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        • Importing a GEO / ENA project
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        • Importing the tutorial data set
        • Adding sample attributes
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        • Viewing DESeq2 results and creating a gene list
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      • Analyzing Single Cell RNA-Seq Data
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        • Importing Feature Barcoding Data
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      • 10x Genomics Visium Spatial Data Analysis
        • Start with pre-processed Space Ranger output files
        • Start with 10x Genomics Visium fastq files
        • Spatial data analysis steps
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        • Import 10x Genomics Xenium Analyzer output
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      • Single Cell RNA-Seq Analysis (Multiple Samples)
        • Getting started with the tutorial data set
        • Classify cells from multiple samples using t-SNE
        • Compare expression between cell types with multiple samples
      • Analyzing Single Cell ATAC-Seq data
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      • Detecting differential gene expression in single cell RNA-Seq analysis
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      • Studying Immunotherapy with Multiomics: Simultaneous Measurement of Gene and Protein
      • How to Integrate ChIP-Seq and RNA-Seq Data
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      • To Boldly Go…
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  • Partek Genomics Suite
    • Installation Guide
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      • Lists
        • Importing a text file list
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        • Starting with a list of genomic regions
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      • Visualizing NGS Data
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      • LOH detection with an allele ratio spreadsheet
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        • Import gene expression data
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    • Tutorials
      • Gene Expression Analysis
        • Importing Affymetrix CEL files
        • Adding sample information
        • Exploring gene expression data
        • Identifying differentially expressed genes using ANOVA
        • Creating gene lists from ANOVA results
        • Performing hierarchical clustering
        • Adding gene annotations
      • Gene Expression Analysis with Batch Effects
        • Importing the data set
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        • Exploring the data set with PCA
        • Detect differentially expressed genes with ANOVA
        • Removing batch effects
        • Creating a gene list using the Venn Diagram
        • Hierarchical clustering using a gene list
        • GO enrichment using a gene list
      • Differential Methylation Analysis
        • Import and normalize methylation data
        • Annotate samples
        • Perform data quality analysis and quality control
        • Detect differentially methylated loci
        • Create a marker list
        • Filter loci with the interactive filter
        • Obtain methylation signatures
        • Visualize methylation at each locus
        • Perform gene set and pathway analysis
        • Detect differentially methylated CpG islands
        • Optional: Add UCSC CpG island annotations
        • Optional: Use MethylationEPIC for CNV analysis
        • Optional: Import a Partek Project from Genome Studio
      • Partek Pathway
        • Performing pathway enrichment
        • Analyzing pathway enrichment in Partek Genomics Suite
        • Analyzing pathway enrichment in Partek Pathway
      • Gene Ontology Enrichment
        • Open a zipped project
        • Perform GO enrichment analysis
      • RNA-Seq Analysis
        • Importing aligned reads
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        • Detecting differential expression in RNA-Seq data
        • Creating a gene list with advanced options
        • Visualizing mapped reads with Chromosome View
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        • Gene Ontology (GO) Enrichment
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      • ChIP-Seq Analysis
        • Importing ChIP-Seq data
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        • Creating a list of enriched regions
        • Identifying novel and known motifs
        • Finding nearest genomic features
        • Visualizing reads and enriched regions
      • Survival Analysis
        • Kaplan-Meier Survival Analysis
        • Cox Regression Analysis
      • Model Selection Tool
      • Copy Number Analysis
        • Importing Copy Number Data
        • Exploring the data with PCA
        • Creating Copy Number from Allele Intensities
        • Detecting regions with copy number variation
        • Creating a list of regions
        • Finding genes with copy number variation
        • Optional: Additional options for annotating regions
        • Optional: GC wave correction for Affymetrix CEL files
        • Optional: Integrating copy number with LOH and AsCN
      • Loss of Heterozygosity
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        • Analyze differentially expressed miRNAs
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      • Promoter Tiling Array
      • Human Exon Array
        • Importing Human Exon Array
        • Gene-level Analysis of Exon Array
        • Alt-Splicing Analysis of Exon Array
      • NCBI GEO Importer
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      • Allele Intensity Import
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      • Unpaired Copy Number Estimation
    • Release Notes
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    • TeamViewer Instructions
  • Getting Help
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On this page
  • How to import a study from GEO / ENA
  • Common Issues
  • Error Message - The project did not yield any data. Double-check the project ID, or try importing the data manually
  • The project was imported, but the Analyses tab is empty and there are no FASTQ files
  • Something is missing or the import failed
  • FAQ
  • What are GEO and ENA?
  • How do I know if a GEO project is also in ENA?
  • Additional Assistance

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  1. Partek Flow
  2. User Manual
  3. Importing Data

Import a GEO / ENA project

PreviousImporting 10x Genomics .bcl FilesNextTask Menu

Last updated 7 months ago

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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 and sample attributes automatically into Partek Flow.

  • On the Homepage click New Project to create a project and give the project a name

  • Click Add data

  • Select fastq as the file type after choosing between Single cell or Bulk as the assay types

  • 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. PRJNA381606)

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

  • Click Finish

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

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:

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.

  • 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

Additional Assistance

GEO -

ENA -

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

https://www.ncbi.nlm.nih.gov/geo/
https://www.ebi.ac.uk/ena
our support page
How to import a study from GEO / ENA
Common Issues
Error Message - The project did not yield any data. Double-check the project ID, or try importing the data manually
The project was imported, but the Analyses tab is empty and there are no FASTQ files
Something is missing or the import failed
FAQ
What are GEO and ENA?
How do I know if a GEO project is also in ENA?