normalization data transformation protocol
GC-RMA summarised and baseline normalised to median of all arrays using GeneSpring GX11.5 ID_REF = VALUE = GC-RMA and baseline normalised to median
array scanning protocol
Affymetrix GeneChip Scanner 3000.
Fragmented and biotinylated cDNA was hybridised to Human U133 Plus 2.0 Affymetrix GeneChips at 45C, 60 rpm for 18 hours. GeneChips were washed and stained with an Affymetrix GeneChip Fluidics station 450, protocol EukGE-WS2v4_450.
500pg mRNA processed using NuGEN Ovation® Whole Blood Solution
sample treatment protocol
Tuberculosis patients, samples taken at beginning and after 2 or 4 weeks of conventional combination therapy (2HRZE/4HR)
human blood, 1ml, diluted 10-fold and cultured with M. tuberculosis H37Rv for 6 days. Supernatant removed and cells lysed in 10ml RNA/DNA Stabilization reagent (Roche Applied Science)
nucleic acid extraction protocol
mRNA Isolation Kit for Blood/Bone Marrow (Roche Applied Science) and Turbo DNA-free™ treatment (Ambion: Applied Biosystems)