title: GSM5466517: roca4; Mus musculus; RNA-Seq
library_construction_protocol: Apoptotic RM1 cells were labeled with CellTrace™ CFSE (ThermoFisher Scientific, C34554), and then co-cultured with macrophages for 16–18 h. Efferocytic and non-efferocytic macrophages were collected and incubated in fluorescence-activated cell sorter (FACS) staining buffer (phosphate buffered saline-1X, 0.2% bovine serum albumin). F4/80 antibody and isotype control were added and incubated for 1 h at 4 °C. F4/80+ only (non-efferocytic macrophages) and F4/80+CFSE+ (efferocytic macrophages) were sorted using a BD FACSAriaTM III (BD biosciences, San Jose, CA, USA) The single cell scRNA-seq libraries were prepared at the University of Michigan Advanced Genomics Core using the 10X Genomics Chromium Next GEM Single Cell 3′ Kit v3.1 (part number 1000268) following the manufacturer's protocol.  Cell suspensions were diluted to target a recovery of 10,000 cells per sample.  The libraries were run on an Agilent TapeStation 4200 (part number G2991BA) for library quality control before sequencing.  Libraries were sequenced at a depth of 50,000 reads/cell on a NovaSeq6000 with the following run configuration: Read 1 - 150 cycles; i7 index read - 8 cycles; Read 2 - 150 cycles.