GEO DataSets

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

Organism:

Mus musculus; Homo sapiens

Type:

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

Platforms:

GPL9318 GPL4134 GPL9442

14 Samples

Download data: TXT, WIG

(Submitter supplied) Wnt signals control three functions of intestinal crypts: maintenance of Lgr5 stem cells, proliferation of transit-amplifying daughters and formation of Paneth cells. Here, we study how the Wnt effector β-catenin/Tcf4 cooperates with the Wnt-activated transcription factor Ascl2 to control a stem cell transcription program. DNA elements that are co-occupied and synergistically regulated by Ascl2 and Tcf4 specifically map to stem cell genes. more...

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9318 GPL9442

6 Samples

Download data: WIG

(Submitter supplied) Wnt signals control three functions of intestinal crypts: maintenance of Lgr5 stem cells, proliferation of transit-amplifying daughters and formation of Paneth cells. Here, we study how the Wnt effector β-catenin/Tcf4 cooperates with the Wnt-activated transcription factor Ascl2 to control a stem cell transcription program. DNA elements that are co-occupied and synergistically regulated by Ascl2 and Tcf4 specifically map to stem cell genes. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL4134

8 Samples

Download data: TXT

(Submitter supplied) The canonical Wnt pathway plays a central role in stem cell maintenance, differentiation and proliferation in the intestinal epithelium. Constitutive, aberrant activity of the TCF4/β-catenin transcriptional complex is the primary transforming factor in colorectal cancer. Despite significant recent inroads, the full complement of Wnt target genes and the mechanisms of regulation remain incompletely understood. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17303

8 Samples

Download data: TXT

(Submitter supplied) We examined mRNA level changes in two mouse enteroids clones expressing different levels of PLAGL2 from a constitutive Piggybac transposon vector.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: XLSX

(Submitter supplied) The small intestinal epithelium is the most rapidly self-renewing tissue of mammals. Proliferative cells are confined to crypts, while differentiated cell types predominantly occupy the villi. We recently demonstrated the existence of a long-lived pool of cycling stem cells defined by Lgr5 expression and intermingled with post-mitotic Paneth cells at crypt bottoms. We have now determined a gene signature for these so called Crypt Base Columnar (CBC) cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL4134

8 Samples

Download data: TXT

(Submitter supplied) The Wnt signaling pathway is deregulated in over 90% of human colorectal cancers. β Catenin, the central signal transducer of the Wnt pathway, can directly modulate gene expression by interacting with transcription factors of the TCF/LEF-family. In the present study we investigate the role of Wnt signaling in the homeostasis of intestinal epithelium using tissue-specific, inducible beta-catenin gene ablation in adult mice. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS2984

Platform:

GPL1261

4 Samples

Download data: CEL, CHP

Analysis of intestinal crypts following inactivation of beta catenin. The mucosa of the intestine is composed of submucosal invaginations called intestinal crypts. Results provide insight into the molecular mechanisms underlying crypt loss as a result of beta-catenin inactivation.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 protocol sets

Platform:

GPL1261

Series:

GSE8818

4 Samples

Download data: CEL, CHP

(Submitter supplied) The gastrointestinal epithelial crypts are clonal units with a high cell turnover, driven by a small population of long-lived, Lgr5-expressing stem cells located in the crypt base. Despite this, depletion of Lgr5+ cells does not lead to severe pathology. Instead, other cell populations, such as secretory and enterocyte precursors are able to de-differentiate, replace Lgr5+ cells, and regenerate the crypt. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL4134

4 Samples

Download data: TXT

(Submitter supplied) There is a gradient of β-catenin expression along the colonic crypt axis with the highest levels at the crypt bottom. However, it remains unclear whether different levels of canonical Wnt signaling exert distinct roles in the colonic epithelium. In the present study, we first showed that the canonical Wnt signaling is active in the proliferative compartment of normal colonic crypts by separating actively proliferating progenitor cells from non-proliferating cells in the colon using transgenic mice expressing a histone H2B-green fluorescent protein (GFP) fusion protein under the control of a tetracycline responsive regulatory element. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

4 Samples

Download data: CEL

(Submitter supplied) Mammalian intestinal epithelium stem cells (IESCs) and their daughter cells require the participation of DNA methylation and the transcription factor Sox9 for proliferation and differentiation. Combining methylated DNA immunoprecipitation with microarray hybridization, we demonstrate that hypomethylation in promoter participates in the aberrant formation of crypts in diabetic db/db mice through ectopic Wnt signaling. more...

Organism:

Mus musculus

Type:

Methylation profiling by array

Platform:

GPL21852

6 Samples

Download data: GFF, TXT, XLSX

(Submitter supplied) Gastric epithelial stem cells are responsible for constant epithelial self-renewal, which is accelerated by infection with the gastric pathogen Helicobacter pylori. However, the mechanism that regulates stem cell turnover in the stomach remains unknown. Here we show that signaling by R-spondin 3 and Wnt hierarchically organizes the stem cell compartment in the antrum, producing two Wnt-responsive populations, which are either Lgr5+ve or Axin2 +ve. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL4134

4 Samples

Download data: TXT

(Submitter supplied) Wnt signaling stimulated by R-spondin (Rspo) via binding to Lgr family members is crucial for stem cell renewal and tissue homeostasis in the gastrointestinal tract. In the stomach, Rspo is secreted by myofibroblasts and controls epithelial gland regeneration by inducing proliferation of Wnt-responsive Axin2+ cells in the isthmus of glands. Infection with Helicobacter pylori results in increased expression of stromal Rspo, leading to an expansion of Axin2+ isthmus stem cells and gland hyperplasia. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: CSV

(Submitter supplied) R-spondin (Rspo) signaling is crucial for stem cell renewal and tissue homeostasis in the gastrointestinal tract. In the stomach, Rspo is secreted from myofibroblasts and controls epithelial gland regeneration by inducing proliferation of Wnt-responsive Axin2+ cells in the isthmus of the gland. Infection with H. pylori results in increased expression of stromal Rspo, leading to an expansion of Axin2+ isthmus stem cells and gland hyperplasia. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

2 Samples

Download data: CSV, H5, TAR

(Submitter supplied) We identify arachidonic acid (AA), as a direct proliferation promoter of intestinal epithelial cells, facilitating small intestinal regeneration. In the transcriptomes, it shows that AA treatment upregulated proliferation-related genes including Wnt signaling target genes, while downregulated differentiation-related genes including enterocyte, goblet cell, Paneth cell, enteroendocrine cell, and tuft cell markers. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: TXT

(Submitter supplied) Organoid technology provides the possibility to culture human colon tissue and patient-derived colorectal cancers (CRC) while maintaining all functional and phenotypic characteristics. Labeling of human colon stem cells (CoSCs), especially in normal and benign tumor organoids, is challenging and therefore limits usability of multi-patient organoid libraries for CoSC research. Here, we developed STAR (STem cell Ascl2 Reporter), a minimal enhancer/promoter element that reports transcriptional activity of ASCL2, a master regulator of LGR5+ CoSC fate. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

18 Samples

Download data: TXT

(Submitter supplied) intestinal mesenchymal stromal cell subset specific accessible elements were analyzed using ATAC-seq Bulk RNA-seq Purpose: The goals of this study are to compare WT and Map3k2 deficient mice colon tissue transcriptome upon Naive and DSS treatment for 1 day Bulk RNA-seq Methods: Colon Tissue mRNA profiles of Naive or 2% DSS treated 16-week-old wild-type (WT) and MEKK2 knockout (Map3k2-/-) mice were generated by deep sequencing, in triplicate, using Illumina NextSeq 500. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL19057 GPL21273

21 Samples

Download data: BED, BW, MTX, RDS, TSV, XLSX

(Submitter supplied) The conserved RNA-binding protein Musashi1 (MSI1) has emerged as a key oncogenic factor in numerous solid tumors, including glioblastoma. However, its mechanism of action has not yet been established comprehensively. We set out to map its impact on the transcriptome in U251 cells using RNA-seq and iCLIP.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL10999 GPL11154

9 Samples

Download data: BED

(Submitter supplied) Functions of Ascl2 in colonic stem cell maintenance and regeneration. We used RNA-sequencing to profile gene expression in regenerating crypt cells and Ascl2-deficient colonic stem cells, and ASCL2 ChIP-seq to identify transcriptional target genes.

Organism:

Mus musculus

Type:

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

Platforms:

GPL21103 GPL19057

19 Samples

Download data: BW, MTX, TSV, TXT

(Submitter supplied) Analysis of vascular endothrial cells and lympatic endotherial cells purified from small intestines

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL21163

6 Samples

Download data: TXT