Transcriptome Profiling of Tumor-Infiltrating Immune Cells

Total RNA was extracted from the cell suspensions of the explant culture, which contained a heterogeneous population of tumor-infiltrating immune cells, using a DNA/RNA/Protein Purification Plus Micro Kit (Norgen, Thorold, ON, Canada). RNA concentrations were determined by Qubit RNA HS (Invitrogen). The cDNA libraries were generated using TruSeq RNA Library Prep Kit (Illumina, San Diego, CA, USA) following the manufacturer’s instructions. The quality of libraries was checked by Agilent High Sensitivity DNA Kit (Agilent Technologies, Santa Clara, CA, USA), and quality-passed DNA (>2000 bp) were quantified and processed, as previously described [23 (link)]. Libraries that passed the quality control were clustered and sequenced on an Illumina HiSeq 4000 instrument using HiSeq 3000/4000 SBS kit (Illumina).