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Bulk ATAC-seq of mouse neural stem and progenitor cells (NSPC) derived from embryonic stem cells, with biallelic Sox2 enhancer cluster deletions

ABSTRACT: Bulk ATAC-seq of mouse neural stem and progenitor cells (NSPC) derived from embryonic stem cells, with biallelic Sox2 enhancer cluster deletions

PROVIDER: PRJNA996595 | ENA |

REPOSITORIES: ENA

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Bulk ATAC-seq of mouse neural stem and progenitor cells (NSPC) derived from embryonic stem cells, with biallelic Sox2 enhancer cluster deletions

Project description:We have generated ATAC-sequencing datasets of the regulome of mouse neural stem and progenitor cells derived from embryonic stem cells, with allele-specific deletions of Sox2 enhancer cluster regions. ATAC-seq experiments were conducted to evaluate the alterations in chromatin accessibility at candidate regulatory elements genome-wide in neural stem and progenitor cells with Sox2 enhancer loss-of-function.

2023-11-13 | GSE237777 | GEO

SuperSeries=Mouse neural stem and progenitor cells (NSPC) derived from embryonic stem cells, with biallelic Sox2 enhancer cluster deletions

Project description:SuperSeries=Mouse neural stem and progenitor cells (NSPC) derived from embryonic stem cells, with biallelic Sox2 enhancer cluster deletions

| PRJNA996589 | ENA

Bulk RNA-seq of mouse neural stem and progenitor cells (NSPC) derived from embryonic stem cells, with allele-specific deletions of a Sox2 enhancer cluster

Project description:We have generated RNA-sequencing datasets of the regulome of mouse neural stem and progenitor cells derived from embryonic stem cells, with allele-specific deletions of Sox2 enhancer cluster regions. RNA-seq experiments were conducted to evaluate the regulatory function of Sox2 candidate enhancers in neural stem and progenitor cells.

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RNA expression in KATOIII cells harboring biallelic deletions of the +22.6-kb site, epithelial-specific enchancer of ABO gene

Project description:Wild-type KATOIII cells and their derived mutant clones B3 and B4 harboring biallelic deletions of the +22.6-kb site, located 22.6 kb downstream from the ABO translation start site

2021-03-22 | GSE169059 | GEO

SuperSeries=Mouse neural stem and progenitor cells (NSPC) derived from embryonic stem cells, with biallelic Sox2 enhancer cluster deletions

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-11-10 | GSE237778 | GEO

Bulk RNA-seq of mouse neural stem and progenitor cells (NSPC) derived from embryonic stem cells, with allele-specific deletions of a Sox2 enhancer cluster

Project description:Bulk RNA-seq of mouse neural stem and progenitor cells (NSPC) derived from embryonic stem cells, with allele-specific deletions of a Sox2 enhancer cluster

| PRJNA996594 | ENA

A Sox2 distal enhancer cluster regulates embryonic stem cell differentiation potential

Project description:We report the effect on genome-wide gene expression after deletion of an enhancer region downstream of Sox2 in F1 ES cells. The Sox2 transcription factor must be robustly transcribed in embryonic stem (ES) cells to maintain pluripotency. Reporter assays reveal novel enhancers, including two enhancers over 100 kb downstream (SRR107 and SRR111) which, through the formation of chromatin loops, localise to the Sox2 promoter in ES cells. Using CRISPR/Cas9 we deleted a region containing these two enhancers, which we term the Sox2 control region (SCR). This deletion revealed that the SCR is required for Sox2 transcription in ES cells. Furthermore, homozygous deletion of this distal Sox2 control region (SCR) caused significant reduction in Sox2 mRNA and protein levels, loss of ES cell colony morphology, genome-wide changes in gene expression and impaired neuroectodermal formation upon spontaneous differentiation to embryoid bodies. Together these data identify a distal control region essential for Sox2 transcription in ES cells. Examination of PolA+ RNA after heterozygous and homozygous enhancer deletion in F1 ES cells (M. musculus129 x M. castaneus).

2014-11-19 | E-GEOD-58339 | biostudies-arrayexpress

A Sox2 distal enhancer cluster regulates embryonic stem cell differentiation potential

2014-11-19 | GSE58339 | GEO

NANOG-OCT4-SOX2 Regulatory Module in Human Embryonic Stem Cells

Project description:This SuperSeries is composed of the following subset Series: GSE34904: NANOG-OCT4-SOX2 Regulatory Module in Human Embryonic Stem Cells (dataset 1) GSE34912: NANOG-OCT4-SOX2 Regulatory Module in Human Embryonic Stem Cells (dataset 2) GSE34918: NANOG-OCT4-SOX2 Regulatory Module in Human Embryonic Stem Cells (dataset 3) GSE34920: NANOG-OCT4-SOX2 Regulatory Module in Human Embryonic Stem Cells (dataset 4) Refer to individual Series

2012-04-05 | E-GEOD-34921 | biostudies-arrayexpress

Sox2-regulatory networks in embryonic and trophoblast stem cells.

Project description:Sox2 is a pleiotropic transcription factor that regulates self-renewal and differentiation capacity in different types of stem cells, raising the possibility that it regulates similar transcriptional programs controlling common stemness. Embryonic stem (ES) cells and trophoblast stem (TS) cells are two developmentally related types of stem cells, which originate from distinct lineages of peri-implantation embryos. We have found that Sox2 is a critical regulator of self-renewal in both of two stem cells. Genome-wide analysis of Sox2 target genes using Affymetrix Exon Arrays and chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) unraveled that it regulates distinct transcriptional networks in ES and TS cells. This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-10-17 | E-GEOD-28455 | biostudies-arrayexpress

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