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Sample GSM380795 Query DataSets for GSM380795
Status Public on Jul 15, 2009
Title CIS_968DMS
Sample type RNA
 
Source name PBMC
Organism Homo sapiens
Characteristics disease state: CIS
cell type: Peripheral blood mononuclear cells
age: 27
gender: Female
time to next relapse(days): 723
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 set34
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 6.457220078
1053_at 5.657800198
117_at 7.001490116
121_at 7.521850109
1255_g_at 2.946860075
1294_at 8.644399643
1316_at 4.851840019
1320_at 3.566179991
1405_i_at 11.25759983
1431_at 3.29501009
1438_at 5.471700191
1487_at 6.923799992
1494_f_at 4.896019936
1598_g_at 7.907849789
160020_at 6.447899818
1729_at 8.383779526
1773_at 5.210999966
177_at 4.39027977
179_at 7.97371006
1861_at 4.962729931

Total number of rows: 22215

Table truncated, full table size 494 Kbytes.




Supplementary file Size Download File type/resource
GSM380795.CEL.gz 1.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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