Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ChIP-seq of NCoR1 in CD8α+ DCs at 6hr of stimulation

ABSTRACT: ChIP-seq of NCoR1 was performed to identify binding sites of NCoR1 in TLR dependent manner. MutuDC1940 cell line were treated with TLR3 ligand poly(I:C) and combined stimulation of TLR9 (CpG-B), TLR3, and IFNg for 6hr.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Mus musculus

SUBMITTER: Sunil Kumar Raghav

PROVIDER: E-MTAB-10991 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

NCoR1, SMRT, Polymerase II and input ChIP-Seq

Project description:ChIP-seq of mouse embryonic fibroblast-adipose like cell line 3T3-L1 to identify binding sites of NCoR1 and SMRT following induction of differentiation, and RNA Pol-II after SMRT knock down

2012-04-23 | E-MTAB-1031 | biostudies-arrayexpress

Cell stage dependent transcriptional response to leukaemic oncogene expression

Project description:Acute myeloid leukemia (AML) is characterized by a block in myeloid differentiation the stage of which is dependent on the nature of the transforming oncogene and the developmental stage of the oncogenic hit. This is also true for the t(8;21) translocation which gives rise to the RUNX1/ETO fusion protein and initiates the most common form of human AML. To understand the molecular principles governing this differential action, we used the differentiation of mouse embryonic stem cells expressing an inducible RUNX1/ETO protein into blood cells as a traceable model combined with genome-wide analyses of transcription factor binding and gene expression. We found that RUNX1/ETO interferes with both the activating and repressive function of its normal counterpart, RUNX1, at early and late stages of blood cell development. However, the response of the transcriptional network to RUNX1/ETO expression is stage-specific, highlighting the molecular mechanisms determining specific target cell expansion after an oncogenic hit. High throughput sequencing data have been used to study RUNX1/ETO role in hematopoietic system

2015-08-26 | E-GEOD-64589 | biostudies-arrayexpress

ChIP-seq of SMRT in CD8α+ DCs at 0hr and 6hr CpG stimulation

Project description:SMRT ChIP-seq were performed to identify binding site of SMRT in CD8α+ DCs at 0hr and 6hr CpG stimulation.

2022-09-20 | E-MTAB-10069 | biostudies-arrayexpress

A crucial role of the ubiquitously expressed transcription factor Sp1 at early stages of hematopoietic specification [ChIP-Seq]

Project description:Mammalian development is regulated by the interplay of tissue-specific and ubiquitously expressed transcription factors, such as Sp1. Sp1 knock-out mice die in utero with multiple phenotypic aberrations, but the underlying molecular mechanism of this differentiation failure has been elusive. Here we used conditional knock-out mice as well as the differentiation of mouse ES cells as a model to address this issue. To this end we examined differentiation potential, global gene expression patterns and Sp1 target regions in Sp1 wild-type and deficient cells representing different stages of hematopoiesis. Sp1-/- cells progress through most embryonic stages of blood cell development but cannot complete terminal differentiation. For most Sp1 target and non-target genes, gene expression is unaffected by Sp1 inactivation. However, Cdx and multiple Hox genes are stage-specific targets of Sp1 and are down-regulated at an early stage. As a consequence, expression of genes involved in hematopoietic specification are progressively deregulated, highlighting the regulatory hierarchy of hematopoietic specification. Our work demonstrates that the early absence of active Sp1 sets a cascade in motion that culminates in a failure of terminal hematopoietic differentiation and emphasizes the role of ubiquitously expressed transcription factors for tissue-specific gene regulation. Two ChIP-Seq data from Sp1 transcription factor obtained from FLK+ and progenitor cells

2014-06-12 | E-GEOD-52496 | biostudies-arrayexpress

An anti-silencer- and SATB1-dependent chromatin hub regulates Rag1 and Rag2 gene expression during thymocyte development

Project description:Rag1 and Rag2 gene expression in CD4+CD8+ double positive (DP) thymocytes depends on the activity of a distant anti-silencer element (ASE) that counteracts the activity of an intergenic silencer. However, the mechanistic basis for ASE activity is unknown. Here we show that the ASE physically interacts with the distant Rag1 and Rag2 gene promoters in DP thymocytes, bringing the two promoters together to form an active chromatin hub. Moreover, we show that the ASE functions as a classical enhancer that can potently activate these promoters in the absence of the silencer or other locus elements. In thymocytes lacking the chromatin organizer SATB1, we identified a partial defect in Tcra gene rearrangement that was associated with reduced expression of Rag1 and Rag2 at the DP stage. SATB1 binds to the ASE and Rag promoters, facilitating inclusion of Rag2 in the chromatin hub and the loading of RNA polymerase II to both the Rag1 and Rag2 promoters. Our results provide a novel framework for understanding ASE function and demonstrate a novel role for SATB1 as a regulator of Rag locus organization and gene expression in DP thymocytes. Sequencing of Satb1-ChIP and input control from 6 wk old thymus

2015-02-25 | E-GEOD-66248 | biostudies-arrayexpress

ChIP-seq of H3K27ac in Control and NCoR1 KD CD8α+ DCs at 0hr, 2hr and 6hr of TLR stimulation

Project description:H3K27ac ChIP-seq was performed to identify active enhancers in different TLR activated control CD8α+ DCs as well as to understand the role of NCoR1 in regulating TLR specific enhacner activity using H3K27ac ChIP-seq performed in NCoR1 KD DCs. MutuDC1940 cell line were treated with TLR3 ligand poly I:C, TLR9 ligand CpG-B and combined stimulation of TLR9 , TLR3, and IFNg for 2hr and 6hr. Recombinant Anti-Histone H3 (acetyl K27) antibody was used to pull down chromatin regions having active enhacner mark in each unstimulated and stimulated condition.

2025-12-03 | E-MTAB-10992 | biostudies-arrayexpress

Genome-wide maps in PDGFB-induced glioma

Project description:We performed genome-wide profiling of oligodendrocyte lineage transcription factor 2 (Olig2) and other histone markers in platelet-derived growth factor subunit B (PDGFB)-induced glioma and genome-occupancy analyses coupled with transcriptome profiling to reveal gene regulatory network. Examination of Olig2, H327Ac, and H3K4me3 genome-wide occupancy in PDGFB-induced Ctrl-T and Olig2cKO brain tumors (gliomas).

2016-05-17 | E-GEOD-80088 | biostudies-arrayexpress

A crucial role of the ubiquitously expressed transcription factor Sp1 at early stages of hematopoietic specification

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-06-12 | E-GEOD-52499 | biostudies-arrayexpress

Chromatin Remodeler CHD7 mutated in CHARGE Syndrome Interacts with Sox10 to Regulate Timing of CNS Myelination and Remyelination [ChIP-seq]

Project description:Mutations in CHD7, encoding ATP-dependent chromodomain-helicase-DNA-binding protein 7, in CHARGE syndrome leads to multiple congenital anomalies including growth retardation, craniofacial malformations and neurological dysfunction. Currently, mechanisms underlying the CNS phenotypes remain poorly understood. Here, we show that Chd7 is a direct transcriptional target of oligodendrogenesis-promoting factors Olig2 and Brg1 and required for proper timing of CNS myelination and remyelination. Genome-occupancy analyses coupled with transcriptome profiling reveal that Chd7 cooperates with Sox10 to target the enhancers of key myelinogenic genes, and identify novel Chd7 target. Examination of Chd7 and Sox10 genomewide occupancy in differentiating oligodendrocytes

2016-02-29 | E-GEOD-72725 | biostudies-arrayexpress

Comprehensive Epigenomic Analysis Reveals Dynamic Regulatory Programs Of Blood Development (ChIP-seq)

Project description:Embryonic hematopoiesis is regulated by the coordinated interaction between transcription factors and the epigenetic regulators driving developmental-stage specific gene expression but how this process drives hematopoietic specification and terminal differentiation is poorly understood. Here we generated RNA-Seq, DNase-Seq and ChIP-Seq data for histone marks and transcription factors from ES-cell derived purified cells representing six sequential stages of blood cell specification and differentiation. Our data reveal the binding patterns of specific transcription factors involved in the priming and maintenance of distal elements and inform how binding impacts on promoter activity. Functional studies based on these data uncovered a previously unrecognised role for Hippo signalling in mammalian hematopoietic specification. Finally, we present a dynamic core regulatory network model for hematopoiesis and demonstrate its utility for the design of reprogramming experiments. Our study represents a powerful resource for studying hematopoiesis and demonstrates how such data can advance our understanding of mammalian development. ChIP-seq data of histone modifications and transcription factors, and RNA-seq data obtained from purified cells representing five sequential stages of murine blood cell specification and differentiation

2016-02-26 | E-GEOD-69096 | 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