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

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 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.

ORGANISM(S): Mus musculus

PROVIDER: GSE68283 | GEO | 2015/11/02

SECONDARY ACCESSION(S): PRJNA282463

REPOSITORIES: GEO

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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

Next Generation Sequencing Analysis of Wild Type and Rfx2-/- Testicular Transcriptomes [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.

2015-11-02 | GSE68284 | GEO

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

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

Next Generation Sequencing Facilitates Quantitative Analysis of Germ Cell-specific Ythdf2 Mutants and Control Transcriptomes

Project description:Given the reported molecular role of YTHDF2 in mRNA stability, we designed to investigate the biological mechanism underlying the defects of germ cell-specific ythdf2 mutants (Ythdf2-vKO) spermatogenesis using high-throughput RNA sequencing (RNA-seq). Testes were obtained from Ythdf2-vKO and control adult mice, then were used for RNA-seq. Our result showed that there were 266 genes (196 up and 70 down) deregulated in Ythdf2-vKO testes (P < 0.05, fold change ＞ 1.5) compared with control adult mice. Based on our previously reported m6A mRNA methylomes of mouse spermaogenic cells (PMID: 28914256), 66% of the upregulated genes (129 genes) in Ythdf2-vKO testes were modified with m6A. Further analysis based on our previously reported single-cell transcriptomics data of mouse spermatogenesis (PMID: 30061742), the 129 upregulated genes with m6A modification in Ythdf2-vKO testes mainly express at early stages of wild-type spermatogenesis. While the 70 down regulated genes in Ythdf2-vKO testes mainly exist at later stages of wild-type spermatogenesis. Our qPCR analysis confirmed the RNA-seq analysis. In summary, our results showed that YTHDF2 is essential for regulation of a wave of transcriptome dynamic transition during mice spermatogenesis.

2022-03-15 | GSE147574 | GEO

Next-Generation Sequencing Analysis of Wild Type and Rfx1-/- or Rfx2-/- or Rfx3-/- Mouse Ependymal Cells

Project description:Purpose: This study was carried out to determine the consequences of inactivating either Rfx1, or Rfx2 or Rfx3 on gene expression during differentiation of mouse multiciliated ependymal cells.

2020-07-13 | GSE145323 | GEO

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