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Cut & Run-seq analysis for transcription factors overexpression in GI-MEN cells

ABSTRACT: Cut & Run-seq analysis for transcription factors overexpression in GI-MEN cells

PROVIDER: PRJNA887091 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21802773_1.fastq.gz	Fastqsanger.gz
	SRR21802773_2.fastq.gz	Fastqsanger.gz
	SRR21802774_1.fastq.gz	Fastqsanger.gz
	SRR21802774_2.fastq.gz	Fastqsanger.gz
	SRR21802775_1.fastq.gz	Fastqsanger.gz

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Cut & Run-seq analysis for transcription factors overexpression in GI-MEN cells

Project description:Cut & Run analysis was performed in an neuroblastoma cell line to analyze DNA bindings of ASCL1-tag-HA in GI-MEN ASCL1-tag-HA cells and GI-MEN ASCL1-tag-HA+4TFs cells; analyze DNA bindings of MYCN, PHOX2B and H3K27ac in, GI-MEN 4TFs cells, and GI-MEN ASCL1-tag-HA+4TFs cells.

2023-11-21 | GSE214793 | GEO

RNA-seq analysis after transcription factors overexpression in GI-MEN cells [Part 2]

Project description:RNA-seq analysis was performed in a Neuroblastoma cell line (GI-MEN) to analyze gene expression changes after ASCL1 ot other TFs overexpression.

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H3K27ac HiChIP analysis in GI-MEN DOX-ASCL1 cells

Project description:H3K27ac HiChIP analysis was performed in GI-MEN DOX-ASCL1 cells to analyze active chromatin-chromatin interactions in GI-MEN DOX-ASCL1 cells.

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RNA-seq analysis after ASCL1 overexpression in GI-MEN cells [Part 1]

Project description:RNA-seq analysis was performed in a Neuroblastoma cell line (GI-MEN) to analyze gene expression changes after ASCL1 overexpression.

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ChIP-seq analysis for H3K27ac in GI-MEN DOX-ASCL1 cells and for ASCL1-HA in GI-MEN DOX-ASCL1-tag-HA cells.

Project description:ChIP-seq analysis was performed in an neuroblastoma cell line to analyze DNA bindings of H3K27ac in GI-MEN DOX-ASCL1 cells and ASCL1-HA in GI-MEN DOX-ASCL1-tag-HA cells.

2023-11-21 | GSE214791 | GEO

ATAC-seq analysis for GI-MEN DOX-ASCL1 cells and GI-MEN DOX-ASCL1-4TFs cells.

Project description:ATAC-seq analysis was performed in an neuroblastoma cell line to analyze chromatin opening of Gi-MEN cells under four different conditions.

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ATAC-seq analysis for GI-MEN DOX-ASCL1 cells and GI-MEN DOX-ASCL1-4TFs cells.

Project description:ATAC-seq analysis for GI-MEN DOX-ASCL1 cells and GI-MEN DOX-ASCL1-4TFs cells.

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RNA-seq analysis after transcription factors overexpression in GI-MEN cells [Part 2]

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Demonstration of CUT&RUN motif footprint analysis using key blood progenitor transcription factors

Project description:We introduce CUT&RUNTools (https://bitbucket.org/qzhudfci/cutruntools/) as a flexible, general pipeline for facilitating the identification of chromatin-associated protein binding and genomic footprinting analysis from antibody-targeted CUT&RUN primary cleavage data. CUT&RUNTools extracts endonuclease cut site information from sequences of short read fragments and produces single-locus binding estimates, aggregate motif footprints, and informative visualizations to support the high-resolution mapping capability of CUT&RUN. We illustrate the functionality of CUT&RUNTools through analysis of CUT&RUN data acquired for GATA1, a master regulator in erythroid lineage cells. Results were compared initially to published GATA1 ChIP-seq data for cells under the same conditions. We performed de novo analysis of CUT&RUN peaks to retrieve not only GATA1’s primary motif, but also the GATA1-TAL1 composite motif, and co-factor motifs GCCCCGCCTC, CMCDCCC, and RTGASTCA that correspond to SP1, KLF1, and NFE2 co-factors. Cofactor binding was verified by independent TAL1 and KLF1 CUT&RUN, and other ChIP-seq experiments. CUT&RUNTools also generated base-pair resolution motif footprint for sequence-specific binding factors, and located likely direct binding sites by quantifying log-odds of binding scores. Overall, CUT&RUNTools should enable biologists to realize advantages of cleavage data provided by CUT&RUN, and make high-quality footprinting analysis accessible to a broad audience.

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Bulk Cut&run and Cut&tag

Project description:Bulk Cut&run and Cut&tag

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