ARG_HPC_snRNAseq

This project contains R code for analysis of single-nucleus RNA-sequencing data from mouse and human hippocampal neurons.

Description of analyses

00_check_read_lengths

• Script to check read 1 files for discrepant read lengths. Should be (and are) exactly 28bp = 16 [BC] + 12 [UMI].

01_align

• Scripts to align sequencing data from all samples using 10x Genomics’ cellranger count version 3.0.2. [here]

02_processing

• Script to build initial SingleCellExperiment (sce) object, filter empty droplets, perform quality control, remove doublets, and build new HPC-only sce object.

03_clustering_annotation

• Script to cluster HPC nuclei, annotate cluster, and build figure 1 plots.

04_broad_de_analysis

• Script to perform initial, sample-level (non-cell type specific) pseudobulk differential expression analysis, perform GO over-representation analysis (ORA), and build figure 2 plots.

05_cell_type_specific_de_analysis

• Script to perform cell type specific pseudobulk differential expression analysis and build figure 3 plots.

06_gsea

• Script to run gene set enrichment analysis (GSEA) on cell type-specific DE analysis results for GO terms within biological process (BP), cellular component (CC), and molecular function (MF) domains.
• Script to process GSEA results, perform semantic similarity clustering of GO terms, and build figure 4 plots.
• Script to make heatmaps for figure 4 plots.

07_nmf

• Script to perform non-negative matrix factorization (NMF) using CoGAPS.
• Script to build figure 5 plots.

Processed data

• File containing SingleCellExperiment object with all nuclei (pre-thalamic neuron removal) [here] https://github.com/Erik-D-Nelson/ARG_HPC_snRNAseq/blob/main/processed_data/sce_total.rda.xz
• File containing SingleCellExperiment object with HPC nuclei only [here] https://github.com/Erik-D-Nelson/ARG_HPC_snRNAseq/blob/main/processed_data/sce_subset.rda.xz