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Sample GSM380741 Query DataSets for GSM380741
Status Public on Jul 15, 2009
Title Definite MS_333AV56
Sample type RNA
 
Source name PBMC
Organism Homo sapiens
Characteristics disease state: Definite MS
cell type: Peripheral blood mononuclear cells
age: 32
gender: Female
time to next relapse(days): NoRelapse
Treatment protocol Peripheral blood mononuclear cells (PBMC) were separated on ficoll-hypaque gradient
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the TRIzol Reagent (Invitrogen, Carlsbad, CA)
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA
 
Hybridization protocol cDNA was synthesized, labeled, hybridized to either HU-133A or HU133A-2 containing 22,215 gene-transcripts according to Affymetrix (Inc, Santa Clara, CA) protocol
Scan protocol Hewlett Packard, GeneArray-TM scanner G2500A
Description working set56
Data processing Data analysis was performed by Partek Genomics Solution software (www.partek.com ). Expression values were computed from raw CEL files by applying the Robust Multi-Chip Average (RMA) background correction algorithm. The RMA correction included: 1) values background correction; 2) quantile normalization; 3) log2 transformation; 4) median polish summarization. In order to avoid the noise caused by variable set effects we normalized each set to pre-saved distribution pattern of a well balanced set used as a reference distribution. To reduce batch effect, Analysis of Variance (ANOVA) multiple model analysis was applied. Source of variation was analyzed; non-relevant batches effects such as array type, working batch, patient age and gender were eliminated.
 
Submission date Mar 16, 2009
Last update date Jul 14, 2009
Contact name Michael Gurevich
E-mail(s) Michael.Gurevich@sheba.health.gov.il
Organization name Sheba Medical Center
Department Multiple Sclerosis Center
Lab Neurogenomics and Neuroimmunology
Street address Tel Hashomer
City Ramat Gan
ZIP/Postal code 52621
Country Israel
 
Platform ID GPL571
Series (1)
GSE15245 Prediction of acute multiple sclerosis relapses by transcription levels of peripheral blood cells

Data table header descriptions
ID_REF
VALUE RMA signal

Data table
ID_REF VALUE
1007_s_at 6.471149921
1053_at 5.632900238
117_at 7.124340057
121_at 7.62845993
1255_g_at 3.128950119
1294_at 8.67977047
1316_at 5.134590149
1320_at 3.596930027
1405_i_at 10.80980015
1431_at 3.525850058
1438_at 5.483950138
1487_at 6.921249866
1494_f_at 4.937079906
1598_g_at 7.921659946
160020_at 6.66301012
1729_at 8.557290077
1773_at 5.44178009
177_at 4.377140045
179_at 8.121390343
1861_at 4.96352005

Total number of rows: 22215

Table truncated, full table size 494 Kbytes.




Supplementary file Size Download File type/resource
GSM380741.CEL.gz 1.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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