|
| Status |
Public on May 04, 2015 |
| Title |
Hepatocellular carcinoma tissue_28t |
| Sample type |
RNA |
| |
|
| Source name |
Expression of hepatocellular carcinoma tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Hepatocellular carcinoma
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After surgical excision, tissue samples for nucleic acids extraction were immediately sliced into aliquots of about 100 mg, snap-frozen in liquid nitrogen and stored at -80°C until use. For RNA extraction, each liver tissue aliquot (100 mg) was kept on ice, immediately homogenized in 2 ml of TriReagent® (Sigma-Aldrich, St. Louis, MO, USA) and the homogenate stored at -80°C until use. RNA was extracted by guanidinium thiocyanate-phenol-chloroform-based method using TRIReagent® (Sigma-Aldrich, St. Louis, MO, USA)
|
| Label |
Cy3
|
| Label protocol |
10 ug of total RNA were utilized to synthesize double-stranded cDNA by Superscript® Double-Stranded cDNA Synthesis Kit (Invitrogen, Carlsbad, CA, USA); 1ug of cDNA was labeled by One-Color DNA Labeling Kit (NimbleGen-Roche, Madison, WI, USA) and 4 ug of Cy3-labeled cDNA were hybridized on the array.
|
| |
|
| Hybridization protocol |
Samples were hybridized on the Human Gene Expression 12x135K Arrays (Nimblegen-Roche, Madison, WI, USA) following manufacturer instructions
|
| Scan protocol |
Microarrays were scanned with Axon GenePix 4400A microarray scanner setting laser power to 100%. PMT gain was set in order to obtain about 1e-5 normalized counts at 65.000 intensity level for both channels.
|
| Description |
Expression analysis of hepatocellular carcinoma tissue
|
| Data processing |
Feature data were extracted, summarized using RMA algorithm and quantile normalized using NimbleScan 2.5 software.
|
| |
|
| Submission date |
Jul 09, 2014 |
| Last update date |
May 05, 2015 |
| Contact name |
Alberto Ferrarini |
| E-mail(s) |
[email protected]
|
| Phone |
+39-045-802-7058
|
| Organization name |
University of Verona
|
| Department |
Scientific and Technological Department
|
| Lab |
Plant Functional Genomics Centre
|
| Street address |
Strada le Grazie, 15
|
| City |
Verona |
| State/province |
Veneto |
| ZIP/Postal code |
37134 |
| Country |
Italy |
| |
|
| Platform ID |
GPL18451 |
| Series (2) |
| GSE59259 |
Expression profiles in alcohol-associated hepatocellular carcinoma |
| GSE59261 |
Expression and DNA methylation profiles in alcohol-associated hepatocellular carcinoma |
|
