GSM9568749: Cell line MALME3M, nontargeting control siRNA, biological rep 2; Homo sapiens; RNA-Seq
At harvest, cells were washed once with PBS and lysed directly in the well using Buffer RLT (Qiagen). Lysates were homogenized using QIAshredder columns (Qiagen, catalog no. 79654), and total RNA was extracted using the RNeasy Mini Kit (Qiagen, catalog no. 74104) following the manufacturer's protocol, including on-column DNase digestion (Qiagen RNase-Free DNase Set, catalog no. 79254). RNA integrity was assessed using the Agilent TapeStation (RNA ScreenTape), and all samples used for sequencing had RINe values > 9. Bulk RNA sequencing libraries were prepared with assistance from the University of Virginia Genome Analysis and Technology Core (RRID: SCR_018883). Poly(A)+ RNA was isolated using the NEB mRNA Isolation Module, followed by library preparation using the NEBNext UltraExpress mRNA Library Prep Kit, according to the manufacturers' instructions. Libraries were sequenced on an Illumina NextSeq 2000 platform using a P3-100 sequencing kit.