Mouse CellCards Multi-Study CellRef 1.0 Atlas
Minzhe Guo1*, Geremy Clair2, Joshua N. Adkins2, Gloria Pryhuber3, Ravi Misra3, Bruce Aronow1, Timothy L. Tickle4, Nathan Salomonis1, Xin Sun5, Edward E. Morrisey6, Jeffrey A. Whitsett1, Yan Xu1*
1Cincinnati Children's Hospital Medical Center, 2Pacific Northwest National Laboratory, 3University of Rochester Medical Center, 4The Broad Institute, 5University of California, San Diego, 6Perelman School of Medicine, University of Pennsylvania, *Corresponding author
The "LungMAP Mouse Lung CellRef" atlas incorporates 37 well-defined and 3 novel (Sox9+/Id2+ DEP ,EPC and PMP) lung cell types (CellCards) catalogued across lung development. This atlas spans sc/snRNA-seq of 95,658 lung cells from 17 samples across 8 timepoints from from embryonic day 16.5 to postnatal day 28, profiled using DropSeq. An accompanying R-shiny app (Azimuth) enables fast supervised annotation of user-provided single-cell RNA-Seq datasets (see below).
LungMAP ID: LMEX0000004397
Organism: mouse
Stages: E16.5-E17.5 | E17.5-E19.5 | P0-P3 | P4-P36
Assay type: Single-cell RNA-seq
Technology: Illumina Drop-Seq
Reference: Guo, et al. (2022)
LungMAP IDAlt IDSpeciesSexAgeAge GroupWeightStrainGenotype
LMSP0000001368E16_batch1Mus musculusE16E16.5-E17.5
LMSP0000001369E16_batch2Mus musculusE16E16.5-E17.5
LMSP0000001370E18_batch1Mus musculusE18E17.5-E19.5
LMSP0000001371E18_batch2Mus musculusE18E17.5-E19.5
LMSP0000001372PND1Mus musculusP1P0-P3
LMSP0000001378PND10_batch1Mus musculusP10P4-P36
LMSP0000001379PND10_batch2Mus musculusP10P4-P36
LMSP0000001380PND14_batch1Mus musculusP14P4-P36
LMSP0000001381PND14_batch2Mus musculusP14P4-P36
LMSP0000001383PND28_batch1Mus musculusP28P4-P36
LMSP0000001382PND28_batch2Mus musculusP28P4-P36
LMSP0000001373PND3_batch1Mus musculusP3P0-P3
LMSP0000001374PND3_batch2Mus musculusP3P0-P3
LMSP0000001375PND7_batch1Mus musculusP7P4-P36
LMSP0000001376PND7_batch2Mus musculusP7P4-P36
LMSP0000001377PND7_batch3Mus musculusP7P4-P36
File Description Size
Cell.Metadata.txt Cell Barcode-level metadata 3.3 MB
LungMAP_MouseLung_CellRef.v1.h5ad HDF5 annotated format single-cell data matrix 391.8 MB
LungMAP_MouseLung_CellRef.v1.1.h5ad HDF5 annotated format single-cell data matrix 404.1 MB
UMAP-coordinates.txt UMAP Coordinates for the Mouse CellRef full dataset 4.3 MB