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Extended data figures and tables
a,b,c, Violin plots of n-count_RNA, n-feature_RNA and Percent_mt (mitochondrial transcripts) distribution in cells from WT, heterozygous or homozygous Ptbp1 KO cortex (a), striatum (b) and substantia nigra (c). Center lines in boxplots are the median and box is the interquartile range (IQR). n = 13198, n = 14732, n = 17071 cells for WT, heterozygous and homozygous Ptbp1 KO cortex; n = 12145, n = 12175, n = 15710 cells for WT, heterozygous and homozygous Ptbp1 KO striatum; n = 5741, n = 4518, n = 2965 cells for WT, heterozygous and homozygous Ptbp1 KO substantia nigra. d,e,f, Expression of cell type-specific marker genes in each cluster defined from cortex (d), striatum (e) and substantia nigra (f) scRNA-seq data.
a, UMAP of cells from striatum of different genotypes (left). Colored clusters are annotated to different cell types based on an established panel of cell markers. Expression of top 10 marker genes in Cluster 10 was compared with other clusters (right). Red text: neuronal genes. b, Expression of GFP, Ptbp1, and Ptbp2 in individual cell clusters from WT (red); green: heterozygous (green), and homozygous (blue) Ptbp1 KO mice.
a, UMAP of cells from substantia nigra of different genotypes. b, Relative quantity of cells in different clusters (indicated at top). c, Expression of GFP, Ptbp1, and Ptbp2 in individual cell clusters from WT (red), heterozygous (green), and homozygous (blue) Ptbp1 KO mice. d, Expression of top 10 marker genes in Cluster 5, compared with other clusters (right). Green text: astrocytic genes, Red text: neuronal genes. e, Identification of potential doublets with DoubletFinder, showing that most cells in Cluster 5 are unlikely to be doublets.
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Hao, Y., Hu, J., Xue, Y. et al. Reply to: Ptbp1 deletion does not induce astrocyte-to-neuron conversion. Nature 618, E8–E13 (2023). https://doi.org/10.1038/s41586-023-06067-8