GEO DataSets

(Submitter supplied) Using single-cell RNA-seq of intestinal epithelial cells we identify surprising expression of MHC class II, which participates in a novel interaction between gut-resident CD4+ T cells and epithelial stem cells, governing the balance between stem cell differentiation and renewal.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

810 Samples

Download data: MTX, TSV, TXT

(Submitter supplied) We report the transcriptomic alterations of Lgr5-eGFP+ intestinal stem cells upon Wnt and R-spondin gain-of-function and loss-of-function in vivo

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

14 Samples

Download data: MTX, TSV

(Submitter supplied) sorted Lgr5-eGFP+ cells under conditions of in vivo Rspo manipulation in reporter mice,

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

10 Samples

Download data: XLSX

(Submitter supplied) Purpose: Transcriptomic exploration for the identification of genes induced upon TGR5 stimulation in intestinal stem cells Methods: For each biological replicate, GFPhi cells were isolated by FACS from intestines from 4 pooled Lgr5-eGFP-IRES-CreERT2 mice. About 200.000 GFPhi cells were then embedded in Matrigel (20.000 per well in 10µL Matrigel drop) and after 4 hours were treated with INT-777 (30µM) or DMSO as control. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23479

6 Samples

Download data: TAB

(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

Platforms:

GPL21273 GPL17021

11 Samples

Download data: TXT

(Submitter supplied) Intestinal stem cells are required for proliferation, differentiation, and regeneration of the intestinal epithelium. Krüppel-like factor 5 regulates intestinal stem cells in both physiologic and pathological conditions and may be a treatment target in certain diseases of the intestine.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21273

5 Samples

Download data: BW

(Submitter supplied) The essential functions of intestinal stem cells (ISCs) are to self-renew and give rise to progenitors that subsequently differentiate to absorptive or secretory cells, thus maintaining homeostasis in the intestinal epithelium. In this study, we analyzed the transcriptomic and epigenetic changes of ISCs with Klf5 deletion to understand the role of KLF5 in ISC identity and functions.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: TXT

(Submitter supplied) Hippo signalling has been implicated as a key regulator of tissue regeneration. In the intestine, ex vivo organoid cultures model aspects of crypt epithelial regeneration. Therefore in order to uncover the Yap regulated transcriptional programs during crypt regeneration we performed RNA-sequencing of Yap wt and Yap deficient organoids, as well as organoids inducibly expressing Yap.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: TXT

(Submitter supplied) Acetylcholine (ACh) has been considered a neurotransmitter residing in central, parasympathetic and neuromuscular synapses of mammals. Here, experiments using crypt-villus organoids that lack nerve and immune cells in culture led us to suggest that endogenous ACh is synthesized in the intestinal epithelium to evoke growth and differentiation of the organoids through activation of muscarinic ACh receptors (mAChRs). more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10333

4 Samples

Download data: TXT

(Submitter supplied) In this experiment, the differential gene expression was examined in intestinal epithelial cells of Mtg16 null mice compared to wild type.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: TSV

(Submitter supplied) The intestinal epithelium is continuously renewed by a pool of intestinal stem cells expressing Lgr5. We show that deletion of the key autophagy gene Atg7 affects the survival of Lgr5+ intestinal stem cells. Mechanistically, this involves defective DNA repair, oxidative stress, and altered interactions with the microbiota. This study highlights the importance of autophagy in maintaining the integrity of intestinal stem cells.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL23092

14 Samples

Download data: CEL

(Submitter supplied) Lgr5+ adult intestinal stem cells are highly proliferative throughout life. Single Lgr5+ stem cells can be cultured into 3D epithelial organoids containing all cell types at nearnormal ratios. Culture conditions to generate the main cell types have been established previously, but signals inducing the various types of enteroendocrine cells (EECs) have remained elusive. Here we generate quiescent Lgr5+ stem cells in vitro by inhibition of the EGF-receptor (EGFR) and mitogen-associated protein kinase (MAPK) signaling pathways in organoids, a state that can be readily reversed. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

58 Samples

Download data: CSV

(Submitter supplied) The Lgr5 receptor is a marker of intestinal stem cells (ISCs) that regulates Wnt/b-catenin signaling. In this study, phenotype analysis of knockin/knockout Lgr5-eGFP-IRES-Cre and Lgr5-DTReGFP embryos revealed that Lgr5 deficiency during Wnt-mediated cytodifferentiation results in amplification of ISCs and early differentiation into Paneth cells, which can be counteracted by in utero treatment with the Wnt inhibitor LGK974. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

45 Samples

Download data: TXT

(Submitter supplied) The intestinal epithelium is the most rapidly self-renewing tissue in adult mammals. We have recently demonstrated the presence of approximately six cycling Lgr5+ stem cells at the bottoms of small intestinal crypts1. We have now established long-term culture conditions under which single crypts undergo multiple crypt fission events, whilst simultanously generating villus-like epithelial domains in which all differentiated cell types are present. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL7202

4 Samples

Download data: TXT

(Submitter supplied) The small intestine has a robust regenerative capacity, and various cell types serve as “cells-of-origin” in the epithelial regeneration process after injury. However, how much each population contributes to regeneration remains unclear. Using lineage tracing, we found that Lgr5-expressing cells’ derivatives contained radioresistant ISCs crucial for epithelial regeneration in the damaged intestine after radiation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

39 Samples

Download data: TXT

(Submitter supplied) We performed 7 single-cell RNAseq experiments to identify progenitor cell populations in the small intestine. To also capture rare intestinal cell populations such as stem cells and secretory cells we not only analyzed crypt cells from wildtype mice but also used two reporter mouse lines: i) the FltpZV/+ mouse line of which we mixed live crypt cells with Fltp Venus reporter (FVR) positive cells at different ratios and ii) Foxa2-Venus fusion (FVF) reporter mice. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

14 Samples

Download data: H5AD, MTX, TSV

(Submitter supplied) Little is known about how metabolites couple tissue stem function with physiology. Here we show that in the mammalian small intestine, the expression of Hmgcs2 (3-hydroxy-3-methylglutaryl-CoA synthetase 2)—the gene encoding the rate-limiting enzyme in the production of ketone bodies, including beta-hydroxybutyrate (ßOHB)—distinguishes the self-renewing Lgr5+ stem cells (ISCs) from differentiated cell types. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

8 Samples

Download data: BED, BW

(Submitter supplied) The goal of this project is to generate transcriptome profiling of Lgr5-GFP high intestinal stem cells (High)/Lgr5-GFP low progenitors (Low) and CD24+C-kit+ Paneth (PA) cells for a systemic analysis of cellular pathways involved in responses to fasting and aging.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

18 Samples

Download data: TXT

(Submitter supplied) We characterized the compositions of cell populations and signaling underlying the lineage commitments of intestinal stem cells upon loss of Hmgcs2.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

4 Samples

Download data: TXT

(Submitter supplied) To follow the changes in the transcriptional programs accompanying the specification of the embryonic Lgr5+ cells we sequenced whole transcriptomes of embryonic intestinal epithelium progenitors (at E13.5 and E15.5). EpCAM positive embryonic gut epithelium was isolated from dissected small intestines using fluorescence activated cell sorting (FACS). Lgr5+ progenitors were purified on the basis of GFP fluorescence from Lgr5GFP-Cre-ERT mice (Barker et al. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

45 Samples

Download data: TSV