What we provide
The aim of DEE2 is to make all RNA-seq data freely available to everyone, even if you don't have coding experience or a powerful computer.
We processed over 2 million RNA-seq samples from NCBI from a several organisms and we provide the processed data to you in the form of gene-level and transcript-level counts. These are useful for understanding gene expression patterns in disease and development. They can also be used for reproduction of original studies, comparison of two or more studies, large-scale data mining, gene network analysis and various machine-learning applications. Read our 2019 journal article to learn more.
Search data
If you're after data from only one or a few studies, this is the tool to try.
Use the data search tool →Data resources
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Hosted data
Statistics about the dataset.
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Bulk data access
Processed transcriptome data and metadata for your data mining pleasure.
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Data-on-demand request service
Can't find a dataset in DEE2? Never fear, we have set up a system to fulfil your requests.
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Browse the catalog of bundles
Each zip file represents an SRA Project.
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Legacy DEE2 search
The old search tool based on individual runs. This is only useful if you want a few samples out of a larger study. It is also much slower than the main search tool.
Documentation
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Citation
Ziemann M, Kaspi A, El-Osta A. Digital expression explorer 2: a repository of uniformly processed RNA sequencing data. Gigascience. 2019 Apr 1;8(4). pii: giz022. DOI:10.1093/gigascience/giz022.
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License and commercial use
DEE2 data is provided under the Creative Commons Attribution-ShareAlike 4.0 (CC BY-SA 4.0) licence. DEE2 software and docker images are provided under the GPLv3 public license which allows academic and commercial use. If your organisation uses DEE2 data for financial benefit, consider supporting DEE2 with a financial contribution which will help the long term viability, expand the dataset and enable new features.
