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Sample GSM827806 Query DataSets for GSM827806
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 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
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]

Data table header descriptions
VALUE MAS5.0 signal intensity

Data table
GC00U902522_at 3
GC00U902726_at 32
GC00U902727_at 5
GC00U902728_at 7
GC00U905129_at 26
GC00U913730_at 53
GC00U916295_at 59
GC00U921637_at 50
GC00U921664_at 62
GC00U921668_at 9
GC00U921857_at 82
GC00U922209_at 99
GC00U922231_at 7
GC00U922298_at 2
GC00U922307_at 6
GC00U922384_at 4
GC00U922430_at 10
GC00U922457_at 47
GC00U922633_at 5
GC00U922796_at 8

Total number of rows: 18862

Table truncated, full table size 342 Kbytes.

Supplementary file Size Download File type/resource
GSM827806.CEL.gz 8.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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