|
| Status |
Public on Sep 14, 2015 |
| Title |
TB09.0217_benign |
| Sample type |
genomic |
| |
|
| Source name |
tissue core
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: prostate
sample type: benign
tumour gleason: N/A
tumour %: N/A
(derived data) iclusterplus group: N/A
extra-capsular extension (ece): see matched tumour sample
positive surgical margins (psm): see matched tumour sample
biochemical relapse (bcr): see matched tumour sample
time to bcr (months): see matched tumour sample
tmprss2: ERG gene fusion status: see matched tumour sample
|
| Treatment protocol |
When available (i.e not CRPC samples), matched tumour and benign tissues were identified and prepared from RP surgical tissue as described in Warren et al. (2013). The Prostate. 73: 194-202. Matched whole blood samples were obtained from selected samples at treatment clinics.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Qiagen AllPrep, according to manufacturer's instructions.
|
| Label |
Cy3 and Cy5
|
| Label protocol |
Standard Illumina label protocol; samples run by AROS (Denmark)
|
| |
|
| Hybridization protocol |
Standard Illumina hyb protocol; samples run by AROS (Denmark)
|
| Scan protocol |
Standard Illumina scan protocol; samples run by AROS (Denmark)
|
| Description |
benign robotic radical prostatectomy tissue from patient TB09.0217
processed data file: A1942_1_processed_matrix.txt, column TB09.0217_3_B
|
| Data processing |
Data were pre-processed and quality checked using ‘Call Rate QC’ (AROS), gender calls from PennCNV (Wang et al., 2007); sample pairings were confirmed using BADGER (Lynch et al., 2012).
Processed data files include Genotype: AA,AB,BB,or NC (no call), GC_Score, Theta, R, B_Allele_Freq and Log_R_Ratio.
|
| |
|
| Submission date |
Aug 11, 2015 |
| Last update date |
Sep 15, 2015 |
| Contact name |
Chandra Chilamakuri |
| E-mail(s) |
datasubmissions@cruk.cam.ac.uk
|
| Organization name |
Cancer Research UK Cambridge Institute
|
| Street address |
Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16104 |
| Series (2) |
| GSE70770 |
Prostate cancer stratification using molecular profiles |
| GSE71965 |
Prostate cancer stratification using molecular profiles [CamCap genotype first set] |
|
