Data publication and dissemination for data associated with the first RNA-seq and Methylation-QTL data

Report from skype call on October 16.
Present: Lude Franke, Michiel van Galen, Bas Heijmans, Leon Mei, Matthijs Moed, Peter-Bram ’t Hoen (minutes)


We intend to make all data generated in BIOS available according to the highest standards required by journals, but making sure that privacy of the data is safeguarded. We will also make sample associated data available, but not the DNA-based genotypes nor the phenotypes

Detailed plan

We will only publish data associated with the first eQTL and meQTL papers. In practice this means Freeze 1 data for RNA-seq (2116 samples) and all qc-passed data for 450K arrays (xx samples). All data will be anonymized and new identifiers will be used for submission. We chose EGA as our repository because it is European, they provide good support and we have experience submitting data there from GoNL and other projects.
The EGA will contain all the privacy-sensitive raw data (fastq, CEL files) and processed data (bam files, gene counts, exon counts etc, normalized array data). These data will be available under controlled access. A data access committee consisting of the BIOS PI will judge the eligibility of the data requests.
Other data that will be submitted to EGA include:

All QC data per sample
Sample data, including cell counts, RIN values, biobank of origin, processing batches, flowcells etc. Please make complete lists.

The results (eQTL, meQTL, other) will be made completely public. eQTL and meQTL results will be provided as flat files but also browsable in a Genome browser like this one:

Who will be responsible?

EGA: Leon together with Pieter Neerinckx (including data access documents)
eQTL browser: Morris Swertz, Patrick Deelen

Time line

Get submission identifiers as soon as possible
Data submitted before April 1, 2015
Data released as soon as paper is accepted

Next steps

Inform other MT members, PIs about this plan.
Lude will check with Morris to pick a new date for the further dissemination and integration of data within BBMRI2.0.

Last modified 8 years ago Last modified on Oct 16, 2014 4:36:41 PM