Computational protocol: Single-Cell Deconvolution of Fibroblast Heterogeneity in Mouse Pulmonary Fibrosis

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Protocol publication

[…] We used Cell Ranger version 1.3.1 (10x Genomics) to process raw sequencing data and Cell Ranger R kit version 2.0.0 and Seurat suite version 2.0.0 (; ) for downstream analysis. For clustering, principal-component analysis was performed for dimension reduction. Top 10 principal components (PCs) were selected by using a permutation-based test implemented in Seurat and passed to t-SNE for clustering visualization. sSeq version 1.0.0 integrated in the Cell Ranger R kit was used for modeling the gene expression with negative binomial distribution to identify genes whose expression was enriched in specific clusters. The Benjamini-Hochberg procedure was used for correcting errors of multiple testing. […]

Pipeline specifications

Software tools Cell Ranger, t-SNE, sSeq
Application scRNA-seq analysis
Organisms Mus musculus, Homo sapiens
Chemicals Bleomycin