HIV Integration analysis in quiescent CD4 T cells

This study examines the sites of HIV integration in quiescent CD4 T cells and compares them to activated T cells. The expression patterns of the sites hosting integration events were determined using microarray analysis data from quiescent and activated CD4 T cells. Integration sites were isolated by inverse PCR analysis. Quiescent and stimulated T cells from different donors were assayed in 10 µg of leukocyte total RNA using a high-density oligonucleotide array (U133a; Affymetrix, Santa Clara, Calif) at baseline and after PSD for genome-wide mRNA expression profiles. All assays were performed by the UCLA DNA Microarray Core (Affymetrix) following the manufacturer's standard protocol, with sample quality assured for RNA concentration and purity using a bioanalyzer (Agilent, Palo Alto, Calif) prior to probe synthesis. Following hybridization of fluorescent complementary RNA probes, microarrays were imaged using a scanner (Affymetrix), and low-level gene expression values were derived using GeneChip Operating Software (GCOS) (Affymetrix) and analyzed using dChip software (Harvard School of Public Health). The data submitted here have been normalized using RMAExpress.