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Sample GSM380734 Query DataSets for GSM380734
Status Public on Jul 15, 2009
Title Definite MS_515AV56
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 6.434329987
1053_at 5.693890095
117_at 6.951220036
121_at 7.871399879
1255_g_at 3.169509888
1294_at 8.493419647
1316_at 5.133200169
1320_at 3.620150089
1405_i_at 10.90530014
1431_at 3.186490059
1438_at 5.483029842
1487_at 7.009009838
1494_f_at 5.190750122
1598_g_at 7.908750057
160020_at 6.858769894
1729_at 8.167460442
1773_at 4.943860054
177_at 4.324880123
179_at 8.326660156
1861_at 4.947350025

Total number of rows: 22215

Table truncated, full table size 494 Kbytes.




Supplementary file Size Download File type/resource
GSM380734.CEL.gz 1.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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