LungMAP Data Explorer

Guided construction of a single cell reference (CellRef) for mouse lung

Updated February 7, 2023

Accurate cell type identification is a key and rate-limiting step in single cell data analysis. Single cell references with comprehensive cell types, reproducible and functional validated cell identities, and common nomenclatures are much needed by the research community to optimize automated cell type annotation and facilitate data integration, sharing, and collaboration. In the present study, we developed a novel computational pipeline to utilize the LungMAP CellCards as a dictionary to consolidate single-cell transcriptomic datasets of 17 mouse lung samples and constructed “LungMAP CellRef” and “LungMAP CellRef Seed” for both normal human and mouse lungs. “CellRef Seed” has an equivalent prediction power and produces consistent cell annotation as does “CellRef” but improves computational efficiency and simplifies its utilization for fast automated cell type annotation and online visualization. This atlas set incorporates 40 mouse well-defined lung cell types catalogued from diverse developmental time points. Using independent datasets, we demonstrated the utility of our CellRefs for automated cell type annotation analysis of both normal and disease lungs. User-friendly web interfaces were developed to support easy access and maximal utilization of the LungMAP CellRefs. LungMAP CellRefs are freely available to the pulmonary research community through fast interactive web interfaces to facilitate hypothesis generation, research discovery, and identification of cell type alterations in disease conditions.

Minzhe GuoCincinnati Children's Hospital Medical
Yan XuCincinnati Children's Hospital Medical Center
Minzhe Guo (Principal Investigator)1
Yan Xu (Principal Investigator)1
1Cincinnati Children's Hospital Medical Center

To reference this project, please use the following link:

Supplementary links are provided by contributors and represent items such as additional data which can’t be hosted here; code that was used to analyze this data; or tools and visualizations associated with this specific dataset.

GEO Series Accessions:

Downloaded data is governed by the LungMAP Data Release Policy.

Analysis Portals

LungMAP AppsLungMAP Apps

Project Label

Guided construction of a single cell reference (CellRef) for mouse lung


Mus musculus

Sample Type


Anatomical Entity

pair of lungs

Organ Part


Selected Cell Types


Disease Status (Specimen)


Disease Status (Donor)


Development Stage

4 development stages

Library Construction Method


Nucleic Acid Source

single cell

Paired End


Analysis Protocol


File Format

3 file formats

Cell Count Estimate


Donor Count

fastq.gz34 file(s)h5ad1 file(s)txt.gz15 file(s)