GSM5851030: FFD+isoleucine [104216-001-033]; Mus musculus; RNA-Seq
Blood samples were obtained from the tail vein in 5h-fasted mice, and body weight, food intake and body composition measurements were acquired at set time points during the study. After 38 weeks mice were sacrificed by gradual-fill CO2 exposure and liver tissues were collected for biochemical measurements and histopathology (snap frozen and formalin fixation, respectively). 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 NovaSeq6000 system for Illumina, (New England Biolabs, Inc. Ipswich, MA, USA), with a paired-end, 150 bp sequencing protocol, 20-35 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.