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

TRAP-seq following Pdx1 depletion

Project description:TRAP-seq following Pdx1 depletion

| PRJNA474185 | ENA

RNA-seq following JunD depletion

Project description:RNA-seq following JunD depletion

| PRJNA474228 | ENA

Differentially expressed genes following PARK2 depletion in Esophageal Squamous Cell Cancer Cell Line

Project description:We konckout PARK2 in Esophageal Squamous Cell Cancer Cell Line EC9706 and then detected differentially expressed genes We konckout PARK2 in Esophageal Squamous Cell Cancer Cell Line EC9706 and then detected differentially expressed genes

2020-03-12 | GSE146808 | GEO

Differentially expressed RNAs in the skin tissue of IRF1 knockout mice following radiation

Project description:Differentially expressed RNAs in the skin tissue of IRF1 knockout mice following radiation

| PRJNA514229 | ENA

Differentially expressed genes following YAP depletion in Esophageal Squamous Cell Cancer Cell Line

Project description:Purpose: Using CRISPR to generate YAP knock-out ESCC cell lines and then detected differentially expressed genes;Results:RNA-seq results showed that the expression of CD24 was regulated by YAP.

2022-12-31 | GSE201646 | GEO

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