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)

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cell_class
 stromal (71)

color cluster count tissue cell_class cell_type
   
adipose tissue fibroblast 8459 adipose tissue stromal fibroblast
   
adipose tissue mesenchymal stem cell 1311 adipose tissue stromal mesenchymal stem cell
   
adipose tissue myofibroblast cell 982 adipose tissue stromal myofibroblast cell
   
adipose tissue smooth muscle cell 16 adipose tissue stromal smooth muscle cell
   
bladder organ fibroblast 4927 bladder organ stromal fibroblast
   
bladder organ myofibroblast cell 1989 bladder organ stromal myofibroblast cell
   
bladder organ pericyte cell 708 bladder organ stromal pericyte cell
   
bladder organ smooth muscle cell 227 bladder organ stromal smooth muscle cell
   
eye fat cell 44 eye stromal fat cell
   
eye fibroblast 95 eye stromal fibroblast
   
eye melanocyte 144 eye stromal melanocyte
   
eye Muller cell 360 eye stromal Muller cell
   
eye radial glial cell 195 eye stromal radial glial cell
   
eye retina horizontal cell 6 eye stromal retina horizontal cell
   
eye retinal bipolar neuron 34 eye stromal retinal bipolar neuron
   
eye retinal ganglion cell 5 eye stromal retinal ganglion cell
   
eye stromal cell 325 eye stromal stromal cell
   
heart cardiac muscle cell 7205 heart stromal cardiac muscle cell
   
heart fibroblast 250 heart stromal fibroblast
   
heart smooth muscle cell 222 heart stromal smooth muscle cell
   
large intestine fibroblast 953 large intestine stromal fibroblast
   
liver fibroblast 76 liver stromal fibroblast
   
lung adventitial cell 373 lung stromal adventitial cell
   
lung bronchial smooth muscle cell 81 lung stromal bronchial smooth muscle cell
   
lung fibroblast 336 lung stromal fibroblast
   
lung myofibroblast cell 10 lung stromal myofibroblast cell
   
lung pericyte cell 213 lung stromal pericyte cell
   
lung smooth muscle cell 25 lung stromal smooth muscle cell
   
lung vascular associated smooth muscl... 80 lung stromal vascular associated smooth muscle cell
   
lymph node stromal cell 111 lymph node stromal stromal cell
   
mammary gland fibroblast 2066 mammary gland stromal fibroblast
   
mammary gland pericyte cell 106 mammary gland stromal pericyte cell
   
mammary gland vascular associated smo... 71 mammary gland stromal vascular associated smooth muscle cell
   
muscle tissue fast muscle cell 266 muscle tissue stromal fast muscle cell
   
muscle tissue mesenchymal stem cell 14148 muscle tissue stromal mesenchymal stem cell
   
muscle tissue pericyte cell 1794 muscle tissue stromal pericyte cell
   
muscle tissue skeletal muscle satelli... 4831 muscle tissue stromal skeletal muscle satellite stem cell
   
muscle tissue slow muscle cell 163 muscle tissue stromal slow muscle cell
   
muscle tissue smooth muscle cell 58 muscle tissue stromal smooth muscle cell
   
muscle tissue tendon cell 234 muscle tissue stromal tendon cell
   
pancreas fibroblast 47 pancreas stromal fibroblast
   
pancreas pancreatic stellate cell 393 pancreas stromal pancreatic stellate cell
   
prostate gland fibroblast 223 prostate gland stromal fibroblast
   
prostate gland smooth muscle cell 285 prostate gland stromal smooth muscle cell
   
prostate gland stromal cell 32 prostate gland stromal stromal cell
   
saliva-secreting gland adventitial cell 442 saliva-secreting gland stromal adventitial cell
   
saliva-secreting gland fibroblast 2169 saliva-secreting gland stromal fibroblast
   
saliva-secreting gland pericyte cell 146 saliva-secreting gland stromal pericyte cell
   
skin of body cell of skeletal muscle 10 skin of body stromal cell of skeletal muscle
   
skin of body melanocyte 64 skin of body stromal melanocyte
   
skin of body muscle cell 437 skin of body stromal muscle cell
   
skin of body smooth muscle cell 13 skin of body stromal smooth muscle cell
   
skin of body stromal cell 2943 skin of body stromal stromal cell
   
small intestine fibroblast 113 small intestine stromal fibroblast
   
thymus fast muscle cell 86 thymus stromal fast muscle cell
   
thymus fibroblast 3924 thymus stromal fibroblast
   
thymus vascular associated smooth mus... 2130 thymus stromal vascular associated smooth muscle cell
   
tongue fibroblast 251 tongue stromal fibroblast
   
tongue pericyte cell 117 tongue stromal pericyte cell
   
tongue Schwann cell 10 tongue stromal Schwann cell
   
tongue tongue muscle cell 60 tongue stromal tongue muscle cell
   
trachea connective tissue cell 249 trachea stromal connective tissue cell
   
trachea fibroblast 1239 trachea stromal fibroblast
   
trachea smooth muscle cell 96 trachea stromal smooth muscle cell
   
uterus fibroblast 3014 uterus stromal fibroblast
   
uterus myometrial cell 199 uterus stromal myometrial cell
   
uterus pericyte cell 95 uterus stromal pericyte cell
   
uterus vascular associated smooth mus... 390 uterus stromal vascular associated smooth muscle cell
   
vasculature fibroblast 5867 vasculature stromal fibroblast
   
vasculature pericyte cell 1193 vasculature stromal pericyte cell
   
vasculature smooth muscle cell 3075 vasculature stromal smooth muscle cell
Data schema/format description and download
Assembly: Human Dec. 2013 (GRCh38/hg38)
Data last updated at UCSC: 2022-05-11 19:58:31

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.