GSM4192525: 5PT-FBScontrol1; Homo sapiens; RNA-Seq
WM164 cells were plated in a 6-well plate at 200,000 cells/well and allowed to attach overnight in normal culture media. Next day, the media was replaced to serum-free RPMI and cells were incubated overnight. Cells were treated with 3μM vemurafenib or vehicle control in 5% FBS/RPMI, or a 1:1 mixture of serum-free media:CSF from patient 1, patient 2 or patient 3 for 8 hours. RNA was extracted using Qiagen's RNeasy Kit, with on-column DNase digestion (Hilden, Germany). RNA samples were reviewed for quality on the Agilent TapeStation followed by quantitation using the Qubit fluorometric assay.  RNAseq libraries were processed using the Ovation Human FFPE RNA-Seq Multiplex System (NuGEN Technologies, San Carlos, CA). Briefly, 100 ng of RNA was used to generate cDNA and a strand-specific library following the manufacturer's protocol.  BioAnalyzer library size assessment and the Kapa Library Quantification Kit were used for library quantification.  The libraries were sequenced on the Illumina NextSeq 500 v2 sequencer with two 75-base paired-end runs in order to generate 25-35 million read pairs per sample.
GEO Accession
GSM4192525