|
| Status |
Public on Feb 15, 2018 |
| Title |
GAT23_Wnt_Rspondin1_NI |
| Sample type |
RNA |
| |
|
| Source name |
GAT23_Wnt_Rspondin1_NI
|
| Organism |
Homo sapiens |
| Characteristics |
patient: GAT23
wnt: Wnt
rspondin: Rspondin1
infection: NI
|
| Treatment protocol |
Cells were cultured in an air-liquid interface and infected with H.pylori as described in the accompanying publication.
|
| Growth protocol |
Gastric primary cells were grown in corresponding media as described in the accompanying publication (materials and methods).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier.
|
| Label |
Cy3-CTP
|
| Label protocol |
RNA was labeled with the single-color Low Input Quick Amp Labeling Kit (Agilent Technologies) according to manufacturer’s instructions.
|
| |
|
| Hybridization protocol |
After precipitation, purification and quantification, 0.75µg labeled samples were hybridized according to the supplier's protocol (Agilent Technologies).
|
| Scan protocol |
Scanning of microarrays was performed with 3µm resolution 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 single-color raw data txt files were further analyzed using R and the associated BioConductor package limma. Background was removed using method normexp with offset 15, followed by quantile normalization.
|
| |
|
| Submission date |
Jan 24, 2017 |
| Last update date |
Feb 15, 2018 |
| 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 |
GPL21272 |
| Series (1) |
| GSE94032 |
Air Liquid Interface Model of Gastric Mucosa and H.pylori Infection |
|
