Gene expression experiments were performed using Illumina Human-HT12 v4.0 array at the Rockefeller University Genomics Facility (New York, NY, USA). Biotin-labeled RNA was prepared using 200 μg of total RNA by MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems, Foster City, CA, USA). Antisense RNA (750 ng) was mixed with hybridisation reagents and heated at 65°C for 5 minutes. After it was cooled to room temperature, hybridization solution was applied to Illumina HumanHT-12 v4 array. The array was scanned using Illumina BeadArray Reader. The scanning was done using standard DirectHyb Gene Expression protocol. The raw data was extracted using Illumina BeadStudio software without normalization. Data has been deposited in the Gene Expression Omnibus database (accession number GSE75605).
GSEA with MSigMB v5.2 software was used to investigate the biological processes and pathways differentially implicated between obinutuzumab treated and PBS or IgG treated PBML cells [47 (link), 48 (link)]. Genes with > 1.5 fold or < 1.5 fold expression ratio were considered to be significantly differentially expressed genes as we and others have previously discussed [48 (link), 49 (link)].
GSEA with MSigMB v5.2 software was used to investigate the biological processes and pathways differentially implicated between obinutuzumab treated and PBS or IgG treated PBML cells [47 (link), 48 (link)]. Genes with > 1.5 fold or < 1.5 fold expression ratio were considered to be significantly differentially expressed genes as we and others have previously discussed [48 (link), 49 (link)].