GSM8174573: Bone marrow, Stroke, scRNA-seq, rep2; Mus musculus; RNA-Seq
Bone marrow cells suspensions were stained with a cocktail of antibodies against markers of the lymphoid lineage (CD3, CD4, CD8a, CD19 and Ter119) and mature neutrophils (Ly6G, see antibodies list). Immediately prior to cell sorting, PI  were also added to label dead cells. Cells were sorted according to the surface markers (FACS Aria II Fusion cell sorter, BD Biosciences, Inc.) and the negative fraction of BM myeloid cells (depleted of lymphoid lineage cells and neutrophils) was collected. After sorting, cells were centrifuged and cautiously resuspended to a final concentration of 1200-1400 cells/ul. Cells were then further processed according to manufacturer's (10X) instructions. The scRNA-seq libraries were prepared using the 10x Chromium Single Cell 3′ Solution. Quality control of all cDNA samples was performed with a Bioanalyzer 2100 (Agilent Technologies) and libraries were quantified with the Qubit dsDNA HS kit. Gene expression libraries were sequenced on an Illumina NextSeq 2000 using 20,000 reads per cell. Libraries were performed according to the manufacter's instructions (single cell 3' v3.1 protocol, dual index, 10x Genomics).