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

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• Click Next
• Choose GEO / ENA 
• Enter the BioProject ID of the data set you would like to download. The format of a BioProject ID is PRJNA followed by one to six numbers (e.g. PRJNA291540PRJNA381606)

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A GEO ID can also be used in the format GSE followed by one to five numbers (e.g. GSE71578). 

• Click Finish

Imported projects from GEO / ENA

The data tab will be populated with sample information. Sample names will be GSM IDs for each sample. Attributes and attribute levels are drawn from the GEO sample characteristics information. 

GEO import populates the data tab. 

Project details are added to the Project settings tab (Figure 4). The project name is the first 54 characters taken from the BioProject ID title. The project description is the BioProject description with the GEO ID and BioProject IDs appended.

The Analyses tab will include an Unaligned reads data node once the data download has started (Figure 5). 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. 

• FASTQ files will be added as an Unaligned reads data node in the Analyses tab

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Common Issues

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

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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.

FAQ

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:

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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

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• 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

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