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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subtissue
 abdomen (59)

color cluster count tissue subtissue cell_class cell_type sex donor assay
   
muscle tissue/abdomen/endothelial/cap... 342 muscle tissue abdomen endothelial capillary endothelial cell male TSP14 10x 3' v3
   
muscle tissue/abdomen/immune/CD4-posi... 25 muscle tissue abdomen immune CD4-positive, alpha-beta T cell male TSP14 10x 3' v3
   
muscle tissue/abdomen/immune/CD8-posi... 25 muscle tissue abdomen immune CD8-positive, alpha-beta T cell male TSP14 10x 3' v3
   
muscle tissue/abdomen/endothelial/end... 22 muscle tissue abdomen endothelial endothelial cell of artery male TSP14 10x 3' v3
   
muscle tissue/abdomen/endothelial/end... 4 muscle tissue abdomen endothelial endothelial cell of lymphatic vessel male TSP14 10x 3' v3
   
muscle tissue/abdomen/endothelial/end... 173 muscle tissue abdomen endothelial endothelial cell of vascular tree male TSP14 10x 3' v3
   
muscle tissue/abdomen/immune/erythroc... 3 muscle tissue abdomen immune erythrocyte male TSP14 10x 3' v3
   
muscle tissue/abdomen/stromal/fast mu... 22 muscle tissue abdomen stromal fast muscle cell male TSP14 10x 3' v3
   
muscle tissue/abdomen/immune/macropha... 147 muscle tissue abdomen immune macrophage male TSP14 10x 3' v3
   
muscle tissue/abdomen/immune/mast cel... 2 muscle tissue abdomen immune mast cell male TSP14 10x 3' v3
   
muscle tissue/abdomen/immune/mature N... 3 muscle tissue abdomen immune mature NK T cell male TSP14 10x 3' v3
   
muscle tissue/abdomen/stromal/mesench... 3787 muscle tissue abdomen stromal mesenchymal stem cell male TSP14 10x 3' v3
   
muscle tissue/abdomen/stromal/pericyt... 360 muscle tissue abdomen stromal pericyte cell male TSP14 10x 3' v3
   
muscle tissue/abdomen/stromal/skeleta... 1113 muscle tissue abdomen stromal skeletal muscle satellite stem cell male TSP14 10x 3' v3
   
muscle tissue/abdomen/stromal/slow mu... 23 muscle tissue abdomen stromal slow muscle cell male TSP14 10x 3' v3
   
muscle tissue/abdomen/stromal/smooth ... 35 muscle tissue abdomen stromal smooth muscle cell male TSP14 10x 3' v3
   
muscle tissue/abdomen/immune/T cell/1... 37 muscle tissue abdomen immune T cell male TSP14 10x 3' v3
   
muscle tissue/abdomen/stromal/tendon ... 19 muscle tissue abdomen stromal tendon cell male TSP14 10x 3' v3
   
skin of body/abdomen/immune/CD1c-posi... 17 skin of body abdomen immune CD1c-positive myeloid dendritic cell male TSP14 10x 3' v3
   
skin of body/abdomen/immune/CD1c-posi... 10 skin of body abdomen immune CD1c-positive myeloid dendritic cell male TSP10 Smart-seq2
   
skin of body/abdomen/immune/CD4-posit... 12 skin of body abdomen immune CD4-positive helper T cell male TSP14 10x 3' v3
   
skin of body/abdomen/immune/CD4-posit... 1 skin of body abdomen immune CD4-positive helper T cell male TSP10 Smart-seq2
   
skin of body/abdomen/immune/CD4-posit... 89 skin of body abdomen immune CD4-positive, alpha-beta memory T cell male TSP14 10x 3' v3
   
skin of body/abdomen/immune/CD4-posit... 5 skin of body abdomen immune CD4-positive, alpha-beta memory T cell male TSP10 Smart-seq2
   
skin of body/abdomen/immune/CD8-posit... 29 skin of body abdomen immune CD8-positive, alpha-beta cytotoxic T ... male TSP14 10x 3' v3
   
skin of body/abdomen/immune/CD8-posit... 2 skin of body abdomen immune CD8-positive, alpha-beta cytotoxic T ... male TSP10 Smart-seq2
   
skin of body/abdomen/immune/CD8-posit... 164 skin of body abdomen immune CD8-positive, alpha-beta memory T cell male TSP14 10x 3' v3
   
skin of body/abdomen/immune/CD8-posit... 24 skin of body abdomen immune CD8-positive, alpha-beta memory T cell male TSP10 Smart-seq2
   
skin of body/abdomen/immune/CD141-pos... 3 skin of body abdomen immune CD141-positive myeloid dendritic cell male TSP14 10x 3' v3
   
skin of body/abdomen/immune/CD141-pos... 3 skin of body abdomen immune CD141-positive myeloid dendritic cell male TSP10 Smart-seq2
   
skin of body/abdomen/endothelial/endo... 139 skin of body abdomen endothelial endothelial cell male TSP14 10x 3' v3
   
skin of body/abdomen/endothelial/endo... 52 skin of body abdomen endothelial endothelial cell male TSP10 Smart-seq2
   
skin of body/abdomen/epithelial/epith... 3 skin of body abdomen epithelial epithelial cell male TSP14 10x 3' v3
   
skin of body/abdomen/epithelial/epith... 6 skin of body abdomen epithelial epithelial cell male TSP10 Smart-seq2
   
skin of body/abdomen/immune/Langerhan... 13 skin of body abdomen immune Langerhans cell male TSP14 10x 3' v3
   
skin of body/abdomen/immune/Langerhan... 3 skin of body abdomen immune Langerhans cell male TSP10 Smart-seq2
   
skin of body/abdomen/immune/macrophag... 90 skin of body abdomen immune macrophage male TSP14 10x 3' v3
   
skin of body/abdomen/immune/macrophag... 103 skin of body abdomen immune macrophage male TSP10 Smart-seq2
   
skin of body/abdomen/immune/mast cell... 51 skin of body abdomen immune mast cell male TSP14 10x 3' v3
   
skin of body/abdomen/immune/mast cell... 92 skin of body abdomen immune mast cell male TSP10 Smart-seq2
   
skin of body/abdomen/immune/mature NK... 118 skin of body abdomen immune mature NK T cell male TSP14 10x 3' v3
   
skin of body/abdomen/immune/mature NK... 14 skin of body abdomen immune mature NK T cell male TSP10 Smart-seq2
   
skin of body/abdomen/stromal/melanocy... 2 skin of body abdomen stromal melanocyte male TSP14 10x 3' v3
   
skin of body/abdomen/stromal/melanocy... 6 skin of body abdomen stromal melanocyte male TSP10 Smart-seq2
   
skin of body/abdomen/stromal/muscle c... 101 skin of body abdomen stromal muscle cell male TSP14 10x 3' v3
   
skin of body/abdomen/stromal/muscle c... 22 skin of body abdomen stromal muscle cell male TSP10 Smart-seq2
   
skin of body/abdomen/immune/naive thy... 17 skin of body abdomen immune naive thymus-derived CD4-positive, al... male TSP14 10x 3' v3
   
skin of body/abdomen/immune/naive thy... 1 skin of body abdomen immune naive thymus-derived CD4-positive, al... male TSP10 Smart-seq2
   
skin of body/abdomen/immune/naive thy... 8 skin of body abdomen immune naive thymus-derived CD8-positive, al... male TSP14 10x 3' v3
   
skin of body/abdomen/immune/naive thy... 2 skin of body abdomen immune naive thymus-derived CD8-positive, al... male TSP10 Smart-seq2
   
skin of body/abdomen/immune/plasma ce... 9 skin of body abdomen immune plasma cell male TSP14 10x 3' v3
   
skin of body/abdomen/immune/plasma ce... 1 skin of body abdomen immune plasma cell male TSP10 Smart-seq2
   
skin of body/abdomen/immune/regulator... 47 skin of body abdomen immune regulatory T cell male TSP14 10x 3' v3
   
skin of body/abdomen/immune/regulator... 1 skin of body abdomen immune regulatory T cell male TSP10 Smart-seq2
   
skin of body/abdomen/stromal/smooth m... 4 skin of body abdomen stromal smooth muscle cell male TSP14 10x 3' v3
   
skin of body/abdomen/stromal/stromal ... 576 skin of body abdomen stromal stromal cell male TSP14 10x 3' v3
   
skin of body/abdomen/stromal/stromal ... 58 skin of body abdomen stromal stromal cell male TSP10 Smart-seq2
   
skin of body/abdomen/immune/T cell/10... 98 skin of body abdomen immune T cell male TSP14 10x 3' v3
   
skin of body/abdomen/immune/T cell/Sm... 11 skin of body abdomen immune T cell male TSP10 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.