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Deprez et al. 2020, Goldfarbmuren et al. 2020, Reyfman et al. 2019, Adams et al. 2020, Habermann et al. 2020 and an unpublished lung biopsy patient cohort.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259k cells from 72 donors from five published (PMIDs: 32726565, 32427931, 30554520, 32832599, 32832598) and one unpublished single cell RNA-seq cohort.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
ClusterCell Cards NameCell Cards MarkersCell OntologyCluster Markers
AF1Alveolar Matrix Fibroblast 1WNT2, TCF21linkSCN7A, ADH1B, C7, LUM, FGFR4, WNT2, COL13A1, TCF21, INMT, CCBE1
AF2Alveolar Matrix Fibroblast 2MFAP5, SCARA5linkSFRP2, PLA2G2A, MFAP5, FBLN1, LAMA2, ADH1B, PI16, LUM, FBN1, SCARA5
aMacAlveolar macrophagesSIGLEC1, ABCG1, FABP4, MARCOlinkSIGLEC1, OLR1, MSR1, SLC11A1, MARCO, PPARG, MRC1, C1QC, MS4A6E, VSIG4
ArterialArterial endothelial cellsGJA5, DKK2linkLDB2, AC007319.1, DKK2, ANO2, PTPRB, GNA14, ERG, ST6GALNAC3, RP3-510L9.1, PREX2
ASMCAirway smooth muscle cellsACTA2, LGR6linkACTG2, DES, CNN1, BCHE, PLN, SBSPON, ACTA2, MYH11, FAM83D, TYRP1
AT1Alveolar type 1 cellsAGER, HOPX, RTKN2linkAGER, RTKN2, CEACAM6, CLDN18, SFTA2, SUSD2, SPOCK2, SCEL, AQP4, ANKRD29
AT2Alveolar type 2 cellsSFTPC, LAMP3linkSFTPA1, SFTPA2, PGC, NAPSA, SLC34A2, LAMP3, SFTPD, ABCA3, SFTA2, LRRK2
BB cellsCD19, CD20linkMS4A1, BANK1, CD79A, CD22, TNFRSF13C, CD19, LINC00926, BLK, PAX5, IGHD
BasalBasal cellsTP63, KRT5linkKRT5, KRT15, KRT17, TP63, FGFBP1, LGALS7B, ADH7, COL17A1, SERPINB13, FGFR3
Basophils/MastBasophils and Mast cellsMS4A2, TPSAB1, TPSB2, KIT, GATA2 linkTPSAB1, TPSB2, CPA3, TPSD1, MS4A2, HPGDS, KIT, C1orf186, SLC18A2, RGS13
Cap1Capillary 1 cellsIL7RH, APLNR, GPIHBP1linkFCN3, SLC6A4, BTNL9, GPIHBP1, TMEM100, PTPRB, VWF, IL7R, VIPR1, FOXF1
Cap2Capillary 2 cellsEDNRB, HPGD, APLN, CA4linkEDNRB, IL1RL1, HPGD, EMCN, SOSTDC1, CA4, VIPR1, FENDRR, PRX, BTNL9
CiliatedCiliated cellsFOXJ1, RSPH1linkC20orf85, RSPH1, C9orf24, TMEM190, C1orf194, FAM183A, PIFO, TPPP3, FOXJ1, AGR3
GobletGoblet cellsMUC5AC, SPDEFlinkMUC5AC, S100P, PSCA, CEACAM5, DHRS9, CYP2F1, SPDEF, SERPINB11, RP1-122P22.4, ERN2
iMacInterstitial macrophagesC1QA, C1QB, C1QC, HLA-DPA1, SLC40A1 linkMCEMP1, TREM1, RP5-839B4.8, MARCO, RETN, VSIG4, C1QC, GLDN, MS4A4A, CCL18
IonocyteIonocytesFOXI1, ASCL3, CFTRlinkASCL3, BPIFA2, CEL, TMEM61, FOXI1, CFTR, CLCNKB, ATP6V1G3, TMPRSS11E, HEPACAM2
LymphaticsLymphatic endothelial cellsPROX1, MMRN1linkCCL21, MMRN1, PROX1, PKHD1L1, LYVE1, SEMA3D, TM4SF18, FLT4, RELN, RP11-322E11.5
maDCDC matureCCL19, CCR7, NCCRP1, LAD1, LAMP3linkCCL22, CCR7, CRLF2, IRF4, TRAF1, ANKRD33B, TNFRSF9, LAMP3, EBI3, ENOX1
mDC1Myeloid DC subset 1CD1C, CD1E, FCGR2B, CLEC10AlinkCLEC10A, MS4A6A, FCGR2B, CSF1R, CD1C, CD1E, F13A1, FCER1A, MS4A4E, JAML
mDC2Myeloid DC subset 2FLT3, CLEC9A, ZBTB46linkWDFY4, IRAK2, CLEC9A, RP11-761N21.1, MCOLN2, CLNK, LGALS2, RAB7B, KIAA0226L, FLT3
MECMyoepithelial cellTP63, ACTA2, SMMHC, MYH11, VIM, KRT5, KRT14linkSFRP1, KRT14, MEG3, KRT23, CHI3L1, FBXO2, COL17A1, NGFR, NTRK2, WIF1
MesothelialMesothelial cellsWT1, UPK3B, FREM2linkPRG4, CALB2, C4B, HAS1, WT1, C4A, RP11-123O22.1, GALNT9, RP11-74M11.2, PLA2G2A
MonocytePatrolling (non-classical) monocytesCD14, CD16linkFCN1, S100A12, CFP, CD300E, CD14, LILRA5, VCAN, MPEG1, RNASE2, LILRB2
MucousMucous cellsMUC5B, SPDEFlinkBPIFB2, MUC5B, AZGP1, TFF1, TCN1, FCGBP, FAM3D, NKX3-1, CRISP3, DEFB1
NKNatural Killer cellsSPTSSB, NKG7, KLRD1, KLRC1linkGNLY, KLRB1, NKG7, GZMA, CCL4, CCL5, PRF1, KLRD1, CD7, GZMB
pDCPlasmacytoid DCCLEC4C, LILRA4, IRF7, PLD4linkCLEC4C, SCT, SHD, LINC01478, LILRA4, KCNK10, RP11-73G16.2, FAM129C, PLD4, LAMP5
PericytePericytesPDGFRB, TRPC6linkPDGFRB, FHL5, COX4I2, GJA4, HIGD1B, PPP1R14A, ACTA2, LAMC3, BGN, HEYL
PlasmaPlasma cellsSDC1, CD38linkJCHAIN, IGHA2, MZB1, IGLV3-1, IGLL5, DERL3, CD27, CD79A, TNFRSF17, FCRL5
pMacProliferative MacrophageMKI67, TOP2A, PTPRC, MARCOlinkMKI67, TOP2A, UBE2C, NUSAP1, CENPF, CTD-2116N17.1, TYMS, CDK1, DIAPH3, TPX2
PNECPulmonary neuroendocrine cellsASCL1, GRP, CALCAlinkGRP, CALCA, SCG2, PCSK1N, ASCL1, CHGA, GP2, SCG5, CHGB, SYT1
SCMFSecondary crest myofibroblastsLTBP2, STC1, FGF18linkDPT, FBLN1, MFAP4, LUM, CCL11, SFRP4, LTBP2, PODN, FBLN2, MMP2
SecretorySecretory cellsSCGB1A1, SCGB3A2linkSERPINB3, CYP2F1, SULT2B1, GABRP, KRT4, ADH7, FAM3D, CLCA2, UPK1B, CHP2
SerousSerous cellsLYZ, LTFlinkLTF, PRB3, PRB4, PIP, C6orf58, DMBT1, AZGP1, TCN1, S100A1, ODAM
TT cellCD3D, CD4, CD8AlinkCD3D, CD3E, CCL5, CD8A, CD2, GZMH, GZMA, CD8B, CD3G, TRBC2
TuftTuft cellsPOU2F3, ASCL2, DCLK1linkPOU2F3, GUCA1A, CTD-2089N3.2, MEX3A, IL23A, OVOL3, MYB, NREP, GNG13, ARL9
VenousVenous endothelial cellsACKR1, PDZRN4, SLC6A2, PRSS23linkACKR1, VWF, CCL23, PLVAP, SELP, CADM3-AS1, EPHB4, MEOX1, TSPAN7, RAMP3
VSMCVascular smooth muscle cellsNTRK3, ITGA7, CNN1linkRERGL, NDUFA4L2, NOTCH3, FRZB, PLN, ITGA7, NTRK2, GJA4, COX4I2, CASQ2