Genomic profiling of offspring liver tissue in response to paternal gut microbiota dysbiosis using whole genome sequencing
Genomic profiling of offspring liver tissue in response to paternal gut microbiota dysbiosis using whole genome sequencing
At 5 weeks of age, specific pathogen free (SPF) male C57BL/6J inbred mice were transferred to a conventional colony facility. The male mice were divided into separate cages (one mouse/cage) and randomly assigned to two groups: (i) Control group, which received regular diet and sterilized water for six successive weeks; (ii) Treated group, which received regular diet and sterilized water supplemented with a cocktail of non-absorbable antibiotics (neomycin 2.5 mg/ml, bacitracin 2.5 mg/ml and pimaricin 1.25microg/ml) for six successive weeks. The water bottle and antibiotics cocktail were replaced freshly every 5 days. At the end of six weeks treatment or 4-week after treatment withdrawal, male mice from both groups were mated with treatment-naive 6 weeks old C57BL/6J inbred female mice. For whole-genome genotyping, F1 offspring liver samples were harvested at postnatal day 17 (P17). Liver tissue samples stored at -80C until processing for whole-genome sequencing. Frozen tissue samples stored in -80C were thawed in ice and gDNA was extracted from F1 liver tissue using DNeasy Blood & Tissue Kit (Qiagen) following the manufacturer's instructions. The quantity and quality of DNA was evaluated on a NanoDrop Spectrophotometer and Agilent TapeStation system (Agilent, CA, USA) to ensure DIN > 7. For library preparation NEBNext Ultra II DNA Library Prep kit was used, following all manufactures guidelines. Amplified libraries were multiplexed and sequenced on an Illumina Hiseq 4000 (PE150).