GSM9772009: VS1046_SCC151_DMSO_rep3_rnaseq; Homo sapiens; RNA-Seq
RNA was extracted from HN-SCC-151 cells using the Direct-zol RNA miniprep kit (Zymo Research, Irvine, CA). For the mouse tumors, 30mg of tissue were sub-sampled from frozen parent samples into pre-chilled Lysing Matrix A 2.0 ml tubes (MP Biomedical).  RNA lysates were generated by adding 700uL of Buffer RLT (Qiagen) containing 1% 2-mercaptoethanol to each tube containing tissue and homogenizing 2 x 30 sec. at high speed in a Bead Ruptor 12 (Omni, Inc.).  12.5 ug of linear polyacrylamide (LPA) (bioWorld cat#10510000) was added to each sample and total RNA was purified with a QIAcube Connect MDx using the RNeasy Mini reagent and protocol (Qiagen) with DNase I treatment.  RNA was eluted in 50uL of RNase-free water. VS912-VS1049: Libraries for HN-SCC-151 cells were prepared using the Illumina® Stranded mRNA Prep and sequenced on NextSeq 2000 P2 with 2x51 bp paired-end reads. VS1752-VS1761: Libraries for MOC1 cells were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (E7760) as described in the manufacturer's manual and sequenced on NextSeq 2000 with 2x101 bp paired-end reads.