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Genome-wide maps of ARID1A binding genes in H9 human embryonic stem cells.

ABSTRACT: Genome-wide maps of ARID1A binding genes in H9 human embryonic stem cells.

PROVIDER: PRJNA578922 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10326131_1.fastq.gz	Fastqsanger.gz
	SRR10326131_2.fastq.gz	Fastqsanger.gz
	SRR10326132_1.fastq.gz	Fastqsanger.gz
	SRR10326132_2.fastq.gz	Fastqsanger.gz

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Genome-wide maps of ARID1A binding genes in H9 human embryonic stem cells

Project description:Genome-wide maps of ARID1A binding genes in H9 human embryonic stem cells

| PRJNA638954 | ENA

Genome-wide maps of ARID1A binding genes in H9 human embryonic stem cells

Project description:We reported loss of ARID1A promoted neurogenesis and inhibited cardiogenesis. Here we used specific ARID1A antibody to pull down ARID1A binding genomic DNA in human embryonic stem cells, which let us know the potential genes regulated by ARID1A during neurogenesis and inhibited cardiogenesis. IgG was used as the control.

2023-06-11 | GSE152324 | GEO

Genome-wide maps of ARID1A binding genes in H9 human embryonic stem cells.

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Genome-wide maps of p53 binding sites in human embryonic stem cell H9 derived trilineage.

Project description:Genome-wide maps of p53 binding sites in human embryonic stem cell H9 derived trilineage.

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Single cell RNA-seq revealed different cell types induced by loss of ARID1A in undifferentiated and differentiation (day 10) H9 hESCs.

Project description:We reported loss of ARID1A promoted neurogenesis and inhibited cardiogenesis. Under microscopy, we observed that spontaneously differentiated cells were induced in ARID1A KO H9 hESCs cultured in mTesR medium. After cardiac differentiation for 10 days, we also observed the cell types were totally different between WT and ARID1A KO cells. We did not know what cells types were. Here scRNA-seq were used to identify the cell types in WT H9 hESCs and ARID1A KO H9 hESCs.

2020-06-19 | GSE139342 | GEO

Genome-wide maps of p53 binding sites in human embryonic stem cell H9 derived trilineage.

Project description:To determine the roles of IFI16-p53 interaction during H9-trilineage specification, we performed ChIP-seq to derive a genome-wide profile of p53-binding genes after IFI16 knockdown by shRNA-1865. p53 binding sites were mapped on Day 2 of trilineage induction.

2020-03-03 | GSE142050 | GEO

Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) revealed genomic chromatin accessibilities change induced by loss of ARID1A in differentiated (day 4) H9 hESCs

Project description:We reported loss of ARID1A promoted neurogenesis and inhibited cardiogenesis. Under microscopy, we observed that spontaneously differentiated cells were induced in ARID1A KO H9 hESCs cultured in mTesR medium. We did not know what cells types were. Here ATAC-seq were used to investigate chromatin accessibilities change in differentiated (day 4) WT H9 hESCs and ARID1A KO hESC cells.

2020-06-19 | GSE139329 | GEO

Arid1a in mouse embryonic cells

Project description:Arid1a in mouse embryonic cells

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Genome-wide analysis of effects of ARID1A depletion in mouse embryonic stem cells

Project description:A degron system is used to deplete ARID1A a subunit of the SWI/SNF complex in mouse embryonic stem cells. Genome wide analysis of chromatin accessibility (ATAC-seq), nucleosome posistioning (MNase-seq), nascent transcription (TT-seq), binding to EP300 and presence of histone H3 K27acetylation (ChIP-seq) amd histone H3K27 tria-methylation (ChIP-seq) allowed us to identify two different pathways responsible for the up and downregulation of transcription following the loss of ARID1A. The rapid depletion of ARID1A generates mini domains of nucleomes at pluripotency transcription factor binding sites. Loss of ARID1A also results in the redistribution of the co-activator EP300. Locations of co-incident EP300 dissociation and lost chromatin accessibility occur adjacent to rapidly downregulated genes. Promoter proximal regions that gain EP300 are linked to genes that are transcriptionally upregulated. Our findings illustrate the importance of both direct and indirect effects in causing rapid changes to gene expression. Only a few genes are directly affected after ARID1A depletion and contribute to pathways associated with cancer and pluripotency establishing the loss of ARID1A phenotype.

2021-10-24 | GSE183278 | GEO

Identification of PAX7-induced transcriptional changes and PAX7 genomic binding during skeletal myogenic differentiation of H9 embryonic stem cells

Project description:Skeletal myogenic commitment of human pluripotent cells can be achieved by doxycycline-inducible expression of the transcription factor PAX7. To gain further insights on PAX7 function during this process, we performed a time course whole transcriptome analysis of differentiating H9 human embryonic stem cells from doxycycline-treated and untreated cultures. In addition, we identified the genomic binding of PAX7 in one of the selected time point (referred as PAX7+ proliferating myogenic progenitors).

2017-06-30 | GSE98976 | GEO

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