Seattle Organismal Molecular Atlases (SOMA)

Gene expression in mouse embryo

Cao, Spielmann et al. Nature (2019)

Species: Mus musculus

Samples: 61 embryos from E9.5 to E13.5

Method: sci-RNA-seq3

Cell count: ~2,000,000

Chromatin accessibility in the adult mouse

Cusanovich, Hill et al. Cell (2018)

Species: Mus musculus

Samples: 13 tissues from 8 wk male mice

Method: sci-ATAC-seq

Cell count: ~100,000

Chromatin accessibility in the developing fly embryo

Cusanovich, Reddington, Garfield et al. Nature (2018)

Species: Drosophila melanogaster

Samples: Whole embryos at 2-4, 6-8, 10-12 hrs

Method: sci-ATAC-seq

Cell count: ~23,000

Gene expression in the worm at the 2nd larval stage

Cao, Packer et al. Science (2017)

Species: Caenorhabditis elegans

Samples: Whole L2 stage worms

Method: sci-RNA-seq

Cell count: ~49,000

Single cell genomics can in principle reveal the molecular definition of every cell type in an entire animal. The Shendure, Trapnell and collaborating labs have begun generating "whole organism" single cell datasets for mouse, worm, fly and other animals, including of gene expression (sci-RNA-seq) and chromatin accessibility (sci-ATAC-seq). This website serves as a data portal and a repository for our analysis code and protocols. We also provide tutorials to assist you in downloading, analyzing and exploring these datasets.