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GenomicsEpigenetic and transcriptional control in hematopoietic development and lineage differentiation
Hematopoiesis is a well-established model system to study molecular mechanisms of lineage-specific differentiation. Key transcription factors (TFs), such as PU.1, NF-E2 and GATA1 are implicated in crucial aspects of distinct hematopoietic lineages. How TFs collaborate with histone modificatons and h...
ORGANISM(S): Mus musculus 
2014-07-28 | E-GEOD-42110 | biostudies-arrayexpress
GenomicsDiscrete Roles of STAT4 and STAT6 Transcription Factors in Tuning Epigenetic Modifications and Transcription during Helper T Cell Differentiation (ChIP-Seq)
Signal transducer and activator of transcription 4 (STAT4) and STAT6 are key factors in the specification of helper T cells; however, their direct roles in driving differentiation are not well understood. Using chromatin immunoprecipitation and massive parallel sequencing, we quantitated the full c...
ORGANISM(S): Mus musculus 
2010-06-18 | E-GEOD-22104 | biostudies-arrayexpress
GenomicsNOTCH1/RBPJ complexes drive target gene expression through dynamic interactions with super-enhancers
The main oncogenic driver in T-lymphoblastic leukemia (T-LL) is NOTCH1, which activates genes by forming chromatin-associated Notch transcription complexes. Gamma-secretase (GSI) inhibitor treatment prevents NOTCH1 nuclear localization, but most genes with NOTCH1 binding sites are insensitive to GSI...
ORGANISM(S): Homo sapiens 
2013-12-27 | E-GEOD-51800 | biostudies-arrayexpress
GenomicsChromatin architecture organized by histone variants H3.3 and H2A.Z in the human genome
To understand how chromatin structure is organized by different histone variants, we have measured the genome-wide distribution of nucleosome core particles (NCPs) containing the histone variants H3.3 and H2A.Z in human cells. We find that a special class of NCPs containing both variants is enriched...
ORGANISM(S): Homo sapiens 
2009-07-26 | E-GEOD-13308 | biostudies-arrayexpress
GenomicsGenome-wide mapping of HATs and HDACs in human CD4+ T cells
Histone acetyltransferases (HATs) and deacetylases (HDACs) function antagonistically to control histone acetylation. As acetylation is a histone mark for active transcription, HATs have been associated with active and HDACs with inactive genes. We describe here genome-wide mapping of HATs and HDACs ...
ORGANISM(S): Homo sapiens 
2009-08-20 | E-GEOD-15735 | biostudies-arrayexpress
GenomicsGenome-wide Definition of Promoter and Enhancer Usage During Neural Induction of Human Embryonic Stem Cells [ChIP-seq]
Genome-wide mapping of transcriptional regulatory elements are essential tools for the understanding of the molecular events orchestrating self-renewal, commitment and differentiation of stem cells. We combined high-throughput identification of nascent, Pol-II-transcribed RNAs by Cap Analysis of Gen...
ORGANISM(S): Homo sapiens 
2015-05-21 | E-GEOD-61265 | biostudies-arrayexpress
GenomicsChromatin Signatures in Multipotent Human HSCs Indicate the Fate of Bivalent Genes during Differentiation
Histone modifications have been implicated in stem cell maintenance and differentiation. We have analyzed genome-wide changes in gene expression and histone modifications during differentiation of multipotent human primary hematopoietic stem cells/progenitor cells (HSCs/HPCs) into erythrocyte precur...
ORGANISM(S): Homo sapiens 
2009-01-09 | E-GEOD-12646 | biostudies-arrayexpress
TranscriptomicsDiscovery of biomarkers predictive of GSI response in triple negative breast cancer and adenoid cystic carcinoma
Next generation sequencing was used to identify Notch mutations in a large collection of diverse solid tumors. NOTCH1 and NOTCH2 rearrangements leading to constitutive receptor activation were confined to triple negative breast cancers (TNBC, 6 of 66 tumors). TNBC cell lines with NOTCH1 rearrangemen...
ORGANISM(S): Homo sapiens 
2014-08-14 | E-GEOD-59810 | biostudies-arrayexpress
TranscriptomicsHistone methylations and gene expression in naïve, central (TCM) and effector (TEM) memory CD8 T cells.
Histone methylations play a major role in regulating the chromatin state and gene expression, yet little is known about their involvement in differential gene expression and function of memory CD8 T cells. Here, we report a genome-wide analysis of two histone H3 methylations (H3K4me3 and H3K27me3) ...
ORGANISM(S): Homo sapiens 
2009-03-06 | E-GEOD-14422 | biostudies-arrayexpress
GenomicsGenome-wide Analysis of Histone Methylations in Memory CD8+ T Cells
Histone methylations play a major role in regulating the chromatin state and gene expression, yet little is known about their involvement in differential gene expression and function of memory CD8 T cells. Here, we report a genome-wide analysis of two histone H3 methylations (H3K4me3 and H3K27me3) ...
ORGANISM(S): Homo sapiens 
2009-06-12 | E-GEOD-12616 | biostudies-arrayexpress
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