|
| Status |
Public on Nov 29, 2021 |
| Title |
9uninfected |
| Sample type |
SRA |
| |
|
| Source name |
stomach mucosa
|
| Organism |
Mus musculus |
| Characteristics |
condition: Uninfected control
|
| 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 |
SAMN12659988 |
| SRA |
SRX6779130 |
