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 tissue subtissue cell_class cell_type sex donor assay
   
blood//immune/alpha-beta T cell/10x 3... 31 blood immune alpha-beta T cell female TSP7 10x 3' v3
   
blood//immune/basophil/10x 3' v3/fema... 7 blood immune basophil female TSP7 10x 3' v3
   
blood//immune/basophil/10x 3' v3/male... 3 blood immune basophil male TSP8 10x 3' v3
   
blood//immune/basophil/10x 3' v3/male... 10 blood immune basophil male TSP10 10x 3' v3
   
blood//immune/basophil/10x 3' v3/male... 9 blood immune basophil male TSP14 10x 3' v3
   
blood//immune/CD4-positive, alpha-bet... 576 blood immune CD4-positive, alpha-beta memory T cell female TSP7 10x 3' v3
   
blood//immune/CD4-positive, alpha-bet... 25 blood immune CD4-positive, alpha-beta memory T cell male TSP8 10x 3' v3
   
blood//immune/CD4-positive, alpha-bet... 137 blood immune CD4-positive, alpha-beta memory T cell male TSP10 10x 3' v3
   
blood//immune/CD4-positive, alpha-bet... 119 blood immune CD4-positive, alpha-beta memory T cell male TSP14 10x 3' v3
   
blood//immune/CD4-positive, alpha-bet... 92 blood immune CD4-positive, alpha-beta memory T cell female TSP7 Smart-seq2
   
blood//immune/CD4-positive, alpha-bet... 1132 blood immune CD4-positive, alpha-beta T cell female TSP1 10x 3' v3
   
blood//immune/CD4-positive, alpha-bet... 1238 blood immune CD4-positive, alpha-beta T cell female TSP2 10x 3' v3
   
blood//immune/CD4-positive, alpha-bet... 158 blood immune CD4-positive, alpha-beta T cell female TSP1 Smart-seq2
   
blood//immune/CD4-positive, alpha-bet... 335 blood immune CD4-positive, alpha-beta T cell female TSP2 Smart-seq2
   
blood//immune/CD8-positive, alpha-bet... 1361 blood immune CD8-positive, alpha-beta cytokine sec... female TSP7 10x 3' v3
   
blood//immune/CD8-positive, alpha-bet... 14 blood immune CD8-positive, alpha-beta cytokine sec... male TSP8 10x 3' v3
   
blood//immune/CD8-positive, alpha-bet... 79 blood immune CD8-positive, alpha-beta cytokine sec... male TSP10 10x 3' v3
   
blood//immune/CD8-positive, alpha-bet... 23 blood immune CD8-positive, alpha-beta cytokine sec... male TSP14 10x 3' v3
   
blood//immune/CD8-positive, alpha-bet... 16 blood immune CD8-positive, alpha-beta cytokine sec... female TSP7 Smart-seq2
   
blood//immune/CD8-positive, alpha-bet... 329 blood immune CD8-positive, alpha-beta T cell female TSP1 10x 3' v3
   
blood//immune/CD8-positive, alpha-bet... 548 blood immune CD8-positive, alpha-beta T cell female TSP2 10x 3' v3
   
blood//immune/CD8-positive, alpha-bet... 174 blood immune CD8-positive, alpha-beta T cell female TSP7 10x 3' v3
   
blood//immune/CD8-positive, alpha-bet... 13 blood immune CD8-positive, alpha-beta T cell male TSP8 10x 3' v3
   
blood//immune/CD8-positive, alpha-bet... 149 blood immune CD8-positive, alpha-beta T cell male TSP10 10x 3' v3
   
blood//immune/CD8-positive, alpha-bet... 16 blood immune CD8-positive, alpha-beta T cell male TSP14 10x 3' v3
   
blood//immune/CD8-positive, alpha-bet... 26 blood immune CD8-positive, alpha-beta T cell female TSP1 Smart-seq2
   
blood//immune/CD8-positive, alpha-bet... 43 blood immune CD8-positive, alpha-beta T cell female TSP2 Smart-seq2
   
blood//immune/CD8-positive, alpha-bet... 24 blood immune CD8-positive, alpha-beta T cell female TSP7 Smart-seq2
   
blood//immune/CD141-positive myeloid ... 7 blood immune CD141-positive myeloid dendritic cell female TSP7 10x 3' v3
   
blood//immune/CD141-positive myeloid ... 1 blood immune CD141-positive myeloid dendritic cell male TSP8 10x 3' v3
   
blood//immune/CD141-positive myeloid ... 5 blood immune CD141-positive myeloid dendritic cell male TSP10 10x 3' v3
   
blood//immune/CD141-positive myeloid ... 2 blood immune CD141-positive myeloid dendritic cell male TSP14 10x 3' v3
   
blood//immune/classical monocyte/10x ... 2846 blood immune classical monocyte female TSP7 10x 3' v3
   
blood//immune/classical monocyte/10x ... 225 blood immune classical monocyte male TSP8 10x 3' v3
   
blood//immune/classical monocyte/10x ... 2053 blood immune classical monocyte male TSP10 10x 3' v3
   
blood//immune/classical monocyte/10x ... 1875 blood immune classical monocyte male TSP14 10x 3' v3
   
blood//immune/classical monocyte/Smar... 212 blood immune classical monocyte female TSP7 Smart-seq2
   
blood//immune/common myeloid progenit... 1 blood immune common myeloid progenitor female TSP1 10x 3' v3
   
blood//immune/common myeloid progenit... 2 blood immune common myeloid progenitor female TSP2 10x 3' v3
   
blood//immune/erythrocyte/10x 3' v3/f... 89 blood immune erythrocyte female TSP1 10x 3' v3
   
blood//immune/erythrocyte/10x 3' v3/f... 319 blood immune erythrocyte female TSP2 10x 3' v3
   
blood//immune/erythrocyte/10x 3' v3/f... 7527 blood immune erythrocyte female TSP7 10x 3' v3
   
blood//immune/erythrocyte/10x 3' v3/m... 1 blood immune erythrocyte male TSP8 10x 3' v3
   
blood//immune/erythrocyte/10x 3' v3/m... 824 blood immune erythrocyte male TSP10 10x 3' v3
   
blood//immune/erythrocyte/10x 3' v3/m... 1637 blood immune erythrocyte male TSP14 10x 3' v3
   
blood//immune/erythrocyte/Smart-seq2/... 1 blood immune erythrocyte female TSP1 Smart-seq2
   
blood//immune/erythrocyte/Smart-seq2/... 14 blood immune erythrocyte female TSP2 Smart-seq2
   
blood//immune/erythrocyte/Smart-seq2/... 72 blood immune erythrocyte female TSP7 Smart-seq2
   
blood//immune/granulocyte/10x 3' v3/f... 2 blood immune granulocyte female TSP2 10x 3' v3
   
blood//immune/hematopoietic stem cell... 2 blood immune hematopoietic stem cell female TSP1 10x 3' v3
   
blood//immune/hematopoietic stem cell... 16 blood immune hematopoietic stem cell female TSP2 10x 3' v3
   
blood//immune/hematopoietic stem cell... 23 blood immune hematopoietic stem cell female TSP7 10x 3' v3
   
blood//immune/hematopoietic stem cell... 1 blood immune hematopoietic stem cell male TSP8 10x 3' v3
   
blood//immune/hematopoietic stem cell... 11 blood immune hematopoietic stem cell male TSP10 10x 3' v3
   
blood//immune/hematopoietic stem cell... 12 blood immune hematopoietic stem cell male TSP14 10x 3' v3
   
blood//immune/hematopoietic stem cell... 5 blood immune hematopoietic stem cell female TSP2 Smart-seq2
   
blood//immune/macrophage/10x 3' v3/fe... 488 blood immune macrophage female TSP2 10x 3' v3
   
blood//immune/mature NK T cell/10x 3'... 115 blood immune mature NK T cell female TSP1 10x 3' v3
   
blood//immune/mature NK T cell/10x 3'... 452 blood immune mature NK T cell female TSP2 10x 3' v3
   
blood//immune/mature NK T cell/10x 3'... 1681 blood immune mature NK T cell female TSP7 10x 3' v3
   
blood//immune/mature NK T cell/10x 3'... 10 blood immune mature NK T cell male TSP8 10x 3' v3
   
blood//immune/mature NK T cell/10x 3'... 514 blood immune mature NK T cell male TSP10 10x 3' v3
   
blood//immune/mature NK T cell/10x 3'... 99 blood immune mature NK T cell male TSP14 10x 3' v3
   
blood//immune/mature NK T cell/Smart-... 11 blood immune mature NK T cell female TSP1 Smart-seq2
   
blood//immune/mature NK T cell/Smart-... 38 blood immune mature NK T cell female TSP2 Smart-seq2
   
blood//immune/mature NK T cell/Smart-... 28 blood immune mature NK T cell female TSP7 Smart-seq2
   
blood//immune/memory B cell/10x 3' v3... 144 blood immune memory B cell female TSP1 10x 3' v3
   
blood//immune/memory B cell/10x 3' v3... 80 blood immune memory B cell female TSP2 10x 3' v3
   
blood//immune/memory B cell/10x 3' v3... 239 blood immune memory B cell female TSP7 10x 3' v3
   
blood//immune/memory B cell/10x 3' v3... 47 blood immune memory B cell male TSP8 10x 3' v3
   
blood//immune/memory B cell/10x 3' v3... 273 blood immune memory B cell male TSP10 10x 3' v3
   
blood//immune/memory B cell/10x 3' v3... 10 blood immune memory B cell male TSP14 10x 3' v3
   
blood//immune/memory B cell/Smart-seq... 24 blood immune memory B cell female TSP1 Smart-seq2
   
blood//immune/memory B cell/Smart-seq... 9 blood immune memory B cell female TSP2 Smart-seq2
   
blood//immune/memory B cell/Smart-seq... 28 blood immune memory B cell female TSP7 Smart-seq2
   
blood//immune/monocyte/10x 3' v3/fema... 1616 blood immune monocyte female TSP1 10x 3' v3
   
blood//immune/monocyte/10x 3' v3/fema... 6819 blood immune monocyte female TSP2 10x 3' v3
   
blood//immune/monocyte/Smart-seq2/fem... 18 blood immune monocyte female TSP1 Smart-seq2
   
blood//immune/monocyte/Smart-seq2/fem... 519 blood immune monocyte female TSP2 Smart-seq2
   
blood//immune/naive B cell/10x 3' v3/... 228 blood immune naive B cell female TSP1 10x 3' v3
   
blood//immune/naive B cell/10x 3' v3/... 338 blood immune naive B cell female TSP2 10x 3' v3
   
blood//immune/naive B cell/10x 3' v3/... 716 blood immune naive B cell female TSP7 10x 3' v3
   
blood//immune/naive B cell/10x 3' v3/... 26 blood immune naive B cell male TSP8 10x 3' v3
   
blood//immune/naive B cell/10x 3' v3/... 766 blood immune naive B cell male TSP10 10x 3' v3
   
blood//immune/naive B cell/10x 3' v3/... 5 blood immune naive B cell male TSP14 10x 3' v3
   
blood//immune/naive B cell/Smart-seq2... 35 blood immune naive B cell female TSP1 Smart-seq2
   
blood//immune/naive B cell/Smart-seq2... 112 blood immune naive B cell female TSP2 Smart-seq2
   
blood//immune/naive B cell/Smart-seq2... 13 blood immune naive B cell female TSP7 Smart-seq2
   
blood//immune/naive thymus-derived CD... 280 blood immune naive thymus-derived CD4-positive, al... female TSP7 10x 3' v3
   
blood//immune/naive thymus-derived CD... 6 blood immune naive thymus-derived CD4-positive, al... male TSP8 10x 3' v3
   
blood//immune/naive thymus-derived CD... 94 blood immune naive thymus-derived CD4-positive, al... male TSP10 10x 3' v3
   
blood//immune/naive thymus-derived CD... 23 blood immune naive thymus-derived CD4-positive, al... male TSP14 10x 3' v3
   
blood//immune/naive thymus-derived CD... 9 blood immune naive thymus-derived CD4-positive, al... female TSP7 Smart-seq2
   
blood//immune/neutrophil/10x 3' v3/fe... 2 blood immune neutrophil female TSP1 10x 3' v3
   
blood//immune/neutrophil/10x 3' v3/fe... 6 blood immune neutrophil female TSP2 10x 3' v3
   
blood//immune/neutrophil/10x 3' v3/fe... 969 blood immune neutrophil female TSP7 10x 3' v3
   
blood//immune/neutrophil/10x 3' v3/ma... 1567 blood immune neutrophil male TSP8 10x 3' v3
   
blood//immune/neutrophil/10x 3' v3/ma... 5834 blood immune neutrophil male TSP14 10x 3' v3
   
blood//immune/neutrophil/Smart-seq2/f... 1 blood immune neutrophil female TSP1 Smart-seq2
   
blood//immune/neutrophil/Smart-seq2/f... 15 blood immune neutrophil female TSP2 Smart-seq2
   
blood//immune/neutrophil/Smart-seq2/f... 62 blood immune neutrophil female TSP7 Smart-seq2
   
blood//immune/non-classical monocyte/... 5 blood immune non-classical monocyte female TSP7 10x 3' v3
   
blood//immune/non-classical monocyte/... 3 blood immune non-classical monocyte male TSP10 10x 3' v3
   
blood//immune/plasma cell/10x 3' v3/f... 1 blood immune plasma cell female TSP2 10x 3' v3
   
blood//immune/plasma cell/10x 3' v3/f... 235 blood immune plasma cell female TSP7 10x 3' v3
   
blood//immune/plasma cell/10x 3' v3/m... 10 blood immune plasma cell male TSP8 10x 3' v3
   
blood//immune/plasma cell/10x 3' v3/m... 33 blood immune plasma cell male TSP10 10x 3' v3
   
blood//immune/plasma cell/10x 3' v3/m... 206 blood immune plasma cell male TSP14 10x 3' v3
   
blood//immune/plasma cell/Smart-seq2/... 3 blood immune plasma cell female TSP7 Smart-seq2
   
blood//immune/plasmablast/10x 3' v3/f... 7 blood immune plasmablast female TSP1 10x 3' v3
   
blood//immune/plasmablast/10x 3' v3/f... 3 blood immune plasmablast female TSP2 10x 3' v3
   
blood//immune/plasmacytoid dendritic ... 9 blood immune plasmacytoid dendritic cell female TSP7 10x 3' v3
   
blood//immune/plasmacytoid dendritic ... 1 blood immune plasmacytoid dendritic cell male TSP10 10x 3' v3
   
blood//immune/plasmacytoid dendritic ... 1 blood immune plasmacytoid dendritic cell male TSP14 10x 3' v3
   
blood//immune/platelet/10x 3' v3/fema... 100 blood immune platelet female TSP7 10x 3' v3
   
blood//immune/platelet/10x 3' v3/male... 1 blood immune platelet male TSP8 10x 3' v3
   
blood//immune/platelet/10x 3' v3/male... 21 blood immune platelet male TSP10 10x 3' v3
   
blood//immune/platelet/10x 3' v3/male... 82 blood immune platelet male TSP14 10x 3' v3
   
blood//immune/platelet/Smart-seq2/fem... 35 blood immune platelet female TSP7 Smart-seq2
   
blood//immune/type I NK T cell/10x 3'... 432 blood immune type I NK T cell female TSP7 10x 3' v3
   
blood//immune/type I NK T cell/10x 3'... 24 blood immune type I NK T cell male TSP8 10x 3' v3
   
blood//immune/type I NK T cell/10x 3'... 34 blood immune type I NK T cell male TSP10 10x 3' v3
   
blood//immune/type I NK T cell/10x 3'... 9 blood immune type I NK T cell male TSP14 10x 3' v3
   
blood//immune/type I NK T cell/Smart-... 19 blood 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.