title: scRNA-seq of homo sapiens: CSF leukocytes
design: CSF samples were collected into round bottom polypropylene tubes and then centrifuged for 10 min at 300 x g. The CSF supernatant was removed and CSF cells were resuspended in 5 ml of X-Vivo15 media (Lonza) and stored at 4C. The samples were then transported to the laboratory of the Department of Neurology with Institute of Translational Neurology at the University Clinic Mnster, Germany for scRNA-seq. Transport time of samples collected in Mnster was 10-30 minutes. Cell suspensions were then centrifuged again for 5 min at 400 x g and then resuspended in 40 _l of media. Out of this volume, 6 _l were used for cell counting and the remaining volume was entirely used for scRNA-seq. Samples were processed with the Chromium Single Cell 5 Library & Gel Bead Kit and barcoded, full-length VDJ segments from T cells were enriched from first-strand cDNA via PCR amplification with the Chromium Single Cell VDJ Enrichment Kit, Human T Cell (from 10X Genomics) following the manufacturers instructions. Further library preparation was performed using the Chromium Single Cell 5' Library Construction Kit (10X Genomics). Sample processing and library preparation was performed according to manufacturer instructions using AMPure XP beads (Beckman Coulter). Sequencing was  carried out on a local Illumina Nextseq 500 using the High-Out 75 cycle kit with a 26-8-0-57 read setup. All the samples were sequenced with a sequencing depth >50,000 reads per cell.