LungMAP Data Explorer

Single-cell multiomic profiling of human lungs reveals cell-type-specific and age-dynamic control of SARS-CoV2 host genes

Updated October 20, 2023

Respiratory failure associated with COVID-19 has placed focus on the lungs. Here, we present single-nucleus accessible chromatin profiles of 90,980 nuclei and matched single-nucleus transcriptomes of 46,500 nuclei in non-diseased lungs from donors of ~30 weeks gestation,~3 years and ~30 years. We mapped candidate cis-regulatory elements (cCREs) and linked them to putative target genes. We identified distal cCREs with age-increased activity linked to SARS-CoV-2 host entry gene TMPRSS2 in alveolar type 2 cells, which had immune regulatory signatures and harbored variants associated with respiratory traits. At the 3p21.31 COVID-19 risk locus, a candidate variant overlapped a distal cCRE linked to SLC6A20, a gene expressed in alveolar cells and with known functional association with the SARS-CoV-2 receptor ACE2. Our findings provide insight into regulatory logic underlying genes implicated in COVID-19 in individual lung cell types across age. More broadly, these datasets will facilitate interpretation of risk loci for lung diseases.

Xin SunUniversity of California, San
Xin Sun (Principle Investigator)1
1University of California, San Diego

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Analysis Portals

LungMAP AppsLungMAP Apps

Project Label



Homo sapiens

Sample Type


Anatomical Entity


Organ Part

middle lobe of right lung

Selected Cell Types


Disease Status (Specimen)


Disease Status (Donor)

2 disease statuses

Development Stage

6 development stages

Library Construction Method

10x 3' v3 sequencing

Nucleic Acid Source

single nucleus

Paired End


Analysis Protocol

0b4eeed3-20be-4bd6-9a4f-0a6c3fe0fb25, c9d53f42-2afb-4b4f-baeb-fd881a51489e

File Format

7 file formats

Cell Count Estimate


Donor Count

barcodes11 file(s)fastq.gz56 file(s)h5ad1 file(s)mtx.gz11 file(s)regions11 file(s)tsv.gz1 file(s)txt.gz1 file(s)