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
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).
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 ID | Alt ID | Species | Sex | Age | Age Group | Weight | Strain | Genotype |
|---|---|---|---|---|---|---|---|---|
| LMSP0000001368 | E16_batch1 | Mus musculus | E16 | E16.5-E17.5 | ||||
| LMSP0000001369 | E16_batch2 | Mus musculus | E16 | E16.5-E17.5 | ||||
| LMSP0000001370 | E18_batch1 | Mus musculus | E18 | E17.5-E19.5 | ||||
| LMSP0000001371 | E18_batch2 | Mus musculus | E18 | E17.5-E19.5 | ||||
| LMSP0000001372 | PND1 | Mus musculus | P1 | P0-P3 | ||||
| LMSP0000001378 | PND10_batch1 | Mus musculus | P10 | P4-P36 | ||||
| LMSP0000001379 | PND10_batch2 | Mus musculus | P10 | P4-P36 | ||||
| LMSP0000001380 | PND14_batch1 | Mus musculus | P14 | P4-P36 | ||||
| LMSP0000001381 | PND14_batch2 | Mus musculus | P14 | P4-P36 | ||||
| LMSP0000001383 | PND28_batch1 | Mus musculus | P28 | P4-P36 | ||||
| LMSP0000001382 | PND28_batch2 | Mus musculus | P28 | P4-P36 | ||||
| LMSP0000001373 | PND3_batch1 | Mus musculus | P3 | P0-P3 | ||||
| LMSP0000001374 | PND3_batch2 | Mus musculus | P3 | P0-P3 | ||||
| LMSP0000001375 | PND7_batch1 | Mus musculus | P7 | P4-P36 | ||||
| LMSP0000001376 | PND7_batch2 | Mus musculus | P7 | P4-P36 | ||||
| LMSP0000001377 | PND7_batch3 | Mus musculus | P7 | P4-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 |