|
| Status |
Public on Mar 01, 2010 |
| Title |
class S, rep45 |
| Sample type |
RNA |
| |
|
| Source name |
Vancouver sample
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: lymphoma
disease status: chronic Hodgkin lymphoma
relapse type: _
age (years): 37
sex: M
disease stage: 2
albumin level: 0
hemoglobin level: 0
lymphocyte percentage: _
white blood count: 0
international prognostic score (ips): 4.7
|
| 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_00403.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 |
|
