Hiscansq sequencing system

RAW264.7, H1819, A7r5, and HEK293 cells were purchased from ATCC^®. A431 cells were a gift of Dr Stanley Cohen (Vanderbilt University, USA). Total RNA from RAW264.7, HEK293, A7r5, H1819, and A413 cells was isolated using TRI REAGENT™ (Sigma-Aldrich) according to the manufacturer’s instructions. RNA quantity was measured with a spectrometer (Nanodrop ND 1000), and RNA quality was analysed on the Agilent 2100 Bioanalyzer using the RNA 6000 Nano Chip (Agilent Technologies, USA). We only included RNA samples with an RIN value above 8. Indexed cDNA libraries were generated using TruSeq RNA Sample Preparation kits v2 (Illumina, USA) according to the manufacturer’s protocol. The average library size was 300 bp as determined on the Agilent 2100 Bioanalyzer with DNA 1000 Chips.
The libraries were sequenced on the Illumina HiScanSQ Sequencing System (Interdisciplinary Centre for Clinical Research, Leipzig), generating on average 11.8 ± 1.5 million 101-bp raw paired-end reads per sample on one flow cell lane.

Total RNA from liver was extracted and indexed cDNA libraries were generated using TruSeq RNA Sample Preparation Kits v2 (Illumina, San Diego, CA, USA). Libraries with an average size of 300 bp were sequenced on Illumina HiScanSQ Sequencing System, performing ten biological replicates for each genotype. Processing and analyses of paired-end reads were performed using an established standard protocol (for details see S1 Methods).