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Status |
Public on Jan 01, 2014 |
Title |
cervical tumour sample 57, batch1, affy_express,rep1 |
Sample type |
RNA |
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|
Source name |
squamous cell carcinoma of the cervix
|
Organism |
Homo sapiens |
Characteristics |
tissue: Cervix disease type: squamous cell carcinoma gender: Female batch: Batch1 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).
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|
|
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).
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|
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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 |
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