Answers.Body: <p>There are several <a href="https://www.ncbi.nlm.nih.gov/geo/browse/?view=series&amp;display=20&amp;zsort=samples" rel="nofollow noreferrer">datasets available on GEO</a>, 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:</p>
  
  <ul>
  <li><a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87650" rel="nofollow noreferrer">GSE87650</a></li>
  <li><a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72874" rel="nofollow noreferrer">GSE72874</a></li>
  <li><a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE56047" rel="nofollow noreferrer">GSE56047</a></li>
  </ul>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-06-03T23:06:42.720Z
Answers.LastActivityDate: 2017-06-03T23:06:42.720Z
Answers.UserDisplayName: user2368936
Answers.Body: <p>Next to OmicsDI the EBI has a special repository for multi-omics datasets: <a href="https://www.ebi.ac.uk/biosamples" rel="nofollow noreferrer">https://www.ebi.ac.uk/biosamples</a></p>
  
  <p>It links the different datasets between repositories, ie. PRIDE for MS/MS based data and ArrayExpress for RNASeq data.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-06-03T11:31:03.630Z
Answers.LastActivityDate: 2017-06-03T11:31:03.630Z
Answers.UserDisplayName: Johannes Griss
Answers.Body: <p>There is a database called <a href="http://www.omicsdi.org/search?q=omics_type:%22Multi-Omics%22" rel="nofollow noreferrer">OmicsDI</a>, where one can search for multi-omics datasets.</p>
  
  <p>Here's a <a href="https://doi.org/10.1101/049205" rel="nofollow noreferrer">link</a> of the associated publication (Perez-Riverol, Yasset, et al. "Omics Discovery Index-Discovering and Linking Public Omics Datasets." bioRxiv (2016): 049205.) for more details. </p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-05-30T12:53:39.583Z
Answers.LastActivityDate: 2017-06-02T08:05:19.020Z
Answers.LastEditDate: 2017-06-02T08:05:19.020Z
Answers.UserDisplayName: user345394
Body: <p>I am searching for a multi-omics dataset which may include genomics, transcriptomics and proteomics (eg. <a href="http://snyderome.stanford.edu/" rel="noreferrer">snyderome</a>).
  I need such a dataset for an introductory data-exploration purpose. So it can be from any host organism and any experimental methods/conditions.</p>
  
  <p>Is there any database/repository where I can find it?</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-05-30T12:36:42.140Z
Comments.Text: 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)?
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-05-30T12:47:37.780Z
Comments.Text: genomics (DNAseq) would be essential. rest any layers (at least two) would work.
Comments.UserDisplayName: user345394
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-05-30T16:06:06.253Z
Comments.Text: 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?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-05-30T22:53:24.997Z
Comments.Text: 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...
Comments.UserDisplayName: Kamil S Jaron
Tags: <multi-omics>
Title: Is there any publicly available multi-omics dataset?
ThreadText: # Is there any publicly available multi-omics dataset?
  
  (Asked by: username_0 on 2017-05-30)
  
  I am searching for a multi-omics dataset which may include genomics, transcriptomics and proteomics (eg. [snyderome](http://snyderome.stanford.edu/)).
  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?
  
  **Tags:** multi-omics
  
  > **Comments:**
  > **username_1**: 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)?  
  > **username_0**: genomics (DNAseq) would be essential. rest any layers (at least two) would work.  
  > **username_2**: 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?  
  > **username_3**: 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...  
  
  ---
  
  ## 3 answers
  
  ### Answer by username_0 on 2017-05-30. Score: 10 | Accepted answer
  
  There is a database called [OmicsDI](http://www.omicsdi.org/search?q=omics_type:%22Multi-Omics%22), where one can search for multi-omics datasets.
  
  Here's a [link](https://doi.org/10.1101/049205) of the associated publication (Perez-Riverol, Yasset, et al. "Omics Discovery Index-Discovering and Linking Public Omics Datasets." bioRxiv (2016): 049205.) for more details.
  
  
  ---
  
  ### Answer by username_4 on 2017-06-03. Score: 3
  
  There are several [datasets available on GEO](https://www.ncbi.nlm.nih.gov/geo/browse/?view=series&display=20&zsort=samples), 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:
  
  * [GSE87650](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87650)
  * [GSE72874](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72874)
  * [GSE56047](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE56047)
  
  
  ---
  
  ### Answer by username_5 on 2017-06-03. Score: 2
  
  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.
  
  
  ---
  
  