GSM8195222: 6cb549ee-a086-427a-a58a-b38f8e5164ac; Homo sapiens; ATAC-seq
RNA-seq: We extracted total RNA from lysed pellets frozen in RLT Plus buffer (collected on day 29) using the Quick-RNA™ MiniPrep Kit (Zymo Research), assessed quality to make sure RNA Integrity number (RIN) was 7.5 or greater. ATAC-seq: ATAC-seq samples were processed as previously described in detail25. Briefly, frozen nuclear pellets of 1x105 CVPC were thawed on ice and tagmented in total volume of 25μl in permeabilization buffer containing digitonin (10mM Tris-HCl pH 7.5, 10mM NaCl, 3mM MgCl2, 0.01% digitonin) and 2.5μl of Tn5 from Nextera DNA Library Preparation Kit (Illumina) for 45-75min at 37°C in a thermomixer (500 RPM shaking). RNA-seq: We prepared indexed libraries using the Illumina TruSeq stranded mRNA kit and sequenced with 150 bp paired-end reads on an Illumina HiSeq 4000 (mean = 91.4M reads). ATAC-seq: To eliminate confounding effects due to index hopping, all libraries within a pool were indexed with unique pairs of i7 and i5 barcodes. Libraries were amplified for 12 cycles using NEBNext® High-Fidelity 2X PCR Master Mix (NEB) in total volume of 25µl in the presence of 800nM of barcoded primers (400nM each) custom synthesized by Integrated DNA Technologies (IDT) and sequenced with 150-bp paired end reads on a HiSeq4000 (mean = 112.9M reads). One RNA-seq and ATAC-seq library was generated for each sample. Four CVPCs with 2 treatments = 8 RNA-seq and 8 ATAC-seq samples.