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Table 2S List of the Probe Sets (Each of Them Corresponding to a Gene Or A

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Table 2s List of the probe sets (each of them corresponding to a gene or a gene family) resulting significantly modulated (see Table 1s) in DPTs following 3 hour Dex and whose increased/decreased modulation was above a chosen cut-off (for log increase > 0.75 and for log decrease < -0.5). In the Affymetrix platform each probe set is represented by an ID number (column 1) linked to a gene or gene family (columns 2 and 3). The modulation of the expression in the treated DPTs is reported as log in 2 basis (a 2 fold increase expression is reported as 1 and a 2 fold decrease expression is reported as –1). To allow comparison, the ID numbers of several data banks corresponding to the probe set ID are reported in columns 6- 14 and 19. Gene Ontology numbers and the pathway(s) in which the gene is involved are reported in columns 15-18. Affymetrix GeneChip Array Murine Genome U74Av2 Array Genome March 2005 (NCBI 34) Version column 1 column 2 column 3 column 4 column 5 column 6 column 7 column 8 column 9 column 10 column 11 column 12 column 13 column 14 Transcript Log2 Fold Representative Entrez RefSeq Transcript Probe Set ID Gene Title Gene Symbol ID (Array UniGene ID Ensembl SwissProt EC RefSeq Protein ID MGI Name Modulation Public ID Gene ID Design) ENSMUSG0 Q9CXH2 /// 95151_at RIKEN cDNA 2810052M02 gene 2810052M02Rik -2.8 5674136 AW061307 Mm.29475 67220 --- NP_075809.1 NM_023320 --- 0000015745 Q9JIY0 ENSMUSG0 P41133 /// 92614_at inhibitor of DNA binding 3 Id3 -2 5663577 M60523 Mm.110 15903 --- NP_032347.1 NM_008321 --- 0000007872 Q545W1 5690864_R ENSMUSG0 160829_at pleckstrin homology-like domain, family A, member 1 Phlda1 -1.7 U44088 Mm.3117 21664 Q62392 --- NP_033370.1 NM_009344 --- C 0000020205 Q61263 /// 5709592_R Q8C795 /// 95887_at sterol O-acyltransferase 1 Soat1 -1.4 AI451008 Mm.28099 --- 20652 --- NP_033256.1 NM_009230 104665 C Q8R3K7 /// Q5XK32 ENSMUSG0 101410_at claudin 4 Cldn4 -1.1 5695544 AB000713 Mm.7339 12740 O35054 --- NP_034033.1 NM_009903 --- 0000047501 ENSMUSG0 O54825 /// 160227_s_at bystin-like Bysl -1.1 5670962 AI132491 Mm.27291 53414 --- NP_058555.2 NM_016859 --- 0000023988 Q543N4 P35951 /// Q91ZJ1 /// 5691030_R ENSMUSG0 160832_at low density lipoprotein receptor Ldlr -1.1 Z19521 Mm.3213 16835 Q8VCT0 /// --- NP_034830.1 NM_010700 96765 C 0000032193 Q6GTJ9 /// Q8CAV5 P00920 /// ENSMUSG0 Q9DCT3 /// 92642_at carbonic anhydrase 2 Car2 -1.1 5663753 M25944 Mm.1186 12349 EC:4.2.1.1 NP_033931.3 NM_009801 --- 0000027562 Q7TPE1 /// Q6LDQ7 ENSMUSG0 P11416 /// 92901_at retinoic acid receptor, alpha Rara -1.1 5705154 M60909 Mm.103336 19401 --- NP_033050.1 NM_009024 97856 0000037992 Q5BLJ8 Q60980 /// Q5K2K0 /// ENSMUSG0 100010_at Kruppel-like factor 3 (basic) Klf3 -1 5694203 U36340 Mm.319499 16599 Q8BV07 /// --- NP_032479.1 NM_008453 1342773 0000029178 Q545J5 /// Q8C7X1 92653_at RIKEN cDNA D530037H12 gene D530037H12Rik -1 5703870 AI482432 --- --- 96893 --- --- --- --- 2138683 Q60980 /// Q5K2K0 /// ENSMUSG0 100011_at Kruppel-like factor 3 (basic) Klf3 -0.9 5694204 AI851658 Mm.319499 16599 Q8BV07 /// --- NP_032479.1 NM_008453 --- 0000029178 Q545J5 /// Q8C7X1 ENSMUSG0 100902_at RIKEN cDNA 2610019F03 gene 2610019F03Rik -0.9 5695053 AI846549 Mm.5727 72148 Q8C5P7 --- NP_776105.1 NM_173744 --- 0000050052 5675893_R ENSMUSG0 Q9CRA4 /// 160388_at sterol-C4-methyl oxidase-like Sc4mol -0.9 AI848668 Mm.30119 66234 --- NP_079712.1 NM_025436 --- C 0000031604 Q543V8 5705151_R ENSMUSG0 92900_at RIKEN cDNA E230012J19 gene Rere -0.9 AU040769 Mm.291274 68703 Q80TZ9 --- XP_204015.2 XM_204015 --- C 0000039852 Q8C9N5 /// ENSMUSG0 Q9CYC2 /// 93614_at Ras-related GTP binding D Rragd -0.9 5706340 AA600647 Mm.34108 52187 --- NP_081767.1 NM_027491 --- 0000028278 Q6GTT2 /// Q7TT45 ENSMUSG0 94197_at UDP-glucose ceramide glucosyltransferase Ugcg -0.9 5708696 D89866 Mm.198803 22234 O88693 --- NP_035803.1 NM_011673 1332243 0000028381 ENSMUSG0 94322_at squalene epoxidase Sqle -0.9 5668876 D42048 Mm.296169 20775 P52019 --- NP_033296.1 NM_009270 --- 0000022351 P34960 /// ENSMUSG0 95339_r_at matrix metalloproteinase 12 Mmp12 -0.9 5709167 M82831 Mm.2055 17381 Q6GX99 /// EC:3.4.24.65 NP_032631.1 NM_008605 97005 0000049723 Q8BJC0 ENSMUSG0 97977_at netrin 1 Ntn1 -0.9 5690862 AA645293 Mm.39095 18208 O09118 --- NP_032770.1 NM_008744 105088 0000020902 ENSMUSG0 98609_at septin 9 Sept9 -0.9 5678263 AJ250723 Mm.38450 53860 Q80UG5 --- NP_059076.1 NM_017380 1858222 0000059248 98756_at RIKEN cDNA 2810043O03 gene 2810043O03Rik -0.9 5715344 W91704 --- --- 72697 --- --- --- --- 1919947 5682019_R ENSMUSG0 160545_at cyclin D3 Ccnd3 -0.8 M86183 Mm.246520 12445 P30282 --- NP_031658.1 NM_007632 88315 C 0000034165 Q99JF5 /// 5688716_R ENSMUSG0 160770_at mevalonate (diphospho) decarboxylase Mvd -0.8 AW049778 Mm.28146 192156 Q8BTM4 /// --- NP_619597.1 NM_138656 --- C 0000006517 Q922D7 Q5FWI0 /// ENSMUSG0 161817_f_at RIKEN cDNA 4930422J18 gene 4930422J18Rik -0.8 5742721 AV376312 Mm.30 74646 Q8BJA4 /// --- NP_083311.1 NM_029035 --- 0000039911 Q9D5L7 ENSMUSG0 P13011 /// 95758_at stearoyl-Coenzyme A desaturase 2 Scd2 -0.8 5674769 M26270 Mm.193096 20250 --- NP_033154.1 NM_009128 --- 0000025203 Q8BH96 P37889 /// ENSMUSG0 100928_at fibulin 2 Fbln2 -0.7 5695133 X75285 Mm.249146 14115 Q8C2U8 /// --- NP_032018.1 NM_007992 95488 0000064080 Q99K58 O35219 /// potassium voltage-gated channel, subfamily H (eag- ENSMUSG0 Q53Z09 /// 100961_at Kcnh2 -0.7 5695237 AF012871 Mm.6539 16511 --- NP_038597.1 NM_013569 1341722 related), member 2 0000038319 Q80WG1 /// Q80XE8 P53986 /// Q8BPS5 /// solute carrier family 16 (monocarboxylic acid ENSMUSG0 101588_at Slc16a1 -0.7 5682940 AF058055 Mm.9086 20501 Q8C2E6 /// --- NP_033222.1 NM_009196 --- transporters), member 1 0000032902 Q8C571 /// Q544N9 102978_at RIKEN cDNA A430104N18 gene A430104N18Rik -0.7 5697376 AI021175 --- --- 78591 --- --- --- --- 1925841 104413_at --- --- -0.7 5699922 AI834976 --- --- --- --- --- --- --- --- Q07916 /// 5689378_R ENSMUSG0 Q6X2R9 /// 160793_at POU domain, class 6, transcription factor 1 Pou6f1 -0.7 AI851313 Mm.28825 19009 --- NP_034257.1 NM_010127 102935 C 0000009739 Q5U4D4 /// Q6X2S0 Q5FWI0 /// ENSMUSG0 161013_f_at RIKEN cDNA 4930422J18 gene 4930422J18Rik -0.7 5700277 AI596360 Mm.30 74646 Q8BJA4 /// --- NP_083311.1 NM_029035 --- 0000039911 Q9D5L7 Q03347 /// Q8BQ09 /// 92399_at runt related transcription factor 1 Runx1 -0.7 5703164 D26532 Mm.4081 --- 12394 --- NP_033951.1 NM_009821 99852 Q8CAV1 /// Q6NSS1 ENSMUSG0 92832_at suppressor of cytokine signaling 1 Socs1 -0.7 5664163 U88325 Mm.130 12703 O35716 --- NP_034026.1 NM_009896 --- 0000038037 Q60790 /// ENSMUSG0 Q6PG24 /// 93319_at RAS p21 protein activator 3 Rasa3 -0.7 5665769 U20238 Mm.18517 19414 --- NP_033051.1 NM_009025 --- 0000031453 Q8C6G4 /// Q925V1 Q8BTY2 /// Solute carrier family 4, sodium bicarbonate 93471_at Slc4a7 -0.7 5706216 AI594427 Mm.258893 --- 218756 Q8BWZ4 /// --- XP_147798.3 XM_147798 --- cotransporter, member 7 Q9JL09 Mid1 interacting protein 1 (gastrulation specific G12- ENSMUSG0 95135_at Mid1ip1 -0.7 5674038 AI844396 Mm.29429 68041 Q9CQ20 --- NP_080800.1 NM_026524 --- like (zebrafish)) 0000008035 Q8BGW5 /// ENSMUSG0 Q8C154 /// 95655_at RIKEN cDNA 5830411E10 gene 5830411E10Rik -0.7 5674236 AA717740 Mm.196290 109019 --- NP_082972.1 NM_028696 1923258 0000026107 Q8C164 /// Q8R2P2 Q01705 /// ENSMUSG0 97497_at Notch gene homolog 1 (Drosophila) Notch1 -0.7 5676563 Z11886 Mm.290610 18128 Q8K428 /// --- NP_032740.2 NM_008714 --- 0000026923 Q8BY39 ENSMUSG0 Q9JMK2 /// 97925_at casein kinase 1, epsilon Csnk1e -0.7 5690604 AB028241 Mm.30199 27373 --- NP_038795.3 NM_013767 --- 0000022433 Q9QUI3 5692333_R ENSMUSG0 O88455 /// 98989_at 7-dehydrocholesterol reductase Dhcr7 -0.7 AF057368 Mm.249342 13360 EC:1.3.1.21 NP_031882.1 NM_007856 --- C 0000058454 Q711T1 ENSMUSG0 Q920E5 /// 99098_at farnesyl diphosphate synthetase Fdps -0.7 5678479 AW045533 Mm.39472 110196 --- NP_608219.1 NM_134469 --- 0000059743 Q5M8R9 O89091 /// ENSMUSG0 99602_at Kruppel-like factor 10 Klf10 -0.7 5679360 AF064088 Mm.4292 21847 Q61596 /// --- NP_038720.1 NM_013692 --- 0000037465 Q8C900 Q9JMH6 /// Q99P49 /// 99985_at thioredoxin reductase 1 Txnrd1 -0.7 5694024 AB027565 Mm.210155 --- 50493 EC:1.8.1.9 NP_056577.2 NM_015762 1354175 Q8CI31 /// Q9CSV5 Q06831 /// Q8BPK5 /// 101430_at SRY-box containing gene 4 Sox4 -0.6 5695610 AW124153 Mm.240627 --- 20677 Q8BQ53 /// --- NP_033264.2 NM_009238 --- Q8CE56 /// Q5SW95 P97443 /// ENSMUSG0 101904_at SET and MYND domain containing 1 Smyd1 -0.6 5696145 U76372 Mm.234274 12180 Q8BMV4 /// --- NP_033892.1 NM_009762 104790 0000055027 Q6DFW7 Q61609 /// ENSMUSG0 Q8CBJ1 /// 103065_at solute carrier family 20, member 1 Slc20a1 -0.6 5684428 M73696 Mm.272675 20515 --- NP_056562.1 NM_015747 108392 0000027397 Q8CF68 /// Q91YQ9 ENSMUSG0 P70338 /// 103259_at growth factor independent 1 Gfi1 -0.6 5697591 U58972 Mm.2078 14581 --- NP_034408.1 NM_010278 103170 0000029275 Q8C287 P51576 /// ENSMUSG0 103971_at purinergic receptor P2X, ligand-gated ion channel, 1 P2rx1 -0.6 5698915 X84896 Mm.25722 18436 Q91WI3 /// --- NP_032797.2 NM_008771 1098235 0000020787 Q5SRU4 Q06831 /// Q8BPK5 /// 5665910_R 160109_at SRY-box containing gene 4 Sox4 -0.6 X70298 Mm.240627 --- 20677 Q8BQ53 /// --- NP_033264.2 NM_009238 98366 C Q8CE56 /// Q5SW95 Q61484 /// Q8BKS2 /// Q8BRB8 /// 5671601_R ENSMUSG0 NP_033773.1 /// NM_009643 /// 160255_at AHNAK nucleoprotein (desmoyokin) Ahnak -0.6 AA657044 Mm.203866 66395 Q8CEX7 /// --- --- C 0000059508 NP_780317.2 NM_175108 Q8CGE7 /// Q8R2L7 /// Q8VDN3 5674813_R ENSMUSG0 Q9D0U0 /// 160359_at RIKEN cDNA 1190002H23 gene 1190002H23Rik -0.6 AI854358 Mm.29811 66214 --- NP_079703.1
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    Supplemental Materials Supplemental Methods Supplemental Figure 1. Immune phenotype of mCD19 targeted CAR T and dose titration of in vivo efficacy. Supplemental Figure 2. Gene expression of fluorescent-protein tagged CAR T cells. Supplemental Figure 3. Fluorescent protein tagged CAR T cells function similarly to non-tagged counterparts. Supplemental Figure 4. Transduction efficiency and immune phenotype of mCD19 targeted CAR T cells for survival study (Figure 2D). Supplemental Figure 5. Transduction efficiency and immune phenotype of CAR T cells used in irradiated CAR T study (Fig. 3B-C). Supplemental Figure 6. Differential gene expression of CD4+ m19-humBBz CAR T cells. Supplemental Figure 7. CAR expression and CD4/CD8 subsets of human CD19 targeted CAR T cells for Figure 5E-G. Supplemental Figure 8. Transduction efficiency and immune phenotype of mCD19 targeted wild type (WT) and TRAF1-/- CAR T cells used for in vivo study (Figure 6D). Supplemental Figure 9. Mutated m19-musBBz CAR T cells have increased NF-κB signaling, improved cytokine production, anti-apoptosis, and in vivo function. Supplemental Figure 10. TRAF and CAR co-expression in human CD19-targeted CAR T cells. Supplemental Figure 11. TRAF2 over-expressed h19BBz CAR T cells show similar in vivo efficacy to h19BBz CAR T cells in an aggressive leukemia model. S1 Supplemental Table 1. Probesets increased in m19z and m1928z vs m19-musBBz CAR T cells. Supplemental Table 2. Probesets increased in m19-musBBz vs m19z and m1928z CAR T cells. Supplemental Table 3. Probesets differentially expressed in m19z vs m19-musBBz CAR T cells. Supplemental Table 4. Probesets differentially expressed in m1928z vs m19-musBBz CAR T cells.
  • Association of Gene Ontology Categories with Decay Rate for Hepg2 Experiments These Tables Show Details for All Gene Ontology Categories

    Association of Gene Ontology Categories with Decay Rate for Hepg2 Experiments These Tables Show Details for All Gene Ontology Categories

    Supplementary Table 1: Association of Gene Ontology Categories with Decay Rate for HepG2 Experiments These tables show details for all Gene Ontology categories. Inferences for manual classification scheme shown at the bottom. Those categories used in Figure 1A are highlighted in bold. Standard Deviations are shown in parentheses. P-values less than 1E-20 are indicated with a "0". Rate r (hour^-1) Half-life < 2hr. Decay % GO Number Category Name Probe Sets Group Non-Group Distribution p-value In-Group Non-Group Representation p-value GO:0006350 transcription 1523 0.221 (0.009) 0.127 (0.002) FASTER 0 13.1 (0.4) 4.5 (0.1) OVER 0 GO:0006351 transcription, DNA-dependent 1498 0.220 (0.009) 0.127 (0.002) FASTER 0 13.0 (0.4) 4.5 (0.1) OVER 0 GO:0006355 regulation of transcription, DNA-dependent 1163 0.230 (0.011) 0.128 (0.002) FASTER 5.00E-21 14.2 (0.5) 4.6 (0.1) OVER 0 GO:0006366 transcription from Pol II promoter 845 0.225 (0.012) 0.130 (0.002) FASTER 1.88E-14 13.0 (0.5) 4.8 (0.1) OVER 0 GO:0006139 nucleobase, nucleoside, nucleotide and nucleic acid metabolism3004 0.173 (0.006) 0.127 (0.002) FASTER 1.28E-12 8.4 (0.2) 4.5 (0.1) OVER 0 GO:0006357 regulation of transcription from Pol II promoter 487 0.231 (0.016) 0.132 (0.002) FASTER 6.05E-10 13.5 (0.6) 4.9 (0.1) OVER 0 GO:0008283 cell proliferation 625 0.189 (0.014) 0.132 (0.002) FASTER 1.95E-05 10.1 (0.6) 5.0 (0.1) OVER 1.50E-20 GO:0006513 monoubiquitination 36 0.305 (0.049) 0.134 (0.002) FASTER 2.69E-04 25.4 (4.4) 5.1 (0.1) OVER 2.04E-06 GO:0007050 cell cycle arrest 57 0.311 (0.054) 0.133 (0.002)
  • Variation in Protein Coding Genes Identifies Information

    Variation in Protein Coding Genes Identifies Information

    bioRxiv preprint doi: https://doi.org/10.1101/679456; this version posted June 21, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Animal complexity and information flow 1 1 2 3 4 5 Variation in protein coding genes identifies information flow as a contributor to 6 animal complexity 7 8 Jack Dean, Daniela Lopes Cardoso and Colin Sharpe* 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Institute of Biological and Biomedical Sciences 25 School of Biological Science 26 University of Portsmouth, 27 Portsmouth, UK 28 PO16 7YH 29 30 * Author for correspondence 31 [email protected] 32 33 Orcid numbers: 34 DLC: 0000-0003-2683-1745 35 CS: 0000-0002-5022-0840 36 37 38 39 40 41 42 43 44 45 46 47 48 49 Abstract bioRxiv preprint doi: https://doi.org/10.1101/679456; this version posted June 21, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Animal complexity and information flow 2 1 Across the metazoans there is a trend towards greater organismal complexity. How 2 complexity is generated, however, is uncertain. Since C.elegans and humans have 3 approximately the same number of genes, the explanation will depend on how genes are 4 used, rather than their absolute number.
  • A Worldwide Map of Swine Short Tandem Repeats and Their

    A Worldwide Map of Swine Short Tandem Repeats and Their

    Wu et al. Genet Sel Evol (2021) 53:39 https://doi.org/10.1186/s12711-021-00631-4 Genetics Selection Evolution RESEARCH ARTICLE Open Access A worldwide map of swine short tandem repeats and their associations with evolutionary and environmental adaptations Zhongzi Wu1, Huanfa Gong1, Mingpeng Zhang1, Xinkai Tong1, Huashui Ai1, Shijun Xiao1, Miguel Perez‑Enciso2,3, Bin Yang1* and Lusheng Huang1* Abstract Background: Short tandem repeats (STRs) are genetic markers with a greater mutation rate than single nucleotide polymorphisms (SNPs) and are widely used in genetic studies and forensics. However, most studies in pigs have focused only on SNPs or on a limited number of STRs. Results: This study screened 394 deep‑sequenced genomes from 22 domesticated pig breeds/populations world‑ wide, wild boars from both Europe and Asia, and numerous outgroup Suidaes, and identifed a set of 878,967 poly‑ morphic STRs (pSTRs), which represents the largest repository of pSTRs in pigs to date. We found multiple lines of evidence that pSTRs in coding regions were afected by purifying selection. The enrichment of trinucleotide pSTRs in coding sequences (CDS), 5′UTR and H3K4me3 regions suggests that trinucleotide STRs serve as important com‑ ponents in the exons and promoters of the corresponding genes. We demonstrated that, compared to SNPs, pSTRs provide comparable or even greater accuracy in determining the breed identity of individuals. We identifed pSTRs that showed signifcant population diferentiation between domestic pigs and wild boars in Asia and Europe. We also observed that some pSTRs were signifcantly associated with environmental variables, such as average annual tem‑ perature or altitude of the originating sites of Chinese indigenous breeds, among which we identifed loss‑of‑function and/or expanded STRs overlapping with genes such as AHR, LAS1L and PDK1.