Omics Data Submission

NCBI-SRA for raw sequencing data (fastq files)

1. Read instructions prior submission at https://submit.ncbi.nlm.nih.gov/about/sra/

2. Then go to the actual submision page at https://submit.ncbi.nlm.nih.gov/subs/sra/  

European Nucleotide Archive (ENA) - an alternative to SRA (fastq files)

1. General instructions at https://www.ebi.ac.uk/ena/browser/submit

-> Interactive submission: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/interactive.html

-> Command-line submission: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli.html

-> Programmatic submission: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/programmatic.html

NCBI-GEO for processed gene expression data (e.g. NGS, microarray, traditional SAGE, RT-PCR, Nanostring)

-> On its main page (https://www.ncbi.nlm.nih.gov/geo/info/submission.html) one can be directed to instructions and actual submission/upload links for each different sort of data

ProteomeXchange for raw and processed proteomics data

http://www.proteomexchange.org/submission/index.html

-> One can be directed to three different repositories (PRIDE, PASSEL, and MassIVE).

-> PRIDE is the most used repository for regular MS/MS data, which users can interactively deposit their data through a locally installed software PX Submission Tool