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

Display mode:   

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


cell_type
Clear
 airway basal cell (1)
 alveolar Type 1 cell (1)
 alveolar Type 2 cell (1)
 artery/vein endothelial cell (1)
 B cell (1)
 basophil/mast cell (1)
 brain SKOR2+ NPSR1+ cell (1)
 brain SLC24A4+ PEX5L+ cell (1)
 bronchial vessel cell (1)
 bronchiolar/alveolar epithelial cell (1)
 capillary endothelial cell (1)
 cholangiocyte (1)
 club cell (1)
 decidual perivascular cell (1)
 dendritic cell (1)
 doublets (1)
 endocardial cell (1)
 endothelial cell (3)
 erythroid cell (1)
 excitatory neuron (1)
 fibroblast (2)
 fibroblast fetal in placenta (1)
 goblet cell (1)
 granule neuron (1)
 heart CLC+ IL5RA+ cell (1)
 heart ELF3+ AGBL2+ cell (1)
 heart SATB2+ LRRC7+ cell (1)
 inhibitory interneuron (1)
 inhibitory neuron (1)
 interneuron PVALB+ (1)
 interneuron SST+ (1)
 interneuron SV2C+ (1)
 interneuron VIP+ (1)
 limbic system neuron (1)
 liver portal endothelial (1)
 liver sinusoidal endothe. 1 (1)
 liver sinusoidal endothe. 2,3 (1)
 lymphatic cell (1)
 lymphoid cell (2)
 macrophage (inflammatory) (1)
 macrophage (noninflammatory) (1)
 macrophage/monocyte (1)
 mesothelial cell (1)
 microglia (1)
 microglial cell (1)
 mucous cell (1)
 myeloid cell (2)
 natural killer cell (1)
 natural killer like (1)
 neuron L2/3 cortex (1)
 neuron L4 cortex (1)
 neuron L5/6 cortico-cortical (1)
 neuron L5/6 corticofugal (1)
 neuron maturing (1)
 neuron NRGN+ I (1)
 neuron NRGN+ II (1)
 neuronal cell (1)
 not assigned (1)
 other immune (1)
 other/rare (1)
 pericyte (2)
 placenta IGFBP1+ DKK1+ cell (1)
 placenta PAEP+ MECOM+ cell (1)
 plasma B cell (1)
 Purkinje neuron (1)
 retinal pigment cell (1)
 stellate (1)
 stellate cell (1)
 T cell alpha/beta (1)
 T cell CD4+ (1)
 T cell CD8+ (1)
 T cell gamma/delta 1 (1)
 T cell gamma/delta 2 (1)
 T cell mucosal (MAIT) (1)
 transit amplifying cell (0)
 unipolar brush cell (1)
See Fewer
color source and cell type count organ cell_class stage↓ cell_type
   
Brain endothelial cell 2668 brain endothelial adult endothelial cell
   
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 myeloid cell 23028 heart immune adult myeloid cell
   
Heart pericyte 77856 heart endothelial adult pericyte
   
Lung fibroblast 2234 lung fibroblast adult fibroblast
   
Lung goblet cell 159 lung secretory adult goblet cell
   
Lung lymphoid cell 13298 lung immune adult lymphoid cell
   
Lung pericyte 1608 lung endothelial adult pericyte
   
Placenta endothelial cell 1260 placenta endothelial adult endothelial cell
   
Placenta myeloid cell 7990 placenta immune adult myeloid cell
View table schema
Data last updated at UCSC: 2022-04-11 21:59:21


new Note: Released May 5, 2022

Description

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
neural
adipose
fibroblast
immune
muscle
hepatocyte
trophoblast
secretory
ciliated
epithelial
endothelial
glia
stem cell or progenitor cell

Methods

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.

Credits

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.

References

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