Good repository for uploading SNP data (from genotyping array) alongside manuscript?

Question

[devenvyas]

I am closing in on finishing a manuscript on some SNP analyses from an Affymetrix genotyping array data. Most reputable journals (including the main one I am targeting) will demand that I make my SNP data publicly accessible prior to publication.

My first manuscript was on mitochondrial genome sequences, so making that data available was obvious (Genbank). However, where I should upload is not clear to me. The binary Plink (bed, bim, fam) files total to less than 30 MB, so I am not quite sure where they should go.

Any suggestions?

[Ahill]

Have you looked at GEO? They apparently support SNP array submissions (e.g. the Affy SNP 6.0 array). Recommendations for human subject data here. Not sure they would accept PLINK binary filesets as-is, but their standard formats would not be too difficult to generate starting from PLINK.

Answer 1

[Medhat]

How to Submit to dbSNP
dbSNP accepts variations from any organism except bacteria

[devenvyas]

I am looking for a good way to just upload a Plink dataset in one place, so I am not sure that dbSNP would be a good place.

Answer 2

[Ahill]

Is this subject-level human SNP data (consented, de-identified?). Are you also reporting phenotypes? EGA (https://www.ebi.ac.uk/ega/submission/array_based) and dbGaP (http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/about.html) accept data from array-based genotyping platforms.

Answer 3

[devenvyas]

This is de-identified, consented human SNP data. Whole mitochondrial genomes for many of them are already on GenBank. It is purely population genetics stuff. There are no phenotype data, just genotype data.

I was looking at the Data Dryad, but unless the article is in one of the sponsoring journals, they charge for storage.