Single-cell RNA sequencing of spinal cord CD133+ DNGR-1 traced and CD133+ non-traced cells

Using CD133 as a pan-ependymal cell marker, we wished to understand whether CD133+ DNGR-1 traced cells constituted a distinct subset of ependymal cells by comparing these at the single cell level with CD133+ non-traced cells purified from spinal cords of DNGR-1 lineage tracer mice. Myelin-depleted single cell suspensions from spinal cords of DNGR-1 lineage traced mice were stained with anti-CD133 AF488, anti-CD45 AF647 and LIVE/DEAD blue dye. LIVE/DEAD- CD45- CDF133+ DNGR-1 traced or LIVE/DEAD- CD45- CDF133+ non-traced cells were FACS sorted into two different tubes and ran onto 10x Chromium. Samples were compared bioinformatically by integration of both samples after identifying 2000 anchor features.