GSM8554367: PDAC PDX, Sample 3, replicate 1; Homo sapiens; RNA-Seq
Total RNA was extracted from cassettes using the AllPrep DNA/RNA FFPE Kit (Qiagen, 80234). RNA was quantified using the Qubit RNA HS Assay Kit (Invitrogen, Q32852) and quality assessed with the 4150 TapeStation System (Agilent) and RNA ScreenTape Analysis Kit (Agilent, 5067-5576). For samples below dv200 30%, a 1.1X or a 1.1X and successive 1.0X bead cleanups was completed using RNAClean XP Beads (Beckman Coulter, A63987) cDNA libraries were prepped with the KAPA Stranded RNA-Seq Kit with RiboErase (HMR) (Roche, KR1151) if total RNA was >25ng and >24% dv200. If dv200 was below 50%, the low input KAPA Prep protocol was used. 17 cycles were used for the final PCR cycle. The remaining samples were prepped using AmpliSeq for Illumina Transcriptome Human Gene Expression Panel (Illumina, 20019170, 20019102).16 cycles were used to amplify target regions in the cDNA