Fig 1: Identification of the main BBB cell types and their proportions in schizophrenia and controls.A Experimental workflow. A.I Representative illustration of the midbrain sections. Blue lines indicate the trimmed regions from the sections. A.II Fluorescence Activated Nucleus Sorting (FANS) isolation strategy to enrich for BBB nuclei. Double negative nuclei (DN), not expressing OLIG2 nor NEUN (gate 1), and NEUN positive nuclei (gate 2) were collected and snRNA sequenced in a ratio of ~6 DN to 1 NEUN nucleus. B B.I UMAP depicting 178,009 nuclei from 29 subjects (15 schizophrenia and 14 controls). Subsequent analyses were carried out considering only the BBB cell types (highlighted inside black dotted rectangles). BBB cell types were annotated according to the expression of cellular-specific genetic markers and extracted from the complete data set (in-silico cell types selection). B.II UMAP depicting 57,522 BBB nuclei. Colors indicate nuclei clusters resulting from unsupervised clustering analysis of nuclei transcriptomic profiles (dim = 50, k = 20, res = 0.1). B.III Dotplot depicting representative marker genes of each of the identified BBB cell types; the five sub-clusters of astrocytes in (B.II) were combined into one cluster. Dot size indicates the fraction of nuclei expressing the gene and the color depicts the gene scaled average expression. C Barplot depicting the percentages of the different BBB cell types per donor (x axis). D Boxplots depicting cell type proportions in schizophrenia and controls. Each dot indicates a sample and horizontal lines indicate the median. The five sub-clusters of astrocytes (B.II) were combined into one cluster. Group comparison was carried out with a generalized linear model and p values were Bonferroni corrected. No significant (adjusted p value < 0.05) differences were observed between schizophrenia and controls.