Tabula Sapiens Tabula Details Track Settings
 
Tabula sapiens full details view

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

+  Description
+  All tracks in this collection (2)

Display mode:      Duplicate track

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 cell_class cell_type↓ sex donor
   
stromal/adventitial cell/male/TSP14 6 stromal adventitial cell male TSP14
   
immune/B cell/female/TSP7 5935 immune B cell female TSP7
   
endothelial/blood vessel endothelial ... 14 endothelial blood vessel endothelial cell male TSP14
   
endothelial/capillary endothelial cel... 364 endothelial capillary endothelial cell male TSP14
   
endothelial/capillary endothelial cel... 88 endothelial capillary endothelial cell female TSP2
   
endothelial/capillary endothelial cel... 83 endothelial capillary endothelial cell female TSP4
   
immune/CD1c-positive myeloid dendriti... 10 immune CD1c-positive myeloid dendritic cell female TSP7
   
immune/CD1c-positive myeloid dendriti... 2 immune CD1c-positive myeloid dendritic cell female TSP2
   
immune/CD1c-positive myeloid dendriti... 21 immune CD1c-positive myeloid dendritic cell male TSP14
   
immune/CD1c-positive myeloid dendriti... 34 immune CD1c-positive myeloid dendritic cell male TSP10
   
immune/CD4-positive helper T cell/mal... 27 immune CD4-positive helper T cell male TSP14
   
immune/CD4-positive helper T cell/mal... 3 immune CD4-positive helper T cell male TSP10
   
immune/CD4-positive, alpha-beta memor... 66 immune CD4-positive, alpha-beta memory T cell female TSP2
   
immune/CD4-positive, alpha-beta memor... 186 immune CD4-positive, alpha-beta memory T cell male TSP14
   
immune/CD4-positive, alpha-beta memor... 8 immune CD4-positive, alpha-beta memory T cell male TSP10
   
immune/CD4-positive, alpha-beta T cel... 57 immune CD4-positive, alpha-beta T cell male TSP14
   
immune/CD4-positive, alpha-beta T cel... 2 immune CD4-positive, alpha-beta T cell female TSP2
   
immune/CD4-positive, alpha-beta T cel... 41 immune CD4-positive, alpha-beta T cell female TSP4
   
immune/CD8-positive, alpha-beta cytot... 42 immune CD8-positive, alpha-beta cytotoxic T ... male TSP14
   
immune/CD8-positive, alpha-beta cytot... 2 immune CD8-positive, alpha-beta cytotoxic T ... male TSP10
   
immune/CD8-positive, alpha-beta memor... 39 immune CD8-positive, alpha-beta memory T cell female TSP2
   
immune/CD8-positive, alpha-beta memor... 274 immune CD8-positive, alpha-beta memory T cell male TSP14
   
immune/CD8-positive, alpha-beta memor... 39 immune CD8-positive, alpha-beta memory T cell male TSP10
   
immune/CD8-positive, alpha-beta T cel... 46 immune CD8-positive, alpha-beta T cell male TSP14
   
immune/CD8-positive, alpha-beta T cel... 112 immune CD8-positive, alpha-beta T cell female TSP4
   
immune/CD141-positive myeloid dendrit... 1 immune CD141-positive myeloid dendritic cell female TSP7
   
immune/CD141-positive myeloid dendrit... 6 immune CD141-positive myeloid dendritic cell male TSP14
   
immune/CD141-positive myeloid dendrit... 6 immune CD141-positive myeloid dendritic cell male TSP10
   
stromal/cell of skeletal muscle/male/... 10 stromal cell of skeletal muscle male TSP14
   
immune/classical monocyte/female/TSP7 30 immune classical monocyte female TSP7
   
immune/effector CD4-positive, alpha-b... 75 immune effector CD4-positive, alpha-beta T cell male TSP14
   
immune/effector CD4-positive, alpha-b... 711 immune effector CD4-positive, alpha-beta T cell female TSP7
   
immune/effector CD8-positive, alpha-b... 34 immune effector CD8-positive, alpha-beta T cell male TSP14
   
immune/effector CD8-positive, alpha-b... 346 immune effector CD8-positive, alpha-beta T cell female TSP7
   
endothelial/endothelial cell/female/TSP7 3 endothelial endothelial cell female TSP7
   
endothelial/endothelial cell/male/TSP14 476 endothelial endothelial cell male TSP14
   
endothelial/endothelial cell/male/TSP10 131 endothelial endothelial cell male TSP10
   
endothelial/endothelial cell of arter... 32 endothelial endothelial cell of artery male TSP14
   
endothelial/endothelial cell of arter... 19 endothelial endothelial cell of artery female TSP2
   
endothelial/endothelial cell of arter... 2 endothelial endothelial cell of artery female TSP4
   
endothelial/endothelial cell of lymph... 22 endothelial endothelial cell of lymphatic vessel male TSP14
   
endothelial/endothelial cell of lymph... 32 endothelial endothelial cell of lymphatic vessel female TSP2
   
endothelial/endothelial cell of lymph... 35 endothelial endothelial cell of lymphatic vessel female TSP4
   
endothelial/endothelial cell of vascu... 227 endothelial endothelial cell of vascular tree male TSP14
   
endothelial/endothelial cell of vascu... 1627 endothelial endothelial cell of vascular tree female TSP2
   
endothelial/endothelial cell of vascu... 128 endothelial endothelial cell of vascular tree female TSP4
   
epithelial/epithelial cell/male/TSP14 5 epithelial epithelial cell male TSP14
   
epithelial/epithelial cell/male/TSP10 42 epithelial epithelial cell male TSP10
   
immune/erythrocyte/female/TSP7 2 immune erythrocyte female TSP7
   
immune/erythrocyte/male/TSP14 4 immune erythrocyte male TSP14
   
immune/erythrocyte/female/TSP2 6 immune erythrocyte female TSP2
   
stromal/fast muscle cell/male/TSP14 44 stromal fast muscle cell male TSP14
   
stromal/fast muscle cell/female/TSP2 3 stromal fast muscle cell female TSP2
   
stromal/fast muscle cell/female/TSP4 39 stromal fast muscle cell female TSP4
   
immune/hematopoietic stem cell/female... 5 immune hematopoietic stem cell female TSP7
   
immune/innate lymphoid cell/female/TSP7 435 immune innate lymphoid cell female TSP7
   
immune/innate lymphoid cell/female/TSP2 3 immune innate lymphoid cell female TSP2
   
immune/intermediate monocyte/female/TSP7 18 immune intermediate monocyte female TSP7
   
immune/intermediate monocyte/female/TSP2 5 immune intermediate monocyte female TSP2
   
immune/Langerhans cell/male/TSP14 17 immune Langerhans cell male TSP14
   
immune/Langerhans cell/male/TSP10 5 immune Langerhans cell male TSP10
   
immune/macrophage/male/TSP14 628 immune macrophage male TSP14
   
immune/macrophage/female/TSP7 4 immune macrophage female TSP7
   
immune/macrophage/female/TSP2 224 immune macrophage female TSP2
   
immune/macrophage/female/TSP4 82 immune macrophage female TSP4
   
immune/macrophage/male/TSP10 190 immune macrophage male TSP10
   
immune/mast cell/female/TSP7 8 immune mast cell female TSP7
   
immune/mast cell/female/TSP2 8 immune mast cell female TSP2
   
immune/mast cell/male/TSP14 71 immune mast cell male TSP14
   
immune/mast cell/female/TSP4 10 immune mast cell female TSP4
   
immune/mast cell/male/TSP10 189 immune mast cell male TSP10
   
immune/mature conventional dendritic ... 1 immune mature conventional dendritic cell female TSP7
   
immune/mature NK T cell/male/TSP14 266 immune mature NK T cell male TSP14
   
immune/mature NK T cell/female/TSP7 50 immune mature NK T cell female TSP7
   
immune/mature NK T cell/female/TSP2 2 immune mature NK T cell female TSP2
   
immune/mature NK T cell/male/TSP10 24 immune mature NK T cell male TSP10
   
stromal/melanocyte/male/TSP14 3 stromal melanocyte male TSP14
   
stromal/melanocyte/male/TSP10 19 stromal melanocyte male TSP10
   
immune/memory B cell/female/TSP2 108 immune memory B cell female TSP2
   
immune/memory B cell/male/TSP10 5 immune memory B cell male TSP10
   
stromal/mesenchymal stem cell/male/TSP14 4858 stromal mesenchymal stem cell male TSP14
   
stromal/mesenchymal stem cell/female/... 1699 stromal mesenchymal stem cell female TSP2
   
stromal/mesenchymal stem cell/female/... 338 stromal mesenchymal stem cell female TSP4
   
epithelial/mesothelial cell/male/TSP14 11 epithelial mesothelial cell male TSP14
   
stromal/muscle cell/male/TSP14 257 stromal muscle cell male TSP14
   
stromal/muscle cell/male/TSP10 35 stromal muscle cell male TSP10
   
immune/naive B cell/female/TSP2 5 immune naive B cell female TSP2
   
immune/naive thymus-derived CD4-posit... 60 immune naive thymus-derived CD4-positive, al... female TSP2
   
immune/naive thymus-derived CD4-posit... 42 immune naive thymus-derived CD4-positive, al... male TSP14
   
immune/naive thymus-derived CD4-posit... 1 immune naive thymus-derived CD4-positive, al... male TSP10
   
immune/naive thymus-derived CD8-posit... 22 immune naive thymus-derived CD8-positive, al... male TSP14
   
immune/naive thymus-derived CD8-posit... 6 immune naive thymus-derived CD8-positive, al... male TSP10
   
immune/neutrophil/male/TSP14 66 immune neutrophil male TSP14
   
immune/neutrophil/female/TSP7 8 immune neutrophil female TSP7
   
immune/non-classical monocyte/female/... 3 immune non-classical monocyte female TSP7
   
stromal/pericyte cell/male/TSP14 373 stromal pericyte cell male TSP14
   
stromal/pericyte cell/female/TSP2 92 stromal pericyte cell female TSP2
   
stromal/pericyte cell/female/TSP4 57 stromal pericyte cell female TSP4
   
immune/plasma cell/female/TSP7 127 immune plasma cell female TSP7
   
immune/plasma cell/female/TSP2 5 immune plasma cell female TSP2
   
immune/plasma cell/male/TSP14 15 immune plasma cell male TSP14
   
immune/plasma cell/male/TSP10 2 immune plasma cell male TSP10
   
immune/regulatory T cell/female/TSP7 50 immune regulatory T cell female TSP7
   
immune/regulatory T cell/male/TSP14 79 immune regulatory T cell male TSP14
   
immune/regulatory T cell/male/TSP10 2 immune regulatory T cell male TSP10
   
epithelial/respiratory goblet cell/ma... 1 epithelial respiratory goblet cell male TSP14
   
stromal/skeletal muscle satellite ste... 1648 stromal skeletal muscle satellite stem cell male TSP14
   
stromal/skeletal muscle satellite ste... 476 stromal skeletal muscle satellite stem cell female TSP2
   
stromal/skeletal muscle satellite ste... 185 stromal skeletal muscle satellite stem cell female TSP4
   
stromal/slow muscle cell/male/TSP14 29 stromal slow muscle cell male TSP14
   
stromal/slow muscle cell/female/TSP2 4 stromal slow muscle cell female TSP2
   
stromal/slow muscle cell/female/TSP4 6 stromal slow muscle cell female TSP4
   
stromal/smooth muscle cell/male/TSP14 61 stromal smooth muscle cell male TSP14
   
stromal/smooth muscle cell/female/TSP4 8 stromal smooth muscle cell female TSP4
   
stromal/stromal cell/male/TSP14 1425 stromal stromal cell male TSP14
   
stromal/stromal cell/male/TSP10 70 stromal stromal cell male TSP10
   
immune/T cell/female/TSP7 339 immune T cell female TSP7
   
immune/T cell/male/TSP14 287 immune T cell male TSP14
   
immune/T cell/female/TSP2 154 immune T cell female TSP2
   
immune/T cell/female/TSP4 2 immune T cell female TSP4
   
immune/T cell/male/TSP10 31 immune T cell male TSP10
   
stromal/tendon cell/male/TSP14 47 stromal tendon cell male TSP14
   
stromal/tendon cell/female/TSP2 15 stromal tendon cell female TSP2
   
stromal/tendon cell/female/TSP4 3 stromal tendon cell female TSP4
   
immune/type I NK T cell/female/TSP7 295 immune type I NK T cell female TSP7
   
epithelial/type II pneumocyte/male/TSP14 867 epithelial type II pneumocyte male TSP14
Data schema/format description and download
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.