Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chromatin profiling by ChIP-seq

ABSTRACT: Chromatin immunoprecipitation analysis of RNAP density and associated histone mark H3K36me3 at introns and exons.

ORGANISM(S): Homo sapiens

SUBMITTER: Tae Hoon Kim

PROVIDER: E-MTAB-744 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Distribution of insulator proteins CP190, dCTCF, Su(Hw) and Mod(mdg4)2.2 in Drosophila S2 cells in the presence or absence of dPARP inhibitor 3AB

Project description:We mapped the localization of insulator proteins in Drosophila S2 cells in the presence or absence of 12mM of 3AB. We found that inhibition of PARylation affects DNA binding of insulator proteins only at a small subsets of genomic sites. Examination of genomic occupancy for insulator proteins in S2 cells with or without 3AB inhibition.

2013-09-15 | E-GEOD-41354 | biostudies-arrayexpress

Transcription elongation analysis by GRO-seq

Project description:Global nuclear run-on sequencing analysis was performed to determine transcription elongation rates across the genome of three human cell lines.

2013-01-10 | E-MTAB-742 | biostudies-arrayexpress

Time course ChIP-seq analysis of the human GM12878 lymphoblasts upon Sendai Virus infection

Project description:Time course ChIP-seqwas performed to determine global changes in histone H3 lysine 27 acetylation (H3K27Ac) at enhancers upon Sendai Virus infection.

2018-10-07 | E-MTAB-6050 | biostudies-arrayexpress

Histone deacetylases positively regulate transcription through the elongation machinery

Project description:Chromatin immunoprecipitation sequencing (ChIP-seq) analysis of elongation factors in breast cancer cells upon HDAC inhibition.

2015-10-20 | E-MTAB-3631 | biostudies-arrayexpress

IMR90_SeV

Project description:Global run-on sequencing analysis of human fetal lung fibroblasts uninfected and infected with Sendai virus for 6 hour was performed to define key transcriptional changes that were induced upon infection at 6 hour time point.

2014-10-28 | E-MTAB-2233 | biostudies-arrayexpress

CTCF loss has limited effects on genome architecture in Drosophila despite critical regulatory functions.

Project description:Proteins co-purifying with recombinantly purified and N-terminally GFP-3C-tagged CTCF N-terminus (amino acids 1-293) produced in bacteria were identified by incubating the tagged bait with soluble nuclear protein extracts from 0-12h hour-old wildtype (OregonR strain) Drosophila melanogaster embryos.

2021-01-18 | PXD019487 | Pride

The RNA-binding protein Rumpelstiltskin antagonizes gypsy chromatin insulator function in a tissue-specific manner

Project description:Chromatin insulators are DNA-protein complexes situated throughout the genome that contribute to higher order organization and demarcation into distinct transcriptional domains. Mounting evidence in different species implicates RNA and RNA-binding proteins as regulators of chromatin insulator activities. Here we identify the Drosophila hnRNP M homolog Rumpelstiltskin (Rump) as an antagonist of gypsy chromatin insulator enhancer-blocking and barrier activities. Despite ubiquitous expression of Rump, improvement of barrier activity is detected only in tissue outside of the central nervous system (CNS) when Rump levels are reduced. Furthermore, rump mutants restore insulator complex localization in an otherwise compromised genetic background only in non-CNS tissues. Rump associates physically with core gypsy insulator proteins, and ChIP-Seq analysis of Rump demonstrates extensive colocalization with a subset of gypsy insulator sites across the genome. The genome-wide binding profile and tissue-specificity of Rump contrast with that of Shep, a recently identified RNA-binding protein that antagonizes gypsy insulator activity exclusively in the CNS. Our findings indicate parallel roles for RNA-binding proteins in mediating tissue-specific regulation of chromatin insulator activity. ChIP-seq of Rump, Mod(mdg4)2.2, Shep, Su(Hw), and CP190 in Drosophila Kc167 cells

2014-04-18 | E-GEOD-51462 | biostudies-arrayexpress

Pervasive Roles of Ubiquitination in Orchestrating the Deubiquitinase Activity and Function of the BAP1/ASXL2 Tumor Suppressor Complex

Project description:The tumor suppressor and deubiquitinase (DUB) BAP1 regulates chromatin-associated processes and is frequently mutated in various malignancies. BAP1 and its drosophila orthologue Calypso assemble DUB complexes with ASXL-1, -2, -3 paralogues and ASX respectively, and these cofactors are required for stimulating their DUB activity. However how the DUB activity of BAP1 is regulated remains largely unknown. Here we show that BAP1 promotes monoubiquitination of ASXLs on the ASXM/DEUBAD domain. ASXL2 monoubiquitination promotes its stability or proteasomal degradation, stimulates BAP1 DUB activity and is required for mammalian cell proliferation. Monoubiquitination of ASXL2 is directly catalyzed by UBE2E family of ubiquitin conjugating enzymes and is regulated by deubiquitination. Monoubiquitination of ASX is regulated by Calypso and is required for drosophila development. We further revealed a switch mechanism that tightly regulate BAP1 function, as a monoubiquitination of BAP1 UCH domain is mutually exclusive with ASXL2 monoubiquitination, thus ensuring highly coordinated DUB-mediated signaling.

2018-09-28 | PXD011124 | Pride

ChIP-chip of RNA Polymerase (RNAP) and RpoD in Salmonella enterica serovar Typhimurium strain SL1344

Project description:ChIP-on-chip analysis of RNAP and RpoD binding to the Salmonella enterica serovar Typhimurium chromosome demonstrated a high degree of overlap between RNAP and RpoD binding and provided us with important insights into the global distribution of these factors. Furthermore this data was correlated with information on the location of 1873 transcription start sites identified by RNA-Seq technology, thereby providing a detailed transcriptional map of Salmonella Typhimurium. Analysis of RNAP, RNAP-Rifampicin and and RpoD binding in Luria Broth (LB)

2012-02-16 | E-GEOD-35827 | biostudies-arrayexpress

Histone deacetylases positively regulate transcription through the elongation machinery

Project description:Global run-on sequencing (GRO-seq) analysis of breast cancer cells upon perturbations of transcription elongation regulators.

2015-10-20 | E-MTAB-3626 | biostudies-arrayexpress