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.

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.