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Status |
Public on Dec 06, 2011 |
Title |
Patient 2, 12 months after start of IFN-beta therapy |
Sample type |
RNA |
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Source name |
Peripheral blood mononuclear cells
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Organism |
Homo sapiens |
Characteristics |
gender: female age at ifn-beta therapy onset (baseline blood sampling): 52 duration from ms diagnosis to therapy initiation (in months): 1 edss at baseline: 2.5 edss after 1 year: 2.5 edss after 2 years: 4.0 edss after 5 years: 4.5 number of relapses during the year prior to treatment: 1 number of relapses during 1-year follow-up: 1 number of relapses during 2-year follow-up: 2 number of relapses during 5-year follow-up: 4 time from start of therapy to the first relapse (in months): 12 completed years of ifn-beta therapy: >=5
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Treatment protocol |
Patients were treated with subcutaneous IFN-beta-1a (Rebif, Merck Serono) at standard doses.
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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.
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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).
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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.
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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 IFN-beta
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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 |
Nov 03, 2011 |
Last update date |
Dec 05, 2012 |
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 |
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Platform ID |
GPL14837 |
Series (1) |
GSE33464 |
Expression data of multiple sclerosis patients receiving subcutaneous Interferon-beta-1a therapy [U133 Plus 2.0] |
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