Multiomic single-cell profiling reveals critical regulators of postnatal brain.

Project Overview - snMultiome This repository contains scripts for the snMultiome postnatal project, focused on the analysis and integration of multi-modal single-cell data, specifically RNA-seq and ATAC-seq. Below is an overview of the scripts used in the project. Further information, including relevant input data files, can be found in synapse under SynID: syn62738189. SnMultiome Analysis - Preprocessing Date: August 2024 Script Name: preprocess_merge.R Description: Pre-processes single-cell RNA-seq and ATAC-seq data from multiple samples using Seurat and Signac, merges data into a single Seurat object, and saves the output. SnMultiome Analysis - Filtering and Clustering Date: August 2024 Script Name: filter_cluster.R Description: Loads a pre-processed Seurat object with multi-modal data (RNA and ATAC-seq), performs filtering, normalization, dimensional reduction, and clustering, then saves the processed object. Outputs: Potential plots for Fig. 1b, e. Variance Partition and crumblr Analysis Date: August 2024 Script Name: VarPart_crumblr.R Description: Performs VariancePartition analysis and crumblr. Outputs: Potential plots for Fig. 1e, Fig. 5b. MAGMA and LDsc Analysis Date: August 2024 Script Name: magma_ldsc.R Description: Analyzes enrichment (MAGMA / LDsc) and TOBIAS results. Outputs: Plots for Fig. 2c, 2e, 3a, 6c, and S6. ABC-Max Analysis Date: August 2024 Script Name: abcmax.R Description: Processes genomic data for various GWAS traits and linkage disequilibrium (LD) buddies, focusing on ABC-MAX analysis (peak overlap with GWAS SNPs and causal genes). Outputs: Plots for Fig. 3-4, Fig. S8-S17, Table S8-S10. Pseudotime analysis using Monocle3 Date: August 2024 Script Name: pseudotime.R Description: Processes a Seurat object, converts it to a Monocle3 cell_data_set, performs trajectory inference, and identifies temporal genes using Moran's I test. Outputs: Potential plots for Fig. 5a, c-d. Hotspot assignment and SCENIC+ correlation with pseudotime Date: August 2024 Script Name: OPCOligo_Hotspot_SCENIC.R Description: Performs module scoring and downstream analysis for Hotspot results and pseudotime, including correlation analysis between pseudotime and SCENIC results. Outputs: Potential plots for Fig. 5e-f, Fig. 6 a-c.