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Zenodo
2026
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| Online Access: | https://doi.org/10.5281/zenodo.20017845 |
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- <p>This record hosts pre-computed Seurat checkpoints for the <a href="https://phipsonlab.github.io/single_cell_workshop/">Single-Cell RNA-seq Workshop</a>, a methods-focused tutorial that analyses single-nucleus RNA-seq data from human heart tissue across foetal, young, and adult developmental stages.</p> <h3>Source data</h3> <p>All checkpoints are derived from the raw count matrix and cell metadata published in <strong>[Zenodo record 18237749](https://zenodo.org/records/18237749)</strong>, which in turn comes from <strong>[Sim et al. (2021), <em>Circulation</em> 143(10):1614–1628](https://doi.org/10.1161/CIRCULATIONAHA.120.051921)</strong>. The four disease samples were excluded; nine healthy samples were used (3 foetal, 3 young, 3 adult).</p> <h3>Files</h3> <ul> <li><strong>01_qc_filtered.rds</strong> — 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<br> unannotated genes removed).</li> <li><strong>02_integrated_clustered.rds </strong>— Module 2 output. 10,000-cell<br> stratified downsample (proportional to per-sample cell counts), then: <ul> <li>SCTransform v2 normalisation with `glmGamPoi`</li> <li>PCA on the top 20 components</li> <li>Harmony integration on `sample`</li> <li>UMAP on the Harmony embedding</li> </ul> </li> </ul> <p>The active identity is resolution 0.4, producing 17 clusters.</p> <ul> <li> <strong>03_annotated.rds</strong>— Module 3 output. Cluster-level marker discovery via <code>Seurat::FindAllMarkers</code>, 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).</li> <li><strong>afternoonSession.zip</strong> — Afternoon session (Module 5, 6, 7) input and intermediate results. Download, unzip and add files to data or results folder according to instructions.</li> </ul> <h3>Reproducibility</h3> <p>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.</p> <p> </p> <div> <p>Original analysis workflow: https://bphipson.github.io/Human_Development_snRNAseq/ </p> <blockquote> <p>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 </p> </blockquote> </div>