Single-Cell RNA-seq Workshop: Processed Heart Development snRNA-seq Checkpoints

This record hosts pre-computed Seurat checkpoints for the Single-Cell RNA-seq Workshop, a methods-focused tutorial that analyses single-nucleus RNA-seq data from human heart tissue across foetal, young, and adult developmental stages.

Source data

All checkpoints are derived from the raw count matrix and cell metadata published in [Zenodo record 18237749](https://zenodo.org/records/18237749), which in turn comes from [Sim et al. (2021), Circulation 143(10):1614–1628](https://doi.org/10.1161/CIRCULATIONAHA.120.051921). The four disease samples were excluded; nine healthy samples were used (3 foetal, 3 young, 3 adult).

Files

01_qc_filtered.rds — Module 1 output. All 9 samples merged into a single Seurat (v5) object after per-cell quality control (`nFeature_RNA ≥ 500`, `nCount_RNA ∈ [2500, 40000]`, `percent.mt ≤ 20`) and gene-level filtering (mitochondrial, ribosomal, sex-chromosome, and unannotated genes removed).

02_integrated_clustered.rds — Module 2 output. 10,000-cell stratified downsample (proportional to per-sample cell counts), then:

SCTransform v2 normalisation with `glmGamPoi`

PCA on the top 20 components

Harmony integration on `sample`

UMAP on the Harmony embedding

The active identity is resolution 0.4, producing 17 clusters.

 03_annotated.rds— Module 3 output. Cluster-level marker discovery via Seurat::FindAllMarkers, plus per-cell `cell_type` and `cell_type_broad` columns from a hand-curated cluster → cell-type mapping (Cardiomyocyte subtypes, Fibroblasts, Endothelial, Macrophages, Epicardial, Neurons, T cells; broad categories also included).

afternoonSession.zip — Afternoon session (Module 5, 6, 7) input and intermediate results. Download, unzip and add files to data or results folder according to instructions.

Reproducibility

Generated with R 4.5.2, Bioconductor 3.22, Seurat 5.4.0, SeuratObject 5.3.0, harmony 1.2.4, glmGamPoi 1.22.0, sctransform 0.4.3, edgeR 4.8.2, limma 3.66.0, speckle 1.10.0. Exact package versions are pinned in [`renv.lock`](https://github.com/phipsonlab/single_cell_workshop/blob/main/renv.lock)  in the workshop repository.

Original analysis workflow: https://bphipson.github.io/Human_Development_snRNAseq/                     

Sim CB, Phipson B, Ziemann M, et al. Sex-Specific Control of Human Heart Maturation by the Progesterone Receptor. Circulation. 2021;143(10):1614-1628. doi:https://doi.org/10.1161/CIRCULATIONAHA.120.051921