Journal: iScience

Article Title: Chrna5 and lynx prototoxins identify acetylcholine super-responder subplate neurons

doi: 10.1016/j.isci.2023.105992

Figure Lengend Snippet: Single-cell transcriptomic analysis reveals Chrna5+ subset to span subplate neuron populations with differential expression of lynx prototoxin genes (A) Single-cell RNA-seq data for 2422 L5-6 glutamatergic neurons in the anterior cingulate cortex (ACA, shown in schematic on the left) was obtained from publicly available datasets (Allen Institute, SMARTSeq ACA and MOP (2018)). ( Right ) Scatterplot showing Chrna5 vs Syt6 expression in log 10 (Copies per million +1) for each neuron, with the frequency distribution shown on the corresponding axes. Neurons were classified into Chrna5+, Chrna5+Syt6+, and Syt6+ groups based on their expression of Chrna5 and Syt6 genes. Cells which expressed neither gene were excluded from subsequent analyses. (B) The major neuronal subclasses within Chrna5+, Chrna5+Syt6+, and Syt6+ groups is indicated by the colorbar on top. NP- Near projecting, CT- Corticothalamic. Heatmap shows expression of subplate and corticothalamic marker genes in each cell in all 3 groups. (C) Dotplot shows summary of subplate and corticothalamic marker expression in Chrna5+, Chrna5+Syt6+, and Syt6+ groups. Dot size indicates the percentage of cells within each group expressing that gene, and color of the dot indicates average expression level relative to other groups. Chrna5+ neurons highly express multiple subplate-marker genes, but not corticothalamic markers. (D) Violin plots show expression of Lynx prototoxin genes Ly6g6e , Lypd1 (Lynx2), and Lypd6b which show highest fold change between Chrna5+ and Chrna5+Syt6+ neurons. (E) Dotplot shows expression of major genes known to modulate cholinergic function, including nicotinic, muscarinic subunits, acetylcholinesterase, and lynx prototoxins in Chrna5+, Chrna5+Syt6+, and Syt6+ neurons. Genes are ordered by decreasing fold change in expression. Dot size indicates the percentage of cells within each group expressing that gene, and color of the dot indicates average expression level relative to other groups. Fold change of all the genes shown in this dotplot are listed in Table S3 . (See Figure S5 for transcriptomic analysis of Chrna5+ neurons in other cortical areas showing conserved subplate markers and lynx prototoxin gene expression across cortical regions).

Article Snippet: Single cell RNAseq data for Anterior Cingulate Cortex (ACA) of adult mice was taken from the ACA and MOP Smart-Seq (2018) database, with cell-type annotations from Whole cortex & Hippocampus Smart-Seq (2019) database from the Allen Institute for Brain Science at https://portal.brain-map.org/atlases-and-data/rnaseq ., Single cell analysis was performed using the R package Seurat (v 4.04)., , Layer 5 and 6 glutamatergic neurons were selected and sorted into three cell classes based on their expression of Chrna5 and Syt6 genes: those expressing only Chrna5 (Chrna5+, n = 243), only Syt6 (Syt6+, n = 834), or both Chrna5 and Syt6 (Chrna5+Syt6+, n = 564).

Techniques: Quantitative Proteomics, RNA Sequencing, Expressing, Marker, Gene Expression

Journal: iScience

Article Title: Investigating microglia-neuron crosstalk by characterizing microglial contamination in human and mouse patch-seq datasets

doi: 10.1016/j.isci.2023.107329

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Article Snippet: Human MTG SMART-seq , Hodge et al., , Allen Institute for Brain Science Cell Types Database.

Techniques: Software

Journal: eLife

Article Title: Microglial trogocytosis and the complement system regulate axonal pruning in vivo

doi: 10.7554/eLife.62167

Figure Lengend Snippet:

Article Snippet: Other , Allen Brain Map Human Multiple Cortical Areas SMART-seq data set , Allen Institute for Brain Science , , .

Techniques: Recombinant, Plasmid Preparation, RNAscope, Multiplex Assay, Software, Transformation Assay