|
| Status |
Public on Nov 03, 2009 |
| Title |
UCNR2_beforeT |
| Sample type |
RNA |
| |
|
| Source name |
Colonic mucosal biopsy from UC non-responder before first infliximab treatment
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Colon
disease: UC
response to infliximab: No
before or after first infliximab treatment: Before first infliximab treatment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Benelux B.V.), according to the manufacturer’s instructions. The total RNA integrity and quantity were assessed with the Agilent 2100 Bioanalyzer (Agilent, Waldbronn, Germany) and Nanodrop ND-1000 spectrophotometer (Nanodrop technologies), respectively.
|
| Label |
biotin
|
| Label protocol |
Total RNA (2 µg) was reverse-transcribed into cDNA using the SuperScript Choice System (Invitrogen, Carlsbad, CA, USA) with oligo-dT primers containing a T7 RNA polymerase promoter site. cDNA was in vitro transcribed to cRNA and biotin labeled using the IVT labeling kit (Affymetrix, Santa Clara, CA, USA), according to Affymetrix expression analysis technical manual 701021Rev.5. Biotinylated cRNA was purified and fragmented. The quality of labeled and fragmented cRNA, respectively, was assessed with the Agilent 2100 Bioanalyzer.
|
| |
|
| Hybridization protocol |
Fragmented cRNA (15 µg) was hybridized overnight to the Human Genome U133 Plus 2.0 Array (Affymetrix).
|
| Scan protocol |
The arrays were washed and stained with streptavidin-phycoerytrin on an automated Fluidics Station (Affymetrix) and scanned on the Affymetrix 3000 GeneScanner.
|
| Description |
Colonic mucosal gene expression data from UC non-responder before first infliximab treatment
|
| Data processing |
The resulting image files (.dat files) were analyzed using Affymetrix GCOS software, and intensity values for each probe cell (.cel file) were calculated. Intensity values were scaled to an average of 150 per array according to the method of global scaling provided in the GCOS.
|
| |
|
| Submission date |
Jan 26, 2009 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Ingrid Arijs |
| E-mail(s) |
[email protected]
|
| Organization name |
KULeuven
|
| Department |
Clinical and Experimental Medicine
|
| Lab |
TARGID - IBD Leuven
|
| Street address |
Herestraat 49
|
| City |
Leuven |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE14580 |
Mucosal gene signatures to predict response to infliximab in patients with ulcerative colitis |
| GSE16879 |
Mucosal expression profiling in patients with inflammatory bowel disease before and after first infliximab treatment |
|
| Relations |
| Reanalyzed by |
GSE119087 |
