GSM6784524: 3172, CAC PDX treated with G007-LK, APC Mut, Replicate 1; Homo sapiens; RNA-Seq
20-30mg frozen tissue was homogenized in 1mL TRIzol Reagent (ThermoFisher catalog # 15596018), phase separation was induced with 200 µL chloroform, and RNA was extracted from the aqueous phase using the miRNeasy Micro Kit (Qiagen catalog # 217084) on the QIAcube Connect (Qiagen) according to the manufacturer's protocol with 350 µL input. Samples were eluted in 15 µL RNase-free water. After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500ng of total RNA with RIN values of 9.2-10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 in a PE50 run, using the HiSeq 3000/4000 SBS Kit (Illumina).  An average of 44 million paired reads was generated per sample. Ribosomal reads represented 1.4-3.0% of the total reads generated and the percent of mRNA bases averaged 67%.