title: NextSeq 500 sequencing; ATAC-sequencing to evaluate the global chromatin dynamics in the absence of hepatic-HMGB1 in livers from mice on fed with chow diet or after a metabolic stress induced by a fasting (6hours)-refeeding (8hours) challenge.
design: ATAC-sequencing to evaluate the global chromatin dynamics in the absence of hepatic-HMGB1 in livers from mice on fed with chow diet or after a metabolic stress induced by a fasting (6hours)-refeeding (8hours) challenge.
library_construction_protocol: Liver biopsies were harvested from control flox and Hmgb1 liver knockout mice in chow diet or after fasting/refeeding challenge Flash-frozen liver biopsies were sent to Active Motif to perform the ATAC-seq assay. The tissue was manually dissociated, isolated nuclei were quantified using a hemocytometer, and 100,000 nuclei were tagmented as previously described (58), with some modifications based on (59) using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter).  Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems).