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
Fetal mixed AFP+ ALB+ cell 182 mixed other fetal mixed AFP+ ALB+ cell
Fetal pancreas acinar cell 11388 pancreas secretory fetal acinar cell
Fetal adrenal gland adrenocortical cell 328920 adrenal gland secretory fetal adrenocortical cell
Fetal eye amacrine cell 7341 eye neural fetal amacrine cell
Fetal thymus antigen presenting cell 465 thymus immune fetal antigen presenting cell
Fetal brain astrocyte 318105 brain glia fetal astrocyte
Fetal eye bipolar neuron 1207 eye neural fetal bipolar neuron
Fetal lung bronchiolar/alveolar epith... 101249 lung epithelial fetal bronchiolar/alveolar epithelial cell
Fetal pancreas CCL19+ CCL21+ cell 206 pancreas other fetal pancreas CCL19+ CCL21+ cell
Fetal heart CLC+ IL5RA+ cell 102 heart other fetal heart CLC+ IL5RA+ cell
Fetal mixed CSH1+ CSH2+ cell 109 mixed other fetal mixed CSH1+ CSH2+ cell
Fetal heart cardiomyocyte 67610 heart muscle fetal cardiomyocyte
Fetal adrenal gland chromaffin cell 21055 adrenal gland secretory fetal chromaffin cell
Fetal mixed ciliated epithelial cell 2886 mixed ciliated fetal ciliated epithelial cell
Fetal eye corneal/conjunctival epithe... 104 eye epithelial fetal corneal/conjunctival epithelial cell
Fetal pancreas ductal cell 4829 pancreas secretory fetal ductal cell
Fetal heart ELF3+ AGBL2+ cell 164 heart other fetal heart ELF3+ AGBL2+ cell
Fetal mixed ENS glial cell 3219 mixed glia fetal enteric nervous system (ENS) glial cell
Fetal mixed ENS neuron 2514 mixed neural fetal enteric nervous system (ENS) neuron
Fetal heart endocardial cell 7398 heart endothelial fetal endocardial cell
Fetal heart epicardial adipose cell 1891 heart adipose fetal epicardial adipose cell
Fetal mixed erythroblast 46707 mixed immune fetal erythroblast
Fetal brain excitatory neuron 1258818 brain neural fetal excitatory neuron
Fetal placenta extravillous trophoblast 1535 placenta trophoblast fetal extravillous trophoblast
Fetal eye ganglion cell 10143 eye neural fetal ganglion cell
Fetal stomach goblet cell 3624 stomach secretory fetal goblet cell
Fetal brain granule neuron 312675 brain neural fetal granule neuron
Fetal liver hematopoietic stem cell 1096 liver stem cell fetal hematopoietic stem cell
Fetal liver hepatoblast 58447 liver hepatocyte fetal hepatoblast
Fetal eye horizontal cell 2300 eye neural fetal horizontal cell
Fetal placenta IGFBP1+ DKK1+ cell 701 placenta other fetal placenta IGFBP1+ DKK1+ cell
Fetal brain inhibitory interneuron 129890 brain neural fetal inhibitory interneuron
Fetal brain inhibitory neuron 350759 brain neural fetal inhibitory neuron
Fetal intestine epithelial cell 24545 intestine epithelial fetal intestinal epithelial cell
Fetal pancreas islet endocrine cell 4768 pancreas secretory fetal islet endocrine cell
Fetal eye lens fibre cell 246 eye other fetal lens fibre cell
Fetal brain limbic system neuron 45989 brain neural fetal limbic system neuron
Fetal mixed lymphatic endothelial cell 7305 mixed endothelial fetal lymphatic endothelial cell
Fetal mixed lymphoid cell 16873 mixed immune fetal lymphoid cell
Fetal stomach MUC13+ DMBT1+ cell 792 stomach other fetal stomach MUC13+ DMBT1+ cell
Fetal mixed megakaryocyte 3498 mixed immune fetal megakaryocyte
Fetal kidney mesangial cell 44177 kidney kidney specific fetal mesangial cell
Fetal mixed mesothelial cell 2048 mixed epithelial fetal mesothelial cell
Fetal kidney metanephric cell 90876 kidney kidney specific fetal metanephric cell
Fetal brain microglial cell 8975 brain immune fetal microglial cell
Fetal mixed myeloid cell 18300 mixed immune fetal myeloid cell
Fetal mixed neuroendocrine cell 1824 mixed secretory fetal neuroendocrine cell
Fetal brain oligodendrocyte 33748 brain glia fetal oligodendrocyte
Fetal placenta PAEP+ MECOM+ cell 287 placenta other fetal placenta PAEP+ MECOM+ cell
Fetal eye PDE11A+ FAM19A2+ cell 806 eye other fetal eye PDE11A+ FAM19A2+ cell
Fetal stomach PDE1C+ ACSM3+ cell 78 stomach other fetal stomach PDE1C+ ACSM3+ cell
Fetal stomach parietal and chief cell 2322 stomach secretory fetal parietal and chief cell
Fetal eye photoreceptor cell 12398 eye neural fetal photoreceptor cell
Fetal brain Purkinje neuron 280377 brain neural fetal Purkinje neuron
Fetal brain retinal pigment cell 704 brain other fetal retinal pigment cell
Fetal brain retinal progenitor/Muller... 14865 brain glia fetal retinal progenitor/Muller glial cell
Fetal heart SATB2+ LRRC7+ cell 318 heart other fetal heart SATB2+ LRRC7+ cell
Fetal brain SKOR2+ NPSR1+ cell 15005 brain other fetal brain SKOR2+ NPSR1+ cell
Fetal brain SLC24A4+ PEX5L+ cell 19722 brain other fetal brain SLC24A4+ PEX5L+ cell
Fetal adrenal gland SLC26A4+ PAEP+ cell 68 adrenal gland other fetal adrenal gland SLC26A4+ PAEP+ cell
Fetal spleen STC2+ TLX1+ cell 4487 spleen other fetal spleen STC2+ TLX1+ cell
Fetal muscle satellite cell 5255 muscle precursor fetal satellite cell
Fetal mixed Schwann cell 1769 mixed glia fetal Schwann cell
Fetal muscle skeletal muscle cell 13516 muscle muscle fetal skeletal muscle cell
Fetal mixed smooth muscle cell 7344 mixed muscle fetal smooth muscle cell
Fetal mixed squamous epithelial cell 2238 mixed epithelial fetal squamous epithelial cell
Fetal liver stellate cell 1743 liver fibroblast fetal stellate cell
Fetal mixed stromal cell 152957 mixed other fetal stromal cell
Fetal adrenal gland sympathoblasts 3805 adrenal gland other fetal sympathoblasts
Fetal placenta syncytiotrophoblast an... 14567 placenta trophoblast fetal syncytiotrophoblast and villous cytot...
Fetal thymus thymic epithelial cell 259 thymus epithelial fetal thymic epithelial cell
Fetal thymus thymocyte 7852 thymus other fetal thymocyte
Fetal placenta trophoblast giant cell 1137 placenta trophoblast fetal trophoblast giant cell
Fetal brain unipolar brush cell 52646 brain neural fetal unipolar brush cell
Fetal kidney ureteric bud cell 9138 kidney other fetal ureteric bud cell
Fetal mixed vascular endothelial cell 75104 mixed endothelial fetal vascular endothelial cell
Fetal mixed visceral neuron 610 mixed neural fetal visceral neuron
Data schema/format description and download
Assembly: Human Dec. 2013 (GRCh38/hg38)
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