Project description:Cut&Run analysis was performed in MOLT-4 cells to analyze the level of H3K27ac and DNA bindings of SMARCA4 and RUNX1 after DMSO or BRM014 treatment.

2024-07-02 | GSE249318 | GEO

Cut&Run analysis for transcription factors in DND-41 cells

Project description:Cut&Run analysis for transcription factors in DND-41 cells

| PRJNA961811 | ENA

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.

2019-08-24 | GSE136251 | GEO

Cut&Run analysis for transcription factors in TAL1-FKBP12 Jurkat cells

Project description:Cut&Run analysis for transcription factors in TAL1-FKBP12 Jurkat cells

| PRJNA938076 | ENA

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

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

| PRJNA887091 | ENA

CUT&RUN LoV-U of beta-catenin, TCF/LEF transcription factors and histone modifications in HEK293T and mouse embryonic hindlimb tissue at 11.5 days post coitum

Project description:In our attempts to profile different regulators of the WNT/b-catenin transcriptional complex, CUT&RUN failed to produce consistent binding patterns of the non-DNA-binding b-catenin. We developed a modified CUT&RUN protocol, which we refer to as LoV-U (Low Volume and Urea), that enables the generation of robust and reproducible b-catenin binding profiles. CUT&RUN-LoV-U can profile all classes of chromatin regulators tested, as shown by datasets targeting the TCF/LEF transcription factors and various histone modifications. CUT&RUN-LoV-U uncovers direct WNT/β-catenin target genes in human cells, as well as in ex vivo cells isolated from developing mouse tissue.

2022-07-16 | E-MTAB-11951 | biostudies-arrayexpress

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