Re: [Geuvadis_rnaseq] RNAseq TC

Dear Thomas, Sorry, but I couldn´t make it yesterday on short notice. I would really llike to discuss the RNAseq project in a smaller round. Especially, the design question (1) is very important and we should seriously consider mixing samples from different populations. Best, Philip Prof. Dr. Philip Rosenstiel Institute of Clinical Molecular Biology University Kiel Schittenhelmstr.12 Building 5 24105 Kiel phone +49/4315971333 mobile +49/1773525080 Von: geuvadis_rnaseq-bounces(a)lists.crg.es [mailto:geuvadis_rnaseq-bounces@lists.crg.es] Im Auftrag von Thomas Giger Gesendet: Dienstag, 19. April 2011 10:43 An: geuvadis_rnaseq(a)lists.crg.es Betreff: [Geuvadis_rnaseq] RNAseq TC Dear All, As we decided yesterday, the people involved in the RNAseq related part of the experiment should have a conference call to discuss open questions. I have written down the following points that should be discussed: 1. As of now we made plans that the different labs analyze samples from one particular population (as listed in the workflow document that I've sent around on April 7). It would be a better experimental design if the samples were randomly distributed among the different labs. Since there is still time to react - do we want to switch the strategy? 2. How long are the library prep / sequencer queue up times in the different labs (once you receive the RNA samples - how long do you think will it take you to analyze them?). If some labs expect to have much larger delays, we could make arrangements that those labs get samples earlier than other labs. This would also mean that we would all use the protocol that is used at the time point when the first lab starts to analyze samples. 3. Which other samples (other than the 500 1KGP European samples) should be analyzed by RNAseq? 4. Specifications for the small RNA protocol. If you know already now, that you would like to have additional things discussed - please let me know and I can make sure that we don't forget about. We would like to schedule the call for either next Tuesday (April 26) or Wednesday (April 27). Please fill in the doodle by the end of this week so that we can select a time where a maximum number of people can attend the call: http://doodle.com/cnfc85cx9ushxzyb cheers, Thomas ------------------------------------------------------------------------ Thomas Giger, Ph.D. Department of Genetic Medicine and Development University of Geneva Medical School 1 Rue Michel-Servet Geneva 1211 Switzerland