GSM5852313: HFD_AHS_liver [s103819-001-028]; Mus musculus; RNA-Seq
Mice were terminated in week 28 by gradual-fill CO2 asphyxiation. At sacrifice, livers and other organs were isolated and immediately snap-frozen in liquid N2. Next Generation Sequencing was performed at Genome Scan (Leiden, the Netherlands). For this, strand-specific cDNA libraries were generated from RNA using oligo-dT magnetic beads, mRNA fragmentation, NEBNext Ultra Directional RNA Library Prep Kit from Illumina, NEB #E7420S/L resulting in 300–500 bp amplified libraries/sample. Libraries were multiplexed, clustered, and sequenced on a Nextseq 500 V2 system for Illumina, (New England Biolabs, Inc. Ipswich, MA, USA), with a single-end, 75 bp sequencing protocol, 13-26 million reads per sample and indexing. Clustering and DNA sequencing using the NovaSeq6000 v1.5 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used yielding paired end reads (2x 150bp). NovaSeq control software NCS v1.7 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.