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
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Description 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).
Dataset ID LMEX0000004397
Assay Type Single-cell RNA-seq
Organism Mouse
Stages E16.5-E17.5 | E17.5-E19.5 | P0-P3 | P4-P36 | P4-P10 | P11-P20 | P21-P41
Cell Count 95658
Technology Illumina Drop-Seq
Reference Guo, et al. (2022)
FileDescriptionSize
Cell.Metadata.txtCell Barcode-level metadata3.3 MB
LungMAP_MouseLung_CellRef.v1.1.h5adHDF5 annotated format single-cell data matrix404.1 MB
LungMAP_MouseLung_CellRef.v1.h5adHDF5 annotated format single-cell data matrix391.8 MB
UMAP-coordinates.txtUMAP Coordinates for the Mouse CellRef full dataset4.3 MB
LungMAP IDAlt IDSpeciesAgeAge Group
LMSP0000001368E16_batch1Mus musculus16 EE16.5-E17.5
LMSP0000001369E16_batch2Mus musculus16 EE16.5-E17.5
LMSP0000001370E18_batch1Mus musculus18 EE17.5-E19.5
LMSP0000001371E18_batch2Mus musculus18 EE17.5-E19.5
LMSP0000001372PND1Mus musculus1 PP0-P3
LMSP0000001378PND10_batch1Mus musculus10 PP4-P10
LMSP0000001379PND10_batch2Mus musculus10 PP4-P10
LMSP0000001380PND14_batch1Mus musculus14 PP11-P20
LMSP0000001381PND14_batch2Mus musculus14 PP11-P20
LMSP0000001383PND28_batch1Mus musculus28 PP21-P41
LMSP0000001382PND28_batch2Mus musculus28 PP21-P41
LMSP0000001373PND3_batch1Mus musculus3 PP0-P3
LMSP0000001374PND3_batch2Mus musculus3 PP0-P3
LMSP0000001375PND7_batch1Mus musculus7 PP4-P10
LMSP0000001376PND7_batch2Mus musculus7 PP4-P10
LMSP0000001377PND7_batch3Mus musculus7 PP4-P10