|
| Status |
Public on Nov 29, 2021 |
| Title |
control vs. lIFN |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Interferon gamma treated cells, replicate 2
|
| Organism |
Mus musculus |
| Characteristics |
treatment: 100ng/ml of recombinant Ifnγ was added to the medium on 2 and 5 day of organoid culture
cell type: Antral, gastric organoids from BL6 mice were grown for 2 days before treatment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
On day 6 RNA was isolatated from the organoids with GeneJET RNA Purification Kit (Thermo Scientific)
|
| Label |
Cy3
|
| Label protocol |
RNA was labeled with the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to manufacturer’s instructions.
|
| |
|
| Channel 2 |
| Source name |
Untreated control cells, replicate 2
|
| Organism |
Mus musculus |
| Characteristics |
treatment: untreated cells
cell type: Antral, gastric organoids from BL6 mice were grown for 2 days before treatment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
On day 6 RNA was isolatated from the organoids with GeneJET RNA Purification Kit (Thermo Scientific)
|
| Label |
Cy5
|
| Label protocol |
RNA was labeled with the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to manufacturer’s instructions.
|
| |
|
| |
| Hybridization protocol |
After precipitation, purification and quantification, labeled samples were hybridized according to the supplier's protocol (Agilent Technologies).
|
| Scan protocol |
Scanning of microarrays was performed with 5µm resolution and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies).
|
| Data processing |
Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.10.1, Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol. The extracted dual-color raw data txt files were further analyzed using R and the associated BioConductor package limma. Agilent FE software processed green and red signals were extracted and within-array normalized using method LOESS was applied.
|
| |
|
| 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 |
GPL4134 |
| Series (2) |
| GSE136658 |
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 [microarray] |
| 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 |
|
