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I am searching for a multi-omics dataset which may include genomics, transcriptomics and proteomics (eg. snyderome). I need such a dataset for an introductory data-exploration purpose. So it can be from any host organism and any experimental methods/conditions.

Is there any database/repository where I can find it?

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  • $\begingroup$ Do you really need all 3 or will any 2 of those work? For "genomics", do you want histone marks (or methylation) or just DNAseq (e.g., for variant calling)? $\endgroup$ – Devon Ryan May 30 '17 at 12:36
  • $\begingroup$ genomics (DNAseq) would be essential. rest any layers (at least two) would work. $\endgroup$ – rraadd88 May 30 '17 at 12:47
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    $\begingroup$ Please edit your question and clarify what you need. Does everything need to be from the same cell or individual? Are you looking for the set of expressed proteins, transcribed RNA and the associated genome sequence? Or maybe those of a specific condition? What's parallel genomics? $\endgroup$ – terdon May 30 '17 at 16:06
  • $\begingroup$ I wanted to make an suggestion for rephrasing the question, but apparently I made the edit. If it does not say now what you wanted, feel free to change it back... $\endgroup$ – Kamil S Jaron May 30 '17 at 22:53
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There is a database called OmicsDI, where one can search for multi-omics datasets.

Here's a link of the associated publication (Perez-Riverol, Yasset, et al. "Omics Discovery Index-Discovering and Linking Public Omics Datasets." bioRxiv (2016): 049205.) for more details.

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There are several datasets available on GEO, though you do have to search for them. For example, here are three data sets that have both Illumina methylation and gene expression microarray profiling:

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Next to OmicsDI the EBI has a special repository for multi-omics datasets: https://www.ebi.ac.uk/biosamples

It links the different datasets between repositories, ie. PRIDE for MS/MS based data and ArrayExpress for RNASeq data.

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