Tabula Sapiens Tabula Tissue Cell Track Settings
 
Tabula sapiens RNA by tissue and cell type

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)


cell_type
Clear
 adventitial cell (1)
 B cell (4)
 basal cell (1)
 basophil (1)
 blood vessel endothelial cell (1)
 bronchial smooth muscle cell (1)
 capillary endothelial cell (2)
 CD1c-positive myeloid dendritic cell (1)
 CD4-positive helper T cell (1)
 CD4-positive, alpha-beta memory T cell (1)
 CD4-positive, alpha-beta T cell (2)
 CD8-positive, alpha-beta cytotoxic T cell (1)
 CD8-positive, alpha-beta memory T cell (1)
 CD8-positive, alpha-beta T cell (3)
 CD141-positive myeloid dendritic cell (1)
 classical monocyte (2)
 club cell (1)
 conjunctival epithelial cell (1)
 corneal epithelial cell (1)
 dendritic cell (3)
 DN1 thymic pro-T cell (1)
 DN3 thymocyte (1)
 DN4 thymocyte (1)
 effector CD4-positive, alpha-beta T cell (2)
 effector CD8-positive, alpha-beta T cell (2)
 endothelial cell (2)
 endothelial cell of artery (2)
 endothelial cell of lymphatic vessel (2)
 epithelial cell of lacrimal sac (1)
 erythrocyte (2)
 erythroid lineage cell (1)
 eye photoreceptor cell (1)
 fast muscle cell (1)
 fat cell (1)
 fibroblast (3)
 hematopoietic stem cell (1)
 immature natural killer cell (1)
 innate lymphoid cell (2)
 intermediate monocyte (2)
 keratocyte (1)
 lung ciliated cell (1)
 lung microvascular endothelial cell (1)
 macrophage (4)
 mast cell (3)
 mature conventional dendritic cell (1)
 mature NK T cell (3)
 medullary thymic epithelial cell (1)
 melanocyte (1)
 memory B cell (2)
 mesothelial cell (2)
 microglial cell (1)
 monocyte (2)
 Muller cell (1)
 myeloid dendritic cell (1)
 myofibroblast cell (1)
 naive B cell (2)
 naive regulatory T cell (1)
 naive thymus-derived CD4-positive, alpha-beta T cell (1)
 neutrophil (2)
 non-classical monocyte (2)
 pericyte cell (1)
 pigmented ciliary epithelial cell (1)
 plasma cell (4)
 plasmacytoid dendritic cell (2)
 pulmonary ionocyte (1)
 radial glial cell (1)
 regulatory T cell (1)
 respiratory goblet cell (1)
 retina horizontal cell (1)
 retinal bipolar neuron (1)
 retinal blood vessel endothelial cell (1)
 retinal ganglion cell (1)
 retinal pigment epithelial cell (1)
 serous cell of epithelium of bronchus (1)
 smooth muscle cell (1)
 stem cell (1)
 stromal cell (2)
 surface ectodermal cell (1)
 T cell (2)
 T follicular helper cell (1)
 thymocyte (1)
 type I NK T cell (1)
 type I pneumocyte (1)
 type II pneumocyte (1)
 vascular associated smooth muscle cell (2)
 vein endothelial cell (2)
See Fewer
color cluster count tissue↓ cell_class cell_type
   
eye B cell 102 eye immune B cell
   
eye fibroblast 95 eye stromal fibroblast
   
eye macrophage 108 eye immune macrophage
   
eye mast cell 5 eye immune mast cell
   
eye T cell 237 eye immune T cell
   
lung B cell 87 lung immune B cell
   
lung fibroblast 336 lung stromal fibroblast
   
lung macrophage 12160 lung immune macrophage
   
lymph node B cell 15249 lymph node immune B cell
   
lymph node macrophage 1148 lymph node immune macrophage
   
lymph node mast cell 143 lymph node immune mast cell
   
lymph node T cell 3848 lymph node immune T cell
   
thymus B cell 1919 thymus immune B cell
   
thymus fibroblast 3924 thymus stromal fibroblast
   
thymus macrophage 461 thymus immune macrophage
   
thymus mast cell 11 thymus immune mast cell
View table schema
Data last updated at UCSC: 2022-05-12 04:58:31

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.