|
| Status |
Public on Aug 08, 2017 |
| Title |
Sample_121 |
| Sample type |
RNA |
| |
|
| Source name |
clinical renal cell carcinoma samples
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: renal cell carcinoma
gender: F
Stage: 1
grade: 3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA (5-20 μg) was used to prepare antisense biotinylated RNA. A subset of cases was added to external poly(A) RNA-positive controls (Affymetrix, Santa Clara, CA).
|
| Label |
biotin
|
| Label protocol |
Synthesis of single-stranded and double-stranded cDNA was done with the use of T7-oligo(dT) primer (Affymetrix). In vitro transcription was done using Enzo Bioarray Transcript Labeling kit (Enzo, Farmingdale, NY).
|
| |
|
| Hybridization protocol |
In vitro transcription was done using Enzo Bioarray Transcript Labeling kit (Enzo, Farmingdale, NY). The biotinylated cRNA was subsequently fragmented, and 10 μg were hybridized to each array at 45°C over 16 hours
|
| Scan protocol |
The HGU133 Plus 2.0 GeneChips contain 54,675 probe sets, representing ∼47,000 transcripts and variants. Scanning was done in a GeneChip 3000 scanner.
|
| Description |
CEL files were pre-processed and normalized using the RMA algorithm through the Affy package of R/Bioconductor.
|
| Data processing |
Quality assessment was done in GeneChip Operating System 1.1.1 (Affymetrix) using global scaling to a target signal of 500. Quality assessment was done using denaturing gel electrophoresis. The CEL file data were analyzed with BioConductor to generate probeset level data.
|
| |
|
| Submission date |
Nov 05, 2015 |
| Last update date |
Aug 08, 2017 |
| Contact name |
Min Han Tan |
| E-mail(s) |
mhtan@ibn.a-star.edu.sg
|
| Phone |
68247110
|
| Organization name |
Institute of Bioengineering and Nanotechnology
|
| Street address |
31 Biopolis Way,
|
| City |
Singapore |
| State/province |
Sinagpore |
| ZIP/Postal code |
138669 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE73731 |
Clear cell renal cell carcinoma (ccRCC) samples |
|
