DESCRIPTION:
We performed single cell RNA sequencing (scRNA-seq) to classify all neuron subtypes in prefrontal cortex (PFC) of adolescent (P21) (N = 4) and adult (P60) (N = 12) male C57BL/6 mice (strain mentioned but not explicit in publication) to characterize the transcriptional changes associated with this period (P21-P60). 12 independent biological replicates were used for each age. Each biological replicate was generated by pooling brain tissue from two mice (see methods for more info). To detect similar populations and identify corresponding cell clusters between the 10,646 P21 cells and the 11, 886 P60 PFC cells, we aligned the two scRNA-seq data sets in t-SNE by cross-correlation analysis (CCA)17 (Fig. (Fig.4a).4a). Using bootstrapped correlation, all clusters identified in the adult PFC are detected in the P21 PFC. Based on the expression of cell type-specific markers, the non-neuronal cells were clustered as: astrocytes (Gja1+), oligodendrocyte (Aspa+), newly formed (NF) oligodendrocytes (Bmp4+), oligodendrocyte precursors (OPC) (Pdgfra+), microglia (C1qa+) and endothelial cells (Flt1+) (Fig. 1c, d). The neurons express Snap25 and can be divided into excitatory (Slc17a7+) and inhibitory (Gad2+) neurons (Fig. 1c, d). We then analyzed transcriptional dynamics in each of the neuron subtypes between adolescence (P21) and adulthood (P60) in mouse. The differentially expressed genes between P21 and P60 cells for each cluster was performed using the “FindMarkers” function from the Seurat package using a likelihood ratio test and correcting for the number of detected unique molecular identifier (UMI) bias. Genelists contain significantly differentiated genes in each cell population cluster with fold change > 1.5 and p < 0.05.
LABEL:
Sig. DEG mouse PFC excitatory neurons (cluster 11) P21 vs. P60_pvalue
SCORE TYPE:
P-Value
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