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TranscriptomicsThe transcription factor CDX2 maintains active enhancer in intestinal villus cells in vivo
This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
ORGANISM(S): Mus musculus 
2013-02-05 | E-GEOD-34568 | 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
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
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
TranscriptomicsTranscription Factors GATA4 and HNF4A Control Distinct Aspects of Intestinal Homeostasis in Conjunction With the Transcription Factor CDX2
To determine whether the intestine-restricted transcription factor (TF) CDX2 functionally interacts with the endoderm-wide TF HNF4A, we crossed tissue-specific conditional Cdx2 and Hnf4a knockout mice to generate compound mutant mice. We used RNA-sequencing to profile gene expression changes in comp...
ORGANISM(S): Mus musculus 
2014-12-08 | E-GEOD-62633 | biostudies-arrayexpress
TranscriptomicsscRNA-seq of intestinal epithelial organoids derived from human fetal duodenum
Here, we used single-cell RNA-sequencing (scRNA-seq) to profile intestinal epithelial only organoids (also known as enteroids) from human fetal duodenum after one passage of in vitro growth. Organoids were grown in the standard 25% LWRN media with either 100 ng/ml of EGF or 1 ng/ml of EREG added.
ORGANISM(S): Homo sapiens 
2022-07-17 | E-MTAB-11912 | biostudies-arrayexpress
UnknownReactive oxygen species stimulate Paneth cell plasticity and diminish antimicrobial function
Not available
S-SCDT-10_1038-S44318-026-00869-Y | biostudies-other
TranscriptomicsMultiomic (Joint snRNA/snATAC) sequencing data of intestinal crypts and epithelial only organoids derived from human fetal duodenum
Here, we used joint single-nuclei RNA-sequencing (snRNA-seq) and single-nuclei ATAC sequencing (scATAC) to profile freshly isolated crypts from the human fetal intestine and matched intestinal epithelial only organoids (also known as enteroids) derived from these crypts after one passage of in vitro...
ORGANISM(S): Homo sapiens 
2022-07-16 | E-MTAB-11908 | biostudies-arrayexpress
UnknownRAB11A and RAB11B control mitotic spindle function in intestinal epithelial progenitor cells of mice
Not available
S-SCDT-10_15252-EMBR_202256240 | biostudies-other
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