GEO DataSets

(Submitter supplied) Purpose: to determine cellular heterogeneity of the murine colonic epithelium and mesenchyme; Summary: We determined 16 disctinct sub-populations of colonic epithelial and mesenchymal cells. Further we found 3 distinct sub-populations of colonic PdgfraEGFP-positive fibroblasts.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

2 Samples

Download data: TXT

(Submitter supplied) 10x Chromium single cell RNA-Seq of colonic mesenchyme cell populations in health and Ulcerative Colitis in human patients and health in DSS-induced colitis in murine colon

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20301 GPL21103

10 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL20301

480 Samples

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(Submitter supplied) Intestinal health is sustained by cooperation between diverse cell types, including epithelial cells, immune cells and stromal cells. Colonic stromal cells provide critical structural support but also regulate mucosal immunity, tolerance and inflammatory responses. Although mucosal stromal cells display substantial variability and plasticity, a paucity of unique genetic markers has precluded the identification of distinct stromal populations and functions. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

192 Samples

Download data: TXT

(Submitter supplied) Intestinal health is sustained by cooperation between diverse cell types, including epithelial cells, immune cells and stromal cells. Colonic stromal cells provide critical structural support but also regulate mucosal immunity, tolerance and inflammatory responses. Although mucosal stromal cells display substantial variability and plasticity, a paucity of unique genetic markers has precluded the identification of distinct stromal populations and functions. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

192 Samples

Download data: TXT

(Submitter supplied) Intestinal health is sustained by cooperation between diverse cell types, including epithelial cells, immune cells and stromal cells. Colonic stromal cells provide critical structural support but also regulate mucosal immunity, tolerance and inflammatory responses. Although mucosal stromal cells display substantial variability and plasticity, a paucity of unique genetic markers has precluded the identification of distinct stromal populations and functions. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

96 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) The study is to define the genetic programs of human colonic cell differentiation, and to identify candidate markers for colonic stem cells and stem cell niche The study assayed the expression of 9 paired normal colon top versus crypts. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL4788 GPL4789 GPL4787

18 Samples

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(Submitter supplied) Signals from the surrounding niche drive proliferation and suppress differentiation of intestinal stem cells (ISCs) at the bottom of intestinal crypts. Among sub-epithelial support cells, deep sub-cryptal CD81+ PDGFRAlo trophocytes alone sustain ISC functions ex vivo. Here we show that mRNA and chromatin profiles of abundant CD81- PDGFRAlo stromal cells resemble those of trophocytes and that both populations provide crucial canonical Wnt ligands. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

1 Sample

Download data: MTX, TSV, TXT

(Submitter supplied) Signals from the surrounding niche drive proliferation and suppress differentiation of intestinal stem cells (ISCs) at the bottom of intestinal crypts. Among sub-epithelial support cells, deep sub-cryptal CD81+ PDGFRAlo trophocytes capably sustain ISC functions ex vivo. Here we show that mRNA and chromatin profiles of abundant CD81- PDGFRAlo mouse stromal cells resemble those of trophocytes and that both populations provide crucial canonical Wnt ligands. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL24247

33 Samples

Download data: BW, MTX, TSV

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

Organism:

Mus musculus

Type:

Expression profiling by array

Platforms:

GPL6246 GPL1261

20 Samples

Download data: CEL

(Submitter supplied) The risk for colon cancer is associated with nutrition, especially high fat and low calcium diets high in red meat. Red meat contains the iron porphyrin pigment heme, which induces cytotoxicity of the colon contents and epithelial hyperproliferation. Using a mouse model, we showed that heme caused damage to the colonic surface epithelium and induced compensatory hyperproliferation. Expression levels of heme- and stress-related genes show that heme affects surface cells and not directly crypt cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

16 Samples

Download data: CEL

(Submitter supplied) The risk for colon cancer is associated with nutrition, especially with diets high in red meat. Red meat contains the iron porphyrin pigment heme, which induces cytotoxicity of the colon contents and epithelial hyperproliferation. Using a mouse model, we showed that heme caused damage to the colonic surface epithelium and induced compensatory hyperproliferation. Expression levels of heme- and stress-related genes show that heme affects surface cells and not directly crypt cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

4 Samples

Download data: CEL

(Submitter supplied) Ihh expression is required for intestinal stem cell niche development. Loss of Ihh leads to disruption of intestinal stem cell niche, which leads to abnormal stem cell development and epithelial cell differentiation.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

6 Samples

Download data: CEL

(Submitter supplied) Wnt/b-catenin signaling supports intestinal homeostasis by regulating proliferation in the crypt. Multiple Wnts are expressed in Paneth as well as other intestinal epithelial and stromal cells. Ex vivo, Wnts secreted by Paneth cells can support intestinal stem cells when Wnt signaling is enhanced with supplemental R-Spondin 1 (RSPO1). However, in vivo, the source of Wnts in the stem cell niche is less clear. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11017

18 Samples

Download data: TXT

(Submitter supplied) The intestinal epithelium requires trophic factors and signaling gradients to maintain proper positioning of Intestinal Stem Cells (ISC) and proper differentiation of ISCs. Because the underlying mesenchyme is composed of numerous cell types, we utilized both transgenic and antibody methods to isolate specific mesenchymal populations including GFP-hi and GFP-lo cells from the murine transgenic PDGFRAH2BEGFP mouse (Jackson, #007669), endothelial and lymphatic endothelial cells via antibody for CD31+LYVE1- and CD31+LYVE1+, respectively. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19057 GPL21103

11 Samples

Download data: CSV, MTX, TSV

(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) Intestinal stem cells are sequestered into crypts generated during postnatal development in mice. During this timeframe, we investigated the transition of the surrounding mesenchymal niche. Using single cell RNA sequencing, we generated transcriptomic libraries from a combination of whole tissue and transgenically labeled fractions, including GFP+ fractions from PdgfraH2BEGFP and GFP-tDt+ fractions from PdgfraH2BEGFP;Myh11CreERT2;Rosa26tDt+ mice, of the intestinal mesenchyme at varying postnatal and adult stages. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

15 Samples

Download data: ZIP

(Submitter supplied) Differential GRO-Seq and ChIP-Seq (H3K27me3) was performed on mouse mini-gut model cells.

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

10 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL15520 GPL18573

31 Samples

Download data: TAR