Merged Cells Track Settings
Single cell RNA expression levels cell types from many organs   (All Single Cell RNA-seq tracks)

Display mode:      Duplicate track

Label: Name or ID of item    Alternative name for item   
Log10(x+1) transform:    View limits maximum: ppm/cell (range 0-10000)

color source and cell type count organ cell_class stage cell_type
Blood B cell 13800 blood immune adult B cell
Blood T cell CD4+ 41001 blood immune adult T cell CD4+
Blood T cell CD8+ 25469 blood immune adult T cell CD8+
Blood dendritic cell 3589 blood immune adult dendritic cell
Blood monocyte 49010 blood immune adult monocyte
Blood natural killer cell 18664 blood immune adult natural killer cell
Blood other 3442 blood immune adult other
Blood T cell other 6789 blood immune adult T cell other
Brain astrocyte (fibrous) 4562 brain glia adult astrocytes (fibrous)
Brain astrocyte (protoplasmic) 7655 brain glia adult astrocytes (protoplasmic)
Brain endothelial cell 2668 brain endothelial adult endothelial cell
Brain interneuron PVALB+ 4037 brain neural adult interneuron PVALB+
Brain interneuron SST+ 4569 brain neural adult interneuron SST+
Brain interneuron SV2C+ 1914 brain neural adult interneuron SV2C+
Brain interneuron VIP+ 5974 brain neural adult interneuron VIP+
Brain neuron L2/3 cortex 13324 brain neural adult neuron L2/3 cortex
Brain neuron L4 cortex 6858 brain neural adult neuron L4 cortex
Brain neuron L5/6 corticofugal 3561 brain neural adult neuron L5/6 corticofugal
Brain neuron L5/6 cortico-cortical 4617 brain neural adult neuron L5/6 cortico-cortical
Brain microglia 3331 brain immune adult microglia
Brain neuron NRGN+ I 3543 brain neural adult neuron NRGN+ I
Brain neuron NRGN+ II 8317 brain neural adult neuron NRGN+ II
Brain neuron maturing 4135 brain neural adult neuron maturing
Brain oligodendrocyte precursor 10123 brain precursor adult oligodendrocyte precursor
Brain oligodendrocyte 15371 brain glia adult oligodendrocyte
Colon enteroendocrine cell 13 colon secretory adult enteroendocrine cell
Colon enterocyte 870 colon epithelial adult enterocyte
Colon goblet cell 765 colon secretory adult goblet cell
Colon Paneth-like cell 349 colon secretory adult Paneth-like cell
Colon enteric progenitor 1784 colon precursor adult enteric progenitor
Colon enteric stem cell 131 colon stem cell adult enteric stem cell
Colon transit amplifying cell 417 colon precursor adult transit amplifying cell
Heart adipocyte 3799 heart adipose adult adipocyte
Heart atrial cardiomyocyte 23483 heart muscle adult atrial cardiomyocyte
Heart endothelial cell 100579 heart endothelial adult endothelial cell
Heart fibroblast 59341 heart fibroblast adult fibroblast
Heart lymphoid cell 17217 heart immune adult lymphoid cell
Heart mesothelial cell 718 heart epithelial adult mesothelial cell
Heart myeloid cell 23028 heart immune adult myeloid cell
Heart neuronal cell 3961 heart neural adult neuronal cell
Heart not assigned 33998 heart other adult not assigned
Heart pericyte 77856 heart endothelial adult pericyte
Heart smooth muscle 16242 heart muscle adult smooth muscle
Heart ventricular cardiomyocyte 125289 heart muscle adult ventricular cardiomyocyte
Heart doublets 623 heart other adult doublets
Ileum enteroendocrine cell 38 ileum secretory adult enteroendocrine cell
Ileum enterocyte 4243 ileum epithelial adult enterocyte
Ileum goblet cell 303 ileum secretory adult goblet cell
Ileum Paneth-like cell 94 ileum secretory adult Paneth-like cell
Ileum enteric progenitor 782 ileum precursor adult enteric progenitor
Ileum enteric stem cell 229 ileum stem cell adult enteric stem cell
Ileum transit amplifying cell 291 ileum precursor adult transit amplifying cell
Kidney ascending vasa recta endothe. 300 kidney endothelial adult ascending vasa recta endothe.
Kidney B cell 975 kidney immune adult B cell
Kidney T cell CD4+ 2435 kidney immune adult T cell CD4+
Kidney T cell CD8+ 991 kidney immune adult T cell CD8+
Kidney connecting tubule 157 kidney kidney specific adult connecting tubule
Kidney descending vasa recta endothe. 192 kidney endothelial adult descending vasa recta endothe.
Kidney epithelial progenitor cell 238 kidney precursor adult epithelial progenitor cell
Kidney fibroblast 145 kidney fibroblast adult fibroblast
Kidney glomerular endothelial cell 622 kidney endothelial adult glomerular endothelial cell
Kidney intercalated cell 829 kidney kidney specific adult intercalated cell
Kidney mononuclear phagocyte 1237 kidney immune adult mononuclear phagocyte
Kidney natural killer cell 2055 kidney immune adult natural killer cell
Kidney other immune 110 kidney immune adult other immune
Kidney pelvic epithelial cell 136 kidney epithelial adult pelvic epithelial cell
Kidney peritubular endothelial cell 851 kidney endothelial adult peritubular endothelial cell
Kidney podocyte 126 kidney kidney specific adult podocyte
Kidney principal cell 88 kidney kidney specific adult principal cell
Kidney proximal tubule cell 28061 kidney kidney specific adult proximal tubule cell
Kidney thick asc. loop of Henle 675 kidney kidney specific adult thick asc. loop of Henle
Kidney transitional urothelium 45 kidney epithelial adult transitional urothelium
Liver B cell 140 liver immune adult B cell
Liver cholangiocyte 121 liver epithelial adult cholangiocyte
Liver erythroid cell 53 liver immune adult erythroid cell
Liver hepatocyte 3498 liver hepatocyte adult hepatocyte
Liver macrophage (inflammatory) 822 liver immune adult macrophage (inflammatory)
Liver liver sinusoidal endothe. 1 340 liver endothelial adult liver sinusoidal endothe. 1
Liver liver sinusoidal endothe. 2,3 301 liver endothelial adult liver sinusoidal endothe. 2,3
Liver natural killer like 520 liver immune adult natural killer like
Liver macrophage (noninflammatory) 326 liver immune adult macrophage (noninflammatory)
Liver plasma B cell 279 liver immune adult plasma B cell
Liver liver portal endothelial 238 liver endothelial adult liver portal endothelial
Liver stellate 20 liver fibroblast adult stellate
Liver T cell alpha/beta 1115 liver immune adult T cell alpha/beta
Liver T cell gamma/delta 1 333 liver immune adult T cell gamma/delta 1
Liver T cell gamma/delta 2 338 liver immune adult T cell gamma/delta 2
Lung smooth muscle (airway) 693 lung muscle adult smooth muscle (airway)
Lung alveolar Type 1 cell 972 lung epithelial adult alveolar Type 1 cell
Lung alveolar Type 2 cell 4483 lung epithelial adult alveolar Type 2 cell
Lung artery/vein endothelial cell 2639 lung endothelial adult artery/vein endothelial cell
Lung airway basal cell 905 lung epithelial adult airway basal cell
Lung basophil/mast cell 1902 lung immune adult basophil/mast cell
Lung bronchial vessel cell 690 lung other adult bronchial vessel cell
Lung capillary endothelial cell 12835 lung endothelial adult capillary endothelial cell
Lung ciliated cell 1409 lung ciliated adult ciliated cell
Lung club cell 931 lung secretory adult club cell
Lung dendritic cell 1115 lung immune adult dendritic cell
Lung fibroblast 2234 lung fibroblast adult fibroblast
Lung goblet cell 159 lung secretory adult goblet cell
Lung lymphatic cell 467 lung other adult lymphatic cell
Lung lymphoid cell 13298 lung immune adult lymphoid cell
Lung macrophage/monocyte 18236 lung immune adult macrophage/monocyte
Lung mucous cell 491 lung secretory adult mucous cell
Lung other/rare 126 lung other adult other/rare
Lung pericyte 1608 lung endothelial adult pericyte
Lung smooth muscle (vascular) 469 lung muscle adult smooth muscle (vascular)
Muscle skeletal muscle ACTA1+ 256 muscle muscle adult skeletal muscle ACTA1+
Muscle smooth muscle ACTA2 MYH11 MYL9+ 1662 muscle muscle adult smooth muscle ACTA2 MYH11 MYL9+
Muscle adipocyte APOD+ CFD+ PLAC9+ 1182 muscle adipose adult adipocyte APOD+ CFD+ PLAC9+
Muscle macrophage C1QA+ CD74+ 614 muscle immune adult macrophage C1QA+ CD74+
Muscle platelets CD36+ VWF+ 1904 muscle immune adult platelets CD36+ VWF+
Muscle endothelial CLDN5+ PECAM1+ 831 muscle endothelial adult endothelial CLDN5+ PECAM1+
Muscle fibroblast COL1A1+ 2744 muscle fibroblast adult fibroblast COL1A1+
Muscle fibroblast DCN+ GSN+ MYOC+ 3489 muscle fibroblast adult fibroblast DCN+ GSN+ MYOC+
Muscle fibroblast FBN1+ MFAP+ CD55+ 2626 muscle fibroblast adult fibroblast FBN1+ MFAP+ CD55+
Muscle erythroblast HBA1+ 62 muscle immune adult erythroblast HBA1+
Muscle endothelial ICAM1+ SELE+ VCAM1+ 875 muscle endothelial adult endothelial ICAM1+ SELE+ VCAM1+
Muscle lymphoid IL7R+ PTPRC+ NKG7+ 1319 muscle immune adult lymphoid IL7R+ PTPRC+ NKG7+
Muscle muscle stem cells PAX7+ DLK1+ 1724 muscle stem cell adult muscle stem cells PAX7+ DLK1+
Muscle muscle stem cells PAX7- MYF5+ 1468 muscle stem cell adult muscle stem cells PAX7- MYF5+
Muscle pericytes RGS5+ MYL9+ 655 muscle endothelial adult pericytes RGS5+ MYL9+
Muscle macrophages (inflammatory) 647 muscle immune adult macrophages (inflammatory)
Pancreas acinar cell 617 pancreas secretory adult acinar cell
Pancreas stellate (activated) 253 pancreas fibroblast adult stellate (activated)
Pancreas islet alpha cell 2251 pancreas secretory adult islet alpha cell
Pancreas islet beta cell 2417 pancreas secretory adult islet beta cell
Pancreas islet delta cell 535 pancreas secretory adult islet delta cell
Pancreas ductal cell 911 pancreas epithelial adult ductal cell
Pancreas endothelial cell 237 pancreas endothelial adult endothelial cell
Pancreas islet epsilon cell 18 pancreas secretory adult islet epsilon cell
Pancreas islet gamma cell 244 pancreas secretory adult islet gamma cell
Pancreas other 68 pancreas other adult other
Pancreas stellate (quiescent) 163 pancreas fibroblast adult stellate (quiescent)
Placenta T cell CD4+ 4950 placenta immune adult T cell CD4+
Placenta T cell CD8+ 2293 placenta immune adult T cell CD8+
Placenta extravillous trophoblast 2360 placenta trophoblast adult extravillous trophoblast
Placenta endothelial cell 1260 placenta endothelial adult endothelial cell
Placenta T cell mucosal (MAIT) 968 placenta immune adult T cell mucosal (MAIT)
Placenta myeloid cell 7990 placenta immune adult myeloid cell
Placenta natural killer cell 12777 placenta immune adult natural killer cell
Placenta other immune 1244 placenta immune adult other immune
Placenta syncytiotrophoblast 1167 placenta trophoblast adult syncytiotrophoblast
Placenta villous cytotrophoblast 8281 placenta trophoblast adult villous cytotrophoblast
Placenta decidual perivascular cell 1830 placenta epithelial adult decidual perivascular cell
Placenta decidual stroma cell 12370 placenta muscle adult decidual stroma cell
Placenta fibroblast fetal in placenta 2215 placenta fibroblast adult fibroblast fetal in placenta
Rectum enteroendocrine cell 66 rectum secretory adult enteroendocrine cell
Rectum enterocyte 584 rectum epithelial adult enterocyte
Rectum goblet cell 899 rectum secretory adult goblet cell
Rectum Paneth-like cell 299 rectum secretory adult Paneth-like cell
Rectum enteric progenitor 1435 rectum precursor adult enteric progenitor
Rectum enteric stem cell 258 rectum stem cell adult enteric stem cell
Rectum transit amplifying cell 256 rectum precursor adult transit amplifying cell
Skin keratinocyte 1399 skin epithelial adult keratinocyte
Skin epidermal stem and progenitors 1187 skin stem cell adult epidermal stem and progenitors
Skin erythrocyte 310 skin immune adult erythrocyte
Skin endothelial lymphatic 294 skin endothelial adult endothelial lymphatic
Skin macrophage/dendritic cell 2228 skin immune adult macrophage/dendritic cell
Skin melanocyte 123 skin other adult melanocyte
Skin fibroblast (mesenchymal) 594 skin fibroblast adult fibroblast (mesenchymal)
Skin pericyte 1220 skin endothelial adult pericyte
Skin fibroblast (pro-inflammatory) 1793 skin fibroblast adult fibroblast (pro-inflammatory)
Skin fibroblast (secretory-papilli.) 1675 skin fibroblast adult fibroblast (secretory-papilli.)
Skin fibroblast (secretory-reticul.) 1886 skin fibroblast adult fibroblast (secretory-reticul.)
Skin T cell 1281 skin immune adult T cell
Skin endothelial vascular cell 1467 skin endothelial adult endothelial vascular cell
Data schema/format description and download
Data last updated at UCSC: 2022-04-11 21:59:21


This track displays single-cell data from 12 papers covering 14 organs. Cells are grouped together by organ and cell type. The cell types are based on annotations published alongside the papers. These were curated at UCSC as much as possible to use the same cell type terminologies across papers and organs. In some cases, we merged together small populations of cells annotated as distinct and related types into a single type so as to have enough cells to call gene expression levels accurate. The gene expression levels are normalized so that the total level of expression for all genes in a single cell or cell type adds up to one million.

Display Conventions and Configuration

The cell types are colored by which class they belong to according to the following table.

Please note, the coloring algorithm allows cells that show some mixed characteristics to = show blended colors so there will be some color variation within a class. In addition, cells with less than 100 transcripts will be a lighter shade and less concentrated in color to represent a low number of transcripts.

Color Cell classification
stem cell or progenitor cell


Each organ or tissue was integrated and curated into the Genome Browser indiviually.

All components were normalized to be in parts per million using the matrixNormalize command available from UCSC. Metadata was cleaned up using the tabToTabDir tool. The major clean-ups were unpacking abbreviations, replacing jargon with standard English, choosing shorted terms to shorten long labels, labeling outliers, etc. Before integration we invited the original data producers as well as local biologists and informaticions to view the data.


Many thanks to the data contributing labs for sharing their high quality research. Thanks to the Cell Browser team including Matt Speir and Max Haeussler, for their work in integratinging these datasets into the Cell Browser. In most cases, their efforts were ahead of our own and we could leverage their work making the job much easier. Within the Genome Browser group, Jim Kent did the initial wrangling, and Brittney Wick did substantial data cleanup and coordination with the labs.


Baron M, Veres A, Wolock SL, Faust AL, Gaujoux R, Vetere A, Ryu JH, Wagner BK, Shen-Orr SS, Klein AM et al. A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure. Cell Syst. 2016 Oct 26;3(4):346-360.e4. PMID: 27667365; PMC: PMC5228327

Cao J, O'Day DR, Pliner HA, Kingsley PD, Deng M, Daza RM, Zager MA, Aldinger KA, Blecher-Gonen R, Zhang F et al. A human cell atlas of fetal gene expression. Science. 2020 Nov 13;370(6518). PMID: 33184181; PMC: PMC7780123

Cao J, Spielmann M, Qiu X, Huang X, Ibrahim DM, Hill AJ, Zhang F, Mundlos S, Christiansen L, Steemers FJ et al. The single-cell transcriptional landscape of mammalian organogenesis. Nature. 2019 Feb;566(7745):496-502. PMID: 30787437; PMC: PMC6434952

De Micheli AJ, Spector JA, Elemento O, Cosgrove BD. A reference single-cell transcriptomic atlas of human skeletal muscle tissue reveals bifurcated muscle stem cell populations. Skelet Muscle. 2020 Jul 6;10(1):19. PMID: 32624006; PMC: PMC7336639

Hao Y, Hao S, Andersen-Nissen E, Mauck WM 3rd, Zheng S, Butler A, Lee MJ, Wilk AJ, Darby C, Zager M et al. Integrated analysis of multimodal single-cell data. Cell. 2021 Jun 24;184(13):3573-3587.e29. PMID: 34062119; PMC: PMC8238499

Litviňuková M, Talavera-López C, Maatz H, Reichart D, Worth CL, Lindberg EL, Kanda M, Polanski K, Heinig M, Lee M et al. Cells of the adult human heart. Nature. 2020 Dec;588(7838):466-472. PMID: 32971526; PMC: PMC7681775

MacParland SA, Liu JC, Ma XZ, Innes BT, Bartczak AM, Gage BK, Manuel J, Khuu N, Echeverri J, Linares I et al. Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations. Nat Commun. 2018 Oct 22;9(1):4383. PMID: 30348985; PMC: PMC6197289

Solé-Boldo L, Raddatz G, Schütz S, Mallm JP, Rippe K, Lonsdorf AS, Rodríguez-Paredes M, Lyko F. Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast priming. Commun Biol. 2020 Apr 23;3(1):188. PMID: 32327715; PMC: PMC7181753

Stewart BJ, Ferdinand JR, Young MD, Mitchell TJ, Loudon KW, Riding AM, Richoz N, Frazer GL, Staniforth JUL, Vieira Braga FA et al. Spatiotemporal immune zonation of the human kidney. Science. 2019 Sep 27;365(6460):1461-1466. PMID: 31604275; PMC: PMC7343525

Travaglini KJ, Nabhan AN, Penland L, Sinha R, Gillich A, Sit RV, Chang S, Conley SD, Mori Y, Seita J et al. A molecular cell atlas of the human lung from single-cell RNA sequencing. Nature. 2020 Nov;587(7835):619-625. PMID: 33208946; PMC: PMC7704697

Velmeshev D, Schirmer L, Jung D, Haeussler M, Perez Y, Mayer S, Bhaduri A, Goyal N, Rowitch DH, Kriegstein AR. Single-cell genomics identifies cell type-specific molecular changes in autism. Science. 2019 May 17;364(6441):685-689. PMID: 31097668; PMC: PMC7678724

Vento-Tormo R, Efremova M, Botting RA, Turco MY, Vento-Tormo M, Meyer KB, Park JE, Stephenson E, Polański K, Goncalves A et al. Single-cell reconstruction of the early maternal-fetal interface in humans. Nature. 2018 Nov;563(7731):347-353. PMID: 30429548

Wang Y, Song W, Wang J, Wang T, Xiong X, Qi Z, Fu W, Yang X, Chen YG. Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine. J Exp Med. 2020 Feb 3;217(2). PMID: 31753849; PMC: PMC7041720