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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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			Action	DRS
	SRR25359912_1.fastq.gz	Fastqsanger.gz
	SRR25359912_2.fastq.gz	Fastqsanger.gz
	SRR25359913_1.fastq.gz	Fastqsanger.gz
	SRR25359913_2.fastq.gz	Fastqsanger.gz
	SRR25359914_1.fastq.gz	Fastqsanger.gz

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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

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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.

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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

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

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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).

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A Sox2 distal enhancer cluster regulates embryonic stem cell differentiation potential

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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.

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Project description:Sox2 has been studied in several types of human solid tumors. The investigators found that Sox2 had higher expression level in colorectal cancer and metastatic tissues than normal tissues. So the investigators assumed that whether Sox2 plays an important role in the progression and migration of colon cancer.

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