- NGI (National Genomics Infrastructure) offers an infrastructure equipped with a comprehensive range of technology platforms for next generation sequencing (NGS) and genotyping.
- Eukaryotic Single-Cell Genomics (ESCG) offers streamlined single cell RNA sequencing, as well as whole genome DNA amplification
- Microbial Single Cell Genomics
In the era of FAIR (Findable, Accessible, Interoperable and Reusable) and Open science, datasets should be made available to the public.
- European Nucleotide Archive (ENA) for raw read data
- ArrayExpress for experiment descriptions and processed expression data
Samples are linked between databases to make sure each part of the dataset is findable. Submitted data can be kept private until the associated research article is published (embargo).
The ENA hosts an instance of the Sequence Read Archive (SRA), the same archive that exists on NCBI. SRA accepts raw sequence data from any sequencing platform, generated in any research project.
There are several ways to submit data to ENA, including extensive documentation on programmatic submissions.
ArrayExpress is tighty integrated with ENA and similar to NCBI's Gene Expression Omnibus database it can be used to archive experimental designs and analysis files based on the raw sequence reads.
ArrayExpress has its own submission portal where information is available on what can be submitted and how.
NBIS is building a local federated version of the European Genome-phenome Archive (EGA) in Sweden (EGA-SE), allowing for the publication of sensitive personal data within a legal framework. Until local EGA is available, the dataset should remain in the secure analysis environment (eg at Bianca on Uppmax). We suggest to make a metadata-only record in the SciLifeLab Data Repository with contact details on how to get access, and for which a DOI (ie a persistent identifier) can be issued. The DOI can then be used in the article to refer to the dataset. Once the Swedish EGA is operational, and the dataset deposited there, the access information can be changed to point at the EGA ID. See https://doi.org/10.17044/scilifelab.12292778, for an example.