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TranscriptomicsZNF804A transcriptome networks in differentiating human neurons derived from induced pluripotent stem cells
The goal of this project is to study transcriptome change by knocking down ZNF804A, a schizophrenia and bipolar disorder candidate gene, in early neurons derived from iPSCs. Neural progenitor cells (NPCs) were developed from human induced pluripotent stem cells (iPSCs) and transduced by two independ...
ORGANISM(S): Homo sapiens 
2014-07-01 | E-GEOD-54112 | biostudies-arrayexpress
TranscriptomicsRNA-Seq of human neurons derived from iPS cells Reveals candidate long non-coding RNAs Involved in neurogenesis and neuropsychiatric disorders.
As a preliminary step towards applying next generation sequencing using neurons derived from patient-specific iPSCs, we have carried out an RNA-Seq analysis on control human neurons. Dramatic changes in the expression of coding genes, long non-coding RNAs (lncRNAs), pseudogenes, and splice isoforms ...
ORGANISM(S): Homo sapiens 
2011-10-06 | E-GEOD-32625 | biostudies-arrayexpress
TranscriptomicsHira-dependent histone H3.3 deposition facilitates PRC2 recruitment at developmental loci in ES cells [CATCH-IT]
Polycomb repressive complex 2 (PRC2) regulates gene expression during lineage specification through trimethylation of lysine 27 on histone H3 (H3K27me3). In Drosophila, polycomb binding sites are dynamic chromatin regions coupled to incorporation of the histone variant H3.3. Here we show in mouse em...
ORGANISM(S): Mus musculus 
2013-09-30 | E-GEOD-42153 | biostudies-arrayexpress
GenomicsHira-dependent histone H3.3 deposition facilitates PRC2 recruitment at developmental loci in ES cells [ChIP-Seq]
Polycomb repressive complex 2 (PRC2) regulates gene expression during lineage specification through trimethylation of lysine 27 on histone H3 (H3K27me3). In Drosophila, polycomb binding sites are dynamic chromatin regions coupled to incorporation of the histone variant H3.3. Here we show in mouse em...
ORGANISM(S): Mus musculus 
2013-09-30 | E-GEOD-42152 | biostudies-arrayexpress
TranscriptomicsHira-dependent histone H3.3 deposition facilitates PRC2 recruitment at developmental loci in ES cells [RNA-Seq]
Polycomb repressive complex 2 (PRC2) regulates gene expression during lineage specification through trimethylation of lysine 27 on histone H3 (H3K27me3). In Drosophila, polycomb binding sites are dynamic chromatin regions coupled to incorporation of the histone variant H3.3. Here we show in mouse em...
ORGANISM(S): Mus musculus 
2013-09-30 | E-GEOD-42154 | biostudies-arrayexpress
GenomicsIdentification of in vivo DNA-binding mechanisms of Pax6 and reconstruction of Pax6-dependent gene regulatory networks during lens and forebrain development
The transcription factor Pax6 is comprised of the paired domain (PD) and homeodomain (HD). In the developing forebrain, Pax6 is expressed in ventricular zone precursor cells and in specific subpopulations of neurons; absence of Pax6 results in disrupted cell proliferation and cell fate specification...
ORGANISM(S): Mus musculus 
2015-07-09 | E-GEOD-66961 | biostudies-arrayexpress
TranscriptomicsTranscriptome of iPSC-derived Neural Cells with Heterozygous Knockout in CHD8
CHD8, encoding Chromodomain helicase DNA binding protein 8, is a top autism spectrum disorders (ASDs) risk gene. To better understanding the molecular links between CHD8 functions and ASD, we have applied the CRISPR/Cas9 technology to knockout one copy of CHD8 in induced pluripotent stem cells (iPSC...
ORGANISM(S): Homo sapiens 
2015-11-05 | E-GEOD-71594 | biostudies-arrayexpress
GenomicsDistinct factors control histone variant H3.3 localization at specific genomic regions
The incorporation of histone H3 variants has been implicated in the epigenetic memory of cellular state. Using genome editing with zinc finger nucleases to tag endogenous H3.3, we report genome-wide profiles of H3 variants in mammalian embryonic stem (ES) cells and neuronal precursor cells. Genome-w...
ORGANISM(S): Mus musculus 
2010-03-04 | E-GEOD-16893 | biostudies-arrayexpress
GenomicsMapping of ETV1 genomic binding sites in gastrointestinal stromal tumor (GIST).
ETV1 is highly expressed in GIST and their presumed precursors--the interstitial cells of Cajal. ETV1 is required for survival for both GIST and ICC and regulates GIST signature genes. Here, using Illumina-Solexa based next-generation sequencing of ETV1 chromatin immunoprecipates (ChIP-Seq), we defi...
ORGANISM(S): Homo sapiens 
2010-10-14 | E-GEOD-22441 | biostudies-arrayexpress
GenomicsGenome-wide mapping of REST-bound sites in human CD4+ T cells
We performed ChIP-seq to identify genome-wide REST (NRSF) binding in the human CD4+ T cells. The data were compared to REST occupancy in additional 15 human cell types analyzed by the ENCODE project (GSE32465) in order to study the dynamics and context-dependent functions of REST-chromatin interacti...
ORGANISM(S): Homo sapiens 
2014-08-06 | E-GEOD-49570 | biostudies-arrayexpress
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