|
| Status |
Public on Mar 05, 2015 |
| Title |
Hepatocellular carcinoma clinical sample, control |
| Sample type |
RNA |
| |
|
| Source name |
Hepatocellular carcinoma clinical sample, control cancer stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
genotype/variation: control
disease state: HCC
|
| Treatment protocol |
Cells were transfected with lentiviral constructs expressing shRNA or shCtrl as described above for 24 hr. Positive cells were selected with puromycin for 5 days. Then, cells were collected for protein and RNA analysis.
|
| Growth protocol |
Cells were seeded on ultra-low attachment culture dishes (Corning) in serum-free medium. DMEM/F12 serum-free medium (Invitrogen) contained 2 mM L-glutamine, 1% sodium pyruvate (Invitrogen), 100 μg/ml penicillin G, and 100 U/ml streptomycin supplemented with 20 ng/ml epithelial growth factor (Invitrogen), 10 ng/ml fibroblast growth factor-2 (Invitrogen), N2 (Invitrogen), and B27 (Invitrogen). HCC Cells were incubated in a CO2 incubator for one to two weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with Trizol from cells according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using Ambion® WT Expression Kit.
|
| |
|
| Hybridization protocol |
Following labeling, 5.5 ug of cDNA was hybridized for 16 hr at 45 ℃ on GeneChip Human Transcriptome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned by using Affymetrix® GeneChip Command Console (AGCC) that installed in GeneChip® Scanner 3000 7G.
|
| Description |
Gene expression data from control of HCC clinical sample
|
| Data processing |
Data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings. Values presented are log2 RMA signal intensity.
|
| |
|
| Submission date |
Mar 04, 2015 |
| Last update date |
Mar 05, 2015 |
| Contact name |
Yanying Wang |
| E-mail(s) |
wangyanying@moon.ibp.ac.cn
|
| Organization name |
Institute of Biophysics, Chinese Academy of Sciences
|
| Street address |
15 Datun Road, Chaoyang District,Beijing 100101, China
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL16686 |
| Series (1) |
| GSE66515 |
Expression data from shlncTCF7 and shCtrl of hepatocellular carcinoma (HCC) clinical sample |
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