geuvadis_rna_analysis

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[Geuvadis_rna_analysis] Geuvadis RNAseq paper accepted in Nature

by Tuuli Lappalainen

Dear all, It is my great pleasure to tell you that the Geuvadis RNAseq paper has been accepted in Nature! Needless to say, I'm extremely happy to finally be at this point, and to be able to thank all of you for your contributions. We wouldn't be here without the hard work from all of you, the huge pool of scientific expertise and insight, and the collaborative spirit that we've had in this project. Please pass my thanks also to technicians and other members of your lab who contributed to this work. It was a really enjoyable experience to work with all of you, and I hope that this will inspire many other collaborations amongst us. I had a lot of fun and I hope you did too! But the most important thing is that I think we can all be proud of the outcome. It's a great paper and a great data set that make an important contribution to the field. We're now going through some final formatting edits, and we'll be in touch about press releases, publication and embargo dates, etc. when we know more. Feel free to share the news with close colleagues, but please don't advertise this yet in the public domain such as social media. The companions papers are in a good shape too: we're waiting for the final confirmation of the acceptance of the QC paper in Nature Biotechnology so more good news will follow, and the splicing paper is under review in Genome Research. best regards, Tuuli PS. Please note that my University of Geneva email address will not work for much longer (in case you didn't know, I'm spending this year at Stanford). Please use tuuli.e.lappalainen(a)gmail.com for future correspondence. -- Tuuli Lappalainen, PhD Department of Genetics, Stanford University School of Medicine Email: tuuli.e.lappalainen(a)gmail.com Tel: +1 415 351 9713 Bustamante lab Department of Genetics 300 Pasteur Dr. Lane L301 Stanford, CA 94305-5120 USA

11 years, 1 month

[Geuvadis_rna_analysis] REMINDER: GEUVADIS final meeting - Registration deadline extended to 06/09/13

by Gabrielle Anne Bertier

Dear all, this is a gentle reminder about the GEUVADIS final meeting. You can still register until this Friday September 6th 2013 Please don’t hesitate to contact me for any question/comment, Kind regards, Gabrielle From: geuvadis_admin-bounces(a)lists.crg.es<mailto:geuvadis_admin-bounces@lists.crg.es> [mailto:geuvadis_admin-bounces@lists.crg.es] On Behalf Of Gabrielle Anne Bertier Sent: Friday, July 19, 2013 15:17 Subject: Update, GEUVADIS final meeting Dear all, Here are a couple of updates on our final meeting: Agenda: we’ve updated the agenda to give more time for young scientists to present their work in the afternoon. Please encourage your lab members to submit abstracts ! Hotel: we're pre-reserved some rooms at a reduced price the Crowne Plaza right next to the World Forum. Crowne Plaza Den Haag - Promenade. Van Stolkweg 1, 2585 JL Den Haag - http://www.crowneplaza.com/denhaag To book your room please contact: l.odekerken(a)crowneplazadenhaag.nl<mailto:l.odekerken@crowneplazadenhaag.nl> Reference: GEUVADIS Annual Meeting individual room:156.8€ + city taxes double room: 182€ + city taxes Reminder: Date: Wednesday November 20th 2013, 9:00-18:00 Place: World forum, the Hague Registration deadline: Friday September 6th 2013 https://docs.google.com/forms/d/14wkUZXjY0v0bfn1Y8xngBTfhieHziif0dB2wHlB4nq… Please don’t hesitate to contact me for any question/comment, Kind regards, Gabrielle Gabrielle Bertier Scientific Project Manager International and Scientific Affairs CRG, Center for Genomic Regulation Carrer Dr. Aiguader, 88 08003 Barcelona, España Phone: +34933160182 email: gabrielle.bertier(a)crg.es<mailto:gabrielle.bertier@crg.es> web: www.geuvadis.eu

11 years, 1 month

[Geuvadis_rna_analysis] GEUVADIS final meeting - Registration deadline extended to 06/09/13

by Gabrielle Anne Bertier

Dear all, please note that the deadline for registration and abstract submission for the GEUVADIS final meeting has been extended to Friday September 6th 2013 Please don’t hesitate to contact me for any question/comment, Kind regards, Gabrielle From: geuvadis_admin-bounces(a)lists.crg.es [mailto:geuvadis_admin-bounces@lists.crg.es] On Behalf Of Gabrielle Anne Bertier Sent: Friday, July 19, 2013 15:17 Subject: Update, GEUVADIS final meeting Dear all, Here are a couple of updates on our final meeting: Agenda: we’ve updated the agenda to give more time for young scientists to present their work in the afternoon. Please encourage your lab members to submit abstracts ! Hotel: we're pre-reserved some rooms at a reduced price the Crowne Plaza right next to the World Forum. Crowne Plaza Den Haag - Promenade. Van Stolkweg 1, 2585 JL Den Haag - http://www.crowneplaza.com/denhaag To book your room please contact: l.odekerken(a)crowneplazadenhaag.nl<mailto:l.odekerken@crowneplazadenhaag.nl> Reference: GEUVADIS Annual Meeting individual room:156.8€ + city taxes double room: 182€ + city taxes Reminder: Date: Wednesday November 20th 2013, 9:00-18:00 Place: World forum, the Hague Registration deadline: 15 August 2013 https://docs.google.com/forms/d/14wkUZXjY0v0bfn1Y8xngBTfhieHziif0dB2wHlB4nq… Please don’t hesitate to contact me for any question/comment, Kind regards, Gabrielle Gabrielle Bertier Scientific Project Manager International and Scientific Affairs CRG, Center for Genomic Regulation Carrer Dr. Aiguader, 88 08003 Barcelona, España Phone: +34933160182 email: gabrielle.bertier(a)crg.es<mailto:gabrielle.bertier@crg.es> web: www.geuvadis.eu

11 years, 1 month

[Geuvadis_rna_analysis] Update, GEUVADIS final meeting

by Gabrielle Anne Bertier

Dear all, Here are a couple of updates on our final meeting: Agenda: we’ve updated the agenda to give more time for young scientists to present their work in the afternoon. Please encourage your lab members to submit abstracts ! Hotel: we're pre-reserved some rooms at a reduced price the Crowne Plaza right next to the World Forum. Crowne Plaza Den Haag - Promenade. Van Stolkweg 1, 2585 JL Den Haag - http://www.crowneplaza.com/denhaag To book your room please contact: l.odekerken(a)crowneplazadenhaag.nl<mailto:l.odekerken@crowneplazadenhaag.nl> Reference: GEUVADIS Annual Meeting individual room:156.8€ + city taxes double room: 182€ + city taxes Reminder: Date: Wednesday November 20th 2013, 9:00-18:00 Place: World forum, the Hague Registration deadline: 15 August 2013 https://docs.google.com/forms/d/14wkUZXjY0v0bfn1Y8xngBTfhieHziif0dB2wHlB4nq… Please don’t hesitate to contact me for any question/comment, Kind regards, Gabrielle Gabrielle Bertier Scientific Project Manager International and Scientific Affairs CRG, Center for Genomic Regulation Carrer Dr. Aiguader, 88 08003 Barcelona, España Phone: +34933160182 email: gabrielle.bertier(a)crg.es<mailto:gabrielle.bertier@crg.es> web: www.geuvadis.eu; www.fliact.eu From: geuvadis_admin-bounces(a)lists.crg.es [mailto:geuvadis_admin-bounces@lists.crg.es] On Behalf Of Gabrielle Anne Bertier Sent: Wednesday, July 03, 2013 15:53 To: geuvadis_partners(a)lists.crg.es; geuvadis_wpl(a)lists.crg.es; geuvadis_rnaseq(a)lists.crg.es; geuvadis_rna_analysis(a)lists.crg.es; geuvadis_exome(a)lists.crg.es Cc: Magali Bartomeus Cistare; Michela Bertero; Magali(a)lists.crg.es; geuvadis_admin(a)lists.crg.es Subject: [Geuvadis_admin] Registration form, GEUVADIS final meeting Importance: High Dear all, Please find below the link to register for the final GEUVADIS meeting. I included a tentative agenda, on which you are welcome to comment. Date: Wednesday November 20th 2013, 9:00-18:00 Place: World forum, the Hague Registration deadline: 15 August 2013 https://docs.google.com/forms/d/14wkUZXjY0v0bfn1Y8xngBTfhieHziif0dB2wHlB4nq… Please indicate the title of existing GEUVADIS posters which we would like to present at the meeting. You also have the possibility to submit an abstract to be selected for a poster presentation or for an oral communication on GEUVADIS Highlights. Remember that our final meeting will take place as a satellite event of the Hands On Biobanks meeting organised in the same place in the 2 following days November 21-22: Hands-on-biobanks meeting http://www.handsonbiobanks.org/2013/ Peter Hoen is organising a GEUVADIS 'Idea-Lab' on Best practices for multi-omics biomarker discoveries. Idea lab will take place on the 21st and the 22nd November. HOB Registration form: http://www.handsonbiobanks.org/2013/registration/ Please don’t hesitate to contact me for any question/comment, Kind regards, Gabrielle Gabrielle Bertier Scientific Project Manager International and Scientific Affairs CRG, Center for Genomic Regulation Carrer Dr. Aiguader, 88 08003 Barcelona, España Phone: +34933160182 email: gabrielle.bertier(a)crg.es<mailto:gabrielle.bertier@crg.es> web: www.geuvadis.eu; www.fliact.eu

11 years, 3 months

[Geuvadis_rna_analysis] Registration form, GEUVADIS final meeting

by Gabrielle Anne Bertier

Dear all, Please find below the link to register for the final GEUVADIS meeting. I included a tentative agenda, on which you are welcome to comment. Date: Wednesday November 20th 2013, 9:00-18:00 Place: World forum, the Hague Registration deadline: 15 August 2013 https://docs.google.com/forms/d/14wkUZXjY0v0bfn1Y8xngBTfhieHziif0dB2wHlB4nq… Please indicate the title of existing GEUVADIS posters which we would like to present at the meeting. You also have the possibility to submit an abstract to be selected for a poster presentation or for an oral communication on GEUVADIS Highlights. Remember that our final meeting will take place as a satellite event of the Hands On Biobanks meeting organised in the same place in the 2 following days November 21-22: Hands-on-biobanks meeting http://www.handsonbiobanks.org/2013/ Peter Hoen is organising a GEUVADIS 'Idea-Lab' on Best practices for multi-omics biomarker discoveries. Idea lab will take place on the 21st and the 22nd November. HOB Registration form: http://www.handsonbiobanks.org/2013/registration/ Please don't hesitate to contact me for any question/comment, Kind regards, Gabrielle Gabrielle Bertier Scientific Project Manager International and Scientific Affairs CRG, Center for Genomic Regulation Carrer Dr. Aiguader, 88 08003 Barcelona, España Phone: +34933160182 email: gabrielle.bertier(a)crg.es<mailto:gabrielle.bertier@crg.es> web: www.geuvadis.eu; www.fliact.eu

11 years, 3 months

[Geuvadis_rna_analysis] Sample sheets, wiki and ftp

by Olof Karlberg

Dear all, I have been trying to figure out how the different samples were multiplexed in the different labs and ran into some problems. The sample sheets on the Wiki (both new and old) lack data in a large number of columns. Does anyone know what has happened to them?. I remember putting it on the ftp and figured the correct versions might still be there but... The ftp-site geuvadis(a)ftp-private.ebi.ac.uk seems non-responding, I get stuck at "logging in..." Was the data moved somewhere else? Regards, Olof

11 years, 6 months

[Geuvadis_rna_analysis] Splicing manuscript

by Michael Sammeth

Dear all**** I attach the current draft of a splicing manuscript based on Geuvadis data. In case please send me any comments until next *Thursday 21st* Best wishes Micha Sammeth

11 years, 7 months

Re: [Geuvadis_rna_analysis] Geuvadis RNAseq manuscript draft

by Tuuli Lappalainen

Dear all, The revised version of the Geuvadis RNAseq main paper has been resubmitted to Nature. The manuscript files are enclosed for your reference. Time to cross fingers again - let's hope for the best! best regards, Tuuli Tuuli Lappalainen, PhD Department of Genetics, Stanford University School of Medicine , and Department of Genetic Medicine and Development, University of Geneva Email: tuuli.e.lappalainen(a)gmail.com / tlappala(a)stanford.edu Tel: +1 415 351 9713 Bustamante lab Department of Genetics 300 Pasteur Dr. Lane L301 Stanford, CA 94305-5120 USA

11 years, 7 months

[Geuvadis_rna_analysis] Geuvadis RNA-seq paper revision

by Tuuli Lappalainen

Dear all, We have revised the Geuvadis RNA-seq paper for Nature; please find the paper and the response letter enclosed. If you have any comments, please send them *by Saturday* - apologies for the tight schedule, we are planning to submit this on Monday. Thanks to all of you who helped me with the revisions. As many of you know, the editor adviced us to make the paper more focused on the key messages, and as a consequence we had to drop some of the analyses - fusion transcripts, soft splicing and RNA editing. I hope that those results can be published in some other context later on. To strengthen the analysis of regulatory variants, I did some additional analysis on regulatory variants underlying allele-specific expression signals, but otherwise the changes in the paper are relatively small. I think that we were able to respond to all the comments really well, and hopefully the editor and reviewers agree. best regards, Tuuli -- Tuuli Lappalainen, PhD Department of Genetics, Stanford University School of Medicine , and Department of Genetic Medicine and Development, University of Geneva Email: tuuli.e.lappalainen(a)gmail.com / tlappala(a)stanford.edu Tel: +1 415 351 9713 Bustamante lab Department of Genetics 300 Pasteur Dr. Lane L301 Stanford, CA 94305-5120 USA

11 years, 7 months

[Geuvadis_rna_analysis] Biology of Genomes abstract

by Tuuli Lappalainen

Dear all, Enclosed please find the abstract of the Geuvadis RNAseq main paper that I'm planning to submit to the Biology of Genomes meeting in Cold Spring Harbor. The deadline is on Friday, so if you have any comments, please send them immediately. Biology of Genomes only allows 18 authors and 12 affiliations, which is why I've had to cut many names from the abstract author list - apologies to those who didn't make it, you will be acknowledged in the poster/talk. best regards, Tuuli -- Tuuli Lappalainen, PhD Department of Genetics, Stanford University School of Medicine , and Department of Genetic Medicine and Development, University of Geneva Email: tuuli.e.lappalainen(a)gmail.com / tlappala(a)stanford.edu Tel: +1 415 351 9713 Bustamante lab Department of Genetics 300 Pasteur Dr. Lane L301 Stanford, CA 94305-5120 USA

11 years, 7 months

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