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Status |
Public on Aug 08, 2017 |
Title |
Sample_41 |
Sample type |
RNA |
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Source name |
clinical renal cell carcinoma samples
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Organism |
Homo sapiens |
Characteristics |
cell type: renal cell carcinoma gender: M Stage: NA grade: 3
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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).
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Label |
biotin
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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).
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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
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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.
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Description |
CEL files were pre-processed and normalized using the RMA algorithm through the Affy package of R/Bioconductor.
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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.
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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
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Phone |
68247110
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Organization name |
Institute of Bioengineering and Nanotechnology
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Street address |
31 Biopolis Way,
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City |
Singapore |
State/province |
Sinagpore |
ZIP/Postal code |
138669 |
Country |
Singapore |
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Platform ID |
GPL570 |
Series (1) |
GSE73731 |
Clear cell renal cell carcinoma (ccRCC) samples |
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