|
| Status |
Public on Apr 24, 2013 |
| Title |
Patient 6, before third IFN-beta injection |
| Sample type |
RNA |
| |
|
| Source name |
Peripheral blood mononuclear cells
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: relapsing-remitting multiple sclerosis
gender: female
age at ifn-beta therapy onset (baseline blood sampling): 27
duration from diagnosis to therapy initiation (in months): 2
edss at baseline: 2.0
edss after 1 year: 1.0
edss after 2 years: 1.5
number of relapses during the year prior to treatment: 3
number of relapses during 1-year follow-up: 2
number of relapses during 2-year follow-up: 2
completed months of ifn-beta therapy: 13
|
| Treatment protocol |
Patients were treated with subcutaneous IFN-beta-1b (Betaferon, Bayer HealthCare) at standard doses.
|
| Growth protocol |
Patient blood samples were taken immediately before first IFN-beta injection as well as two days, four days and one month post therapy initiation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Peripheral blood mononuclear cells were separated using isopycnic centrifugation (Ficoll), and total RNA enriched with small RNAs was isolated using the mirVana miRNA isolation kit (Invitrogen) according to the manufacturers' protocols.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix 3' IVT protocol from 200 ng 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. The 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 2.2.0, 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 19,204 human genes.
|
| |
|
| Submission date |
Apr 22, 2013 |
| Last update date |
Aug 06, 2013 |
| Contact name |
Michael Hecker |
| E-mail(s) |
michael.hecker@rocketmail.com
|
| 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 |
GPL15445 |
| Series (2) |
| GSE46280 |
Expression data of multiple sclerosis patients receiving Interferon-beta therapy [HG-U133_Plus_2] |
| GSE46293 |
Expression data of multiple sclerosis patients receiving Interferon-beta therapy |
|
