Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Strand-specific RNA-seq analysis after Ssrp1 knockout in embryonic stem cells

ABSTRACT: Strand-specific RNA-seq analysis after Ssrp1 knockout in embryonic stem cells

PROVIDER: PRJNA655887 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12411180_1.fastq.gz	Fastqsanger.gz
	SRR12411180_2.fastq.gz	Fastqsanger.gz
	SRR12411181_1.fastq.gz	Fastqsanger.gz
	SRR12411181_2.fastq.gz	Fastqsanger.gz
	SRR12411182_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Strand-specific RNA-seq analysis after Ssrp1 knockout in embryonic stem cells

2020-08-23 | GSE155863 | GEO

RNA-seq analysis after Ssrp1 knockout or Usp7 depletion in embryonic stem cells

Project description:Endogenous retrovirus MERVL is specifically expressed in a minority of embryonic stem cells. To determine the restrain mechanism of MERVL, we knocked out Ssrp1 and analyzed the effect on the expression of transposable elements and coding genes. Ssrp1 further interacts with ubiquitin specific protease Usp7. We knocked down usp7 and analyzed the effect on the expression of MERVL. It turns out the deletion of ssrp1 or usp7 would lead to upregulation of MERVL. This study extends our understandings of the machanism by novel factors regulates MERVL.

2020-08-23 | GSE141788 | GEO

RNA-seq analysis after Ssrp1 knockout or Usp7 depletion in embryonic stem cells

Project description:RNA-seq analysis after Ssrp1 knockout or Usp7 depletion in embryonic stem cells

| PRJNA594729 | ENA

Ssrp1 co-immunoprecipitation and mass spectrometry

Project description:Endogenous retroviruses (ERVs) were usually silenced by various histone modifications on histone H3 variants and respective histone chaperones in embryonic stem cells (ESCs). However, it is still unknown whether chaperones of other histones could repress ERVs. Here, we show that H2A/H2B histone chaperone FACT plays a critical role in silencing ERVs and ERV-derived cryptic promoters in ESCs. Loss of FACT component Ssrp1 activated MERVL whereas the re-introduction of Ssrp1 rescued the phenotype. Additionally, Ssrp1 interacted with MERVL and suppressed cryptic transcription of MERVL-fused genes. Remarkably, Ssrp1 interacted with and recruited H2B deubiquitinase Usp7 to Ssrp1 target genes. Suppression of Usp7 caused similar phenotypes as loss of Ssrp1. Furthermore, Usp7 acted by deubiquitinating H2Bub and thereby repressed the expression of MERVL-fused genes. Taken together, our study uncovers a unique mechanism by which FACT complex silences ERVs and ERV-derived cryptic promoters in ESCs.

2020-08-24 | PXD017351 | Pride

ChIP-seq for SSRP1

Project description:SSRP1 ChIP-seq was performed in E14 cells

2024-02-20 | GSE167180 | GEO

ChIP-seq for SSRP1

Project description:ChIP-seq for SSRP1

| PRJNA703674 | ENA

The polyA+ transcriptomes of mouse embryonic stem cells and their derived neural precursors from strand-specific RNA-Seq

Project description:We have examined the nuclear (nuc) and cytoplasmic (cyt) polyA+ transcriptomes of undifferentiated mouse embryonic stem cells (un) and cells differentiated to neural precursors (d5) using strand-specific RNA-Seq. The 46C mouse embryonic stem cell line was used for this study. Two cell types were examined: undifferentiated mouse embryonic stem cells (un) and cells differentiated to neural precursors (d5). For each cell type, cells were fractionated to nuclear and cytoplasmic components. RNAs were extracted from each component and were fragmented enzymatically for library construction. For each cell type and component, strand-specific RNA-Seq libraries were generated using at least two different fragmentation protocols.

2012-08-01 | E-GEOD-38990 | biostudies-arrayexpress

The polyA+ transcriptomes of mouse embryonic stem cells and their derived neural precursors from strand-specific RNA-Seq

2012-08-01 | GSE38990 | GEO

Comparison of E14.5 embryonic kidney transcriptomes (Grb2 ureteric-specific knockout vs wild-type)

Project description:Comparison of E14.5 embryonic kidney transcriptomes (Grb2 ureteric-specific knockout vs wild-type)

| PRJNA684494 | ENA

Strand-specific RNA-seq analysis of three streptomycetes

Project description:Strand-specific RNA-seq analysis of three streptomycetes

| PRJNA196870 | ENA