> For the complete documentation index, see [llms.txt](https://academy.dnanexus.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://academy.dnanexus.com/public-datasets-on-the-dnanexus-platform/target-validation/the-genotype-tissue-expression-gtex-dataset.md).
# The Genotype-Tissue Expression (GTEx) Dataset
## Necessary Disclaimers and Legal
The user is responsible for reviewing and complying with the license requirements of the software, notebooks, and data referenced in this documentation.
Users are responsible for the costs associated with analyzing the GTEx dataset and its storage in their project spaces.
Instance type availability and pricing are subject to the contract between the user or the user’s organization and DNAnexus.
## Citations for GTEx dataset
The latest publication regarding GTEx, [The human and non-human primate developmental GTEx projects (2025)](https://www.nature.com/articles/s41586-024-08244-9), is available on the GTEx Portal website and describes recent updates: the developmental Genotype-Tissue Expression (dGTEx) which integrates gene expression, regulatory, and genetic data across human and non-human primate development. Users can also find more information about GTEx in previous publications:
[The GTEx Consortium atlas of genetic regulatory effects across human tissues (2020)](https://www.science.org/doi/10.1126/science.aaz1776).
[The Genotype-Tissue Expression (GTEx) project (2013)](https://www.nature.com/articles/ng.2653).
More publications related to GTEx are listed in the [GTEx Portal- Publication section](https://gtexportal.org/home/publicationsPage).
More information about the GTEx dataset can be found in the [GTEx Portal Website](https://gtexportal.org/home/).
## Overview of the GTEx Dataset
The Adult Genotype-Tissue Expression (GTEx) project is a comprehensive public resource for studying tissue-specific gene expression and genetic regulation, developed by the National Center for Biotechnology Information (NCBI) at the National Institutes of Health (NIH). GTEx provides two major open-access datasets:
* Adult GTEx: RNA-seq, scRNA-seq, QTL, long-read RNA-seq, haplotype expression, and variant data
* Enhancing GTEx (eGTEx): DNA methylation, proteomics, and telomere measurements
The original GTEx study design profiled 54 non-diseased human tissue sites collected from nearly 1,000 donors. In the final release (GTEx v11), enhanced quality control, histopathology review, and expression-based assessment refined tissue annotations. Selected samples from v8 were re-annotated, and tissue definitions were expanded to finer anatomical subregions and cell-enriched preparations. As a result, GTEx v11 sample metadata contains 70 tissue annotations, reflecting updated and corrected tissue site assignments. For more information about tissue and other metadata files, refer to the following folder: /GTEx/dataset/gtex\_open\_access/adult\_gtex/annotations/v11/metadata\_files/
Recently, two additional datasets have been added to GTEx Open Access Data:
* Non-Human Primate Developmental GTEx (NHP-dGTEx): consists of tissues from 24 organs from 12 rhesus macaque and 12 common marmoset individuals at each of 6-8 developmental stages, including prenatal developmental stages. Please refer to [the project description](https://gtexportal.org/home/aboutNHPdGtex) to learn more about this data.
* Developmental Genotype-Tissue Expression: includes up to 75 tissues from 30 donors for each of the following age groups: postnatal (0-2 years), early childhood (2-8 years), pre-pubertal (\~8-12.5 years), post-pubertal (\~12.5-18 years). Please refer to [the project description](https://gtexportal.org/home/aboutdGTEx) to learn more about this data.
## Where to Access GTEx Open Access Data
The following files are available for the GTEx Open Access Data:
* Adult GTEx
* Enhancing GTEx
* Non-Human Primate Developmental GTEx
* Developmental Genotype-Tissue Expression
Three notebooks to showcase how to query and integrate datasets from GTEx can be found here on the platform. The file endings are .ipynb.
To use notebooks, please copy notebooks into your own project space. Details on how to copy the notebooks are provided in the section titled "Copying GTEx demo notebooks into a Project".
## Running analyses on DNAnexus
### Copying GTEx dataset and demo notebooks into a Project
To try our demo analysis, please copy the dataset and demo notebooks from this project into your own project. Here are the steps to copy the notebook into a Project Space:
1. Create a project for your GTEx and enrichment analysis, billed to your own organization. Tutorials on how to set up a project can be [found on this page](https://academy.dnanexus.com/overview-of-the-platform/setting-up-a-project).
2. Go to Resources Tab and find the project titled “Public Datasets AWS US (East)” and select the folder "GTEx".
3. Select "Copy" on the top right menu, and select the project that you created in Step 1.
4. Then, go to the project space you created in Step 1 to start exploring the GTEx dataset and notebooks.
5. To run the JupyterLab Notebooks, refer to the Academy Documentation's [JupyterLab section](https://academy.dnanexus.com/interactivecloudcomputing/jupyterlab/introduction), which covers both [regular](https://academy.dnanexus.com/interactivecloudcomputing/jupyterlab/running_notebook) and [Spark](https://academy.dnanexus.com/interactivecloudcomputing/jupyterlab/running-a-spark-jupyterlab-notebook) execution.
Note: The GTEx Open Access data is over 500 GB. We suggest either using the data directly from 'Public Datasets AWS US (East)' or copying only the interested datasets to your project.
### Example GTEx notebooks
We prepared three notebooks for demo analysis using GTEx data. Among them, two are optimized for the [JupyterLab with Spark Cluster](https://platform.dnanexus.com/panx/tool/app/app-J2PfkXj005PyVJQJ133B9k1v):
* GTEx\_v11\_Pancreas\_ProteinCoding\_GeneExpression\_Spark.ipynb – Configured for instance type mem1\_ssd1\_v2\_x16 with an Instance Count: 2.
* GTEx\_v11\_QTL\_Target\_Evaluation\_PCSK9\_Spark.ipynb – Configured for instance type mem1\_ssd1\_v2\_x16 with an Instance Count: 3.
* Please follow the command-line instructions provided within the notebook to download the necessary data before running it.
The third notebook, the GTEx official tutorial ("GTEx\_data\_tutorial.ipynb"), is optimized for the [JupyterLab with Python, R, Stata, ML, Image Processing](https://platform.dnanexus.com/panx/tool/app/app-J6B38V00ybbkyqqp8XppK2yF) (version 2.11) and uses the default instance. Please use the snapshot snapshot-target\_validation-jupyterlab.tar.gz when starting the job. The snapshot is available in the 'Notebook\_snapshot' folder in 'Public Datasets AWS US (East)'.
To use the snapshot, choose this snapshot in the Snapshot box when you start the JupyterLab.
