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Links from GEO DataSets

Items: 20

1.

Id2 controls specification of Lgr5+ intestinal stem cell progenitors during gut development

(Submitter supplied) To follow the changes in the transcriptional programs accompanying the specification of the adult ISCs we sequenced whole transcriptomes of embryonic intestinal epithelium progenitors (at E11.5 and E12.5) and adult ISCs. EpCAM positive embryonic gut epithelium was isolated from dissected small intestines using fluorescence activated cell sorting (FACS). Adult ISCs were purified on the basis of GFP fluorescence from crypts of Lgr5GFP-Cre-ERT mice (Barker et al. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
41 Samples
Download data: TSV
Series
Accession:
GSE90470
ID:
200090470
2.

Krüppel-like factor 5 regulates stemness, lineage specification, and regeneration of intestinal epithelial stem cells

(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
Series
Accession:
GSE131278
ID:
200131278
3.

Krüppel-like Factor 5 Regulates Stemness, Lineage Specification, and Regeneration of Intestinal Epithelial Stem Cells

(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
Series
Accession:
GSE131265
ID:
200131265
4.

Krüppel-like factor 5 regulates stemness, lineage specification, and regeneration of intestinal epithelial stem cells [RNA-seq]

(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
Series
Accession:
GSE122278
ID:
200122278
5.

Distinct populations of embryonic epithelial progenitors generate Lgr5+ intestinal stem cells

(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
Series
Accession:
GSE104727
ID:
200104727
6.

Transcriptomic profiling of small intestinal crypts upon MEX3A deletion

(Submitter supplied) The effort to better understand intestinal stem cell (ISC) identity and regulation remains a challenge. We have been studying the RNA-binding protein MEX3A as a putative ISC marker. In that context, we have generated the first Mex3a knockout (KO) mouse model and show MEX3A is crucial for maintenance of the Lgr5+ ISC pool. As part of a phenotypic characterization pipeline, we have performed transcriptomic profiling (RNA-sequencing) of isolated Mex3a KO small intestinal crypts and compared it against small intestinal crypts isolated from age-matched wild-type controls.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL24247 GPL21103
6 Samples
Download data: XLSX
Series
Accession:
GSE141191
ID:
200141191
7.

Compared gene expression profile of Lgr5-expressing and deficient stem cells in the intestine

(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
Series
Accession:
GSE135362
ID:
200135362
8.

Yap dependent reprogramming of Lgr5+ stem cells drives intestinal regeneration and cancer

(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
Series
Accession:
GSE66567
ID:
200066567
9.

Altered cell lineage differentiation in fetal LGR5-null mice

(Submitter supplied) The molecular mechanisms controlling stem cell renewal and lineage commitment are still poorly understood due to lack of reliable markers. In the adult small intestine, an example of high rate self-renewing tissue, four different epithelial cell lineages (enterocytes, Goblet, enteroendocrine and Paneth cells) are generated from a pool of stem cells localised at the bottom of the crypts of Lieberkühn. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6943
8 Samples
Download data: GPR
Series
Accession:
GSE13337
ID:
200013337
10.

Autophagy maintains intestinal stem cell integrity

(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
Series
Accession:
GSE136952
ID:
200136952
11.

Gene expression profiles in the embryonic midgut of Id2 knockout and wild-type mice

(Submitter supplied) Id2 knockout mice develop heterotopic gastric tissues in the small intestine during development. To gain a mechanistic insight into the cell fate conversion in the Id2 knockout midgut endoderm, we performed microarray analysis using RNA samples extracted from midgut tissues at E13.5.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL2995
6 Samples
Download data: TXT
Series
Accession:
GSE43014
ID:
200043014
12.

Gene expression signature of fast and slow cycling intestinal crypt base columnar cell populations

(Submitter supplied) The identification of Lgr5 as an intestinal stem cell marker has made it possible to isolate and study primary stem cells from small intestine. Using the cell cycle specific expression og the mKi67 gene, we generated a novel Ki67-RFP knock-in allele which identifies dividing cells. Using Lgr5-GFP;Ki67-RFP mice, we isolated CBCs with distinct Wnt signaling levels and cell cycle features, and analyzed their global gene expression pattern using microarrays. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL11533
10 Samples
Download data: CEL
Series
Accession:
GSE52813
ID:
200052813
13.

TCF7L1 controls tuft cell differentiation

(Submitter supplied) To study the functions of Tcf7l1 during gut development, we have ablated Tcf7l1 specifically in the intestinal epithelium using Shh-Cre. To determine transcriptional changes upon loss of Tcf7l1, we have isolated EpCAM-positive epithelial cells from mouse embryos using fluorescence activated cell sorting (FACS) and performed RNA-sequencing analysis.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19057
6 Samples
Download data: BW, TSV
Series
Accession:
GSE226187
ID:
200226187
14.

Identification of Lgr5-independent spheroid-generating progenitors of the mouse fetal intestinal epithelium

(Submitter supplied) Immortal spheroids were generated from fetal mouse intestine using the culture system developed to culture organoids from adult intestinal epithelium. Spheroids are made of a monostratified polarized epithelium displaying a poorly differentiated intestinal phenotype. The proportion of spheroids generated from intestinal explants progressively decreases from fetal to postnatal period, with a corresponding increase in production of organoids. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6943
4 Samples
Download data: GPR
Series
Accession:
GSE49803
ID:
200049803
15.

ID2 controls differentiation of entero-endocrine cells in mouse small intestine

(Submitter supplied) Aim: The mammalian gut is the largest endocrine organ. Dozens of hormones secreted by enteroendocrine cells regulate a variety of physiological functions of the gut but also of the pancreas and brain. Here, we examined the role of the helix-loop-helix transcription factor ID2 during the differentiation of intestinal stem cells along the enteroendocrine lineage. Methods: To assess the functions of ID2 in the adult mouse small intestine, we used single-cell RNA sequencing, genetically modified mice, and organoid assays. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19057
6 Samples
Download data: TXT
Series
Accession:
GSE178586
ID:
200178586
16.

T helper cells modulate intestinal stem cell renewal and differentiation

(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
Series
Accession:
GSE106510
ID:
200106510
17.

Essential role of Arid1a in intestinal stem cell maintenance and homeostasis through Sox9 regulation (ChIP-Seq)

(Submitter supplied) Arid1a, a subunit of the SWI/SNF chromatin remodeling complex, have been reported in multiple human cancers, however, its functional role in intestinal homeostasis remains unclear. To investigate the role of Arid1a in murine intestine, we have employed ChIP experiments in intestinal spheroid cells generated from crypt cells of wild type mice. ChIP assay revealed that Arid1a binds directly to the Sox9 promoter to support its expression.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17021
1 Sample
Download data: BED, TXT
Series
Accession:
GSE121658
ID:
200121658
18.

Dynamic Reorganization of Chromatin Accessibility Signatures during Dedifferentiation of Secretory Precursors into Lgr5+ Intestinal Stem Cells

(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
Series
Accession:
GSE83394
ID:
200083394
19.

Signals controlling maintenance and differentiation of embryonic gastric epithelial progenitors

(Submitter supplied) A dozen of cells expressing various marker genes was defined as adult gastric epithelial stem cells. Do these cells represent different cell types or they are just the same cell with cycling expression of different marker genes? The origin of the adult stem cells could answer this question. Yet, the identity of the embryonic gastric progenitors was not known. We performed single cell RNA-sequencing to characterize cellular composition of the embryonic stomach at the time of initiation of cytodifferentiation. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19057
576 Samples
Download data: TSV
Series
Accession:
GSE137908
ID:
200137908
20.

Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform:
GPL17021
74 Samples
Download data: TSV
Series
Accession:
GSE89684
ID:
200089684
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