DOCSLIB.ORG

Cellular-Resolution Gene Expression Profiling in the Neonatal Marmoset Brain Reveals Dynamic Species- and Region-Specific Differences

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Cellular-Resolution Gene Expression Profiling in the Neonatal Marmoset Brain Reveals Dynamic Species- and Region-Specific Differences Cellular-resolution gene expression profiling in the neonatal marmoset brain reveals dynamic species- and region-specific differences Yoshiaki Kitaa, Hirozumi Nishibea, Yan Wanga, Tsutomu Hashikawaa, Satomi S. Kikuchia, Mami Ua, Aya C. Yoshidaa, Chihiro Yoshidaa, Takashi Kawaseb, Shin Ishiib, Henrik Skibbec, and Tomomi Shimogoria,1 aLaboratory for Molecular Mechanisms of Brain Development, Center for Brain Science, RIKEN, Saitama 351-0198, Japan; bIntegrated Systems Biology Laboratory, Department of Systems Science, Graduate School of Informatics, Kyoto University, Kyoto 606-8501, Japan; and cBrain Image Analysis Unit, Center for Brain Science, RIKEN, Saitama 351-0198, Japan Edited by Edward M. Callaway, Salk Institute for Biological Studies, La Jolla, CA, and approved March 12, 2021 (received for review September 25, 2020) Precise spatiotemporal control of gene expression in the develop- (12). However, these studies are highly resource intensive, re- ing brain is critical for neural circuit formation, and comprehensive quiring substantial time and cost. Consequently, such efforts expression mapping in the developing primate brain is crucial to have been limited, focusing on a few brain regions in limited species understand brain function in health and disease. Here, we devel- (13). Thus, interspecific comparison of brain-cell heterogeneity has oped an unbiased, automated, large-scale, cellular-resolution in situ not been possible. hybridization (ISH)–based gene expression profiling system (GePS) Here, we describe the development and implementation of an and companion analysis to reveal gene expression patterns in the unbiased gene expression profiling system (GePS) for use with neonatal New World marmoset cortex, thalamus, and striatum the Marmoset Gene Atlas (MGA) (https://gene-atlas.brainminds. that are distinct from those in mice. Gene-ontology analysis of riken.jp/) (14), which is adaptable for use with other atlases. The marmoset-specific genes revealed associations with catalytic activ- system, developed as a part of “Brain Mapping by Integrated ity in the visual cortex and neuropsychiatric disorders in the thal- Neurotechnologies for Disease Studies (Brain/MINDS),” a brain amus. Cortically expressed genes with clear area boundaries were mapping program in Japan (15, 16), enables systematic and au- used in a three-dimensional cortical surface mapping algorithm to de- tomatic analysis of gene expression across brain regions. Brain/ NEUROSCIENCE lineate higher-order cortical areas not evident in two-dimensional ISH MINDS aims to develop knowledge-based tools to explore primate- data. GePS provides a powerful platform to elucidate the molecular specific brain structure, function, and connectivity in health and mechanisms underlying primate neurobiology and developmental disease. Specifically, we analyzed the expression patterns of identi- psychiatric and neurological disorders. fied risk genes for psychiatric disorders in the neonatal marmoset brain. There are >2,000 gene expression profiles for the neonatal gene expression | database | nonhuman primate | evolution | common-marmoset brain in the MGA. Although each ISH section developmental disorder is complemented by an adjacent neuroanatomically stained section (visualizing the Nissl substance), enabling users to compare gene he mammalian brain contains many functionally distinct re- expression against a brain atlas, mapping gene expression patterns Tgions that are extensively interconnected, enabling rapid and accurate information processing. Each region contains diverse Significance cell types that differ in their molecular, morphological, electrophys- iological, and functional characteristics (1, 2). Advanced neurosci- The MGA contains a large gene expression dataset from the ence technologies, which are generally optimized and extensively developing brain of the common marmoset. However, the data applied in mice, provide complicated approaches to analyze represent the gene expression patterns across the entire brain, these characteristics and model the genetic basis of this regional- and methods to isolate region-specific gene expression pat- and cell-type diversity. However, clear cognitive differences arise terns will provide important information regarding primate from interspecies differences in these key characteristics, and most brain structure, function, and cellular and molecular organiza- contemporary technologies are difficult to apply in species whose tion. We have developed a system, GePS, that systematically study involves extensive ethical, practical, and experimental im- identifies genes expressed in selected regions of the common pediments. The ability to compare gene expression patterns be- marmoset brain. Comprehensive, comparative gene expression tween primates and model species such as mice is crucial for analysis with mice revealed many genes with species- and understanding the human brain (3, 4). region-specific expression. Moreover, by combining GePS with Recent developments in technologies, such as microarray, single- the gene expression comparison and cortical area projection cell RNA-sequencing (RNA-seq), and Drop-seq, have allowed for mapping systems, we were able to provide further insight into high-resolution genome-wide expression analysis in specific regions the molecular organization of these species- and region- of the brain or in thousands of individual cells simultaneously specific gene expression patterns. (5–10). However, these methods provide limited anatomical in- formation and no morphological observations. Slide-seq solves Author contributions: S.I., H.S., and T.S. designed research; Y.K., H.N., Y.W., T.H., S.S.K., these problems by transferring RNA from tissue sections onto a M.U., A.C.Y., C.Y., T.K., and H.S. performed research; T.S. analyzed data; and T.S. wrote surface covered in DNA-barcoded beads, allowing the preserva- the paper. tion of positional information (11). However, the unbiased nature The authors declare no competing interest. of next-generation sequencing technologies may hinder the mo- This article is a PNAS Direct Submission. lecular identification of specific cell types or their direct analysis. This open access article is distributed under Creative Commons Attribution-NonCommercial- In situ hybridization (ISH) databases of humans and nonhuman NoDerivatives License 4.0 (CC BY-NC-ND). primates (NHPs) have revealed brain gene expression profiles at 1To whom correspondence may be addressed. Email: [email protected]. cellular resolution, while preserving key morphological and ana- This article contains supporting information online at https://www.pnas.org/lookup/suppl/ tomical characteristics, ultimately providing important informa- doi:10.1073/pnas.2020125118/-/DCSupplemental. tion about the genetic conservation of analogous brain regions Published April 26, 2021. PNAS 2021 Vol. 118 No. 18 e2020125118 https://doi.org/10.1073/pnas.2020125118 | 1of11 Downloaded by guest on September 23, 2021 over the entire brain is both time and labor intensive. A large mouse comparisons of signal-to-noise ratios in a given grid area were ISH database, the Allen Brain Atlas (ABA; http://developingmouse. performed to determine whether the nitro blue tetrazolium/ brain-map.org/), demonstrated that an anatomic gene expression 5-bromo-4-chloro-3-indolyl-phosphate reaction provided a posi- atlas (AGEA) can characterize local gene expression in the tive signal. Fig. 1A shows a Nissl substance-stained section from mouse brain without prior knowledge of classical anatomy (17). the reference atlas, with a position indicator to search for genes To enhance the MGA in this manner, we developed GePS to expressed within the selected area. All ISH sections were over- systematically and automatically identify gene expression pat- laid with a grid (Fig. 1 A and B), and the gene expression de- terns in specific regions of the neonatal marmoset brain. tection software was used to sum the number and intensities of GePS, including the gene expression comparison system and expressing pixels (Fig. 1C). Different grids were tested (from cortical surface projection mapping function, is publicly available 20 × 20 pixel grids to 200 × 200 pixel grids), and we concluded as an open resource on our website (https://gene-atlas.brainminds. that 200 × 200 pixel grids provide the most accurate result. When riken.jp/). It provides primate-specific whole brain–gene expres- grid size becomes smaller, a chance to pick dust, scratch, and sion patterns and will be a valuable platform in the field of primate background becomes higher and provides false-positive results neuroscience, helping reveal primate-specific brain functions and more often. Therefore, we decided to use 200 × 200 pixel grids connections and providing insights into brain evolution and for the automated signal identification system. Fig. 1C depicts the pathology. grid system for detecting the positivesignalineachgrid(redsquares indicate 200 × 200 pixel grids). The anatomical location of the Results position indicator on the reference atlas was then transferred to a The MGA contains coronally sectioned ISH data from marmoset grid position on a selected plane of ISH data. When the sections brains at different ages, including 2,000 gene expression profiles had rostral–caudal misalignment, the software also searched for from neonatal common-marmoset brains. To enable automatic, gene expression in one rostral section and one caudal section ∼200 systematic, and unbiased comparisons of gene
Load more

Recommended publications
  • Blueprint Genetics ANOS1 Single Gene Test
    ANOS1 single gene test Test code: S00125 Phenotype information Kallmann syndrome Alternative gene names KALIG-1, WFDC19 Some regions of the gene are duplicated in the genome leading to limited sensitivity within the regions. Thus, low-quality variants are filtered out from the duplicated regions and only high-quality variants confirmed by other methods are reported out. Read more. Panels that include the ANOS1 gene Kallmann Syndrome Panel Abnormal Genitalia/ Disorders of Sex Development Panel Test Strengths The strengths of this test include: CAP accredited laboratory CLIA-certified personnel performing clinical testing in a CLIA-certified laboratory Powerful sequencing technologies, advanced target enrichment methods and precision bioinformatics pipelines ensure superior analytical performance Careful construction of clinically effective and scientifically justified gene panels Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level Our publicly available analytic validation demonstrating complete details of test performance ~2,000 non-coding disease causing variants in our clinical grade NGS assay for panels (please see ‘Non-coding disease causing variants covered by this test’) Our rigorous variant classification scheme Our systematic clinical interpretation workflow using proprietary software enabling accurate and traceable processing of NGS data Our comprehensive clinical statements Test Limitations This test does not detect the following: Complex inversions Gene conversions
    [Show full text]
  • Polymorphisms of the BARX1 and ADAMTS17 Locus Genes in Individuals with Gastroesophageal Reflux Disease
    J Neurogastroenterol Motil, Vol. 25 No. 3 July, 2019 pISSN: 2093-0879 eISSN: 2093-0887 https://doi.org/10.5056/jnm18183 JNM Journal of Neurogastroenterology and Motility Original Article Polymorphisms of the BARX1 and ADAMTS17 Locus Genes in Individuals With Gastroesophageal Reflux Disease Alexandra Argyrou,1 Evangelia Legaki,1 Christos Koutserimpas,2 Maria Gazouli,1* Ioannis Papaconstantinou,3 George Gkiokas,3 and George Karamanolis4 1Department of Basic Medical Sciences, Laboratory of Biology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece; 22nd Department of General Surgery, “Sismanoglio General Hospital of Athens, Athens, Greece; 32nd Department of Surgery, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece; and 4Gastroenterology Unit, 2nd Department of Surgery, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece Background/Aims Gastroesophageal reflux disease (GERD) represents a common condition having a substantial impact on the patients’ quality of life, as well as the health system. According to many studies, the BARX1 and ADAMTS17 genes have been suggested as genetic risk loci for the development of GERD and its complications. The purpose of this study is to investigate the potential association between GERD and BARX1 and ADAMTS17 polymorphisms. Methods The present is a prospective cohort study of 160 GERD patients and 180 healthy control subjects of Greek origin, examined for BARX1 and ADAMTS17 polymorphisms (rs11789015 and rs4965272) and a potential correlation to GERD. Results The rs11789015 AG and GG genotypes were found to be significantly associated with GERD (P = 0.032; OR, 1.65; 95% CI, 1.06- 2.57 and P = 0.033; OR, 3.00; 95% CI, 1.15-7.82, respectively), as well as the G allele (P = 0.007; OR, 1.60; 95% CI, 1.14- 2.24).
    [Show full text]
  • From Bipotent Neuromesodermal Progenitors to Neural-Mesodermal Interactions During Embryonic Development
    International Journal of Molecular Sciences Review From Bipotent Neuromesodermal Progenitors to Neural-Mesodermal Interactions during Embryonic Development Nitza Kahane and Chaya Kalcheim * Department of Medical Neurobiology, Institute of Medical Research Israel-Canada (IMRIC) and the Edmond and Lily Safra Center for Brain Sciences (ELSC), Hebrew University of Jerusalem-Hadassah Medical School, P.O. Box 12272, Jerusalem 9112102, Israel; [email protected] * Correspondence: [email protected] Abstract: To ensure the formation of a properly patterned embryo, multiple processes must operate harmoniously at sequential phases of development. This is implemented by mutual interactions between cells and tissues that together regulate the segregation and specification of cells, their growth and morphogenesis. The formation of the spinal cord and paraxial mesoderm derivatives exquisitely illustrate these processes. Following early gastrulation, while the vertebrate body elongates, a pop- ulation of bipotent neuromesodermal progenitors resident in the posterior region of the embryo generate both neural and mesodermal lineages. At later stages, the somitic mesoderm regulates aspects of neural patterning and differentiation of both central and peripheral neural progenitors. Reciprocally, neural precursors influence the paraxial mesoderm to regulate somite-derived myogen- esis and additional processes by distinct mechanisms. Central to this crosstalk is the activity of the axial notochord, which, via sonic hedgehog signaling, plays pivotal roles in neural, skeletal muscle and cartilage ontogeny. Here, we discuss the cellular and molecular basis underlying this complex Citation: Kahane, N.; Kalcheim, C. developmental plan, with a focus on the logic of sonic hedgehog activities in the coordination of the From Bipotent Neuromesodermal Progenitors to Neural-Mesodermal neural-mesodermal axis.
    [Show full text]
  • Supplementary Table 3 Complete List of RNA-Sequencing Analysis of Gene Expression Changed by ≥ Tenfold Between Xenograft and Cells Cultured in 10%O2
    Supplementary Table 3 Complete list of RNA-Sequencing analysis of gene expression changed by ≥ tenfold between xenograft and cells cultured in 10%O2 Expr Log2 Ratio Symbol Entrez Gene Name (culture/xenograft) -7.182 PGM5 phosphoglucomutase 5 -6.883 GPBAR1 G protein-coupled bile acid receptor 1 -6.683 CPVL carboxypeptidase, vitellogenic like -6.398 MTMR9LP myotubularin related protein 9-like, pseudogene -6.131 SCN7A sodium voltage-gated channel alpha subunit 7 -6.115 POPDC2 popeye domain containing 2 -6.014 LGI1 leucine rich glioma inactivated 1 -5.86 SCN1A sodium voltage-gated channel alpha subunit 1 -5.713 C6 complement C6 -5.365 ANGPTL1 angiopoietin like 1 -5.327 TNN tenascin N -5.228 DHRS2 dehydrogenase/reductase 2 leucine rich repeat and fibronectin type III domain -5.115 LRFN2 containing 2 -5.076 FOXO6 forkhead box O6 -5.035 ETNPPL ethanolamine-phosphate phospho-lyase -4.993 MYO15A myosin XVA -4.972 IGF1 insulin like growth factor 1 -4.956 DLG2 discs large MAGUK scaffold protein 2 -4.86 SCML4 sex comb on midleg like 4 (Drosophila) Src homology 2 domain containing transforming -4.816 SHD protein D -4.764 PLP1 proteolipid protein 1 -4.764 TSPAN32 tetraspanin 32 -4.713 N4BP3 NEDD4 binding protein 3 -4.705 MYOC myocilin -4.646 CLEC3B C-type lectin domain family 3 member B -4.646 C7 complement C7 -4.62 TGM2 transglutaminase 2 -4.562 COL9A1 collagen type IX alpha 1 chain -4.55 SOSTDC1 sclerostin domain containing 1 -4.55 OGN osteoglycin -4.505 DAPL1 death associated protein like 1 -4.491 C10orf105 chromosome 10 open reading frame 105 -4.491
    [Show full text]
  • Slit1 and Slit2 Cooperate to Prevent Premature Midline Crossing of Retinal Axons in the Mouse Visual System
    Neuron, Vol. 33, 219–232, January 17, 2002, Copyright 2002 by Cell Press Slit1 and Slit2 Cooperate to Prevent Premature Midline Crossing of Retinal Axons in the Mouse Visual System Andrew S. Plump,1,2,6 Lynda Erskine,3,6,7 midbrain. Some axons do not cross, projecting to the Christelle Sabatier,1 Katja Brose,1 same targets but ipsilaterally. As with many other brain Charles J. Epstein,2 Corey S. Goodman,4 commissures, formation of the optic chiasm occurs at Carol A. Mason,3 and Marc Tessier-Lavigne1,5,8 an invariant position along the antero-posterior axis of 1 Departments of Anatomy and the developing forebrain. Mechanisms must therefore of Biochemistry and Biophysics exist not only to direct divergence at the midline but also Howard Hughes Medical Institute to prevent retinal axons from crossing at inappropriate 2 Division of Medical Genetics locations. University of California, San Francisco While significant progress in recent years has led to San Francisco, California 94143 a greater understanding of the factors that help establish 3 Departments of Pathology, Anatomy, a topographic map within the retina and its targets and Cell Biology (O’Leary et al., 1999), less progress has been made in Center for Neurobiology and Behavior identifying the rudimentary axon guidance cues that es- Columbia University College of Physicians tablish the basic trajectories within the vertebrate visual and Surgeons system, particularly those that function at the midline New York, New York 10032 to regulate the positioning and decussation of retinal 4 Department of Molecular and Cell Biology axons. In mammals, chondroitin sulfate proteoglycans Howard Hughes Medical Institute (CSPGs), L1, netrin-1, and specific EphB ligands are University of California, Berkeley important for guidance within the retina (Birgbauer et Berkeley, California 94720 al., 2000; Brittis et al., 1992, 1995; Deiner et al., 1997; Snow et al., 1991).
    [Show full text]
  • Novel Mutations in ANOS1 and FGFR1 Genes Agnieszka Gach1* , Iwona Pinkier1, Maria Szarras-Czapnik2, Agata Sakowicz3 and Lucjusz Jakubowski1
    Gach et al. Reproductive Biology and Endocrinology (2020) 18:8 https://doi.org/10.1186/s12958-020-0568-6 RESEARCH Open Access Expanding the mutational spectrum of monogenic hypogonadotropic hypogonadism: novel mutations in ANOS1 and FGFR1 genes Agnieszka Gach1* , Iwona Pinkier1, Maria Szarras-Czapnik2, Agata Sakowicz3 and Lucjusz Jakubowski1 Abstract Background: Congenital hypogonadotropic hypogonadism (CHH) is a rare disease, triggered by defective GnRH secretion, that is usually diagnosed in late adolescence or early adulthood due to the lack of spontaneous pubertal development. To date more than 30 genes have been associated with CHH pathogenesis with X-linked recessive, autosomal dominant, autosomal recessive and oligogenic modes of inheritance. Defective sense of smell is present in about 50–60% of CHH patients and called Kallmann syndrome (KS), in contrast to patients with normal sense of smell referred to as normosmic CHH. ANOS1 and FGFR1 genes are all well established in the pathogenesis of CHH and have been extensively studied in many reported cohorts. Due to rarity and heterogenicity of the condition the mutational spectrum, even in classical CHH genes, have yet to be fully characterized. Methods: To address this issue we screened for ANOS1 and FGFR1 variants in a cohort of 47 unrelated CHH subjects using targeted panel sequencing. All potentially pathogenic variants have been validated with Sanger sequencing. Results: Sequencing revealed two ANOS1 and four FGFR1 mutations in six subjects, of which five are novel and one had been previously reported in CHH. Novel variants include a single base pair deletion c.313delT in exon 3 of ANOS1, three missense variants of FGFR1 predicted to result in the single amino acid substitutions c.331C > T (p.R111C), c.1964 T > C (p.L655P) and c.2167G > A (p.E723K) and a 15 bp deletion c.374_388delTGCCCGCAGACTCCG in exon 4 of FGFR1.
    [Show full text]
  • Sequence Analysis of Familial Neurodevelopmental Disorders
    SEQUENCE ANALYSIS OF FAMILIAL NEURODEVELOPMENTAL DISORDERS by Joseph Mark Tilghman A dissertation submitted to Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland December 2020 © 2020 Joseph Tilghman All Rights Reserved Abstract: In the practice of human genetics, there is a gulf between the study of Mendelian and complex inheritance. When diagnosis of families affected by presumed monogenic syndromes is undertaken by genomic sequencing, these families are typically considered to have been solved only when a single gene or variant showing apparently Mendelian inheritance is discovered. However, about half of such families remain unexplained through this approach. On the other hand, common regulatory variants conferring low risk of disease still predominate our understanding of individual disease risk in complex disorders, despite rapidly increasing access to rare variant genotypes through sequencing. This dissertation utilizes primarily exome sequencing across several developmental disorders (having different levels of genetic complexity) to investigate how to best use an individual’s combination of rare and common variants to explain genetic risk, phenotypic heterogeneity, and the molecular bases of disorders ranging from those presumed to be monogenic to those known to be highly complex. The study described in Chapter 2 addresses putatively monogenic syndromes, where we used exome sequencing of four probands having syndromic neurodevelopmental disorders from an Israeli-Arab founder population to diagnose recessive and dominant disorders, highlighting the need to consider diverse modes of inheritance and phenotypic heterogeneity. In the study described in Chapter 3, we address the case of a relatively tractable multifactorial disorder, Hirschsprung disease.
    [Show full text]
  • Systematic Data-Querying of Large Pediatric Biorepository Identifies Novel Ehlers-Danlos Syndrome Variant Akshatha Desai1, John J
    Desai et al. BMC Musculoskeletal Disorders (2016) 17:80 DOI 10.1186/s12891-016-0936-8 RESEARCH ARTICLE Open Access Systematic data-querying of large pediatric biorepository identifies novel Ehlers-Danlos Syndrome variant Akshatha Desai1, John J. Connolly1, Michael March1, Cuiping Hou1, Rosetta Chiavacci1, Cecilia Kim1, Gholson Lyon1, Dexter Hadley1 and Hakon Hakonarson1,2* Abstract Background: Ehlers Danlos Syndrome is a rare form of inherited connective tissue disorder, which primarily affects skin, joints, muscle, and blood cells. The current study aimed at finding the mutation that causing EDS type VII C also known as “Dermatosparaxis” in this family. Methods: Through systematic data querying of the electronic medical records (EMRs) of over 80,000 individuals, we recently identified an EDS family that indicate an autosomal dominant inheritance. The family was consented for genomic analysis of their de-identified data. After a negative screen for known mutations, we performed whole genome sequencing on the male proband, his affected father, and unaffected mother. We filtered the list of non- synonymous variants that are common between the affected individuals. Results: The analysis of non-synonymous variants lead to identifying a novel mutation in the ADAMTSL2 (p. Gly421Ser) gene in the affected individuals. Sanger sequencing confirmed the mutation. Conclusion: Our work is significant not only because it sheds new light on the pathophysiology of EDS for the affected family and the field at large, but also because it demonstrates the utility of unbiased large-scale clinical recruitment in deciphering the genetic etiology of rare mendelian diseases. With unbiased large-scale clinical recruitment we strive to sequence as many rare mendelian diseases as possible, and this work in EDS serves as a successful proof of concept to that effect.
    [Show full text]
  • Supplementary Table 1: Adhesion Genes Data Set
    Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like,
    [Show full text]
  • Gene Expression Profiling of Corpus Luteum Reveals the Importance Of
    bioRxiv preprint doi: https://doi.org/10.1101/673558; this version posted February 27, 2020. 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. 1 Gene expression profiling of corpus luteum reveals the 2 importance of immune system during early pregnancy in 3 domestic sheep. 4 Kisun Pokharel1, Jaana Peippo2 Melak Weldenegodguad1, Mervi Honkatukia2, Meng-Hua Li3*, Juha 5 Kantanen1* 6 1 Natural Resources Institute Finland (Luke), Jokioinen, Finland 7 2 Nordgen – The Nordic Genetic Resources Center, Ås, Norway 8 3 College of Animal Science and Technology, China Agriculture University, Beijing, China 9 * Correspondence: MHL, [email protected]; JK, [email protected] 10 Abstract: The majority of pregnancy loss in ruminants occurs during the preimplantation stage, which is thus 11 the most critical period determining reproductive success. While ovulation rate is the major determinant of 12 litter size in sheep, interactions among the conceptus, corpus luteum and endometrium are essential for 13 pregnancy success. Here, we performed a comparative transcriptome study by sequencing total mRNA from 14 corpus luteum (CL) collected during the preimplantation stage of pregnancy in Finnsheep, Texel and F1 15 crosses, and mapping the RNA-Seq reads to the latest Rambouillet reference genome. A total of 21,287 genes 16 were expressed in our dataset. Highly expressed autosomal genes in the CL were associated with biological 17 processes such as progesterone formation (STAR, CYP11A1, and HSD3B1) and embryo implantation (eg.
    [Show full text]
  • Mouse Slit1 Conditional Knockout Project (CRISPR/Cas9)
    https://www.alphaknockout.com Mouse Slit1 Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Slit1 conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Slit1 gene (NCBI Reference Sequence: NM_015748 ; Ensembl: ENSMUSG00000025020 ) is located on Mouse chromosome 19. 37 exons are identified, with the ATG start codon in exon 1 and the TAA stop codon in exon 37 (Transcript: ENSMUST00000025993). Exon 6~8 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Slit1 gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-332I24 as template. Cas9, gRNA and targeting vector will be co-injected into fertilized eggs for cKO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Mice homozygous for a reporter allele exhibit normal interneuron numbers and morphology. Exon 6 starts from about 10.58% of the coding region. The knockout of Exon 6~8 will result in frameshift of the gene. The size of intron 5 for 5'-loxP site insertion: 992 bp, and the size of intron 8 for 3'-loxP site insertion: 1117 bp. The size of effective cKO region: ~1526 bp. The cKO region does not have any other known gene. Page 1 of 7 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 5 6 7 8 9 10 11 37 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Slit1 Homology arm cKO region loxP site Page 2 of 7 https://www.alphaknockout.com Overview of the Dot Plot Window size: 10 bp Forward Reverse Complement Sequence 12 Note: The sequence of homologous arms and cKO region is aligned with itself to determine if there are tandem repeats.
    [Show full text]
  • Análise Integrativa De Perfis Transcricionais De Pacientes Com
    UNIVERSIDADE DE SÃO PAULO FACULDADE DE MEDICINA DE RIBEIRÃO PRETO PROGRAMA DE PÓS-GRADUAÇÃO EM GENÉTICA ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas Ribeirão Preto – 2012 ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas Tese apresentada à Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo para obtenção do título de Doutor em Ciências. Área de Concentração: Genética Orientador: Prof. Dr. Eduardo Antonio Donadi Co-orientador: Prof. Dr. Geraldo A. S. Passos Ribeirão Preto – 2012 AUTORIZO A REPRODUÇÃO E DIVULGAÇÃO TOTAL OU PARCIAL DESTE TRABALHO, POR QUALQUER MEIO CONVENCIONAL OU ELETRÔNICO, PARA FINS DE ESTUDO E PESQUISA, DESDE QUE CITADA A FONTE. FICHA CATALOGRÁFICA Evangelista, Adriane Feijó Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas. Ribeirão Preto, 2012 192p. Tese de Doutorado apresentada à Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo. Área de Concentração: Genética. Orientador: Donadi, Eduardo Antonio Co-orientador: Passos, Geraldo A. 1. Expressão gênica – microarrays 2. Análise bioinformática por module maps 3. Diabetes mellitus tipo 1 4. Diabetes mellitus tipo 2 5. Diabetes mellitus gestacional FOLHA DE APROVAÇÃO ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas.
    [Show full text]