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How to import a study from GEO / ENA

If a project is publicly available in the Gene Expression Omnibus (GEO) and European Nucleotide Archive (ENA) databases, you can import associated FASTQ files, sample attributes, and project details automatically into Partek Flow.

  • Click Projects at the top of the page
  • Click Import project 

Figure 1. Importing project invoke

  • Choose GEO / ENA project for Select files from 
  • Type the BioProject ID or the GEO Accession number

Figure 2. Enter the Bioproject ID in the Import project dialog

The format of a BioProject ID is PRJNA followed by one to six numbers (e.g., PRJNA291540). The format of a GEO Accession number is GSE followed by one to five numbers  (e.g., GSE71578). 

  • Click Import project at the bottom 

The Analyses tab will include an Unaligned reads data node once the data download has started (Figure 3). It may take a while for the download to complete depending on the size of the data. FASTQ files are downloaded from the ENA BioProject page. 

Figure 3. FASTQ files will be added as an Unaligned reads data node in the Analyses tab

Common Issues

Error Message - The project did not yield any data. Double-check the project ID, or try importing the data manually

If the study is not publicly available in both GEO and ENA, project import will not succeed.

The project was imported, but the Analyses tab is empty and there are no FASTQ files

If there is an ENA project, but the FASTQ files are not available through ENA, the project will be created, but data will not be imported. 

Something is missing or the import failed

A variety of other issues and irregularities can cause imports to not succeed or partially succeed, including, but not limited to, a BioProject having multiple associated GSE IDs, incomplete information on the GEO or ENA page, and either the GEO or ENA project not being publicly available. 


What are GEO and ENA? 

The Gene Expression Omnibus (GEO) and the European Nucleotide Archive (ENA) are web-accessible public repositories for genomic data and experiments. Access and learn more about their resources at their respective websites:


ENA - 

How do I know if a GEO project is also in ENA?

You can search ENA using the GEO ID (e.g., GSE71578) to check if there is a matching ENA project (Figure 6). 

Figure 4. Searching ENA using a GEO ID
Open the Study result to view the BioProject ID (e.g., PRJNA381606) and a table with information about the samples and files included in the project (Figure 7). 

Figure 5. ENA Study page

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

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