Digital Expression Explorer 2

Digital Expression Explorer 2 (DEE2) is a repository of uniformly processed RNA-seq data mined from public data obtained from NCBI Sequence Read Archive.

Did you know that DEE2 has an R package which enables convenient access of these data? Visit getDEE2 on Bioconductor to learn more.

Hosted RNA-seq data

Select an organism of interest

Search for data sets of interest

Search accession numbers Multiple accessions can be separated by commas. Try GSE63462,SRP070529,SRR401430 for A. thaliana.

Search for keywords Case-insensitive.
Try "ethanol" for S. cerevisiae.

More sophisticated keyword searches can be done at GEO and SRA, to identify studies and accession numbers of interest.

Keyword searches in mouse and human take up to a minute to complete.

Browse the metadata catalogue here.

Can't find your project of interest in our dataset? Try requesting a SRA project to be added to the express queue here (experimental).


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.

License and commercial use

DEE2 software and data 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.