title: RNAseq of LDHC silenced breast cancer cells
design: Total RNA was isolated using the PureLink RNA Mini kit (Ambion). Total RNA was depleted from ribosomal RNA and random primed for cDNA synthesis using the TruSeq stranded total RNA kit (Illumina, USA). The FASTQ files were trimmed to remove adaptor sequences using flexbar (v3.0.3) and aligned to GRCh37/hg19. Reads were counted to genomic features using subreads (v1.5.5).  reference genome using hisat2 (v2.0.5), resulting in an average 10-15M aligned reads. RNA-seq data was corrected for GC content and normalized within and between lanes using the R package EDASeq (v2.12.0), and quantile normalized using the preprocessCore (v1.36.0).