This repository contains single-cell RNA sequencing analysis of cardiac interstitial cells from WT and Hyaluronan Mediated Motility Receptor(Hmmr) overexpressing (OE) mice, 3 days (n = 3, 4) and 7 days (n = 3, 4) after acute myocardial infarction. Data were processed with the Seurat toolkit, using SCTransform normalization and reference-based integration with reciprocal PCA. WT samples were used as reference, OE samples as query.
Sequencing data, including fastq files and cellranger outputs can be found at ArrayExpress accession E-MTAB-12852, a public link will be available upon publication or request.
To recreate the full analysis you can follow the steps below. If you would like to process the data with your own custom workflow, a final list of cells (barcodes + metadata) after preprocessing, doublet removal and low-quality cluster removal can be found in:
data/basic_annotation.csv(all interstitial cells)data/mac_annotation.csv(re-clustered macrophage subset)
The following scRNA-seq-specific libraries were used:
- Seurat v4.0.1
- DoubletFinder v2.0.3
- ComplexHeatmap v2.13.1
- miloR v.1.2.0
- SingleCellExperiment v1.16.0
- scater v1.22.0
- edgeR v3.36.0
- clusterProfiler v4.2.1
- enrichplot v1.14.1
- org.Mm.eg.db v3.14.0
- yulab.utils v0.0.4
- condiments v1.2.0
- tradeSeq v1.8.0
- slingshot v2.2.1
To reproduce the analysis, clone this repository and place the filtered feature count matrices inside the data folder. It should then contain the following:
scRNAseq-Hmmr-OE/data/
day_3_filtered_feature_bc_matrix
day_7_filtered_feature_bc_matrix
basic_annotation.csv
canonical_markers.csv
cell_migration_GO_0016477.csv
leukocyte_chemotaxis_GO_0030595.csv
mac_annotation.csv
seurat_cell_cycle.csv
0-Hmmr-OE-complete-analysis.R will create all necessary directories and run the full analysis in the appropriate order. Each analysis step can also be run individually for better interactivity, starting from 1-Hmmr-OE-preprocessing.R. The estimated total memory needed to hold and process the resulting Seurat objects is ~120GB.
