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Track collection: Tabula Sapiens single cell RNA data from many tissues

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 adventitial cell (4)
 alpha-beta T cell (1)
 B cell (3)
 basal cell (3)
 basophil (5)
 blood vessel endothelial cell (1)
 bronchial smooth muscle cell (2)
 capillary endothelial cell (3)
 CD1c-positive myeloid dendritic cell (10)
 CD4-positive helper T cell (3)
 CD4-positive, alpha-beta memory T cell (14)
 CD4-positive, alpha-beta T cell (7)
 CD8-positive, alpha-beta cytokine secreting effector T cell (4)
 CD8-positive, alpha-beta cytotoxic T cell (3)
 CD8-positive, alpha-beta memory T cell (10)
 CD8-positive, alpha-beta T cell (12)
 CD141-positive myeloid dendritic cell (14)
 classical monocyte (13)
 club cell (3)
 common myeloid progenitor (2)
 dendritic cell (2)
 effector CD4-positive, alpha-beta T cell (3)
 effector CD8-positive, alpha-beta T cell (2)
 endothelial cell (11)
 endothelial cell of artery (3)
 endothelial cell of lymphatic vessel (2)
 epithelial cell (3)
 erythrocyte (13)
 fibroblast (2)
 granulocyte (1)
 hematopoietic stem cell (9)
 innate lymphoid cell (7)
 intermediate monocyte (6)
 Langerhans cell (3)
 lung ciliated cell (3)
 lung microvascular endothelial cell (2)
 macrophage (16)
 mast cell (5)
 mature conventional dendritic cell (1)
 mature NK T cell (22)
 melanocyte (3)
 memory B cell (16)
 mesothelial cell (1)
 monocyte (4)
 muscle cell (3)
 myofibroblast cell (1)
 naive B cell (16)
 naive thymus-derived CD4-positive, alpha-beta T cell (14)
 naive thymus-derived CD8-positive, alpha-beta T cell (8)
 neutrophil (15)
 non-classical monocyte (5)
 pericyte cell (2)
 plasma cell (19)
 plasmablast (2)
 plasmacytoid dendritic cell (8)
 platelet (7)
 regulatory T cell (11)
 respiratory goblet cell (5)
 serous cell of epithelium of bronchus (2)
 smooth muscle cell (3)
 stromal cell (4)
 T cell (4)
 type I NK T cell (8)
 type I pneumocyte (3)
 type II pneumocyte (5)
 vascular associated smooth muscle cell (3)
 vein endothelial cell (3)
See Fewer
color↓ cluster count cell_class cell_type sex donor assay
   
immune/plasma cell/Smart-seq2/female/... 1 immune plasma cell female TSP1 Smart-seq2
   
immune/plasma cell/Smart-seq2/male/TSP10 1 immune plasma cell male TSP10 Smart-seq2
   
immune/macrophage/Smart-seq2/female/TSP7 10 immune macrophage female TSP7 Smart-seq2
   
immune/macrophage/Smart-seq2/female/TSP2 18 immune macrophage female TSP2 Smart-seq2
   
immune/mast cell/10x 3' v3/female/TSP2 16 immune mast cell female TSP2 10x 3' v3
   
immune/mature NK T cell/Smart-seq2/fe... 14 immune mature NK T cell female TSP1 Smart-seq2
   
immune/mature NK T cell/Smart-seq2/ma... 14 immune mature NK T cell male TSP10 Smart-seq2
   
immune/macrophage/Smart-seq2/female/TSP1 21 immune macrophage female TSP1 Smart-seq2
   
immune/plasma cell/10x 3' v3/female/TSP1 34 immune plasma cell female TSP1 10x 3' v3
   
immune/plasma cell/10x 3' v3/male/TSP10 40 immune plasma cell male TSP10 10x 3' v3
   
immune/mast cell/10x 3' v3/male/TSP14 66 immune mast cell male TSP14 10x 3' v3
   
immune/mature NK T cell/Smart-seq2/fe... 84 immune mature NK T cell female TSP7 Smart-seq2
   
immune/mast cell/Smart-seq2/male/TSP10 92 immune mast cell male TSP10 Smart-seq2
   
immune/macrophage/10x 3' v3/female/TSP2 978 immune macrophage female TSP2 10x 3' v3
   
immune/mature NK T cell/10x 3' v3/fem... 121 immune mature NK T cell female TSP1 10x 3' v3
   
immune/mature NK T cell/10x 3' v3/fem... 1204 immune mature NK T cell female TSP2 10x 3' v3
   
immune/mature NK T cell/10x 3' v3/fem... 2206 immune mature NK T cell female TSP7 10x 3' v3
   
immune/mature NK T cell/10x 3' v3/mal... 857 immune mature NK T cell male TSP10 10x 3' v3
   
immune/mature NK T cell/10x 3' v3/mal... 1719 immune mature NK T cell male TSP14 10x 3' v3
   
immune/mature NK T cell/Smart-seq2/fe... 150 immune mature NK T cell female TSP2 Smart-seq2
   
immune/plasma cell/10x 3' v3/female/TSP2 954 immune plasma cell female TSP2 10x 3' v3
   
immune/plasma cell/10x 3' v3/female/TSP7 643 immune plasma cell female TSP7 10x 3' v3
   
immune/plasma cell/10x 3' v3/male/TSP14 4136 immune plasma cell male TSP14 10x 3' v3
   
immune/plasma cell/Smart-seq2/female/... 132 immune plasma cell female TSP7 Smart-seq2
   
immune/macrophage/10x 3' v3/female/TSP1 8530 immune macrophage female TSP1 10x 3' v3
   
immune/plasma cell/Smart-seq2/female/... 113 immune plasma cell female TSP2 Smart-seq2
   
immune/macrophage/10x 3' v3/male/TSP14 1588 immune macrophage male TSP14 10x 3' v3
   
immune/macrophage/Smart-seq2/male/TSP10 103 immune macrophage male TSP10 Smart-seq2
   
immune/macrophage/10x 3' v3/male/TSP10 528 immune macrophage male TSP10 10x 3' v3
   
immune/mast cell/10x 3' v3/male/TSP10 389 immune mast cell male TSP10 10x 3' v3
   
immune/macrophage/10x 3' v3/female/TSP7 360 immune macrophage female TSP7 10x 3' v3
View table schema
Data last updated at UCSC: 2022-05-12 04:59:08

Description

This track shows data from The Tabula Sapiens: a multiple organ single cell transcriptomic atlas of humans. The dataset covers ~500,000 cells from a total of 24 human tissues and organs from all regions of the body using both droplet-based and plate-based single-cell RNA-sequencing (scRNA-seq). Samples were taken from the human bladder, blood, bone marrow, eye, fat, heart, kidney, large intestine, liver, lung, lymph node, mammary, muscle, pancreas, prostate, salivary gland, skin, small intestine, spleen, thymus, tongue, trachea, uterus, and vasculature. The dataset includes 264,009 immune cells, 102,580 epithelial cells, 32,701 endothelial cells, and 81,529 stromal cells. A total of 475 distinct cell types were identified.

This track collection contains two bar chart tracks of RNA expression. The first track, Tabula Tissue Cell allows cells to be grouped together and faceted on up to 3 categories: tissue, cell class, and cell type. The second track, Tabula Details allows cells to be grouped together and faceted on up to 7 categories: tissue, cell class, cell type, subtissue, sex, donor, and assay.

Please see tabula-sapiens-portal.ds.czbiohub.org for further interactive displays and additional data.

Display Conventions and Configuration

The cell types are colored by which compartment they belong to according to the following table. In addition, cells found in the Tabula Details track with less than 100 transcripts will be a lighter shade and less concentrated in color to represent a low number of transcripts.

Color Cell Compartment
epithelial
endothelial
germline
immune
stromal

Methods

All tissues

36 tissue specimens comprising 24 unique tissues and organs were collected from 15 human donors (TSP1-15) with a mean age of 51 years. Tissue specimens were collected at various hospital locations in the Northern California region and transported on ice in less than one hour to preserve cell viability. Single cell suspensions from each organ were prepared in tissue expert laboratories at Stanford and UCSF. For each tissue, the dissociated cells were sorted using MACS and FACS to balance immune, stromal, epithelial, and endothelial cell types.

Sequencing libraries for all tissues were prepared using 10x 3' v3.1, 10x 5' v2, and Smart-seq2 (SS2) protocols for Illumina sequencing. Two 10x reactions per organ were loaded with 7,000 cells each with the goal to yield 10,000 QC-passed cells. Four 384-well Smartseq2 plates were run per organ. In most organs, one plate was used for each compartment (epithelial, endothelial, immune, and stromal), however, to capture rare cells, some organ experts allocated cells across the four plates differently. Sequencing runs for droplet libraries were loaded onto the NovaSeq S4 flow cell in sets of 16 to 20 libraries of approximately 5,000 cells per library with the goal of generating 50,000 to 75,000 reads per cell. Plate libraries were run in sets of 20 plates on Novaseq S4 flow cells to allow generating 1M reads per cell, depending on library quality. 152 10x reactions were performed, yielding 454,069 cells passing QC, and 161 smartseq2 plates were processed, yielding 27,051 cells passing QC.

Tissues collected from the same donor were used to study the clonal distribution of T cells between tissues, to understand the tissue specific mutation rate in B cells, and to analyze the cell cycle state and proliferative potential of shared cell types across tissues. RNA splicing analysis was also used to characterize cell type specific splicing and its variation across individuals.

For detailed methods and information on donors for each organ or tissue please refer to Quake et al, 2021 or the Tabula Sapiens website.

Errata

Some cell types, particularly in the intestines, are duplicated due to the use of multiple ontologies for the same cell type. In a future version, we plan to pool the data from these duplicates.

Data Access

The raw bar chart data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be queried from our REST API. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.

The cell/gene matrix and cell-level metadata was downloaded from the UCSC Cell Browser. The UCSC command line utility matrixClusterColumns, matrixToBarChart, and bedToBigBed were used to transform these into a bar chart format bigBed file that can be visualized. The UCSC utilities can be found on our download server.

Credits

Thanks to the Tabula Sapiens Consortium who worked on producing and publishing this data set. The data were integrated into the UCSC Genome Browser by Jim Kent, Brittney Wick, and Rachel Schwartz.

References

The Tabula Sapiens Consortium, Quake SR., The Tabula Sapiens: A Multiple Organ Single Cell Transcriptomic Atlas of Humans. bioRxiv. 2021 March 4.; doi: https://doi.org/10.1101/2021.07.19.452956.