ID: 600134.0001 disease: multiple sclerosis visit: Baseline treatment: untreated gender: male tissue: whole blood data set: discovery
Extracted molecule
total RNA
Extraction protocol
Blood was drawn into PAXgene collection tubes and RNA was isolated using the PAXgene Blood RNA kit (Qiagen, Valencia, CA), following manufacturer’s instructions except for an additional washing step before RNA elution. DNA was digested on columns using the RNase-free DNase Set (Qiagen, Valencia, CA).
Label
biotin
Label protocol
1ug of total RNA that had been put through the ribo minus protocol was labelled using the Affymetrix GeneChip WT Sense Target Labeling and Control Reagent kit.
Hybridization protocol
5.5ug of ssDNA was fragmented before hybridization using the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
Scan protocol
Microarrays were scanned using the Affymetrix GeneChip Scanner 3000 7G.
Description
600134.0001A.CEL whole blood of untreated MS patient, sample 600134.0001A, Interferon Analysis, discovery data set re-analyzed
Data processing
Microarray data were processed in R using the R package “aroma.affymetrix”. Data were background corrected (RMAbackgroundCorrection) and quantile normalized before core probe sets were summarized to transcript level, using a custom made cdf file. This cdf file excludes all probes known to span single nucleotide polymorphisms (SNPs), which could interfere with hybridization and thus introduce noise (Duan, S., Zhang, W., Bleibel, W.K., Cox, N.J. and Dolan, M.E. (2008) SNPinProbe_1.0: a database for filtering out probes in the Affymetrix GeneChip human exon 1.0 ST array potentially affected by SNPs. Bioinformation, 2, 469-470). probe group file/meta-probeset file; HuEx-1_0-st-v2,core,na31,hg19,HB20110919,noSNPs.cdf
