NextSeq 500 paired end sequencing; RNA-seq of PBMCs to investigate peptide vaccine immunotherapy biomarkers and response patterns in pediatric gliomas
RNA-seq of PBMCs to investigate peptide vaccine immunotherapy biomarkers and response patterns in pediatric gliomas
Samples were collected in accordance with our approved IRB (University of Pittsburgh Medical Center). PBMCs were isolated from whole blood using FicollTM, according to the manufacturers protocol, at the Immune Monitoring and Cell Production Laboratory (IMCPL) at the Hillman Cancer Center (Pittsburgh, PA).    PBMCs were collected from LGG patients at multiple time relative to the initial peptide vaccine treatment including, 0 weeks (w; pretreatment), 6w, 16w, and when available 34w, 70w, and 86w time points.  Dnase-1-treated RNA was isolated using a Direct-zol RNA isolation kit (Zymo). RNA quality and concentration was determined by RNA Screen Tape (Agilent) using a 4200 TapeStation (Agilent). All RNA integrity numbers (RIN) exceeded RIN-8. mRNA libraries were prepared using TruSeq Stranded mRNA (PolyA+) Library Prep Kit High Throughput (Illumina)
Experimental Factor: response to treatment
partial response
Experimental Factor: time
34