|
| Status |
Public on Sep 15, 2020 |
| Title |
Hep_wt_3 |
| Sample type |
RNA |
| |
|
| Source name |
hepatocyte_wt
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
genotype: WT
|
| Growth protocol |
Primary hepatocytes were isolated through a perfusion with EGTA and collagenase buffer. Primary hepatocytes were cultivated for 4 hours. Medium change was performed to remove non-adherent cells. Cells were cultivated for another 20 hours and after this RNA extraction performed. Only samples with a RIN higher than 7 were used for expression profiling analysis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Nucleo Spin RNA II kit (Macherey Nagel) according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
|
| |
|
| Hybridization protocol |
Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.
|
| Scan protocol |
Affymetrix GeneArray Scanner3000
|
| Description |
primary isolated hepatocytes
WT
|
| Data processing |
The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-2_0-type from Affymetrix. A Custom CDF Version 20 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary
|
| |
|
| Submission date |
Mar 08, 2019 |
| Last update date |
Sep 16, 2020 |
| Contact name |
Carsten Sticht |
| Organization name |
University Heidelberg
|
| Department |
ZMF
|
| Street address |
Theodor-Kutzer-Ufer
|
| City |
Mannheim |
| ZIP/Postal code |
68169 |
| Country |
Germany |
| |
|
| Platform ID |
GPL22598 |
| Series (2) |
| GSE128043 |
Yes-Associated Protein (YAP) Induces a Secretome Phenotype and Transcriptionally Regulates Plasminogen Activator Inhibitor-1 (PAI-1) Expression in Hepatocarcinogenesis |
| GSE128047 |
An endothelial subtype-specific communication network orchestrates capillarization in liver tumorigenesis via the Hgf/c-Met pathway |
|
