Fig. 1: Post-hoc transcriptomic identification of recorded neurons.
From: A transcriptomic axis predicts state modulation of cortical interneurons
a, Three-dimensional (3D) representation of an example reference z-stack (white: GCaMP6m, expressed in all neurons, red: mCherry, expressed in inhibitory neurons) . b, Digital sagittal section of this z-stack (maximum intensity projection, 15-μm slice); colours as in a. Scale bar, 100 µm. c, Portion of ex vivo slice aligned to section in b after 72-fold mRNA detection with coppaFISH. Dots represent detected mRNAs (colour code: top of i). Scale bar, 100 µm. d, Expanded view of dashed rectangle in b,c showing in vivo mCherry fluorescence (red) and ex vivo Gad1 mRNA detection (blue). Scale bar, 20 µm. e, mRNAs detected in this same region, plotted as in c. White lines indicate two functional imaging planes. Grey background: DAPI stain for cell nuclei. Scale bar, 20 µm. f, Hierarchical classification of in-vivo-recorded cells into 5 subclasses, 11 types and 35 subtypes. Within each type, subtypes are sorted by their mean first transcriptomic principal component (tPC1) score (see Fig. 5b). Lect1 is also known as Cnmd; Fam19a1 is also known as Tafa1. g, Higher-magnification view of cells 1 and 2 from e. Gene detections are indicated by coloured letters (code: top of i). Grey background: DAPI image. Below: pie charts indicating probabilities of assignment to subtypes. Scale bars, 5 µm. h, Deconvolved calcium traces for the two example cells, together with running speed. i, Mean expression of the 72 genes (pseudocoloured as log(1 + gene count)) for the 35 subtypes, ordered as in f (n = 4 mice). Left: number of unique cells of each subtype. Nov is also known as Ccn3. j, Comparison of the median cortical depth of each subtype found using coppaFISH (as a fraction of total depth; n = 14 sections from a brain in which mRNAs were detected down to layer 6), and its median cortical depth found independently using Patch-seq7 (Pearson correlation: r = 0.91, P = 1 × 10−13; analysis of covariance (ANCOVA) controlling for subclasses and types: F(1) = 163.6, P = 6 × 10−12). Only subtypes with at least four cells for each dataset were considered. Symbols for subtypes imaged in vivo are shown in f; for subtypes too deep to image, symbols are shown on the right.
