Journal: Cell Reports Methods

Article Title: Development and application of a barcoded rabies viral tracing method for mapping brain-wide inputs to single neurons

doi: 10.1016/j.crmeth.2025.101244

Figure Lengend Snippet: Investigation on the brain-wide synaptic connectome of mPFC neurons through BRT (A) Schematic representation of the plasmid constructs used for recovering CVS-N2cΔG rabies virus. N, P, L, and M denote the rabies nucleoprotein, phosphoprotein, large polymerase protein, and matrix protein, respectively. The sequence of the barcode region is shown below the diagram. (B and C) Schematic of the experimental setup: barcoded rabies virus is injected into the mPFC (B). After 9 days, the starter region was processed for scRNA-seq, while input regions were isolated and processed for bulk barcode sequencing (C). (D) UMAP embedding of mPFC cells from the reference data and cells from RV-infected animals. (E) UMAP embedding of cells from each animal. (F) Dot plot displaying the expression levels of RVΔG-mRuby-barcodes within each cell. (G) Dot plot summarizing the expression of key marker genes across transcriptomic subclasses. Vertical and horizontal lines delineate groups of genes and their associated subclasses. (H) Integration of unique barcodes to trace both local and long-range inputs for individual starter cells. (I) Comprehensive analysis showing the inputome and the transcriptomic subclass for each starter cell. Each column represents an individual starter cell. Rectangles between “Number of input cells” and “Input regions” indicate the types of each starter cell. The heatmap colors represent the relative strength of inputs from each brain region, with points below indicating the total barcode counts detected across all input regions for each starter cell.

Article Snippet: Meanwhile, we sequentially separated the long-range input regions from anterior to posterior under the microscope (MacroView MVX10, Olympus).

Techniques: Plasmid Preparation, Construct, Virus, Sequencing, Injection, Isolation, Infection, Expressing, Marker

Journal: Cell Reports Methods

Article Title: Development and application of a barcoded rabies viral tracing method for mapping brain-wide inputs to single neurons

doi: 10.1016/j.crmeth.2025.101244

Figure Lengend Snippet: High complexity of the long-range innervations of mPFC neurons (A) Binarized representation of input regions to all starter cells, clustered hierarchically using Euclidean distances. Black marks indicate the presence of a connection from an input region to a starter cell, with starter cells that have no detected barcodes in any input region also included. (B) Bar graph showing the percentage of starter cells that receive inputs from each input region. (C) Bar graph depicting the frequency distribution of input region numbers contributing to each starter cell. (D) Matrix displaying the conditional probabilities between pairs of input regions. The probability P(A|B) represents the likelihood that if a starter cell receives input from region B, it also receives input from region A. (E) Top panel: visualization of the bias in conditional probabilities between observed and randomized conditions. Hierarchical clustering was applied using Euclidean distances to group input regions. Bottom panel: violin plot depicting the distribution of input regions contributing to starter cells that receive input from a particular input region. (F) Significant positive correlation between the number of local input cells and the number of long-range input regions ( r = 0.71, p < 0.01, Spearman’s rank correlation). (G) Violin plots comparing the distribution of the number of input regions per starter cell, grouped according to the size of the local input cell population (∗Kruskal-Wallis rank-sum test followed by post hoc two-sided Dunn’s test, Bonferroni corrected p value < 0.01).

Article Snippet: Meanwhile, we sequentially separated the long-range input regions from anterior to posterior under the microscope (MacroView MVX10, Olympus).

Techniques: