Single cell RNA sequencing of mouse brain hematopoietic cells after brain ischemia model

We performed scRNA-seq of brain CD45+ hematopoietic cells from the brain of Cd300a-fl/fl and Cd300a-fl/fl Lys2-Cre mice 0, 1 and 3 hrs after the reperfusion of middle cerebral artery occlusion (MCAO). Overall design: Brain PI-CD45+ hematopoietic cells were sorted by flow cytometry from Cd300a-fl/fl and Cd300a-fl/fl Lys2-Cre mice 0, 1 and 3 hrs after the reperfusion of MCAO. Three brains were pooled per each sample. Re-staining of PI of sorted samples were measured by flow cytometry, and the viability of all samples were more than 85%. Single cells were processed through the Chromium Single Cell Platform using the Chromium Single Cell 3' Library and Gel Bead Kit v3 (10X Genomics, PN-1000092) and the Chromium Single Cell B Chip Kit (10X Genomics, PN-1000074) as per the manufacturer's protocol. The sequencing of libraries was performed at Macrogen Japan (Kyoto, Japan) using an Illumina HiSeq X. Processed files were generated from Cell Ranger (10X Genomics) pipeline.