|
| Status |
Public on Apr 15, 2017 |
| Title |
CPCG0099-F2 |
| Sample type |
RNA |
| |
|
| Source name |
Fresh Frozen primary prostate tumour extraction
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: prostrate
|
| Treatment protocol |
For RNA extractions, ice cold tumour tissue maintained on RNAase-free microscope slides was macro-dissected from 10 µm sections and transferred to an Eppendorf tube on ice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue was digested and total RNA was extracted using the mirVana miRNA Isolation Kit (Life Technologies).
|
| Label |
biotin
|
| Label protocol |
As per manufacturer (Affymetrix)
|
| |
|
| Hybridization protocol |
Hybridization was performed by Affymetrix according to the platform protocol
|
| Scan protocol |
Scanning was performed by Affymetrix
|
| Data processing |
Quantitated intensity files (CEL files) for each array were loaded into the R statistical environment (v3.0.2).
Files generated for batch 1 (HuGene2.0 arrays) were loaded and normalized using the RMA algorithm available in the oligo package for R (v1.26.2), using the default platform design information (pd.hugene.2.0.st v3.8.0).
Each batch was examined for spatial and distributional homogeneity; no outliers were identified
Normalized batch 1 transcript clusters were mapped to EntrezGene IDs and gene symbols using the hugene20sttranscriptcluster.db (v2.12.1) available from Bioconductor.
|
| |
|
| Submission date |
Apr 18, 2014 |
| Last update date |
Apr 15, 2017 |
| Contact name |
Nicholas J Harding |
| E-mail(s) |
nicholas.harding@oicr.on.ca
|
| Phone |
4167320720
|
| Organization name |
OICR
|
| Department |
Informatics and Biocomputing Platform
|
| Lab |
Boutros
|
| Street address |
101 College St
|
| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M5G 0A3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL16686 |
| Series (1) |
| GSE56916 |
Canadian Prostate Cancer GEnome NEtwork – HuGene RNA expression |
|
