Human - Lung - Cell Cards
Overview
Modalities: RNA
Cells in Reference: 7,400
Species: Human
Reference Dataset(s): Integration from Deprez et al. 2020, Goldfarbmuren et al. 2020, Reyfman et al. 2019, Adams et al. 2020, Habermann et al. 2020 and an unpublished lung biopsy patient cohort.
Demo Dataset(s): Human 24 year old male LGEA, LungMAP, h5 file
This LungMAP scRNA-Seq reference is associated with the Lung CellCards resource. This initial reference integrated 259k cells from 72 donors from five published (PMIDs: 32726565, 32427931, 30554520, 32832599, 32832598) and one unpublished single cell RNA-seq cohort. It consists of non-diseased adult and pediatric healthy lung single-cell 10x Genomics captures (3’ v2 and v3). Sparse matrices were integrated from different donors using the software Batchlor. Preliminary cell types were called based on Leiden clustering analysis and expression patterns of LungMAP cell card markers. UMAP embeddings were generated using monocle3. This reference, along with a corresponding single-nucleus specific version of this atlas, is under active construction. We expect to release the beta version of the reference in November 2021.
Annotation Details
annotation.l1
Cluster | Cell Cards Name | Cell Cards Markers | Cell Ontology | Cluster Markers |
---|---|---|---|---|
AF1 | Alveolar Matrix Fibroblast 1 | WNT2, TCF21 | link | SCN7A, ADH1B, C7, LUM, FGFR4, WNT2, COL13A1, TCF21, INMT, CCBE1 |
AF2 | Alveolar Matrix Fibroblast 2 | MFAP5, SCARA5 | link | SFRP2, PLA2G2A, MFAP5, FBLN1, LAMA2, ADH1B, PI16, LUM, FBN1, SCARA5 |
aMac | Alveolar macrophages | SIGLEC1, ABCG1, FABP4, MARCO | link | SIGLEC1, OLR1, MSR1, SLC11A1, MARCO, PPARG, MRC1, C1QC, MS4A6E, VSIG4 |
Arterial | Arterial endothelial cells | GJA5, DKK2 | link | LDB2, AC007319.1, DKK2, ANO2, PTPRB, GNA14, ERG, ST6GALNAC3, RP3-510L9.1, PREX2 |
ASMC | Airway smooth muscle cells | ACTA2, LGR6 | link | ACTG2, DES, CNN1, BCHE, PLN, SBSPON, ACTA2, MYH11, FAM83D, TYRP1 |
AT1 | Alveolar type 1 cells | AGER, HOPX, RTKN2 | link | AGER, RTKN2, CEACAM6, CLDN18, SFTA2, SUSD2, SPOCK2, SCEL, AQP4, ANKRD29 |
AT2 | Alveolar type 2 cells | SFTPC, LAMP3 | link | SFTPA1, SFTPA2, PGC, NAPSA, SLC34A2, LAMP3, SFTPD, ABCA3, SFTA2, LRRK2 |
B | B cells | CD19, CD20 | link | MS4A1, BANK1, CD79A, CD22, TNFRSF13C, CD19, LINC00926, BLK, PAX5, IGHD |
Basal | Basal cells | TP63, KRT5 | link | KRT5, KRT15, KRT17, TP63, FGFBP1, LGALS7B, ADH7, COL17A1, SERPINB13, FGFR3 |
Basophils/Mast | Basophils and Mast cells | MS4A2, TPSAB1, TPSB2, KIT, GATA2 | link | TPSAB1, TPSB2, CPA3, TPSD1, MS4A2, HPGDS, KIT, C1orf186, SLC18A2, RGS13 |
Cap1 | Capillary 1 cells | IL7RH, APLNR, GPIHBP1 | link | FCN3, SLC6A4, BTNL9, GPIHBP1, TMEM100, PTPRB, VWF, IL7R, VIPR1, FOXF1 |
Cap2 | Capillary 2 cells | EDNRB, HPGD, APLN, CA4 | link | EDNRB, IL1RL1, HPGD, EMCN, SOSTDC1, CA4, VIPR1, FENDRR, PRX, BTNL9 |
Ciliated | Ciliated cells | FOXJ1, RSPH1 | link | C20orf85, RSPH1, C9orf24, TMEM190, C1orf194, FAM183A, PIFO, TPPP3, FOXJ1, AGR3 |
Goblet | Goblet cells | MUC5AC, SPDEF | link | MUC5AC, S100P, PSCA, CEACAM5, DHRS9, CYP2F1, SPDEF, SERPINB11, RP1-122P22.4, ERN2 |
iMac | Interstitial macrophages | C1QA, C1QB, C1QC, HLA-DPA1, SLC40A1 | link | MCEMP1, TREM1, RP5-839B4.8, MARCO, RETN, VSIG4, C1QC, GLDN, MS4A4A, CCL18 |
Ionocyte | Ionocytes | FOXI1, ASCL3, CFTR | link | ASCL3, BPIFA2, CEL, TMEM61, FOXI1, CFTR, CLCNKB, ATP6V1G3, TMPRSS11E, HEPACAM2 |
Lymphatics | Lymphatic endothelial cells | PROX1, MMRN1 | link | CCL21, MMRN1, PROX1, PKHD1L1, LYVE1, SEMA3D, TM4SF18, FLT4, RELN, RP11-322E11.5 |
maDC | DC mature | CCL19, CCR7, NCCRP1, LAD1, LAMP3 | link | CCL22, CCR7, CRLF2, IRF4, TRAF1, ANKRD33B, TNFRSF9, LAMP3, EBI3, ENOX1 |
mDC1 | Myeloid DC subset 1 | CD1C, CD1E, FCGR2B, CLEC10A | link | CLEC10A, MS4A6A, FCGR2B, CSF1R, CD1C, CD1E, F13A1, FCER1A, MS4A4E, JAML |
mDC2 | Myeloid DC subset 2 | FLT3, CLEC9A, ZBTB46 | link | WDFY4, IRAK2, CLEC9A, RP11-761N21.1, MCOLN2, CLNK, LGALS2, RAB7B, KIAA0226L, FLT3 |
MEC | Myoepithelial cell | TP63, ACTA2, SMMHC, MYH11, VIM, KRT5, KRT14 | link | SFRP1, KRT14, MEG3, KRT23, CHI3L1, FBXO2, COL17A1, NGFR, NTRK2, WIF1 |
Mesothelial | Mesothelial cells | WT1, UPK3B, FREM2 | link | PRG4, CALB2, C4B, HAS1, WT1, C4A, RP11-123O22.1, GALNT9, RP11-74M11.2, PLA2G2A |
Monocyte | Patrolling (non-classical) monocytes | CD14, CD16 | link | FCN1, S100A12, CFP, CD300E, CD14, LILRA5, VCAN, MPEG1, RNASE2, LILRB2 |
Mucous | Mucous cells | MUC5B, SPDEF | link | BPIFB2, MUC5B, AZGP1, TFF1, TCN1, FCGBP, FAM3D, NKX3-1, CRISP3, DEFB1 |
NK | Natural Killer cells | SPTSSB, NKG7, KLRD1, KLRC1 | link | GNLY, KLRB1, NKG7, GZMA, CCL4, CCL5, PRF1, KLRD1, CD7, GZMB |
pDC | Plasmacytoid DC | CLEC4C, LILRA4, IRF7, PLD4 | link | CLEC4C, SCT, SHD, LINC01478, LILRA4, KCNK10, RP11-73G16.2, FAM129C, PLD4, LAMP5 |
Pericyte | Pericytes | PDGFRB, TRPC6 | link | PDGFRB, FHL5, COX4I2, GJA4, HIGD1B, PPP1R14A, ACTA2, LAMC3, BGN, HEYL |
Plasma | Plasma cells | SDC1, CD38 | link | JCHAIN, IGHA2, MZB1, IGLV3-1, IGLL5, DERL3, CD27, CD79A, TNFRSF17, FCRL5 |
pMac | Proliferative Macrophage | MKI67, TOP2A, PTPRC, MARCO | link | MKI67, TOP2A, UBE2C, NUSAP1, CENPF, CTD-2116N17.1, TYMS, CDK1, DIAPH3, TPX2 |
PNEC | Pulmonary neuroendocrine cells | ASCL1, GRP, CALCA | link | GRP, CALCA, SCG2, PCSK1N, ASCL1, CHGA, GP2, SCG5, CHGB, SYT1 |
SCMF | Secondary crest myofibroblasts | LTBP2, STC1, FGF18 | link | DPT, FBLN1, MFAP4, LUM, CCL11, SFRP4, LTBP2, PODN, FBLN2, MMP2 |
Secretory | Secretory cells | SCGB1A1, SCGB3A2 | link | SERPINB3, CYP2F1, SULT2B1, GABRP, KRT4, ADH7, FAM3D, CLCA2, UPK1B, CHP2 |
Serous | Serous cells | LYZ, LTF | link | LTF, PRB3, PRB4, PIP, C6orf58, DMBT1, AZGP1, TCN1, S100A1, ODAM |
T | T cell | CD3D, CD4, CD8A | link | CD3D, CD3E, CCL5, CD8A, CD2, GZMH, GZMA, CD8B, CD3G, TRBC2 |
Tuft | Tuft cells | POU2F3, ASCL2, DCLK1 | link | POU2F3, GUCA1A, CTD-2089N3.2, MEX3A, IL23A, OVOL3, MYB, NREP, GNG13, ARL9 |
Venous | Venous endothelial cells | ACKR1, PDZRN4, SLC6A2, PRSS23 | link | ACKR1, VWF, CCL23, PLVAP, SELP, CADM3-AS1, EPHB4, MEOX1, TSPAN7, RAMP3 |
VSMC | Vascular smooth muscle cells | NTRK3, ITGA7, CNN1 | link | RERGL, NDUFA4L2, NOTCH3, FRZB, PLN, ITGA7, NTRK2, GJA4, COX4I2, CASQ2 |