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Profiling of Gata1 binding in primary erythroid cells by CUT&RUN

ABSTRACT: Profiling of Gata1 binding in primary erythroid cells by CUT&RUN

PROVIDER: PRJNA719369 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14134900_1.fastq.gz	Fastqsanger.gz
	SRR14134900_2.fastq.gz	Fastqsanger.gz
	SRR14134901_1.fastq.gz	Fastqsanger.gz
	SRR14134901_2.fastq.gz	Fastqsanger.gz
	SRR14134902_1.fastq.gz	Fastqsanger.gz

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Profiling of Gata1 binding in primary erythroid cells by CUT&RUN

Project description:The chromatin landscape of developing erythroblasts changes dramatically during differentiation. We have profiled the change in Gata1 binding in primary erythroid cells entering terminal differentiation using CUT&RUN.

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Profiling of Gata2 binding in primary erythroid cells by CUT&RUN

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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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Project description:Profiling of Nf-e2 binding in primary erythroid cells by CUT&RUN

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CUT&RUN HUDEP1 OE SOX6-Flag

Project description:SOX6 CUT&RUN on HUDEP1 over expressing SOX6-Flag. The experiment is done using and anti Flag Ab to assist the genome wide binding profile of SOX6 in HUDEP1 (Human Umbilical cord blood-Derived Erythroid Progenitor-1).

2023-04-07 | E-MTAB-12800 | biostudies-arrayexpress

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