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excludeAdditional Assistance


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.


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

Numbered figure captions
SubtitleTextEnter the Bioproject ID in the Import project dialog
AnchorNameGEO/ENA import

Image Added


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). 


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 (Figure 23).


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SubtitleTextGEO import populates the data tab
AnchorNameData tab after GEO ENA import

Project details are added to the Project settings tab (Figure 34). 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.


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SubtitleTextProject details from ENA
AnchorNameProject settings page GEO ENA import

The Analyses tab will include an Unaligned reads data node once the data download has started (Figure 45). 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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SubtitleTextFASTQ files will be added as an Unaligned reads data node in the Analyses tab
AnchorNameAnalyses tab after GEO ENA import

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



You can search ENA using the GEO ID (e.g., GSE71578) to check if there is a matching ENA project (Figure 56). 


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SubtitleTextSearching ENA using a GEO ID
AnchorNameSearching ENA for GEO project

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 67). 


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SubtitleTextENA Study page
AnchorNameENA Study page