geuvadis_rnaseq September 2011

geuvadis_rnaseq@lists.crg.es

5 participants
9 discussions

by Tuuli Lappalainen

Dear all, For the mRNA sequencing of the Geuvadis samples, we suggest using the latest Illumina sample prep kit for HiSeq with 24 indexes: TruSeq RNA Sample Prep Kit V2 Set A and Set B (RS-122-2001 and RS-122-2002) As we agreed on the call, you should let me know this week if you don't agree with using this kit - otherwise we'll go forward with this, and everyone should to order the kits as necessary to prepare for receiving the RNAs in the end of October or early November. Please see the attachment for full information from Illumina for ordering - as you know, it is absolutely critical that we all follow the same protocol. best regards, Tuuli -- Tuuli Lappalainen, PhD Department of Genetic Medicine and Development University of Geneva Medical School CMU / Rue Michel-Servet 1 1211 Geneva 4 Switzerland Tel. +41-(0)22-3795550 tuuli.lappalainen(a)unige.ch

12 years, 11 months

[Geuvadis_rnaseq] Geuvadis RNAseq and 1000 Genomes

by Tuuli Lappalainen

Dear all, I would like to ask your opinion on potential collaboration in the future between the Geuvadis RNA sequencing project and the 1000 Genomes Consortium. There will be a 1000g project meeting in Montreal in mid-November that I will attend - me and Manolis belong to the 1000g analysis group. In the Phase 1 of the project there is now increasing interest to analyze functional consequences of the discovered variants, also in the regulatory context. There's no doubt that the Geuvadis dataset will be hugely valuable in annotating regulatory variation, which is of interest to many people. The vast majority of the work will naturally happen within the Geuvadis framework. However, the really unique property of our dataset is the combination of genome and transcriptome sequence data, and in my opinion the expertise that the 1000g people have in analyzing genome sequence might help us to get the most out of our data, benefiting us all. So, what would you think of exploring the possibilities for collaboration? We suggest that I will let relevant people from the 1000g consortium to know about Geuvadis, and discuss if there would be joint interests - open the door a little bit, so to say. It goes without saying all external collaborations would be conditional to full acceptance by the partners and all due credit to the Geuvadis project. Please let me know what you think by early October. best regards, Tuuli -- Tuuli Lappalainen, PhD Department of Genetic Medicine and Development University of Geneva Medical School CMU / Rue Michel-Servet 1 1211 Geneva 4 Switzerland Tel. +41-(0)22-3795550 tuuli.lappalainen(a)unige.ch

12 years, 11 months

[Geuvadis_rnaseq] Geuvadis RNAseq and 1000 Genomes

by Gabrielle Anne Bertier

FYI, from Tuuli -------- Original Message -------- Dear all, I would like to ask your opinion on potential collaboration in the future between the Geuvadis RNA sequencing project and the 1000 Genomes Consortium. There will be a 1000g project meeting in Montreal in mid-November that I will attend - me and Manolis belong to the 1000g analysis group. In the Phase 1 of the project there is now increasing interest to analyze functional consequences of the discovered variants, also in the regulatory context. There's no doubt that the Geuvadis dataset will be hugely valuable in annotating regulatory variation, which is of interest to many people. The vast majority of the work will naturally happen within the Geuvadis framework. However, the really unique property of our dataset is the combination of genome and transcriptome sequence data, and in my opinion the expertise that the 1000g people have in analyzing genome sequence might help us to get the most out of our data, benefiting us all. So, what would you think of exploring the possibilities for collaboration? We suggest that I will let relevant people from the 1000g consortium to know about Geuvadis, and discuss if there would be joint interests - open the door a little bit, so to say. It goes without saying all external collaborations would be conditional to full acceptance by the partners and all due credit to the Geuvadis project. Please let me know what you think by early October. best regards, Tuuli -- Tuuli Lappalainen, PhD Department of Genetic Medicine and Development University of Geneva Medical School CMU / Rue Michel-Servet 1 1211 Geneva 4 Switzerland Tel. +41-(0)22-3795550 tuuli.lappalainen(a)unige.ch<mailto:tuuli.lappalainen@unige.ch>

12 years, 11 months

[Geuvadis_rnaseq] Geuvadis mRNAseq kit

by Gabrielle Anne Bertier

FYI, from Tuuli Lappalainen -------- Original Message -------- Subject: Geuvadis mRNAseq kit Date: Tue, 27 Sep 2011 10:29:00 +0200 From: Tuuli Lappalainen <Tuuli.Lappalainen(a)unige.ch><mailto:Tuuli.Lappalainen@unige.ch> To: geuvadis_rnaseq(a)lists.crg.es<mailto:geuvadis_rnaseq@lists.crg.es> <geuvadis_rnaseq(a)lists.crg.es><mailto:geuvadis_rnaseq@lists.crg.es> Dear all, For the mRNA sequencing of the Geuvadis samples, we suggest using the latest Illumina sample prep kit for HiSeq with 24 indexes: TruSeq RNA Sample Prep Kit V2 Set A and Set B (RS-122-2001 and RS-122-2002) As we agreed on the call, you should let me know this week if you don't agree with using this kit - otherwise we'll go forward with this, and everyone should to order the kits as necessary to prepare for receiving the RNAs in the end of October or early November. Please see the attachment for full information from Illumina for ordering - as you know, it is absolutely critical that we all follow the same protocol. best regards, Tuuli -- Tuuli Lappalainen, PhD Department of Genetic Medicine and Development University of Geneva Medical School CMU / Rue Michel-Servet 1 1211 Geneva 4 Switzerland Tel. +41-(0)22-3795550 tuuli.lappalainen(a)unige.ch<mailto:tuuli.lappalainen@unige.ch>

12 years, 11 months

[Geuvadis_rnaseq] Geuvadis mRNAseq kit

by Tuuli Lappalainen

Dear all, For the mRNA sequencing of the Geuvadis samples, we suggest using the latest Illumina sample prep kit for HiSeq with 24 indexes: TruSeq RNA Sample Prep Kit V2 Set A and Set B (RS-122-2001 and RS-122-2002) As we agreed on the call, you should let me know by the end of September if you object - otherwise we'll go forward with this, and everyone should to order the kits as necessary to prepare for receiving the RNAs in the end of October or early November. Please see the attachment for full information from Illumina for ordering - as you know, it is absolutely critical that we all follow the same protocol. best regards, Tuuli -- Tuuli Lappalainen, PhD Department of Genetic Medicine and Development University of Geneva Medical School CMU / Rue Michel-Servet 1 1211 Geneva 4 Switzerland Tel. +41-(0)22-3795550 tuuli.lappalainen(a)unige.ch

12 years, 12 months

Re: [Geuvadis_rnaseq] SCHEDULE CHANGE GEUVADIS RNA-seq TC 16.09.11 17:00 CET

by Gabrielle Anne Bertier

Dear all, it should be working now If calling from Spain: 902 125 136 If calling from outside Spain: +34 91 495 18 99 Participant Pin-Code: 764989* Gabrielle From: P.A.C._t_Hoen(a)lumc.nl [mailto:P.A.C._t_Hoen@lumc.nl] Sent: viernes, 16 de septiembre de 2011 17:09 To: Gabrielle Anne Bertier; geuvadis_rnaseq(a)lists.crg.es Cc: geuvadis_wpl(a)lists.crg.es; G.J.B.van_Ommen(a)lumc.nl; Rut Carbonell Garcia; p.rosenstiel(a)mucosa.de Subject: RE: SCHEDULE CHANGE GEUVADIS RNA-seq TC 16.09.11 17:00 CET Dear all I could not connect to this TC. Others could? Peter ________________________________ From: Gabrielle Anne Bertier [mailto:gabrielle.bertier@crg.eu] Sent: Wednesday, September 14, 2011 7:00 PM To: Gabrielle Anne Bertier; geuvadis_rnaseq(a)lists.crg.es Cc: geuvadis_wpl(a)lists.crg.es; Hoen, P.A.C. 't (HG); Ommen, G.J.B. van (HG); Rut Carbonell Garcia; Rosenstiel, Philip Subject: SCHEDULE CHANGE GEUVADIS RNA-seq TC 16.09.11 17:00 CET Dear all, To the best convenience of a majority of participants, note that the schedule for the RNAseq TC has been shifted to 17:00 CET. Details: Date: Friday 16. Sept; Time: 17:00-18:00 CET If calling from Spain: 902 125 136 If calling from outside Spain: +34 91 495 18 99 Participant Pin-Code: 764989* Kind regards, Gabrielle From: geuvadis_wpl-bounces(a)lists.crg.es<mailto:geuvadis_wpl-bounces@lists.crg.es> [mailto:geuvadis_wpl-bounces@lists.crg.es]<mailto:%5bmailto:geuvadis_wpl-bounces@lists.crg.es%5d> On Behalf Of Gabrielle Anne Bertier Sent: jueves, 01 de septiembre de 2011 17:27 To: geuvadis_rnaseq(a)lists.crg.es<mailto:geuvadis_rnaseq@lists.crg.es> Cc: Michela Bertero; geuvadis_wpl(a)lists.crg.es<mailto:geuvadis_wpl@lists.crg.es> Subject: [Geuvadis_wpl] RNA-seq strandedness benchmark Dear all, Please find below a message from Philip about RNA study results. We will setup a doodle for a TC to discuss these results. Please be so kind as to pass this on to any relevant person, and let me know if there's anyone I should add to the Geuvadis RNAseq mailing list. Kind regards, Gabrielle Gabrielle Bertier Scientific 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(a)crg.es<mailto:gabrielle.bertier@crg.es> web: www.geuvadis.eu From: Rosenstiel, Philip [mailto:p.rosenstiel@mucosa.de]<mailto:%5bmailto:p.rosenstiel@mucosa.de%5d> Sent: jueves, 01 de septiembre de 2011 17:08 To: Gabrielle Anne Bertier; Manolis Dermitzakis Cc: Xavier Estivill Subject: WG: RNA-seq strandedness benchmark Dear RNA friends of gEUVADIS, Several weeks ago we have committed to perform the benchmarking study for strandedness protocols in the 5 samples with both Illumina GAIIx and SoliD V4 protocols. Matthias has put a lot of work into this and we would like to discuss the results with you and see how to proceed from here. I think the results are very interesting and are worth following up/finishing. Best, Philip & Matthias Prof. Dr. Philip Rosenstiel Institute of Clinical Molecular Biology University Kiel Schittenhelmstr.12 Building 5 24105 Kiel phone +49/4315971333 mobile +49/1773525080 -- 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(a)molgen.mpg.de<mailto:sudbrak@molgen.mpg.de>

13 years

Re: [Geuvadis_rnaseq] [Geuvadis_wpl] GEUVADIS RNA-seq TC 16.09.11 17:00 CET

by Gabrielle Anne Bertier

Dear all, we are experiencing technical problems. We should be able to connect in 5 minutes. Sorry for the inconvenience. Gabrielle -----Original Message----- From: Manolis Dermitzakis [mailto:Emmanouil.Dermitzakis@unige.ch] Sent: viernes, 16 de septiembre de 2011 17:02 To: Gabrielle Anne Bertier Cc: geuvadis_rnaseq(a)lists.crg.es; geuvadis_wpl(a)lists.crg.es; kslopez(a)pcb.ub.cat; Rut Carbonell Garcia Subject: Re: [Geuvadis_wpl] GEUVADIS RNA-seq TC 16.09.11 17:00 CET Gabrielle The pin code is wrong Please send us the correct one Thanks, Manolis ------------------------------------------ Emmanouil (Manolis) Dermitzakis, PhD Louis-Jeantet Professor Department of Genetic Medicine and Development University of Geneva Medical School 1 Rue Michel-Servet (CMU office 9088) Geneva 1211 Switzerland Email: emmanouil.dermitzakis(a)unige.ch Tel: +41 (0) 22 379 5483 Fax: +41 (0) 22 379 5706 website: http://funpopgen.unige.ch/ Admin assistant: Ancilla Stefani, Tel: +41 22 379 5551 e-mail: Ancilla.Stefani(a)unige.ch ------------------------------------------ Gabrielle Anne Bertier wrote: > > FYI, please find below an email from Matthias Barann > > Reminder: > > RNAseq TC > > Date: Today *Friday 16. Sept;* > > Time: *17:00-18:00 CET* > > If calling from Spain: 902 125 136 > > If calling from outside Spain: +34 91 495 18 99 > > Participant Pin-Code: 764989* > > > > Kind regards, > > Gabrielle > > ---------- Forwarded message ---------- > From: *Matthias Barann* <mbarann(a)gmail.com <mailto:mbarann@gmail.com>> > Date: 2011/9/16 > Subject: Re: [Geuvadis_rnaseq] SCHEDULE CHANGE GEUVADIS RNA-seq TC > 16.09.11 17:00 CET > > > Dear all, > > please see attatched an excel sheet with some data regarding the > stranded protocols for illumina and solid, which we will discuss > during the telephone conference at 17:00 CET. > > best wishes, > Matthias > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Geuvadis_wpl mailing list > Geuvadis_wpl(a)lists.crg.es > http://davinci.crg.es/mailman/listinfo/geuvadis_wpl

13 years

[Geuvadis_rnaseq] GEUVADIS RNA-seq TC 16.09.11 17:00 CET

by Gabrielle Anne Bertier

FYI, please find below an email from Matthias Barann Reminder: RNAseq TC Date: Today Friday 16. Sept; Time: 17:00-18:00 CET If calling from Spain: 902 125 136 If calling from outside Spain: +34 91 495 18 99 Participant Pin-Code: 764989* Kind regards, Gabrielle ---------- Forwarded message ---------- From: Matthias Barann <mbarann(a)gmail.com<mailto:mbarann@gmail.com>> Date: 2011/9/16 Subject: Re: [Geuvadis_rnaseq] SCHEDULE CHANGE GEUVADIS RNA-seq TC 16.09.11 17:00 CET Dear all, please see attatched an excel sheet with some data regarding the stranded protocols for illumina and solid, which we will discuss during the telephone conference at 17:00 CET. best wishes, Matthias

13 years

[Geuvadis_rnaseq] RNA-seq strandedness benchmark

by Gabrielle Anne Bertier

Dear all, Please find below a message from Philip about RNA study results. We will setup a doodle for a TC to discuss these results. Please be so kind as to pass this on to any relevant person, and let me know if there's anyone I should add to the Geuvadis RNAseq mailing list. Kind regards, Gabrielle Gabrielle Bertier Scientific 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(a)crg.es<mailto:gabrielle.bertier@crg.es> web: www.geuvadis.eu From: Rosenstiel, Philip [mailto:p.rosenstiel@mucosa.de]<mailto:[mailto:p.rosenstiel@mucosa.de]> Sent: jueves, 01 de septiembre de 2011 17:08 To: Gabrielle Anne Bertier; Manolis Dermitzakis Cc: Xavier Estivill Subject: WG: RNA-seq strandedness benchmark Dear RNA friends of gEUVADIS, Several weeks ago we have committed to perform the benchmarking study for strandedness protocols in the 5 samples with both Illumina GAIIx and SoliD V4 protocols. Matthias has put a lot of work into this and we would like to discuss the results with you and see how to proceed from here. I think the results are very interesting and are worth following up/finishing. Best, Philip & Matthias Prof. Dr. Philip Rosenstiel Institute of Clinical Molecular Biology University Kiel Schittenhelmstr.12 Building 5 24105 Kiel phone +49/4315971333 mobile +49/1773525080 -- 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(a)molgen.mpg.de<mailto:sudbrak@molgen.mpg.de>

13 years

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geuvadis_rnaseq September 2011