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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
TranscriptomicsThe transcription factor CDX2 maintains active enhancer in intestinal villus cells in vivo (expression data)
We established whether partner transcription factor binding, chromatin structure, or gene expression is compromised upon loss of partner factors cdx2 or hnf4a in mouse intestinal villi This metadata file describes the gene expression componant of that data Intestinal epithelia were collected from mo...
ORGANISM(S): Mus musculus 
2013-02-05 | E-GEOD-34567 | biostudies-arrayexpress
TranscriptomicsTCF4 and CDX2, major transcription factors for intestinal function, converge on the same cis-regulatory regions
Surprisingly few pathways signal between cells, raising questions about mechanisms for tissue-specific responses. In particular, Wnt ligands signal in many mammalian tissues, including the intestinal epithelium, where constitutive signaling causes cancer. Genome-wide analysis of DNA cis-regulatory r...
ORGANISM(S): Homo sapiens 
2010-08-11 | E-GEOD-22572 | biostudies-arrayexpress
GenomicsHistone methylation and transcription factor binding during intestinal cell differentation
Cell differentiation requires epigenetic modulation of tissue-specific genes and activities of master transcriptional regulators, which are recognized for their dominant control over cellular programs. Using novel epigenomic methods, we characterized enhancer elements specifically modified in differ...
ORGANISM(S): Mus musculus 
2010-11-17 | E-GEOD-23436 | biostudies-arrayexpress
TranscriptomicsGenome-wide analyses of GATA6 occupancy and functions provide insights into its oncogenic mechanisms in human gastric cancer (microarray)
To identifiy core GATA6 functions and transcriptional targets in human gastric cancer, including additional subservient transcriptional regulators via integrative analysis of GATA6 transcription factor occupancy, gene dependency, and tumor synexpression. This study used Affymetrix U133A 2.0 gene chi...
ORGANISM(S): Homo sapiens 
2013-12-02 | E-GEOD-43196 | biostudies-arrayexpress
TranscriptomicsSOX15 governs a transcriptional program in human esophageal stratified epithelium and in a subset of esophageal adenocarcinomas
We identified spatially restricted transcription factors and found SOX15 expression confined to stratified esophageal epithelium, with attenuation in Barrett's esophagus. SOX15 binds esophagus-specific loci and its loss in human esophageal cells affected esophagus-specific transcripts [RNA-Seq] Tota...
ORGANISM(S): Homo sapiens 
2015-11-09 | E-GEOD-62909 | biostudies-arrayexpress
TranscriptomicsDistinct processes and transcriptional targets underlie CDX2 requirements in intestinal stem cells and differentiated villus cells
To define target genes of the intestine-restricted transcription factor (TF) CDX2 in intestinal stem cells, we performed chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq). We used RNA-sequencing to profile gene expression changes during cell differentiation from mouse ...
ORGANISM(S): Mus musculus 
2015-09-15 | E-GEOD-70766 | biostudies-arrayexpress
TranscriptomicsExpression data from mouse proximal intestinal epithelial Lgr5(hi) stem cells and differentiated villus cells (enterocytes from Atoh1 conditional knockout)
We used microarrays to detail the differentail gene expression between intestinal Lgr5(hi) stem cells and differentiated cells Assay the differential gene expression using total RNA from flow cytometry sorted Lgr5(hi) cells and EDTA isolated enterocytes from Atoh1 conditional knockout
ORGANISM(S): Mus musculus 
2012-10-13 | E-GEOD-41541 | biostudies-arrayexpress
TranscriptomicsGene expression in intestinal epithelial crypt and villus cell populations
We analyzed gene expression profiles in isolated mouse LGR5+ intestinal stem cells, lineage-specific enterocyte and secretory progenitors, and terminally differentiated villus enterocytes. Gene Ontology analyses of cell type-specific transcripts indicated their expected biological functions. We hybr...
ORGANISM(S): Mus musculus 
2014-01-06 | E-GEOD-51398 | biostudies-arrayexpress
TranscriptomicsEngineered stomach tissue as a renewable source of functional beta-cells for blood glucose regulation
The gastrointestinal (GI) epithelium is a highly regenerative tissue with the potential to provide a renewable source of insulin+ cells using cellular reprogramming. Here, we describe the antral stomach as a previously unrecognized source highly amenable to conversion into functional insulin-secret...
ORGANISM(S): Mus musculus 
2016-01-09 | E-GEOD-76686 | biostudies-arrayexpress
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