Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR4436664_1.fastq.gz | Fastqsanger.gz | |||
| SRR4436664_2.fastq.gz | Fastqsanger.gz | |||
| SRR4436665_1.fastq.gz | Fastqsanger.gz | |||
| SRR4436665_2.fastq.gz | Fastqsanger.gz | |||
| SRR4436666_1.fastq.gz | Fastqsanger.gz |
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Project description:Analysis of gene expression and alternate splicing effects of retinoic acid treatment on gestational day 15 rat fetal testes in whole testis culture Retinoic acid exposure in cultured fetal testis has previously been demonstrated to have significant effects on the histology of the fetal testis in multiple species, as well as to alter the meiotic states of germ cells. However, previous experiments have not analyzed the mechanisms by which retinoic acid exposure leads to altered tubulogenesis and loss of seminiferous cord structure. This experiment demonstrated that retinoic acid exposure activated signaling pathways that promote the ovary development program and oppose normal testis development in mid-gestational rat fetal testes.
2017-09-26 | GSE101634 | GEO
Project description:Embryonic day 13 (E13), E14, and E16 rat testes and ovaries were used for microarray analysis, as well as E13 testis organ cultures that undergo testis morphogenesis and develop seminiferous cords in vitro. A list of 109 genes resulted from a selective analysis for genes present in male gonadal development and with a 1.5-fold change in expression between E13 and E16. Characterization of these 109 genes potentially important for testis development revealed that cytoskeletal-associated proteins, extracellular matrix factors, and signaling factors were highly represented. Throughout the developmental period (E13-E16), sex-enriched transcripts were more prevalent in the male with 34 of the 109 genes having testis-enriched expression during sex determination. In ovaries, the total number of transcripts with a 1.5-fold change in expression between E13 and E16 was similar to the testis, but none of those genes were both ovary enriched and regulated during the developmental period. Genes conserved in sex determination were identified by comparing changing transcripts in the rat analysis herein, to transcripts altered in previously published mouse studies of gonadal sex determination. A comparison of changing mouse and rat transcripts identified 43 genes with species conservation in sex determination and testis development. Profiles of gene expression during E13-E16 rat testis and ovary development are presented and candidate genes for involvement in sex determination and testis differentiation are identified. Analysis of cellular pathways did not reveal any specific pathways involving multiple candidate genes. However, the genes and gene network identified influence numerous cellular processes with cellular differentiation, proliferation, focal contact, RNA localization, and development being predominant. Keywords: expression analysis, testis, ovary, sex determination
2008-02-20 | GSE10558 | GEO
Project description:We report the RNAseq-based transcriptome profiles of adult male rat liver and testis following 14 day exposure to myclobutanil. A treatment-related change in mRNA levels were observed in both liver and testis.
2020-12-15 | GSE139098 | GEO
Project description:2-hydroxy-4-methoxybenzophenone (HMB) has been reported to have weak estrogenic activity by in vivo and in vitro studies, making it a chemical with potential reproductive concern. To explore if perinatal HMB exposure altered the gene expression profiling in the rat testis, we analyzed whole genome and mitochondria-related gene expression profiling on the testis ontained from Sprague-Dawley rat offspring exposed prenatally and lactationally to varying dose of HMB.
2018-08-31 | GSE111262 | GEO
Project description:Background Digital gene expression (DGE) profiling has become an established tool to study RNA expression. Here, we provide an in-depth analysis of small RNA DGE profiles from two different rat strains (BN-Lx and SHR) from six different rat tissues (spleen, liver, brain, testis, heart, kidney). We describe the expression patterns of known and novel micro (mi)RNAs and piwi-interacting (pi)RNAs. We confirmed the expression of 589 known miRNAs and identified 56 miRNAs homologous to known human or mouse miRNAs, as well as 45 new rat miRNAs. Furthermore, we confirmed specific A to I editing in brain for mir-376a/b/c and identified mir-377 as a novel editing target. In accordance with earlier findings, we observed a highly tissue-specific expression pattern for all tissues analyzed. The brain was found to express the highest number of tissue-specific miRNAs, followed by testis. Notably, our experiments also revealed robust strain-specific differential miRNA expression in the liver that is caused by genetic variation between the strains. Finally, we identified two types of germline-specific piRNAs in testis, mapping either to transposons or in strand-specific clusters. Taken together, the small RNA compendium described here advances the annotation of small RNAs in the rat genome. Strain and tissue-specific expression patterns furthermore provide a strong basis for studying the role of small RNAs in regulatory networks as well as biological process like physiology and neurobiology that are extensively studied in this model system.
2010-02-17 | GSE19054 | GEO
Project description:Background: Eleven linker histone subtypes are reported in mammals. Linker histones establish and maintain higher order chromatin structure. HILS1 is a spermatid-specific linker histone and its expression overlaps with the chromatin reorganization process during spermiogenesis; however, role of HILS1 in chromatin restructuring is largely unknown. Method: Genome-wide occupancy of the rat HILS1 protein was studied by ChIP-sequencing of pulldown DNA isolated from nuclei of 50-60 days old rat testis, using anti HILS1 antibody. Conclusion: Present study revealed that HILS1 is preferentially associated Line L1 elements in rat spermatids.
2018-10-02 | GSE98116 | GEO
Project description:Male germ cell development is dependent on the orchestrated regulation of gene networks. TAF7 like (Taf7l) is situated on the X chromosome and has been implicated in testis development. We examined the biology of TAF7L in testis development using the rat. Taf7l disruption resulted in male infertility due to compromised testis development and failed sperm production. An arrest in the progression of meiosis was observed.
2024-07-17 | GSE241840 | GEO
Project description:The current study investigates the direct effects of in utero vinclozolin exposure on the developing rat testis transcriptome. Vinclozolin is a commonly used fungicide in agriculture and is an endocrine disruptor with anti-androgenic activity. Previous studies have demonstrated that exposure to vinclozolin during embryonic gonadal sex determination induces epigenetic modifications of the germ line and transgenerational adult onset disease states that include spermatogenic cell defects, prostate disease, kidney disease, and tumor development. An investigation of the molecular actions of vinclozolin was initiated through an analysis of direct actions on the F1 generation embryonic testis development. Microarray analyses were performed to compare control and vinclozolin treated testis transcriptomes at embryonic day 13, 14 and 16. A total of 576 differentially expressed genes were identified and the major cellular functions and pathways associated with these altered transcripts were examined. The sets of regulated genes at the different development periods were found to be transiently altered and distinct. Interestingly, genes previously shown to be regulated during normal male sex determination were not altered by vinclozolin treatment. Categorization by major known functions of all 576 genes altered by in utero vinclozolin exposure demonstrates transcription, signaling, cytoskeletal and extra cellular matrix associated transcripts are highly represented. Specific cellular process and pathway analyses suggest the involvement of Wnt and calcium signaling, vascular development and epigenetic mechanisms as potential mediators of the direct F1 generation actions of vinclozolin. For Samples 1-12: We used microarrays to determine genes expressed differentially between control and in utero Vinclozolin treated E13, E14, and E16 rat testis. For Samples 13-16: We used microarrays to determine genes expressed differentially between control and in vitro Vinclozolin treated E13 cultured rat testis. For Samples 17-20: We used microarrays to determine genes expressed differentially between control and in vitro Flutamide treated rat E13 cultured testis.
2010-02-14 | GSE20245 | GEO