6 May
2011
6 May
'11
4:36 p.m.
Dear Thomas, thank you very much for these minutes.
I would like to remind you all that our first official deliverable for WP4, D4.1 due on
November 2011 is the following: Database for RNAseq pilot project.
Also due in November 2011 are the following Milestones
MS10 Database established and functional for pilot project.
MS11 Selection of pilot samples completed.
Find below a description of the first task of the WP as in the Grant Agreement.
Kind regards,
Gabrielle
Task 4.1 RNA sequencing in 500 pilot samples
For the pilot RNA sequencing project, samples will be selected from the set of individuals
that have been selected for exon resequencing in WP5. RNAseq will be performed with
standard protocols as described by Mortazavi et al. (Nature Methods 2008). Each RNA sample
will be sequenced at a depth of at least 20 million reads with a paired end protocol.
Coordination of data processing, data sharing and data analysis will be modelled using
this dataset. We are in the process of piloting this approach by RNAseq of the same 5 RNA
samples from individuals of the CEU panel of the HapMap3 and 1000GP projects in 8
different sequencing centres across Europe. The data has been produced and we are in the
process of finalizing the plans for centralized deposit of the data and joint analysis. A
database for samples and clinical data sets will be implemented (WP3) to facilitate the
project and to monitor its progress (WP1). A web-based service will enable both project
partners and external collaborators to enter all information relevant for the project.
Completed entries will be required for samples participating in the pilot project. The
structure of the databases will be such that will facilitate the deposit of various types
of functional genomics datasets such as ChIPseq, GROseq, and methylation-seq.
Gabrielle Bertier
Project Manager
International Collaboration and Sponsorship Office
CRG, Center for Genomic Regulation
Carrer Dr. Aiguader, 88
08003 Barcelona, España
Tel: +34933160374
Mobile: +34639960656
email: gabrielle.bertier@crg.es<mailto:gabrielle.bertier@crg.es>
web: www.geuvadis.eu
-----Original Message-----
From: geuvadis_rnaseq-bounces(a)lists.crg.es [mailto:geuvadis_rnaseq-bounces@lists.crg.es]
On Behalf Of Thomas Giger
Sent: viernes, 06 de mayo de 2011 15:48
To: geuvadis_rnaseq(a)lists.crg.es
Subject: [Geuvadis_rnaseq] Minutes Geuvadis RNAseq TC on May 6
Dear All,
thanks a lot for participating in the TC today.
Please find attached to this message a word document containing the minutes of the
particular points that were discussed. This document contains very important information
on changes of the experimental design - please read it.
Please don't hesitate to ask me if I am unclear or if I missed something.
cheers,
Thomas