Extended Data Fig. 3: Quality control and differential analysis of whole brain transcriptional activity and anatomical connectivity.

a, Number of counts per region throughout the brain with transcriptional activity. Dashed line represents the median number of counts in each region. b, As in a, for spinal cord-projecting neuron counts. c, Number of transcriptionally active cells across the whole brain for each brain. Brains are colored by experimental group. Distribution reflects the variance across regions within each brain (n = 3 mice per group). Box plots reflect the median, with the limits of the box as the first and third quartile, and the range represented by the plot whiskers. d, As in c, for spinal cord-projecting neuron counts (n = 3 mice per group). Box plots reflect the median, with the limits of the box as the first and third quartile, and the range represented by the plot whiskers. e, Number of regions with transcriptionally active cells throughout the whole brain, for each brain. Brains are colored by experimental group. f, As in e, for spinal cord-projecting neuron counts. g, Number of transcriptionally active cells in each major region of the brain, for each brain. Brains are colored by experimental group (n = 3 mice per group). Box plots reflect the median, with the limits of the box as the first and third quartile, and the range represented by the plot whiskers. h, As in g, for spinal cord-projecting neuron counts (n = 3 mice per group). Box plots reflect the median, with the limits of the box as the first and third quartile, and the range represented by the plot whiskers. i, Spike plot indicating the number of transcriptionally active cells in each region of the brain (x-axis). Plots are faceted by major region of the brain (horizontal) and experimental group (vertical). Each spike represents the counts for a single region. j, As in i, for spinal cord-projecting neuron counts. k, Mean-variance relationship for count data from transcriptionally active cells and spinal cord-projecting neurons. l, Volcano plots indicate differential analysis of each comparison outlined in k. Colored dots represent those meeting statistical significance. FC: Fold Change.