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Sample GSM1049544 Query DataSets for GSM1049544
Status Public on Dec 07, 2012
Title Patient 4, before month 1 GA injection
Sample type RNA
Source name Patient 4, before month 1 GA injection
Organism Homo sapiens
Characteristics disease: multiple sclerosis
cell: CD14+ monocytes
gender: female
age at ga therapy onset (baseline blood sampling): 38
duration from ms diagnosis to therapy initiation (in months): 9
edss at baseline: 1.0
edss after 1 year: 1.5
edss after 2 years: 1.5
edss after 5 years: 3.0
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: 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 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
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]

Data table header descriptions
VALUE MAS5.0 processed and normalized data

Data table
GC00U902522_at 3
GC00U902726_at 12
GC00U902727_at 36
GC00U902728_at 2
GC00U905129_at 18
GC00U913730_at 37
GC00U916295_at 20
GC00U921637_at 53
GC00U921664_at 76
GC00U921668_at 23
GC00U921857_at 7
GC00U922209_at 78
GC00U922231_at 3
GC00U922298_at 3
GC00U922307_at 31
GC00U922384_at 3
GC00U922430_at 32
GC00U922457_at 62
GC00U922633_at 41
GC00U922796_at 5

Total number of rows: 18862

Table truncated, full table size 340 Kbytes.

Supplementary file Size Download File type/resource
GSM1049544_Pat04_month_1.CEL.gz 5.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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