The Collaborative OPen Omics (COPO) platform facilitated its first single-cell data submission in January 2026 after development and testing of the new workflow was completed in 2025.
The submission was part of the project, longread_singlecell_transcriptomics_approaches, which involved long-read single-cell RNA sequencing technologies using matched with cDNA generated with the 10x Genomics platform. It used a Minimum Information about any (x) Sequence (MIxS) single-cell submission type and included metadata covering person, study, dissociation, cell suspension, library preparation, sequencing, raw data processing and data files. The submission employed the European Nucleotide Archive (ENA) default sample checklist.
Highlights include:
- First successful use of single-cell submission workflow in COPO which demonstrates the platform's readiness for more single-cell metadata upload
- Validation of long-read single-cell RNA sequencing metadata handling ensures that complex experimental metadata can be captured accurately
- Integration with European Nucleotide Archive (ENA) workflows confirmed which includes the proper use of the various supported sample checklists types such as the default sample checklist
- Uploaded samples are automatically prefilled in the single-cell spreadsheet with minimal sample metadata. This reduces time to complete the single-cell manifest.
- Support for various types of single-cell submissions such as MIxS has been proven thereby, enabling standardised metadata capture
- Enhanced traceability of samples and associated data from project, to metadata and through processed data files
- Proof of concept for end-to-end submission automation which reduces manual data entry and potential errors
- Foundation for future single-cell submissions which makes it easier for other users to use COPO submit single-cell data
- Samples and single-cell metadata as well as the data files are publicly available (after the data is published) which allow others to cite them in publications or for reviewers to verify that reported results match the underlying metadata.
To view this Single-cell submission, please see the following links:
- ENA Project PRJEB106558
- ENA Project PRJEB106558 XML(XML will be downloaded)
See also the Single-cell website and Single-cell documentation for more information.