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Sample GSM4054581 Query DataSets for GSM4054581
Status Public on Nov 29, 2021
Title 1infected
Sample type SRA
 
Source name stomach mucosa
Organism Mus musculus
Characteristics condition: Helicobacter pylori infection
Treatment protocol 3x Myh11CreErt2/Rosa26-mTmG mice were infected with H. pylori for 2 months and 3x uninfected mice were used as a control, 2 days before sacrifizing mice were intraperitoneally injected with one dose (4mg/25g BW) of Tamoxifen to induce Myh11+ lineage.
Growth protocol not applicable
Extracted molecule total RNA
Extraction protocol Stomach tissues were sorted for Myh11+ myofibroblasts (GFP) and RNA was isolated from sorted cells using Qiagen RNeasy Plus Micro Kit
cDNA was generated from total RNA using SMART-Seq® v4 Ultra® Low Input RNA Kit resulting in enrichment of polyA RNA. Libraries were generated from cDNA using Nextera XT DNA Library Preparation Kit.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Data processing Reads were aligned against GRCm38 using STAR v2.4
Per-gene expression levels were determined by counting reads per gene using htseq-count against gene models from Ensembl, version Mus_musculus.GRCm38.76
Genome_build: GRCm38
Supplementary_files_format_and_content: htseq-count output as tab-separated text file. Columns: Ensembl gene id, read count
 
Submission date Aug 29, 2019
Last update date Nov 30, 2021
Contact name Thomas F Meyer
E-mail(s) tfm@mpiib-berlin.mpg.de
Phone 03028 460 404
Organization name Max Planck Institute for Infection Biology
Department Molecular Biology
Street address Chariteplatz 1
City Berlin
ZIP/Postal code 10117
Country Germany
 
Platform ID GPL18480
Series (2)
GSE136653 Bmp2 -driven terminal differentiation of the stomach epithelium is induced by an autocrine Bmp2 positive feedback loop and inhibited by H. pylori via Interferon gamma signaling [RNA-seq]
GSE136660 Bmp2 -driven terminal differentiation of the stomach epithelium is induced by an autocrine Bmp2 positive feedback loop and inhibited by H. pylori via Interferon gamma signaling
Relations
BioSample SAMN12659992
SRA SRX6779126

Supplementary file Size Download File type/resource
GSM4054581_1infected_sorted.counts.txt.gz 138.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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