GSM9365074: SUDHL4 cells, DMSO treatment, 4 hours, bio rep 3; Homo sapiens; RNA-Seq
Cells were plated at 1M/mL. For KP422 cells, cells were harvested in TRIsure (Bioline 38033). RNA was extracted using Direct-zol RNA MicroPrep columns (Zymo R2062) treated with DNAseI. For RL, SUDHL4, and OCILY19 cells, cells were harvested in Zymo DNA/RNA Shield (R1100). For sequencing library preparation for KP422 cells, polyA-tailed mRNA was enriched (NEB E7490) and prepared into paired-end libraries (NEB E7765) and indexed (NEB E7335). Library size distributions were confirmed using an Agilent Bioanalyzer and High Sensitivity DNA reagents (Agilent 5067) and concentrations determined by qPCR. For sequencing library preparation for RL, SUDHL4, and OCILY19 cells, 3' end counting was used (Plasmidsaurus): polyA mRNA was captured, reverse transcribed, and barcoded with a unique molecular identifier; then, double-stranded cDNA was generated and tagmented; finally, libraries were amplified using Illumina index primers for sequencing.