title: GSM8333672: RNA-08, 24.0 % DV200, incubation time 5 min, rep 26; Homo sapiens; RNA-Seq
library_construction_protocol: RNA was extracted using the RNAstorm™ FFPE RNA Extraction Kit (Biotium, Fremont, CA) according to the manufacturer's instructions. RNA quantity was assessed with the High Sensitivity RNA Qubit assay (Thermo Fisher Scientific, Waltham, MA). RNA quality was assessed using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA). RNAseq libraries for OncoPrism-HNSCC ICI response prediction were prepared using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Inc., Greenland, NH), following the manufacturer's instructions. Library RNA input was 40 ng total RNA for all samples unless otherwise specified. UMI Second Strand Synthesis Module for QuantSeq FWD (Lexogen, Inc., Greenland, NH) replaced Second Strand Synthesis Mix 1 in the workflow. All samples were processed with two OncoPrism-HNSCC positive controls and a No Template Control. The positive (high or medium scoring) controls were RNA extracted from RM-HNSCC samples as described above. Final libraries were sequenced to a minimum depth of 10 million single-end 75 base pair reads on a NextSeq500 (Illumina, San Diego, CA), following the manufacturer's protocols.