Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA132465 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description: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 compromised. Lethality was accelerated in mice lacking both Cdx2 and its homolog Cdx1, with exaggeration of defects in crypt cell replication and enterocyte differentiation. Cdx2 occupancy correlated with hundreds of transcripts that fell but not with equal numbers that rose with Cdx loss, indicating a predominantly activating role at intestinal cis-regulatory regions. Integrated consideration of a mutant phenotype and cistrome hence reveals the continued and distinct requirement in adults of a master developmental regulator that activates tissue-specific genes. Cdx2 ChIP-seq in mouse villus, and gene expression data from Cdx1, Cdx2 and compound knockout mouse intestine
2011-04-13 | E-GEOD-24633 | biostudies-arrayexpress
Project description: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 intestinal stem cells to mature villus cells, as well as genes perturbed in intestinal stem cells upon loss of Cdx2. We find thousands of genes that change in expression during cell differentiation, including known stem cell and mature markers. Upon loss of Cdx2, hundreds of genes are up and down-regulated in intestinal stem cells, some of which are also bound by CDX2 nearby and constitute candidate direct target genes. CDX2 ChIP-Seq analysis of isolated mouse intestinal stem cells. RNA seq analysis of control mouse villus cells, control intestinal stem cells and Cdx2-deleted intestinal stem cells.
2015-09-15 | E-GEOD-70766 | biostudies-arrayexpress
Project description:We report differentially expressed genes due to Cdx loss in mouse large intestinal tissue using RNA-seq. We report Cdx2 binding sites and chromatin accessibilty for target genes occupied by Cdx2 in mouse large intestinal tissue using ChIP-seq and ATAC-seq.
2023-04-25 | GSE185334 | GEO
Project description: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 compromised. Lethality was accelerated in mice lacking both Cdx2 and its homolog Cdx1, with exaggeration of defects in crypt cell replication and enterocyte differentiation. Cdx2 occupancy correlated with hundreds of transcripts that fell but not with equal numbers that rose with Cdx loss, indicating a predominantly activating role at intestinal cis-regulatory regions. Integrated consideration of a mutant phenotype and cistrome hence reveals the continued and distinct requirement in adults of a master developmental regulator that activates tissue-specific genes.
2011-04-13 | GSE24633 | GEO
Project description: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 intestinal stem cells to mature villus cells, as well as genes perturbed in intestinal stem cells upon loss of Cdx2. We find thousands of genes that change in expression during cell differentiation, including known stem cell and mature markers. Upon loss of Cdx2, hundreds of genes are up and down-regulated in intestinal stem cells, some of which are also bound by CDX2 nearby and constitute candidate direct target genes.
2015-09-15 | GSE70766 | GEO
Project description:The transcription factor CDX2 maintains active enhancer in intestinal villus cells in vivo (expression data)
| PRJNA156203 | ENA
Project description:We used microarrays to identify the gene expression accompanied with growth arrest caused by the transduction of CDX1 or CDX2. Ectopic expression of CDXs causes intestinal metaplasia, which is thought to be precancerous legion of gastric cancer. On the contrary, there were some studies reported that CDX2 positive gastric cancers showed better prognosis or tumor suppressive activity. To evaluate the effect of exogenous CDX expression in gastric cancer cells, we transducted CDX1 or CDX2 in two CDX negative expression cell lines, MKN7 and TMK1.
2020-11-27 | GSE107433 | GEO
Project description:Important lineage regulators, such as the intestinal lineage regulator CDX2, can function over the timespan of intestinal development. The consequences of CDX2 knockout in the embryo versus in the adult are quite distinct. The data below provide a rationale for these divergent transcription factor functions in distinct developmental contexts, with unique binding patterns of CDX2 observed via ChIP-seq and unique gene regulatory targets defined via RNA-seq. The dynamic gene regulatory program controlled by CDX2 is conserved in mice and humans.
2019-02-18 | GSE115314 | GEO
Project description: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 differentiating intestinal epithelial cells and found enrichment of transcription factor-binding motifs corresponding to CDX2, a master regulator of the intestine. Directed investigation revealed surprising lability in CDX2 occupancy of the genome, with redistribution from hundreds of sites occupied only in progenitors to thousands of new sites in mature cells. Knockout mice confirmed distinct Cdx2 requirements in dividing and differentiated adult intestinal cells, including responsibility for the active enhancer configuration associated with maturity. Dynamic CDX2 occupancy corresponds with condition-specific gene expression and, importantly, to differential co-occupancy with other tissue-restricted transcription factors: HNF4A in mature cells and GATA6 in progenitors. These results reveal dynamic, context-specific functions and mechanisms of a master transcription factor within a cell lineage. H3K4me2, CDX2, GATA6, and HNF4A ChIP-seq patterns were mapped in proliferating and 26 day post-confluent (differentatied) Caco-2 intestinal cell lines and compared to published expression data or newly generated Cdx2 knockout mouse intestine expression data
2010-11-17 | E-GEOD-23436 | biostudies-arrayexpress