PFC-MERFISH

Spatially resolved single cell transcriptome profiling of mouse PFC

We employed MERFISH, an imaging-based single cell spatial transcriptome technology, to decode organizational heterogeneity of cells in mouse prefrontal cortex (PFC).

Dependencies

These scripts are based on R (version 4.0.5)

Platform: x86_64-conda-linux-gnu (64-bit).

Running under: Ubuntu 20.04.3 LTS.

R packges

Seurat_4.0.5, SeuratObject_4.0.2, harmony_1.0, dplyr_1.0.7, ggplot2_3.3.5, cowplot_1.1.1, wholebrain_0.1.1, iSpatial_1.0.0, e1071_1.7-9, etc.

Main Scripts

• merFISH_pipeline.R: A pipeline for analyzing MERFISH data
• run_merFISH_pipeline.R: A script for integrating mulitple samples
• Neuron_projecting.R: A script for prediting extatitory neuron projection
• integrate_scRNA_merFISH.R: Integrate MERFISH and scRNA-seq data
• merFISH_Pain_0329.R: A script for identifying Pain related subtypes and genes

Data Visualization

UCSC Cell brower was used for MERFISH data visulization: Access

Supportive data

Single cell RNA-seq of PFC

single cell RNA-seq data including projection information