GSM6394992: chow, 104616-001-001; Mus musculus; RNA-Seq
5h-fasted blood samples for EDTA plasma isolation were collected from the tail vein at set intervals. Also body weight and food intake measurements were acquired repeatedly. A few days before sacrifice a functional gut permeability test was performed. Mice were sacrificed after a 5-h fast. At sacrifice blood for EDTA plasma and serum was collected via heart puncture, organs were isolated and weighed, and mucosal microbiota from ileum and colon was collected. 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 II Directional RNA Library Prep Kit from Illumina, NEB #E7760S/L resulting in 300–500 bp amplified libraries/sample. Libraries (1.1nM) 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). 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.