Chunk #62 — STAR Methods — METHOD DETAILS — Characterization of single-cell suspensions — Cell class, type and subtype acquisition bias

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Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain.

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label GABAergic (Gad1/Gad2) and glutamatergic (Slc17a6/Slc17a7/Slc17a8) populations (Advanced Cell Diagnostic Biosystems). We counted a total of 487,003 glutamatergic and GABAergic neurons total from n=3 mice using a custom pipeline in CellProfiler. To evaluate representations at the level of subtypes, we focused on cortical interneurons, using smFISH probes against Pvalb, Sst and Vip. We quantified n=68,734 interneurons, calling cells as single, double and triple-positive population using a second custom CellProfiler pipeline (n= 3 mice).