|
| Status |
Public on Dec 07, 2012 |
| Title |
Patient 3, before week 1 GA injection |
| Sample type |
RNA |
| |
|
| Source name |
Patient 3, before week 1 GA injection
|
| Organism |
Homo sapiens |
| Characteristics |
disease: multiple sclerosis
cell: CD14+ monocytes
gender: female
age at ga therapy onset (baseline blood sampling): 37
duration from ms diagnosis to therapy initiation (in months): 33
edss at baseline: 1.0
edss after 1 year: 1.5
edss after 2 years: 1.5
edss after 5 years: 2.0
number of relapses during the year prior to treatment: 0
number of relapses during 12-month follow-up: 0
number of relapses during 2-year follow-up: 0
number of relapses during 5-year follow-up: 0
time from start of therapy to the first relapse (in months): >60
completed years of ga therapy: >=5
|
| Treatment protocol |
Patients were treated with subcutaneous GA (Copaxone, Teva) at standard doses.
|
| Growth protocol |
Patient blood samples were taken immediately before first GA injection as well as one day, one week, one month and two months post therapy initiation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CD14+ monocytes were isolated using magnetic-activated cell sorting (MACS), and monocytes were lysed using chaotropic buffer and cleaned by RNeasy (Qiagen) according to the manufacturers' protocols.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100-200 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. 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 GA
|
| 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 |
Dec 05, 2012 |
| Last update date |
Jan 17, 2014 |
| 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) |
| GSE42763 |
Expression data of multiple sclerosis patients receiving glatiramer acetate therapy [U133 Plus 2.0] |
|
