GEO DataSets

(Submitter supplied) Intestinal differentiation during endoderm development We used RNA-sequencing to profile gene expression changes during the embryonic development of the gastrointestinal tract.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

74 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21626 GPL21697

21 Samples

Download data: BW, TXT

(Submitter supplied) 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. more...

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by array

Platforms:

GPL9115 GPL10773

17 Samples

Download data: BED, BW, CEL, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by array

Platforms:

GPL10773 GPL11002

23 Samples

Download data: BED, CEL, TXT

(Submitter supplied) 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

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10773

12 Samples

Download data: CEL

(Submitter supplied) 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

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

11 Samples

Download data: BED, TXT

(Submitter supplied) 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 compound mutant mice compared to control mice. The compound mutant mice had a significantly worse phenotype than either single mutant, and gene expression was significantly perturbed in compound mutants compared to control mice.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

4 Samples

Download data: TXT

(Submitter supplied) HNF4 paralogs are redundantly required for proper villus elongation, differentiation and maturation in the developing gut. We find 5,391 chromatin regions become inaccessible upon HNF4 loss, and HNF4 binding sequences are most enriched in these regions. Genes nearby these 5,391 HNF4 dependent regions are associated with villus differentiation/maturation.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21626

3 Samples

Download data: BED, BW

(Submitter supplied) 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. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19057 GPL13112

11 Samples

Download data: BED, BW, GTF, TXT

(Submitter supplied) 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. more...

Organism:

Mus musculus

Type:

Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9250 GPL11044

13 Samples

Download data: BED, CEL, TXT, XLS

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

54 Samples

Download data

(Submitter supplied) Embryos originate from fertilized eggs and are shaped through continuous cell division and differentiation, accompanied by dramatic changes in transcription, translation, and metabolism. Epigenetic information and transcription factors (TFs) play indispensable roles in regulating these processes. Recently, the trophoblast regulator TFAP2C was found to be essential in initiating the earliest cell fate decisions. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

12 Samples

Download data: XLSX

(Submitter supplied) Embryos, originating from fertilized eggs, undergo continuous cell division and differentiation, accompanied by dramatic changes in transcription, translation, and metabolism. Epigenetic information and transcription factors (TFs) play indispensable roles in regulating these processes. Recently, the trophoblast regulator TFAP2C was identified as crucial in initiating early cell fate decisions. However, Tfap2c transcripts persist in both the inner cell mass (ICM) and trophectoderm (TE) of blastocysts, prompting inquiry into its function in post-lineage establishment. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

42 Samples

Download data: BW

(Submitter supplied) Transcriptional profiling of undifferentiated HIEC cells stably infected with a retroviral inducible expression vector (RevTet system) comparing DOX-induced HIEC pTetON with DOX-induced HIEC cells expressing either HNF1 and CDX2 or HNF1, CDX2 plus GATA4. Keywords: Differential gene expression

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6854

8 Samples

Download data: TAV

(Submitter supplied) The first lineage decisions during mouse development lead to establishment of embryonic and extraembryonic tissues. The transcription factor Cdx2 plays a central role by repressing pluripotency genes, such as Oct4 and promoting trophoblast fate at the blastocyst stage. Here we show that the transcription factor Gata3 is coexpressed with Cdx2 in the blastocyst and that overexpression of Gata3 in embryonic stem cells is sufficient to induce expression of trophoblast genes. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Datasets:

GDS3948 GDS3949

Platform:

GPL1261

24 Samples

Download data: CEL, CHP

(Submitter supplied) To identify whether Cdx2 or Gata3 can activate trophoblast specific gene expression when expressed in R1 ES cells. To assess the dependency of Gata3 activity on Cdx2, Gata3 was also expressed in Cdx2-null ES cells. Keywords: gene expression

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

10 Samples

Download data: CEL, CHP

(Submitter supplied) To characterized the changes in gene expression during the differentiation of TS cells. TS cells can be derived from two time point during embryogenesis, cell lines tested were from each of these time points. Keywords: time course

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

14 Samples

Download data: CEL, CHP

Analysis of R1 embryonic stem (ES) cells overexpressing transcription factor Cdx2 or Gata3 and cultured under trophoblast stem (TS) cell derivation conditions. Gata3-expressing Cdx2-null ES cells also examined. Results provide insight into the roles of Gata3 and Cdx2 in trophoblast development.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 genotype/variation, 3 protocol sets

Platform:

GPL1261

Series:

GSE12999

10 Samples

Download data: CEL, CHP

Analysis of trophoblast stem (TS) cell lines TS3.5 and TS6.5 derived from 2 time points during embryogenesis (from blastocyst and E6.5 embryos, respectively) and differentiated over 6 days. Results provide insight into the molecular basis of trophoblast development.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 cell line, 2 protocol, 7 time sets

Platform:

GPL1261

Series:

GSE12999

14 Samples

Download data: CEL, CHP

(Submitter supplied) Stomach and intestinal adult epithelia harbor stem cells that are responsible for their continuous regeneration. Stomach and intestinal stem cells differ in their differentiation program and in the gene repertoire that they express. We show that single adult Lgr5-positive stem cells, isolated from 3D cultured small intestinal organoids, require Cdx2 to maintain their intestinal identity and are converted cell-autonomously into stomach-pyloric stem cells in the absence of this transcription factor.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

16 Samples

Download data: TXT