Files in this Data Supplement:

• Appendix 1 - (Microsoft Word) (24.5 kb). Glossary.
• Appendix 2 - (TIF) (7.22 MB). RNA quality. RNA digestion plot shows that RNA was not degraded and that the quality was good.
• Appendix 3 - (TIF) (7.82 MB). Normalization of the data. Quantile normalization performed simultaneously on the 57 chip datasets from the index cohort (stroke patients, n=38, controls, n=39). The result of normalization is seen with Boxplots shown prior to quantile normalization of all the samples, and post quantile normalization.
• Appendix 4 - (TIF) (11.5 MB). Multiple comparison correction procedures. The expression set was compared univariately between the stroke patients and controls using t-tests and by subsequent permutation analysis. Parametric tests were assigned a raw p cut-off significance value of <0.05, with subsequent multiple comparison correction using Bonferroni, Sidak SS procedure, Sidak SD procedure, Holm’s procedure, Hoschberg’s procedure and Benjamini and Yekutieli techniques.
• Appendix 5 - (Microsoft Word) (34.5 kb). Primers for real-time PCR.
• Appendix 6 - (Microsoft Excel) (344 kb). GENE LIST: False Discovery Rate listing (Benjamini and Yekutieli). Gene listing from false discovery rate set that includes 771 gene probes from 637 genes in order of significance. Columns include: Affymetrix probe ID#, t-statistic, control mean, control variance, patient mean, patient variance, gene title, gene symbol, Unigene ID, no. of multiple probes, GO biological process description, GO molecular function description, GO cellular component description, pathway and pathway hyperlink.
• Appendix 7 - (Microsoft Excel) (116 kb). GENE LIST: Bonferroni listing. Gene listing from Bonferroni dataset that includes 231 gene probes from 190 genes in order of significance. Columns include: Affymetrix probe ID#, t-statistic, control mean, control variance, patient mean, patient variance, gene title, gene symbol, Unigene ID, no. of multiple probes, GO biological process description, GO molecular function description, GO cellular component description, pathway and pathway hyperlink.
• Appendix 8 - (Microsoft Excel) (52 kb). GENE LIST: Westfall and Young list. This gene list from the permutation dataset includes 101 gene probes from 82 genes that were significantly different between stroke patients and control subjects: some genes had more than one probe on the HU133A microarray. Columns include: Affymetrix probe ID#, t-statistic, gene title, gene symbol, Unigene ID, no. of multiple probes, GO biological process description, GO molecular function description, GO cellular component description, pathway and pathway hyperlink.