GEO DataSets

(Submitter supplied) The weekly turnover of the intestinal epithelium is driven by multipotent, Lgr5+, crypt base columnar cells (CBCs). In response to injury, however, Lgr5+ cells are lost but then re-emerge and are required for successful recovery. How these resurgent Lgr5+ stem cells arise is unclear. We transcriptionally profiled single cells from regenerating intestinal epithelia and identified a unique cell type we term the revival stem cell (rSC). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21493

192 Samples

Download data: CSV

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21493

196 Samples

Download data: MTX, TSV

(Submitter supplied) The weekly turnover of the intestinal epithelium is driven by multipotent, Lgr5+, crypt base columnar cells (CBCs). In response to injury, however, Lgr5+ cells are lost but then re-emerge and are required for successful recovery. How these resurgent Lgr5+ stem cells arise is unclear. We transcriptionally profiled single cells from regenerating intestinal epithelia and identified a unique cell type we term the revival stem cell (rSC). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21493

4 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) The intestinal epithelium undergoes DNA damage response, regenerative response and homeostasis after suffering irradiation. To understand the dynamic change of intestinal epithelium during the irrradiation recovery, we performed single cell RNA sequencing on irradiation-resistant +4 cells in homeostasis and its lineages at different time points after radiation.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

7 Samples

Download data: MTX, TSV

(Submitter supplied) The currently accepted intestinal epithelial cell organization model equates crypt base columnar (CBC) cells, marked by high levels of Lgr5 expression, with the intestinal stem cell (ISC). However, recent intestinal regeneration studies have uncovered limitations of the ‘Lgr5-CBC’ model, leading to two major views: one favoring the presence of a quiescent reserve stem cell population, the other calling for differentiated cell plasticity. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL24247

6 Samples

Download data: H5, TSV

(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) Mist1+CD24hi cells and Mist1+CD24lo cells in mouse small intestine were separatedly sorted, and RNAs were isolated. Mice were treated with irradiation, Lgr5-DT ablation, doxorubicin, or NICD expression before sorting.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

21 Samples

Download data: CEL, CHP

(Submitter supplied) The intestinal epithelium is continuously regenerated by highly proliferative Lgr5+ intestinal stem cells (ISCs). The existence of a population of quiescent ISCs has been suggested yet its identity and features remain controversial. Here we describe that the expression of the RNA-binding protein Mex3a labels a subpopulation of Lgr5+ cells that divide less frequently and contribute to regenerate all intestinal lineages with slow kinetics. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

400 Samples

Download data: 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) 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 identification of Lgr5 as an intestinal stem cell marker has made it possible to isolate and study primary intestinal stem cells. Transcriptional differences between intestinal stem cells can be explored by the use of the Lgr5-eGFP-ires-CreERT2 knock-in mouse. In this mouse model GFP expression is driven from the Lgr5 locus, leading to highest GFP levels in the Lgr5 positive cells. Yet, due to the stability of the GFP protein, it is distributed upon cell division to the daughter cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL4134

8 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

Expression profiling by array

Platforms:

GPL11180 GPL4134

10 Samples

Download data: CEL, TXT

(Submitter supplied) The identification of Lgr5 as an intestinal stem cell marker has made it possible to isolate and study primary intestinal stem cells. Applying quantitative mass spectrometry as well as transcriptomic analysis, we profiled the protein and gene changes between FACS-sorted Lgr5+ve stem cells and their immediate undifferentiated daughter cells. The overall comparison of mRNA and protein levels revealed a high level of correlation, implying that the initial control of intestinal stem cell biology occurs largely at the mRNA level. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11180

6 Samples

Download data: CEL

(Submitter supplied) The identification of Lgr5 as an intestinal stem cell marker has made it possible to isolate and study primary intestinal stem cells. Applying quantitative mass spectrometry as well as transcriptomic analysis, we profiled the protein and gene changes between FACS-sorted Lgr5+ve stem cells and their immediate undifferentiated daughter cells. The overall comparison of mRNA and protein levels revealed a high level of correlation, implying that the initial control of intestinal stem cell biology occurs largely at the mRNA level. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL4134

4 Samples

Download data: TXT

(Submitter supplied) To define differences in chormatin accessibility and histome modifications in intestinal stem and epithelial cells, we performed ATAC-seq and ChIP-seq. We used RNA-sequencing to profile gene expression changes during intestinal stem cell differentiation into different cell types. We find that gene expression is correlated with the chromatin accessibility and reveals differences between intestinal stem cells types.

Organism:

Mus musculus

Type:

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

Platform:

GPL19057

49 Samples

Download data: BW, TXT

(Submitter supplied) Using 3' droplet-based single-cell sequencing, we performed the transcriptional profiling of mouse large intestinal epithelial cells at the single-cell level.

Organism:

Mus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31136

1 Sample

Download data: MTX, TSV

(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) The Wnt target gene Lgr5 marks actively dividing stem cells in Wnt-driven, self-renewing tissues such as small intestine and colon, stomach and hair follicles. A 3D culture system allows long-term clonal expansion of single Lgr5+ stem cells into transplantable organoids that retain many characteristics of the original epithelial architecture. A crucial component of the culture medium is the Wnt agonist Rspo, the recently discovered ligand of Lgr5. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL4134

28 Samples

Download data: TXT