title: scRNA-seq of Homo Sapiens: adult meninges
design: Cell suspensions were prepared according to the manufacturers protocol (10x genomics) for 3 v3 single cell sequencing or 5 single cell sequencing with TCR enrichment (Additional File 1: Table S1). For both methods, gel beads in emulsion (GEMs) were generated from a mixture of cell suspension combined with the GEM beads subjected to emulsion production by the Chromium Controller. cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps. Purified cDNA was amplified for 10-14 cycles before being cleaned up using SPRIselect beads. Samples were then run on a tape station or Bioanalyzer to determine the cDNA concentration. TCR enrichments were done on the full-length cDNA 5 gene expression libraries (GEX). Both GEX and Enriched TCR libraries were prepared as recommended by the 10x Genomics Chromium Single Cell V(D)J Reagent Kits (v1 Chemistry) user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform for 3v3 libraries, the Chromium Single Cell 3 GEM, Library & Gel Bead Kit v3 (PN-1000075) with the Chromium Single Cell Chip B Kit (PN-1000154) were used. For 5 libraries the Chromium Single Cell 5 Library and Gel Bead Kit (PN-1000006), Chromium Single Cell A Chip Kit (PN-1000152), Chromium Single Cell V(D)J Enrichment Kit, Human, T cell (96 rxns) (PN-1000005), and Chromium Single Index Kit T (PN-1000213) were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 151x10x10x151 sequencing recipe according to manufacturer protocol for 5 sequencing and a 28x8x98 sequencing recipe according to manufacturer protocol for 3v3 sequencing. For both sequencing approaches, a median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression Library and 5000 reads/cell for each V(D)J (Tcell) library generated from the 5 sequencing library.