|
| Status |
Public on Dec 22, 2014 |
| Title |
IBD38 colon biopsy |
| Sample type |
RNA |
| |
|
| Source name |
colon biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis (ibdu, uc, nomoa): UC
|
| Treatment protocol |
The immunosuppressive treatment of the patients before the biopsy was based on individual treatment regiments; the treatment after the biopsy was adjusted based on the histopathological diagnosis.
|
| Growth protocol |
All human colon biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).
|
| Label |
biotin
|
| Label protocol |
Total RNA (0.3µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array
|
| |
|
| Hybridization protocol |
(Affymetrix, Santa Clara, CA). Amplified RNA (10ug) was hybridized for 16 hr at 45C on GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).
|
| Description |
colon biopsy, (U of A/Cedars-Sinai)
|
| Data processing |
Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.
|
| |
|
| Submission date |
Oct 28, 2013 |
| Last update date |
Dec 22, 2014 |
| Contact name |
Jessica Chang |
| E-mail(s) |
jjchang@ualberta.ca
|
| Organization name |
University of Alberta
|
| Department |
Medicine
|
| Lab |
ATAGC
|
| Street address |
250 Heritage Medical Research Centre
|
| City |
Edmonton |
| ZIP/Postal code |
T6G 2S2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL15207 |
| Series (1) |
| GSE51785 |
Molecular patterns in human ulcerative colitis and correlation with response to infliximab |
|
