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

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 immune (50)

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 microglia 3331 brain immune adult microglia
Fetal thymus antigen presenting cell 465 thymus immune fetal antigen presenting cell
Fetal mixed erythroblast 46707 mixed immune fetal erythroblast
Fetal mixed lymphoid cell 16873 mixed immune fetal lymphoid cell
Fetal mixed megakaryocyte 3498 mixed immune fetal megakaryocyte
Fetal brain microglial cell 8975 brain immune fetal microglial cell
Fetal mixed myeloid cell 18300 mixed immune fetal myeloid cell
Heart lymphoid cell 17217 heart immune adult lymphoid cell
Heart myeloid cell 23028 heart immune adult myeloid cell
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 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
Liver B cell 140 liver immune adult B cell
Liver erythroid cell 53 liver immune adult erythroid cell
Liver macrophage (inflammatory) 822 liver immune adult macrophage (inflammatory)
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 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 basophil/mast cell 1902 lung immune adult basophil/mast cell
Lung dendritic cell 1115 lung immune adult dendritic cell
Lung lymphoid cell 13298 lung immune adult lymphoid cell
Lung macrophage/monocyte 18236 lung immune adult macrophage/monocyte
Muscle macrophage C1QA+ CD74+ 614 muscle immune adult macrophage C1QA+ CD74+
Muscle platelets CD36+ VWF+ 1904 muscle immune adult platelets CD36+ VWF+
Muscle erythroblast HBA1+ 62 muscle immune adult erythroblast HBA1+
Muscle lymphoid IL7R+ PTPRC+ NKG7+ 1319 muscle immune adult lymphoid IL7R+ PTPRC+ NKG7+
Muscle macrophages (inflammatory) 647 muscle immune adult macrophages (inflammatory)
Placenta T cell CD4+ 4950 placenta immune adult T cell CD4+
Placenta T cell CD8+ 2293 placenta immune adult T cell CD8+
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
Skin erythrocyte 310 skin immune adult erythrocyte
Skin macrophage/dendritic cell 2228 skin immune adult macrophage/dendritic cell
Skin T cell 1281 skin immune adult T 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