Extended Data Fig. 3: Subcellular RNA correction to minimize effect of potential ambient contamination and developmental stage agnostic analysis.

(a) To minimize effects of potential ambient contamination in the GC preparation, transcriptomes obtained from sorted GC samples are corrected for their respective input material, that is RNA extracted from the unsorted GCF. (b/c) GC transcripts for CPN and CThPN are defined as those having a higher abundance in sorted GCs than in GCF. (d) Correction for input material results in exclusion of likely ambient contaminants, for example marker genes for various non-neuronal cell types (grey), while preserving a class of robustly GC transcripts (red). (e) GO term enrichment comparing GC genes to likely contaminants from the GCF. (f) Principal component analysis of CPN (light and dark red) and CThPN (light and dark blue) soma transcriptomes collected at developmental stage P1 (light colors) and P3 (dark colors). Data show striking separation according to subtype and additional distinction within each subtype cluster across developmental stages. (g) Heatmap of correlated soma samples for CPN (red) and CThPN (blue) at P1 (lighter color) and P3 (darker color). LUT reflects pairwise Euclidean distance between the log2 TPMs of all genes in a sample. (h) Principal component analysis of CPN (light and dark red) and CThPN (light and dark blue) GC transcriptomes collected at developmental stage P1 (light colors) and P3 (dark colors). Data show striking separation according to subtype and additional, but less distinct separation within each subtype cluster across developmental stages. (i) Representative images of coronal brain sections from intersectional transgenic mice (genotype indicated on top) showing CThPN having reached the thalamus at P1, innervating and branching into the different thalamic nuclei at P3 and having established circuitry at P7. (j) ASD and schizophrenia disease-associated genes are enriched (95% confidence interval) in soma- and GC-enriched transcriptomes. Both CPN and CThPN soma-localized and GC- localized transcriptomes show enrichment for ASD-associated genes, based on comparison with two independent data sets. Cross-referencing with two independent GWAS studies for schizophrenia additionally revealed that CThPN soma- and GC-localized transcriptomes are also enriched for schizophrenia-associated genes. There is no enrichment detected with genes associated with bipolar disorder in either CPN or CThPN transcriptomes, serving as a neuropsychiatric disease control, highlighting specificity in ASD and schizophrenia.