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

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


color cluster count tissue subtissue cell_class cell_type sex donor assay
   
spleen//immune/CD1c-positive myeloid ... 22 spleen immune CD1c-positive myeloid dendritic cell female TSP2 10x 3' v3
   
spleen//immune/CD1c-positive myeloid ... 2 spleen immune CD1c-positive myeloid dendritic cell female TSP7 10x 3' v3
   
spleen//immune/CD1c-positive myeloid ... 24 spleen immune CD1c-positive myeloid dendritic cell male TSP14 10x 3' v3
   
spleen//immune/CD1c-positive myeloid ... 3 spleen immune CD1c-positive myeloid dendritic cell female TSP2 Smart-seq2
   
spleen//immune/CD4-positive, alpha-be... 278 spleen immune CD4-positive, alpha-beta memory T cell female TSP2 10x 3' v3
   
spleen//immune/CD4-positive, alpha-be... 342 spleen immune CD4-positive, alpha-beta memory T cell female TSP7 10x 3' v3
   
spleen//immune/CD4-positive, alpha-be... 1042 spleen immune CD4-positive, alpha-beta memory T cell male TSP14 10x 3' v3
   
spleen//immune/CD4-positive, alpha-be... 30 spleen immune CD4-positive, alpha-beta memory T cell female TSP2 Smart-seq2
   
spleen//immune/CD4-positive, alpha-be... 79 spleen immune CD4-positive, alpha-beta memory T cell female TSP7 Smart-seq2
   
spleen//immune/CD8-positive, alpha-be... 630 spleen immune CD8-positive, alpha-beta memory T cell female TSP2 10x 3' v3
   
spleen//immune/CD8-positive, alpha-be... 577 spleen immune CD8-positive, alpha-beta memory T cell female TSP7 10x 3' v3
   
spleen//immune/CD8-positive, alpha-be... 2756 spleen immune CD8-positive, alpha-beta memory T cell male TSP14 10x 3' v3
   
spleen//immune/CD8-positive, alpha-be... 192 spleen immune CD8-positive, alpha-beta memory T cell female TSP2 Smart-seq2
   
spleen//immune/CD8-positive, alpha-be... 146 spleen immune CD8-positive, alpha-beta memory T cell female TSP7 Smart-seq2
   
spleen//immune/CD8-positive, alpha-be... 41 spleen immune CD8-positive, alpha-beta T cell female TSP2 10x 3' v3
   
spleen//immune/CD8-positive, alpha-be... 2 spleen immune CD8-positive, alpha-beta T cell female TSP2 Smart-seq2
   
spleen//immune/CD141-positive myeloid... 32 spleen immune CD141-positive myeloid dendritic cell female TSP2 10x 3' v3
   
spleen//immune/CD141-positive myeloid... 14 spleen immune CD141-positive myeloid dendritic cell female TSP7 10x 3' v3
   
spleen//immune/CD141-positive myeloid... 1 spleen immune CD141-positive myeloid dendritic cell male TSP14 10x 3' v3
   
spleen//immune/CD141-positive myeloid... 1 spleen immune CD141-positive myeloid dendritic cell female TSP2 Smart-seq2
   
spleen//immune/CD141-positive myeloid... 3 spleen immune CD141-positive myeloid dendritic cell female TSP7 Smart-seq2
   
spleen//immune/classical monocyte/10x... 828 spleen immune classical monocyte female TSP2 10x 3' v3
   
spleen//immune/classical monocyte/10x... 327 spleen immune classical monocyte female TSP7 10x 3' v3
   
spleen//immune/classical monocyte/10x... 2959 spleen immune classical monocyte male TSP14 10x 3' v3
   
spleen//immune/classical monocyte/Sma... 165 spleen immune classical monocyte female TSP2 Smart-seq2
   
spleen//immune/classical monocyte/Sma... 164 spleen immune classical monocyte female TSP7 Smart-seq2
   
spleen//endothelial/endothelial cell/... 156 spleen endothelial endothelial cell female TSP2 10x 3' v3
   
spleen//endothelial/endothelial cell/... 287 spleen endothelial endothelial cell female TSP7 10x 3' v3
   
spleen//endothelial/endothelial cell/... 128 spleen endothelial endothelial cell male TSP14 10x 3' v3
   
spleen//endothelial/endothelial cell/... 2 spleen endothelial endothelial cell female TSP2 Smart-seq2
   
spleen//endothelial/endothelial cell/... 23 spleen endothelial endothelial cell female TSP7 Smart-seq2
   
spleen//immune/erythrocyte/10x 3' v3/... 22 spleen immune erythrocyte female TSP2 10x 3' v3
   
spleen//immune/erythrocyte/10x 3' v3/... 16 spleen immune erythrocyte female TSP7 10x 3' v3
   
spleen//immune/erythrocyte/10x 3' v3/... 126 spleen immune erythrocyte male TSP14 10x 3' v3
   
spleen//immune/erythrocyte/Smart-seq2... 6 spleen immune erythrocyte female TSP2 Smart-seq2
   
spleen//immune/hematopoietic stem cel... 28 spleen immune hematopoietic stem cell female TSP7 10x 3' v3
   
spleen//immune/hematopoietic stem cel... 45 spleen immune hematopoietic stem cell male TSP14 10x 3' v3
   
spleen//immune/innate lymphoid cell/1... 27 spleen immune innate lymphoid cell female TSP2 10x 3' v3
   
spleen//immune/innate lymphoid cell/1... 21 spleen immune innate lymphoid cell female TSP7 10x 3' v3
   
spleen//immune/innate lymphoid cell/1... 66 spleen immune innate lymphoid cell male TSP14 10x 3' v3
   
spleen//immune/innate lymphoid cell/S... 3 spleen immune innate lymphoid cell female TSP7 Smart-seq2
   
spleen//immune/intermediate monocyte/... 95 spleen immune intermediate monocyte female TSP7 10x 3' v3
   
spleen//immune/intermediate monocyte/... 30 spleen immune intermediate monocyte male TSP14 10x 3' v3
   
spleen//immune/intermediate monocyte/... 6 spleen immune intermediate monocyte female TSP7 Smart-seq2
   
spleen//immune/macrophage/10x 3' v3/f... 430 spleen immune macrophage female TSP2 10x 3' v3
   
spleen//immune/macrophage/10x 3' v3/f... 360 spleen immune macrophage female TSP7 10x 3' v3
   
spleen//immune/macrophage/10x 3' v3/m... 522 spleen immune macrophage male TSP14 10x 3' v3
   
spleen//immune/macrophage/Smart-seq2/... 13 spleen immune macrophage female TSP2 Smart-seq2
   
spleen//immune/macrophage/Smart-seq2/... 10 spleen immune macrophage female TSP7 Smart-seq2
   
spleen//immune/mature NK T cell/10x 3... 551 spleen immune mature NK T cell female TSP2 10x 3' v3
   
spleen//immune/mature NK T cell/10x 3... 525 spleen immune mature NK T cell female TSP7 10x 3' v3
   
spleen//immune/mature NK T cell/10x 3... 1239 spleen immune mature NK T cell male TSP14 10x 3' v3
   
spleen//immune/mature NK T cell/Smart... 68 spleen immune mature NK T cell female TSP2 Smart-seq2
   
spleen//immune/mature NK T cell/Smart... 56 spleen immune mature NK T cell female TSP7 Smart-seq2
   
spleen//immune/memory B cell/10x 3' v... 1779 spleen immune memory B cell female TSP2 10x 3' v3
   
spleen//immune/memory B cell/10x 3' v... 1362 spleen immune memory B cell female TSP7 10x 3' v3
   
spleen//immune/memory B cell/10x 3' v... 2775 spleen immune memory B cell male TSP14 10x 3' v3
   
spleen//immune/memory B cell/Smart-se... 290 spleen immune memory B cell female TSP2 Smart-seq2
   
spleen//immune/memory B cell/Smart-se... 254 spleen immune memory B cell female TSP7 Smart-seq2
   
spleen//immune/naive B cell/10x 3' v3... 562 spleen immune naive B cell female TSP2 10x 3' v3
   
spleen//immune/naive B cell/10x 3' v3... 350 spleen immune naive B cell female TSP7 10x 3' v3
   
spleen//immune/naive B cell/10x 3' v3... 78 spleen immune naive B cell male TSP14 10x 3' v3
   
spleen//immune/naive B cell/Smart-seq... 4 spleen immune naive B cell female TSP2 Smart-seq2
   
spleen//immune/naive B cell/Smart-seq... 50 spleen immune naive B cell female TSP7 Smart-seq2
   
spleen//immune/naive thymus-derived C... 189 spleen immune naive thymus-derived CD4-positive, al... female TSP2 10x 3' v3
   
spleen//immune/naive thymus-derived C... 310 spleen immune naive thymus-derived CD4-positive, al... female TSP7 10x 3' v3
   
spleen//immune/naive thymus-derived C... 661 spleen immune naive thymus-derived CD4-positive, al... male TSP14 10x 3' v3
   
spleen//immune/naive thymus-derived C... 47 spleen immune naive thymus-derived CD4-positive, al... female TSP2 Smart-seq2
   
spleen//immune/naive thymus-derived C... 54 spleen immune naive thymus-derived CD4-positive, al... female TSP7 Smart-seq2
   
spleen//immune/naive thymus-derived C... 359 spleen immune naive thymus-derived CD8-positive, al... female TSP2 10x 3' v3
   
spleen//immune/naive thymus-derived C... 126 spleen immune naive thymus-derived CD8-positive, al... female TSP7 10x 3' v3
   
spleen//immune/naive thymus-derived C... 88 spleen immune naive thymus-derived CD8-positive, al... male TSP14 10x 3' v3
   
spleen//immune/naive thymus-derived C... 19 spleen immune naive thymus-derived CD8-positive, al... female TSP2 Smart-seq2
   
spleen//immune/naive thymus-derived C... 18 spleen immune naive thymus-derived CD8-positive, al... female TSP7 Smart-seq2
   
spleen//immune/neutrophil/10x 3' v3/f... 24 spleen immune neutrophil female TSP2 10x 3' v3
   
spleen//immune/neutrophil/10x 3' v3/f... 570 spleen immune neutrophil female TSP7 10x 3' v3
   
spleen//immune/neutrophil/10x 3' v3/m... 3814 spleen immune neutrophil male TSP14 10x 3' v3
   
spleen//immune/neutrophil/Smart-seq2/... 29 spleen immune neutrophil female TSP2 Smart-seq2
   
spleen//immune/neutrophil/Smart-seq2/... 102 spleen immune neutrophil female TSP7 Smart-seq2
   
spleen//immune/plasma cell/10x 3' v3/... 749 spleen immune plasma cell female TSP2 10x 3' v3
   
spleen//immune/plasma cell/10x 3' v3/... 408 spleen immune plasma cell female TSP7 10x 3' v3
   
spleen//immune/plasma cell/10x 3' v3/... 1829 spleen immune plasma cell male TSP14 10x 3' v3
   
spleen//immune/plasma cell/Smart-seq2... 56 spleen immune plasma cell female TSP2 Smart-seq2
   
spleen//immune/plasma cell/Smart-seq2... 129 spleen immune plasma cell female TSP7 Smart-seq2
   
spleen//immune/plasmacytoid dendritic... 2 spleen immune plasmacytoid dendritic cell female TSP2 10x 3' v3
   
spleen//immune/plasmacytoid dendritic... 37 spleen immune plasmacytoid dendritic cell male TSP14 10x 3' v3
   
spleen//immune/plasmacytoid dendritic... 4 spleen immune plasmacytoid dendritic cell female TSP2 Smart-seq2
   
spleen//immune/platelet/10x 3' v3/fem... 8 spleen immune platelet female TSP7 10x 3' v3
   
spleen//immune/platelet/10x 3' v3/mal... 10 spleen immune platelet male TSP14 10x 3' v3
   
spleen//immune/platelet/Smart-seq2/fe... 11 spleen immune platelet female TSP2 Smart-seq2
   
spleen//immune/regulatory T cell/10x ... 17 spleen immune regulatory T cell female TSP2 10x 3' v3
   
spleen//immune/regulatory T cell/10x ... 75 spleen immune regulatory T cell female TSP7 10x 3' v3
   
spleen//immune/regulatory T cell/10x ... 145 spleen immune regulatory T cell male TSP14 10x 3' v3
   
spleen//immune/regulatory T cell/Smar... 39 spleen immune regulatory T cell female TSP2 Smart-seq2
   
spleen//immune/regulatory T cell/Smar... 12 spleen immune regulatory T cell female TSP7 Smart-seq2
   
spleen//immune/type I NK T cell/10x 3... 391 spleen immune type I NK T cell female TSP7 10x 3' v3
   
spleen//immune/type I NK T cell/10x 3... 589 spleen immune type I NK T cell male TSP14 10x 3' v3
   
spleen//immune/type I NK T cell/Smart... 58 spleen immune type I NK T cell female TSP7 Smart-seq2
Data schema/format description and download
Assembly: Human Dec. 2013 (GRCh38/hg38)
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.