A total of 1 µg of RNA per sample was used to synthesize 50-bp-long single-end mRNA libraries with an Illumina TruSeq Stranded mRNA Library Prep Kit. The integrity and quantity of the libraries were determined on the Bioanalyzer using the DNA 12000 Kit (Agilent). The barcoded libraries were pooled and sequenced on an Illumina HiSeq 4000, with an average depth of 20 million reads per sample. The raw reads were mapped to the human genome build GRCh38, and gene level counts were determined using Spliced Transcripts Alignment to a Reference, version 2.5 (71 (link)). Subsequent data processing followed the method outlined in ref. 72 (link).
Madsen R.R., Knox R.G., Pearce W., Lopez S., Mahler-Araujo B., McGranahan N., Vanhaesebroeck B, & Semple R.K. (2019). Oncogenic PIK3CA promotes cellular stemness in an allele dose-dependent manner. Proceedings of the National Academy of Sciences of the United States of America, 116(17), 8380-8389.
Other organizations :
Wellcome Trust, National Institute for Health Research, The Queen's Medical Research Institute, University of Edinburgh, Wellcome/MRC Institute of Metabolic Science, Medical Research Council, University of Cambridge, University College London, London Cancer, CRUK Lung Cancer Centre of Excellence, Cancer Research UK, Cambridge University Hospitals NHS Foundation Trust, National Health Service
Sequencing depth (average of 20 million reads per sample)
Genome build used for mapping (GRCh38)
controls
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