Iscan confocal scanner

Genome-wide transcriptional profiles were collected from peripheral blood leukocytes sampled at baseline and week 12 from 56 older adults with major depression who were randomly selected for testing and randomized to either vilazodone or paroxetine. Peripheral blood mononuclear cells were isolated by Ficoll density gradient centrifugation of antecubital venipuncture samples drawn between 10:00 and 11:00 a.m. at baseline and 16 weeks later following the completion of intervention procedures. RNA samples were extracted using the Qiagen RNeasy system, assessed for suitable integrity using an Agilent 2200 TapeStation, and quantitated by Ribogreen assay. Labeled cRNA was synthesized from 100 ng of total RNA using the Ambion Totalprep 96 kit. Amplified and labeled samples were hybridized to Illumina HT-12 v4 expression chips in the UCLA Neuroscience Genomics Core Laboratory according to the standard Illumina protocol. Post-hybridization washing and staining was done using a SciGene Little Dipper robotic processing platform, and arrays were scanned using an Illumina iScan confocal scanner.

Biological genomic analyses were conducted on a randomly selected subsection of the larger clinical trial. RNA samples were quality checked using an Agilent 2200 (Agilent Technologies, Santa Clara, CA, USA) tapestation and quantitated with ribogreen. Total RNA of 100–200 ng was used for amplification/labeling using the Ambion total prep 96 kit. Amplified and labeled samples were hybridized to Illumina expression chips according to the standard Illumina protocol (Cole et al., 2011 (link)). Post-hybridization washing and staining were carried out using a SciGene Little Dipper robotic processing platform. Chips were scanned on our Illumina iScan confocal scanner.