|
| Status |
Public on Jan 01, 2015 |
| Title |
UC_active_2 [mRNA] |
| Sample type |
RNA |
| |
|
| Source name |
colonic mucosal biopsy from UC patient with active disease
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: colon
disease: UC
disease activity: active
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions. RNA quality and quantity were assessed with a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies) and a 2100 Bioanalyzer (Agilent) using the Agilent RNA 6000 Nano kit.
|
| Label |
biotin
|
| Label protocol |
Total RNA (150 ng) was reverse-transcribed into cDNA, followed by the generation of cRNA and ss DNA using the GeneChip WT Synthesis and Amplification kit (Ambion). Fragmented DNA is labeled with biotin (GeneChip WT terminal Labeling kit).
|
| |
|
| Hybridization protocol |
Hybridization to GeneChip Human Gene 1.0ST arrays (Affymetrix) was performed at 45°C for 17 hours. The arrays were washed and stained on an automated Fluidics Station (Affymetrix).
|
| Scan protocol |
Microarrays were scanned on the Affymetrix 3000 GeneScanner. Intensity values for each probe cell (.cel file) were calculated using Affymetrix GeneChip Command Console (AGCC).
|
| Description |
colonic mucosal gene expression data from UC patient with active disease
|
| Data processing |
Quality assessment and outlier detection was performed before and after normalization using the Bioconductor package arrayQualityMetrics. Data were analyzed using the RMA algorithm with the aroma.affymetrix package (R version 2.15.0).
|
| |
|
| Submission date |
Jul 17, 2013 |
| Last update date |
Jan 01, 2015 |
| Contact name |
Jan Van der Goten |
| E-mail(s) |
jan.vandergoten@med.kuleuven.be
|
| Organization name |
KU Leuven
|
| Department |
Clinical and Experimental Medicine
|
| Lab |
TARGID - IBD Leuven
|
| Street address |
Herestraat 49 bus 701
|
| City |
Leuven |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL6244 |
| Series (2) |
| GSE48958 |
Mucosal gene expression profiling in (un)inflamed colon of patients with ulcerative colitis (UC) |
| GSE48959 |
Mucosal expression profiling in (un)inflamed colon of patients with ulcerative colitis (UC) |
|
