Genomestudio project software

RNA was isolated from 5 × 10⁵ DCs on day 5 using total RNA isolation RNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. Yield and quality of RNA samples were evaluated with NanoDrop 1000 spectrophotometer (Thermo Scientific, Waltham, MA, USA) and RNA integrity (RIN score) was analyzed with Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) or LabChip GX/GX II (Caliper LifeSciences, Hopkinton, MA, USA). A total of 40 samples, corresponding to 10 healthy donors under four experimental conditions were considered for microarray analysis (Figure S1 in Supplementary Material). All RNA samples used for microarrays showed A260/A280 values between 1.8 and 2.2, and RIN scores >7. RNA samples were reverse transcribed, amplified, and labeled using an Illumina^® TotalPrep™ RNA Amplification Kit, and cDNA was hybridized onto Illumina Human HT-12 v4 BeadChips (Illumina, San Diego, CA, USA), covering the whole human genome. Expression data were extracted with GenomeStudio Project Software from Illumina.

Total RNA was isolated from 5 × 10⁵ moDCs using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions. Yield and quality of RNA samples were evaluated with NanoDrop 1000 spectrophotometer (Thermo Scientific, Waltham, MA, USA) and RNA Integrity (RIN score) was analyzed with Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) or LabChip GX/GX II (Caliper LifeSciences, Hopkinton, MA USA). A total of 76 samples, corresponding to DCs derived from 9 RA patients and 10 healthy donors under 4 experimental conditions were considered for microarray analysis (Figure S1 in Supplementary Material). All RNA samples used for microarrays showed A260/A280 values between 1.8 and 2.2, and RIN scores >7. RNA samples were reverse transcribed, amplified, and labeled using a Illumina^® TotalPrepTM RNA Amplification Kit, and cRNA was hybridized onto Illumina Human HT-12 v4 BeadChips (Illumina, San Diego, CA, USA), covering the whole human genome. Expression data were extracted with GenomeStudio Project Software from Illumina.