6 protocols
normalization data transformation protocol
Microarray data was normalized using Chipster software, according to Smyth GK, Speed T. Normalization of cDNA microarray data. Methods. 2003;31:265-273.; Ritchie ME, Silver J, Oshlack A, et al. A comparison of background correction methods for two-colour microarrays. Bioinformatics. 2007;23:2700-2707.
array scanning protocol
iScan, Genome Studio software v2011.1 (Illumina)
nucleic acid hybridization to array protocol
Standard Illumina hybridization protocol
nucleic acid labeling protocol
Standard Illumina labelling protocol
nucleic acid extraction protocol
RNA was isolated from fresh or frozen sorted MNCs or from whole blood samples using miRNeasy kit (Qiagen).
Sample collection method
Mononuclear cells (MNCs) were separated from peripheral blood (PB) using Ficoll gradient separation (GE Healthcare) and CD8+ T cells were further separated with magnetic beads separation: PB MNCs were labeled with CD8 MicroBeads (Miltenyi Biotech) according to instructions by the manufacturer and separated with an AutoMACS cell sorter (Miltenyi Biotech). NK cells were negatively selected using Dynabeads Untouched Human NK cells-kit (Invitrogen). Purity of the sorted fractions was confirmed by flow cytometry (FACSAria, Becton Dickinson).