Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cut and Run from Caki-1, MCF7, and U251 cell lines with NRF1 and CTCF

ABSTRACT: We performed a Cut & Run assay in the associated cell lines to profile the direct binding of NRF1 and CTCF at the promoters of target genes.

ORGANISM(S): Homo sapiens

PROVIDER: GSE240699 | GEO | 2023/08/11

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Cut and Run from Caki-1, MCF7, and U251 cell lines with NRF1 and CTCF

Project description:Cut and Run from Caki-1, MCF7, and U251 cell lines with NRF1 and CTCF

| PRJNA1004633 | ENA

Identification of CTCF binding sites through CUT&RUN sequencing in the neuroblastoma cell line CLB-GA.

Project description:CUT&RUN sequencing to define binding sites for CTCF and IgG in the neuroblastoma cell line CLB-GA.

2023-02-23 | E-MTAB-12586 | biostudies-arrayexpress

Bulk Cut&run and Cut&tag

Project description:Bulk Cut&run and Cut&tag

| PRJNA686390 | ENA

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

Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag

Project description:Here we describe successful implementation of CUT&RUN for profiling protein-DNA interactions in zebrafish embryos. We apply modified a CUT&RUN method to generate high resolution maps of enrichment for H3K4me3, H3K27me3, H3K9me3, and RNA polymerase II during zebrafish gastrulation. Using this data, we identify a conserved subset of developmental genes that are enriched in both H3K4me3 and H3K27me3 during gastrulation, and we demonstrate the increased effectiveness of CUT&RUN for detecting protein enrichment at repetitive sequences with reduced mappability. Our work demonstrates the power of combining CUT&RUN with the strengths of the zebrafish system to better understand the changing embryonic chromatin landscape and its roles in shaping development.

2021-06-17 | GSE178343 | GEO

CUT&RUN analysis for NOP16-mediated H3K27me3 alteration in MDA-MB231 cells [CUT&RUN-seq]

Project description:The goal of CUT&RUN-seq is to identify the global alteration of H3K27me3 levels by NOP16 overexpression or deletion in triple negative breast cancer cell line MDA-MB231 cells. Three (or Two) biological replicates were assigned for each group and in total 6 groups were prepared for these CUT&RUN-seq libraries. We mapped about 20 million reads per sample to hg38 human reference genome, and counted and normalized each reads number and identified H3K27me3 distribution.

2023-12-31 | GSE192496 | GEO

CUT&RUN-seq of DPPA2 in Esg1-tdTomato reporter mESC line

Project description:Enrichment of DPPA2 was assessed by CUT&RUN-sequencing in wildtype Esg1-tdTomato reporter mESC line.

2021-11-23 | E-MTAB-11182 | biostudies-arrayexpress

CUT&RUN LoV-U for SMAD4 in human melanoma cells

Project description:CUT&RUN LoV-U was performed against SMAD4 using two different antibodies in M170117 human melanoma cells under 4 conditions: Control (DMSO), TGFb, MEKi and TGFb + MEKi (Both).

2024-04-22 | E-MTAB-13951 | biostudies-arrayexpress

Epigenomic profiling of TASOR in Hela cells using CUT&RUN and CUT&Tag

Project description:Targeted epigenomic profiling methods CUT&RUN and CUT&Tag were used to examine TASOR genome binding and TASOR-regulated H3K9me3 deposition on chromatin.

2020-08-05 | GSE155693 | GEO

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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data