Cross Tissue Nuclei Cross Tissue Nuclei Track Settings
 
Cross tissue nuclei RNA by tissue and cell type

Track collection: Single Nuclei sequenced across many tissues

+  Description
+  All tracks in this collection (3)

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)

color cluster count tissue cell_class cell_subclass cell_type
   
Breast/Stromal/Adipocyte/Adipocyte 1761 Breast Stromal Adipocyte Adipocyte
   
Breast/Endothelial/Endothelial cell/E... 119 Breast Endothelial Endothelial cell Endothelial cell (lymphatic)
   
Breast/Endothelial/Endothelial cell/E... 762 Breast Endothelial Endothelial cell Endothelial cell (vascular)
   
Breast/Epithelial/Epithelial cell/Epi... 4849 Breast Epithelial Epithelial cell Epithelial cell (luminal)
   
Breast/Stromal/Fibroblast/Fibroblast 819 Breast Stromal Fibroblast Fibroblast
   
Breast/Immune/Immune (myeloid)/Immune... 358 Breast Immune Immune (myeloid) Immune (DC/macrophage)
   
Breast/Epithelial/Epithelial cell/Myo... 950 Breast Epithelial Epithelial cell Myoepithelial (basal)
   
Breast/Stromal/Muscle/Pericyte/SMC 152 Breast Stromal Muscle Pericyte/SMC
   
Esophagus mucosa/Endothelial/Endothel... 1567 Esophagus mucosa Endothelial Endothelial cell Endothelial cell (lymphatic)
   
Esophagus mucosa/Endothelial/Endothel... 3111 Esophagus mucosa Endothelial Endothelial cell Endothelial cell (vascular)
   
Esophagus mucosa/Epithelial/Epithelia... 8152 Esophagus mucosa Epithelial Epithelial cell Epithelial cell (basal)
   
Esophagus mucosa/Epithelial/Epithelia... 2771 Esophagus mucosa Epithelial Epithelial cell Epithelial cell (squamous)
   
Esophagus mucosa/Epithelial/Epithelia... 2404 Esophagus mucosa Epithelial Epithelial cell Epithelial cell (suprabasal)
   
Esophagus mucosa/Stromal/Fibroblast/F... 2815 Esophagus mucosa Stromal Fibroblast Fibroblast
   
Esophagus mucosa/Immune/Immune (lymph... 157 Esophagus mucosa Immune Immune (lymphocyte) Immune (B cell)
   
Esophagus mucosa/Immune/Immune (myelo... 96 Esophagus mucosa Immune Immune (myeloid) Immune (DC)
   
Esophagus mucosa/Immune/Immune (myelo... 1262 Esophagus mucosa Immune Immune (myeloid) Immune (DC/macrophage)
   
Esophagus mucosa/Immune/Immune (myelo... 40 Esophagus mucosa Immune Immune (myeloid) Immune (mast cell)
   
Esophagus mucosa/Immune/Immune (lymph... 29 Esophagus mucosa Immune Immune (lymphocyte) Immune (NK cell)
   
Esophagus mucosa/Immune/Immune (lymph... 1632 Esophagus mucosa Immune Immune (lymphocyte) Immune (T cell)
   
Esophagus mucosa/Epithelial/Epithelia... 457 Esophagus mucosa Epithelial Epithelial cell Mucous cell
   
Esophagus mucosa/Stromal/Stromal/Myof... 989 Esophagus mucosa Stromal Stromal Myofibroblast
   
Esophagus mucosa/Epithelial/Epithelia... 12 Esophagus mucosa Epithelial Epithelial cell Neuroendocrine
   
Esophagus mucosa/Stromal/Muscle/Peric... 501 Esophagus mucosa Stromal Muscle Pericyte/SMC
   
Esophagus mucosa/Glia/Glia/Schwann cell 65 Esophagus mucosa Glia Glia Schwann cell
   
Esophagus muscularis/Stromal/Adipocyt... 175 Esophagus muscularis Stromal Adipocyte Adipocyte
   
Esophagus muscularis/Endothelial/Endo... 1217 Esophagus muscularis Endothelial Endothelial cell Endothelial cell (lymphatic)
   
Esophagus muscularis/Endothelial/Endo... 3244 Esophagus muscularis Endothelial Endothelial cell Endothelial cell (vascular)
   
Esophagus muscularis/Stromal/Fibrobla... 10409 Esophagus muscularis Stromal Fibroblast Fibroblast
   
Esophagus muscularis/Stromal/Muscle/ICCs 237 Esophagus muscularis Stromal Muscle ICCs
   
Esophagus muscularis/Immune/Immune (l... 17 Esophagus muscularis Immune Immune (lymphocyte) Immune (B cell)
   
Esophagus muscularis/Immune/Immune (m... 2242 Esophagus muscularis Immune Immune (myeloid) Immune (DC/macrophage)
   
Esophagus muscularis/Immune/Immune (m... 721 Esophagus muscularis Immune Immune (myeloid) Immune (mast cell)
   
Esophagus muscularis/Immune/Immune (l... 34 Esophagus muscularis Immune Immune (lymphocyte) Immune (NK cell)
   
Esophagus muscularis/Immune/Immune (l... 250 Esophagus muscularis Immune Immune (lymphocyte) Immune (T cell)
   
Esophagus muscularis/Stromal/Muscle/M... 13662 Esophagus muscularis Stromal Muscle Myocyte (smooth muscle)
   
Esophagus muscularis/Neuron/Neuron/Ne... 25 Esophagus muscularis Neuron Neuron Neuronal
   
Esophagus muscularis/Stromal/Muscle/P... 970 Esophagus muscularis Stromal Muscle Pericyte/SMC
   
Esophagus muscularis/Glia/Glia/Schwan... 970 Esophagus muscularis Glia Glia Schwann cell
   
Heart/Stromal/Adipocyte/Adipocyte 193 Heart Stromal Adipocyte Adipocyte
   
Heart/Endothelial/Endothelial cell/En... 565 Heart Endothelial Endothelial cell Endothelial cell (lymphatic)
   
Heart/Endothelial/Endothelial cell/En... 7070 Heart Endothelial Endothelial cell Endothelial cell (vascular)
   
Heart/Stromal/Fibroblast/Fibroblast 9287 Heart Stromal Fibroblast Fibroblast
   
Heart/Immune/Immune (lymphocyte)/Immu... 22 Heart Immune Immune (lymphocyte) Immune (B cell)
   
Heart/Immune/Immune (myeloid)/Immune ... 6320 Heart Immune Immune (myeloid) Immune (DC/macrophage)
   
Heart/Immune/Immune (myeloid)/Immune ... 79 Heart Immune Immune (myeloid) Immune (mast cell)
   
Heart/Immune/Immune (lymphocyte)/Immu... 319 Heart Immune Immune (lymphocyte) Immune (NK cell)
   
Heart/Immune/Immune (lymphocyte)/Immu... 357 Heart Immune Immune (lymphocyte) Immune (T cell)
   
Heart/Stromal/Muscle/Myocyte (cardiac) 7041 Heart Stromal Muscle Myocyte (cardiac)
   
Heart/Stromal/Muscle/Myocyte (cardiac... 2585 Heart Stromal Muscle Myocyte (cardiac, cytoplasmic)
   
Heart/Stromal/Muscle/Pericyte/SMC 2438 Heart Stromal Muscle Pericyte/SMC
   
Heart/Glia/Glia/Schwann cell 298 Heart Glia Glia Schwann cell
   
Lung/Endothelial/Endothelial cell/End... 334 Lung Endothelial Endothelial cell Endothelial cell (lymphatic)
   
Lung/Endothelial/Endothelial cell/End... 2412 Lung Endothelial Endothelial cell Endothelial cell (vascular)
   
Lung/Epithelial/Epithelial cell/Epith... 7274 Lung Epithelial Epithelial cell Epithelial cell (alveolar type I)
   
Lung/Epithelial/Epithelial cell/Epith... 15103 Lung Epithelial Epithelial cell Epithelial cell (alveolar type II)
   
Lung/Epithelial/Epithelial cell/Epith... 142 Lung Epithelial Epithelial cell Epithelial cell (basal)
   
Lung/Epithelial/Epithelial cell/Epith... 896 Lung Epithelial Epithelial cell Epithelial cell (ciliated)
   
Lung/Epithelial/Epithelial cell/Epith... 660 Lung Epithelial Epithelial cell Epithelial cell (club)
   
Lung/Stromal/Fibroblast/Fibroblast 1476 Lung Stromal Fibroblast Fibroblast
   
Lung/Immune/Immune (myeloid)/Immune (... 5121 Lung Immune Immune (myeloid) Immune (alveolar macrophage)
   
Lung/Immune/Immune (lymphocyte)/Immun... 56 Lung Immune Immune (lymphocyte) Immune (B cell)
   
Lung/Immune/Immune (myeloid)/Immune (... 921 Lung Immune Immune (myeloid) Immune (DC/macrophage)
   
Lung/Immune/Immune (myeloid)/Immune (... 57 Lung Immune Immune (myeloid) Immune (mast cell)
   
Lung/Immune/Immune (lymphocyte)/Immun... 56 Lung Immune Immune (lymphocyte) Immune (NK cell)
   
Lung/Immune/Immune (lymphocyte)/Immun... 613 Lung Immune Immune (lymphocyte) Immune (T cell)
   
Lung/Stromal/Muscle/Pericyte/SMC 163 Lung Stromal Muscle Pericyte/SMC
   
Prostate/Endothelial/Endothelial cell... 251 Prostate Endothelial Endothelial cell Endothelial cell (lymphatic)
   
Prostate/Endothelial/Endothelial cell... 2575 Prostate Endothelial Endothelial cell Endothelial cell (vascular)
   
Prostate/Epithelial/Epithelial cell/E... 7300 Prostate Epithelial Epithelial cell Epithelial cell (basal)
   
Prostate/Epithelial/Epithelial cell/E... 3009 Prostate Epithelial Epithelial cell Epithelial cell (club)
   
Prostate/Epithelial/Epithelial cell/E... 1578 Prostate Epithelial Epithelial cell Epithelial cell (Hillock)
   
Prostate/Epithelial/Epithelial cell/E... 11107 Prostate Epithelial Epithelial cell Epithelial cell (luminal)
   
Prostate/Stromal/Fibroblast/Fibroblast 1142 Prostate Stromal Fibroblast Fibroblast
   
Prostate/Immune/Immune (lymphocyte)/I... 32 Prostate Immune Immune (lymphocyte) Immune (B cell)
   
Prostate/Immune/Immune (myeloid)/Immu... 1014 Prostate Immune Immune (myeloid) Immune (DC/macrophage)
   
Prostate/Immune/Immune (myeloid)/Immu... 14 Prostate Immune Immune (myeloid) Immune (mast cell)
   
Prostate/Immune/Immune (lymphocyte)/I... 36 Prostate Immune Immune (lymphocyte) Immune (NK cell)
   
Prostate/Immune/Immune (lymphocyte)/I... 614 Prostate Immune Immune (lymphocyte) Immune (T cell)
   
Prostate/Stromal/Muscle/Myocyte (smoo... 2018 Prostate Stromal Muscle Myocyte (smooth muscle)
   
Prostate/Epithelial/Epithelial cell/N... 79 Prostate Epithelial Epithelial cell Neuroendocrine
   
Prostate/Stromal/Muscle/Pericyte/SMC 225 Prostate Stromal Muscle Pericyte/SMC
   
Prostate/Glia/Glia/Schwann cell 67 Prostate Glia Glia Schwann cell
   
Skeletal muscle/Stromal/Adipocyte/Adi... 159 Skeletal muscle Stromal Adipocyte Adipocyte
   
Skeletal muscle/Endothelial/Endotheli... 207 Skeletal muscle Endothelial Endothelial cell Endothelial cell (lymphatic)
   
Skeletal muscle/Endothelial/Endotheli... 1124 Skeletal muscle Endothelial Endothelial cell Endothelial cell (vascular)
   
Skeletal muscle/Stromal/Fibroblast/Fi... 5944 Skeletal muscle Stromal Fibroblast Fibroblast
   
Skeletal muscle/Immune/Immune (myeloi... 721 Skeletal muscle Immune Immune (myeloid) Immune (DC/macrophage)
   
Skeletal muscle/Immune/Immune (myeloi... 16 Skeletal muscle Immune Immune (myeloid) Immune (mast cell)
   
Skeletal muscle/Immune/Immune (lympho... 33 Skeletal muscle Immune Immune (lymphocyte) Immune (NK cell)
   
Skeletal muscle/Immune/Immune (lympho... 67 Skeletal muscle Immune Immune (lymphocyte) Immune (T cell)
   
Skeletal muscle/Stromal/Muscle/Myocyt... 95 Skeletal muscle Stromal Muscle Myocyte (NMJ-rich)
   
Skeletal muscle/Stromal/Muscle/Myocyt... 20772 Skeletal muscle Stromal Muscle Myocyte (sk. muscle)
   
Skeletal muscle/Stromal/Muscle/Myocyt... 769 Skeletal muscle Stromal Muscle Myocyte (sk. muscle, cytoplasmic)
   
Skeletal muscle/Stromal/Muscle/Pericy... 448 Skeletal muscle Stromal Muscle Pericyte/SMC
   
Skeletal muscle/Stromal/Muscle/Satell... 487 Skeletal muscle Stromal Muscle Satellite cell
   
Skeletal muscle/Glia/Glia/Schwann cell 35 Skeletal muscle Glia Glia Schwann cell
   
Skin/Other/Other/ 452 Skin Other Other
   
Skin/Stromal/Adipocyte/Adipocyte 62 Skin Stromal Adipocyte Adipocyte
   
Skin/Endothelial/Endothelial cell/End... 293 Skin Endothelial Endothelial cell Endothelial cell (lymphatic)
   
Skin/Endothelial/Endothelial cell/End... 730 Skin Endothelial Endothelial cell Endothelial cell (vascular)
   
Skin/Epithelial/Epithelial cell (kera... 1320 Skin Epithelial Epithelial cell (keratinocyte) Epithelial cell (basal keratinocyte)
   
Skin/Epithelial/Epithelial cell/Epith... 72 Skin Epithelial Epithelial cell Epithelial cell (cornified keratinocyte)
   
Skin/Epithelial/Epithelial cell (kera... 195 Skin Epithelial Epithelial cell (keratinocyte) Epithelial cell (mature keratinocyte)
   
Skin/Epithelial/Epithelial cell (kera... 432 Skin Epithelial Epithelial cell (keratinocyte) Epithelial cell (suprabasal keratinoc...
   
Skin/Stromal/Fibroblast/Fibroblast 529 Skin Stromal Fibroblast Fibroblast
   
Skin/Immune/Immune (myeloid)/Immune (... 121 Skin Immune Immune (myeloid) Immune (DC/macrophage)
   
Skin/Immune/Immune (myeloid)/Immune (... 48 Skin Immune Immune (myeloid) Immune (Langerhans)
   
Skin/Immune/Immune (myeloid)/Immune (... 10 Skin Immune Immune (myeloid) Immune (mast cell)
   
Skin/Immune/Immune (lymphocyte)/Immun... 75 Skin Immune Immune (lymphocyte) Immune (T cell)
   
Skin/Epithelial/Melanocyte/Melanocyte 272 Skin Epithelial Melanocyte Melanocyte
   
Skin/Stromal/Muscle/Pericyte/SMC 186 Skin Stromal Muscle Pericyte/SMC
   
Skin/Epithelial/Epithelial cell/Sebac... 230 Skin Epithelial Epithelial cell Sebaceous gland cell
   
Skin/Epithelial/Epithelial cell/Sweat... 300 Skin Epithelial Epithelial cell Sweat gland cell
Data schema/format description and download
Assembly: Human Dec. 2013 (GRCh38/hg38)
Data last updated at UCSC: 2022-11-09 15:52:51

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