|
| Status |
Public on Aug 31, 2010 |
| Title |
peripheral blood collected on day 3 from a pediatric non-responder to IVCS therapy SID_3609 |
| Sample type |
RNA |
| |
|
| Source name |
peripheral blood, 3 days on IVCS therapy
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral blood
age (in years): 15.848385331144
therapy_response: No
d3_pucai: 45
d5_pucai: 50
batch: 2
|
| Treatment protocol |
Blood samples were collected in PAXgene tubes (PreAnalytiX, QIAGEN) and were incubated at room temperaturte between 2 and 24 hours priot to being frozen at -20°C. Samples were then stored at -80°C until extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from all samples using the PAXgene Blood RNA Kit (QIAGEN).
|
| Label |
biotin
|
| Label protocol |
Samples were labeled using Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay - 100 ng Total RNA Labeling Protocol
|
| |
|
| Hybridization protocol |
Samples were hybridized using Affymetrix GeneChip Hybridization, Wash and Stain Kit
|
| Scan protocol |
Affymetrix Gene ChIP Scanner 3000 7G
|
| Data processing |
Probesets lacking annotation information were removed from further analysis. Raw data were background corrected, log transformed, and quantile normalized using a robust multi-array average (RMA) algorithm in R. All 40 samples were scaled using the R function “scale” (http://www.r-project.org/), and then correlated with a binary intravenous-corticosteroid therapy response variableusing the local-pooled error (LPE) method for detection of significance while controlling for batch effects.
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.r4.mps
|
| |
|
| Submission date |
Apr 06, 2010 |
| Last update date |
Apr 06, 2010 |
| Contact name |
Boyko Kabakchiev |
| Organization name |
Mount Sinai Hospital
|
| Department |
Samuel Lunenfeld Research Institute
|
| Lab |
Silverberg Lab
|
| Street address |
60 Murray Street, Room L3-004
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5T 3L9 |
| Country |
Canada |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE21231 |
Gene expression changes associated with resistance to intravenous corticosteroid therapy in children with severe ulcerative colitis |
|
