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Sparse gene (row) by cell (column) matrices split by organs.

To compare cell types across organs, we randomly sampled 5,000 cells per cell type per organ (or in cases where less than 5,000 cells of a given cell type were represented in a given organ, all cells were taken). The data comprise gene count information including a total of 377,456 cells.

Annotation files for cell by gene count matrices

We performed DE gene analysis to identify differentially expressed genes across main cell types within each organ. We the idenfied genes that are differentially expressed across 77 main cell types across organs.

Garnett faciliates automated cell type classification from single-cell expression data. Garnett works by taking single-cell data, along with a cell type definition (marker) file, and training a regression-based classifier. Once a classifier is trained for a tissue/sample type, it can be applied to classify future datasets from similar tissues.

Matrix of normalized gene expression values (transcripts per million)

The proportion of cells in which a given gene was detected (UMI > 0)