Epigenetic transgenerational inheritance of altered stress responses

David Crewsa,1,2, Ross Gillettea, Samuel V. Scarpinoa, Mohan Manikkamb, Marina I. Savenkovab, and Michael K. Skinnerb,1,2 aSection of Integrative Biology, University of Texas at Austin, Austin, TX 78712; and bCenter for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164

Edited by Fred H. Gage, The Salk Institute, San Diego, CA, and approved April 18, 2012 (received for review November 15, 2011)

Ancestral environmental exposures have previously been shown to stress has focused on the earliest life stages (fetus and neonate) or promote epigenetic transgenerational inheritance and influence all adulthood, with relatively few studies on adolescence (9–11). It is aspects of an individual’s life history. In addition, proximate life during this period that adrenarche and pubarche occur and the events such as chronic stress have documented effects on the de- individual graduates from dependence to independence, assum- velopment of physiological, neural, and behavioral phenotypes in ing the properties of maturity. Stress experienced during adoles- adulthood. We used a systems biology approach to investigate in cence has enduring effects, including neural remodeling, male rats the interaction of the ancestral modifications carried trans- sensitivity to drugs of abuse, impaired learning and memory, and generationally in the germ line and the proximate modifications in- altered emotional behaviors in adulthood (12–15). The current volving chronic restraint stress during adolescence. We find that study shows that the effects of chronic restraint stress (CRS) a single exposure to a common-use fungicide (vinclozolin) three gen- during adolescence on the adult physiological, behavioral, and erations removed alters the physiology, behavior, metabolic activity, neural phenotypes become more profound when considered in and transcriptome in discrete brain nuclei in descendant males, caus- the context of epigenetic transgenerational inheritance. ing them to respond differently to chronic restraint stress. This alter- We investigated this complex phenotypic response with a unique ation of baseline brain development promotes a change in neural statistical approach for multidimensional phenotype analysis (16). genomic activity that correlates with changes in physiology and be- Systems biology attempts to understand how molecular- to organ- havior, revealing the interaction of genetics, environment, and epi- ism-level processes are involved in the emergence of complex NEUROSCIENCE genetic transgenerational inheritance in the shaping of the adult phenotypes. Emergence was originally formulated by Weiss (17, 18) phenotype. This is an important demonstration in an animal that to mean “phenotypes, and the mechanisms that underlie them, ancestral exposure to an environmental compound modifies how depend on, and subordinate to, the law which rules the complex as descendants of these progenitor individuals perceive and respond aunit.” Systems biology approaches have recently been used to to a stress challenge experienced during their own life history. examine the phenotype at the molecular level of genetics or epigenetics (19). The current study tests the hypothesis that henotype is determined by both inherited and experienced a combination of an environmentally induced epigenetic trans- Pfactors. Traditionally, the former are regarded as a result of generational inheritance (lineage) and context-dependent stress genetic inheritance, and the latter encompass events in the indi- (stress) interact and promote alterations in brain development and vidual’s personal life history. Study of how the environment shapes genome activity (gene networks) that alter the adult phenotype at the phenotype was initially referred to as “epigenesis” (1) and later all levels. termed “epigenetics” by Waddington (2). The current definition for epigenetics used in this study is “molecular factors or processes Results that regulate genome activity independent of DNA sequence and In social animals, the presence of conspecifics is another pow- are mitotically stable” (3). The model used in the current study erful force shaping how an individual responds to abiotic and involves an epigenetic transgenerational inheritance of a behav- biotic stimuli (Fig. S1A). When housed together individuals tend ioral phenotype (4) induced by an environmental toxicant (5) and to be less sensitive to stressors that, if experienced alone, are transmitted through the germ line, involving a permanent alter- debilitating or lethal (20). Social status also influences sensitivity ation in the sperm epigenome (i.e., DNA methylation) (6). The to negative allostatic factors, with subordinate individuals often epigenetic transgenerational inheritance of this altered sperm faring more poorly than dominant individuals. Social housing epigenome modifies the subsequent development and epigenomes also modulates both the stress response (21) and the behavior of of all cells and tissues, including the brain, to promote phenotypic fi variation (7). Although no direct epigenetic measurements were transgenerationally epigenetically modi ed individuals (22). made in the current study, the epigenetic model and role of epi- Thus, individuals from each lineage were housed together in genetics in development provides the molecular basis of the dyads; half of the dyads were exposed to CRS. observations presented. The development of brain and behavior involves at least two distinct epigenetic programming mechanisms (3, 8). “Germ line- Author contributions: D.C. and M.K.S. designed research; R.G., M.M., and M.I.S. per- dependent” epigenetic change occurs when the modified epi- formed research; D.C., R.G., S.V.S., M.M., M.I.S., and M.K.S. analyzed data; and D.C., genome is permanently incorporated into the germ line to man- R.G., S.V.S., M.M., M.I.S., and M.K.S. wrote the paper. ifest each generation in the absence of the causative agent. The authors declare no conflict of interest. “Context-dependent” epigenetic change occurs when the envi- This article is a PNAS Direct Submission. ronmental factors that bring about the epigenetic modification Freely available online through the PNAS open access option. persist in the environment. Most research in epigenetics today Data deposition: All microarray CEL files reported in this study have been deposited in the falls within this context-dependent category. Although both have Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. been attributed with “generational” properties, only germ line- GSE26737). dependent epigenetic modification is epigenetic transgenera- 1D.C. and M.K.S. contributed equally to this work. tional inheritance (5, 7). The life-history approach to the study of 2To whom correspondence may be addressed. E-mail: [email protected] or skinner@ behavioral development emphasizes both the continuity and in- wsu.edu. terplay between the internal and external environmental charac- This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. teristic of the specific life stages. Most research on the effects of 1073/pnas.1118514109/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1118514109 PNAS | June 5, 2012 | vol. 109 | no. 23 | 9143–9148 Physiological Phenotype. Body weight (BW) and gonadosomatic and adrenosomatic indices. The pattern of BW gain differs according to lineage and stress (Fig. S1B). There is no difference in BW be- tween vinclozolin-lineage (V-L) and control-lineage (C-L) males at birth or at weaning. As expected, shipping stress depresses BW in all animals. The effect of lineage is observed in the nonstress groups with V-L males gaining weight more rapidly and becoming heavier than C-L males (P = 0.02). CRS depresses gain in both lineages: within 2 d of onset of CRS, weight gain (average per- centage gain relative to previous weight) in stress animals is half that of nonstress males regardless of lineage; on the cessation of CRS, BW increases in both lineages. Interestingly, there is no in- teraction of lineage and stress. Finally, stress attenuates the dif- ference in BW between the lineages: in the nonstress dyads, V-L males are ∼25 g heavier than C-L males are, whereas, in the stress dyads, the weight differences are less than 5 g (Fig. S1BInset). There are no lineage effects in gonadosomatic or adrenosomatic indices, but males experiencing CRS have larger testes than do nonstress males in the V-L group and V-L stress males have larger adrenals than C-L stress males do (both P = 0.03). When con- sidering the dyad, males in stress dyads have larger testes and adrenals (P = 0.03 and 0.02, respectively) than do males in non- stress dyads. Finally, within-dyad analysis reveals that, in the stress dyads, V-L males have larger adrenals than do C-L males (P = 0.01); this effect is not seen in nonstress dyads (Fig. S2A). Hormonal indices. With a single exception, CRS results in lower corticosterone (CORT) levels in both the C-L and V-L groups (Fig. S1C). Lineage, but not stress, influences circulating tes- tosterone (TESTO) levels (F1, 63 = 2.11, P = 0.04). In stress animals, TESTO levels are significantly higher in V-L males relative to C-L males (P = 0.01). There is no significant differ- ence in circulating concentrations in leptin across lineage or stress conditions, perhaps because BW is stable and unchanging by the time of death [postnatal day (PND) 120].

Behavioral Phenotype. In the forced-swim (FS) test, there is no difference according to lineage or stress condition in terms of distance, speed, latency to immobility, or time mobile measures, even after controlling for BW differences. In the open-field (OF) test, C-L nonstress males spend more time in the corners of the OF than do V-L nonstress males (Fig. 1A). Exposure to CRS has Fig. 1. Behavior analysis. (A) In OF tests, C-L nonstress males spent more opposite effects in the two lineages (Fig. 1A): C-L males move time in corners than did V-L nonstress males. (B) Heat map showing occu- ’ out of corners and into the center, indicating greater exploration, pancy for group means in the OF from the bird s eye view. Red indicates whereas V-L males move from the center into corners, indicating greater time spent at any given position. Arrows indicate change in activity as a consequence of stress. (C) Overhead view of group mean tracing of greater anxiety [interaction between lineage and stress (F = 1, 56 movement within a schematic of the testing chamber for animals in Soc 1. 3.89, P = 0.05)] (Fig. 1B). Considering the dyad, V-L males in “E” indicates an empty stimulus cage; “A” indicates a stimulus cage con- nonstress condition cross the center more frequently (P = 0.01), taining an animal. (D) Overhead view of group mean tracing of movement whereas, in the stress condition, they cross the center faster (P = within a schematic of the testing chamber for animals in Soc 2. “N” indicates 0.04) than C-L males do. There is also an effect of stress in- a stimulus cage containing a novel male; “F” indicates a stimulus cage dependent of lineage: stressed males move faster through the containing a familiar animal. (E) Evidence of transgenerational epigenetic center than do nonstressed males (P = 0.01), indicating that modification on response to CRS on social bonding. CRS increases anxiety later in adulthood (Fig. S2B). In sociability test 1 (Soc 1) (Fig. 1C), lineage effects are re- stricted to the stress dyads, with V-L males traveling farther and stress males display greater affiliation behavior with the familiar faster than the C-L males do (both P = 0.04) and choosing to individual. In C-L males, there is no effect of stress, but mean associate with the stimulus animal more than nonstress individ- center time decreases in Soc 2, a difference significant only in the uals (P = 0.03). In general, CRS affects line crossing (P = 0.04) stress condition (P = 0.03). Similarly, V-L stress males tend to and latency to first entry into the chamber containing the stim- spend more time in the animal chamber in Soc 1 than do V-L ulus animal (P = 0.01). In the nonstress dyads, V-L males visit nonstress males and in Soc 2; this difference becomes significant the stimulus animal for longer periods and move between (P = 0.03), again suggesting formation of a social bond with the chambers less than did C-L males do (both P = 0.04) (Fig. S2B). familiar animal. See Fig. 2B and Fig. S2B for landscape analysis. In Soc 2, C-L nonstress males spend more time with the novel stimulus male than with the familiar stimulus male (P = 0.01) Brain Metabolism Phenotype. Previous research on the neural and (Fig. 1 D and E). Only V-L males show effects of stress, traveling behavioral consequences of CRS has identified 15 brain regions farther (P = 0.04) and faster (P = 0.05) than V-L nonstress that play a role in stress reactivity as well as learning and memory males do; they also spend less time in the center compartment (Tables S1 and S2 ). Assessing metabolic activity by using cyto- (P = 0.01) and more time with the familiar and novel stimulus chrome histochemistry (23) in these nuclei, we find that nine nuclei males (P = 0.03). Comparison of the two tests reveals that, in capture 87% of the variance: basolateral amygdala (BLA), medial Soc 1, V-L stress males tend to spend less time in the center amygdala (MeAmy), central amygdala (CeAmy), anterior cortical compartment than do V-L nonstress males, a difference that amygdala (CoAmy), posteromedial cortical amygdala (PMCo), becomes significant in Soc 2 (P = 0.01), suggesting that V-L medial posterior dorsal amygdala (MePD), stria terminalis (ST),

9144 | www.pnas.org/cgi/doi/10.1073/pnas.1118514109 Crews et al. NEUROSCIENCE

Fig. 2. Phenotype analysis at different levels of biological organization. Leftmost columns depict effects of lineage (difference between C-L and V-L) under nonstress and stress conditions. An asterisk above a peak or a valley indicates a significant effect of treatment in that behavioral test (P < 0.05). Differences in phenotype calculated by permutation analysis on this dataset yielded the p results shown beneath each landscape, indicating the degree to which the landscape is changed. A peak for a trait indicates a greater result in V-L (V ) males, whereas a valley indicates a greater result in C-L (C ) males. Rightmost columns depict effects of stress (difference between nonstress and stress) in C-L and V-L males. A peak for a trait indicates a greater result in stress (S ) conditions, whereas a valley indicates a greater result in nonstress (NS ) conditions. Nodes represent group means of percentage maximum or Z scores (see SI Materials and Methods for specifics). (A) Body phenotype. Clockwise nodes: BW; ASI, adrenosomatic index; CORT; Lept, leptin level; TESTO; and GSI, gonadosomatic index. (B) Behavior phenotype. Clockwise nodes: Soc 2, measure of social novelty and working memory; OF; FS; and Soc 1, measure of social approach, anxiety, and exploration. (C) Brain metabolism phenotype. Clockwise nodes: BLA, CeAmy, MeAmy, CA1, CA3, CoAmy, PMCo, MePD, and ST. (D) Essential phenotype or the three most influential measures from each category (physiology, behavior, and brain). Clockwise nodes: TESTO, CORT, OF, Soc 1, Soc 2, MePD metabolic activity, ST metabolic activity, CA1 metabolic activity, and BW. and CA1 and CA3 areas of the hippocampus (Table S2). V-L show a 10% decrease in activity in the CA1 and an ∼9% decrease males subjected to CRS show an approximately 10% decrease in in activity in the CA3 relative to males that were not subjected to overall activity in the brain, but other experimental groups are CRS. This effect indicates a general decrease in activity within the relatively unchanged (Fig. 2C and Fig. S2C and Tables S1 and S2). hippocampus in animals that have been subjected to both vinclo- fi Speci c nuclei show both lineage and stress effects. The PMCo zolin and CRS, whereas animals that were subjected to either V-L males in both stress and nonstress groups show a substan- vinclozolin or CRS (but not both) do not show great changes in tial decrease (13% and 17%, respectively) in metabolic activity activity. See Fig. S2C for landscape analysis. within the PMCo (P = 0.03,0.04, respectively) relative to C-L males. In the MeAmy, C-L stress males show an 8.4% increase in Essential Phenotype. An essential phenotype landscape was con- activity. In the MePD, V-L stress males show a marked decrease structed by combining the three measures from each level of in activity relative to C-L stress males (∼18%, P < 0.01), whereas, analysis that best differentiate between groups as determined by in C-L stress males, there was only a 9% increase in activity. In the ST, V-L males that have been subjected to CRS show an ∼12% discriminant function analysis (DFA) followed by permutation increase in activity relative to C-L males also subjected to CRS analysis. This analysis determined how changes within and be- (P = 0.02). In V-L males, CRS results in a 10% increase in activity tween phenotype classes are correlated with and separate from the (P = 0.05). The CA1 and CA3 of the hippocampus show effects effects of lineage versus the effects of CRS (Fig. 2D), revealing (i) similar to one another. In animals that have been subjected to no significant difference between C-L and V-L males; (ii) V-L CRS, the CA1 shows an ∼7% decrease in activity, and the CA3 males perceive and respond to CRS differently than do C-L males; shows an 11% decrease in activity in V-L animals relative to C-L and (iii) CRS affects males of both lineages to the same approxi- males. Similarly, in V-L animals, males that were subjected to CRS mate degree, albeit it in different ways on different traits.

Crews et al. PNAS | June 5, 2012 | vol. 109 | no. 23 | 9145 Brain Genomics and Gene Networks. For the genomic and gene (24). The direct-connection (i.e., interaction) gene networks were network studies, RNA was derived from 1-mm punches from the identified for the CRTX and the CA1 regions (Fig. 3). These CA1 and CA3 of the hippocampus, BLA, and the primary and networks identify how the genes with altered expression are con- secondary motor cortex (CRTX) from each individual (Fig. S3). nected and associated with the changes in the brain regions and The comparisons made to assess alterations in gene expression are behavior. Interestingly, the two regions have distinct networks. shown in Table S3, with the C-L nonstress males considered as the The BLA and the CA3 have direct neural and gene network baseline or “normal” brain. The number of genes with significant connections, and their individually identified gene networks also differences in expression with a minimum fold change of 1.2 (fold identify the indirectly connected genes and cellular processes they > > change 1.2) and mean difference of 10 are presented for all regulate. The direct-connection gene networks of the CRTX and comparisons in Table S3 and Dataset S1. The altered gene sets are CA1 provide novel networks of genes involved in the regulation of – – each given a list number 1 16 and involve 23 377 genes, the brain regions and behavioral alterations. The gene networks depending on the comparison and brain region analyzed. Each identified involve a combination of lineage and stress factors that brain region, both within and between lineage and stress con- cannot be segregated. Similar analysis for each of the individual ditions, has its own set of distinct genes with negligible overlap. comparisons of lineage and stress for each region separately Indeed, only a single gene, ribosomal protein L21, is common (Fig. demonstrated no other major direct-connection gene network, but S4). A complete list of the genes with altered expression for each – all had indirectly connected gene networks. Thus, each of the gene brain region and comparison is presented in Dataset S1 (lists 1 16) networks identified is unique and specific to brain region, lineage, and categorized to various cellular functions and processes (Fig. or stress condition. Observations indicate that each brain region S5), with receptors and binding proteins, metabolism, transcrip- has a different altered gene set and gene network involved in the tion, signal transduction, and development being highly repre- lineage and stress comparisons. These gene networks are directly sented. Various comparisons of lineage and stress conditions have genes that share common gene functional categories but are in- associated with the behavioral alterations observed and are spec- dependent in their patterns of change according to lineage and ulated to, in part, be causally related. Because neither the lineage stress. Analysis of the altered gene sets correlated to specificsig- nor the stress effects promote genetic mutations, but they do naling pathways, and cellular processes show the top 20 pathways promote epigenetic alterations (7), epigenetics is the basal mo- lecular process involved, as previously documented (6). Therefore, in multiple comparative lists (Tables S3 and S4). The highest fi correlated pathway is olfactory transduction, with 78 genes altered the germ line-dependent transgenerational modi cation and the fi among all of the comparisons (Fig. S6). Nearly all of the com- context-dependent stress response modi cation promotes an parative gene lists had the highest number of altered genes in this epigenetic reprogramming of these brain regions that alters the fi pathway. Other brain-related pathways affected by lineage and gene networks and pathways identi ed to promote the altered stress are neuroactive ligand–receptor interaction, Huntington behavioral phenotypes observed. disease, Alzheimer’s disease, axon guidance, and Parkinson dis- A validation of the gene expression of the microarray data was ease (Tables S3 and S4). Two of the more ubiquitous pathways performed with a quantitative PCR (qPCR) analysis of selected affected are the calcium signaling pathway and the MAPK sig- genes from the gene networks that were highly connected and naling pathway (Fig. S7). Although unique gene sets exist for each critical to the regulation of the gene network. These genes were brain region analyzed, the lineage and stress altered gene sets are angiotensinogen (Agt) and connective tissue growth factor (Ctgf) associated with common signaling pathways and cellular pro- (Fig. 3A), insulin-like growth factor binding protein 5 (Igfbp5) (Fig. cesses. Interestingly, a number of brain-specific pathways associ- 3B), and brain-derived neurotrophic factor (Bdnf)(Fig. S8A). The ated with neurodegenerative disease were identified. altered gene expression for all four genes had similar trends for the The final genomic analysis of the brain region transcriptome microarray and qPCR (Agt: 1.34 vs. 1.6; Ctgf: 1.31 vs. 1.92; Igfbp5: comparisons involved identification of gene networks by using 1.70 vs. 1.36; and Bdnf: 1.21 vs. 1.63, respectively), and all had global literature analysis software with the altered brain gene sets statistically significant differences (P < 0.05). Therefore, the qPCR

Fig. 3. Direct-connection networks for genes in CRTX (gene lists 5–8; A) or CA1 (gene lists 9–12; B) obtained by global literature analysis using Pathway Studio 7.0 software (Ariadne Genomics). (A) For cortex, only 22 directly connected genes of 330 unique genes (no ESTs included) from combined lists 1–4 are shown. (B) For CA1, 47 genes of 430 unique genes (no ESTs included) from combined lists 9–12 are shown. The rest of genes are not connected and not shown.

9146 | www.pnas.org/cgi/doi/10.1073/pnas.1118514109 Crews et al. validated the microarray data for these critical genes in the various adolescence. Landscape analyses reveal that, depending on the gene networks identified. phenotype, different relationships emerge. For example, at all three levels (physiological, behavioral, and brain metabolism), the Discussion effects of lineage are most apparent in the stress condition, sug- Our observations illustrate a “two-hit” model where the “hits” gesting that V-L males respond differently after CRS than do C-L span generations, in this instance the first hit (transgenerational males. In the physiological landscape (Fig. 2A), TESTO and epigenetic inheritance) predisposing a future generation to re- CORT are mostly responsive to the effect of lineage but only in the spond to a second hit (CRS during second adolescence), which stress condition. In both lineages, CRS slows weight gain, yet the further alters the adult phenotype. The first hit of this model V-L nonstress males gain weight more rapidly. The most notable corresponds to the exposure of a gestating female to the fungicide effects in the behavioral landscape are the reversed effects of stress vinclozolin occurring three generations earlier. As demonstrated in the OF between C-L and V-L males (Fig. 2B). C-L stress males previously, vinclozolin exposure predisposes males to develop show lower anxiety, defined by fewer entries and less time in the a variety of adult-onset diseases earlier than normal (5, 7), effects center arena, whereas animals not exposed to CRS show elevated still detectable in males over four subsequent generations without anxiety. This effect is reversed in the V-L animals: Stressed males diminution (5). These alterations in brain and behavior occur in show higher levels of anxiety, which is consistent with the findings young animals, months before the onset of these diseases (4, 22). of Soc 1 and 2. In the nonstress condition, V-L males show Most research on the neural substrates of the studied behaviors a heightened state of anxiety compared with C-L males. In C-L has focused on the amygdala and hippocampus. Because these males, there is little effect of CRS on anxiety, as defined by the (and other) brain areas have glucocorticoid receptors (25), the willingness to explore novel social interactions. However, in V-L role stress plays in plasticity in these regions has received much males, anxiety state is decreased after CRS even beyond that dis- attention. The amygdala is an assemblage of nuclei and has no played by C-L males. The brain metabolism landscape (Fig. 2C) reliable structural or functional definition (26). The traditional shows that the amygdaloid nuclei are differentially affected by guiding concept has been that of a “chemosensory” amygdala lineage. For example, cytochrome oxidase activity in PMCo is with its divisions based on input from the main or olfactory higher in C-L males regardless of stress condition. The MePD amygdala (for processing odor cues) versus the accessory or shows opposite effects after CRS (pronounced increase in C-L vomeronasal amygdala (for processing pheromonal cues). The males and decrease in V-L males). In the MeAmy, cytochrome “extended” amygdala concept relates to a functionally integrated oxidase activity is opposite in the lineages, depending on stress. series of nuclei (27). Regardless of the definition used, amygda- We also see that the ST, and not the bed nucleus of the ST (BnST), – loid nuclei are involved in activation of the hypothalamo pitui- is markedly changed, indicating that activity in this major pathway NEUROSCIENCE tary–adrenal (HPA) axis both via their role in the control of is being modified by lineage. In CA1 and CA3, stress decreases pituitary adrenocorticotropic hormone release by stressors and metabolic activity in the V-L males but has no such effect in the integration of behavioral responses to fear and/or anxiety- C-L males. provoking conditions (28). The hippocampus both receives and Although the primary focus of the current study is a systems sends projections to the amygdaloid nuclei, including CA1 and biology approach to understanding how the brain responds to CA3 (29–32). Traditionally, the hippocampus is thought to inhibit ancestral exposures and environmental stress, a more targeted stress-induced activation of the HPA (28). Although the amyg- approach that considers specific genes can also provide insights dala and hippocampus tend to be studied separately for their into the general pathways and processes identified. Considering roles in emotional behaviors and learning and memory, re- genes important in stress reactivity, V-L males have higher levels spectively, both structures are involved (33, 34). of BDNF (P = 0.03) in the BLA, whereas C-L males have higher We find that this ancestral exposure promotes weight gain and, levels of catechol-O-methyltransferase (COMT; P = 0.02) in as such, provides pivotal empirical evidence that exposure to an CA1. The effects of CRS are observed in the BLA (COMT is endocrine disruptor in generations past results in substantial higher in C-L nonstress males, P = 0.003) and the CA1 [mela- weight gain in the descendants. We also replicate the finding that nocortin 4 receptor (Mc4r) is higher in the C-L stress group, P = this transgenerational epigenetic modification influences how 0.008]. Depending on the nucleus, gene expression can be neg- individuals respond to events in their own life history (4, 22) as atively correlated: CRS in C-L animals increases expression of well as the work of others that CRS experience influences an dopamine receptor D2 >1.5-fold in the BLA but decreases it by individual’s physiological and behavioral phenotypes as an adult. >1.5-fold in the CA3. The effects of the interaction of lineage CRS has an immediate and long-lasting effect on BW that cor- and CRS are observed in the CA1 [cytochrome P450, family 19, relates with CORT secretion later in life (35–38) as well as subfamily A, polypeptide 1 (Cyp19a1) is lower in the V-L stress a negative relationship between stress and CORT and TESTO condition, P = 0.03], CA3 [melanocortin 3 receptor (Mc3r) and (39, 40). The behavioral tests measuring emotionality, anxiety, nuclear receptor subfamily 3, group C, member 1 (Nr3c1) are learning, and memory also reveal the well-established effects of higher in the V-L stress group, P = 0.04 and 0.03, respectively], CRS. We find a lack of effect of stress (or lineage) in the FS test and CRTX [nuclear respiratory factor 1 (Nrf1) is higher in the (36, 41). CRS has a profound effect on the structure and function V-L stress condition, P = 0.02]. However, in a genome-wide of the hippocampus (42), and, with a single exception in the context, the reductionist approach and consideration of in- CRTX, differential expression of apoptosis genes of >1.2 is re- dividual genes is not overly informative. stricted to the CA1 and CA3 (Fig. S3). GST (Gsp) genes are Further analysis of the systems biology of these coordinated thought to be involved in stress-related oxidative damage in the phenomena used a more extensive molecular investigation. A pyramidal cells of the CA1 and CA3, and, in mice, CRS down- bioinformatics analysis of the altered brain transcriptomes regulates Gsp in these regions (43). A similar down-regulation is revealed gene networks associated with each brain region. These observed in the present study in CA1 (but not CA3) in both C-L regional-specific gene networks provide a molecular basis for and V-L males. Thus, for some traits, lineage and CRS have the physiological and behavioral alterations observed. Although effects independent of each other. Equally important, other the gene networks were distinct, many of the altered genes in the traits, such as circulating levels of leptin and FS, show no evi- various regions were in similar signaling pathways. For example, dence that either epigenetic modification has an effect. Finally, the olfactory transduction pathway was affected by nearly all of the fact that C-L and V-L individuals were housed together the lineage and stress comparisons (Tables S3 and S4 and Fig. S6). (dyad) yet responded differently further emphasizes that the An olfactory receptor promoter has been shown to have an epi- transgenerational epigenetic modification fundamentally alters genetic transgenerational alteration in sperm (6). CRS altered 17 how the individual responds to a common challenge. genes in the CA1 of V-L males and in the CRTX of C-L males. What is significant about this study is that ancestral exposure to Why should genes involved in olfaction be expressed in areas of an endocrine disruptor changes how individuals respond to CRS in the brain not involved with olfaction and taste? Olfactory and

Crews et al. PNAS | June 5, 2012 | vol. 109 | no. 23 | 9147 vomeronasal receptors as a group are among the most rapidly bringing “the phenotype into being” (2) down to the molecular evolving of all genes and have been linked to higher processing basis of this phenomena. centers in the brain as well as to behavior (44, 45). Such findings may indicate the neurobiological and neuromolecular basis of the Materials and Methods Proust effect, a phenomenon in which an involuntary memory Detailed materials and methods and corresponding references are presented reaction is triggered by an olfactory input (46). This approach also in SI Materials and Methods. In brief, two different cohorts of male rats of identifies brain signaling pathways associated with neurodegen- the F3 generation of V-L and C-L produced at Washington State University erative disease (Table S4). Thus, the altered comparative gene were shipped to the University of Texas at Austin on the day after weaning sets and gene networks identified are anticipated to be critical in (Fig. S1A). Rats were randomly pair-housed (one of each lineage) and the vinclozolin lineage and stress effects on the physiological and remained in these dyads throughout the duration of the study. On the day behavioral phenotypes observed. after the last behavioral test, the animals were killed by rapid decapitation, How an ancestral environmental exposure modifies the germ- and tissue and blood samples were taken within 3 min (Fig. S9A, A and B). line epigenome and promotes epigenetic transgenerational in- Brain regions were isolated, and RNA for animals from different litters was heritance is critical in any consideration of tissue function. The pooled to generate three different pools with the highest biological varia- exposure to CRS during adolescence clearly influences subsequent tion possible to be used in the microarray analysis. brain development and behavior but is itself altered by ancestral exposures and epigenetic transgenerational inheritance. The mo- ACKNOWLEDGMENTS. We thank R. Tracey, L. Walker, D. Walker, and lecular basis of this environmental influence on phenotype involves Y. Matsumoto for technical assistance as well as H. Johnson for assistance in preparation of the manuscript. We thank Drs. A. Gore, C. Guerrero- unique gene networks associated with these altered phenotypes. As Bosagna, H. Hofmann, and M. Montfils for critical input and comments on such, it is one of the few systems biology approaches to link an- the manuscript. This work was supported in part by National Institutes of cestral and context-dependent environmental factors to illustrate Health Grants ES 017538 (to D.C.) and ES 012974 (to M.K.S.).

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9148 | www.pnas.org/cgi/doi/10.1073/pnas.1118514109 Crews et al. Supporting Information

Crews et al. 10.1073/pnas.1118514109 SI Materials and Methods and no red light. At 3:30 PM, animals were immediately re- Animal Housing Protocol. F3 generation vinclozolin-lineage (V-L) moved from the restraint cages by removing the binder clip and DMSO control-lineage (C-L) male rats were selected out of closest to the animal’s nose, allowing them to crawl out of the littersfrom untreated F2 generationmothers in M.K.S.’s laboratory restraint into their home cage at will. As each animal was placed at Washington State University (WSU) according to established back in its home cage, it was scanned to confirm identity and protocols (1). Briefly, approximately four different F0 generation correct cage mate placement. The animals were then transported females were used to generate different lineages for the F1–F3 back to the housing room and placed back in their original generations with no sibling or cousin breeding to avoid inbreeding housing rack. Dyads that were not to be stressed were left in the artifacts. Gestating female F0 generation Sprague–Dawley rats housing room, untouched. Restraint cages and binder clips were were injected with the fungicide vinclozolin (100 mg/kg) daily washed after stressing each day with soap and water and left to during fetal gonadal sex determination (embryonic days 8–14), dry for the next day’s stressing. and the F1 generation were bred to generate the F2 generation, Twice a week (Tuesday and Friday), after the animals had been and then the F2 were bred to generate the F3 generation (1). At stressed, animals were weighed, beginning at 4:00 PM. While each approximately postnatal day (PND) 10 (before weaning), each dyad was being weighed, the animals were handled for about animal was injected with a small microchip (AVID) s.c. between 3 min each to allow the animal to become accustomed with the the shoulder blades. The animals were then shipped to D.C.’s experimenter and to prevent any unnecessary stress while the laboratory at the University of Texas at Austin (UTA) from WSU animals had to be handled for stressing or behavioral testing. on PND 22, 1 d after weaning. Upon arrival at the UTA, one After the initial 21 d of CRS, all animals were left in the housing animal from each lineage (control and vinclozolin) was pair- room constantly and were only removed for handling, weighing, housed (one control and one vinclozolin animal) and remained in and behavioral testing on scheduled days. these dyads throughout the duration of the study. Because of the natural variation in dates of breeding, there was a 4-d spread of Animal Groups and Numbers. There were four treatment groups: birth date of animals in the first cohort, but all animals were born V-L stress (VS), V-L nonstress (VNS), C-L stress (CS), and C-L on the same day in the second cohort. However, all pair-housed nonstress (CNS). A subset of each group was not tested (4, 2, 4, and animals were no more than 1 d apart in birth age and were paired 2, respectively); all remaining dyads were behaviorally tested. Two randomly to prevent an age effect on cage mates. cohorts of animals were run, the first in January and the second in fi Each dyad of animals was randomly placed in a six-wide, ve- May. Cohort sample sizes are shown in the following table: high metal housing rack in standard translucent polycarbonate rat cages (46 cm × 24 cm × 20.5 cm) with ad libitum access to tap water and standard rat chow (rodent chow 5LL2 Prolab RMH Cohort CNS VNS CS VS 1800 diet; Purina). The animal room was on a 14-h/10-h light/ 1881110 dark schedule. For environmental enrichment, a 7-cm-diameter 28899 PVC pipe was placed in each cage. Total 16 16 20 19 Uterine and litter sex ratios can influence adult phenotype (2– 4), and so the sex ratio of each litter was determined at birth and weaning. The litters were then divided according to criteria de- Body Weight (BW). Animals were weighed every 3–8 d from PND scribed in de Medeiros et al. (4). Equal (E) litters (n = 5 litters 21 (at weaning) to PND 108. Analysis focused on two questions: totaling 20 animals) containing equal numbers of males and fe- how do the groups differ through time or at any one point in time males (or no more than 1 individual more of either sex). Male- and how does weight change within a group as a function of time biased (Mb) litters (n = 5; 23 animals) contained ≥50% males. and experience. The first question was addressed by using Female-biased (Fb) litters (n = 9; 42 animals) contained ≥50% a three-way ANOVA with repeated measures. females. All of the litters that provided animals in the study The second question was addressed in the following manner. could be divided into one of these three groups. Differences in BW between a stress group and a nonstress group Chronic Restraint Stress (CRS). The day after receipt at UTA, half of and between V-L and C-L were compared at each time point the dyads were randomly chosen to be administered a CRS (PNDs 21, 29, 32, 37, 40, 46, 52, 57, 61, 67, 71, 79, 81, 88, 96, 102, treatment. This paradigm entailed 6 h of daily CRS consecutively and 108). The effect of CRS on BW was compared between and for 21 d and duplicated the methodology of ref. 5. The restraint within lineages at each time point. apparatus consisted of a 25.4-cm2 metal wire mesh folded in half The nonparametric Wilcoxon rank-sum test was used to an- and bound with a plastic mold that allowed for two openings and alyze the association between a lineage and stress treatment prevented any rough edges. The front and rear openings of the because of the asymmetric distribution of BW in each group. restraint cage were clipped shut with binder clips with an addi- All statistical comparison was performed with JMP 8.0 (SAS tional binder clip on one side of the animal to allow for adjust- Institute); P values < 0.05 were considered to be statistically ment of the size of the restraint as the animals grew. Animals to significant. be stressed were removed from the animal housing room at 9:00 AM and transported to a procedural room separate from the Behavioral Testing. Beginning at PND 114, each individual received housing room. Each animal was hand-placed in a restraint at 1 h four different behavioral tests with behavior quantified by using the after lights off (9:30 AM) by either allowing the animal to enter automated Stoelting ANY-maze video-tracking system. Each test the restraint on its own will or gently coaxing the animal into the was separated by 48 h. All of the dyads (V-L and its yoked C-L cage restraint. Extra care was taken to not forcefully place the animals mate) were tested in open-field (OF), forced-swim (FS), and two in the restraint as to prevent any unnecessary stress. Stressing social-affiliation tests. The order of the tests was counterbalanced was performed between 9:30 AM and 3:30 PM, with lights off to treatment, although the OF test was obligatory to the last day of

Crews et al. www.pnas.org/cgi/content/short/1118514109 1of17 testing because it was performed during the light phase to control closure with vertical rods spaced at 1 cm apart to prevent fighting for the time between tests. Animals were then killed 42 h later. and biting but allowing for facial recognition and investigation. After each trial, the apparatus was cleaned with 70% (vol) ethanol For sociability test 1 (Soc 1), the blockades to the two side and allowed to dry before the next test. chambers were removed after the habituation period, allowing the The FS and sociability tests were performed during the dark experimental rat to explore any of the three chambers. The cycle, beginning at 1 h after lights off (9:30 AM). The test arenas position (left or right) of the stimulus animal was systematically were softly illuminated with red lights, positioned as to not affect rotated between trials. The experimental rat was given 10 min to ANY-maze tracking. The OF was performed during the light cycle become familiar with the stimulus animal. ANY-maze was under illumination, beginning at 1 h after lights on (7:30 PM). instructed to record the time spent in the chamber with animal 1 To prevent ambiguities in testing each animal, a scanning versus the center and other chambers (containing an empty cage). system was used that automatically scanned the identity of the In Soc 2, a second stimulus animal (novel animal), pair-housed animal, via an AVID identification microchip, that was auto- with the first animal (familiar animal) was placed in the empty matically entered into ANY-maze and began each test. cage in the opposite chamber. The experimental rat then had the FS test. This test was based on the methods of Porsolt et al. (6). choice of associating with the familiar rat or with the novel rat or However, because there was no intermittent treatment to ad- not associating with either. ANY-maze was instructed to record minister, a single 15-min paradigm was used. Animals were the time spent with the novel animal versus the time spent with the × placed in a 19 cm 50 cm Plexiglas cylinder with 40 cm of water. familiar animal versus the time spent in the center arena (no Each animal was allowed 15 min in the cylinder with no possi- animal). After this second 10-min period, the rat being tested was bility of escape (a piece of clear glass was placed over each ap- returned to its home cage, and the arena and metal enclosures paratus to prevent escape). The ANY-maze system was then were wiped down with 70% ethanol and allowed to air-dry. instructed to measure the time that each animal was immobile, fi de ned as no more movement than necessary to keep the head Hormone Assays. The hormone RIAs were performed by the above the water to breathe. The depth of the water was such that Hormone Assay Core Laboratory at the Center for Reproductive an animal would not be able to balance itself on the bottom of Biology, WSU. Circulating concentrations of corticosterone the tank with its tail. If an animal sank to the bottom of the tank (CORT), testosterone (TESTO), and leptin were determined by and exhaled their breath under water, they were immediately “ fi ” commercial assays (TESTO and CORT from Siemens Medical removed from the tank and scored as a did not nish. Water Solutions with coefficients of variation at less than 6.18% and for the FS was tap water that had been placed in containers 6.7%, respectively). Each cohort was analyzed in separate assays overnight to allow the temperature of the water to come up to – for TESTO and CORT, with the latter hormone conducted in room temperature (23 25 °C). After each trial, the water was a single assay. The leptin commercial assay was from Millipore poured out and the cylinder was rinsed with water, rinsed with with a coefficient of variance less than 7.3%. 70% ethanol, rinsed with water again, and then filled with room temperature water. After each trial, each animal was hand-dried Brain Processing. For each dyad, the brain of each male was cut in the with a towel and placed back into its cage with a red light directly sagittal plane at the midline (Fig. S8A, A–D). Each half was com- above the cage for warming the animal from hypothermia. bined with the complementary half of the other individual (alter- OF test. Each animal was tested in a 100 cm × 100 cm × 40 cm “ ” × nating the right and left halves) such that each brain consisted of apparatus partitioned into four equivalent arenas of 50 cm symmetrical halves of the V-L and a C-L male pair. One “com- 50 cm each). A soft white light bulb (60 W) was placed directly bined” brain was prepared for cryostat sections (40 μm) in three over the enclosure. No other ambient lights were on during alternating sets: the first set was for cytochrome oxidase histo- testing. Each animal was placed at the corner where the partition chemistry (8) and the second and third sets were kept for future met (i.e., in the center of the 100 cm × 100 cm arena) to rule out studies, such as in situ hybridization and immunohistochemistry of initial placement of the animal in the arena as a factor affecting behavior. The animal was then allowed a 15-min period to roam target genes for better resolution of gene expression. The other combined brain was prepared for punches of discrete nuclei by first the arena with no interruption. A 10-cm perimeter border – around the edges of the arena was drawn digitally in ANY-maze slicing in 2-mm sections with a Zivic brain matrix (Fig. S8A, E G. and defined as an “outer region,” and anything inside of that The following coordinates are relative to bregma based on the 10-cm border was defined as the “inner region.” ANY-maze was Paxinos and Watson (9) rat brain atlas: the beginning of each − − − instructed to calculate the time in the inner region versus the blocked slice was +0.36, 1.64, 3.64, and 5.64. The following time in the outer region as well as the following measures: total areas were taken using a 1-mm punch (Stoelting): primary and distance traveled (m), average speed (m/s), number of line secondary motor cortex (CRTX) at the level of the basolateral crossings, time in inside zone (s), number of entries into the amygdala (BLA), BLA, and CA1 and CA3 of the hippocampus. outside zone, and time in outside zone (s). To obtain a measure Tissue punches were placed singly in 1-mL Eppendorf tubes con- of time spent in corners, the OF was divided into 25 equal seg- taining 200 μL of TRIzol. All brain analyses (microarray and cy- ments, and the four corner segments were summed. After the tochrome oxidase histochemistry) were conducted after all tissues 15-min trial period, each animal was removed and returned to its had been collected so that material from all individuals could be home cage. The arena floor and walls were cleaned with 70% done in a single run for each procedure. ethanol and left to air-dry before the beginning of the next trial. Tests for sociability. Two tests for sociability were modeled after Cytochrome Oxidase and Brain Nuclei. Behavior is a function of protocols in Moy et al. (7). A 100 cm × 100 cm × 40 cm Plexiglas brain activity, which obtains ∼90% of its energy from the aerobic enclosure (Stoelting) was partitioned into three arenas by 40-cm metabolism of glucose (8). Cytochrome oxidase (COX) is a rate- high walls with a 10 cm × 11 cm opening to allow movement of the limiting enzyme in oxidative phosphorylation. COX activity re- rat between arenas. At the beginning of the test, the animal was flects the metabolic history of brain areas, and COX levels and/ allowed to become accustomed to its environment for 5 min. The or activity constrain the activity of a neuron, thereby limiting the center arena was used for this, and the entrances to the two side likelihood of a behavior (10). Thus, factors that constrain brain arenas were blocked by standard poster board taped to the wall of metabolism also constrain behavior. Considering that behavior the arena. A 5-min habituation period preceded each test. All results from coordinated activity in networks of specific brain stimulus animals were PND 120 intact Sprague–Dawley male rats nuclei (11), information on the metabolic activity in neural from Harlan. The stimulus animal cage was a 15 cm × 30 cm en- networks is of interest.

Crews et al. www.pnas.org/cgi/content/short/1118514109 2of17 Metabolism is assessed by cytochrome oxidase histochemistry four separate ANOVAs. There was a significant effect of lineage in in 14 discrete brain regions (Tables S1 and S2): All regions but the PC1 and PC3 (F1, 32 = 7.54, qFDR = 0.02; F1, 32 = 7.31, qFDR = CRTX have been implicated in the neural and behavioral con- 0.021), stress in PC1 (F1, 32 = 17.88, qFDR = 0.002), and dyad in sequences of response to CRS. PC2 and PC4 (F34, 32 = 2.59, qFDR = 0.013; F34, 32 =7.31, The primary disadvantage of the split-brain method is that qFDR = 0.008), where qFDR is the false discovery rate q value. midline nuclei such as the paraventricular nucleus (PVN) and PCA of the combined behavioral tests revealed that the first anteroventral periventricular nucleus (AvPv) are damaged and in three principal components account for 93% of the variance (Fig. most instances cannot be imaged with confidence. For example, S2B). A MANOVA of the principal component scores for effects the PVN is integral to the stress response (12). Although we were of lineage, stress, and dyad revealed no significant effects vari- able to obtain total metabolic measurements for the PVN, the ation. The individual importance of each axis was explored post sample sizes were limited (two or more per group). The PVN in hoc by using four separate ANOVAs, again with no statistically C-L males had substantially higher activity (>35%) than V-L significant effects of lineage, stress, dyad, or their interactions. males in the nonstress condition (P = 0.02); this effect was re- PCA of the essential phenotype captured 69% of the variance duced to ∼10% difference in the stress condition. Only the C-L observed among and between the groups. males showed a response to CRS (32% decrease; P < 0.01), PCA revealed that nine brain nuclei capture 87% of the var- whereas the V-L males showed an approximately 10% change in iance: BLA, medial amygdala (MeAmy), central amygdala the stress condition. (CeAmy), anterior cortical amygdala (CoAmy), posteromedial cortical amygdala (PMCo), medial posterior dorsal amygdala Landscape Analysis. The functional landscape analysis developed (MePD), stria terminalis (ST), and CA1 and CA3 of the hip- involves principal component analysis (PCA) followed by dis- pocampus. The first four principal component axes account for criminant function analysis (DFA) and permutation analysis to >92% of the variation. The first principal component likely determine whether the targeted traits at each level of biological represents a measure of general activity in the sampled brain organization (physiology, behavior, and brain nuclei metabolism) regions, with all nuclei except ST strongly loading onto the axis are different between groups (11, 13). Performing a traditional (Fig. S2C). The second axis is dominated by CA1 and CA2, and PCA requires either omitting individuals with missing data the third axis is almost entirely determined by ST. The fourth points or imputing the missing data. We opted for an alternative axis accounts for slightly more than 5% of the variation and is method for PCA termed probabilistic PCA (PPCA), capable of strongly determined by PMCo and, to a lesser extent, CA1, CA3, accommodating missing data (13). Before the analysis, in- and CoAmy. To test for the effect of lineage, stress, and their dividuals with greater than 50% of their data missing were re- interaction, we used the principal component scores as response moved (n = 5 individuals), and the data were recentered to variables in a MANOVA. Housing dyad (dyad) is also included mean 0 and scaled via vector normalization. The remaining as a covariate. There is a significant effect of lineage (F1, 29 = missing data were imputed during PPCA (n = 36 data points) < < (14). Unlike traditional PCA, PPCA can handle missing data 8.99, P 0.001) and dyad (F1, 29 = 3.14, P 0.001), a trend toward a significant interaction (F1, 29 = 2.56, P = 0.063), and (14). In PPCA, an expectation-maximization algorithm is used to fi fit a Gaussian latent-variable model (14). The maximum-likeli- a nonsigni cant effect of CRS. The individual importance of each hood estimate for the missing data was determined from the axis is explored post hoc by using four ANOVAs. The overall result is a strong effect of vinclozolin on the response to CRS. observed conditional distributions for individuals with complete fi data (13, 14). All data-preprocessing and PCA were carried out The rst and fourth principal component axes contribute to lin- using the MultiDimBio (13) R package (v0.0.2) and bio- eage (F1, 29 = 6.55, P = 0.028; F1, 29 = 8.60, P = 0.021) and dyad conductor (release 2.8) R package pcaMethods (v1.32.0) (15). effects (F1, 29 = 4.04, P = 0.001; F1, 29 = 2.35, P = 0.024). The The imputed data account for 6% of the total dataset. third principal component accounts for the interaction between A multivariate ANOVA (MANOVA) was conducted on the lineage and CRS (F1, 29 = 4.64, qFDR = 0.055), and the second results of the PPCA. Lineage, stress, their interaction, and principal component only contributes to the effect of dyad fi housing dyad were included in the model. The interaction be- (F1, 29 = 2.48, qFDR = 0.022). There is a signi cant effect of dyad tween dyad and the other group variables was not modeled be- in the MANOVA and all ANOVAs, except for the PC3 ANOVA. cause the effect of dyad should be random with respect to lineage and stress. The number of unique housing dyads also preclude this RNA Preparation. From each individual, 1-mm punches were taken analysis because there are not enough degrees of freedom. Post from the CA1 and CA3 of the hippocampus, the BLA, and the hoc analysis was carried out with four ANOVAs, one for each CRTX. After RNA isolation, three different pools, each con- principal component axis. Significance was determined by using taining three different males, were generated in each of the four a false discovery rate correction as implemented in the R package conditions. Microarray analysis was performed on each pool in fdrtools (16). All analyses were performed with R v2.12.2 (17). triplicate, involving three different experiments and aged animal The effects of lineage and stress on the physiological, behav- pools. The sample histograms for raw data for all 48 arrays are ioral, brain metabolism, and essential phenotypes were analyzed shown in Fig. S3 and after preprocessing (,SI Materials and (Fig. 2 A–D, respectively). Methods) all arrays corresponded well with no outlying arrays. PCA was performed on six measures of body phenotype: leptin Individual rats were homogenized in 200 μL of TRIzol, and then level, TESTO level, CORT level, adrenal weight, testes weight, and 600 μL of TRIzol was added to final volume of 800 μL. Samples animal BW. The first four principal components were maintained were stored at −80 °C or −20 °C until RNA extraction. Then, and account for 81% of the variance (Fig. S2A). The first and 100 μL of the above TRIzol homogenate from four randomly second principal components (PC1 and PC2) were organ/animal chosen individuals within the same tissue/treatment group were weight and circulating hormones, respectively. The third principal pooled together for one RNA sample (one microarray biological component (PC3) was dominated by leptin levels, and the fourth replica). Samples from the same set of four dyads were pooled for principal component (PC4) related adrenal size to CORT levels. A one vinclozolin or control replica for all four brain areas, stress or MANOVA of the principal component scores for effects of line- nonstress. For microarray analysis, three biological replicas were age, stress, and dyad revealed a significant effect of lineage prepared as above for each brain area/treatment group. A total of Χ (F1, 32 = 4.49, P = 0.006), stress (F1, 32 = 4.00, P = 0.011), and dyad 48 samples/chips were analyzed: 4 (brain areas) 2 (control or Χ Χ (F34, 32 = 4.49, P = 0.006) but no significant interaction. The in- vinclozolin) 2 (stress or nonstress) 3 (biological replicas). dividual importance of each axis was explored post hoc by using RNA was extracted from pooled TRIzol samples according to

Crews et al. www.pnas.org/cgi/content/short/1118514109 3of17 standard TRIzol extraction protocols (Invitrogen) and stored in C-L stress condition or V-L nonstress condition versus V-L stress aqueous solution at −80 °C until microarray analysis. condition) or lineage effects within stress (i.e., V-L stress con- dition versus C-L stress condition or V-L nonstress condition Microarray Analysis. The microarray analysis was performed by the versus C-L nonstress condition). t test statistics are indicated as Genomics Core Laboratory at the Center for Reproductive Biology, being either one- or two-tailed analyses depending on a priori fl WSU, by using standard Affymetrix reagents and protocol. Brie y, hypotheses of each of the measures. That is, if directionality was mRNA was transcribed into cDNA with random primers, cRNA hypothesized, statistics are displayed as one-tailed analyses with was transcribed, and single-stranded sense DNA was synthesized, a significance α = 0.05. fragmented, and labeled with biotin. Biotin-labeled ssDNA was To clarify social interactions and rule out the confounding then hybridized to the Rat Gene 1.0 ST microarrays containing effects of differences between cage mates (social context), sta- more than 29,000 transcripts (Affymetrix). Hybridized chips were fi tistics were performed on a matched-pair basis. As previously scanned on an Affymetrix Scanner 3000. CEL les containing raw described, animals were pair-housed with an animal of the other data were then preprocessed and analyzed with Partek Genomic lineage (C-L with V-L). The value of each measure for each C-L Suite 6.5 software using an RMA GC content-adjusted algorithm. animal was subtracted from the measure for its V-L cage mate, Raw data preprocessing was performed in four groups, one for creating a difference score for each measure. Because the each of four brain areas (BLA, CRTX, CA1, and CA3; Fig. S4 B, C, resulting scores were not normally distributed, based on the E, and F). Comparison of raw data array histogram graphs for Kolmogorov–Smirnov test for normality, they were compared each brain tissue demonstrated the data for all 12 chips belonging to one of four tissues were similar and appropriate for further with nonparametric statistics. To compare the effects of CRS between dyads, the same difference scores described above were preprocessing and analysis as a whole group (Fig. S4 A and D). – Preprocessing of raw data involved multiple testing corrections compared with a Kruskal Wallis one-way ANOVA. To de- and false discovery rate corrections (18). termine an effect of lineage within each dyad, a pair-matched The microarray quantitative data involves hybridization signals signed-rank Wilcoxon test was performed. In all these tests, fi < from an average of 28 different oligonucleotides arrayed for each statistical signi cance was P 0.05. gene, and the hybridization must be consistent to allow a statistically In addition to traditional comparisons, a combined Z score of significant quantitative measure of gene expression and regulation. In multiple measures was composed for each behavioral test based contrast, a quantitative PCR (qPCR) procedure only uses two oli- on the work of Bellani et al. (20). Each measure was prechosen gonucleotides, and primer bias is a major factor in this type of anal- as a measure of anxiety or sociability whereupon it was trans- ysis. Therefore, we did not attempt to use PCR-based approaches for formed to a Z value. These Z values were then summed for each gene expression measurement because we feel the microarray animal within each behavioral test. These sum scores of Z val- analysis is more accurate and reproducible without the primer bias ueswerethencomparedinatwo-wayANOVAandbyt tests, as found in PCR-based approaches, as previously described (18). described above. The combined and averaged Z scores for each All microarray CEL files from this study have been deposited in group were plotted onto a surface map to create a behavioral the Gene Expression Omnibus (GEO) database, www.ncbi.nlm. phenotype of that group. To determine the change in a pheno- nih.gov/geo (accession no. GSE26737), all arrays combined with type relative to a stress or lineage condition, surface plots were one accession number. For gene annotation, Affymetrix anno- subtracted across lineage or stress, but not both, to elucidate tation file RaGene1_0stv1.na31.rn4.transcript.csv was used un- those effects (Z2–Z1). All significance levels were restricted to less otherwise specified. α =0.05. At death, each animal’s adrenals and testes were removed and Gene Network and Pathways. Global literature analysis of differ- weighed for analysis. The weights of these organs were compared entially expressed gene lists for each tissue or treatment group was as whole weights and as an index to BW, thus controlling for performed by using Pathway Studio software (Ariadne Genomics), total size of the animal. As with the statistical analyses on be- which performs an interaction analysis and builds subnetworks of havioral measures, organ weight data were parsed into their genes and cell processes connected to each other. Resulting lists of respective groups and compared via a two-way ANOVA and t differentially expressed genes for each treatment and each tissue tests. The same interdyad comparison described above was used were analyzed for KEGG (Kyoto Encyclopedia of Genes and to determine any effects of social context. All significance levels Genomes, Kyoto University, Japan) pathway enrichment with were restricted to α = 0.05. Pathway-Express, a web-based tool freely available as part of the Hormone assays were performed at WSU, and subsequent Onto-Tools (http://vortex.cs.wayne.edu) (19), and the Search statistical analyses were performed at UTA. CORT, TESTO, and Pathway tool at http://www.genome.jp/kegg/pathway.html. leptin were measured by RIA and were compared both directly Other Statistical Analysis. All measures for behavioral analysis were and as an index of organ weight (e.g., TESTO to testes weight). As acquired automatically from the ANY-maze behavioral tracking with the statistical analyses on behavioral measures, hormone data program (Stoelting). Visual confirmation of the system was were parsed into their respective groups and compared via a two- performed as each animal was tested to ensure accuracy. All way ANOVA and t tests. The same interdyad comparison de- behavioral measures were formatted for use in SPSS to perform scribed above was used to determine any effects of social context. fi α statistical analyses in two basic variations, parametric and non- All signi cance levels were restricted to = 0.05. In the instance parametric. Several parametric statistics were used. of CORT levels, there appeared to be an effect of litter sex ratio. For the behavioral tests, a two-way ANOVA (stress × lineage) Although the litter sex ratio of the V-L and C-L does not differ in was performed on each of the measures obtained from ANY- the colony at large, post hoc analysis of the data revealed that maze looking for main effects of stress, main effects of lineage, males from equal and female-biased litters exhibit a significant and interactions as well as for each Hochberg’s GT2 post hoc decline (averaging 39%) in CORT levels as a consequence of analysis applied. Significance was determined at α < 0.05. Ad- CRS in both C-L and V-L groups, whereas males from male-bi- ditionally, t tests were performed on a 2 × 2 design looking for ased litters exhibit a significant elevation (31%) in CORT levels. stress effects within lineage (i.e., C-L nonstress condition versus There is no effect of litter sex ratio for either TESTO or leptin.

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Crews et al. www.pnas.org/cgi/content/short/1118514109 5of17 Fig. S1. Experimental design and phenotypic analysis. (A) Paradigm to test the interaction of germ line-dependent (V-L) and context-dependent (CRS during adolescence) epigenetic effects on morphology, physiology, behavior, metabolism, and gene networks in the brain. Individual male rats were weaned at PND 21 and then shipped from WSU to UTA. On receipt, each V-L male was paired with a vehicle C-L male and housed together thereafter. On the day after receipt, half of the pairs were subjected to a regimen of CRS daily for 6 h for 21 d, whereas the other half of the pairs were not stressed. (B) Effects of germ line- dependent (V-L) and context-dependent (stress) epigenetic modifications on BW. Animals were weighed at weaning (PND 21) at WSU and again on receipt at UTA (PND 25). Illustrated is group mean BW (g) ± SEM. Purple, C-L nonstress condition; blue, V-L nonstress condition; yellow, C-L stress condition; and red, V-L stress condition. BW in each group was also compared. C-L stress condition and V-L stress condition are significantly lower than C-L nonstress condition at PND 29 (P = 0.003 and P = 0.012, respectively), PND 32 (P < 0.001 for both), PND 37 (P < 0.001 for both), PND 40 (P < 0.001 for both), PND 46 (P = 0.007 and P = 0.008, respectively), and PND 52 (P = 0.016 and P = 0.003, respectively). At PND 57 only, C-L stress group has a lower BW than C-L nonstress group (P = 0.009). V-L nonstress condition had a significantly higher BW than C-L nonstress condition at PND 46 (P = 0.048), PND 52 (P = 0.013), PND 61 (P = 0.021), and PND 67 (P = 0.046). In the nonstress groups, the V-L males had higher BW than did C-L at PND 52 (P = 0.026) and PND 96 (P = 0.046). There was no significant BW difference between the C-L stress condition and V-L stress condition males. In C-L, CRS had a significant effect on BW at PND 29 (P = 0.002), PND 32.5 (P < 0.002), PND 37 (P < 0.001), PND 40 (P < 0.001), PND 46 (P = 0.003), PND 52 (P = 0.003), PND 57 (P = 0.003), PND 61 (P = 0.028), and PND 67 (P = 0.03). In the nonstress groups, V-L males tend to have a higher BW than C-L males do at PND 52 and PND 96. However, this lineage-specific BW difference was not seen in stress groups. CRS resulted in a decrease in BW in both lineages. This effect diminished after animals had recovered from the CRS treatment (PND 67) in the C-L males. However, Legend continued on following page

Crews et al. www.pnas.org/cgi/content/short/1118514109 6of17 BW in the stress condition continued to be lower than in the nonstress condition in the V-L animals. Exposure to CRS did not seem to have differential effect between two lineages; however, it had a significant effect within a lineage, particularly in V-L males. In these males, the decrease in BW because of the CRS lasted longer than in the C-L males. Therefore, the transgenerational influence of vinclozolin does not affect BW in a synergistic fashion with exposure to CRS; rather, it changes sensitivity toward to external stress during this important life-history stage. (Inset) Graph shows the moving average (n = 3 consecutive weighings) of weight differences within each dyad for stress (red) and nonstress (blue) (V-L minus C-L). (C) Circulating concentrations of CORT and TESTO in V-L and C-L males that received CRS (gray bars). Comparison is with males that did not receive CRS (white bars).

Fig. S2. (Continued)

Crews et al. www.pnas.org/cgi/content/short/1118514109 7of17 Fig. S2. (Continued)

Crews et al. www.pnas.org/cgi/content/short/1118514109 8of17 Fig. S2. Phenotype analysis. (A) Relative importance for each physiological trait (leptin, TESTO, CORT, adrenal weight, testes weight, and BW) across the four principal component axes. On the left are the four principal component axes (PC1–PC4). The loading score for each nuclei is transformed into the relative weight by taking the absolute value and dividing by the sum of the loadings across all nuclei. A value of 1 indicates that the axis is entirely determined by that nucleus, whereas a value of 0 indicates that nucleus contributes no information to that axis. On the right are the interaction plots for each principal componentaxis.NS,not significant. PC1: stress (F =17.8816,P < 0.001, qFDR = 0.002), lineage (F =7.5362,P = 0.001, qFDR = 0.019), interaction (NS). PC2: stress (NS), lineage (NS), interaction (NS). PC3: stress (NS), lineage (F =7.3091,P = 0.01, qFDR = 0.021), interaction (NS). PC4: stress (NS), lineage (NS), interaction (NS). Significance for both main effects and interactions were determined by using ANOVAs and a false discovery rate correction (with qFDR < 0.05 being significant). (B) Relative importance for each behavioral trait (FS, OF, Soc 1, and Soc 2) across the three principal component axes. On the left are the three principal component axes (PC1–PC3). The loading score for each nuclei is transformed into the relative weight by taking the absolute value and dividing by the sum of the loadings across all nuclei. A value of 1 indicates that the axis is entirely determined by that nucleus, whereas a value of 0 indicates that nucleus contributes no information to that axis. On the right are the interaction plots for each principal component axis. NS, not significant. PC1: stress (NS), lineage (NS), interaction (NS). PC2: stress (NS), lineage (NS), interaction (NS). PC3: stress (NS), lineage (NS), interaction (NS). Significance for both main effects and interactions were determined by using ANOVAs and a false discovery rate correction (with qFDR < 0.05 being significant). (C) Relative importance for metabolic activity in each brain nucleus (BLA, MeAmy, CeAmy, CoAmy, PMCo, CA1, CA3, MePD, and ST) measured across the first four principal component axes. On the left are the four principal component axes (PC1–PC4). The loading score for each nuclei is transformed into the relative weight by taking the absolute value and dividing by the sum of the loadings across all nuclei. A value of 1 indicates that the axis is entirely determined by that nucleus, whereas a value of 0 indicates that nucleus contributes no information to that axis. On the right are the interaction plots for each principal component axis. An interaction plot represents the effect of treatment and stress for each of the four axes. NS, not significant. PC1; stress, (NS), lineage (F =6.545,P = 0.016, qFDR = 0.028), interaction (NS). PC2: stress (NS), lineage (NS), interaction (NS). PC3: stress (NS), lineage (NS), interaction (F =4.639,P = 0.040, qFDR = 0.055). PC4: stress (NS), lineage (F =8.60,P = 0.007, qFDR = 0.021). Significance for both main effects and interactions were determined by using ANOVAs and a false discovery rate correction (with qFDR < 0.05 being significant).

Crews et al. www.pnas.org/cgi/content/short/1118514109 9of17 Fig. S3. Sample histograms and box plots for raw microarray signals (A and D) or for signals preprocessed with RMA GC content-adjusted algorithm (B, C, E, and D) for CRTX (A and C), BLA (A and B), CA1 (D and E), and CA3 (D and F).

Crews et al. www.pnas.org/cgi/content/short/1118514109 10 of 17 Fig. S4. Venn diagrams of four differentially expressed gene lists obtained by contrasting VNS V-L nonstress condition vs. C-L nonstress condition (NstV vs. NstC), V-L stress condition vs. C-L stress condition (StV vs. StC), C-L stress condition vs. C-L nonstress condition (StC vs. NstC), or V-L stress condition vs. V-L nonstress condition (StV vs. NstV) shown for CRTX (C), BLA (A), CA1 (B), and CA3 (D). (E, F, G, and H) Venn diagrams for the same lists showing how each of the four brain regions overlap. Numbers in brackets show number of differentially expressed probe sets.

Crews et al. www.pnas.org/cgi/content/short/1118514109 11 of 17 Fig. S5. Bar graph showing the number of genes differentially expressed and associated with functional categories in the brain. (A) BLA. (B) CRTX. (C) CA1. (D) CA3. Yellow, V-L nonstress vs. C-L nonstress differentially expressed genes (lists 1, 5, 9, and 13); green, V-L stress vs. C-L stress (lists 2, 6, 10, and 14); blue, C-L stress vs. C-L nonstress (lists 3, 7, 11, and 15); and red, V-L stress vs. V-L nonstress (lists 4, 8, 12, 16).

Fig. S6. Olfactory transduction pathway (Kyoto Encyclopedia of Genes and Genomes, http://www.genome.jp/kegg/) showing genes affected by either CRS during adolescence (stress) or transgenerational epigenetic modification by vinclozolin (lineage) at least in one of four studied brain regions: CRTX, BLA, CA1, or CA3. Red box, up-regulated ; blue boxes, down-regulated; green boxes, not affected. Extended lists of genes for two pathway entities (R and PKA) are shown in beige boxes.

Crews et al. www.pnas.org/cgi/content/short/1118514109 12 of 17 Fig. S7. Calcium signaling pathway (A) and MAPK signaling pathway (B) (Kyoto Encyclopedia of Genes and Genomes, http://www.genome.jp/kegg/) showing genes affected by either stress or lineage at least in one of four studied brain regions: CRTX, BLA, CA1, and CA3. Red boxes are up-regulated; blue boxes are down-regulated; and green boxes are not affected.

Crews et al. www.pnas.org/cgi/content/short/1118514109 13 of 17 Fig. S8. Subnetworks of shortest connections including cell processes for genes affected by either stress or lineage in BLA (combined gene lists 1–4; A) or CA3 (combined gene lists 13–16; B) obtained by global literature analysis using Pathway Studio 7.0 software (Ariadne Genomics). (A) For BLA, 49 affected genes of 125 genes (no ESTs included) are shown as red or blue. (B) For CA3, 60 affected genes of 198 genes (no ESTs) are shown as red or blue. The rest of affected genes are not connected and not shown. Oval and circle, protein; diamond, ligand; ice cream cone, receptor; circle/oval on tripod platform, transcription factor; crescent, protein kinase and kinase; irregular polygon, phosphatase. Red, up-regulated genes; blue, down-regulated genes; arrows with plus sign, positive regulation/activation; arrows with minus sign, negative regulation/inhibition; gray arrows, regulation; lilac, expression; purple, binding; green, promoter binding.

Crews et al. www.pnas.org/cgi/content/short/1118514109 14 of 17 Fig. S9. Images of different stages of brain processing. (A) Rats from one dyad were processed simultaneously. Before freezing, the brain was cut sagittally along the midline. The symmetrical brain halves were then recombined with one side from the vinclozolin individual and the other from the control individual; the sides used were alternated to control for possible asymmetries in activity. One such “brain” was used for metabolic studies and the other for RNA studies. (AA) Brain in sagittal block. (AB) Razor cutting brain along midline in sagittal plane. (AC) Two halves of brain shown. (AD) Recombining of brain halves; one half is from the V-L individual and the other from the C-L individual in the dyad. (AE) Brain being blocked into 2-mm slices. (AF) Target slices of recombined brain. (AG) Frozen slices of recombined brain showing 1-mm punches on one half (one individual) of sampled brain areas. (B) Cytochrome oxidase histo- chemistry of 40-μm sections of a recombined brain (left half is from V-L individual and right half is from C-L individual). Different levels indicate different brain regions analyzed: BLA, CA1, and CA3.

Crews et al. www.pnas.org/cgi/content/short/1118514109 15 of 17 Table S1. Metabolic activity (abundance of cytochrome oxidase) in brain nuclei in V-L and C-L male rats that received CRS during adolescence Mean activity value Percentage of maximum Percentage change

CNS vs. CS vs. CNS vs. VNS vs. Nucleus CNS VNS CS VS CNS VNS CS VS VNS VS CS VS

BLA 207.70 198.80 213.36 200.69 97.3 93.2 100.0 94.1 −4.2 −5.9 2.7 0.9 BnSTl 208.82 204.36 203.06 207.47 100.0 97.9 97.2 99.4 −2.1 2.1 −2.8 1.5 BnSTm 205.58 197.59 204.33 201.59 100.0 96.1 99.4 98.1 −3.9 −1.3 −0.6 1.9 CA1 157.95 157.41 152.34 141.65 100.0 99.7 96.4 89.7 −0.3 −6.8 −3.6 −10.0 CA3 159.54 156.31 160.11 142.16 99.6 97.6 100.0 88.8 −2.0 −11.2 0.4 −8.8 CeAmy 175.72 178.02 174.78 168.64 98.7 100.0 98.2 94.7 1.3 −3.5 −0.5 −5.3 CoAmy 159.91 152.69 161.40 157.46 99.1 94.6 100.0 97.6 −4.5 −2.4 0.9 3.0 CRTX 223.69 236.90 235.57 229.76 94.4 100.0 99.4 97.0 5.6 −2.5 5.0 −3.0 MeAmy 152.50 162.73 166.48 165.13 91.6 97.7 100.0 99.2 6.1 −0.8 8.4 1.4 MePD 205.56 203.31 226.58 185.28 90.7 89.7 100.0 81.8 −1.0 −18.2 9.3 −8.0 MPOA 201.14 197.50 198.19 189.12 100.0 98.2 98.5 94.0 −1.8 −4.5 −1.5 −4.2 PMCo 221.05 182.06 210.09 180.53 100.0 82.4 95.0 81.7 −17.64 −13.4 −5.0 −0.7 ST 245.28 247.57 241.44 274.92 89.2 90.0 87.8 100.0 0.8 12.2 −1.4 10.0 VMH 202.36 191.03 207.71 202.27 97.4 92.0 100.0 97.4 −5.5 −2.6 2.6 5.4

Control Non-Stress meAmy; MePD Control Stress

CA3; MePD; PMCo Lineage Stress Effect PMCo; ST Effect

Vinclozolin Non-Stress CA1, CCAA3, MePD, ST Vinclozolin Stress

Boldface values in the percentage change columns indicate comparisons that were equal to or greater than 8% change. Schematic indicates those bolded nuclei in terms of comparison (lineage comparisons vertical vs. stress comparisons horizontal), indicated in the center cell of the 3 × 3 grid.

Table S2. Abbreviations for brain nuclei imaged for cytochrome histochemistry abundance (per ref. 1) Abbreviation Definition

BLA Basolateral amygdaloid nucleus BnSTl Bed nucleus of the stria terminalis, anterolateral division BnSTm Bed nucleus of the stria terminalis, anteromedial division CA1 CA1 area of the hippocampus CA3 CA3 area of the hippocampus CeAmy Central amygdaloid nucleus CoAmy Anterior cortical amygdaloid nucleus CRTX Primary and secondary motor cortex MeAmy Medial amygdaloid nucleus MePD Medial amygdaloid nucleus, posterior dorsal part MPOA Medial preoptic area PMCo Posteromedial cortical amygdaloid nucleus PVN Periventricular hypothalamic nucleus ST Stria terminalis VMH Ventromedial hypothalamic nucleus

1. Paxinos G, Watson C (2007) The Rat Brain in Stereotaxic Coordinates (Academic, New York).

Crews et al. www.pnas.org/cgi/content/short/1118514109 16 of 17 Table S3. Altered gene sets for V-L and C-L male rats subjected to CRS during adolescence List no. Effect Comparison No. of altered genes

BLA 1 Lineage Nonstress V-L vs. nonstress C-L 79 2 Lineage Stress V-L vs. stress C-L 101 3 Stress Stress C-L vs. nonstress C-L 81 4 Stress Stress V-L vs. nonstress V-L 62 CRTX 5 Lineage Nonstress V-L vs. nonstress C-L 118 6 Lineage Stress V-L vs. stress C-L 142 7 Stress Stress C-L vs. nonstress C-L 290 8 Stress Stress V-L vs. nonstress V-L 96 CA1 9 Lineage Nonstress V-L vs. nonstress C-L 68 10 Lineage Stress V-L vs. stress C-L 155 11 Stress Stress C-L vs. nonstress C-L 118 12 Stress Stress V-L vs. nonstress V-L 379 CA3 13 Lineage Nonstress V-L vs. nonstress C-L 64 14 Lineage Stress V-L vs. stress C-L 23 15 Stress Stress C-L vs. nonstress C-L 50 16 Stress Stress V-L vs. nonstress V-L 202

Table S4. Number of altered genes in specific brain regions according to signaling pathways and cellular processes No. of genes altered in tissue list no.

BLA CRTX CA1 CA3 No. of altered Pathway name genes 123456 7 8910111213141516

Olfactory transduction 78 3 4 1 4 6 8 17 2 3 9 3 17 4 2 9 Calcium signaling pathway 18 1 1 4 3 1 1 6 1 1 Neuroactive ligand–receptor interaction 16 1 1 2 3 2 7 MAPK signaling pathway 13 1 2 1 1 1 2 1 4 1 2 Huntington disease 13 1 1 1 1 2 1 4 3 1 Pathways in cancer 12 1 1 2 1 1 1 1 3 1 2 Endocytosis 11 1 1 2 1 2 4 1 2 Alzheimer’s disease 11 1 2 4 3 1 Cell adhesion molecules (CAMs) 10 1 1 3 3 1 3 Cytokine–cytokine receptor interaction 10 4 5 5 Axon guidance 9 3 1 1 2 1 3 Metabolism of xenobiotics by P450 9 1 1 1 2 4 1 Drug metabolism, cytochrome P450 9 1 1 1 2 4 1 Phagosome 9 2 1 1 4 4 Oxidative phosphorylation 9 1 1 2 4 1 Parkinson disease 9 1 2 1 4 2 Retinol metabolism 8 1 1 1 1 2 1 2 Regulation of actin cytoskeleton 8 1 1 1 2 1 2 PPAR signaling pathway 8 1 2 1 4 1

Dataset S1. Genes expressed differentially in four brain regions in lineage and stress comparisons

Dataset S1 (PDF)

Crews et al. www.pnas.org/cgi/content/short/1118514109 17 of 17 Supplemental Dataset S1.

Genes Expressed Differentially in Four F3-Rat Brain Regions in Lineage and Stress Comparisons (16 gene lists)

1

List 1. Genes Expressed Differentially in Non-Stressed F3-Vinclozolin Rat Basolateral Amygdala as Compared to Non-Stressed F3-Control ('Nst-Vin vs Nst-Con' contrast), 79 genes and EST's GenBank_Reference Mean Affymetrix Gene Symbol Ratio Gene Title Sequence _diff ID Epigenetics RNA (guanine-9-) methyltransferase domain Rg9mtd1 NM_001008337 -25 0.83 10750795 containing 1 LOC365114 ENSRNOT00000018945 -36 0.82 10703187 similar to High mobility group protein 1 (HMG-1) Growth Factors Bmp5 NM_001108168 15 1.24 10911711 bone morphogenetic protein 5 Mid1 NM_022927 -44 0.83 10937624 midline 1 Immune Response Spag6 NM_001034960 62 1.23 10752563 sperm associated antigen 6 Metabolism & Transport Doc2b NM_031142 -25 0.83 10744970 double C2-like domains, beta Retsat NM_145084 94 1.26 10856424 retinol saturase (all trans retinol 13,14 reductase) Proteolysis serine (or cysteine) peptidase inhibitor, clade A, Serpina3k NM_012657 -47 0.68 10891991 member 3K Receptors & Binding Proteins killer cell lectin-like receptor, subfamily A, member Klra5 NM_198746 16 1.27 10866236 5 Ly49s5 ENSRNOT00000045309 23 1.22 10866180 Ly49 stimulatory receptor 4 Olr1149 NM_001000874 17 1.29 10915281 olfactory receptor 1149 Olr1233 NM_001001084 -42 0.76 10909168 olfactory receptor 1233 Olr1571 ENSRNOT00000034210 24 1.27 10752574 olfactory receptor 1571 Htr5b NM_024395 -15 0.81 10767186 5-hydroxytryptamine (serotonin) receptor 5B Efcab1 NM_001106930 42 1.29 10931558 EF hand calcium binding domain 1 Signaling Stac2 NM_001108834 38 1.28 10746842 SH3 and cysteine rich domain 2 MAS-related G protein-coupled receptor, member Mrgprb5 NM_001002284 47 1.21 10707154 B5 Sh2d1b1 ENSRNOT00000048692 -10 0.79 10765469 SH2 domain protein 1B1 Tpte NM_001108877 10 1.22 10792456 transmembrane phosphatase with tensin homology Transcription Npas4 NM_153626 31 1.20 10727717 neuronal PAS domain protein 4 Set NM_001012504 -164 0.80 10749869 SET nuclear oncogene Translation & Protein Modification RGD1564552 ENSRNOT00000050803 -141 0.73 10799888 similar to ribosomal protein L21 Miscellaneous & Unknown similar to Leukosialin precursor (Leucocyte LOC288521 BC079301 -12 0.76 10760760 sialoglycoprotein) (Sialophorin) (CD43) (W3 RGD1311849 ENSRNOT00000058387 26 1.22 10869837 similar to mKIAA1797 protein RGD1565119 ENSRNOT00000048106 -14 0.79 10776873 similar to Mitochondrial carrier triple repeat 1 Ccdc162 ENSRNOT00000000340 13 1.25 10833727 coiled-coil domain containing 162 rno-mir-21 rno-mir-21 30 1.25 10745931 XM_002725832 -9 0.80 10831802 rCG44733-like 2 LOC100363863 EST's LOC363737 ENSRNOT00000032643 -9 0.78 10750089 hypothetical LOC363737 XR_008519 -24 0.82 10732906 XR_008445 -121 0.78 10880562 XR_007871 -198 0.83 10927699 XR_007680 15 1.27 10791977 XR_007365 -115 0.83 10813246 XR_006323 -10 0.82 10923292 XR_005743 -7 0.82 10937252 XR_005657 -20 0.79 10898947 XR_005430 63 1.24 10877896 XM_226468 36 1.30 10807925 NC_001665 -1186 0.74 10930595 ENSRNOT00000060361 29 1.25 10889368 ENSRNOT00000053328 -232 0.76 10855946 ENSRNOT00000053029 32 1.25 10774265 ENSRNOT00000052710 -101 0.79 10838282 59896131, 41350416 12 1.30 10769693 --- -1953 0.74 10930580 --- -127 0.81 10772758 --- -88 0.83 10811008 --- -80 0.80 10761245 --- -58 0.82 10711498 --- -49 0.77 10864479 --- -42 0.79 10832081 --- -15 0.76 10795677 --- -13 0.82 10836152 --- -7 0.79 10870488 --- 4 1.23 10814661 --- 6 1.23 10932910 --- 7 1.21 10936478 --- 8 1.20 10709532 --- 8 1.22 10799500 --- 8 1.24 10768128 --- 9 1.28 10716744 --- 10 1.24 10702076 --- 12 1.27 10884614 --- 12 1.23 10815913 --- 12 1.27 10820963 --- 12 1.22 10781972 --- 13 1.26 10785259 --- 14 1.21 10782889 --- 18 1.24 10893434 --- 19 1.22 10861656 --- 19 1.20 10917344 --- 20 1.22 10816647 --- 21 1.23 10726652 --- 21 1.29 10776796 --- 27 1.23 10813005 --- 28 1.30 10815350 --- 29 1.24 10873885

List 2. Genes Expressed Differentially in Stressed F3-Vinclozolin Rat Basolateral Amygdala as Compared to Stressed F3-Control ('St-Vin vs St-Con' contrast), 101 genes and EST's Gene Symbol GenBank_Reference Mean Ratio Affymetrix Gene Title

3 Sequence _diff ID Cell Cycle Cdca3 NM_001007648 -46 0.80 10858707 cell division cycle associated 3 Cytoskeleton- ECM Pcdhb6 NM_001014780 47 1.24 10801176 protocadherin beta 6 Development oligodendrocytic myelin paranodal and inner loop Opalin NM_001017386 -66 0.79 10730148 protein Mtpn AY951952 -11 0.83 10861826 myotrophin Growth Factors Bdnf NM_012513 25 1.21 10852620 brain derived neurotrophic factor Metabolism & Transport Kcnt2 NM_198762 79 1.26 10764460 potassium channel, subfamily T, member 2 LOC685173 XM_001062675 -18 0.77 10899693 similar to carbonic anhydrase 13 Proteolysis serine (or cysteine) peptidase inhibitor, clade B, RGD1560658 ENSRNOT00000022681 10 1.31 10798126 member 1b Receptors & Binding Proteins Olr1171 NM_001001005 17 1.28 10915295 olfactory receptor 1171 Olr1742 NM_001001424 13 1.26 10827655 olfactory receptor 1742 Olr349 NM_001001019 23 1.32 10729045 olfactory receptor 349 Olr679 NM_001000354 16 1.23 10847168 olfactory receptor 679 Olr720 NM_001001067 28 1.21 10847229 olfactory receptor 720 Signaling ArfGAP with RhoGAP domain, ankyrin repeat and Arap2 ENSRNOT00000044580 -18 0.78 10772895 PH domain 2 Ctxn2 NM_001162935 36 1.25 10839365 cortexin 2 RGD1562952 ENSRNOT00000061017 -238 0.72 10812779 similar to Erbb2 interacting protein isoform 2 Transcription similar to High mobility group protein 1 (HMG-1) (High mobility group protein B1) (Amphoterin) LOC365114 ENSRNOT00000018945 -37 0.83 10703187 (Heparin-binding protein p30) Set NM_001012504 -189 0.80 10749869 SET nuclear oncogene Translation & Protein Modification Rps27a ENSRNOT00000042383 -110 0.81 10734318 similar to thymosin, beta 4 RGD1562547 ENSRNOT00000049211 -62 0.82 10901960 similar to ribosomal protein L31 similar to Eukaryotic translation initiation factor 5 RGD1564400 ENSRNOT00000033258 -87 0.81 10836556 (eIF-5) RGD1564552 ENSRNOT00000050803 -112 0.78 10799888 similar to ribosomal protein L21 Miscellaneous & Unknown LOC686096 XM_002730304 -116 0.82 10939909 similar to basic transcription factor 3 EST's MGC72627 BC061963 55 1.20 10853407 similar to RIKEN cDNA A330021E22 RGD1560493 ENSRNOT00000032053 21 1.24 10937331 similar to chromosome X open reading frame 45 XR_008237 -38 0.80 10926160 XR_007324 -23 0.80 10877933 XR_007098 -20 0.83 10707370 XR_009222 -50 0.69 10729312 XR_008445 -162 0.72 10880562 4 XR_007232 -14 0.75 10784444 XR_005958 -9 0.82 10793706 XR_008485 -12 0.83 10794940 XR_008126 9 1.29 10822090 XR_007395 -13 0.70 10850440 XR_009494 -8 0.82 10739816 NC_001665 -1372 0.60 10930588 6683748 -70 0.79 10748234 ENSRNOT00000059477 -105 0.69 10791602 ENSRNOT00000057420 -105 0.69 10833416 ENSRNOT00000056786 -145 0.67 10939699 ENSRNOT00000054649 -189 0.82 10930226 ENSRNOT00000054517 -107 0.67 10797013 ENSRNOT00000053934 -363 0.82 10722465 ENSRNOT00000052710 -130 0.76 10838282 ENSRNOT00000052697 12 1.27 10878963 ENSRNOT00000052541 -30 0.69 10911811 ENSRNOT00000018011 -15 0.76 10926819

ENSRNOT00000039948 -36 0.82 10767044 --- -263 0.74 10722451 --- -583 0.80 10722481 --- -83 0.81 10869614 --- -65 0.83 10846749 --- -58 0.81 10756253 --- -58 0.81 10756255 --- -54 0.77 10858497 --- -35 0.79 10853681 --- -28 0.80 10764400 --- -21 0.78 10907958 --- -20 0.71 10925371 --- -17 0.78 10769398 --- -16 0.79 10773706 --- -13 0.78 10746252 --- -12 0.81 10776665 --- -11 0.83 10795677 --- -5 0.81 10757702 --- 6 1.20 10853227 --- 7 1.22 10724580 --- 8 1.22 10751226 --- 8 1.30 10718406 --- 9 1.23 10823430 --- 9 1.20 10782954 --- 9 1.24 10931079 --- 10 1.26 10812884 --- 11 1.27 10870012 --- 11 1.25 10785259 --- 11 1.22 10778575 --- 12 1.21 10717396 --- 12 1.28 10922247 --- 12 1.22 10795717 --- 13 1.26 10857000 --- 13 1.25 10781972 --- 13 1.32 10893404 --- 13 1.23 10887074 --- 13 1.23 10752096

5 --- 14 1.20 10711257 --- 15 1.26 10707254 --- 17 1.20 10792099 --- 17 1.26 10890570 --- 17 1.29 10917318 --- 18 1.23 10868794 --- 25 1.43 10939931 --- 25 1.41 10920630 --- 25 1.24 10939899 --- 27 1.23 10801707 --- 29 1.23 10909070 --- 30 1.30 10772554 --- 39 1.31 10846650 --- 40 1.29 10791561

List 3. Genes Expressed Differentially in Stressed F3-Control Rat Basolateral Amygdala as Compared to Non- Stressed F3-Control ('Str-Con vs Nst-Con' contrast), 81 genes and EST's GenBank_Reference Mean Affymetrix Gene Symbol Ratio Gene Title Sequence _diff ID Cytoskeleton- ECM Tspan33 NM_001109227 -85 0.81 10854199 tetraspanin 33 Coro1a NM_130411 -152 0.76 10725806 coronin, actin binding protein 1A Dbnl NM_031352 -56 0.83 10773999 drebrin-like Development Baalc NM_144762 -53 0.82 10896250 brain and acute leukemia, cytoplasmic Cpne4 NM_001109003 -141 0.62 10912718 copine IV Nell2 NM_031070 -274 0.83 10906546 NEL-like 2 (chicken) Ntng2 NM_001107825 -26 0.83 10844082 netrin G2 similar to Discs, large homolog 5 (Placenta and RGD1563738 ENSRNOT00000052026 20 1.29 10909263 prostate DLG) Sprn NM_001031845 -83 0.79 10726620 shadow of prion protein homolog (zebrafish) Synj2 NM_001113371 -106 0.67 10702829 synaptojanin 2 Synpo2 ENSRNOT00000019931 8 1.20 10826541 synaptopodin 2 Tmem59l BC089056 -110 0.81 10787556 transmembrane protein 59-like transient receptor potential cation channel, Trpc4 NM_080396 -83 0.62 10815352 subfamily C, member 4 Epigenetics Cog7 NM_001033889 -41 0.82 10725427 component of oligomeric golgi complex 7 Growth Factors Bdnf NM_012513 -25 0.83 10852620 brain derived neurotrophic factor Fgf1 NM_012846 9 1.26 10804127 fibroblast growth factor 1 Immune Response Igha BC092592 18 1.29 10892572 immunoglobulin heavy chain, alpha killer cell lectin-like receptor, subfamily A, member Klra7 XM_578407 23 1.45 10866140 7 Mal2 NM_198786 -356 0.72 10896533 mal, T-cell differentiation protein 2 Metabolism & Transport potassium inwardly-rectifying channel, subfamily J, Kcnj9 NM_053834 -20 0.81 10770022 member 9 Kcnn2 NM_019314 -67 0.82 10801520 potassium intermediate Kcnt2 NM_198762 -125 0.71 10764460 potassium channel, subfamily T, member 2 Atp6v1a NM_001108318 -536 0.81 10823609 ATPase, H+ transporting, lysosomal V1 subunit A

6 Cth NM_017074 -25 0.83 10827517 cystathionase (cystathionine gamma-lyase) Fetub NM_053348 -26 0.78 10755148 fetuin B Msra NM_053307 -42 0.78 10784517 methionine sulfoxide reductase A Ppap2a NM_022538 -114 0.78 10813048 phosphatidic acid phosphatase type 2A Syp NM_012664 -568 0.82 10937103 synaptophysin Faah NM_024132 -82 0.77 10871182 fatty acid amide hydrolase LOC685173 XM_001062675 16 1.25 10899693 similar to carbonic anhydrase 13 Proteolysis Prcp NM_001106281 -45 0.82 10708672 prolylcarboxypeptidase (angiotensinase C) Receptors & Binding Proteins Olr98 NM_001000143 16 1.22 10709432 olfactory receptor 98 RGD1560871 ENSRNOT00000022951 -71 0.79 10863960 similar to plexin 1 Nrp1 NM_145098 -45 0.70 10808959 neuropilin 1 Signaling CKLF-like MARVEL transmembrane domain Cmtm4 NM_001172151 -83 0.83 10805716 containing 4 Ehd3 NM_138890 -108 0.79 10888596 EH-domain containing 3 Hpcal4 NM_017357 -255 0.81 10871732 hippocalcin-like 4 Ifi27l1 NM_203410 -168 0.79 10886573 interferon, alpha-inducible protein 27 protein kinase, cAMP dependent regulatory, type I, Prkar1b NM_001033679 -204 0.80 10757119 beta RGD1561667 ENSRNOT00000059957 25 1.24 10703287 similar to putative protein kinase src homology 2 domain-containing transforming Shd NM_001108223 -29 0.82 10931523 protein D Tmem74 ENSRNOT00000006791 -47 0.77 10903560 transmembrane protein 74 Srgap1 ENSRNOT00000006180 35 1.36 10902765 SLIT-ROBO Rho GTPase activating protein 1 Translation & Protein Modification Bin1 NM_053959 -210 0.83 10800760 bridging integrator 1 Ccdc32 NM_001024245 -111 0.80 10848499 coiled-coil domain containing 32 Dnajb1 NM_001108441 -74 0.77 10810295 DnaJ (Hsp40) homolog, subfamily B, member 1 Translation RGD1562547 ENSRNOT00000049211 67 1.24 10901960 similar to ribosomal protein L31 Rps21 NM_031111 104 1.23 10873649 ribosomal protein S21 Miscellaneous & Unknown Fam40a ENSRNOT00000025036 -46 0.80 10825830 family with sequence similarity 40, member A LOC501427 ENSRNOT00000061060 9 1.26 10779531 similar to Spetex-2F protein Wdr1 NM_001014135 -165 0.83 10773205 WD repeat domain 1 EST's LOC498145 NM_001017485 -57 0.81 10760393 similar to RIKEN cDNA 2810453I06 ENSRNOT00000048364 -14 0.76 10900112 ENSRNOT00000052541 27 1.39 10911811 ENSRNOT00000057420 112 1.49 10833416 ENSRNOT00000059477 112 1.49 10791602 NC_001665 1587 1.35 10930595 NC_001665 1419 1.69 10930588 --- -51 0.70 10755315 --- -18 0.77 10917318 --- -15 0.82 10782179 --- -11 0.75 10707639 --- -9 0.81 10850610 --- -8 0.83 10931079 --- -5 0.83 10891491 7 --- 8 1.30 10856117 --- 9 1.30 10850313 XR_007232 10 1.23 10784444 --- 10 1.27 10909127 --- 10 1.24 10702076 --- 11 1.22 10776665 XR_008088 12 1.24 10786415 --- 12 1.23 10818253 --- 34 1.25 10853681 --- 36 1.21 10847062 --- 45 1.36 10914009 --- 51 1.28 10858497 --- 66 1.28 10756253 --- 66 1.28 10756255 --- 807 1.26 10930622 --- 969 1.29 10930560

List 4. Genes Expressed Differentially in Stressed F3-Vinclozolin Rat Basolateral Amygdala as Compared to Non-Stressed F3-Vinclozolin ('Str-Vin vs Nst-Vin' contrast), 62 genes and EST's

GenBank_Reference Mean Affymetrix Gene Symbol Ratio Gene Title Sequence _diff ID Development ganglioside-induced differentiation-associated Gdap1l1 NM_001107798 -47 0.83 10842001 protein 1-like 1 similar to Discs large homolog 5 (Placenta and LOC689690 ENSRNOT00000052385 39 1.44 10809503 prostate DLG) (Discs large protein P-dlg) Nptx2 NM_001034199 -106 0.74 10760290 neuronal pentraxin 2 similar to Discs, large homolog 5 (Placenta and RGD1563738 ENSRNOT00000052026 15 1.21 10916360 prostate DLG) Sntb2 NM_001168674 37 1.21 10807601 syntrophin, beta 2 Electron Transport cytochrome P450, family 26, subfamily b, Cyp26b1 NM_181087 -31 0.77 10863608 polypeptide 1 Epigenetics LOC689244 ENSRNOT00000061517 127 1.50 10756280 similar to chromobox homolog 3 LOC501799 ENSRNOT00000061397 163 1.34 10756257 similar to chromobox homolog 3 Immune Response Igsf21 ENSRNOT00000051793 -52 0.81 10880936 immunoglobin superfamily, member 21 RT1-CE10 NM_001008833 29 1.26 10828001 RT1 class I, locus CE10 Metabolism & Transport potassium voltage gated channel, shaker related Kcna6 NM_023954 -75 0.81 10865738 subfamily, member 6 potassium inwardly-rectifying channel, subfamily J, Kcnj9 NM_053834 -20 0.82 10770022 member 9 Alas2 NM_013197 17 1.21 10932912 aminolevulinate, delta-, synthase 2 Decr1 NM_057197 51 1.23 10875631 2,4-dienoyl CoA reductase 1, mitochondrial Hpgd NM_024390 17 1.29 10791522 hydroxyprostaglandin dehydrogenase 15 (NAD) Proteolysis similar to ubiquitin-conjugating enzyme E2G 1 RGD1559940 ENSRNOT00000038310 12 1.20 10900050 (UBC7 homolog, C. elegans) Receptors & Binding

8 Proteins Olr1093 NM_001001388 41 1.23 10901100 olfactory receptor 1093 Olr1117 NM_001000884 -15 0.81 10915199 olfactory receptor 1117 Olr668 NM_001000348 -12 0.80 10847146 olfactory receptor 668 Olr995 NM_001000938 16 1.30 10893373 olfactory receptor 995 Grm2 NM_001105711 -65 0.67 10919953 glutamate receptor, metabotropic 2 LOC304239 ENSRNOT00000049215 37 1.27 10756334 similar to RalA binding protein 1 Vom2r1 NM_001099460 27 1.24 10701668 vomeronasal 2 receptor, 3 Vom2r2 ENSRNOT00000051591 8 1.20 10701636 vomeronasal 2 receptor, 2 Signaling Arrb2 NM_012911 -43 0.82 10735205 arrestin, beta 2 Exph5 ENSRNOT00000039336 -19 0.81 10909987 exophilin 5 RGD1560209 ENSRNOT00000047232 15 1.20 10796831 similar to MAP Sh2d1b1 ENSRNOT00000048692 9 1.24 10765469 SH2 domain protein 1B1 Stac2 NM_001108834 -36 0.79 10746842 SH3 and cysteine rich domain 2 Transcription Junb NM_021836 -25 0.80 10806585 jun B proto-oncogene Mtpn AY951952 -11 0.82 10861826 myotrophin Znf622 NM_001034912 -94 0.83 10813934 family with sequence similarity 134, member B Miscellaneous & Unknown LOC501427 ENSRNOT00000061060 8 1.28 10779531 similar to Spetex-2F protein RGD1561734 ENSRNOT00000056348 -53 0.79 10925933 similar to KIAA1913 EST's LOC363337 BC082068 31 1.21 10931083 similar to RIKEN cDNA 1700081O22 XR_007680 -14 0.79 10791977 XR_006025 -5 0.80 10775566 XM_001080565 51 1.21 10729852 NC_001665 1455 1.43 10930595 NC_001665 804 1.62 10930588 ENSRNOT00000055830 66 1.23 10859162 ENSRNOT00000053106 -12 0.83 10908229 ENSRNOT00000053029 -30 0.82 10774265 ENSRNOT00000040251 -9 0.83 10868279 59896131, 41350416 -14 0.72 10769693 --- -31 0.75 10815350 --- -54 0.83 10871661 --- -23 0.76 10775577 --- -11 0.83 10932132 --- -9 0.81 10929592 --- -7 0.81 10729120 --- 5 1.22 10746914 --- 5 1.24 10852168 --- 11 1.29 10857203 --- 19 1.21 10809071 --- 25 1.28 10802574 --- 37 1.22 10864479 --- 48 1.42 10726672 --- 151 1.21 10718134 --- 763 1.27 10930560 --- 930 1.36 10930622 --- 2253 1.41 10930580

List 5. Genes Expressed Differentially in Non-Stressed F3-Vinclozolin Rat Cortex Region as Compared to Non- Stressed F3-Control ('Nst-Vin vs Nst-Con' contrast), 118 genes and EST's Gene Symbol GenBank_Reference Mean Ratio Affymetrix Gene Title

9 Sequence _diff ID Cytoskeleton- ECM Pcdhb19 ENSRNOT00000060484 28 1.22 10801204 protocadherin beta 19 Development Egln2 NM_001004083 57 1.22 10719958 EGL nine homolog 2 (C. elegans) similar to Vomeronasal secretory protein 2 precursor (Vomeronasal secretory protein II) (VNSP II) LOC681385 ENSRNOT00000067576 6 1.23 10843857 (Lipocalin-4) Electron Transport cytochrome P450, family 2, subfamily r, Cyp2r1 NM_001108499 -13 0.79 10725045 polypeptide 1 LOC305698 ENSRNOT00000049636 -28 0.83 10779240 similar to RIKEN cDNA 1700001F09 Epigenetics Mettl11a NM_001025019 33 1.20 10835252 methyltransferase like 11A Hist1h4b NM_022686 125 1.20 10798490 histone cluster 1, H4b Growth Factors Ccl27 NM_001108660 90 1.22 10876193 chemokine (C-C motif) ligand 27 Hormones Gphb5 NM_001007013 -12 0.83 10890626 glycoprotein hormone beta 5 Pth NM_017044 12 1.21 10724987 parathyroid hormone Immune Response Btnl7 NM_212488 -40 0.82 10828335 butyrophilin-like 7 Ly6b NM_139257 6 1.25 10904590 lymphocyte antigen 6 complex, locus B Slamf9 NM_001105971 -12 0.83 10765746 SLAM family member 9 Metabolism & Transport Akr1b7 NM_053781 6 1.22 10854427 aldo-keto reductase family 1, member B7 aldo-keto reductase family 1, member D1 (delta 4-3- Akr1d1 NM_138884 -15 0.78 10854548 ketosteroid-5-beta-reductase) Apool NM_001014105 -23 0.81 10934700 apolipoprotein O-like Bphl NM_001037206 13 1.25 10798100 biphenyl hydrolase-like (serine hydrolase) Commd8 NM_001106004 -28 0.83 10772517 COMM domain containing 8 NADH dehydrogenase (ubiquinone) 1 alpha Ndufa1 NM_001108813 66 1.20 10931991 subcomplex, 1 Nqo2 NM_001004214 -58 0.69 10798119 NAD(P)H dehydrogenase, quinone 2 platelet-activating factor acetylhydrolase, isoform Pafah1b3 NM_053654 -48 0.82 10719817 1b, subunit 3 Sepw1 NM_013027 68 1.21 10719212 selenoprotein W, 1 Mgst1 NM_134349 23 1.21 10859392 microsomal glutathione S-transferase 1 Cerkl ENSRNOT00000043238 6 1.20 10846671 ceramide kinase-like Proteolysis Slpil2 NM_001008872 13 1.29 10851573 antileukoproteinase-like 2 Receptors & Binding Proteins Agtr1b NM_031009 -17 0.82 10822516 angiotensin II receptor, type 1b Epha8 ENSRNOT00000017559 -15 0.81 10880738 Eph receptor A8 Igfbp6 NM_013104 -149 0.62 10899465 insulin-like growth factor binding protein 6 Olr1060 NM_001000698 26 1.68 10900087 olfactory receptor 1060 Olr1237 NM_001000963 11 1.28 10909176 olfactory receptor 1237 Olr1560 NM_001001009 27 1.22 10750649 olfactory receptor 1560 Olr29 NM_001000691 24 1.35 10723519 olfactory receptor 29 Olr481 NM_001000684 -13 0.83 10846950 olfactory receptor 481 10 Olr631 NM_001000339 -49 0.81 10847113 olfactory receptor 631 Olr703 NM_001000359 7 1.20 10847193 olfactory receptor 703 Olr724 NM_001000573 -12 0.80 10847233 olfactory receptor 724 Taar8a NM_175599 8 1.23 10717268 trace amine-associated receptor 8a Signaling LOC689617 ENSRNOT00000058250 36 1.36 10815215 similar to GTPase activating protein testicular GAP1 Mrgprb4 ENSRNOT00000045792 -43 0.73 10722218 MAS-related GPR, member B4 Rassf9 NM_022959 -12 0.83 10895247 Ras association (RalGDS Scube1 NM_001134884 38 1.21 10905843 signal peptide, CUB domain, EGF-like 1 Snx11 NM_001012012 51 1.23 10746594 sorting nexin 11 Transcription coiled-coil-helix-coiled-coil-helix domain Chchd2 NM_001015019 113 1.31 10930091 containing 2 coiled-coil-helix-coiled-coil-helix domain Chchd6 NM_001106608 90 1.23 10863993 containing 6 Fbxo23 NM_001013138 122 1.27 10797368 F-box only protein 23 Nola2 NM_001105779 90 1.21 10733380 NHP2 ribonucleoprotein homolog (yeast) Ry1 NM_001108636 -53 0.81 10782583 small nuclear ribonucleoprotein 27kDa (U4 Top1mt NM_001002798 16 1.21 10904612 topoisomerase (DNA) I, mitochondrial Translation & Protein Modification RGD1564552 ENSRNOT00000050803 -97 0.69 10799888 similar to ribosomal protein L21 Rpl22l1 NM_001108548 -73 0.82 10814650 ribosomal protein L22 like 1 Rpl36 NM_022504 91 1.36 10772984 ribosomal protein L36 Miscellaneous & Unknown LOC501427 ENSRNOT00000061060 -14 0.72 10779531 similar to Spetex-2F protein Lrrn4 ENSRNOT00000040802 -30 0.82 10850170 leucine rich repeat neuronal 4 Magohb ENSRNOT00000013725 -18 0.81 10866265 mago-nashi homolog B (Drosophila) RGD1310587 NM_001100857 -17 0.83 10770517 similar to hypothetical protein FLJ14146 RGD1565493 XM_002729803 -11 0.83 10903280 similar to DKFZP434I092 protein Samd12 NM_001130562 -79 0.82 10903721 sterile alpha motif domain containing 12 Ttc36 NM_001005546 -34 0.80 10916876 tetratricopeptide repeat domain 36 RGD1565166 NM_001105762 10 1.22 10731622 similar to MGC45438 protein RGD1566243 NM_001134635 -6 0.82 10909777 similar to protein of unknown function UTP3, small subunit (SSU) processome component, Utp3 NM_001012036 22 1.20 10776064 homolog (S. cerevisiae) EST's RGD1309501 NM_001127537 -30 0.79 10774403 hypothetical LOC305552 LOC306766 NM_001014007 114 1.31 10794172 hypothetical LOC306766 RGD1310794 BC093393 -23 0.81 10853515 similar to RIKEN cDNA C030048B08 XR_008339 -35 0.75 10845365 XR_009246 12 1.30 10731555 XR_009095 -17 0.81 10828152 XR_008340 -50 0.79 10717829 XR_007585 29 1.46 10934560 NC_001665 30 1.35 10930610 K02909 70 1.21 10918820 ENSRNOT00000060122 -31 0.83 10884046 ENSRNOT00000056786 -108 0.60 10939699 ENSRNOT00000053279 311 1.35 10708691 ENSRNOT00000042423 28 1.24 10938712 37727288 -278 0.69 10760298 --- -85 0.73 10827665 --- -60 0.83 10798921

11 --- -45 0.79 10932187 --- -41 0.77 10767747 --- -39 0.80 10726221 --- -35 0.82 10914901 --- -35 0.83 10803509 --- -34 0.66 10866205 --- -34 0.82 10760005 --- -31 0.69 10717085 --- -30 0.82 10888682 --- -28 0.80 10927840 --- -27 0.81 10795400 --- -21 0.82 10820761 --- -21 0.80 10750470 --- -14 0.83 10848414 --- -12 0.75 10873723 --- -10 0.82 10802574 --- -10 0.83 10813889 --- -10 0.83 10823935 --- -10 0.83 10877538 --- -9 0.81 10706465 --- -9 0.74 10841294 --- -8 0.82 10769229 --- -7 0.79 10740841 --- -5 0.80 10746914 --- 8 1.22 10711995 --- 8 1.33 10891491 --- 9 1.26 10744141 --- 11 1.24 10772782 --- 13 1.20 10778675 --- 13 1.21 10822356 --- 14 1.36 10896378 --- 14 1.28 10814299 --- 16 1.38 10877749 --- 21 1.33 10917344 --- 26 1.25 10909137 --- 27 1.21 10884820 --- 34 1.22 10826602 --- 44 1.40 10856228 --- 56 1.26 10714842 --- 184 1.25 10805225

List 6. Genes Expressed Differentially in Stressed F3-Vinclozolin Rat Cortex Region as Compared to Stressed F3- Control ('St-Vin vs St-Con' contrast), 142 genes and EST's GenBank_Reference Mean Affymetrix Gene Symbol Ratio Gene Title Sequence _diff ID Development Robld3 NM_001106441 -30 0.78 10824344 roadblock domain containing 3 RGD1559751 ENSRNOT00000058177 -14 0.80 10805591 similar to n-chimaerin Syt2 NM_012665 -84 0.83 10764174 synaptotagmin II Vof16 NM_147207 91 1.58 10909382 ischemia related factor vof-16 Electron Transport Gpx8 NM_001106411 29 1.23 10821367 glutathione peroxidase 8 Epigenetics LOC501799 ENSRNOT00000061397 100 1.38 10759844 similar to chromobox homolog 3 Hist1h2bc NM_001109400 44 1.34 10798475 histone cluster 1, H2bc

12 Mkx ENSRNOT00000025623 -24 0.82 10798902 mohawk homeobox Growth Factors Ctgf NM_022266 47 1.31 10717233 connective tissue growth factor Hdgfl1 NM_133549 12 1.24 10795072 hepatoma derived growth factor-like 1 Immune Response RT1-S2 NM_001008857 15 1.35 10827789 RT1 class Ib, locus S2 Igha BC092592 20 1.34 10892572 immunoglobulin heavy chain, alpha Metabolism & Transport Akr1c19 NM_001100576 8 1.20 10796050 aldo-keto reductase family 1, member C19 Cml1 NM_021668 -34 0.82 10863692 camello-like 1 Fth1 BC081845 43 1.26 10713831 ferritin, heavy polypeptide 1 Gnpnat1 NM_001134756 71 1.22 10782846 glucosamine-phosphate N-acetyltransferase 1 hydroxy-delta-5-steroid dehydrogenase, 3 beta- and Hsd3b6 NM_017265 -27 0.82 10825349 steroid delta-isomerase 6 Klk8 NM_001107509 -27 0.80 10706424 kallikrein related-peptidase 8 low density lipoprotein-related protein 1B (deleted Lrp1b NM_001107843 54 1.23 10844966 in tumors) phosphatidylinositol glycan anchor biosynthesis, Piga NM_001108816 53 1.25 10937719 class A Pln NM_022707 18 1.24 10830174 phospholamban similar to ATP synthase, H+ transporting, LOC679586 ENSRNOT00000048808 -31 0.81 10920350 mitochondrial F0 complex, subunit G RGD1565045 ENSRNOT00000015997 -11 0.81 10716502 similar to carboxylesterase isoenzyme gene RGD1561777 ENSRNOT00000035047 -31 0.76 10833617 similar to Na+ dependent glucose transporter 1 Proteolysis Ube2n BC090072 26 1.42 10759435 ubiquitin-conjugating enzyme E2N Receptors & Binding Proteins Fabp7 NM_030832 115 1.27 10830223 fatty acid binding protein 7, brain Hcrtr2 NM_013074 22 1.20 10918761 hypocretin (orexin) receptor 2 Igfbp6 NM_013104 -82 0.67 10899465 insulin-like growth factor binding protein 6 Lhcgr NM_012978 -8 0.81 10888343 luteinizing hormone Olr1199 NM_001000819 -19 0.77 10909109 olfactory receptor 1199 Olr1223 NM_001000441 32 1.47 10909149 olfactory receptor 1223 Olr14 NM_001000695 11 1.26 10723503 olfactory receptor 14 Olr1627 NM_001000091 -10 0.83 10779790 olfactory receptor 1627 Olr1701 NM_001001114 41 1.21 10830802 olfactory receptor 1701 Olr421 NM_001000824 -14 0.80 10844764 olfactory receptor 421 Olr550 NM_001000322 -41 0.82 10847051 olfactory receptor 550 Olr850 NM_001000401 -5 0.82 10876763 olfactory receptor 850 LOC690821 ENSRNOT00000047245 -9 0.82 10908225 similar to olfactory receptor Olr1185 LOC304239 ENSRNOT00000049215 25 1.39 10834046 similar to RalA binding protein 1 P2rx5 NM_080780 -19 0.83 10735647 purinergic receptor P2X, ligand-gated ion channel, 5 Signaling Cyr61 NM_031327 11 1.20 10827231 cysteine-rich, angiogenic inducer, 61 Ibsp NM_012587 -16 0.81 10775365 integrin-binding sialoprotein Pef1 NM_001007651 -28 0.76 10901111 penta-EF hand domain containing 1 pleckstrin homology domain containing, family O Plekho2 ENSRNOT00000042633 -47 0.78 10918288 member 2 Prkacb NM_001077645 -40 0.77 10827305 protein kinase, cAMP dependent, catalytic, beta Pygm NM_012638 -73 0.83 10713382 phosphorylase, glycogen, muscle Stk10 NM_019206 48 1.25 10741887 serine Trib2 NM_001108015 -35 0.83 10889263 tribbles homolog 2 (Drosophila) 13 Transcription Casc5 ENSRNOT00000067081 -16 0.79 10838743 cancer susceptibility candidate 5 Ccdc112 NM_001109124 29 1.23 10804371 coiled-coil domain containing 112 Ccdc153 NM_001013953 -14 0.78 10909463 coiled-coil domain containing 153 Dpf3 ENSRNOT00000010703 -23 0.83 10891013 D4, zinc and double PHD fingers, family 3 Hlf ENSRNOT00000055664 -41 0.81 10746209 hepatic leukemia factor Npas4 NM_153626 192 1.53 10727717 neuronal PAS domain protein 4 Nr4a2 NM_019328 41 1.23 10845384 nuclear receptor subfamily 4, group A, member 2 Polr2j NM_001105921 -36 0.82 10761070 polymerase (RNA) II (DNA directed) polypeptide J reprimo, TP53 dependent G2 arrest mediator Rprm NM_001044276 78 1.52 10845372 candidate Txnip NM_001008767 170 1.48 10817552 thioredoxin interacting protein Zcchc12 NM_001014065 40 1.27 10936360 zinc finger, CCHC domain containing 12 Zfp280b NM_001106384 -12 0.83 10832460 zinc finger protein 280b Zfp354a NM_052798 -11 0.83 10733310 zinc finger protein 354A Zfpm2 NM_001130501 32 1.24 10896337 zinc finger protein, multitype 2 Translation & Protein Modification RGD1561635 ENSRNOT00000032135 -10 0.81 10764811 similar to 40S ribosomal protein S17 RGD1564552 ENSRNOT00000050803 -45 0.80 10799888 similar to ribosomal protein L21 Miscellaneous & Unknown FAM50A NM_001170573 27 1.24 10940358 family with sequence similarity 50, member A LOC680227 NM_001047974 -7 0.82 10934517 LRRGT00193

LOC100363176 XM_002725742 -43 0.75 10728981 mCG145114-like Spetex-2A ENSRNOT00000061476 14 1.29 10782777 Spetex-2B protein Trim59 NM_001108945 29 1.21 10823591 tripartite motif-containing 59 RGD1562420 ENSRNOT00000007683 -31 0.69 10887809 similar to hypothetical protein rno-mir-9-1 rno-mir-9-1 36 1.24 10816485 EST's LOC500492 XR_005747 30 1.22 10877982 NM_001111127 66 1.38 10798473 J01884 -51 0.77 10830454 ENSRNOT00000057306 -274 0.78 10815996 ENSRNOT00000054517 -39 0.76 10797013 ENSRNOT00000053338 -25 0.83 10791520 ENSRNOT00000053279 -252 0.79 10708691 ENSRNOT00000053268 287 1.42 10909356 ENSRNOT00000053042 69 1.53 10937568 ENSRNOT00000052741 24 1.30 10726878 ENSRNOT00000052710 -74 0.72 10838282 ENSRNOT00000025383 103 1.24 10920986 AF272707 -22 0.80 10867318 AF188753 -183 0.78 10855185 XR_005716 -11 0.83 10875005 XM_221100 60 1.26 10748601 XR_006516 -45 0.82 10759585 XR_006465 -13 0.72 10902361 XR_005810 -37 0.83 10849861 XR_007276 -23 0.83 10933574 XR_007404 -113 0.80 10845645 XM_001066244 -44 0.82 10905605 --- -621 0.81 10761253 --- -411 0.75 10758031

14 --- -91 0.79 10898938 --- -58 0.81 10937523 --- -52 0.74 10935698 --- -47 0.81 10729345 --- -44 0.71 10774100 --- -43 0.73 10713873 --- -42 0.78 10758033 --- -37 0.76 10883797 --- -35 0.80 10845397 --- -35 0.78 10759465 --- -26 0.75 10767278 --- -22 0.76 10903965 --- -20 0.77 10836352 --- -18 0.82 10718598 --- -16 0.82 10820280 --- -13 0.82 10840477 --- -13 0.79 10800629 --- -10 0.82 10937800 --- -10 0.83 10842472 --- -10 0.79 10871417 --- -8 0.83 10882530 --- -7 0.75 10902418 --- -6 0.82 10723555 --- 8 1.34 10925452 --- 9 1.22 10927207 --- 10 1.24 10759459 --- 18 1.26 10846962 --- 18 1.36 10925371 --- 18 1.25 10720518 --- 19 1.40 10908227 --- 20 1.24 10830161 --- 26 1.23 10900073 --- 26 1.42 10756268 --- 26 1.42 10756270 --- 26 1.42 10756272 --- 26 1.42 10759445 --- 29 1.52 10865347 --- 32 1.37 10726672 --- 36 1.22 10924669 --- 36 1.20 10843845 --- 50 1.40 10765036 --- 50 1.20 10828841 --- 64 1.25 10815955 --- 73 1.45 10939061 --- 172 1.22 10748763 --- 237 1.52 10752799 --- 257 1.32 10718134

List 7. Genes Expressed Differentially in Stressed F3-Control Rat Cortex Region as Compared to Non-Stressed F3-Control ('Str-Con vs Nst-Con' contrast), 290 genes and EST's GenBank_Reference Mean Affymetrix Gene Symbol Ratio Gene Title Sequence _diff ID Apoptosis Tnfaip8l1 XM_236787 -23 0.81 10931477 tumor necrosis factor, alpha-induced protein 8-like 1 Cell Cycle Ccne2 NM_001108656 -15 0.81 10867614 cyclin E2

15 Fcho2 ENSRNOT00000020692 -88 0.82 10820770 FCH domain only 2 RGD1562871 NM_001106935 -15 0.83 10934664 similar to BMI1-like protein Cytoskeleton- ECM Afap1 NM_080900 17 1.28 10777450 actin filament associated protein 1 capping protein (actin filament) muscle Z-line, alpha Capza1 NM_001109625 -143 0.82 10825686 1 carcinoembryonic antigen-related cell adhesion Ceacam11 NM_001025404 9 1.26 10704634 molecule 11 Cspg4 NM_031022 -31 0.77 10910237 chondroitin sulfate proteoglycan 4 Cldn16 NM_131905 -7 0.82 10755027 claudin 16 Emilin1 NM_001106710 -20 0.82 10888953 elastin microfibril interfacer 1 Gm52 NM_001014771 -27 0.78 10757808 envelope glycoprotein syncytin-A Krtap4-7 ENSRNOT00000068237 -53 0.69 10747166 keratin associated protein 4-5 Nvl NM_001105980 -44 0.78 10770351 nuclear VCP-like Papln NM_001108039 -16 0.81 10885823 papilin, proteoglycan-like sulfated glycoprotein Pcdh19 NM_001169129 32 1.21 10939226 protocadherin 19 RGD1564515 ENSRNOT00000056894 -10 0.80 10896803 similar to alpha 1B-glycoprotein RGD1564955 ENSRNOT00000033044 7 1.23 10939640 similar to fibrous sheath interacting protein 2 similar to Myosin regulatory light chain 2-A, RGD1309537 NM_001135017 38 1.26 10930421 smooth muscle isoform (Myosin RLC-A) LOC290704 ENSRNOT00000059673 -9 0.79 10787918 similar to palladin Smtnl1 ENSRNOT00000009903 19 1.21 10846862 smoothelin-like 1 Tpm2 NM_001024345 18 1.23 10876324 tropomyosin 2, beta Development Egln2 NM_001004083 59 1.23 10719958 EGL nine homolog 2 (C. elegans) Fancl ENSRNOT00000029513 -23 0.72 10774612 Fanconi anemia, complementation group L Fignl2 ENSRNOT00000044982 38 1.23 10907335 fidgetin-like 2 similar to Vomeronasal secretory protein 2 precursor (Vomeronasal secretory protein II) (VNSP II) LOC681385 ENSRNOT00000067576 10 1.35 10843857 (Lipocalin-4) similar to spermatogenesis associated glutamate (E)- LOC685226 ENSRNOT00000045972 60 1.67 10806527 rich protein 4d LOC687994 ENSRNOT00000030501 -56 0.83 10867109 similar to 82-kD FMRP Interacting Protein Olfml1 NM_001013192 -85 0.75 10709687 olfactomedin-like 1 polymerase (RNA) III (DNA directed) polypeptide Polr3k NM_001014259 -186 0.77 10843132 K Retnlg NM_181625 10 1.22 10753861 resistin-like gamma Spata4 NM_001002852 6 1.22 10793083 spermatogenesis associated 4 Sytl5 NM_178333 22 1.21 10936877 synaptotagmin-like 5 transient receptor potential cation channel, Trpa1 NM_207608 -9 0.79 10867111 subfamily A, member 1 Wbscr27 NM_001109499 -24 0.76 10761247 Williams Beuren syndrome chromosome region 27 Electron Transport Cox6c1 NM_173303 -22 0.78 10811879 cytochrome c oxidase subunit VIc-1 cytochrome P450, family 2, subfamily j, polypeptide Cyp2j3 NM_175766 27 1.21 10878170 3 Piwil2 NM_001107276 -18 0.81 10785031 piwi-like 2 (Drosophila) Epigenetics As3mt NM_080890 -12 0.80 10715875 arsenic (+3 oxidation state) methyltransferase Dmap1 NM_001015006 -22 0.80 10938804 DNA methyltransferase 1-associated protein 1 Hist2h2bb ENSRNOT00000042005 50 1.27 10817539 histone cluster 2, H2bb Hist2h4 NM_001123469 173 1.37 10825151 histone cluster 2, H4 Hist3h2bb NM_001109641 9 1.21 10742987 histone cluster 3, H2bb Hmgb2 NM_017187 8 1.26 10791497 high mobility group box 2 Golgi 16 Apparatus RGP1 retrograde golgi transport homolog (S. Rgp1 ENSRNOT00000064419 53 1.21 10868541 cerevisiae) Growth Factors Amh NM_012902 15 1.26 10900405 anti-Mullerian hormone Artn NM_053397 -14 0.79 10879084 artemin Edn2 NM_012549 -12 0.80 10871623 endothelin 2 Ccr9 NM_172329 8 1.20 10914601 chemokine (C-C motif) receptor 9 Il18 NM_019165 -16 0.81 10909874 interleukin 18 Ing5 NM_001108810 -18 0.83 10925660 inhibitor of growth family, member 5 Hormones Pth NM_017044 14 1.25 10724987 parathyroid hormone Immune Response Obp3 NM_147215 9 1.21 10877229 alpha-2u globulin PGCL4 C4bpa NM_012516 -8 0.82 10767422 complement component 4 binding protein, alpha Ly6b NM_139257 8 1.34 10904590 lymphocyte antigen 6 complex, locus B Mup4 NM_198784 11 1.21 10877251 major urinary protein 4 RT1-CE2 NM_001008840 22 1.50 10831129 RT1 class I, locus CE2 RT1-S2 NM_001008857 -21 0.67 10827789 RT1 class Ib, locus S2 Slamf9 NM_001105971 -16 0.77 10765746 SLAM family member 9 Metabolism & Transport Aadacl2 ENSRNOT00000067870 7 1.25 10815616 arylacetamide deacetylase-like 2 Abhd1 NM_001008520 54 1.28 10888931 abhydrolase domain containing 1 Acot1 NM_031315 6 1.24 10885857 acyl-CoA thioesterase 1 Akr1b7 NM_053781 9 1.31 10854427 aldo-keto reductase family 1, member B7 aldo-keto reductase family 1, member D1 (delta 4-3- Akr1d1 NM_138884 -15 0.78 10854548 ketosteroid-5-beta-reductase) Apoa2 NM_013112 -19 0.82 10765530 apolipoprotein A-II Apool NM_001014105 -26 0.79 10934700 apolipoprotein O-like Bphl NM_001037206 16 1.28 10798100 biphenyl hydrolase-like (serine hydrolase) Coq10b NM_001009671 -88 0.76 10923338 coenzyme Q10 homolog B (S. cerevisiae) Dhrs7c ENSRNOT00000036752 -8 0.79 10734701 dehydrogenase Eno3 NM_012949 15 1.23 10735331 enolase 3, beta, muscle Fth1 BC081845 -52 0.76 10713831 ferritin, heavy polypeptide 1 Gnpnat1 NM_001134756 -82 0.80 10782846 glucosamine-phosphate N-acetyltransferase 1 Guf1 NM_001107215 -89 0.82 10776646 GUF1 GTPase homolog (S. cerevisiae) Gykl1 NM_134341 13 1.31 10801717 glycerol kinase-like 1 Klk1c10 NM_001135173 -22 0.74 10721283 T-kininogenase low density lipoprotein-related protein 1B (deleted Lrp1b NM_001107843 -207 0.79 10844988 in tumors) Mgst1 NM_134349 28 1.25 10859392 microsomal glutathione S-transferase 1 phosphatidylinositol glycan anchor biosynthesis, Pigw NM_194461 -43 0.83 10745782 class W Plch1 ENSRNOT00000013280 8 1.21 10823432 phospholipase C, eta 1 RGD1561057 ENSRNOT00000043238 7 1.23 10846671 ceramide kinase-like RGD1561777 ENSRNOT00000035047 28 1.28 10833617 similar to Na+ dependent glucose transporter 1 Scd4 ENSRNOT00000017834 40 1.20 10715552 stearoyl-coenzyme A desaturase 4 Slc10a4 NM_001008555 -20 0.79 10776582 solute carrier family 10 (sodium Proteolysis Adamtsl4 NM_001034012 -13 0.78 10833985 ADAMTS-like 4 angiotensinogen (serpin peptidase inhibitor, clade A, Agt NM_134432 92 1.34 10811900 member 8) Hpn NM_017112 -12 0.82 10720891 hepsin Pomp NM_001100942 43 1.28 10760041 proteasome maturation protein 17 proteasome (prosome, macropain) assembly Psmg4 NM_001129879 -17 0.82 10798096 chaperone 4 Rnf113a1 NM_001014791 -15 0.82 10936285 ring finger protein 113A1 Rnft1 ENSRNOT00000005064 -93 0.81 10737380 ring finger protein, transmembrane 1 Usp30 NM_001107153 44 1.26 10762857 ubiquitin specific peptidase 30 Receptors & Binding Proteins ATP-binding cassette, sub-family A (ABC1), Abca17 NM_001031637 8 1.22 10741044 member 17 Acvr2b NM_031554 10 1.23 10914230 activin A receptor, type IIB Gpr179 ENSRNOT00000055427 -11 0.79 10746701 G protein-coupled receptor 179 leukocyte immunoglobulin-like receptor, subfamily Lilrb3 NM_031713 -12 0.82 10703666 B (with TM and ITIM domains), member 3 Ly49i6 NM_001009718 8 1.28 10866207 Ly49 inhibitory receptor 6 Mtnr1b NM_001100641 -12 0.83 10915124 melatonin receptor 1B Olr1060 NM_001000698 29 1.74 10900087 olfactory receptor 1060 Olr1297 NM_001000461 17 1.24 10916342 olfactory receptor 1297 Olr130 NM_001001272 -13 0.76 10724337 olfactory receptor 130 Olr1431 NM_001000778 -15 0.80 10733862 olfactory receptor 1431 Olr1567 NM_001000043 11 1.25 10752235 olfactory receptor 1567 Olr1607 NM_001000534 -21 0.80 10779355 olfactory receptor 1607 Olr1664 NM_001001007 8 1.22 10795357 olfactory receptor 1664 Olr222 NM_001000201 -22 0.76 10724611 olfactory receptor 222 Olr29 NM_001000691 22 1.34 10723519 olfactory receptor 29 Olr315 NM_001000243 23 1.25 10712086 olfactory receptor 315 Olr485 NM_001000307 -8 0.82 10846958 olfactory receptor 485 Olr551 NM_001000670 -12 0.76 10847053 olfactory receptor 551 Olr664 NM_001000347 11 1.20 10837619 olfactory receptor 664 Olr703 NM_001000359 8 1.24 10847193 olfactory receptor 703 Olr771 NM_001000610 -22 0.74 10838435 olfactory receptor 771 Olr813 NM_001000846 -6 0.82 10855100 olfactory receptor 813 Olr830 NM_001000900 11 1.26 10858158 olfactory receptor 830 Olr855 NM_001000409 -9 0.82 10871502 olfactory receptor 855 Olr862 NM_001001071 -27 0.81 10879329 olfactory receptor 862 Olr905 NM_001001355 19 1.20 10893392 olfactory receptor 905 Olr93 NM_001000141 -20 0.78 10724262 olfactory receptor 93 P2rx7 NM_019256 -20 0.81 10761992 purinergic receptor P2X, ligand-gated ion channel, 7 Prokr2 NM_138978 -16 0.81 10850137 prokineticin receptor 2 PVR NM_017076 -12 0.82 10719616 poliovirus receptor V1rc28 NM_001009513 17 1.20 10855844 vomeronasal 1 receptor, C28 V1rd6 NM_001008923 6 1.20 10703890 vomeronasal 1 receptor, D6 Vom2r7 NM_001099463 10 1.27 10703233 vomeronasal 2 receptor, 7 Vom2r-ps53 ENSRNOT00000012225 12 1.25 10719051 vomeronasal 2 receptor, pseudogene 53 Signaling Akap14 NM_021703 8 1.24 10931995 A kinase (PRKA) anchor protein 14 Chka NM_017127 -48 0.83 10712706 choline kinase alpha Frmpd1 NM_001107937 25 1.23 10868693 FERM and PDZ domain containing 1 Grtp1 ENSRNOT00000057740 -15 0.82 10789500 growth hormone regulated TBC protein 1 Gna15 NM_053542 8 1.20 10893474 guanine nucleotide binding protein, alpha 15 Gnas NM_001159653 -7 0.83 10842657 GNAS complex locus LOC689617 ENSRNOT00000058250 64 1.63 10815215 similar to GTPase activating protein testicular GAP1 menage a trois homolog 1, cyclin H assembly factor Mnat1 NM_153472 -32 0.80 10885207 (Xenopus laevis) Mrgprb4 ENSRNOT00000045792 -42 0.73 10722218 MAS-related GPR, member B4 Musk NM_031061 -17 0.80 10869213 muscle, skeletal, receptor tyrosine kinase

18 Pih1d1 NM_001024868 -14 0.79 10706724 PIH1 domain containing 1 RGD1561231 ENSRNOT00000047232 12 1.21 10795701 similar to MAP Socs6 ENSRNOT00000058179 -25 0.81 10805585 suppressor of cytokine signaling 6 Sppl2a NM_001107770 -110 0.82 10849598 signal peptide peptidase-like 2A Susd5 ENSRNOT00000028675 -13 0.83 10913963 sushi domain containing 5 Transcription Bwk1 NM_198743 -72 0.83 10842879 Bwk1 leukemia-related gene Cass4 ENSRNOT00000035245 -13 0.82 10842525 Cas scaffolding protein family member 4 Ccdc114 NM_001126277 -10 0.82 10707003 coiled-coil domain containing 114 Ccdc153 NM_001013953 15 1.30 10909463 coiled-coil domain containing 153 Dmrta2 NM_001107951 9 1.22 10870971 DMRT-like family A2 Duxbl ENSRNOT00000052224 11 1.21 10786197 double homeobox B-like Gtf2h4 NM_212501 29 1.24 10827936 general transcription factor II H, polypeptide 4 Hoxd10 NM_001107094 -28 0.81 10837003 homeo box D10 Hrasls NM_001105871 31 1.20 10754987 HRAS-like suppressor Lmx1a NM_001105967 -12 0.81 10765424 LIM homeobox transcription factor 1 alpha similar to Zinc finger protein 354A (Transcription factor 17) (Renal transcription factor Kid-1) (Kidney, LOC499110 ENSRNOT00000041861 27 1.21 10705431 ischemia, and developmentally regulated protein 1) Nusap1 NM_001107762 -10 0.81 10838843 nucleolar and spindle associated protein 1 Rfx6 NM_001106388 12 1.21 10830105 regulatory factor X, 6 similar to ETS domain transcription factor ERF RGD1563034 ENSRNOT00000021187 8 1.28 10719719 (Ets2 repressor factor) Srfbp1 NM_001005536 -27 0.83 10801698 serum response factor binding protein 1 RGD1564386 XM_001074961 8 1.20 10824792 similar to TDPOZ3 Zfp278 NM_001107231 9 1.23 10773683 zinc finger protein 278 Znf295 NM_001107105 -35 0.78 10753513 zinc finger protein 295 Znf307 ENSRNOT00000024797 -20 0.82 10798513 zinc finger protein 307 Ddx18 NM_001006996 -37 0.81 10767189 DEAD (Asp-Glu-Ala-Asp) box polypeptide 18 Translation & Protein Modification LOC681338 ENSRNOT00000047517 5 1.24 10928032 similar to ribosomal protein L31 LOC683597 ENSRNOT00000030099 -9 0.83 10877637 similar to ribosomal protein L9 Mtrf1l NM_001025723 -33 0.82 10717785 mitochondrial translational release factor 1-like RGD1564062 ENSRNOT00000033738 -48 0.76 10798841 similar to ribosomal protein L27a RGD1564552 ENSRNOT00000050803 -89 0.72 10799888 similar to ribosomal protein L21 Mrpl1 NM_001105997 -52 0.83 10775719 mitochondrial ribosomal protein L1 Rpl3 NM_198753 203 1.27 10905530 ribosomal protein L3 Rps9 NM_031108 184 1.26 10718510 ribosomal protein S9 TAF9 RNA polymerase II, TATA box binding Taf9 NM_001037310 -62 0.83 10812748 protein (TBP)-associated factor Miscellaneous & Unknown Fam133b BC094528 -57 0.65 10936823 family with sequence similarity 133, member B LOC686013 ENSRNOT00000007407 6 1.24 10810203 hypothetical protein LOC686013 LOC689425 NM_001135002 -16 0.82 10828752 hypothetical protein LOC689425 LOC690206 NM_001109567 -20 0.75 10873029 hypothetical protein LOC690206 LOC690422 ENSRNOT00000029223 -10 0.83 10887627 hypothetical protein LOC690422 LOC499542 NM_001047943 9 1.21 10821984 LRRGT00178 Rwdd2a NM_001108773 -8 0.79 10912048 RWD domain containing 2A RGD1561161 NM_001134510 -11 0.80 10813119 similar to BC067074 protein RGD1565493 XM_002729803 -24 0.82 10903288 similar to DKFZP434I092 protein RGD1310587 NM_001100857 -19 0.80 10770517 similar to hypothetical protein FLJ14146 RGD1562310 NM_001109066 16 1.24 10762420 similar to hypothetical protein FLJ21415 RGD1311269 NR_033170 28 1.24 10928207 similar to hypothetical protein FLJ37953 RGD1308165 NM_001108664 -27 0.83 10868982 similar to hypothetical protein MGC17337 19 RGD1562039 ENSRNOT00000049790 30 1.21 10939072 similar to MGC82337 protein RGD1563945 ENSRNOT00000061140 -21 0.82 10936645 similar to mKIAA0215 protein similar to NACHT, leucine rich repeat and PYD RGD1560291 XM_001078928 -13 0.81 10901121 containing 4A LOC501427 ENSRNOT00000061060 -12 0.77 10779531 similar to Spetex-2F protein Samd12 NM_001130562 -85 0.81 10903721 sterile alpha motif domain containing 12 Ttc36 NM_001005546 -38 0.77 10916876 tetratricopeptide repeat domain 36 Tmco5a ENSRNOT00000006809 11 1.22 10838571 transmembrane and coiled-coil domains 5A Tmem156 NM_001025138 9 1.25 10772760 transmembrane protein 156 UTP23, small subunit (SSU) processome Utp23 NM_001126266 -23 0.82 10896499 component, homolog (yeast) ESTs similar to RIKEN cDNA 2610301B20; EST MGC94199 BC079168 -64 0.80 10867596 AI428449 RGD1308251 NM_001108697 44 1.26 10882071 similar to RIKEN cDNA 2810405K02 XR_009246 17 1.40 10731555 XR_008340 -68 0.71 10717829 XR_008339 -56 0.60 10845365 XR_008033 -7 0.79 10796881 XR_007931 -50 0.78 10836964 XR_007585 35 1.56 10934560 XR_007179 -25 0.78 10830126 XR_007098 -37 0.62 10707370 XR_006082 6 1.25 10934692 XR_006046 -35 0.75 10703137 XR_005716 23 1.58 10875005 XM_001074777 -170 0.73 10721276 ENSRNOT00000056786 -124 0.54 10939699 ENSRNOT00000055830 22 1.34 10859174 ENSRNOT00000042423 31 1.27 10938712 ENSRNOT00000002166 -5 0.82 10836988 AF272707 34 1.45 10867318

ENSRNOT00000009117 -13 0.77 10867916 --- -173 0.83 10732837 --- -141 0.76 10805311 --- -130 0.70 10742507 --- -106 0.66 10827665 --- -93 0.73 10848956 --- -84 0.64 10903520 --- -80 0.83 10768364 --- -79 0.77 10798921 --- -73 0.79 10934980 --- -69 0.80 10810417 --- -66 0.78 10817114 --- -64 0.82 10833808 --- -64 0.59 10914009 --- -52 0.77 10723231 --- -47 0.81 10932054 --- -44 0.82 10716630 --- -41 0.67 10830161 --- -39 0.80 10914901 --- -38 0.61 10866205 --- -38 0.73 10795400 --- -27 0.80 10877992 --- -25 0.79 10818137

20 --- -19 0.79 10840363 --- -19 0.78 10713011 --- -18 0.77 10724240 --- -17 0.65 10873723 --- -16 0.76 10732217 --- -15 0.76 10725541 --- -15 0.77 10925371 --- -14 0.78 10824526 --- -12 0.82 10892481 --- -11 0.76 10706465 --- -11 0.79 10727600 --- -10 0.82 10802574 --- -10 0.77 10927158 --- -9 0.75 10740841 --- -8 0.76 10706238 --- -6 0.82 10901139 --- 6 1.20 10856127 --- 6 1.20 10833090 --- 7 1.25 10856177 --- 8 1.24 10789696 --- 8 1.24 10719036 --- 9 1.33 10778804 --- 9 1.23 10862942 --- 9 1.26 10711995 --- 9 1.30 10899717 --- 9 1.22 10787805 --- 9 1.24 10882530 --- 9 1.26 10938066 --- 10 1.41 10798792 --- 10 1.26 10785598 --- 10 1.34 10702317 --- 10 1.44 10891491 --- 11 1.31 10781995 --- 11 1.27 10782889 --- 13 1.37 10759597 --- 14 1.29 10887052 --- 15 1.32 10852413 --- 16 1.38 10847172 --- 17 1.21 10704147 --- 19 1.25 10887066 --- 19 1.37 10814299 --- 19 1.26 10816483 --- 22 1.35 10755550 --- 24 1.38 10917344 --- 25 1.37 10809067 --- 26 1.33 10750898 --- 27 1.41 10903965 --- 27 1.78 10932699 --- 29 1.26 10878640 --- 29 1.27 10730659 --- 29 1.29 10751799 --- 31 1.31 10909137 --- 35 1.30 10888388 --- 44 1.43 10914898 --- 50 1.98 10767278 --- 57 1.57 10713873

21 --- 84 1.58 10934710 --- 84 1.78 10856228

List 8. Genes Expressed Differentially in Stressed F3-Vinclozolin Rat Cortex Region as Compared to Non- Stressed F3-Vinclozolin ('Str-Vin vs Nst-Vin' contrast), 96 genes and EST's GenBank_Reference Mean Affymetrix Gene Symbol Ratio Gene Title Sequence _diff ID Development Reln NM_080394 -67 0.81 10853020 reelin similar to Discs, large homolog 5 (Placenta and RGD1563738 ENSRNOT00000052026 17 1.34 10916270 prostate DLG) Epigenetics LOC501799 ENSRNOT00000061397 107 1.75 10759485 similar to chromobox homolog 3 Growth Factors Ctgf NM_022266 43 1.28 10717233 connective tissue growth factor Fgf9 NM_012952 -80 0.81 10780813 fibroblast growth factor 9 Immune Response Btnl4 NM_001166344 7 1.27 10828340 butyrophilin-like 4 Metabolism & Transport Acot1 NM_031315 5 1.20 10885857 acyl-CoA thioesterase 1 solute carrier family 32 (GABA vesicular Slc32a1 NM_031782 -78 0.80 10841774 transporter), member 1 Lrp12 NM_001134883 -81 0.82 10903503 low density lipoprotein-related protein 12 Pcbd1 NM_001007601 -16 0.82 10830003 pterin-4 alpha-carbinolamine dehydratase phosphatidylinositol glycan anchor biosynthesis, Piga NM_001108816 45 1.20 10937719 class A phospholipase A2, group VII (platelet-activating Pla2g7 NM_001009353 56 1.21 10926683 factor acetylhydrolase, plasma) Proteolysis Ube2n BC090072 33 1.58 10759435 ubiquitin-conjugating enzyme E2N Receptors & Binding Proteins Ddr2 NM_031764 -17 0.78 10769695 discoidin domain receptor tyrosine kinase 2 Igfbp6 NM_013104 -78 0.68 10899465 insulin-like growth factor binding protein 6 Olr1559 NM_001000049 -16 0.83 10750647 olfactory receptor 1559 Olr213 NM_001000735 14 1.25 10724601 olfactory receptor 213 Olr756 NM_001000614 -9 0.79 10838414 olfactory receptor 756 Olr862 NM_001001071 -24 0.82 10879329 olfactory receptor 862 LOC304239 ENSRNOT00000049215 26 1.40 10834046 similar to RalA binding protein 1 Vom2r1 NM_001099460 20 1.21 10701668 vomeronasal 2 receptor, 3 Vom2r2 ENSRNOT00000051591 9 1.25 10701636 vomeronasal 2 receptor, 2 Signaling RGD1560808 ENSRNOT00000048991 29 1.35 10718191 similar to putative protein kinase RGD1560825 ENSRNOT00000059958 22 1.25 10703256 similar to putative protein kinase RGD1561667 ENSRNOT00000059957 17 1.25 10703287 similar to putative protein kinase RGD1564858 ENSRNOT00000047604 15 1.23 10703274 similar to putative protein kinase RGD1565231 ENSRNOT00000065348 25 1.24 10718188 similar to putative protein kinase Transcription coiled-coil-helix-coiled-coil-helix domain Chchd2 NM_001015019 -99 0.79 10930091 containing 2 Klhl20 NM_001107192 -46 0.80 10769204 kelch-like 20 (Drosophila) Med21 NM_001107895 -46 0.83 10859655 mediator complex subunit 21

22 RGD1560135 ENSRNOT00000040584 27 1.23 10830272 similar to double homeobox, 4 RGD1563747 ENSRNOT00000040887 29 1.25 10833468 similar to double homeobox, 4 RGD1565550 ENSRNOT00000040584 36 1.26 10830279 similar to double homeobox, 4 Txnip NM_001008767 142 1.37 10817552 thioredoxin interacting protein Zcchc5 ENSRNOT00000003296 -14 0.83 10938988 zinc finger, CCHC domain containing 5 Translation & Protein Modification Mrpl45 NM_001105834 -53 0.83 10737815 mitochondrial ribosomal protein L45 Rnaseh2b NM_001007007 -34 0.80 10780937 ribonuclease H2, subunit B RGD1564095 ENSRNOT00000061899 21 1.28 10867377 similar to 60S acidic ribosomal protein P2 RGD1565170 ENSRNOT00000043836 -16 0.73 10780763 similar to 60S ribosomal protein L23a RGD1559877 ENSRNOT00000049689 23 1.39 10800511 similar to 60S ribosomal protein L29 (P23) RGD1564552 ENSRNOT00000050803 -37 0.83 10799888 similar to ribosomal protein L21 Miscellaneous & Unknown LOC498544 AY383688 9 1.20 10702078 hypothetical protein LOC498544 Spetex-2A ENSRNOT00000061476 14 1.29 10782777 Spetex-2B protein Mir196a NR_031913 8 1.24 10899597 microRNA mir-196a EST's RGD1559459 ENSRNOT00000065079 -5 0.80 10771998 similar to Expressed sequence AI788959 XR_008286 -23 0.75 10934032 XR_008099 -50 0.82 10798900 XR_007963 16 1.25 10903522 XR_007931 -33 0.83 10836964 NC_001665 -282 0.62 10930569 ENSRNOT00000054517 -70 0.64 10797013 ENSRNOT00000053929 113 1.35 10839872 ENSRNOT00000053328 -180 0.72 10855946 ENSRNOT00000053279 -241 0.80 10708691 ENSRNOT00000053042 78 1.64 10937568 ENSRNOT00000052710 -107 0.64 10838282 ENSRNOT00000052661 -739 0.73 10722437 ENSRNOT00000052661 -739 0.73 10722441 ENSRNOT00000052507 -802 0.68 10722471 ENSRNOT00000048364 -12 0.77 10900112 ENSRNOT00000006888 22 1.22 10892493 AF188753 -209 0.76 10855185 ENSRNOT00000039948 32 1.28 10767044 --- 55 1.23 10748601 --- -1073 0.46 10722449 --- -829 0.76 10761253 --- -620 0.61 10722481 --- -596 0.76 10722461 --- -545 0.70 10722433 --- -381 0.76 10758031 --- -236 0.56 10722451 --- -190 0.59 10722427 --- -165 0.78 10848027 --- -103 0.82 10846928 --- -98 0.73 10722459 --- -48 0.82 10787706 --- -32 0.81 10884738 --- -21 0.77 10831804 --- -11 0.81 10894798 --- 8 1.22 10850313

23 --- 9 1.23 10860595 --- 12 1.21 10714183 --- 12 1.34 10769229 --- 14 1.32 10785598 --- 14 1.32 10774339 --- 25 1.20 10771525 --- 26 1.20 10888388 --- 29 1.31 10734368 --- 33 1.58 10756268 --- 33 1.58 10756270 --- 33 1.58 10756272 --- 33 1.58 10759445 --- 56 1.31 10934710 --- 72 1.51 10933038

List 9. Genes Expressed Differentially in Non-Stressed F3-Vinclozolin Rat CA1 of the Hippocampus as Compared to Non- Stressed F3-Control ('Nst-Vin vs Nst-Con' contrast), 68 genes and EST's GenBank_Reference Mean Affymetrix Gene Symbol Ratio Gene Title Sequence _diff ID Apoptosis Ankdd1a ENSRNOT00000033512 16 1.29 10918281 ankyrin repeat and death domain containing 1A RGD1563348 NM_001114939 13 1.30 10912076 similar to Selenoprotein H RGD1559610 BC168964 73 1.21 10879679 similar to CGI-94 protein Cytoskeleton- ECM Gpc4 NM_001014108 65 1.32 10939744 glypican 4 Kb23 NM_001008813 33 1.21 10907369 type II keratin Kb23 Pcdh8 NM_022868 49 1.24 10785461 protocadherin 8 Pcdhb19 ENSRNOT00000060484 40 1.27 10801204 protocadherin beta 19 Rimbp2 NM_001100488 82 1.25 10758064 RIMS binding protein 2 Scg3 NM_053856 196 1.20 10918738 secretogranin III Epigenetics dapper, antagonist of beta-catenin, homolog 3 Dact3 ENSRNOT00000043203 69 1.20 10704555 (Xenopus laevis) Immune Response complement component 1, q subcomponent binding C1qbp NM_019259 84 1.20 10744568 protein C1ql3 NM_001109403 235 1.42 10799733 complement component 1, q subcomponent-like 3 Metabolism & Transport Atp11a NM_001107324 -213 0.72 10792859 ATPase, class VI, type 11A Car14 NM_001109655 -118 0.62 10825100 carbonic anhydrase 14 Chi3l4 ENSRNOT00000055968 7 1.20 10825770 chitinase 3-like 4 Lrp12 NM_001134883 114 1.24 10903501 low density lipoprotein-related protein 12 Slc8a2 NM_078619 163 1.24 10704437 solute carrier family 8 (sodium Retsat NM_145084 166 1.36 10856424 retinol saturase (all trans retinol 13,14 reductase) Sulf1 NM_134378 -67 0.71 10874981 sulfatase 1 Proteolysis Rnf213 ENSRNOT00000004904 -16 0.82 10740016 ring finger protein 213 Receptors & Binding Proteins Olr1320 NM_001000471 19 1.28 10909285 olfactory receptor 1320 Olr1424 NM_001000779 10 1.24 10742937 olfactory receptor 1424 Olr221 NM_001000200 -13 0.82 10724609 olfactory receptor 221 Olr711 NM_001000625 -6 0.83 10847213 olfactory receptor 711 24 Signaling Calcoco2 XM_220903 6 1.24 10746588 calcium binding and coiled-coil domain 2 Akap5 NM_133515 71 1.20 10885393 A kinase (PRKA) anchor protein 5 Defb42 NM_001037532 -151 0.83 10784446 defensin beta 42 Enpp2 NM_057104 -2109 0.42 10903736 ectonucleotide pyrophosphatase pleckstrin homology domain containing, family O Plekho2 ENSRNOT00000042633 27 1.22 10918288 member 2 Prosapip1 NM_172022 130 1.23 10849927 ProSAPiP1 protein Rab40b NM_001107076 63 1.20 10749809 Rab40b, member RAS oncogene family RGD1561955 ENSRNOT00000058079 93 1.35 10785405 similar to diacylglycerol kinase eta Smad1 NM_013130 38 1.24 10806981 SMAD family member 1 Smpdl3b NM_001025737 55 1.28 10880339 sphingomyelin phosphodiesterase, acid-like 3B Transcription Bhlhe41 AF009329 102 1.29 10867026 basic helix-loop-helix family, member e41 Baz1b ENSRNOT00000001975 77 1.20 10761209 bromodomain adjacent to zinc finger domain, 1B Casc5 ENSRNOT00000067081 51 1.40 10838741 cancer susceptibility candidate 5 Ccdc34 NM_001108587 29 1.21 10838373 coiled-coil domain containing 34 Dnajc8 NM_001013168 148 1.21 10880372 DnaJ (Hsp40) homolog, subfamily C, member 8 Kbtbd11 NM_001107326 42 1.33 10792660 kelch repeat and BTB (POZ) domain containing 11 Klhl12 NM_153730 44 1.22 10764126 kelch-like 12 (Drosophila) Mitf ENSRNOT00000051121 -22 0.81 10857435 microphthalmia-associated transcription factor similar to high mobility group nucleosomal binding LOC691642 XM_002726878 19 1.27 10894417 domain 1 similar to transcription elongation factor B (SIII), LOC680767 ENSRNOT00000060096 133 1.22 10760816 polypeptide 1 Translation & Protein Modification RGD1559743 XM_001077121 -21 0.82 10920785 similar to 40S ribosomal protein S16 Miscellaneous & Unknown UTP18, small subunit (SSU) processome Utp18 NM_001135039 58 1.22 10746256 component, homolog (yeast) RGD1308601 NM_001107374 63 1.24 10805304 similar to hypothetical protein EST's --- -164 0.82 10750114 --- -108 0.71 10716702 --- -58 0.83 10740505 --- -48 0.81 10923727 --- -46 0.78 10830161 --- -45 0.82 10820145 --- -41 0.76 10892648 --- -40 0.75 10788099 --- -27 0.82 10932580 --- -15 0.82 10887022 --- -15 0.82 10887038 --- -12 0.83 10787822 --- 7 1.23 10823674 --- 10 1.25 10722713 --- 11 1.36 10850319 --- 14 1.22 10707254 --- 14 1.25 10749852 --- 17 1.23 10827347 --- 18 1.21 10804461 --- 23 1.23 10887336 --- 74 1.26 10809882

25

List 10. Genes Expressed Differentially in Stressed F3-Vinclozolin Rat CA1 of the Hippocampus as Compared to Stressed F3-Control ('St-Vin vs St-Con' contrast), 155 genes and EST's GenBank_Reference Mean Affymetrix Gene Symbol Ratio Gene Title Sequence _diff ID Apoptosis tumor necrosis factor (ligand) superfamily, member Tnfsf4 NM_053552 -24 0.79 10765092 4 Tnfaip8l3 ENSRNOT00000038830 -10 0.80 10917501 tumor necrosis factor, alpha-induced protein 8-like 3 Cell Cycle Cspp1 ENSRNOT00000030345 -84 0.79 10875091 centrosome and spindle pole associated protein 1 Cytoskeleton- ECM Bgn NM_017087 48 1.38 10935890 biglycan carcinoembryonic antigen-related cell adhesion Ceacam10 NM_173339 9 1.28 10705034 molecule 10 Myom2 NM_001169141 -9 0.83 10792621 myomesin 2 LOC680489 NM_001109415 -19 0.81 10938099 similar to claudin 1 twinfilin, actin-binding protein, homolog 1 Twf1 NM_001008521 9 1.22 10871693 (Drosophila) Development Auts2 ENSRNOT00000044800 -42 0.81 10761299 autism susceptibility candidate 2 Nlgn1 NM_053868 -86 0.83 10822545 neuroligin 1 Syt17 NM_138849 203 1.26 10725235 synaptotagmin XVII Sntg1 ENSRNOT00000009679 -71 0.83 10867345 syntrophin, gamma 1 Tert NM_053423 -18 0.83 10717517 telomerase reverse transcriptase Tor1b NM_001039197 39 1.25 10835261 torsin family 1, member B Vgll3 ENSRNOT00000042316 -37 0.74 10749839 vestigial like 3 (Drosophila) Electron Transport cytochrome P450, family 2, subfamily c, Cyp2c13 NM_138514 -32 0.82 10930762 polypeptide 13

LOC100174910 NM_001131003 -90 0.78 10804552 glutaredoxin-like protein Epigenetics Brd8 NM_001008509 57 1.22 10803774 bromodomain containing 8 Growth Factors Gdf10 NM_024375 -25 0.76 10786905 growth differentiation factor 10 Gdf9 NM_021672 41 1.23 10733506 growth differentiation factor 9 Il15 NM_013129 -15 0.82 10806899 interleukin 15 Kng1l1 NM_001009628 -49 0.72 10755135 kininogen 1-like 1 LOC360228 NM_001003706 -25 0.80 10736875 WDNM1 homolog Sept12 NM_001100865 -11 0.81 10731699 septin 12 Tgfb2 NM_031131 150 1.37 10770577 transforming growth factor, beta 2 Immune Response Il22 ENSRNOT00000009776 -15 0.82 10895618 interleukin 22 LOC688858 XM_001068599 -181 0.82 10759581 similar to CD209a antigen RT1-DMb NM_198740 37 1.26 10831620 RT1 class II, locus DMb RT1-M6-1 NM_001008852 -45 0.74 10827686 RT1 class I, locus M6, gene 1 Metabolism & Transport Dio2 NM_031720 24 1.22 10891402 deiodinase, iodothyronine, type II dolichyl-diphosphooligosaccharide-protein Ddost NM_001012104 234 1.22 10873303 glycosyltransferase Mocos NM_001108425 -12 0.82 10800546 molybdenum cofactor sulfurase 26 Por NM_031576 73 1.21 10761162 P450 (cytochrome) oxidoreductase Ppid NM_001004279 -243 0.83 10816008 peptidylprolyl isomerase D (cyclophilin D) RGD1565145 ENSRNOT00000017696 -12 0.80 10914045 similar to cysteine sulfinic acid decarboxylase Ttpal NM_001106537 61 1.22 10842032 tocopherol (alpha) transfer protein-like Proteolysis Klk15 ENSRNOT00000038353 -16 0.83 10706498 kallikrein-related peptidase 15 LOC688812 XR_085983 -31 0.79 10756117 similar to ubiquitin-activating enzyme E1C Pm20d2 NM_001107922 16 1.23 10875853 peptidase M20 domain containing 2 Prcp NM_001106281 91 1.32 10708672 prolylcarboxypeptidase (angiotensinase C) Ubc NM_017314 284 1.26 10758134 ubiquitin C Ubd NM_053299 -31 0.83 10830854 ubiquitin D Receptors & Binding Proteins Gfra1 NM_012959 92 1.30 10731075 GDNF family receptor alpha 1 Ifngr1 NM_053783 96 1.22 10701924 interferon gamma receptor 1 LOC304239 ENSRNOT00000049215 -45 0.72 10756334 similar to RalA binding protein 1 Olr1057 NM_001000072 -14 0.83 10900081 olfactory receptor 1057 Olr1405 NM_001001012 -31 0.82 10733296 olfactory receptor 1405 Olr160 NM_001000738 -23 0.81 10709507 olfactory receptor 160 Olr1734 NM_001001119 -8 0.76 10827639 olfactory receptor 1734 Olr542 NM_001000566 -30 0.70 10847042 olfactory receptor 542 Olr582 NM_001000662 -35 0.67 10837545 olfactory receptor 582 Olr584 NM_001000661 -13 0.83 10847074 olfactory receptor 584 Olr629 NM_001001058 -24 0.76 10847109 olfactory receptor 629 Olr720 NM_001001067 -26 0.82 10847229 olfactory receptor 720 Olr734 NM_001000617 -22 0.81 10847242 olfactory receptor 734 Olr996 NM_001000700 30 1.37 10893375 olfactory receptor 996 Paqr5 NM_001014092 21 1.21 10918055 progestin and adipoQ receptor family member V Robo3 NM_001108135 -15 0.81 10916201 roundabout homolog 3 (Drosophila) Tlr2 NM_198769 10 1.26 10823970 toll-like receptor 2 Vom2r66 ENSRNOT00000051621 66 1.32 10774903 vomeronasal 2 receptor, 66 Vom2r-ps27 ENSRNOT00000051051 -17 0.83 10718403 vomeronasal 2 receptor, pseudogene 27 Signaling Ebag9 NM_001009665 77 1.20 10896486 estrogen receptor binding site associated, antigen, 9 Gbp4 ENSRNOT00000022648 -12 0.83 10819512 guanylate binding protein 4 SMEK homolog 1, suppressor of mek1 Smek1 NM_001108050 94 1.21 10891719 (Dictyostelium) Sh3bp4 NM_022693 105 1.38 10925264 SH3-domain binding protein 4 Transcription Ccdc37 ENSRNOT00000024222 -15 0.76 10864025 coiled-coil domain containing 37 Dnajc11 NM_001108694 83 1.21 10874223 DnaJ (Hsp40) homolog, subfamily C, member 11 Dnajc30 NM_001109024 21 1.30 10761225 DnaJ (Hsp40) homolog, subfamily C, member 30 Elk1 NM_001108059 72 1.22 10936520 ELK1, member of ETS oncogene family Gtf2ird1 NM_001001504 -16 0.82 10757829 GTF2I repeat domain containing 1 Hint1 ENSRNOT00000006471 -13 0.78 10862836 histidine triad nucleotide binding protein 1 Luzp1 AF181259 -16 0.83 10873012 leucine zipper protein 1 Ldoc1l ENSRNOT00000039588 83 1.29 10905915 leucine zipper, down-regulated in cancer 1-like similar to Zinc finger protein 84 (Zinc finger protein LOC691468 XM_002724499 42 1.22 10733914 HPF2) Tdpoz1 XM_345239 40 1.20 10824790 TD and POZ domain containing 1 transcriptional adaptor 2 (ADA2 homolog, yeast)- Tada2b NM_001170455 -44 0.81 10773358 beta Zfp212 ENSRNOT00000009054 -64 0.83 10855203 Zinc finger protein 212 Znf307 ENSRNOT00000024797 -31 0.81 10795315 zinc finger protein 307 Znf488 ENSRNOT00000031496 13 1.24 10790433 zinc finger protein 488

27 Translation & Protein Modification LOC362863 NM_001170605 -13 0.83 10894643 first gene upstream of Nt5dc3 Ptrh1 NM_001108580 -23 0.82 10835624 peptidyl-tRNA hydrolase 1 homolog (S. cerevisiae) Polr1b NM_031773 37 1.22 10839751 polymerase (RNA) I polypeptide B Rplp2 NM_001030021 367 1.24 10776809 ribosomal protein, large P2 RGD1563551 ENSRNOT00000047507 -7 0.79 10865372 similar to ribosomal protein L31 Miscellaneous & Unknown

LOC100192313 NM_001136261 250 1.20 10902333 hypothetical protein LOC100192313 LOC502684 NM_001025060 -12 0.76 10840826 hypothetical protein LOC502684 LOC691649 ENSRNOT00000005237 110 1.23 10734061 hypothetical protein LOC691649 Rcan3 NM_001012746 33 1.32 10880610 RCAN family member 3 RGD1564171 NM_001109186 -35 0.72 10816879 RGD1564171 RGD1311188 BC162017 44 1.21 10897118 similar to 1500031N24Rik protein MGC94282 NR_027366 20 1.28 10865838 similar to 5930416I19Rik protein RGD1564129 ENSRNOT00000038189 -7 0.83 10795611 similar to hypothetical protein 4930474N05 RGD1563072 NM_001107981 58 1.23 10872059 similar to hypothetical protein FLJ38984 Ttc21a ENSRNOT00000043831 -13 0.79 10914271 tetratricopeptide repeat domain 21A Tsku NM_001009965 -33 0.81 10723822 tsukushin EST's RGD1311575 ENSRNOT00000002908 -32 0.81 10776361 hypothetical LOC289568 RGD1306462 BC097453 -13 0.83 10906065 similar to RIKEN cDNA 1700019P01 RGD1306446 NM_001008554 -9 0.82 10772030 similar to RIKEN cDNA 9930032O22 gene --- -202 0.79 10855185 --- -126 0.80 10932269 --- -75 0.82 10890648 --- -64 0.74 10831148 --- -57 0.80 10894227 --- -51 0.78 10872129 --- -49 0.79 10788314 --- -44 0.81 10914901 --- -44 0.70 10807957 --- -41 0.68 10818911 --- -39 0.82 10820213 --- -37 0.78 10804712 --- -35 0.77 10796438 --- -35 0.81 10746789 --- -33 0.76 10883023 --- -30 0.77 10914877 --- -29 0.70 10840477 --- -28 0.81 10717953 --- -28 0.54 10736193 --- -27 0.76 10790465 --- -27 0.77 10726483 --- -26 0.66 10723687 --- -26 0.61 10776289 --- -25 0.79 10893305 --- -21 0.77 10802574 --- -21 0.78 10755550 --- -20 0.78 10771204 --- -18 0.65 10807883 --- -15 0.82 10850090 --- -14 0.75 10877567

28 --- -13 0.75 10701666 --- -12 0.82 10725517 --- -12 0.78 10830185 --- -11 0.81 10894874 --- -11 0.83 10764047 --- -10 0.80 10763316 --- -10 0.79 10890166 --- -10 0.82 10754929 --- -9 0.80 10803721 --- -8 0.76 10933227 --- -8 0.79 10729120 --- -8 0.83 10839972 --- -8 0.81 10776737 --- -7 0.82 10863051 --- 5 1.21 10814661 --- 8 1.20 10877368 --- 9 1.22 10894850 --- 12 1.32 10886244 --- 13 1.24 10823498 --- 22 1.59 10850319 --- 27 1.21 10764400 --- 31 1.35 10934042 --- 32 1.22 10896201 --- 42 1.21 10880526 --- 46 1.24 10797939 --- 68 1.60 10722816 --- 111 1.22 10708560

List 11. Genes Expressed Differentially in Stressed F3-Control Rat CA1 of the Hippocampus as Compared to Non-Stressed F3-Control ('Str-Con vs Nst-Con' contrast), 118 genes and EST's GenBank_Reference Mean Affymetrix Gene Symbol Ratio Gene Title Sequence _diff ID Cytoskeleton- ECM Glycam1 NM_012794 -65 0.79 10907749 glycosylation dependent cell adhesion molecule 1 Kb23 NM_001008813 32 1.20 10907369 type II keratin Kb23 Kif27 NM_198050 -20 0.78 10793846 kinesin family member 27 Lamb2 NM_012974 -44 0.78 10793140 laminin, beta 2 LIM domain containing preferred translocation Lpp NM_001013864 -34 0.78 10755069 partner in lipoma Development Atn1 NM_017228 57 1.22 10865487 atrophin 1 Pbxip1 NM_001100976 -51 0.79 10816807 pre-B-cell leukemia homeobox interacting protein 1 Pinx1 NM_001083337 -24 0.80 10781014 PIN2-interacting protein 1 Rex2 ENSRNOT00000040918 52 1.28 10873880 reduced expression 2 Rhox11 NM_001024873 13 1.25 10936270 reproductive homeobox 11 Electron Transport Cox8b NM_012786 -10 0.81 10726669 cytochrome c oxidase, subunit VIIIb Etfb NM_001004220 -65 0.81 10706339 electron-transfer-flavoprotein, beta polypeptide Prdx4 NM_053512 -40 0.82 10933699 peroxiredoxin 4 Pet112l ENSRNOT00000057128 -64 0.82 10816176 PET112-like (yeast) Tmem126a NM_001011557 -30 0.81 10723639 transmembrane protein 126A Epigenetics core-binding factor, runt domain, alpha subunit 2; Cbfa2t3 NM_001108453 12 1.21 10811688 translocated to, 3

29 Growth Factors Igf2r NM_012756 -91 0.80 10702996 insulin-like growth factor 2 receptor Mif NM_031051 -270 0.83 10829649 macrophage migration inhibitory factor Immune Response Mr1 NM_001100635 -23 0.82 10768819 major histocompatibility complex, class I-related LOC287167 NM_001013853 -93 0.78 10741765 globin, alpha Metabolism & Transport Acaa2 NM_130433 -46 0.80 10802691 acetyl-Coenzyme A acyltransferase 2 Aldh2 NM_032416 -87 0.76 10758663 aldehyde dehydrogenase 2 family (mitochondrial) Apoc1 NM_012824 -26 0.74 10719524 apolipoprotein C-I ATP synthase, H+ transporting, mitochondrial F0 Atp5g1 NM_017311 -134 0.83 10746583 complex, subunit C1 (subunit 9) ATP synthase, H+ transporting, mitochondrial F0 Atp5g2 NM_133556 -180 0.82 10907634 complex, subunit C2 (subunit 9) Decr1 NM_057197 -53 0.83 10875631 2,4-dienoyl CoA reductase 1, mitochondrial Grhpr NM_001113754 -50 0.83 10868673 glyoxylate reductase Gsta3 NM_031509 -304 0.81 10926958 glutathione S-transferase A3 Gsta4 NM_001106840 -29 0.69 10911797 glutathione S-transferase alpha 4 Hba-a2 NM_013096 -1385 0.63 10741756 hemoglobin alpha, adult chain 2 Hbb NM_033234 -300 0.64 10724311 hemoglobin, beta Idh2 NM_001014161 -129 0.74 10723020 isocitrate dehydrogenase 2 (NADP+), mitochondrial similar to Nucleoside diphosphate kinase homolog 5 LOC682386 ENSRNOT00000027244 -37 0.80 10803759 (NDK-H 5) (NDP kinase homolog 5) (nm23-M5) Ndufab1 NM_001106294 -209 0.77 10725474 NADH dehydrogenase (ubiquinone) 1, alpha Odc1 NM_012615 -137 0.82 10883785 ornithine decarboxylase 1 Pex14 NM_172063 50 1.27 10881648 peroxisomal biogenesis factor 14 Prodh NM_001135778 -122 0.75 10752352 proline dehydrogenase sulfotransferase family, cytosolic, 1A, phenol- Sult1a1 NM_031834 -60 0.78 10725782 preferring, member 1 Tcn2 NM_022534 -127 0.74 10778028 transcobalamin 2 Urod NM_019209 -74 0.82 10878926 uroporphyrinogen decarboxylase Proteolysis Rnf213 ENSRNOT00000004904 -16 0.81 10740016 ring finger protein 213 Cst3 NM_012837 -809 0.83 10850563 cystatin C Mcpt4l1 XM_001056983 11 1.21 10780538 mast cell protease 4-like 1 LOC688812 XR_085983 26 1.22 10756117 similar to ubiquitin-activating enzyme E1C Receptors & Binding Proteins

LOC100363058 XM_002742441 -17 0.79 10709757 olfactory receptor 480-like Mt2A NM_001137564 -171 0.78 10827989 metallothionein 2A Mt2A NM_001137564 -326 0.81 10809399 metallothionein 2A Olr1320 NM_001000471 16 1.24 10909285 olfactory receptor 1320 Olr567 NM_001000326 -12 0.82 10847060 olfactory receptor 567 Olr760 NM_001001069 28 1.33 10848105 olfactory receptor 760 Vom2r-ps27 ENSRNOT00000051051 17 1.21 10718403 vomeronasal 2 receptor, pseudogene 27 Signaling Ctnnal1 NM_001106649 -78 0.77 10876896 catenin (cadherin associated protein), alpha-like 1 Dusp5 NM_133578 -28 0.77 10716080 dual specificity phosphatase 5 Fkbp14 NM_001013210 -66 0.75 10862643 FK506 binding protein 14 Fxyd1 NM_031648 -261 0.80 10720878 FXYD domain-containing ion transport regulator 1 Mark2 NM_021699 98 1.22 10728396 MAP Magmas NM_001100136 -24 0.83 10731783 mitochondria-associated protein involved in 30 granulocyte-macrophage colony-stimulating factor signal transduction Nek6 NM_182953 -38 0.83 10835964 NIMA (never in mitosis gene a)-related kinase 6 Transcription E2f5 ENSRNOT00000014361 -22 0.75 10718609 E2F transcription factor 5 gonadotropin inducible ovarian transcription factor Giot1 NM_133563 68 1.25 10900841 1 Id3 NM_013058 -49 0.83 10872972 inhibitor of DNA binding 3 polymerase (RNA) III (DNA directed) polypeptide Polr3k NM_001014259 -158 0.82 10843132 K Zcchc11 NM_001107953 54 1.20 10870777 zinc finger, CCHC domain containing 11 Translation & Protein Modification Mrpl54 NM_001106770 -102 0.79 10893586 mitochondrial ribosomal protein L54 M-phase phosphoprotein 10 (U3 small nucleolar Mphosph10 NM_001106340 40 1.21 10722566 ribonucleoprotein) similar to 60S ribosomal protein L17 (L23) (Amino LOC499485 XM_002725892 22 1.23 10820047 acid starvation-induced protein) (ASI) RGD1563579 ENSRNOT00000057412 15 1.20 10939086 similar to 60S ribosomal protein L29 (P23) Serp1 NM_030835 -201 0.80 10823309 stress-associated endoplasmic reticulum protein 1 Miscellaneous & Unknown Fam100a BC079459 77 1.20 10731734 family with sequence similarity 100, member A

LOC100364350 XM_002725175 -64 0.81 10790658 NACHT and WD repeat domain containing 1-like RGD1562420 ENSRNOT00000007683 44 1.39 10887809 similar to hypothetical protein RGD1560187 NM_001173556 -140 0.83 10880897 similar to Hypothetical UPF0327 protein RGD1561667 XM_217999 16 1.23 10703216 similar to putative protein kinase Tmem147 NM_001038494 -41 0.83 10720767 transmembrane protein 147 Tmem38b NM_001014191 -37 0.78 10869151 transmembrane protein 38B EST's RGD1311378 BC166836 -42 0.83 10842513 similar to RIKEN cDNA 2010011I20 --- -81 0.78 10827665 --- -56 0.83 10731138 --- -49 0.75 10859627 --- -31 0.77 10904356 --- -28 0.79 10827448 --- -28 0.76 10779792 --- -26 0.64 10938173 --- -26 0.77 10730021 --- -22 0.82 10933128 --- -22 0.77 10870890 --- -21 0.81 10903058 --- -18 0.79 10939164 --- -12 0.83 10861356 --- -9 0.79 10765728 --- -9 0.79 10905970 --- 13 1.37 10774341 --- 13 1.26 10766994 --- 14 1.23 10717798 --- 17 1.28 10707376 --- 19 1.21 10801535 --- 23 1.21 10822348 --- 25 1.33 10853149 --- 28 1.57 10723687 --- 29 1.39 10859772 31 --- 29 1.30 10805577 --- 30 1.20 10736417 --- 33 1.21 10884738 --- 39 1.31 10792132 --- 42 1.21 10768369 --- 50 1.20 10795260 --- 50 1.20 10940007 --- 54 1.67 10922266 --- 70 1.21 10741664 --- 103 1.58 10791602 --- 103 1.58 10833416 --- 108 1.24 10930569 --- 122 1.44 10809882 --- 140 1.21 10805722 --- 142 1.66 10939699 --- 350 1.39 10820008 --- 754 1.34 10930602

List 12. Genes Expressed Differentially in Stressed F3-Vinclozolin Rat CA1 of the Hippocampus as Compared to Non-Stressed F3-Vinclozolin ('Str-Vin vs Nst-Vin' contrast), 379 genes and EST's GenBank_Reference Mean Affymetrix Gene Symbol Ratio Gene Title Sequence _diff ID Apoptosis Bace2 NM_001002802 -35 0.71 10750513 beta-site APP-cleaving enzyme 2 Dap3 NM_001011950 -83 0.81 10824373 death associated protein 3 TRAF-interacting protein with forkhead- Tifab NM_001025029 -14 0.82 10793961 associated domain, family member B tumor necrosis factor (ligand) superfamily, Tnfsf4 NM_053552 -22 0.80 10765092 member 4 ENSRNOT000000388 tumor necrosis factor, alpha-induced protein 8- Tnfaip8l3 30 -18 0.70 10917501 like 3 Cell Cycle Cenpc1 NM_001004098 -73 0.79 10772107 centromere protein C 1 Cep70 NM_001017470 -56 0.78 10912464 centrosomal protein 70kDa ENSRNOT000000303 centrosome and spindle pole associated protein Cspp1 45 -128 0.71 10875091 1 minichromosome maintenance complex Mcm8 NM_001106514 -17 0.80 10840112 component 8 Prc1 NM_001107529 -29 0.73 10708214 protein regulator of cytokinesis 1 Cytoskeleton- ECM Cdh8 NM_053393 -335 0.61 10805767 cadherin 8 carcinoembryonic antigen-related cell adhesion Ceacam10 NM_173339 9.6 1.30 10705034 molecule 10 Crtac1 NM_134401 -121 0.73 10715431 cartilage acidic protein 1 Dynlrb2 NM_001108451 -42 0.62 10811283 dynein light chain roadblock-type 2 Gjb6 NM_053388 -134 0.79 10784120 gap junction protein, beta 6 Fank1 NM_001008347 -14 0.78 10711777 fibronectin type 3 and ankyrin repeat domains 1 Hapln1 NM_019189 -92 0.81 10812399 hyaluronan and proteoglycan link protein 1 Krt17 NM_212545 8 1.22 10747296 keratin 17 killer cell lectin-like receptor, subfamily A, Klra5 NM_198746 -13 0.78 10866236 member 5 LOC290704 ENSRNOT000000596 14 1.28 10787918 similar to palladin

32 73 Marveld2 NM_001108936 -15 0.72 10820965 MARVEL domain containing 2 MOCO sulphurase C-terminal domain Mosc1 NM_001100811 -9 0.83 10770503 containing 1 Myom2 NM_001169141 -11 0.80 10792621 myomesin 2 ENSRNOT000000465 similar to Contactin associated protein-like 3 RGD1563615 25 53 1.24 10793444 precursor (Cell recognition molecule Caspr3) Tbca NM_001013245 -51 0.78 10899579 tubulin folding cofactor A Ttll3 NM_001108640 -20 0.81 10857767 tubulin tyrosine ligase-like family, member 3 ENSRNOT000000230 Ttll4 67 -45 0.81 10924392 tubulin tyrosine ligase-like family, member 4 Development cat eye syndrome chromosome region, Cecr6 XM_001058567 20 1.25 10865198 candidate 6 homolog (human) Crygb NM_001109875 -9.9 0.80 10928555 crystallin, gamma B Gsc2 NM_001108846 17 1.24 10752382 goosecoid homeobox 2 Gtl3 NM_001037978 -113 0.78 10805895 gene trap locus 3 Lce1l NM_001109493 -48 0.76 10824769 late cornified envelope 1L Lhx2 NM_001106571 -87 0.78 10835958 LIM homeobox 2 Meox1 NM_001108837 23 1.20 10747682 mesenchyme homeobox 1 Myocd NM_182667 22 1.26 10743652 myocardin Ntn1 AY028417 56 1.52 10743781 netrin 1 Nlgn1 NM_053868 -156 0.73 10822545 neuroligin 1 Popdc2 NM_199113 -22 0.83 10754179 popeye domain containing 2 Ptov1 NM_001008304 -95 0.80 10721504 prostate tumor overexpressed 1 Robo3 NM_001108135 -21 0.75 10916201 roundabout homolog 3 (Drosophila) Tecpr1 NM_001037191 -81 0.82 10756638 tectonin beta-propeller repeat containing 1 ENSRNOT000000423 Vgll3 16 -44 0.71 10749839 vestigial like 3 (Drosophila) Rcan3 NM_001012746 37 1.37 10880610 RCAN family member 3 Syt17 NM_138849 193 1.25 10725235 synaptotagmin XVII ENSRNOT000000096 Sntg1 79 -100 0.77 10867345 syntrophin, gamma 1 Tert NM_053423 -22 0.80 10717517 telomerase reverse transcriptase Vasn NM_001109382 41 1.21 10740701 vasorin DNA Repair Rad52 NM_001106617 -46 0.80 10858260 RAD52 homolog (S. cerevisiae) Electron Transport COX18 cytochrome c oxidase assembly Cox18 NM_001106000 -95 0.81 10771819 homolog (S. cerevisiae) Etfb NM_001004220 -110 0.67 10706339 electron-transfer-flavoprotein, beta polypeptide

LOC10017491 0 NM_001131003 -129 0.71 10804552 glutaredoxin-like protein Prdx6 NM_053576 -362 0.66 10769218 peroxiredoxin 6 Pdcl NM_022247 -115 0.83 10844776 phosducin-like ENSRNOT000000029 Pdcl2 53 -12 0.74 10772243 phosducin-like 2 ENSRNOT000000508 LOC691211 23 -9.9 0.79 10724991 similar to Cytochrome c, somatic Epigenetics 33 DPH5 homolog Dph5 NM_001017449 -32 0.82 10818581 (S. cerevisiae) HFM1, ATP-dependent DNA helicase homolog (S. Hfm1 XM_002724927 -17 0.80 10771099 cerevisiae) Hdac8 NM_001126373 -65 0.78 10938734 histone deacetylase 8 Tbx20 NM_001108132 12 1.20 10915817 T-box 20 Growth Factors Angpt1 NM_053546 -30 0.69 10903529 angiopoietin 1 Dner BC086329 -186 0.80 10929482 delta Gdf10 NM_024375 -30 0.72 10786905 growth differentiation factor 10 Il15 NM_013129 -19 0.78 10806899 interleukin 15 Kng1l1 NM_001009628 -63 0.66 10755135 kininogen 1-like 1 Rxfp1 NM_201417 133 1.80 10823819 relaxin Tgfb2 NM_031131 212 1.62 10770577 transforming growth factor, beta 2 wingless-type MMTV integration site family, Wnt7a NM_001100473 -48 0.75 10864094 member 7A Immune Response Cd244 NM_022259 -13 0.77 10765625 Cd244 molecule, natural killer cell receptor 2B4 Cd302 NM_001013916 -35 0.82 10845508 CD302 molecule Cd5l NM_001025685 -31 0.77 10816270 Cd5 molecule-like Igh-1a BC088254 -12 0.81 10892533 immunoglobulin heavy chain 1a (serum IgG2a) Il22 ENSRNOT00000009776 -15 0.82 10895618 interleukin 22 LOC688858 XM_001068599 -224 0.78 10759581 similar to CD209a antigen RT1-M6-1 NM_001008852 -49 0.72 10827686 RT1 class I, locus M6, gene 1 RT1-M6-2 NM_001008853 -36 0.71 10827691 RT1 class I, locus M6, gene 2 Spag8 NM_001173555 -14 0.83 10876426 sperm associated antigen 8 Metabolism & Transport Aadacl2 ENSRNOT00000067870 -8 0.82 10815616 arylacetamide deacetylase-like 2 Abhd3 NM_001106162 -276 0.80 10803207 abhydrolase domain containing 3 Acsbg1 NM_134389 -230 0.81 10917568 acyl-CoA synthetase bubblegum family member 1 Adh1 NM_019286 27 1.27 10819379 alcohol dehydrogenase 1 (class I) Adsl NM_001130503 -63 0.83 10897854 adenylosuccinate lyase Apof NM_001024351 -16 0.80 10893064 apolipoprotein F Ass1 NM_013157 27 1.37 10835355 argininosuccinate synthetase 1 ATP synthase, H+ transporting, mitochondrial F1 Atp5o NM_138883 -101 0.83 10753198 complex, O subunit carbamoyl-phosphate synthetase 2, aspartate Cad NM_001105710 -20 0.82 10888872 transcarbamylase, and dihydroorotase Coq9 NM_001035257 -60 0.81 10809251 coenzyme Q9 homolog (S. cerevisiae) Crot NM_031987 -58 0.80 10860548 carnitine O-octanoyltransferase glycine cleavage system protein H (aminomethyl Gcsh NM_133598 -127 0.80 10811293 carrier) Gk NM_024381 -79 0.77 10938219 glycerol kinase Gstm5 NM_172038 -245 0.81 10818291 glutathione S-transferase, mu 5 Gstm7 NM_031154 -296 0.78 10825890 glutathione S-transferase, mu 7 Hsd11b1 NM_017080 -226 0.67 10770795 hydroxysteroid 11-beta dehydrogenase 1 potassium voltage-gated channel, subfamily Q, Kcnq5l ENSRNOT00000040034 -337 0.57 10926975 member 5-like Peci NM_001006966 -75 0.80 10794769 peroxisomal D3,D2-enoyl-CoA isomerase Pgcp NM_031640 -53 0.80 10896028 plasma glutamate carboxypeptidase Phyh NM_053674 -136 0.81 10799558 phytanoyl-CoA 2-hydroxylase Ppcdc NM_001108763 -16 0.83 10917754 phosphopantothenoylcysteine decarboxylase Ppid NM_001004279 -399 0.75 10816008 peptidylprolyl isomerase D (cyclophilin D) Prodh NM_001135778 -134 0.70 10752352 proline dehydrogenase 34 Pygb NM_013188 -296 0.78 10840700 phosphorylase, glycogen; brain Sephs2 NM_001079889 50 1.20 10725993 selenophosphate synthetase 2 Slc14a1 NM_019346 -166 0.80 10805335 solute carrier family 14 (urea transporter), member 1 solute carrier family 16, member 3 (monocarboxylic Slc16a3 NM_030834 39 1.26 10740209 acid transporter 4) Slc45a2 NM_001107653 -9 0.82 10813686 solute carrier family 45, member 2 translocase of inner mitochondrial membrane 17 Timm17a NM_019351 -152 0.80 10890170 homolog A (yeast) translocase of inner mitochondrial membrane 8 Timm8a1 NM_053370 -119 0.81 10939289 homolog a1 (yeast) Tst NM_012808 -82 0.83 10905284 thiosulfate sulfurtransferase Ugt2b NM_031533 -9 0.80 10771951 UDP glycosyltransferase 2 family, polypeptide B Urod NM_019209 -83 0.79 10878926 uroporphyrinogen decarboxylase Proteolysis homocysteine-inducible, endoplasmic reticulum Herpud1 NM_053523 -74 0.80 10809328 stress-inducible, ubiquitin-like domain member 1 Htra1 NM_031721 -397 0.74 10711566 HtrA serine peptidase 1 Kdelc1 NM_001108217 -57 0.83 10923000 KDEL (Lys-Asp-Glu-Leu) containing 1 Klk15 ENSRNOT00000038353 -27 0.75 10706498 kallikrein-related peptidase 15 LOC360228 NM_001003706 -33 0.75 10736875 WDNM1 homolog Osgep NM_001100510 -22 0.79 10783147 O-sialoglycoprotein endopeptidase Prep NM_031324 -64 0.78 10830654 prolyl endopeptidase Prss23 NM_001007691 -34 0.82 10708541 protease, serine, 23 Rnf146 NM_001012060 -165 0.80 10702424 ring finger protein 146 Timp4 NM_001109393 -70 0.81 10864732 tissue inhibitor of metalloproteinase 4 Ubc NM_017314 350 1.34 10758134 ubiquitin C ubiquitin protein ligase E3 component n-recognin 7 Ubr7 NM_001007705 -74 0.82 10886494 (putative) Usp3 NM_001025424 -20 0.81 10918345 ubiquitin specific peptidase 3 Receptors & Binding Proteins Adora2b NM_017161 -36 0.76 10734291 adenosine A2B receptor Adra1d NM_024483 -81 0.75 10850087 adrenergic, alpha-1D-, receptor Bdkrb1 NM_030851 -17 0.83 10886644 bradykinin receptor B1 Efcab2 NM_001105977 -24 0.70 10766065 EF-hand calcium binding domain 2 Efcab6 ENSRNOT00000015447 16 1.34 10905871 EF-hand calcium binding domain 6 Fgfr3 NM_053429 -64 0.79 10777748 fibroblast growth factor receptor 3 gamma-aminobutyric acid (GABA) A receptor, Gabrg1 NM_080586 -432 0.65 10772544 gamma 1 Gfral ENSRNOT00000052341 -9.8 0.82 10918752 GDNF family receptor alpha like Ifngr2 NM_001108313 -129 0.76 10750211 interferon gamma receptor 2 Igfbp5 NM_012817 212 1.70 10928837 insulin-like growth factor binding protein 5 Iscu NM_001105936 -121 0.83 10762887 iron-sulfur cluster scaffold homolog (E. coli) MGC112715 NM_001044300 59 1.22 10829993 platelet receptor Gi24 Mt2A NM_001137564 -626 0.67 10809399 metallothionein 2A Mt2A NM_001137564 -346 0.61 10827989 metallothionein 2A Olr1069 NM_001000522 -12 0.78 10900095 olfactory receptor 1069 Olr1088 ENSRNOT00000012907 25 1.22 10900905 olfactory receptor 1088 Olr120 NM_001000154 -21 0.75 10724297 olfactory receptor 120 Olr1321 NM_001000792 10.4 1.22 10909287 olfactory receptor 1321 Olr1418 NM_001000008 -12 0.79 10742927 olfactory receptor 1418 Olr1557 NM_001000050 -10.1 0.75 10753565 olfactory receptor 1557 Olr1640 NM_001000099 -12 0.82 10783355 olfactory receptor 1640 Olr1714 NM_214456 -56 0.81 10830818 olfactory receptor 1714 Olr1734 NM_001001119 -9 0.74 10827639 olfactory receptor 1734 Olr221 NM_001000200 24 1.41 10724609 olfactory receptor 221 35 Olr423 NM_001000391 12 1.25 10835879 olfactory receptor 423 Olr495 NM_001000310 11 1.28 10846974 olfactory receptor 495 Olr560 NM_001000325 -13 0.83 10837518 olfactory receptor 560 Olr582 NM_001000662 -42 0.63 10837545 olfactory receptor 582 Olr584 NM_001000661 -20 0.76 10847074 olfactory receptor 584 Olr629 NM_001001058 -29 0.72 10847109 olfactory receptor 629 Olr689 NM_001000997 45 1.31 10847176 olfactory receptor 689 Olr734 NM_001000617 -28 0.78 10847242 olfactory receptor 734 Olr809 NM_001000849 17 1.25 10855092 olfactory receptor 809 Olr828 NM_001000991 35 1.30 10858150 olfactory receptor 828 Olr996 NM_001000700 33 1.42 10893375 olfactory receptor 996 Ptbp2 NM_001005555 -290 0.80 10826418 polypyrimidine tract binding protein 2 Sec14l2 NM_053801 -98 0.82 10778043 SEC14-like 2 (S. cerevisiae) Tlr2 NM_198769 10.0 1.25 10823970 toll-like receptor 2 Trhr NM_013047 -23 0.72 10896394 thyrotropin releasing hormone receptor V1rd23 NM_001008947 -16 0.83 10718780 vomeronasal 1 receptor, D23 V1rg6 NM_001008957 -14 0.78 10894297 vomeronasal 1 receptor, G6 Vom2r66 ENSRNOT00000051621 74 1.37 10774903 vomeronasal 2 receptor, 66 Signaling Anxa6 NM_024156 -464 0.50 10742712 annexin A6 Arhgap1 NM_001107747 127 1.28 10837960 Rho GTPase activating protein 1 Aurkb NM_053749 -12 0.77 10734853 aurora kinase B diazepam binding inhibitor (GABA receptor Dbi NM_031853 -92 0.78 10931154 modulator, acyl-Coenzyme A binding protein) Dusp4 NM_022199 -51 0.75 10792035 dual specificity phosphatase 4 Efna1 NM_053599 23 1.25 10824439 ephrin A1 Gbp4 ENSRNOT00000022648 -18 0.76 10819512 guanylate binding protein 4 Gm2a NM_172335 -99 0.82 10733690 GM2 ganglioside activator Gpr139 NM_001024241 17 1.24 10725286 G protein-coupled receptor 139 glutamate receptor, ionotropic, N-methyl D- Grin2c NM_012575 -57 0.81 10748891 aspartate 2C Ick NM_138886 92 1.39 10911780 intestinal cell kinase Igtp NM_001008765 -10.1 0.82 10733790 interferon gamma induced GTPase Inpp5j NM_133562 -84 0.75 10777958 inositol polyphosphate-5-phosphatase J LOC304239 ENSRNOT00000049215 -66 0.63 10756334 similar to RalA binding protein 1 Map6d1 NM_001108844 77 1.23 10752200 MAP6 domain containing 1 similar to Microsomal signal peptidase 23 kDa MGC109340 NM_001024267 -167 0.77 10935036 subunit (SPase 22 kDa subunit) (SPC22 Ndrg3 NM_001013923 277 1.22 10851210 N-myc downstream regulated gene 3 Nek6 NM_182953 -64 0.75 10835964 NIMA (never in mitosis gene a)-related kinase 6 Pdk2 NM_030872 -161 0.82 10746469 pyruvate dehydrogenase kinase, isozyme 2 protein kinase (cAMP-dependent, catalytic) Pkib NM_001076553 -13 0.82 10830216 inhibitor beta pleckstrin homology domain containing, family O Plekho2 ENSRNOT00000042633 -48 0.68 10918288 member 2 Pygm NM_012638 -95 0.77 10713382 phosphorylase, glycogen, muscle similar to GABA(A) receptor-associated protein like RGD1562165 ENSRNOT00000029187 -11 0.82 10876836 2 Rilpl2 NM_001004205 -24 0.81 10758212 Rab interacting lysosomal protein-like 2 Rit1 NM_001109185 -89 0.82 10816607 Ras-like without CAAX 1 Src homology 3 domain-containing guanine Sgef ENSRNOT00000019553 -73 0.73 10815663 nucleotide exchange factor Sh3bp4 NM_022693 128 1.50 10925264 SH3-domain binding protein 4 signaling lymphocytic activation molecule family Slamf1 NM_001109078 16 1.23 10765639 member 1 Socs4 NM_001107256 -37 0.83 10779668 suppressor of cytokine signaling 4 Srp14 NM_001106497 -125 0.81 10848434 signal recognition particle 14 36 Transcription Ankdd1a ENSRNOT00000033512 -19 0.73 10918281 ankyrin repeat and death domain containing 1A Ankrd60 ENSRNOT00000055082 -16 0.82 10852149 ankyrin repeat domain 60 Ccdc129 ENSRNOT00000045930 -19 0.72 10855741 coiled-coil domain containing 129 Ccdc148 NM_001107732 -28 0.78 10845443 coiled-coil domain containing 148 Ccdc153 NM_001013953 -72 0.56 10909463 coiled-coil domain containing 153 Ccdc30 ENSRNOT00000011325 -41 0.81 10871570 coiled-coil domain containing 30 Ccdc37 ENSRNOT00000024222 -21 0.69 10864025 coiled-coil domain containing 37 Ccdc46 NM_001105849 -22 0.76 10739277 coiled-coil domain containing 46 CAP-GLY domain containing linker protein family, Clip4 NM_001013942 -117 0.69 10888620 member 4 Creb3l3 NM_001012115 18 1.22 10893630 cAMP responsive element binding protein 3-like 3 E2f5 ENSRNOT00000014361 -25 0.72 10718609 E2F transcription factor 5 Elk1 NM_001108059 78 1.24 10936520 ELK1, member of ETS oncogene family Foxj2 NM_001109352 42 1.23 10858529 forkhead box J2 Gtf2ird1 NM_001001504 -18 0.80 10757829 GTF2I repeat domain containing 1 Haus1 NM_138864 36 1.25 10805313 HAUS augmin-like complex, subunit 1 Hint1 ENSRNOT00000006471 -20 0.70 10862836 histidine triad nucleotide binding protein 1 Kbtbd11 NM_001107326 -43 0.74 10792660 kelch repeat and BTB (POZ) domain containing 11 Klhl36 NM_001017511 -19 0.81 10808356 kelch-like 36 (Drosophila) Luzp1 AF181259 -20 0.80 10873012 leucine zipper protein 1 March3 NM_001007759 -40 0.73 10804541 membrane-associated ring finger (C3HC4) 3 nucleolar complex associated 4 homolog (S. Noc4l NM_001014129 -40 0.81 10759342 cerevisiae) Nop58 NM_021754 -117 0.82 10923670 nucleolar protein NOP58 Nutf2 NM_001007629 -117 0.80 10807386 nuclear transport factor 2 Ovca2 NM_001109036 -74 0.81 10744904 candidate tumor suppressor in ovarian cancer 2 Pnrc1 NM_173322 237 1.20 10875863 proline-rich nuclear receptor coactivator 1 polymerase (RNA) III (DNA directed) polypeptide Polr3k NM_001014259 -204 0.77 10843132 K Ppara NM_013196 -16 0.79 10898359 peroxisome proliferator activated receptor alpha RGD1565987 ENSRNOT00000048737 -47 0.79 10877694 similar to F-box and leucine-rich repeat protein 18 RGD1565987 ENSRNOT00000048737 -46 0.80 10756806 similar to F-box and leucine-rich repeat protein 18 Ssx1 ENSRNOT00000030146 -9 0.82 10936947 synovial sarcoma, X breakpoint 1 transcriptional adaptor 2 (ADA2 homolog, yeast)- Tada2b NM_001170455 -54 0.77 10773358 beta Zcchc3 ENSRNOT00000009859 17 1.21 10850793 zinc finger, CCHC domain containing 3 Zcchc6 ENSRNOT00000067726 136 1.36 10793708 zinc finger, CCHC domain containing 6 Zfp212 ENSRNOT00000009054 -76 0.80 10855203 Zinc finger protein 212 Znf488 ENSRNOT00000031496 15 1.30 10790433 zinc finger protein 488 Translation & Protein Modification CWC22 spliceosome-associated protein homolog Cwc22 ENSRNOT00000037684 -66 0.75 10846661 (S. cerevisiae) Eif4e3 NM_001106612 -159 0.62 10864425 eukaryotic translation initiation factor 4E member 3 LOC500148 NM_001035253 57 1.29 10862792 similar to 40S ribosomal protein S7 (S8) LSM3 homolog, U6 small nuclear RNA associated Lsm3 NM_001106611 -134 0.80 10857310 (S. cerevisiae) Mrps16 NM_001109518 -69 0.81 10779159 mitochondrial ribosomal protein S16 queuine tRNA-ribosyltransferase domain containing Qtrtd1 ENSRNOT00000000317 -30 0.81 10751196 1 Rbm45 NM_153306 -65 0.81 10837056 RNA binding motif protein 45 RGD1560186 ENSRNOT00000049634 -9 0.78 10766758 similar to ribosomal protein L37 RGD1561736 XM_001061583 -80 0.76 10940411 similar to ribosomal protein L10 RGD1563551 ENSRNOT00000047507 -9 0.75 10865372 similar to ribosomal protein L31 RGD1565117 ENSRNOT00000045687 9 1.22 10895828 similar to 40S ribosomal protein S26 37 Rnase4 NM_020082 -87 0.78 10779832 ribonuclease, RNase A family 4 Rpl28 NM_022697 -186 0.81 10718863 ribosomal protein L28 Rplp2 NM_001030021 366 1.24 10776809 ribosomal protein, large P2 Miscellaneous & Unknown Btbd16 NM_001017464 -11 0.82 10711532 BTB (POZ) domain containing 16 Dtwd1 NM_001013921 33 1.23 10839438 DTW domain containing 1 Dydc2 NM_001134797 12 1.20 10790647 DPY30 domain containing 2 Fam123c ENSRNOT00000033700 -24 0.73 10922449 family with sequence similarity 123C Fam158a BC086432 -54 0.83 10783799 family with sequence similarity 158, member A Fam198b NM_199105 32 1.29 10816017 family with sequence similarity 198, member B

LOC100359838 XM_002728978 14 1.23 10833596 ret finger protein-like 4-like

LOC100364350 XM_002725175 -69 0.79 10790658 NACHT and WD repeat domain containing 1-like LOC362863 NM_001170605 -14 0.82 10894643 first gene upstream of Nt5dc3 LOC363306 ENSRNOT00000043269 86 1.27 10921328 hypothetical protein LOC363306 LOC502684 NM_001025060 -17 0.68 10840826 hypothetical protein LOC502684 LOC679307 ENSRNOT00000038733 -12 0.73 10774245 hypothetical protein LOC679307 LOC687395 ENSRNOT00000006406 -139 0.82 10838278 similar to CG9240-PA Lsmd1 NM_001105794 -149 0.80 10734970 LSM domain containing 1 Luc7l3 NM_001108291 -202 0.76 10746286 LUC7-like 3 (S. cerevisiae) MGC94282 NR_027366 23 1.32 10865838 similar to 5930416I19Rik protein Mterfd2 NM_001037209 -32 0.78 10929991 MTERF domain containing 2 Ptcd3 NM_001134718 -105 0.80 10863158 Pentatricopeptide repeat domain 3 RGD1305089 NM_001106730 -80 0.81 10884648 similar to 1110008L16Rik protein RGD1310641 NM_001079701 -14 0.78 10875910 similar to hypothetical protein RGD1559961 NM_001163736 -71 0.80 10745785 similar to novel protein RGD1563072 NM_001107981 73 1.31 10872059 similar to hypothetical protein FLJ38984 RGD1565059 NM_001127562 -18 0.83 10823456 similar to hypothetical protein E130311K13 Rtn4ip1 NM_001107644 -72 0.76 10830630 reticulon 4 interacting protein 1 Tlcd1 NM_001013858 -91 0.76 10745214 TLC domain containing 1 Tmem186 NM_001025756 -38 0.83 10731596 transmembrane protein 186 Tmem208 NM_001106179 -64 0.82 10807211 transmembrane protein 208 transmembrane and tetratricopeptide repeat Tmtc2 XM_001080732 -77 0.78 10902080 containing 2 Tsku NM_001009965 -32 0.82 10723822 tsukushin ttc21a ENSRNOT00000043831 -22 0.68 10914271 tetratricopeptide repeat domain 21A Wdr60 ENSRNOT00000006144 -40 0.82 10892677 WD repeat domain 60 Yjefn3 ENSRNOT00000065345 -26 0.78 10787684 YjeF N-terminal domain containing 3 EST's RGD1311575 ENSRNOT00000002908 -46 0.75 10776361 hypothetical LOC289568 LOC499565 NM_001047946 -12 0.81 10814179 LRRGT00038 LOC689296 NM_001109531 -14 0.80 10890190 similar to expressed sequence C79407 RGD1306462 BC097453 -13 0.83 10906065 similar to RIKEN cDNA 1700019P01 RGD1305457 NM_001009430 15 1.25 10894842 similar to RIKEN cDNA 1700023M03 LOC497940 BC079326 -9 0.77 10744306 similar to RIKEN cDNA 2810408A11 RGD1565158 ENSRNOT00000061709 -36 0.71 10740325 similar to RIKEN cDNA 4921537P18 RGD1306446 NM_001008554 -10.3 0.81 10772030 similar to RIKEN cDNA 9930032O22 gene --- -702 0.76 10886848 --- -270 0.83 10865696 --- -170 0.75 10932269 --- -92 0.71 10894227 --- -91 0.74 10906590 --- -68 0.60 10914877 --- -65 0.61 10807957

38 --- -63 0.79 10783318 --- -63 0.78 10721694 --- -61 0.76 10758724 --- -53 0.77 10729852 --- -52 0.75 10749975 --- -49 0.83 10869187 --- -47 0.80 10914901 --- -47 0.64 10782509 --- -46 0.78 10738221 --- -45 0.74 10804712 --- -44 0.48 10776289 --- -42 0.79 10878965 --- -40 0.69 10726483 --- -39 0.77 10897004 --- -38 0.64 10802574 --- -36 0.65 10840477 --- -33 0.77 10717953 --- -33 0.78 10796438 --- -31 0.83 10812493 --- -30 0.81 10798486 --- -27 0.83 10938820 --- -25 0.81 10736814 --- -24 0.54 10800599 --- -22 0.80 10701814 --- -22 0.77 10755550 --- -22 0.60 10807883 --- -21 0.74 10818656 --- -20 0.77 10729554 --- -19 0.81 10706224 --- -19 0.76 10781888 --- -18 0.75 10764047 --- -17 0.81 10705392 --- -17 0.82 10840180 --- -17 0.70 10701666 --- -16 0.72 10708304 --- -16 0.81 10876998 --- -13 0.83 10717011 --- -13 0.83 10719289 --- -13 0.83 10841596 --- -12 0.75 10803721 --- -12 0.80 10894874 --- -12 0.76 10908152 --- -11 0.81 10719036 --- -11 0.79 10763316 --- -11 0.77 10839972 --- -11 0.80 10788343 --- -11 0.82 10860416 --- -11 0.82 10827409 --- -10.5 0.77 10890166 --- -10.4 0.80 10830185 --- -10.3 0.83 10910545 --- -10.2 0.75 10776737 --- -9.5 0.74 10752253 --- -9 0.82 10862921 --- -9 0.81 10876750 --- -9 0.78 10863051

39 --- -9 0.78 10729120 --- -9 0.78 10934683 --- -8 0.79 10905970 --- -8 0.80 10791547 --- -7 0.82 10708451 --- -7 0.82 10703566 --- 9 1.23 10788345 --- 9 1.22 10874046 --- 11 1.26 10894850 --- 14 1.21 10868595 --- 14 1.35 10935227 --- 16 1.44 10886244 --- 18 1.23 10742118 --- 21 1.36 10816498 --- 21 1.50 10774341 --- 24 1.25 10801535 --- 25 1.32 10777433 --- 27 1.21 10764400 --- 28 1.30 10823676 --- 29 1.33 10731606 --- 33 1.29 10930576 --- 34 1.43 10838077 --- 42 1.33 10896201 --- 51 1.38 10863026 --- 53 1.28 10880526 --- 64 1.37 10797939 --- 68 1.59 10722816 --- 70 1.23 10833808 --- 111 1.29 10925808 --- 149 1.23 10833287 --- 161 1.28 10813246 --- 176 1.54 10741664 --- 195 1.24 10867364

List 13. Genes Expressed Differentially in Non-Stressed F3-Vinclozolin Rat CA3 of the Hippocampus as Compared to Non-Stressed F3-Control ('Nst-Vin vs Nst-Con' contrast), 64 genes and EST's GenBank_Reference Mean Affymetrix Gene Symbol Ratio Gene Title Sequence _diff ID

Apoptosis

Bfar NM_001013125 80 1.20 10731229 bifunctional apoptosis regulator

Development

Pno1 NM_199083 117 1.24 10778568 partner of NOB1 homolog (S. cerevisiae)

similar to vitamin A-deficient testicular protein 11- LOC689303 ENSRNOT00000041918 -13 0.75 10797584 like

Growth Factors

Kng1 NM_012696 8 1.20 10751988 kininogen 1

Prl8a7 NM_022537 -11 0.83 10795057 prolactin family 8, subfamily a, member 7

40 Immune Response

similar to [Human Ig rearranged gamma chain mRNA, V_J_C region and complete cds.], gene LOC502812 XM_002729360 23 1.27 10863000 product

Metabolism & Transport

Acaa2 NM_130433 -70 0.79 10802691 acetyl-Coenzyme A acyltransferase 2

Chi3l4 XM_001069770 -17 0.82 10825768 chitinase 3-like 4

potassium voltage-gated channel, subfamily F, Kcnf1 NM_001169104 -62 0.81 10889326 member 1

Pop5 NM_001105752 60 1.31 10762717 processing of precursor 5, ribonuclease P

RGD1560402 XM_574850 -57 0.81 10812969 similar to Phosphoglycerate kinase 1

UDP glucuronosyltransferase 2 family, polypeptide Ugt2b34 ENSRNOT00000002728 11 1.23 10771993 B34

Proteolysis

Serpinb3 NM_001008887 -9 0.82 10766988 serine protease inhibitor B3

Ube2n NM_053928 200 1.20 10860546 ubiquitin-conjugating enzyme E2N

Receptors & Binding Proteins

Olr1545 NM_001001105 -26 0.73 10750630 olfactory receptor 1545

Epha5 NM_001169137 221 1.20 10772128 Eph receptor A5

Fgfr1 NM_024146 153 1.23 10792304 Fibroblast growth factor receptor 1

Wbp2 NM_138975 155 1.21 10749108 WW domain binding protein 2

similar to mannose-6-phosphate receptor binding LOC365559 ENSRNOT00000035259 -19 0.82 10832838 protein 1

Wipf3 NM_147211 102 1.21 10855637 WAS

Signaling

Rcn3 NM_001008694 25 1.21 10721641 reticulocalbin 3, EF-hand calcium binding domain

Sipa1l3 ENSRNOT00000038929 159 1.25 10720504 signal-induced proliferation-associated 1 like 3

Tbc1d25 NM_001106955 50 1.23 10932416 TBC1 domain family, member 25

similar to calcium/calmodulin-dependent protein RGD1560691 NM_001107365 204 1.23 10796307 kinase 1D

Transcription

41 Nrip3 NM_001108498 412 1.21 10724785 nuclear receptor interacting protein 3

Miscellaneous & Unknown Fam50a NM_001170573 -40 0.81 10940358 family with sequence similarity 50, member A LOC502894 NM_001025064 90 1.24 10884921 hypothetical protein LOC502894 LOC678714 ENSRNOT00000051350 -74 0.80 10862027 hypothetical protein LOC678714 RGD1563774 ENSRNOT00000045483 -12 0.80 10875576 similar to hypothetical protein 4930474N05 Tmem60 ENSRNOT00000018040 90 1.24 10860269 transmembrane protein 60 EST's RGD1566265 NM_001134589 97 1.22 10939002 similar to RIKEN cDNA 2610002M06 RGD1306282 ENSRNOT00000038294 13 1.26 10902621 similar to RIKEN cDNA 4432406C05 BC090072 -30 0.64 10759435 --- -241 0.80 10813353 --- -130 0.77 10794749 --- -117 0.74 10838153 --- -83 0.58 10939888 --- -70 0.74 10908655 --- -60 0.74 10878386 --- -58 0.61 10859195 --- -57 0.63 10928205 --- -56 0.81 10860184 --- -46 0.81 10857448 --- -39 0.73 10778586 --- -34 0.69 10902762 --- -33 0.74 10933576 --- -30 0.64 10756268 --- -30 0.64 10756270 --- -30 0.64 10756272 --- -30 0.64 10759445 --- -28 0.76 10703289 --- -25 0.77 10789042 --- -23 0.72 10714409 --- -21 0.83 10722413 --- -20 0.79 10909129 --- -16 0.82 10936019 --- -16 0.79 10861395 --- -16 0.83 10800386 --- -12 0.82 10885297 --- 20 1.35 10920741 --- 20 1.42 10888777 --- 24 1.23 10714177 --- 52 1.21 10852671 --- 70 1.39 10937568 EST's RGD1566265 NM_001134589 97 1.22 10939002 similar to RIKEN cDNA 2610002M06 RGD1306282 ENSRNOT00000038294 13 1.26 10902621 similar to RIKEN cDNA 4432406C05 BC090072 -30 0.64 10759435 --- -241 0.80 10813353 --- -130 0.77 10794749 --- -117 0.74 10838153 --- -83 0.58 10939888 --- -70 0.74 10908655 --- -60 0.74 10878386 --- -58 0.61 10859195 --- -57 0.63 10928205

42 --- -56 0.81 10860184 --- -46 0.81 10857448 --- -39 0.73 10778586 --- -34 0.69 10902762 --- -33 0.74 10933576 --- -30 0.64 10756268 --- -30 0.64 10756270 --- -30 0.64 10756272 --- -30 0.64 10759445 --- -28 0.76 10703289 --- -25 0.77 10789042 --- -23 0.72 10714409 --- -21 0.83 10722413 --- -20 0.79 10909129 --- -16 0.82 10936019 --- -16 0.79 10861395 --- -16 0.83 10800386 --- -12 0.82 10885297 --- 20 1.35 10920741 --- 20 1.42 10888777 --- 24 1.23 10714177 --- 52 1.21 10852671 --- 70 1.39 10937568

List 14. Genes Expressed Differentially in Stressed F3-Vinclozolin Rat CA3 of the Hippocampus as Compared to Stressed F3-Control ('St-Vin vs St-Con' contrast), 23 genes and EST's GenBank_Reference Mean Affymetrix Gene Symbol Ratio Gene Title Sequence _diff ID Cell Cycle Cspp1 ENSRNOT00000008480 -105 0.83 10875093 centrosome and spindle pole associated protein 1 Immune Response Cd38 NM_013127 -30 0.82 10777232 CD38 molecule Receptors & Binding Proteins Olr1443 NM_001000018 25 1.22 10733884 olfactory receptor 1443 Olr1567 NM_001000043 16 1.23 10752235 olfactory receptor 1567 Olr666 NM_001000924 13 1.21 10847144 olfactory receptor 666 Olr921 NM_001001385 44 1.29 10900010 olfactory receptor 921 Signaling Rab25 NM_001107687 17 1.20 10824339 RAB25, member RAS oncogene family Transcription Zbtb41 ENSRNOT00000015596 -153 0.82 10764404 zinc finger and BTB domain containing 41 Translation & Protein Modification RGD1565170 ENSRNOT00000043836 20 1.32 10780763 similar to 60S ribosomal protein L23a Miscellaneous & Unknown Fam75a4 BC085936 -13 0.77 10796941 family with sequence similarity 75, member A4 RGD1563482 NM_001109065 -25 0.82 10761736 similar to hypothetical protein FLJ38663 EST's --- -419 0.80 10886870 --- -275 0.81 10886890 --- -227 0.81 10886988

43 --- -140 0.82 10908810 --- -92 0.82 10870979 --- -22 0.80 10938245 --- -15 0.82 10892616 --- 12 1.24 10759473 --- 18 1.21 10724999 --- 21 1.35 10703461 --- 59 1.39 10726672 --- 392 1.33 10902859

List 15. Genes Expressed Differentially in Stressed F3-Control Rat CA3 of the Hippocampus as Compared to Non-Stressed F3-Control ('Str-Con vs Nst-Con' contrast), 50 genes and EST's GenBank_Reference Mean Affymetrix Gene Symbol Ratio Gene Title Sequence _diff ID Cell Cycle Cdk2ap2 NM_001109498 -38 0.83 10712786 CDK2-associated protein 2 Cytoskeleton- ECM Lce1c ENSRNOT00000012420 -6 0.82 10824752 late cornified envelope 1C Spock3 NM_001107310 -227 0.80 10791346 sparc Growth Factors Kng1 NM_012696 10.5 1.27 10751988 kininogen 1 Immune Response LOC287167 NM_001013853 -85 0.82 10741765 globin, alpha Metabolism & Transport Acaa2 NM_130433 -60 0.82 10802691 acetyl-Coenzyme A acyltransferase 2 ATPase, H+ transporting, lysosomal accessory Atp6ap1l ENSRNOT00000044237 -52 0.77 10820308 protein 1-like Hbb NM_033234 -374 0.63 10724311 hemoglobin, beta MGC72973 NM_198776 -324 0.63 10724319 beta-glo Hba-a2 NM_013096 -1192 0.70 10741756 hemoglobin alpha, adult chain 2 Hbb NM_033234 -311 0.72 10724315 hemoglobin, beta Proteolysis Rnf135 ENSRNOT00000005428 8 1.22 10736636 ring finger protein 135 Receptors & Binding Proteins Olr1222 NM_001000440 12 1.20 10909147 olfactory receptor 1222 Olr582 NM_001000662 24 1.25 10837545 olfactory receptor 582 Olr654 NM_001000636 41 1.28 10847125 olfactory receptor 654 Snupn NM_001004270 -74 0.82 10910252 snurportin 1 Signaling Ctnnal1 NM_001106649 -90 0.81 10876896 catenin (cadherin associated protein), alpha-like 1 Sfn XM_001065560 50 1.20 10872572 stratifin Transcription leucine rich repeat and coiled-coil domain Lrrcc1 NM_001100645 98 1.21 10822290 containing 1 similar to High mobility group protein 1 (HMG-1) (High mobility group protein B1) (Amphoterin) LOC500210 XM_002726403 9.8 1.22 10863370 (Heparin-binding protein p30) Yeats2 NM_001109057 -61 0.81 10755501 YEATS domain containing 2

44 Miscellaneous & Unknown Fam102b NM_001163568 -94 0.83 10826137 family with sequence similarity 102, member B RGD1562660 ENSRNOT00000044160 -59 0.76 10809906 RGD1562660 RGD1563774 ENSRNOT00000045483 -11 0.83 10875576 similar to hypothetical protein 4930474N05 EST's

LOC100365935 BC160895 59 1.20 10833346 rCG22129-like --- -78 0.66 10726672 --- -70 0.81 10798900 --- -66 0.71 10878386 --- -47 0.67 10778586 --- -35 0.71 10722413 --- -32 0.83 10843159 --- -29 0.74 10703289 --- -27 0.81 10844062 --- -20 0.82 10881476 --- -16 0.80 10861395 --- -15 0.79 10744141 --- -12 0.82 10857000 --- 10.3 1.24 10857203 --- 13 1.27 10742245 --- 16 1.24 10894848 --- 18 1.23 10791329 --- 19 1.24 10894798 --- 23 1.31 10717136 --- 25 1.27 10877933 --- 25 1.21 10898117 --- 51 1.22 10867699 --- 57 1.22 10940126 --- 65 1.20 10774605 --- 72 1.26 10923212 --- 75 1.47 10866205

List 16. Genes Expressed Differentially in Stressed F3-Vinclozolin Rat CA3 of the Hippocampus as Compared to Non- Stressed F3-Vinclozolin ('Str-Vin vs Nst-Vin' contrast), 202 genes and EST's GenBank_Reference Mean Affymetrix Gene Symbol Ratio Gene Title Sequence _diff ID Apoptosis Snn NM_001034083 -162 0.81 10740408 stannin Cell Cycle Ccnk NM_001109672 -50 0.83 10886714 cyclin K Cnnm1 NM_001107593 -111 0.83 10730272 cyclin M1 Cspp1 ENSRNOT00000008480 -120 0.83 10875087 centrosome and spindle pole associated protein 1 RGD1563620 ENSRNOT00000033132 -146 0.82 10815924 similar to retinoblastoma binding protein 4 Cytoskeleton- ECM Cadm2 NM_001047102 -330 0.80 10752679 cell adhesion molecule 2 Elmo2 NM_001134955 -168 0.82 10851753 engulfment and cell motility 2 Fxc1 NM_053371 9 1.27 10833834 fractured callus expressed transcript 1 Jph1 NM_001106630 -105 0.77 10867081 junctophilin 1 Krtap14l ENSRNOT00000064058 52 1.51 10752948 keratin associated protein 14 like Lum NM_031050 15 1.21 10895083 lumican Mast3 NM_001134796 -121 0.81 10787447 microtubule associated serine Mfap3 NM_001007609 -68 0.83 10733726 microfibrillar-associated protein 3 microtubule associated monoxygenase, calponin and Mical2 NM_001139508 -184 0.80 10709951 LIM domain containing 2 45 Pcdh1 ENSRNOT00000026324 -197 0.83 10804117 protocadherin 1 Development Clmn NM_001106755 -177 0.78 10892035 calmin Bbx NM_001079938 -72 0.82 10750900 bobby sox homolog (Drosophila) Shisa6 ENSRNOT00000057509 -200 0.77 10743715 shisa homolog 6 (Xenopus laevis) Dpy19l3 NM_001135835 -196 0.83 10721126 dpy-19-like 3 (C. elegans) Lrrc8b NM_001107204 -106 0.79 10775278 leucine rich repeat containing 8 family, member B Msl1 NM_001107048 -126 0.82 10738071 male-specific lethal 1 homolog (Drosophila) neural precursor cell expressed, developmentally Nedd4l NM_001008300 -192 0.83 10802231 down-regulated 4-like Odz3 NM_001169133 -91 0.78 10788086 odz, odd Oz Sez6 ENSRNOT00000048543 -234 0.82 10736119 seizure related 6 homolog (mouse) sema domain, immunoglobulin domain (Ig), short Sema3e NM_001106579 -180 0.81 10860457 basic domain, secreted, (semaphorin) 3E Skil ENSRNOT00000013191 -169 0.79 10822637 SKI-like oncogene similar to vitamin A-deficient testicular protein 11- LOC689303 ENSRNOT00000041918 11 1.27 10797584 like Syn3 NM_017109 -23 0.83 10894465 synapsin III Sncg NM_031688 47 1.20 10790471 synuclein, gamma (breast cancer-specific protein 1) Wasf1 NM_001025114 -374 0.80 10833952 WAS protein family, member 1 Epigenetics Hist1h2bc NM_001109400 -90 0.81 10798488 histone cluster 1, H2bc Hist1h2bn NM_001106114 -51 0.82 10798494 histone cluster 1, H2bn Mir483 NR_032112 173 1.31 10727006 microRNA mir-483 Brd2 NM_212495 -100 0.82 10828364 bromodomain containing 2 Prmt8 ENSRNOT00000006878 -184 0.83 10865790 protein arginine methyltransferase 8 Golgi Apparatus golgi associated, gamma adaptin ear containing, Gga3 NM_001108304 -106 0.82 10748973 ARF binding protein 3 Immune Response Nfat5 NM_001107425 -119 0.80 10807638 nuclear factor of activated T-cells 5 similar to OX-2 membrane glycoprotein precursor LOC685767 ENSRNOT00000048964 20 1.22 10751086 (MRC OX-2 antigen) (CD200 antigen) Metabolism & Transport Aldh1a2 NM_053896 34 1.31 10911380 aldehyde dehydrogenase 1 family, member A2 Aox4 ENSRNOT00000033068 -208 0.80 10923476 aldehyde oxidase 4 Bco2 NM_001127712 38 1.21 10917215 beta-carotene oxygenase 2 Cacnb4 NM_001105733 -114 0.83 10845306 calcium channel, voltage-dependent, beta 4 subunit calcium channel, voltage-dependent, gamma subunit Cacng8 NM_080696 -172 0.82 10718561 8 Commd10 NM_001004276 -155 0.83 10801584 COMM domain containing 10 cytochrome P450, family 4, subfamily a, Cyp4a2 NM_001044770 42 1.27 10878780 polypeptide 2 ELOVL family member 6, elongation of long chain Elovl6 NM_134383 -111 0.83 10819005 fatty acids (yeast) Hs6st2 ENSRNOT00000040165 -84 0.74 10939725 heparan sulfate 6-O-sulfotransferase 2 intraflagellar transport 88 homolog Ift88 NM_001107266 -54 0.82 10780765 (Chlamydomonas) potassium voltage-gated channel, Shal-related Kcnd2 NM_031730 -291 0.82 10853905 subfamily, member 2 Kcnn2 NM_019314 -177 0.81 10801520 potassium intermediate Nup205 NM_001108620 -45 0.83 10854494 nucleoporin 205 Plcb1 NM_001077641 -196 0.83 10840142 phospholipase C, beta 1 (phosphoinositide-specific) Scn3b NM_139097 -487 0.83 10909328 sodium channel, voltage-gated, type III, beta 46 ST8 alpha-N-acetyl-neuraminide alpha-2,8- St8sia3 NM_013029 -234 0.83 10802222 sialyltransferase 3 transient receptor potential cation channel, Trpc5 NM_080898 -222 0.72 10932726 subfamily C, member 5 Trak2 NM_133560 -207 0.81 10928307 trafficking protein, kinesin binding 2 Proteolysis Adam23 NM_001029899 -143 0.82 10923877 ADAM metallopeptidase domain 23 Dpp6 NM_022850 -258 0.81 10859886 dipeptidylpeptidase 6 HECT, C2 and WW domain containing E3 ubiquitin Hecw2 NM_001108218 -113 0.83 10928001 protein ligase 2 Receptors & Binding Proteins Baiap2 NM_057196 -190 0.83 10740094 BAI1-associated protein 2 Cttnbp2 NM_001114401 -245 0.83 10861171 cortactin binding protein 2 Epha5 NM_001169137 -226 0.83 10772128 EphA5 Lphn3 NM_130822 -184 0.82 10776264 latrophilin 3 Lrp6 NM_001107892 -96 0.82 10866374 low density lipoprotein receptor-related protein 6 Olr105 NM_001000146 91 1.21 10724274 olfactory receptor 105 Olr1143 NM_001001017 56 1.20 10908171 olfactory receptor 1143 Olr1226 NM_001000442 48 1.27 10909154 olfactory receptor 1226 Olr1364 NM_001000858 139 1.23 10740780 olfactory receptor 1364 Olr1400 NM_001001096 23 1.20 10733098 olfactory receptor 1400 Olr1567 NM_001000043 17 1.25 10752235 olfactory receptor 1567 Olr1637 NM_001000503 52 1.22 10783186 olfactory receptor 1637 Olr1714 NM_214456 83 1.32 10830818 olfactory receptor 1714 Olr1726 NM_001000896 102 1.34 10830830 olfactory receptor 1726 Olr546 NM_001001054 73 1.30 10847049 olfactory receptor 546 Olr566 NM_001000665 26 1.22 10837528 olfactory receptor 566 Olr712 NM_001000624 9 1.27 10847215 olfactory receptor 712 Olr886 NM_001001382 17 1.23 10899979 olfactory receptor 886 Olr921 NM_001001385 46 1.31 10900010 olfactory receptor 921 RGD1566059 ENSRNOT00000046220 54 1.28 10838423 similar to olfactory receptor Olfr1289 sortilin-related receptor, LDLR class A repeats- Sorl1 NM_053519 -227 0.83 10916493 containing V1rc1 NM_001008906 24 1.22 10855806 vomeronasal 1 receptor, C1 Vom2r24 NM_001099493 32 1.27 10703632 vomeronasal 2 receptor, 24 Vom2r56 NM_001099484 13 1.26 10901190 vomeronasal 2 receptor, 56 Signaling Csrnp3 ENSRNOT00000007197 -120 0.81 10836490 cysteine-serine-rich nuclear protein 3 Defb49 NM_001037527 55 1.21 10926837 defensin beta 49 Defa24 NM_001013053 16 1.21 10792538 defensin, alpha, 24 Dixdc1 NM_001037654 -72 0.79 10917260 DIX domain containing 1 Dgki NM_198782 -129 0.80 10861843 diacylglycerol kinase, iota Dclk2 NM_001009691 -179 0.79 10824091 doublecortin-like kinase 2 Frmd4b ENSRNOT00000010717 -51 0.81 10864371 FERM domain containing 4B Jak1 NM_053466 -219 0.83 10878286 Janus kinase 1 Ksr1 NM_001108284 -72 0.82 10745303 kinase suppressor of ras 1 protein phosphatase 1, regulatory (inhibitor) subunit Ppp1r9a NM_053473 -149 0.83 10853614 9A Rab11fip2 NM_001107447 -128 0.83 10731140 RAB11 family interacting protein 2 (class I) Sipa1l3 ENSRNOT00000038929 -187 0.76 10720504 signal-induced proliferation-associated 1 like 3 Sh3bp4 NM_022693 -55 0.82 10925264 SH3-domain binding protein 4 Snx19 NM_001108131 -129 0.79 10908764 sorting nexin 19 Snx32 ENSRNOT00000036745 -56 0.81 10727884 sorting nexin 32 Tbc1d25 NM_001106955 -49 0.82 10932416 TBC1 domain family, member 25 Transcription 47 Ankrd45 ENSRNOT00000003857 -161 0.82 10765051 ankyrin repeat domain 45 Ahctf1 ENSRNOT00000035875 -131 0.80 10770261 AT hook containing transcription factor 1 Bcl6 NM_001107084 -80 0.80 10751931 B-cell CLL Cnot7 NM_001107313 -196 0.82 10788414 CCR4-NOT transcription complex, subunit 7 Dnajb5 NM_001108004 -114 0.83 10868428 DnaJ (Hsp40) homolog, subfamily B, member 5 E2f5 ENSRNOT00000014361 -39 0.65 10718609 E2F transcription factor 5 Ing2 NM_001106083 -63 0.82 10788134 inhibitor of growth family, member 2 Med14 ENSRNOT00000066480 -177 0.83 10932279 mediator complex subunit 14 Myt1l NM_053888 -157 0.83 10884001 myelin transcription factor 1-like Mef2d NM_030860 -91 0.81 10816470 myocyte enhancer factor 2D PDX1 C-terminal inhibiting factor 1 Tdpoz1 XM_345239 45 1.21 10824790 TD and POZ domain containing 1 Tcf3 NM_001107865 59 1.21 10863277 transcription factor 3 Yeats2 NM_001109057 -59 0.82 10755501 YEATS domain containing 2 Zbtb45 NM_001107478 -26 0.82 10704281 zinc finger and BTB domain containing 45 Zeb2 NM_001033701 -317 0.81 10845072 zinc finger E-box binding homeobox 2 Zfp354b ENSRNOT00000004902 -14 0.83 10742466 zinc finger protein 354B Zfp462 ENSRNOT00000047225 -121 0.71 10869158 zinc finger protein 462 Znf667 NM_001008557 -62 0.83 10718696 zinc finger protein 667 Dhx57 ENSRNOT00000037705 -66 0.82 10887990 DEAH (Asp-Glu-Ala-Asp Translation & Protein Modification Eif1b NM_001106867 -197 0.82 10914349 eukaryotic translation initiation factor 1B Eif4g3 NM_001106693 -133 0.83 10873226 eukaryotic translation initiation factor 4 gamma, 3 IMP3, U3 small nucleolar ribonucleoprotein, Imp3 NM_001108152 -171 0.83 10910249 homolog (yeast) PRP38 pre-mRNA processing factor 38 (yeast) Prpf38b NM_001024305 -86 0.83 10826130 domain containing B RGD1559743 XM_001077121 22 1.21 10920785 similar to 40S ribosomal protein S16 RGD1559955 ENSRNOT00000046179 72 1.35 10925757 similar to 40S ribosomal protein S17 Miscellaneous & Unknown Fam102b NM_001163568 -109 0.81 10826137 family with sequence similarity 102, member B LOC681205 ENSRNOT00000020640 15 1.23 10921453 hypothetical protein LOC681205 LOC685340 ENSRNOT00000039568 10 1.23 10933970 hypothetical protein LOC685340 Prb1 L17318 241 1.24 10866332 proline-rich protein BstNI subfamily 1 RGD1562660 ENSRNOT00000044160 -34 0.83 10809906 RGD1562660 RGD1563065 ENSRNOT00000002978 -105 0.76 10772788 similar to 3110047P20Rik protein RGD1308297 BC082039 -166 0.82 10785745 similar to CG10084-PA RGD1564195 ENSRNOT00000049044 -79 0.82 10725914 similar to hypothetical protein RGD1306556 ENSRNOT00000000901 -35 0.80 10759227 similar to hypothetical protein A530094D01 RGD1564200 NM_001108969 -104 0.81 10867587 similar to hypothetical protein MGC34646 RGD1560883 ENSRNOT00000018479 -50 0.83 10812297 similar to KIAA0825 protein Trim2 NM_001108552 -344 0.83 10824017 tripartite motif-containing 2 EST's LOC290577 XM_002725158 40 1.33 10786993 hypothetical LOC290577 RGD1564814 ENSRNOT00000038133 28 1.25 10775737 similar to CDNA sequence BC061212 RGD1305664 ENSRNOT00000004829 -102 0.81 10743626 similar to KIAA0672 gene product --- -103 0.78 10722718 --- -88 0.83 10867008 --- -77 0.81 10743702 --- -73 0.82 10869817 --- -72 0.83 10801258 --- -72 0.83 10924669

48 --- -71 0.81 10869614 --- -52 0.81 10743680 --- -52 0.81 10743699 --- -48 0.78 10765036 --- -48 0.82 10758033 --- -46 0.80 10765038 --- -29 0.79 10761268 --- -28 0.59 10888777 --- -23 0.82 10714177 --- -21 0.77 10815350 --- -18 0.81 10749977 --- -17 0.83 10882888 --- -13 0.81 10857000 --- -10 0.78 10887693 --- 7 1.24 10933227 --- 9 1.30 10850313 --- 10 1.23 10794940 --- 11 1.29 10788028 --- 11 1.21 10796768 --- 12 1.24 10806925 --- 14 1.27 10908156 --- 14 1.31 10892794 --- 15 1.26 10886267 --- 15 1.24 10822733 --- 17 1.21 10718428 --- 17 1.22 10787820 --- 18 1.21 10884694 --- 21 1.25 10789042 --- 22 1.23 10934042 --- 26 1.34 10828152 --- 26 1.77 10850319 --- 26 1.22 10769619 --- 28 1.30 10877933 --- 28 1.53 10703461 --- 33 1.23 10927211 --- 33 1.36 10933576 --- 40 1.24 10715188 --- 41 1.23 10904230 --- 41 1.21 10901836 --- 42 1.27 10797939 --- 46 1.26 10800328 --- 47 1.20 10717353 --- 52 1.30 10704169 --- 53 1.30 10773461 --- 55 1.25 10934978 --- 55 1.24 10913627 --- 68 1.76 10859195 --- 69 1.27 10802272 --- 125 1.25 10892656 --- 128 1.25 10934792 --- 211 1.26 10737708 --- 246 1.37 10719159 --- 346 1.24 10909581 --- 415 1.35 10902859 --- 685 1.39 10788070 --- 733 1.52 10815996

49

50