Extended Data Fig. 7: AAV-mediated pooled in vivo CRISPR screening.
From: Distinct subnetworks of the thalamic reticular nucleus
a, Schematics of the AAV-mediated pooled CRISPR–Cas9 in vivo screen. b, List of pools and genes selected for knockout in the CRISPR–Cas9 screening. TRN enriched refers to genes differentially expressed between Pvalb+ neurons from TRN and from M2 cortex, somatosensory cortex, striatum, and hippocampus. c, A heat map showing the expression pattern of the selected genes in the TRN neurons. The selected disease-risk genes are labelled on the right side. d, A heat map showing the differentially expressed disease-risk genes in Spp1+ versus Ecel1+ neurons: autism spectrum disorder (ASD, purple) and schizophrenia (orange). e, Violin plots showing a list of genes differentially expressed between Pvalb+ neurons in TRN compared and Pvalb+ neurons in the four other brain regions including hippocampus (HP), secondary motor cortex (M2), somatosensory cortex (SCX), and striatum (STR). f, Violin plots confirming the TRN-enriched gene list as shown in e in additional brain regions using the mousebrain.org datasets. CB: cerebellum; Hypoth: hypothalamus; MBd: medial basal nucleus dorsal part; MBV: medial basal nucleus ventral part; SC: spinal cord; Thal: thalamus. g, Violin plots showing selected differentially expressed disease-risk genes compared to the Pvalb+ neurons in the other four brain regions as indicated. HP: hippocampus; M2: secondary motor cortex; SCX: somatosensory cortex; STR: striatum. For e and g, nHP = 90, nM2 = 97, nSCX = 116, nSTR = 13, nTRN = 671 cells; For (f), nCA1 = 136, nCB = 477, nHypoth = 156, nMBb = 331, nMBv = 209, nMedulla = 121, nPons = 199, nSC = 69, nThal = 54, nTRN = 501 cells. The violin plots width is based off of a Gaussian kernel density estimate of the data (estimated by the standard density function in R with default parameters), scaled to have maximum width equal to 1.
