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Next Generation Sequencing Analysis of Wild Type and Rfx2-/- Testicular Transcriptomes [RNA-Seq P21]

ABSTRACT: Purpose: This study was carried out to determine the consequences of the Rfx2-/- genotype on spermatogenesis in the mouse Methods: RNA was extracted from decapsulated testes of 21 day old mixed background mice of either genotype. Deep sequencing was used to determine quantitative expression of the genomes from independent replicates of each genotype Results: RNA-Seq analysis identified some 105 genes that are down regulated at least 2-fold in Rfx2-/- testes, with ~50 being reduced at least 10-fold Conclusion: Spermatogenesis undergoes complete arrest just prior to the end of the round spermatid period of sperm development in mutant mice. Sequencing results showed that approximately 105 genes were downregulated 2 fold or more in the testes of mutant mice. Comparison of similar studies of targeted mutations in genes for other transcription factor demonstrate that Rfx2 has a large and nearly unique set of genes that depend on it directly or indirectly. A large number of downregulated genes are identified with cilia function.

ORGANISM(S): Mus musculus

PROVIDER: GSE68284 | GEO | 2015/11/02

SECONDARY ACCESSION(S): PRJNA282462

REPOSITORIES: GEO

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Next Generation Sequencing Analysis of Wild Type and Rfx2-/- Testicular Transcriptomes at post natal day 21 [RNA-Seq P21]

Project description:Purpose: This study was carried out to determine the consequences of the Rfx2-/- genotype on spermatogenesis in the mouse Methods: RNA was extracted from decapsulated testes of 21 day old mixed background mice of either genotype. Deep sequencing was used to determine quantitative expression of the genomes from independent replicates of each genotype Results: RNA-Seq analysis identified some 105 genes that are down regulated at least 2-fold in Rfx2-/- testes, with ~50 being reduced at least 10-fold Conclusion: Spermatogenesis undergoes complete arrest just prior to the end of the round spermatid period of sperm development in mutant mice. Sequencing results showed that approximately 105 genes were downregulated 2 fold or more in the testes of mutant mice. Comparison of similar studies of targeted mutations in genes for other transcription factor demonstrate that Rfx2 has a large and nearly unique set of genes that depend on it directly or indirectly. A large number of downregulated genes are identified with cilia function. Testicular mRNA profiles were determined by deep sequencing using testes from 5 independent wild type and 6 independent Rfx2-/- mice

2015-11-02 | E-GEOD-68284 | biostudies-arrayexpress

Next Generation Sequencing Analysis of Wild Type and Rfx2-/- Testicular Transcriptomes [ChIP-Seq]

Project description:Purpose: This study was carried out to determine the consequences of the Rfx2-/- genotype on spermatogenesis in the mouse Methods: DNA was extracted from decapsulated testes of 21 day old mice. ChIP sequencing was used to determine the binding sites of RFX2. Results: ChIP-Seq analysis identified ~880 binding sites of RFX2 near TSS. Conclusion: Spermatogenesis undergoes complete arrest just prior to the end of the round spermatid period of sperm development in mutant mice. Sequencing results showed that approximately 105 genes were downregulated 2 fold or more in the testes of mutant mice. Comparison of similar studies of targeted mutations in genes for other transcription factor demonstrate that Rfx2 has a large and nearly unique set of genes that depend on it directly or indirectly. A large number of downregulated genes are identified with cilia function.

2015-11-02 | GSE68282 | GEO

Next Generation Sequencing Analysis of Wild Type and Rfx2-/- Testicular Transcriptomes [ChIP-Seq]

2015-11-02 | E-GEOD-68282 | biostudies-arrayexpress

Next Generation Sequencing Analysis of Wild Type and Rfx2-/- Testicular Transcriptomes [RNA-Seq P30]

Project description:Purpose: This study was carried out to determine the consequences of the Rfx2-/- genotype on spermatogenesis in the mouse Methods: RNA was extracted from decapsulated testes of 29-30 day old mixed background mice of either genotype. Deep sequencing was used to determine quantitative expression of the genomes from independent replicates of each genotype Results: RNA-Seq analysis identified some 640 genes that are down regulated at least 2-fold in Rfx2-/- testes, with ~150 being reduced at least 10-fold Conclusion: Spermatogenesis undergoes complete arrest just prior to the end of the round spermatid period of sperm development in mutant mice. Sequencing results showed that approximately 640 genes were downregulated 2 fold or more in the testes of mutant mice. Comparison of similar studies of targeted mutations in genes for other transcription factor demonstrate that Rfx2 has a large and nearly unique set of genes that depend on it directly or indirectly. A large number of downregulated genes are identified with cilia function.

2015-11-02 | GSE68283 | GEO

Next Generation Sequencing Analysis of Wild Type and Rfx2-/- Testicular Transcriptomes at post natal day 30 [RNA-Seq P30]

Project description:Purpose: This study was carried out to determine the consequences of the Rfx2-/- genotype on spermatogenesis in the mouse Methods: RNA was extracted from decapsulated testes of 29-30 day old mixed background mice of either genotype. Deep sequencing was used to determine quantitative expression of the genomes from independent replicates of each genotype Results: RNA-Seq analysis identified some 640 genes that are down regulated at least 2-fold in Rfx2-/- testes, with ~150 being reduced at least 10-fold Conclusion: Spermatogenesis undergoes complete arrest just prior to the end of the round spermatid period of sperm development in mutant mice. Sequencing results showed that approximately 640 genes were downregulated 2 fold or more in the testes of mutant mice. Comparison of similar studies of targeted mutations in genes for other transcription factor demonstrate that Rfx2 has a large and nearly unique set of genes that depend on it directly or indirectly. A large number of downregulated genes are identified with cilia function. Testicular mRNA profiles were determined by deep sequencing using testes from 5 independent wild type and 4 independent Rfx2-/- mice

2015-11-02 | E-GEOD-68283 | biostudies-arrayexpress

Transcription Factor RFX2 Is a Key Regulator of Mouse Spermiogenesis

Project description:To identify RFX2-dependent genes during spermatogenesis, We chose 24-day-old wild-type and mutant testes samples. Spermiogenesis in mutants was normal before this time point while massive round spermatids detached from the tubules thereafter. RNAs were isolated from the total testicular cells.

2017-02-09 | GSE74961 | GEO

Coordinated genomic control of ciliogenesis and cell movement by Rfx2

2013-12-12 | GSE50593 | GEO

Coordinated genomic control of ciliogenesis and cell movement by Rfx2

Project description:We have performed a systems-level analysis of the RFX/Daf-19 family transcription factor, Rfx2. Using a combination of high-throughput sequencing of Rfx2-regulated transcripts and chromosomal binding sites, we provide a comprehensive accounting of the target genes by which Rfx2 controls ciliogenesis and cilia beating in vertebrates. RNA-seq: two biological replicates for control and RFX2 knockdown by morpholino injection, ChIP-seq: RFX2-GFP pulldown with GFP antibody, GFP only expression used as control

2013-12-12 | E-GEOD-50593 | biostudies-arrayexpress

A comparative profile of the mRNA and microRNA transcriptome in immature and mature bovine testes

Project description:This study aim to screening potential regulators of fecundity, the bovine testes of immature and mature in Chinese Red Steppes were performed by a genome-wide analysis of mRNAs and miRNAs. Compared with born testicular tissue, 6051 upregulated genes and 7104 downregulated genes in adult bovine testicular tissue were identified as differentially expressed genes (DEGs) (log2FC>1 or <－1 , FDR <0.05). The DEGs were significantly enriched in 808 GO terms (p <0.05), which are involved in sperm biological activity, including male gonad development, male genitalia development, spermatogenesis, sperm motility, spermatid development, sperm chromatin condensation, etc. Moreover, DEGs were also significantly enriched in 105 KEGG pathways (p <0.05), such as focal adhesion, cGMP-PKG signaling pathway and calcium signaling pathway, etc. To explore the miRNA-regulated gene expression network integrated analysis was used between DEGs and differentially expressed miRNAs (DERs). Correlation prediction and analysis found that 896 differentially expressed target genes were negatively correlated with the expression levels of 31 differentially expressed bovine miRNAs. Our results identified novel candidate DEGs and DERs correlated with male reproduction, which will be valuable for future genetic and epigenetic studies of sperm development and maturity, as well as provided valuable insights into the molecular mechanisms of the male fertility and spermatogenesis in cattle.

2020-12-31 | GSE137464 | GEO

EWSR1 is critical for post-meiotic transcription and spermiogenesis

Project description:Spermatogenesis is precisely controlled by complex gene expression programs. During mammalian male germ cell development, a crucial feature is the repression of transcription before spermatid elongation. Previously, we discovered that RNA-binding protein EWSR1 plays an important role in meiotic recombination and is highly expressed in late meiotic cells and post-meiotic cells. Here, we used a Ewsr1 pachytene stage-specific knockout mouse model to study its roles at late meiotic prophase I and in spermatozoa maturation. We show that loss of EWSR1 at this stage does not affect proper meiosis completion, but the developing germ cells exhibit defects in spermatid elongation and chromocenter formation. In the Ewsr1 conditional knockout testes, expression of many genes regulating spermatid differentiation is impaired, suggesting that EWSR1 may play important role in regulation of spermiogenesis related mRNA synthesis and spermatid differentiation.

2021-06-01 | GSE120989 | GEO

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