|
| Status |
Public on Dec 06, 2011 |
| Title |
Patient 1, before first IFN-beta injection |
| Sample type |
RNA |
| |
|
| Source name |
Peripheral blood mononuclear cells
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
age at ifn-beta therapy onset (baseline blood sampling): 40
duration from ms diagnosis to therapy initiation (in months): 33
edss at baseline: 3.0
edss after 1 year: 2.5
edss after 2 years: 3.0
edss after 5 years: 3.5
number of relapses during the year prior to treatment: 0
number of relapses during 1-year follow-up: 0
number of relapses during 2-year follow-up: 1
number of relapses during 5-year follow-up: 3
time from start of therapy to the first relapse (in months): 20
completed years of ifn-beta therapy: >=5
|
| Treatment protocol |
Patients were treated with subcutaneous IFN-beta-1a (Rebif, Merck Serono) at standard doses.
|
| Growth protocol |
Patient blood samples were taken immediately before first IFN-beta injection as well as two days, one month, one year and two years post therapy initiation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Blood was separated using isopycnic centrifugation (Ficoll), and peripheral blood mononuclear cells were lysed using chaotropic buffer and cleaned by RNeasy (Qiagen) according to the manufacturers' protocol.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 µg total RNA (Expression Analysis Technical Manual, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 µg of cRNA were hybridized for 16 h at 45°C on Affymetrix HG-U133 Plus 2.0 arrays. Microarrays were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
|
| Description |
Gene expression data from a multiple sclerosis patient treated with IFN-beta
|
| Data processing |
The raw probe-level signals were converted to expression values using the MAS5.0 algorithm and custom GeneAnnot-based chip definition files (version 2.1.0, available at http://www.xlab.unimo.it/GA_CDF). Data normalization was performed by a loess fit to the data with span=0.05 (using R package affy). Each chip yielded mRNA levels of 18,862 human genes.
|
| |
|
| Submission date |
Nov 03, 2011 |
| Last update date |
Dec 05, 2012 |
| Contact name |
Michael Hecker |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Rostock
|
| Department |
Department of Neurology
|
| Lab |
Division of Neuroimmunology
|
| Street address |
Gehlsheimer Str. 20
|
| City |
Rostock |
| ZIP/Postal code |
18147 |
| Country |
Germany |
| |
|
| Platform ID |
GPL14837 |
| Series (1) |
| GSE33464 |
Expression data of multiple sclerosis patients receiving subcutaneous Interferon-beta-1a therapy [U133 Plus 2.0] |
|
