|
| Status |
Public on Jan 01, 2015 |
| Title |
UC_active_5 [miRNA] |
| 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 miRVAna miRNA isolation Kit (Ambion), according to the manufacturer's instructions. The integrity and quantity of total RNA and small RNA were assessed with a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies) and a 2100 Bioanalyzer (Agilent) using the Agilent RNA 6000 Nano kit and the Agilent Small RNA kit, respectively.
|
| Label |
biotin
|
| Label protocol |
Total RNA (250 ng) was used in a tailing reaction followed by ligation of the biotinylated signal molecule, using the FlashTag™ Biotin HSR RNA Labeling Kit (Genesphere) protocol for Affymetrix GeneChip miRNA arrays. As recommended, the labeling efficiency is verified with the ELOSA QC assay (Genesphere).
|
| |
|
| Hybridization protocol |
Incubation at 99°C for 5 minutes, followed by 45°C for another 5 minutes. Hybridization to GeneChip miRNA 2.0 arrays (Affymetrix) was performed under rotation (60 rpm) at 48°C for 16 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 microRNA expression data from UC patient with active disease
|
| Data processing |
Quality control of the array data was performed with the Affymetrix miRNA QC Tool, version 1.1.1.0. Data were analyzed using RMA method in Bioconductor (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 |
GPL14613 |
| Series (2) |
| GSE48957 |
Mucosal miRNA 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) |
|
