Fig. 1

scRNAseq of fresh and cryopreserved CSF cells. A Graphical schema depicting the experimental design (created with BioRender.com). Freshly collected CSF was spun and the resulting CSF cells were counted, cells were then immediately divided into either FRE which was immediately processed on the 10x Chromium Controller to capture single cells or cryopreserved with protocols for FBS and/or REC and/or DNA for downstream processing basing on the total cell count. The cryopreserved fractions were later thawed and run on the 10x Chromium Controller, and the resulting data were analyzed together. B Uniform Manifold Approximation and Projection (UMAP) plot of all the cells of samples from CSF A, B, and C, annotated to depict the FRE or FBS or REC protocols. C UMAP plot of all the cells of samples from CSF A, B, and C in protocols FRE, FBS and REC annotated to depict the cell types clustered using Azimuth peripheral blood mononuclear cells (PBMC) reference atlas at L1 resolution. D Dot plot depicting the concordance between respective cell-type specific enriched marker gene expression of all the cells from samples CSF A, B, and C (on the y-axis) as characterized by earlier published CSF scRNAseq studies that are correspondingly identified and clustered accordingly (on the x-axis) by Azimuth reference atlas at L1 resolution