Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression in WT and Stat6 KO intestinal stem cells

ABSTRACT: Gene expression in WT and Stat6 KO intestinal stem cells

PROVIDER: PRJNA508407 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8281296.fastq.gz	Fastqsanger.gz
	SRR8281297.fastq.gz	Fastqsanger.gz

Items per page:

1 - 2 of 2

Similar Datasets

Gene expression in WT and Stat6 KO intestinal stem cells

Project description:Purpose: To examine the expression profile of WT and Stat6 KO intestinal stem cells. Methods: We isolated Lgr5+ ISCs from the intestine tissue, and generated Stat6 KO ISCs through CRISPR/Cas9 approach. Results: Many genes are changed upon Stat6 KO cells. We pay special attention on Wnt/β-catenin signaling that is the most critical pathway in ISCs, and discovered Stat6 drove the expression of Wnt target genes. Conclusions: Stat6 crosstalks with Wnt signaling to drive ISC self-renewal.

2018-12-05 | GSE123353 | GEO

Stat6 occupancy profiling by high throughput sequencing from wild-type(WT) or Trim24-deficient(Trim24-KO) mouse peritoneal macrophages stimulated with IL-4 for 1 hour .

Project description:To identify the potential genes that regulated by Trim24 through Stat6 DNA binding activity, we immunoprecipitated chromatin from WT or Trim24-KO macrophages stimulated with IL-4, and analyzed the precipitated DNA with deep sequencing (ChIP-Seq).

2019-09-06 | GSE134167 | GEO

RNA-seq analysis of SIRT6 and STAT6 regulated genes in intestinal epithelial cells (IECs)

Project description:To investigate the roles of SIRT6 and IL4/IL13-STAT6 pathway in intestinal epithelium homeostasis, we generated IEC-specifc Sirt6 knockout mice and transgenic mice with IEC-specific overexpression of constitutively activated STAT6 (STAT6vt). IECs from these mice were isolated and RNA were extracted and performed RNAseq analysis.

2022-05-15 | GSE202470 | GEO

ATAC-sequencing mice small intestinal epithelium with intestinal epithelium specific LSD1 knock out compared to wild type

Project description:To study the epigenetic regulation of intestinal epithelium we focus on the role of chromatin modulators. Lysine-specific histone demethylase 1a (KDM1A, LSD1) is one of the enzymes that can erase the H3K4me1/2 mark. To assess the role of LSD1 in intestinal epithelium we studied wild type (WT) (Villin-Cre -; Lsd1f/f) and intestinal-epithelial-specific knock-out (KO) (Villin-Cre+; Lsd1f/f) mice. We found that KO mice completely lack Paneth cells, and have altered stem cell characteristics compared to WT littermates. To assess genome-wide ATAC levels in WT and KO small intestines, we isolated intestinal epithelium tissue from wild type mice and LSD1 KO mice. This tissue was digested to single cells and performed ATAC seq as described in the protocols.

2021-03-23 | E-MTAB-8718 | biostudies-arrayexpress

Whole transcriptomes analyses of intestinal epithelial cells (IECs) isolated from Mst4F/F Villincre (Mst4 KO) mice and wildtype (WT) mice

Project description:Purpose: To explore the molecular mechanisms of MST4 regulating intestinal stem cell homeostasis, RNA sequencing was performed to analyze the geome-wide change of MST4 KO IECs compared to those of WT mice. Methods: Total mRNA was extracted from IECs which were isolated from small intestines of Mst4 KO mice and WT mice (8 weeks) in triplicate respectively. Then RNA quality was assessed using an Agilent Bioanalyzer 2100 and the sample reads were sequenced using Illumina Hiseq 4000 platform. As a reasult, we got the transcript data using Hisat2 followed by Stringtie. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: We mapped about 60 million sequence reads per sample to the mouse genome and identified about 50,000 transcripts in IECs of mice. Apprioximately 2,000 transcripts showed different expression between Mst4 KO and WT IECs, with a fold change ≥2 and p value <0.05. Gene set enrichment analysis (GSEA) showed a significantly negative enrichment of Wnt/b-catenin target genes and altered expression of 15 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Conclusion: Our study present the datiled transcripts analysis of IECs isolated from small intestines, with biologic replicates. Based on RNA-seq transcriptome characterization , we conclude a molecular mechanism of MST4 regulating intestinal stem cell homeostasis and provide a framework to understand the crosstalk of MST4 and Wnt/b-catenin signaling.

2021-09-15 | GSE132565 | GEO

WT and ATRX KO

Project description:WT and ATRX KO

| PRJNA254835 | ENA

Transcription profiling of mouse WT and E2A-KO bone marrow stem and progenitor cell subfractions.

Project description:Expression profiling of WT and E2A-KO LSK FLT3- and LMPP protenitor cells. Experiment Overall Design: LSK FLT3- and LMPP stem/progenitor cells from WT and E2A-KO mice were FACS sorted. Subsequently RNA was extracted, labelled and hybridized to Affymetrix microarrays. Goal of experiment was to investigate expression changes between WT and KO LMPP cells.

2008-10-25 | E-GEOD-11982 | biostudies-arrayexpress

mRNAseq and proteomic data set of one week old WT (Chop wt/wt CkmmCre wt/wt Dars2 fl/fl), Chop KO (Chop ko/ko CkmmCre wt/wt Dars2 fl/fl), Dars2 KO (Chop wt/wt CkmmCre tg/wt Dars2 fl/fl) and DKO (Chop ko/ko CkmmCre tg/wt Dars2 fl/fl) mice

Project description:mRNAseq and proteomic data set of one week old WT (Chop wt/wt CkmmCre wt/wt Dars2 fl/fl), Chop KO (Chop ko/ko CkmmCre wt/wt Dars2 fl/fl), Dars2 KO (Chop wt/wt CkmmCre tg/wt Dars2 fl/fl) and DKO (Chop ko/ko CkmmCre tg/wt Dars2 fl/fl) mice

| PRJNA627135 | ENA

mRNA profiles of WT and STAT6-/- mice colon tissue

Project description:mRNA profiles of WT and STAT6-/- mice colon tissue

| PRJNA451477 | ENA

ChIP-sequencing of the H3K4me1/2 in crypts from mice intestinal epithelium with intestinal epithelium specific LSD1 knock out compared to wild type

Project description:To study the epigenetic regulation of intestinal epithelium we focus on the role of chromatin modulators. Lysine-specific histone demethylase 1a (KDM1A, LSD1) is one of the enzymes that can erase the H3K4me1/2 mark. To assess the role of LSD1 in intestinal epithelium we studied wild type (WT) (Villin-Cre -; Lsd1f/f) and intestinal-epithelial-specific knock-out (KO) (Villin-Cre+; Lsd1f/f) mice. We found that KO mice completely lack Paneth cells, and have altered stem cell characteristics compared to WT littermates. To assess genome-wide H3K4me1/2 levels in WT and KO small intestines, we sorted small intestinal crypt cells, fixed them, isolated chromatin, and performed ChIP using an H3K4me1 and an H3K4me2 antibody as described in the protocols.

2020-11-16 | E-MTAB-7871 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data