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Genome wide analysis of STAT3-mediated transcription and binding sites in mouse female germ stem cell (RNA-seq)

ABSTRACT: Genome wide analysis of STAT3-mediated transcription and binding sites in mouse female germ stem cell (RNA-seq)

PROVIDER: PRJEB23416 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2193450_1.fastq.gz	Fastqsanger.gz
	ERR2193450_2.fastq.gz	Fastqsanger.gz
	ERR2193451_1.fastq.gz	Fastqsanger.gz
	ERR2193451_2.fastq.gz	Fastqsanger.gz
	ERR2193452_1.fastq.gz	Fastqsanger.gz

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Genome wide analysis of STAT3-mediated transcription and binding sites in mouse female germ stem cell (ChIP-seq)

Project description:Activation of JAK-STAT3 signaling by leukemia inhibitory factor (LIF) is required for maintaining self-renewal of mouse embryonic stem cells (mESCs). STAT3 perform cell type-specific roles in different cell type, here we revisit the role of STAT3 using mouse female germ stem cell (mFGSCs). We applied CRISPR/Cas9 system to generate Stat3 knockout FGSCs and then observed cell growth inhibition and cell cycle arrest in KO cell line. By combining genome wide ChIP-Seq and RNA-Seq, we identified 5990 STAT3 binding sites and discovered serval genes specific regulated by STAT3 that were involved in stem cell proliferation and female gonad development in FGSCs. In general, we identify key roles of STAT3 for sustains self-renewal and proliferation for FGSCs in this study.

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Genome wide analysis of STAT3-mediated transcription and binding sites in mouse female germ stem cell (RNA-seq)

2017-12-20 | E-MTAB-6162 | biostudies-arrayexpress

Genome wide analysis of STAT3-mediated transcription and binding sites in mouse female germ stem cell (ChIP-seq)

Project description:Genome wide analysis of STAT3-mediated transcription and binding sites in mouse female germ stem cell (ChIP-seq)

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Genome-Wide Discovery of STAT3 Functional Binding Sites

Project description:STAT3 is a transcription factor playing a crucial role in inflammation, immunity and oncogenesis, able to induce distinct subsets of target genes in different cell types or under different conditions. Identification of direct transcriptional targets however has only defined a relatively limited set of genes, not sufficient to explain its variegated functions. In order to improve our understanding of the STAT3 transcriptional network we decided to develop a computational approach for the discovery of STAT3 functional binding sites. Upon generating a Positional Weight Matrix to define STAT3 binding sites, we applied a loglikelihood ratio scoring function and were able to assign affinity scores with very high specificity (93.5%) as measured by EMSA. STAT3 binding sites scoring above a stringent threshold have been identified genome-wide in Homo sapiens and Mus musculus and selected for phylogenetic conservation by genomic sequence alignment using eight vertebrate species. Validation was carried out on a subset of predicted sites within genes previously identified as STAT3-responsive by microarray analysis. The high percentage of sites able to bind STAT3 in vivo, as assessed by Chromatin Immunoprecipitation (ChIP) analysis, revealed the high predictive power of our method.

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