|
Status |
Public on Apr 15, 2017 |
Title |
CPCG0102-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 |
|