Cell line mixture bulk RNA-seq data for benchmarking somatic mutation detection
The goal of the experiment is to construct libraries with pseudo somatic variants using germline variants from different cell lines, to provide a benchmarking dataset for somatic variant detection from RNA-seq data using RNA-MosaicHunter. Six human lymphoblastoid cell lines (GM12878, GM18620, GM18865, GM19141, GM20126, and GM20904) were used. All cell lines were maintained in RPMI 1640 medium (Corning, Cat# 10-040-CV) supplemented with 2 mM L-glutamine and 15% Fetal Bovine Serum (Gibco). Two biological replicates of the cell mixture were independently prepared, each consisting of 5 million viable cells as determined by a trypan blue exclusion assay. For each replicate, the six cell lines were mixed based on cell counts in the following proportions: GM12878 (45%), GM18620 (20%), GM18865 (10%), GM19141 (10%), GM20126 (10%), and GM20904 (5%). Total RNA was isolated using the Quick-RNA Miniprep kit (Zymo Research, Cat# R1055) according to the manufacturer protocol. For each replicate, a stranded mRNA-seq library was constructed using the Illumina Stranded mRNA Prep kit and sequenced on an Illumina NovaSeqX platform to generate approximately 160 million 151 bp paired-end reads per library.