Abstract

The Human Cell Atlas is a large international collaborative effort to map all cell types of the human body. Single cell RNA sequencing can generate high quality data for the delivery of such an atlas.

We obtained lung, oesophagus and spleen samples from 12 healthy organ donors to create single cell RNA sequencing (sc-RNA-seq) dataset of 240,000 cells. This includes the largest published datasets on human oesophagus and spleen to date, which we provide in an easy to browse data portal: www.tissuestabilitycellatlas.org.

In lung, 57,020 cells represented 25 cell types including ciliated, alveolar types 1 and 2 cells, fibroblasts, muscle and endothelial cells both from blood and lymph vessels, as well as cell types identified from the immune compartment including NK, T and B-cells, two types of macrophages, monocytes and dendritic cells. Oesophagus yielded 87,947 cells with over 90% belonging to the four major epithelial cell types: upper, stratified, suprabasal and dividing cells of the suprabasal layer. We further defined rare cells from the mucous glands and the duct with frequency of

In addition to high resolution map of the cell composition of the three tissues we provide insights into the tissue architecture and considerations for limitations of the sampling for providing Human Cell Atlas. Furthermore, we describe both intra and inter-individual variability especially in the immune compartment, and describe dissociation-related gene expression by comparison to the bulk RNA sequencing.

Overall, we have generated detailed annotations on three primary human tissues: spleen, oesophagus and lung. This dataset of over 240,000 single cells presents a significant resource for further investigation of the biology of these tissues and contains the largest oesophagus and spleen datasets to date. In addition, we make available WGS data from thirteen healthy donors including clinical metadata, allowing for future tissue-specific, single cell eQTL studies.