Somatic cells in testes
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE366 | GEO | 2003/05/06
SECONDARY ACCESSION(S): PRJNA84865
REPOSITORIES: GEO
Similar Datasets
Project description:Gene expression profiles of somatic cells of fetal and adult testis. To identify genes developmentally regulated in the somatic cells of the testis, serial analysis of gene expression (SAGE) has been used to generate gene expression profiles from these cells in the fetal and adult mouse. To avoid germ cell transcripts, a fetal SAGE library was generated from germ cell-free fetal Wv/Wv mice, and an adult SAGE library was generated from adult testes depleted of germ cells with busulfan. The combined SAGE libraries contained 147570 tags identifying 12976 unique transcripts. Of these transcripts, 3607 were present in only the fetal library and 3941 were present in only the adult library. Most of the abundant differentially expressed tags in the adult testis library were from characterized genes, whereas 3' rapid amplification of complementary ends was required to identify most differentially expressed tags in the fetal library. These fetal tags were mostly associated with uncharacterized UniGene clusters. These data provide a comprehensive and quantitative analysis of gene expression in the somatic cells of the fetal and adult testis (including unknown transcripts) and identify genes differentially expressed in these cells during testis development. These differentially regulated genes are likely to provide insight into mechanisms regulating testis function both during development and in the adult animal. Keywords: other
2003-05-06 | E-GEOD-366 | biostudies-arrayexpress
Project description:Following sex determination, XY and XX gonads develop into a testis and an ovary, respectively. Depending on the sex of the gonad, resident germ cells will subsequently be committed to either spermatogenesis or oogenesis. In this study we took advantage of the Wv/Wv mouse genetic model, in which gonads are almost devoided of germ cells, to uncover gene expression underlying fetal germ cell development.
2010-12-20 | GSE23908 | GEO
Project description:Following sex determination, XY and XX gonads develop into a testis and an ovary, respectively. Depending on the sex of the gonad, resident germ cells will subsequently be committed to either spermatogenesis or oogenesis. In this study we took advantage of the Wv/Wv mouse genetic model, in which gonads are almost devoided of germ cells, to uncover gene expression underlying fetal germ cell development. Male and Female gonads were collected at 12, 14 and 16 days post coitum (dpc) from wild-type and Wv/Wv mouse embryos. Total RNAs were extracted and hybridized on Affymetrix microarrays. Expression signals from male and female gonads or from wild-type and mutant gonads were compared to identify sexually dimorphic genes as well as genes expressed in germ cell during fetal gonad development.
2010-12-20 | E-GEOD-23908 | biostudies-arrayexpress
Project description:Accumulated evidence proves that mature spermatozoa contain a complex yet specific mRNA, which could provide information of the past events of spermatogenesis. Our aim was to quantitatively microdissect these mRNA transcripts by a digital approach. SAGE was used to study the mRNA transcripts from ejaculate of an individual and of a pool of 10 fertile men. SAGE library from individual produced 20237 raw tags representing 2459 unique tags (those tags that show at least twice in the library), and that from pooled 10 men generated 21052 raw tags representing 2712 unique tags. The SAGE view of ejaculate of fertile men has revealed a large number of transcripts, which occur in steady frequencies and probably have important implications in the spermatogenesis and fertilization. Keywords: normal gene expression profile
2005-11-11 | GSE3587 | GEO
Project description:Increasing evidence suggests that low-abundant transcripts may play fundamental roles in biological processes. In an attempt to estimate the prevalence of low-abundant transcripts in eukaryotic genomes, we performed a transcriptome analysis in Drosophila using the SAGE technique. We collected 244,313 SAGE tags from transcripts expressed in Drosophila embryonic, larval, pupae, adult, and testicular tissue. From these SAGE tags, we identified 40,823 unique SAGE tags. Our analysis showed that 55% of the 40,823 unique SAGE tags are novel without matches in currently known Drosophila transcripts, and most of the novel SAGE tags have low copy numbers. Further analysis indicated that these novel SAGE tags represent novel low-abundant transcripts expressed from loci outside of currently annotated exons including the intergenic and intronic regions, and antisense of the currently annotated exons in the Drosophila genome. Our study reveals the presence of a significant number of novel low-abundant transcripts in Drosophila, and highlights the need to isolate these novel low-abundant transcripts for further biological studies. Keywords: other
2005-06-03 | GSE2347 | GEO
Project description:Increasing evidence suggests that low-abundant transcripts may play fundamental roles in biological processes. In an attempt to estimate the prevalence of low-abundant transcripts in eukaryotic genomes, we performed a transcriptome analysis in Drosophila using the SAGE technique. We collected 244,313 SAGE tags from transcripts expressed in Drosophila embryonic, larval, pupae, adult, and testicular tissue. From these SAGE tags, we identified 40,823 unique SAGE tags. Our analysis showed that 55% of the 40,823 unique SAGE tags are novel without matches in currently known Drosophila transcripts, and most of the novel SAGE tags have low copy numbers. Further analysis indicated that these novel SAGE tags represent novel low-abundant transcripts expressed from loci outside of currently annotated exons including the intergenic and intronic regions, and antisense of the currently annotated exons in the Drosophila genome. Our study reveals the presence of a significant number of novel low-abundant transcripts in Drosophila, and highlights the need to isolate these novel low-abundant transcripts for further biological studies. Keywords: other
2005-06-03 | E-GEOD-2347 | biostudies-arrayexpress
Project description:Spermatogenesis has been well studied in rodents and invertebrates, but remains poorly understood in humans. As a step towards illuminating human spermatogenesis, we used single-cell RNA-sequencing (scRNAseq) analysis to analyze neonatal and adult human testes. Clustering analysis of neonatal testes revealed 3 germ subsets, including cells with characteristics of primordial germ cells (PGCs), and more differentiated cells with gene expression profiles similar with adult spermatogonial stem cells (SSCs). We identified markers for these neonatal subsets, including protein markers for the PGC-like (PGCL) subset. Clustering analysis of the adult testis revealed 9 germ and 3 somatic cell subsets. Among the germ cell clusters are 4 undifferentiated spermatogonia (SPG) states, each marked by specific genes. One of the SPG states has characteristics suggesting it is enriched for SSCs. We identified protein markers specific for this state, including cell-surface proteins that we used to enrich for these cells. We mapped the timeline of male germ cell development from PGCs through fetal germ cells to differentiating adult SPG stages. We also defined somatic cell subsets in the human testis and traced their developmental trajectories. Together, our data provides a blueprint for understanding the development of the male germline and supporting somatic cells in humans. The germ cell subset markers we identified are candidates to be used for clinical applications, including SSC therapy for treating infertility.
2018-12-22 | GSE124263 | GEO
Project description:Adult male grass shrimp were exposed for 96 hours to LC50 concentrations of either Fipronil, Endosulfan, or Cadmium, as well as a Carrier Control exposure. RNA was extracted from whole-body homogenates using the RNABee kit. Tags were clustered to identify tags diagnostic of the different exposures. Keywords: SAGE, Grass shrimp, ecotoxicogenomics 3 randomly selected shrimp were pooled for each library. Libraries were constructed using the I-SAGE long kit from Invitrogen.
2006-05-18 | E-GEOD-4853 | biostudies-arrayexpress
Project description:The abundant and widespread coccolithophore Emiliania huxleyi plays an important role in mediating CO2 exchange between the ocean and the atmosphere through its impact on marine photosynthesis and calcification. Here, we use long serial analysis of gene expression (SAGE) to identify E. huxleyi genes responsive to nitrogen (N) or phosphorus (P) starvation. Long SAGE is an elegant approach for examining quantitative and comprehensive gene expression patterns without a priori knowledge of gene sequences via the detection of 21-bp nucleotide sequence tags. E. huxleyi appears to have a robust transcriptional-level response to macronutrient deficiency, with 42 tags uniquely present or up-regulated twofold or greater in the N-starved library and 128 tags uniquely present or up-regulated twofold or greater in the P-starved library. The expression patterns of several tags were validated with reverse transcriptase PCR. Roughly 48% of these differentially expressed tags could be mapped to publicly available genomic or expressed sequence tag (EST) sequence data. For example, in the P-starved library a number of the tags mapped to genes with a role in P scavenging, including a putative phosphate-repressible permease and a putative polyphosphate synthetase. In short, the long SAGE analyses have (i) identified many new differentially regulated gene sequences, (ii) assigned regulation data to EST sequences with no database homology and unknown function, and (iii) highlighted previously uncharacterized aspects of E. huxleyi N and P physiology. To this end, our long SAGE libraries provide a new public resource for gene discovery and transcriptional analysis in this biogeochemically important marine organism. Keywords: Emiliania, gene expression, nutrients, SAGE, phosphate, nitrogen
2007-07-07 | GSE8376 | GEO
Project description:Recent improvements in the development of methods for isolating functionally validated populations of nearly pure (>20%) murine hematopoietic stem cells (HSCs) have made it possible to analyze the molecular basis of the properties of these cells with increased precision. One intriguing feature of HSCs is the change they undergo in many of their key properties during development a change that affects the control of their self-renewal, cycling status, differentiated progeny output and steel factor sensitivity. To investigate how these differences are mediated, we undertook a genome-wide analysis of the transcripts present in highly purified fetal and adult HSCs using an adaptation of the LongSAGE methodology that allows its application to small numbers of cells (10 ng of RNA) by inclusion of an initial PCR amplification step that preserves the transcript repertoire while excluding less than 0.25% of the transcripts. The LongSAGE methodology was adopted because it is sequence-based and thus quantitative and independent of prior knowledge of expressed genes or variations in their hybridization to matching or related cDNAs, ESTs or derived oligos. A suspension of 10,000 lin-Sca-1+CD43+Mac1+ fetal liver (FL) cells (20% pure HSCs as determined by 16-week limiting dilution and single cell transplantation experiments) was obtained from embryonic day 14.5 fetuses. From these cells, we generated a 160,000-tag LongSAGE library containing 7865 tags that map uniquely to the mouse genome (using the RefSeq database through DiscoverySpace; www.bcgsc.ca/DiscoverySpace). A suspension of 3700 CD45midlin-Rho-SP cells (30% pure HSCs) was isolated from adult mouse bone marrow (BM) and then used to generate a 37,000-tag LongSAGE library (956 uniquely mapped tags). Both of these libraries contained tags identifying transcripts that have been previously reported to be associated with HSCs from FL and/or adult BM, including c-kit, pbx-1, tgf-, cul-4a, PrP, c-myc, robo1, sox17, as well as a number of Smarc transcripts, ubiquitin ligase transcripts and TNF-related transcripts. As a first test of the utility of the libraries, we looked for differences in the expression of genes that have been broadly associated with differences in cellular proliferative activity. This comparison identified many such tags in the FL HSC library that were absent from the adult BM HSC library, including multiple cyclins (A2, B2, C, D1, D2, D3, E1, F, H, I, J L1, L2), cdc20, cdc5b, and plk, as well as 34 of the top 50 proliferation genes identified by Venezia et al (PLoS Biology, 2004) to be selectively expressed in adult BM HSCs that had been stimulated to proliferate. Other transcripts that were present at significantly higher levels in the FL HSC library (95% C.I. using Audic Claverie statistics) included msl2, rbx1, lmo2, pfn1, and 16 members of the tripartite motif protein (trim) family. Conversely, many transcripts for components of the proteosome, involved in nucleic acid binding, and transcripts coding for proteins with receptor activity were present at higher levels (or uniquely) in the adult BM HSC library. Taken together, these findings establish the validity and potential of these permanent HSC transcriptome resources for further investigation of mechanisms that determine the different biology of fetal and adult HSCs. RNA was collected from E14.5 fetal livers and 10-12 week old adult bone marrow with the phenotypes that isolate highly purified hematopoietic stem cells (Lin-/CD45+/SP/Rho- for bone marrow and Lin-/Mac1+/CD43+/Sca1+ for fetal liver)
2008-10-18 | E-GEOD-13243 | biostudies-arrayexpress