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 
  
  

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

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

• Click Import project at the bottom 

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

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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

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. 

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:

GEO - https://www.ncbi.nlm.nih.gov/geo/

ENA - https://www.ebi.ac.uk/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). 

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). 

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