Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

52 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chromatin immunoprecipitation of mouse B3 pre-B cells and VL3 thymocytes to identify cohesin and CTCF binding sites

ABSTRACT: Identification of cohesin (Rad21) and CTCF binding sites in ~2% of the mouse genome in B3 pre-B cells stably expressing FLAG-tagged Rad21 using anti-FLAG (Sigma F3165) and anti-CTCF (Upstate 07729) antibodies

ORGANISM(S): Mus musculus

SUBMITTER: Mikhail Spivakov Marion Leleu

PROVIDER: E-TABM-401 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

ChIP-chip by array of mouse embryonic stem cells to analyze Jarid2 binding

Project description:Analysis of the binding of Jarid2 in mouse ES cells using a Flag tagged version of Jarid2 and a anti-Flag antibody.

2010-04-13 | E-TABM-963 | biostudies-arrayexpress

Genome-wide identification of CTCF and Cohesin binding sites in neonatal mouse brain

Project description:ChIP-seq for CTCF and Rad21 in 3 week old mouse brain from reciprocal BxC and CxB crosses. One biological replicate of each. Examination of CTCF and Cohesin binding sites in neonetal mouse brain

2013-06-20 | E-GEOD-35140 | biostudies-arrayexpress

ChIP-sequencing in human monocyte differentiation (3D-MO)

Project description:This dataset consists of ChIP-seq data from human monocytes, monocyte-derived dendritic cells as well as monocyte-derived cells that were subjected to siRNA treatment targeting CTCF or RAD21. ChIP-sequencing was done for H3K27, RAD21 and CTCF. In total, the data set includes 120 samples.

2022-06-24 | E-MTAB-10849 | biostudies-arrayexpress

ChIP-seq for CTCF and Rad21 in Rag1M-bM-^HM-^R/M-bM-^HM-^R pro-B cells

Project description:Genome-wide ChIP data of CTCF and Rad21 binding in Rag1M-bM-^HM-^R/M-bM-^HM-^R pro-B cells CTCF and Rad21 binding in Rag1M-bM-^HM-^R/M-bM-^HM-^R pro-B

2011-06-07 | E-GEOD-26257 | biostudies-arrayexpress

Genomic localization of Topoisomerase II beta

Project description:ChIP-seq of Top2b, CTCF, Rad21, H3K4me2, H3K36me3 in mouse liver. ChIP-exo of CTCF, Rad21 and Top2b

2016-08-05 | E-MTAB-3587 | biostudies-arrayexpress

ChIP-seq of CTCF, RAD21, and TOP2B binding sites in three human tissue samples with hepatocellular carcinoma

Project description:The roles of topoisomerases in somatic mutagenesis in cancer are poorly understood and their DNA-binding landscape remains largely unmapped. Here we generated genome-wide DNA-binding maps of TOP2B, CTCF, and RAD21 in human hepatocellular carcinoma samples.

2024-02-01 | E-MTAB-13301 | biostudies-arrayexpress

Cohesin regulates gene expression through spatial clustering of enhancer elements

Project description:H3K27Ac ChIP-seq in wild type and cohesin-deficient thymocytes Rad21 was deleted in CD4+ CD8+ double positive (DP) thymocytes by crossing a Rad21 floxed allele with a Cd4-driven Cre transgene. DP positive thymocytes were FACS-sorted from control and Rad21-/- littermates, which were then used to perform chromatin immunoprecipitation for histone H3 acetylated on lysine 27 (H3K27Ac).

2015-02-12 | E-GEOD-61428 | biostudies-arrayexpress

Histone modification and transcription factor ChIPseq of Xenopus laevis epithelial progenitors

Project description:To determine the positions of promoters and enhancers in developing Xenopus laevis epithelial progenitors, we performed ChIPseq on the histone modifications H3K4me3 and H3K27ac. We also performed ChIPseq on the transcription factors foxj1 (in the presence or absence of rfx2), myb (in the presence or absence of multicilin), and rad21. Some embryos were harvested as wild-types; in other experiments, we injected embryos with mRNAs encoding FLAG-foxj1 (with and without rfx2 morpholino) or GFP-myb (with and without an inducible form of multicilin (mcidas-HGR)). We then isolated epithelial progenitors surgically and, when injected with multicilin, induced at mid-stage 11. We then harvested chromatin at 9 hours after induction (roughly stage 18) and performed ChIPseq using antibodies against endogenous targets (H3K4me3, H3K27ac, rad21) or protein tags (FLAG, GFP). We then sequenced these libraries, aligned the reads to the X. laevis genome (version 9.1) with bwa mem and called peaks with HOMER, using input as background.

2016-02-23 | E-GEOD-78176 | biostudies-arrayexpress

ChIP-seq analyses of CTCF binding in liver samples from CAST/EiJ and SPRET/EiJ (Mus spretus) mice, and of the cohesin subunit RAD21 in C57BL/6J mouse liver

Project description:We explored the relationship between the evolutionary dynamics of CTCF binding and the functional stability of higher order genome structures, by performing ChIP-seq experiments in closely related Mus species or strains and intersecting with Hi-C-derived topologically associating domains (TADs) and expression data. All experiments were performed in adult male liver samples in 3 biological replicates and with an input control set. We also generated RAD21 (cohesin subunit) ChIP-seq from a replicate of adult male mouse (C57BL/6J) liver to determine localization of cohesin with respect to CTCF.

2019-11-20 | E-MTAB-8014 | biostudies-arrayexpress

Gene expression in human monocyte differentiation (3D-MO)

Project description:This dataset consists of RNA-seq data data from human monocytes, monocyte-derived dendritic cells or monocyte-derived macrophages as well as monocyte-derived cells that were subjected to siRNA treatment targeting CTCF or RAD21. In total, it includes 63 samples.

2022-06-20 | E-MTAB-10844 | biostudies-arrayexpress

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