Extended Data Fig. 2. Quality check of the scRNA-seq analysis.

a-c, Quality control of individual extracted neurons after sequencing. Neurons with a low total detected gene number (n = 14), or a high mitochondrial gene (n = 2), or ERCC (n = 7) percentage (orange) were excluded from further analysis. Each symbol represents a neuron. d, e, Quantification of the number of the total detected genes (d) and cPcdh isoforms (e) in our clone dataset (n = 188). Each symbol represents a neuron. f, Histogram of the number of the detected cPcdh isoforms per neuron in our clone dataset (n = 188). g, h, Quantification of the number of the total detected gene (g) and cPcdh isoforms (h) in the previously published randomly collected neocortical excitatory neuron scRNA-seq dataset from the Allen Institute⁴² (n = 4,152). Each symbol represents a neuron. i, Histogram of the number of the detected cPcdh isoforms in the previously published randomly collected neocortical excitatory neuron scRNA-seq dataset from the Allen Institute⁴² (n = 4,152). j, Quantification of the number of the total detected cPcdh isoforms in clonally related excitatory neurons from different neocortical regions (motor cortex/MO, n = 32; somatosensory cortex/SS, n = 116; visual cortex/VIS, n = 40). k, Pearson correlation analysis between the average expression level of each cPcdh isoform in clonally related excitatory neurons of SS (n = 116) and VIS (n = 40). Each dot represents a cPcdh isoform. The grey bar indicates the 95% confidence interval. A similar display is used in subsequent panels (l-n). l, Pearson correlation analysis between the average expression level of each cPcdh isoform in clonally related excitatory neurons of SS (n = 116) and MO (n = 32). m, Pearson correlation analysis between the average expression level of each cPcdh isoform in clonally related excitatory neurons of MO (n = 32) and VIS (n = 40). n, Pearson correlation analysis between the average expression level of each cPcdh isoform in randomly collected excitatory neurons of MO (n = 3,893) and VIS (n = 7,347) in the previously published scRNA-seq datasets from the Allen Institute⁵⁴. o, Frequency distribution of the mean similarities of cPcdh isoform expression pattern in the non-clonal dataset (n = 1,000 trails, grey bars), and the mean similarity of the clonal dataset (red line) from 32 clones. The non-clonal dataset was generated by a random permutation of the clonal dataset and statistics were performed using the permutation test (see Methods). p, Quantification of the pair-wise similarity of cPcdh isoform expression for clonally related neocortical excitatory neurons in the same or different layers per clone (same layers, n = 31; different layers, n = 20). q, Quantification of the pair-wise similarity of cPcdh isoform expression for neurons in the same or different layers of the randomly collected 150 neocortical excitatory neurons from the previously published Allen Institute dataset⁴² (same layers, n = 600; different layers, n = 400). r, Quantification of the pair-wise similarity of cPcdh isoform expression for randomly collected excitatory neurons across different layers from the previously published Allen Institute dataset⁴² (L2/3-L2/3, n = 200; L2/3-L5, n = 200; L2/3-L6, n = 200). The n numbers indicate neurons (a-n), clones (p), and neuron pairs (q, r). Data are representative of at least three independent experiments. One-way ANOVA test without adjusted P value (j); Two-tailed Pearson correlation analysis (k-n); One-tailed permutation test (o); Two-tailed unpaired Student’s t-test (p-r). Box plots as in Fig. 1.