----------------- Dear Thomas, Stefan Schreiber and Philip Rosenstiel will be attending the DDW in Chicago, May 6 - 10. They asked me to announce that they will not be able to attend the teleconference therefore. With best regards, Christiane Dr. Christiane Wolf-Schwerin Personal Assistant to Prof. Schreiber University Hospital Schleswig-Holstein Institute for Clinical Molecular Biology Schittenhelmstr. 12 24105 Kiel, Germany phone: +49 (0)431/597-2350 fax: +49 (0)431/597-1434 From: geuvadis_rnaseq-bounces(a)lists.crg.es [mailto:geuvadis_rnaseq-bounces@lists.crg.es] On Behalf Of Ralf Sudbrak Sent: jueves, 28 de abril de 2011 17:14 To: geuvadis_rnaseq(a)lists.crg.es Subject: Re: [Geuvadis_rnaseq] Geuvadis RNAseq TC details Dear Thomas, as my vote in the doodle poll indicated, I am not available at the 6th of May, but I trust the consortium that the scientifically best approach will be chosen. Until the 13.5. I am traveling and might have only limited email access. Best wishes Ralf On 26.04.2011 11:27, Thomas Giger wrote: Dear All, thank you for having filled in the doodle. The Geuvadis RNAseq phone conference will take place on May 6 from 11am - 12pm CEST. To participate in this call you have to do the following: - if you call in from Switzerland dial: +41 58 262 07 22 - otherwise from other countries please find enclosed the list with the "local access numbers for teleconferences" and dial the number corresponding to your country. Then enter the PIN: 611683 In case you need assistance during the call - dial "OO" (nil nil) to get in touch with an operator. 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 already know 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. Looking forward to talk to you soon, Thomas = ------------------------------------------------------------------------ Thomas Giger, Ph.D. Department of Genetic Medicine and Development University of Geneva Medical School 1 Rue Michel-Servet Geneva 1211 Switzerland _______________________________________________ Geuvadis_rnaseq mailing list Geuvadis_rnaseq@lists.crg.es<mailto:Geuvadis_rnaseq@lists.crg.es> http://davinci.crg.es/mailman/listinfo/geuvadis_rnaseq -- Dr. Ralf Sudbrak EU Coordinator MPG Cluster Berlin-Brandenburg c/o Max Planck Institute for Molecular Genetics Ihnestr. 63 - 73 D-14195 Berlin Germany Fon: +49 (30) 8413 1612 Fax: +49 (30) 8413 1380 sudbrak@molgen.mpg.de<mailto:sudbrak@molgen.mpg.de>

Hi Thomas et al. I'll join. Petr is on holidays but has sent his comments on the topic list which I cc below. Bw GJ 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? I would say the random design is preferred. 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. 3-4 months 3. Which other samples (other than the 500 1KGP European samples) should be analyzed by RNAseq? Disease related samples for which we are also analyzing exomes, e.g. intestinal expression profiles for IBD 4. Specifications for the small RNA protocol. We suggest 36 cycles single end sequencing aiming for at least 3 million reads per sample. Prof dr GertJan B. van Ommen Head, Department of Human Genetics Center for Human and Clinical Genetics Leiden University Medical Center Director, Center For Medical Systems Biology Visiting address: Building 2, Zone S-4-P, Room S04-046 Einthovenweg 20 P.O.Box 9600, 2300 RC Leiden NL Tel +31-71-526 9401 / 9400 Fax +31-71-526 8285 Email gjvo@lumc.nl<mailto:gjvo@lumc.nl> Website: <http://www.humgen.nl>; <http://www.cmsb.nl> =========== NB: This communication is intended for use by the addressee. It may contain confidential or privileged information. Therefore no right or title whatsoever shall be deemed to have given regarding the content of the communication or its enclosures. If you receive this communication unintentionally, please immediately notify the sender and delete the original, copies and enclosures. From: geuvadis_rnaseq-bounces(a)lists.crg.es [mailto:geuvadis_rnaseq-bounces@lists.crg.es] On Behalf Of Thomas Giger Sent: vrijdag 6 mei 2011 10:38 To: geuvadis_rnaseq(a)lists.crg.es Subject: [Geuvadis_rnaseq] Geuvadis RNAseq TC 11am - local Access numbers Dear All, please find attached to this message the local Access numbers for joining the TC at 11am. cheers, Thomas Begin forwarded message: From: Thomas Giger <Thomas.Giger@unige.ch<mailto:Thomas.Giger@unige.ch>> Date: April 26, 2011 11:27:49 AM GMT+02:00 To: geuvadis_rnaseq@lists.crg.es<mailto:geuvadis_rnaseq@lists.crg.es>, Manolis Dermitzakis <Emmanouil.Dermitzakis@unige.ch<mailto:Emmanouil.Dermitzakis@unige.ch>> Subject: [Geuvadis_rnaseq] Geuvadis RNAseq TC details Dear All, thank you for having filled in the doodle. The Geuvadis RNAseq phone conference will take place on May 6 from 11am - 12pm CEST. To participate in this call you have to do the following: - if you call in from Switzerland dial: +41 58 262 07 22 - otherwise from other countries please find enclosed the list with the "local access numbers for teleconferences" and dial the number corresponding to your country. Then enter the PIN: 611683 In case you need assistance during the call - dial "OO" (nil nil) to get in touch with an operator. 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 already know 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. Looking forward to talk to you soon, Thomas