Guided construction of a single cell reference (CellRef) for mouse lung
Updated February 7, 2023Accurate 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.
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Analysis Portals

Project Label
Guided construction of a single cell reference (CellRef) for mouse lungSpecies
Mus musculus
Sample Type
specimens
Anatomical Entity
pair of lungs
Organ Part
Unspecified
Selected Cell Types
Unspecified
Disease Status (Specimen)
Unspecified
Disease Status (Donor)
Unspecified
Development Stage
Library Construction Method
Drop-seq
Nucleic Acid Source
single cell
Paired End
falseAnalysis Protocol
a9a30412-66a1-4c3e-a226-d46e6b169902File Format
Cell Count Estimate
UnspecifiedDonor Count
16