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

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

PROVIDER: PRJNA606759 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11089526.fastq.gz	Fastqsanger.gz
	SRR11089527.fastq.gz	Fastqsanger.gz
	SRR11089528.fastq.gz	Fastqsanger.gz
	SRR11089529.fastq.gz	Fastqsanger.gz
	SRR11089530.fastq.gz	Fastqsanger.gz

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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

Next-Generation Sequencing Analysis of ChIP

Project description:Purpose: This study was carried out to determine RFX1 or RFX2 or RFX3 binding sites in nuclei of multiciliated ependymal cells. Methods: DNA was extracted from ependymal cell cultures. ChIP-sequencing was used to determine the binding sites of RFX1 , RFX2 or RFX3.

2020-07-13 | GSE144758 | GEO

Study of RFX1 and RFX3 binding sites in the mouse genome

Project description:The aim of the study was to identify RFX1 and RFX2 binding sites in mouse pancreatic beta cells. Chromatin immunoprecipitation experiments were performed with the mouse MIN6 beta cell line and antibodies raised against RFX1 and RFX3. Immunoprecipitated DNA was sequenced using the Genome Analyzer II (Illumina). Antibodies were described in Reith W, Ucla C, Barras E, Gaud A, Durand B, Herrero-Sanchez C, Kobr M, Mach B : RFX1, a transactivator of hepatitis B virus enhancer I, belongs to a novel family of homodimeric and heterodimeric DNA-binding proteins. Mol Cell Biol 1994;14:1230–1244

2015-08-22 | E-GEOD-72272 | biostudies-arrayexpress

Study of RFX1 and RFX3 binding sites in the mouse genome

Project description:The aim of the study was to identify RFX1 and RFX2 binding sites in mouse pancreatic beta cells.

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Next-Generation Sequencing Analysis of Mouse Ependymal Cells

Project description:Next-Generation Sequencing Analysis of Mouse Ependymal Cells

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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. Testicular RFX2 binding sites were determined by deep sequencing using testes from 2 independentWT mice

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

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

2015-11-02 | GSE68282 | GEO

ChIP-seq for RFX1

Project description:ChIP-seq for RFX1

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RNA-seq Analysis of RFX1-dependent Genes in Fusarium graminearum Z-3639

Project description:Fusarium graminearum is a major pathogen of Fusarium head blight in wheat, barley, and rice, as well as ear rot and stalk rot in maize. Regulatory Factor X (RFX) transcription factors are well-conserved in animals and fungi, but their functions are diverse, ranging from DNA-damage response to ciliary gene regulation. We investigated the role of the sole RFX transcription factor, RFX1, in F. graminearum. Deletion of rfx1 resulted in multiple defects in hyphal growth, conidiation, virulence, and sexual development. Deletion mutants of rfx1 were more sensitive to various types of DNA damage than the wild-type strain. Septum formation was inhibited and micronuclei were produced in the rfx1 deletion mutants. The results of the neutral comet assay demonstrated that disruption of rfx1 function caused spontaneous DNA double-strand breaks. To understand regulatory mechanisms of rfx1 in F. graminearum, we obtained and analyzed genome-wide transcription profiles generated from the RNA-sequencing data of the wild-type and M-NM-^Trfx1 strains. RNA-sequencing-based transcriptomic analysis revealed that RFX1 suppressed the expression of many genes, including genes for the repair of DNA damage. 2 samples examined: mycelia harvested 24 h after inoculation of wild-type conidia in complete medium; mycelia harvested 32 h after inoculation of M-NM-^Trfx1 conidia in complete medium

2014-01-28 | E-GEOD-52198 | 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

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