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Genome wide chromatin changes in Wild Type and DDX5 knockdown of GC cells [RNA polymerase II ChIP-seq]

ABSTRACT: Genome wide chromatin changes in Wild Type and DDX5 knockdown of GC cells [RNA polymerase II ChIP-seq]

PROVIDER: PRJNA610572 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11244973.fastq.gz	Fastqsanger.gz
	SRR11244974.fastq.gz	Fastqsanger.gz
	SRR11244975.fastq.gz	Fastqsanger.gz
	SRR11244976.fastq.gz	Fastqsanger.gz

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Similar Datasets

Genome wide chromatin changes in Wild Type and DDX5 knockdown of GC cells [RNA polymerase II ChIP-seq]

Project description:DDX5 (DEAD-Box Helicase 5) plays a role as an adaptor molecule, is involved in a variety of cellular processes. Here, we performed ChIP-seq with antibody specific for RNA Polymerase II in HGC-27 cells after transduction with lentivirus harboring DDX5 shRNA or non-targeting shRNA.

2021-11-10 | GSE146430 | GEO

Next-Generation Sequencing Facilitates Quantitative Analysis of Wild Type and DDX5 knockdown of GC Transcriptomes

Project description:Next-Generation Sequencing Facilitates Quantitative Analysis of Wild Type and DDX5 knockdown of GC Transcriptomes

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Genome wide chromatin and transcriptome changes of Wild Type and DDX5 knockdown of GC cells

Project description:Genome wide chromatin and transcriptome changes of Wild Type and DDX5 knockdown of GC cells

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Next-Generation Sequencing Facilitates Quantitative Analysis of Wild Type and DDX5 knockdown of GC Transcriptomes

Project description:We aimed to detect the mRNA expression levels in HGC-27 cells after transduction with lentivirus harboring DDX5 shRNA or non-targeting shRNA.

2021-11-10 | GSE146429 | GEO

Effect of DDX5/DDX17 on genome-wide RNA Polymerase II distribution in SH-SY5Y cells

Project description:This project includes ChIP of total RNA pol II in human SH-SY5Y neuroblastoma cells following the joint depletion of RNA helicases DDX5 and DDX17 to determine the genome-wide effect of DDX5/DDX17 on RNA Pol II distribution.

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Knockdown of IGFBP7 decreases FGF2 expression in GC.

Project description:Knockdown of IGFBP7 decreases FGF2 expression in GC.

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Analysis of the genome-wide distribution of RNA Pol II in a neuroblastoma cell line under silencing of RNA helicases DDX5 and DDX17

Project description:DEAD-box RNA helicases DDX5 and DDX17 regulate gene expression at different levels such as transcription and splicing, but the underlying mechanisms are not fully understood. A calibrated ChIP-seq analysis of total RNA Polymerase II was carried out in DDX5/DDX17-depleted SH-SY5Y cells to analyse the contribution of DDX5/DDX17 to RNAPII distribution. Univ Lyon, ENS de Lyon, CNRS UMR 5239, INSERM U1293, Laboratory of Biology and Modelling of the Cell, 46 Allée d'Italie, F-69007, Lyon, France. Corresponding author: cyril.bourgeois@inserm.fr

2022-08-04 | GSE183517 | GEO

Effect of DDX5/DDX17 on genome-wide RNA Polymerase II distribution in SH-SY5Y cells

Project description:Effect of DDX5/DDX17 on genome-wide RNA Polymerase II distribution in SH-SY5Y cells

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DDX5 in colonic tumors

Project description:The Asp-Glu-Ala-Asp (DEAD)-box RNA binding protein, DDX5, is ubiquitously expressed in many cell types, yet its role in RNA metabolism and its downstream function in vivo has not been fully elucidated. In the intestine, DDX5 is highly expressed in the intestinal epithelial cell (IECs) and contributes to tumorigenesis. Here, we used a conditional mouse lines where DDX5 is knocked out in IECs upon Tamoxifen administration to uncover mechanisms underlying DDX5 functions in colon tumors.

2021-12-03 | GSE146014 | GEO

Genome-wide R-loop analysis defines unique roles for DDX5, XRN2, and PRMT5 in DNA/RNA hybrid resolution

Project description:DDX5, XRN2, and PRMT5 have been shown to resolve DNA/RNA hybrids (R-loops) at RNA polymerase II transcription termination sites at few genomic loci. Herein, we perform genome-wide R-loop mapping using classical DNA/RNA immunoprecipitation and high-throughput sequencing (DRIP-seq) of loci regulated by DDX5, XRN2, and PRMT5. We observed hundreds to thousands of R-loop gains and losses at transcribed loci in DDX5-, XRN2-, and PRMT5-deficient U2OS cells. R-loop gains were characteristic of highly transcribed genes located at gene-rich regions, whereas R-loop losses were observed in low-density gene areas. DDX5, XRN2, and PRMT5 shared many R-loop gain loci at transcription termination sites, consistent with their coordinated role in RNA polymerase II transcription termination. DDX5-depleted cells had unique R-loop gain peaks near the transcription start site that did not overlap with those of siXRN2 and siPRMT5 cells, suggesting a role for DDX5 in transcription initiation independent of XRN2 and PRMT5. Moreover, we observed that the accumulated R-loops at certain loci in siDDX5, siXRN2, and siPRMT5 cells near the transcription start site of genes led to antisense intergenic transcription. Our findings define unique and shared roles of DDX5, XRN2, and PRMT5 in DNA/RNA hybrid regulation.

2020-08-08 | GSE155865 | GEO

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