Changes between Initial Version and Version 1 of data_dissemination


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Timestamp:
Oct 16, 2014 4:36:41 PM (10 years ago)
Author:
pacthoen
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  • data_dissemination

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     1= Data publication and dissemination for data associated with the first RNA-seq and Methylation-QTL data =
     2
     3Report from skype call on October 16.[[BR]]
     4Present: Lude Franke, Michiel van Galen, Bas Heijmans, Leon Mei, Matthijs Moed, Peter-Bram ’t Hoen (minutes)
     5
     6== Summary ==
     7We 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
     8
     9== Detailed plan ==
     10We 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.
     11We 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.[[BR]]
     12The 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.[[BR]]
     13Other data that will be submitted to EGA include:
     14 All QC data per sample[[BR]]
     15 Sample data, including cell counts, RIN values, biobank of origin, processing batches, flowcells etc. Please make complete lists.[[BR]]
     16The 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: http://molgenis.nl/ase
     17
     18== Who will be responsible? ==
     19EGA: Leon together with Pieter Neerinckx (including data access documents)[[BR]]
     20eQTL browser: Morris Swertz, Patrick Deelen
     21
     22== Time line ==
     23 Get submission identifiers as soon as possible[[BR]]
     24 Data submitted before April 1, 2015[[BR]]
     25 Data released as soon as paper is accepted[[BR]]
     26
     27== Next steps ==
     28Inform other MT members, PIs about this plan.[[BR]]
     29Lude will check with Morris to pick a new date for the further dissemination and integration of data within BBMRI2.0.