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Free public dataset tool

Download GEO FASTQ datasets online

Paste a GEO accession to find every linked sequencing run and public FASTQ source. Download the files to your computer, or sign up and analyze an eligible RNA-seq dataset in NotchBio for free.

NCBI GEONCBI SRAENADDBJ

GEO dataset search

Enter a GEO accession

No sign-up required

Also accepts SRR, SRP, PRJNA, ERR, DRR, ERP, PRJEB, and other public archive accessions.

Examples:

Download locally

Choose what you want to download

Both options use your selected runs. FASTQ data transfers directly from the public ENA mirror to your computer.

GEO to FASTQ

From an NCBI GEO record to the raw reads

GEO is the publication-facing record at NCBI. Raw high-throughput sequencing reads are normally attached through SRA run accessions such as SRR, then mirrored among the International Nucleotide Sequence Database Collaboration partners.

This downloader resolves that chain for you. It shows the GEO sample, run accession, library layout, expected file size, checksum, and the exact public ENA HTTPS path used for each FASTQ.

Read the command-line GEO and SRA tutorial
  1. 01
    Paste GSE or GSM

    Start with the accession from a paper or GEO record.

  2. 02
    Review linked runs

    Check sample titles, assay, layout, platform, sizes, and paths.

  3. 03
    Download or analyze

    Save files locally, or import an RNA-seq subset into a NotchBio project.

Common questions

Downloading GEO datasets

How do I download FASTQ files from GEO?

Enter the GSE or GSM accession above. The tool resolves the linked sequencing runs and lists direct public FASTQ paths when ENA has mirrored them.

Can I download every run in a GSE?

Yes. There is no NotchBio file-count limit for local downloads. For larger studies, use the resumable download-manager bundle.

Why does a valid GEO accession have no FASTQ?

The record may contain microarray or processed data, may not link to raw sequencing runs, may be controlled-access, or may still be synchronizing across archives.

Are GEO downloads free?

Public FASTQ downloads are free and go directly from ENA to your computer. Importing samples into NotchBio follows your account’s sample-import allowance.

What do NCBI, ENA, and DDBJ have to do with GEO?

GEO is hosted by NCBI. Its linked raw runs participate in the INSDC archive network, whose partners include NCBI SRA, ENA, and DDBJ.

Can NotchBio analyze the dataset?

NotchBio can import compatible bulk RNA-seq FASTQs. The Free tier supports 16 imported samples and one complete analysis run.