|
Status |
Public on Mar 01, 2010 |
Title |
class S, rep71 |
Sample type |
RNA |
|
|
Source name |
Vancouver sample
|
Organism |
Homo sapiens |
Characteristics |
tissue type: lymphoma disease status: chronic Hodgkin lymphoma relapse type: _ age (years): 31 sex: M disease stage: 2 albumin level: 34 hemoglobin level: 105 lymphocyte percentage: 7 white blood count: 14 international prognostic score (ips): 4
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted from multiple (10-20x) 20µm freshly cut tissue sections after mechanical homogenization using Allprep RNA extraction kits.
|
Label |
biotin
|
Label protocol |
1-8 µg of extracted RNA were used to prepared biotinylated cRNA in a one-cycle reaction following routine protocols including reverse transcription and labeling in-vitro transcription reactions.
|
|
|
Hybridization protocol |
11µg of labeled cRNA were hybridized on the array overnight. The arrays were washed and stained using Affymetrix Fluidics Station 450.
|
Scan protocol |
Arrays were scanned using Affymetrix GeneChip Scanner.
|
Description |
VAN_00487.CEL
|
Data processing |
The data were analyzed with Bioconductor (R), and normalized and summaried using the rma function in the affy package. The quality control thresholds used were present call rates >20% and normalized unscaled standard errors <1.05 (NUSE). Batch-normalization was performed using ComBat.
|
|
|
Submission date |
Sep 01, 2009 |
Last update date |
Feb 16, 2010 |
Contact name |
Christian Steidl |
E-mail(s) |
csteidl@bccancer.bc.ca
|
Phone |
1-604-675-8046
|
Organization name |
BC Cancer Agency
|
Department |
Pathology
|
Lab |
Steidl lab
|
Street address |
675 West 10th Avenue
|
City |
Vancouver |
State/province |
BC |
ZIP/Postal code |
V5Z 1L3 |
Country |
Canada |
|
|
Platform ID |
GPL570 |
Series (1) |
GSE17920 |
Expression data of diagnostic biopsy samples from Hodgkin lymphoma patients |
|