Description
This track collection shows data from
Single-nucleus cross-tissue molecular reference maps toward
understanding disease gene function. The dataset covers ~200,000 single nuclei
from a total of 16 human donors across 25 samples, using 4 different sample preparation
protocols followed by droplet based single-cell RNA-seq. The samples were obtained from
frozen tissue as part of the Genotype-Tissue Expression (GTEx) project.
Samples were taken from the esophagus, skeletal muscle, heart, lung, prostate, breast,
and skin. The dataset includes 43 broad cell classes, some specific to certain tissues
and some shared across all tissue types.
This track collection contains three bar chart tracks of RNA expression. The first track,
Cross Tissue Nuclei, allows
cells to be grouped together and faceted on up to 4 categories: tissue, cell class, cell subclass,
and cell type. The second track,
Cross Tissue Details, allows
cells to be grouped together and faceted on up to 7 categories: tissue, cell class, cell subclass,
cell type, granular cell type, sex, and donor. The third track,
GTEx Immune Atlas,
allows cells to be grouped together and faceted on up to 5 categories: tissue, cell type, cell
class, sex, and donor.
Please see the
GTEx portal
for further interactive displays and additional data.
Display Conventions and Configuration
Tissue-cell type combinations in the Full and Combined tracks are
colored by which cell type they belong to in the below table:
| Color |
Cell Type |
| Endothelial |
| Epithelial |
| Glia |
| Immune |
| Neuron |
| Stromal |
| Other |
Tissue-cell type combinations in the Immune Atlas track are shaded according
to the below table:
| Color |
Cell Type |
| Inflammatory Macrophage |
| Lung Macrophage |
| Monocyte/Macrophage FCGR3A High |
| Monocyte/Macrophage FCGR3A Low |
| Macrophage HLAII High |
| Macrophage LYVE1 High |
| Proliferating Macrophage |
| Dendritic Cell 1 |
| Dendritic Cell 2 |
| Mature Dendritic Cell |
| Langerhans |
| CD14+ Monocyte |
| CD16+ Monocyte |
| LAM-like |
| Other |
Methods
Using the previously collected tissue samples from the Genotype-Tissue Expression
project, nuclei were isolated using four different protocols and sequenced
using droplet based single cell RNA-seq. CellBender v2.1 and other standard quality
control techniques were applied, resulting in 209,126 nuclei profiles across eight
tissues, with a mean of 918 genes and 1519 transcripts per profile.
Data from all samples was integrated with a conditional variation autoencoder
in order to correct for multiple sources of variation like sex, and protocol
while preserving tissue and cell type specific effects.
For detailed methods, please refer to Eraslan et al, or the
GTEx portal website.
UCSC Methods
The gene expression files were downloaded from the
GTEx portal. The UCSC command line utilities matrixClusterColumns,
matrixToBarChartBed, 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.
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.
Credits
Thanks to the GTEx Consortium for creating and analyzing these data.
References
Eraslan G, Drokhlyansky E, Anand S, Fiskin E, Subramanian A, Slyper M, Wang J, Van Wittenberghe N,
Rouhana JM, Waldman J et al.
Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function.
Science. 2022 May 13;376(6594):eabl4290.
PMID: 35549429; PMC: PMC9383269
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US Server