|
| Status |
Public on Jun 29, 2021 |
| Title |
Liver_NASH-HCC_NonTumoral_Adjacent_17 |
| Sample type |
RNA |
| |
|
| Source name |
NY5682
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Non-tumoral NASH liver adjacent to HCC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
50ng of total mRNA was isolated from FFPE samples using the miRNeasy FFPE kit (Qiagen). The Qiacube system (Qiagen) was used to automatize the extraction process. DNA FFPE kits (Qiagen).
|
| Label |
biotin
|
| Label protocol |
Double-stranded cDNAs were synthesized from total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA.
|
| |
|
| Hybridization protocol |
Total mRNA was prepared for hybridization using the GeneChip 3’ IVT Pico Kit assay (Thermo Fisher) following the manufacturer’s protocols. Samples were hybridized to the Human Genome U219 Array (Affymetrix) also following the manufacturer protocols.
|
| Scan protocol |
Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.
|
| Data processing |
Gene expression profiles that passed the quality control were submitted to the GenePattern ExpressionFileCreator Module20 to generate the final dataset. In this last step, the background was corrected with the Robust Multi-array Average (RMA) algorithm and data were normalized using quantiles.
|
| |
|
| Submission date |
Jan 13, 2021 |
| Last update date |
Jun 29, 2021 |
| Contact name |
Marta Piqué |
| Organization name |
IDIBAPS
|
| Street address |
Rosselló, 153
|
| City |
Barcelona |
| State/province |
Barcelona |
| ZIP/Postal code |
08036 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13667 |
| Series (1) |
| GSE164760 |
Molecular characterization of hepatocellular carcinoma in patients with non-alcoholic steatohepatitis |
|
