Human Lung Cell Atlas

Human lung diagramAlthough single cell RNA sequencing studies have begun providing compendia of cell expression profiles, it has proven more difficult to systematically identify and localize all molecular cell types in individual organs to create a full molecular cell atlas. From droplet- and plate-based single cell RNA sequencing applied to ~75,000 human lung and blood cells, combined with a multi-pronged cell annotation approach that includes extensive tissue localization, we have defined the gene expression profiles and anatomical locations of 58 cell populations in the human lung, including 41 of 45 previously known cell types or subtypes and 14 new ones. Learn more in our manuscript and our GitHub repository.


Explore the data in your browser on hosted by the Chan Zuckerberg Initiative:

SmartSeq2 10x

Data availability

Thank you for your interest in obtaining access to Dr. Krasnow’s and Dr. Quake's lung single-cell RNA sequencing datasets. De-identified, non-raw data (count/UMI tables, metadata, and Seurat and scanpy objects for your own bioinformatic piplines) can be downloaded directly from Synapse. Because of human patient privacy considerations, in order to access raw sequencing reads, you must first establish an account with the European Genome-phenome Archive (EGA), submit a request to access EGAC00001001536, and sign a Data Access Agreement (DAA). You will receive a separate email from the Data Access Committee (DAC) containing additional instructions once your EGA request has been submitted.