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Status |
Public on Dec 07, 2012 |
Title |
Patient 1, before first GA injection |
Sample type |
RNA |
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|
Source name |
Patient 1, before first GA injection
|
Organism |
Homo sapiens |
Characteristics |
disease: multiple sclerosis cell: CD14+ monocytes gender: female age at ga therapy onset (baseline blood sampling): 41 duration from ms diagnosis to therapy initiation (in months): 0 edss at baseline: 1.5 edss after 1 year: 1.5 edss after 2 years: 1.5 edss after 5 years: NA number of relapses during the year prior to treatment: 1 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: NA time from start of therapy to the first relapse (in months): >36 completed years of ga therapy: >=3
|
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).
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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.
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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.
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Submission date |
Dec 05, 2012 |
Last update date |
Jan 17, 2014 |
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 |
GPL14837 |
Series (1) |
GSE42763 |
Expression data of multiple sclerosis patients receiving glatiramer acetate therapy [U133 Plus 2.0] |
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