Published: 20 July 2023| Version 1 | DOI: 10.17632/9486bvt38w.1
Farhoud Faraji


Single cell RNAseq data of epithelia at 15 days post transgene induction.


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Single cell gene expression data was processed from the Illumina sequencer files using Cell Ranger (v5.0.0) and its prebuilt mouse reference genome. Individual sample data was then processed and merged using the Seurat (v4.3.0) SCTransform pipeline. Low quality cells (mitochondrial percentage >7, features <1000 and >5500, transcripts per cell >30,000) were filtered prior to data scaling and normalization. After filtering, data was transformed using SCTransform with default parameters, regressing on percent mitochondrial content. Principal component analysis was performed with RunPCA, using the top 50 PCs. Dimensionality reduction was performed with RunUMAP, using the top 30 dimensions. Nearest-neighbor analysis was performed using FindNeighbors using the top 30 dimensions and with k.param set to 50. Clustering was performed with FindClusters with resolution 0.3. Marker genes were calculated using FindAllMarkers with default parameters. Cluster identities were assigned by analysis of differential gene expression.


University of California San Diego Health Sciences


Single-Cell RNA Sequencing


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