Question: Suitable Public Repository For Disparate Data Types?
2
gravatar for Bio_X2Y
8.3 years ago by
Bio_X2Y3.7k
Ireland
Bio_X2Y3.7k wrote:

We're currently analyzing a number of clinical samples using a range of platforms, e.g.

  • Genomics (e.g. DNA sequencing, SNP analysis)
  • Transcriptomics (e.g. RNA-Seq, microarrays)
  • Proteomics (e.g. IHC)

Ultimately, we plan to disseminate our work into the public domain. This will include raw data, and various integrative analyses.

Is there any public repository that would be suitable for storing ALL these kinds of data? (as opposed to spreading the files over a number of specialized databases like NCBI GEO and dbSNP)

We're effectively looking for a simple file store, ideally one that has been adopted by other research groups, and which is likely to remain available on a long-term basis.

Any thoughts or suggestions? Thanks

data open • 1.6k views
ADD COMMENTlink modified 5.9 years ago by alaincoletta110 • written 8.3 years ago by Bio_X2Y3.7k
6
gravatar for Pierre Lindenbaum
8.3 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum120k wrote:

Is there any kind of public data repository that would be suitable for holding ALL these kinds of data?

Dryad http://datadryad.org ?

Dryad is an international repository of data underlying peer-reviewed articles in the basic and applied biosciences. Dryad enables scientists to validate published findings, explore new analysis methodologies, repurpose data for research questions unanticipated by the original authors, and perform synthetic studies. Dryad is governed by a consortium of journals that collaboratively promote data archiving and ensure the sustainability of the repository.

another suggestion, why not https://github.com ? (e.g. see msporny who posted his personal DNA: https://github.com/msporny/dna )

ADD COMMENTlink written 8.3 years ago by Pierre Lindenbaum120k
1

+1 for Dyrad. It's on my list to submit work from our lab there.

ADD REPLYlink written 8.3 years ago by Casey Bergman18k

Accepted for Dryad, looks interesting.

ADD REPLYlink written 8.3 years ago by Bio_X2Y3.7k
3
gravatar for Casey Bergman
8.3 years ago by
Casey Bergman18k
Athens, GA, USA
Casey Bergman18k wrote:

Pierre's suggestion to use Dryad is probably wiser since it has better meta-data archiving, but you could also try BioTorrents if you plan to release all of your raw sequencing data.

ADD COMMENTlink written 8.3 years ago by Casey Bergman18k

I wasn't aware of BioTorrents, thanks for pointing it out.

ADD REPLYlink written 8.3 years ago by Bio_X2Y3.7k
0
gravatar for alaincoletta
5.9 years ago by
alaincoletta110
Belgium
alaincoletta110 wrote:

Check InSilico DB (https://insilicodb.org): 100,000s of manually curated profiles pre-processed and ready to analyse freely available. RNA-Seq data is pre-processed with tophat-cufflinks-cuffdiff-cummeRbund. and ready to analyse. See https://insilicodb.org/differential-gene-expression-heatmap-from-rnaseq-data-using-cummerbund/ for a step-by-step example.

Highly accessed Genome Biology paper: http://genomebiology.com/2012/13/11/R104

ADD COMMENTlink written 5.9 years ago by alaincoletta110
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