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.
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US Server