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ProteomicsCTCF ChIP-MS from crosslinked chromatin in mouse embryonic stem cells (mESCs) and motor neurons (MNs)
To identify CTCF partners and co-localizing proteins from crosslinked chromatin in mESCs and MNs in endogenous conditions. The goal is to identify proteins within each sample with respect to wild-type control for each.
ORGANISM(S): Mus musculus (Mouse) 
2022-02-15 | PXD030543 | Pride
Mouse Crosslinked chromatin Ctcf chip-ms Ctcf partners Lc-ms/ms 
GenomicsGenome-wide analysis of the role of FOG-1 in GATA-1 chromatin occupancy
We report ChIP-Seq data for GATA-1 and the FOG-binding mutant of GATA-1 (GATA-1^V205G) in G1ME cells, a Gata1-null cell line with both erythroid and megakaryocytic differentiation potential. We introduced HA-tagged GATA-1 or V205G into G1ME cells via retroviral transduction. The cells were crossli...
ORGANISM(S): Mus musculus 
2012-07-30 | E-GEOD-35644 | biostudies-arrayexpress
GenomicsChromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants (ChIP-seq)
Chromatin-based functional genomic analyses and genomewide association studies (GWASs) together implicate enhancers as critical elements influencing gene expression and risk for common diseases. Here, we performed systematic chromatin and transcriptome pro- filing in human pancreatic islets. Integra...
ORGANISM(S): Homo sapiens 
2013-11-08 | E-GEOD-51311 | biostudies-arrayexpress
ProteomicsCharacterization of chromatin associated RNA-binding proteins by SPACE
Chromatin processes such as DNA replication, transcription and RNA processing are mediated by intermolecular transactions among proteins, RNAs and the genome. Although DNA-protein and RNA-protein interactions have been studied extensively, reliable and efficient identification of chromatin-associate...
ORGANISM(S): Mus musculus (Mouse) 
2021-11-25 | PXD023903 | Pride
Proteomics Pluripotency Idr Chromatin Dazl Rbp 
TranscriptomicsThe genomic landscape of cohesin-associated chromatin interactions
Cohesin is implicated in establishing tissue-specific DNA loops that target enhancers to promoters, and also localizes to sites bound by the insulator protein CTCF, which blocks enhancer-promoter communication. However, cohesin-associated interactions have not been characterized on a genome-wide sca...
ORGANISM(S): Mus musculus 
2013-05-22 | E-GEOD-42237 | biostudies-arrayexpress
GenomicsMapping Novel Chromatin Regions Using Sono-Seq
We found that sonication of crosslinked chromatin produces breaks at non-random sites in DNA and can be used to map sites of high chromatin accessibility when combined with high-throughput tag sequencing using the GA II platform from Illumina. This technique, which we named Sono-Seq, can be a simple...
ORGANISM(S): Homo sapiens 
2008-12-18 | E-GEOD-14022 | biostudies-arrayexpress
TranscriptomicsChromatin immunopreciptitation of Drosophila DNA using antibodies against RMA polymerase II CTD repeats
Crosslinked chromatin from wild type flies was sonicated into small fragments, and used in ChIP reactions using a monoclonal antibody, 8WG16, against RNA polymerase II CTD repeats. Input material was removed prior to chIP, and a control chIP was incubated with normal rabbit IgG. The Input and IPed...
ORGANISM(S): Drosophila melanogaster 
2008-05-20 | E-MEXP-1520 | biostudies-arrayexpress
ProteomicsPRC1-CBX8 chromatin crosslinking
XL-MS to identify interaction sites of PRC1-CBX8 with chromatin
ORGANISM(S): Homo sapiens (Human) 
2024-12-30 | PXD039589 | Pride
Cbx8 Polycomb Prc1 Chromatin 
ProteomicsProteomic profiling reveals distinct phases to the restoration of chromatin following DNA replication
Chromatin organization must be maintained during cell proliferation to preserve cellular identity and genome integrity. However, DNA replication results in transient displacement of DNA bound proteins, and it is unclear how they regain access to newly replicated DNA. Using quantitative MS-based prot...
ORGANISM(S): Homo sapiens (Human) 
2023-02-02 | PXD038113 | Pride
Proteomics Lc-ms Tmt 
GenomicsThe nucleosomal barrier to promoter escape by RNA Polymerase II is overcome by the chromatin remodeler Chd1 [HiSeq]
We use a metabolic labeling strategy for directly measuring nucleosome turnover to determine the role of chromatin remodeler Chd1 on chromatin dynamics in mouse embryonic fibroblasts expressing with wildtype-Chd1 and dominant negative K510R-Chd1. We find that expression of K5 10R-Chd1 decreases nucl...
ORGANISM(S): Mus musculus 
2014-04-15 | E-GEOD-52501 | biostudies-arrayexpress
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