10X Genomics single-cell RNA-Seq data set of CreER mice

The liver is organized into zones in which hepatocytes express different metabolic enzymes. The cells most responsible for liver repopulation and regeneration remain undefined because fate-mapping has only been performed on a few hepatocyte subsets. Fourteen mouse fate mapping strains were used to systematically compare distinct subsets of hepatocytes. During homeostasis, cells from both periportal zone 1 and pericentral zone 3 contracted in number, whereas cells from midlobular zone 2 expanded in number. These cells, which are sheltered from common injuries, also contributed to regeneration after pericentral and periportal injuries. Zone 2 repopulation was driven by the IGFBP2-mTOR-CCND1 axis. Hence, different regions of the lobule exhibit differences in their contributions to hepatocyte turnover, and zone 2 is the primary source of new hepatocytes during homeostasis and regeneration. Primary hepatocytes were isolated with a two-step collagenase perfusion method described previously. Cells were washed and resuspended in hepatocyte washing medium (Life, 17704024). Single cell libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Reagents Kit v3. For each sample, 8,000 hepatocytes were loaded to target ~5,000 cells after recovery according to the manufacturer's protocol. Single cell libraries were generated and sequenced using the 150 bp paired-end Illumina NextSeq500 in the UTSW Children’s Research Institute Sequencing Facility. 10X scRNA-seq data was preprocessed using the Cellranger v3.0.2 software. We used the mkfastq and count commands to process the 10x single-cell RNA-seq output into cells by gene expression count matrix, and used the aggr command to pool sequencing runs from 4 mice. All parameters were set to default except for the “force-cells” parameter, which was set to 4000.