|
| Status |
Public on Jan 01, 2014 |
| Title |
cervical tumour sample 1, batch2, affy_express, rep1 |
| Sample type |
RNA |
| |
|
| Source name |
squamous cell carcinoma of the cervix
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Cervix
disease type: squamous cell carcinoma
gender: Female
batch: Batch2
protocol: Affymetrix Express
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from flash-frozen cervix tissues embedded in Optimal Cutting Temperature (OCT) storage medium using the Norgen Total RNA Purification Kit (Norgen Biotek, Thorold, ON), according to manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
50ng of total RNA was reverse transcribed into double-stranded cDNA and linearly amplified using the WT-Ovation Pico Kit (NuGEN Technologies, San Carlos, CA). The cDNA was fragmented and biotin labeled using the FL-Ovation cDNA biotin Module v2 (NuGEN). 200ng of total RNA was reverse transcribed into double-stranded cDNA with the GeneChip One-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA) and linearly amplified using the GeneChip 3' IVT Express Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Standard Affymetrix procedures
|
| Scan protocol |
Standard Affymetrix procedures
|
| Description |
Affymetrix Express
|
| Data processing |
All analyses were performed in R (v2.15.2). Data processing was performed for each sample using RMA (affy package, v1.36.0 ) for pre-processing and updated Entrez GeneID annotation(hgu133plus2hsentrezgcdf package, v15.0.0).
|
| |
|
| Submission date |
Dec 05, 2012 |
| Last update date |
Jan 01, 2014 |
| Contact name |
Rui Yan |
| E-mail(s) |
rui.yan@oicr.on.ca
|
| Organization name |
Ontario Institute for Cancer Research
|
| Department |
Informatics and Bio-computing Platform
|
| Street address |
101 College Street
|
| City |
Toronto |
| ZIP/Postal code |
M5G 0A3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL16356 |
| Series (1) |
| GSE42764 |
Identification and Correction of Amplification Protocol Bias in Microarray Studies |
|
