Construction of a human cell landscape at single-cell level
Xiaoping Han, Ziming Zhou, Lijiang Fei, Huiyu Sun, Renying Wang, Yao Chen, Haide Chen, Jingjing Wang, Huanna Tang, Wenhao Ge, Yincong Zhou, Fang Ye, Mengmeng Jiang, Junqing Wu, Yanyu Xiao, Xiaoning Jia, Tingyue Zhang, Xiaojie Ma, Qi Zhang, Xueli Bai, Shujing Lai, Chengxuan Yu, Lijun Zhu, Rui Lin, Yuchi Gao, Min Wang, Yiqing Wu, Jianming Zhang, Renya Zhan, Saiyong Zhu, Hailan Hu, Changchun Wang, Ming Chen, He Huang, Tingbo Liang, Jianghua Chen, Weilin Wang, Dan Zhang, Guoji Guo
Abstract
Single-cell analysis is a valuable tool for dissecting cellular heterogeneity in complex systems1. However, a comprehensive single-cell atlas has not been achieved for humans. Here we use single-cell mRNA sequencing to determine the cell-type composition of all major human organs and construct a scheme for the human cell landscape (HCL). We have uncovered a single-cell hierarchy for many tissues that have not been well characterized. We established a ‘single-cell HCL analysis’ pipeline that helps to define human cell identity. Finally, we performed a single-cell comparative analysis of landscapes from human and mouse to identify conserved genetic networks. We found that stem and progenitor cells exhibit strong transcriptomic stochasticity, whereas differentiated cells are more distinct. Our results provide a useful resource for the study of human biology.
Datasets
1. Construction of a human cell landscape at single-cell level
Metadata
disease_ontology_term_id
self_reported_ethnicity_ontology_term_id
tissue_original
assay_ontology_term_id
tissue_ontology_term_id
author_cell_type
cell_type_ontology_term_id
development_stage_ontology_term_id
sex_ontology_term_id
organism_ontology_term_id
donor_id
suspension_type
tissue_type
cell_type
assay
disease
organism
sex
tissue
self_reported_ethnicity
development_stage
HANCESTRO:0027599926 cells FetalIntestine23516 cells AdultAdrenalGland23197 cells AdultPeripheralBlood17331 cells AdultTransverseColon16994 cells CordBloodCD34P16904 cells FetalAdrenalGland14416 cells FetalMaleGonad13211 cells AdultEsophagus11364 cells ChorionicVillus9898 cells AdultGallbladder9769 cells AdultTemporalLobe9544 cells AdultBoneMarrow8704 cells AdultCerebellum7324 cells FetalFemaleGonad6941 cells AdultFallopiantube6556 cells FetalSpinalCord5916 cells NeonatalAdrenalGland5863 cells AdultEpityphlon4486 cells AdultSigmoidColon3281 cells AdultAscendingColon2026 cells UBERON:000211345630 cells UBERON:000236943476 cells UBERON:000204833698 cells UBERON:000210728501 cells UBERON:000126428473 cells UBERON:000163026120 cells UBERON:000016023516 cells UBERON:001216823498 cells UBERON:000094522577 cells UBERON:000097719695 cells UBERON:000017817331 cells UBERON:000115716994 cells UBERON:000210615806 cells UBERON:000095513625 cells UBERON:000047313211 cells UBERON:000368812812 cells UBERON:000204612647 cells UBERON:000104311364 cells UBERON:000094810783 cells B cell (Plasmocyte)27737 cells Fetal mesenchymal progenitor22915 cells Fasciculata cell22652 cells Smooth muscle cell22077 cells Fetal stromal cell21405 cells Epithelial cell18927 cells Fetal epithelial progenitor18559 cells Endothelial cell17205 cells Enterocyte progenitor16008 cells Erythroid cell13110 cells Endothelial cell (APC)12859 cells Erythroid progenitor cell (RP high)12049 cells Fetal enterocyte11745 cells Hepatocyte/Endodermal cell11260 cells Fetal fibroblast10880 cells Oligodendrocyte7771 cells Thyroid follicular cell7302 cells Stratified epithelial cell6498 cells Neutrophil (RPS high)6324 cells Antigen presenting cell (RPS high)6211 cells Fetal chondrocyte5758 cells Pancreas exocrine cell5568 cells Gastric chief cell4973 cells Proliferating T cell4767 cells Intercalated cell4450 cells Epithelial cell (intermediated)4104 cells Sinusoidal endothelial cell4086 cells Primordial germ cell3969 cells Fetal skeletal muscle cell3851 cells Endothelial cell (endothelial to mesenchymal transition)3799 cells Fetal acinar cell3284 cells Ventricle cardiomyocyte3007 cells Mesothelial cell2663 cells Ureteric bud cell2555 cells Proximal tubule progenitor2023 cells Gastric endocrine cell1962 cells Fetal endocrine cell1591 cells Immature sertoli cell (Pre-Sertoli cell)1192 cells Intermediated cell540 cells Kidney intercalated cell138 cells Adrenal gland inflammatory cell91 cells HsapDv:000004971529 cells HsapDv:000004862207 cells HsapDv:000014642093 cells HsapDv:000014039296 cells HsapDv:000005037957 cells HsapDv:000006329616 cells HsapDv:000008229361 cells HsapDv:000013523304 cells HsapDv:000014521571 cells HsapDv:000011719467 cells HsapDv:000014318436 cells HsapDv:000011517746 cells HsapDv:000014116989 cells HsapDv:000013916789 cells HsapDv:000015515872 cells HsapDv:000004714433 cells HsapDv:000020911229 cells HsapDv:000015110168 cells HsapDv:000015010022 cells NCBITaxon:9606599926 cells epithelial cell82683 cells endothelial cell33863 cells mesenchymal stem cell22915 cells smooth muscle cell22077 cells erythroid lineage cell13110 cells erythroid progenitor cell12049 cells cord blood hematopoietic stem cell9056 cells kidney loop of Henle epithelial cell8628 cells oligodendrocyte7771 cells type II pneumocyte7403 cells thyroid follicular cell7302 cells stratified epithelial cell6498 cells professional antigen presenting cell6211 cells epithelial cell of exocrine pancreas5568 cells alternatively activated macrophage5467 cells renal intercalated cell4588 cells primordial germ cell3969 cells cell of skeletal muscle3851 cells ventricular cardiac muscle cell3007 cells mesothelial cell2663 cells epithelial cell of proximal tubule2023 cells embryonic stem cell1644 cells inflammatory cell91 cells microwell-seq599926 cells umbilical cord blood23498 cells transverse colon16994 cells chorionic villus9898 cells vermiform appendix4486 cells ascending colon2026 cells embryonic stem cell1660 cells 12th week post-fertilization human stage71529 cells 11th week post-fertilization human stage62207 cells 52-year-old human stage42093 cells 46-year-old human stage39296 cells 13th week post-fertilization human stage37957 cells 26th week post-fertilization human stage29616 cells newborn human stage29361 cells 41-year-old human stage23304 cells 51-year-old human stage21571 cells 23-year-old human stage19467 cells 49-year-old human stage18436 cells 21-year-old human stage17746 cells 47-year-old human stage16989 cells 45-year-old human stage16789 cells 61-year-old human stage15872 cells 10th week post-fertilization human stage14433 cells 83-year-old human stage11229 cells 57-year-old human stage10168 cells 56-year-old human stage10022 cells 43-year-old human stage9727 cells 66-year-old human stage9153 cells embryonic human stage8276 cells 62-year-old human stage8076 cells 63-year-old human stage7775 cells 55-year-old human stage7324 cells 25-year-old human stage7160 cells 64-year-old human stage5549 cells 30-year-old human stage5296 cells 58-year-old human stage5031 cells 59-year-old human stage4669 cells 32-year-old human stage2750 cells 34-year-old human stage2719 cells 14th week post-fertilization human stage2547 cells 60-year-old human stage2261 cells 27-year-old human stage2156 cells 36-year-old human stage1372 cells Analyze this study
Source data
https://cellxgene.cziscience.com/collections/38833785-fac5-48fd-944a-0f62a4c23ed1
Alias names
GSE134355, PMID32214235
Cite this study
Han, X., Zhou, Z., Fei, L., Sun, H., Wang, R., Chen, Y., Chen, H., Wang, J., Tang, H., Ge, W. and Zhou, Y., 2020. Construction of a human cell landscape at single-cell level. Nature, 581(7808), pp.303-309. https://doi.org/10.1038/s41586-020-2157-4
