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TranscriptomicsExpression data from TOP-GFP sorted colon cancer cells
Colon cancers typically contain tumor cell populations with differential WNT signaling activity. Colon cancer cells with high WNT-activity have been attributed increase tumorigenic potential and stem cell characteristics. We extracted tumor cells with differential WNT activity using fluorescent repo...
ORGANISM(S): Homo sapiens 
2012-02-16 | E-GEOD-32408 | biostudies-arrayexpress
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
TranscriptomicsCdx2 transcription factor binding in intestinal villus and gene expression profiling in Cdx mutant mice
We conditionally inactivated mouse Cdx2, a dominant regulator of intestinal development, and mapped its genome occupancy in adult intestinal villi. Although homeotic transformation, observed in Cdx2-null embryos, was absent in mutant adults, gene expression and cell morphology were vitally compromis...
ORGANISM(S): Mus musculus 
2011-04-13 | E-GEOD-24633 | 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
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
GenomicsThe transcription factor CDX2 maintains active enhancer in intestinal villus cells in vivo (ChIP-seq 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 ChIP-seq componant of that data Intestinal epithelia were collected from mouse je...
ORGANISM(S): Mus musculus 
2013-02-05 | E-GEOD-34566 | 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
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
GenomicsAnalyses of the chromatin and transcriptional basis for lateral inhibition in isolated intestinal epithelial cells.
We analyzed chromatin modifications, DNaseI-hypersensitive sites, and occupancy of a key secretory-lineage transcription factor, ATOH1. We found that lateral inhibition in the intestine occurs through ATOH1 exerting direct control within a broadly permissive chromatin state that is established in st...
ORGANISM(S): Mus musculus 
2014-01-06 | E-GEOD-51458 | biostudies-arrayexpress
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