array scanning and feature extraction protocol
P-AFFY-6 Affymetrix CEL analysis
Affymetrix Generic Hybridization
nucleic acid labeling protocol
P-AFFY-2 Affymetrix biotin labelling
Blood samples (9 mL) were collected in EDTA-tubes at baseline and at week 2 of cART. The EDTA blood tubes were centrifuged at 1500 rpm for 10 minutes at room temperature. Peripheral blood mononuclear cells (PBMCs) were isolated from the blood fraction by Ficoll-Paque Plus gradient separation (GE Healthcare, Little Chalfont, UK). PBMCs were washed once with 50 mL HBSS (Gibco-Invitrogen, Carlsbad, USA) and once with 50 mL RPMI supplemented (Lonza BioWitthaker, Walkersville, MD, USA) with 100U/ml penicillin and 100 mg/mL streptomycin. PBMC pellets were resuspended in cold cryomedium (containing 40% RPMI, 10% DMSO and 50% human serum) and transferred to cryotubes. PBMCs were cryopreserved in liquid nitrogen prior further processing.
(Parameters: start time = 2.0, time unit = weeks, min temperature = 20, temperature unit = C, media = Cryomedium )
The RMA procedure was followed to normalize data within arrays (probeset summarization, background correction and log2-transformation) and between arrays (quantile normalization). The RMA-normalized expression values as obtained with the xps 1.8.0 package of BioConductor (www.bioconductor.org). About 90% of the identifiers found in the normalised data file are ?ǣtranscript cluster Ids?ÇØ in the NetAffx annotation file (?ǣHuGene-1_1-st-v1.na30.1.hg19.probeset?ÇØ annotation file from Affymetrix Technical Documentation, release 30). The remaining ~10% of identifiers are ?ǣprobeset_ids?ÇØ in the annotation file. Both types of identifiers can be found in the ArrayExpress array design file A-MEXP-2212.
Total RNA and protein fractions were isolated from Trizol lysates by chloroform extraction and isopropanol precipitation respectively, as per the manufacturer??Æs recommendations. Due to the low number of monocytes obtained from very limited PBMC samples, the RNA extraction required addition of RNase-free glycogen (Invitrogen, Carlsbad, CA, USA) as RNA carrier to enhance RNA precipitation and avoid the loss of samples. Using the Ambion WT Expression Kit, per sample, an amount of 100 ng of total RNA spiked with bacterial poly-A RNA positive controls (Affymetrix) was converted to double stranded cDNA in a reverse transcription reaction. Next the sample was converted and amplified to antisense cRNA in an in vitro transcription reaction which was subsequently converted to single stranded sense cDNA.
(Parameters: Extracted product = total_RNA, Amplification = RNA polymerases)
Monocytes were isolated from the cryopreserved PBMC samples using positive magnetic selection on CD14 (Miltenyi-Biotec, Bergisch Gladbach, Germany) according to the manufacturer??Æs instruction. Purified monocytes were immediately lysed in 1 mL Trizol (Invitrogen, Carlsbad, CA, USA) and lysates were stored at -80???C.