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. 2017 Jul 20;7:6031. doi: 10.1038/s41598-017-04426-w

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© The Author(s) 2017

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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SNS reveals excitatory neuron identity. (a) Overview of the SNS pipeline. S1 mouse cortex was dissociated to single nuclei for NeuN+ and DAPI+ sorting and capture on C1 chips for modified SmartSeq (SmartSeq+) reactions. Inset shows DAPI positive nuclei in the C1 capture site. (b) Comparison of nuclear data sets with 100 random single S1 cortical or CA1 hippocampal data sets². Top panel: Pearson correlation (r) coefficients for comparison of ERCC TPM values with their input quantities. Bottom panel: proportion of genomic reads mapping to coding sequences (CDS Exons), introns, or untranslated regions (3′ or 5′ UTRs). (c) t-SNE plots showing cluster distribution of hippocampal CA1, cortical S1 cells and cortical S1 nuclei. (d) t-SNE plots as in (c) showing positive expression levels (low – gray; high – blue) of cell type marker genes for oligodendrocytes (Mbp), astrocytes (Aldoc), endothelial cells (Cldn5), mural cells (Acta2), neurons (Thy1), inhibitory neurons (Gad1), excitatory neurons (Slc17a7), and excitatory neuron subtypes Rasgrf2 (layer 2–3), Rorb (layer 4), Plcxd2 (layer 5), FoxP2 (layer 6) and Nr4a2 (layer 6b)^{2, 29}. (e) t-SNE plots showing expected identity of cluster groupings based on markers in (d) (Table S1, ambiguous data sets defined in Methods are shown in gray).