Which accession numbers should be cited in publication?

Please cite accession numbers according to journal instructions.
It is recommended to cite accession numbers assigned to your data submissions, e.g. the DDBJ nucleotide sequence or DRA Run accession numbers.
Please cite a BioProject accession to reference all data from the project. It is necessary that metadata are described to enable users understand relationship between data in the publication and in the databases.

DDBJ

Cite accession number(s) assigned to nucleotide sequence(s).
Prefix Letter List

DRA

Cite Run accession number(s) (prefix DRR) assigned to sequencing reads. Metadata
Please cite a BioProject accession to reference all data from the project. It is necessary that metadata are described to enable users understand relationship between data in the publication and in the databases.
Because data cannot be added to existing DRA submission, more than one DRA submission accessions will be created after data addition (Update). Therefore, citing DRA submission accessions (prefix DRA) is not recommended. Instead, we recommend to cite a BioProject accession.

GEA

Cite Experiment accession “E-GEAD-n”.
GEA Accession

MetaboBank

Cite Study accession “MTBKSn”.
MetaboBank Accession

BioProject

If an individual BioProject needs to be referenced, state that “The data have been deposited with links to BioProject accession number PRJDBxxxxxx in the DDBJ BioProject database.” along with the accession numbers assigned to the data submissions.

BioSample

If an individual BioSample needs to be referenced, state that “BioSample metadata are available in the DDBJ BioSample database under accession number SAMDxxxxxxxx”.