geuvadis_rnaseq

geuvadis_rnaseq@lists.crg.es

97 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 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

13 years, 8 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, 8 months

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, 8 months

[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, 8 months

[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, 8 months

[Geuvadis_rnaseq] TC Minutes and important deadlines

by Gabrielle Anne Bertier

Dear all, You will find attached the last WPL TC Minutes. Comments are welcome. Action points: - Annual Meeting: 29.11 morning Workshop on Medical NGS. -Thomas Meitinger- Suggestions of External Speakers can be made until the end of August. (Leena Peltonen School 21-25 August 2011) - WP5: Plan -Parkinson's disease and mental retardation- has to be shaped before the annual meeting and finalised in Toulouse. Because of the summer holidays, some WPL could not attend the TC. Manolis, Alvis, could you give us a short update on your WP ? Please remember that we have several Deliverables due in November: Nov. 2011 D1.3 Geuvadis Website Evaluation CRG Please fill in the survey<https://spreadsheets.google.com/spreadsheet/viewform?hl=en_US&formkey=dDlPd…> before September 19th 2011 Nov. 2011 D1.4 Communication CRG Develop a transparent communication strategy. Nov. 2011 D2.1 Quality Control of Sequence Data UU Definition of standards for quality control of sequence data Nov. 2011 D4.1 Database for RNAseq pilot ptoject UNIGE Nov. 2011 D5.1 Database for Exomeseq pilot ptoject HMGU Nov. 2011 D6.1 Documentation Inserm Relevant documentation for European Commission and internal ELSI policy established Nov. 2011 D6.2 ELSI database Inserm ELSI Database: Database of ELSI experts and list of relevant ELSI initiatives and events As mentioned in the table, please be so kind as to fill in the survey<https://spreadsheets.google.com/spreadsheet/viewform?hl=en_US&formkey=dDlPd…> we've prepared to assess the use of our project website before September 19th 2011. https://spreadsheets.google.com/spreadsheet/viewform?hl=en_US&formkey=dDlPd… We also set up the registration page<https://spreadsheets.google.com/spreadsheet/viewform?formkey=dDFkdktiQ1Y0Rz…> for our next annual meeting in Toulouse. Please register as soon as possible and before October 10th 2011. You will also find this registration sheet as well as all useful information for the annual meeting on our intranet dedicated page. https://spreadsheets.google.com/spreadsheet/viewform?formkey=dDFkdktiQ1Y0Rz… For any question don't hesitate to contact me, I wish you a very nice summer ! Kind regards, Gabrielle Dealines Reminder: 2011 August September October November Deadline/ Action 21-25: Leena Peltonen School 19: Fill-in website survey<https://spreadsheets.google.com/spreadsheet/viewform?hl=en_US&formkey=dDlPd…> 10: Registration<https://spreadsheets.google.com/spreadsheet/viewform?formkey=dDFkdktiQ1Y0Rz…> for Annual Meeting 28-29: Annual Meeting 31: Suggestions of Ext. Speakers to T. Meitinger for 29.11 morning Workshop on Medical NGS. WP5 plan shaping 30: Deliverables: D1.3, D1.4, D2.1, D4.1, D5.1, D6.1, D6.2

13 years, 10 months

[Geuvadis_rnaseq] REMINDER: Registration deadline August 8th -ENGAGE RNA-seq Course, 12th-13th September 2011, EBI, Hinxton, UK

by Gabrielle Anne Bertier

FYI; This course is open to maximum of 10 GEUVADIS participants. From: Shen Huei-Yi <huei-yi.shen(a)thl.fi<mailto:huei-yi.shen@thl.fi>> Date: 22 de julio de 2011 13:50:39 GMT+02:00 To: "everyone(a)euengage.org<mailto:everyone@euengage.org>" <everyone(a)euengage.org<mailto:everyone@euengage.org>> Subject: [Everyone] REMINDER: Registration deadline August 8th -ENGAGE RNA-seq Course, 12th-13th September 2011, EBI, Hinxton, UK Dear all, We would like to remind you that there are only two weeks left to sign up for the ENGAGE RNA-seq course to be held on 12th-13th September at EBI, Hinxton, UK. The registration deadline is 8th of August. The course with covers data analysis of RNA-Seq experiments including topics on: short read alignment, data handling and visualisation, region identification, differential expression, data quality assessment and statistical analysis, using R/Bioconductor. This course is recommended for advanced PhD students and post-doctoral researchers who are applying or planning to apply high throughput sequencing technologies and bioinformatics methods in their research. Both lecture and practical sessions are included in the program. Invited Speakers: *Peter 't Hoen, Leiden University Medical Center, Netherlands *Angela Goncalves, EBI-EMBL, UK *Mar Gonzales Porta, EBI-EMBL, UK *Thomas J. Hardcastle, Cambridge University, UK *Gabriella Rustici, EBI-EMBL, UK More details on the program, please visit the course webpage at: http://embl-web.ungerboeck.com/reg/reg_p1_form.aspx?oc=20&ct=GBPNORMAL&even… Link to the registration page: http://embl-web.ungerboeck.com/reg/reg_p1_form.aspx?oc=20&ct=GBPNORMAL&even… Best regards, Huei-yi and Maxine -------------------------------------------------------------------------------- Huei-yi Shen, PhD Project Coordinator Institute for Molecular Medicine Finland FIMM, University of Helsinki National Institute for Health and Welfare (THL) Tel: +358-20-610 8334; Fax: +358-20-610 8480 Email:huei-yi.shen@thl.fi;huei-yi.shen@helsinki.fi<mailto:huei-yi.shen@helsinki.fi>

13 years, 10 months

[Geuvadis_rnaseq] new Postdoc in Geneva RNAseq Analysis Team

by Gabrielle Anne Bertier

FYI From: Thomas Giger <Thomas.Giger(a)unige.ch<mailto:Thomas.Giger@unige.ch>> Date: July 4, 2011 1:12:56 PM GMT+02:00 To: geuvadis_rnaseq(a)lists.crg.es<mailto:geuvadis_rnaseq@lists.crg.es> Subject: new Postdoc in RNAseq Analysis Team Dear All, I would like to introduce Tuuli Lappalainen to the Geuvadis consortium. Tuuli is a senior postdoc in the Dermitzakis lab in Geneva. She will take over my spot in the consortium coordinating the transcriptome sequencing of 500 samples of the 1000 genomes project. You can contact Tuuli by her e-mail address: Tuuli.Lappalainen(a)unige.ch<mailto:Tuuli.Lappalainen@unige.ch> Since I will leave the consortium by the end of the week, I wanted to thank all of you for your collaboration and wish you all the best for the future! kindest regards, Thomas ------------------------------------------------------------------------ Thomas Giger, Ph.D. Department of Genetic Medicine and Development University of Geneva Medical School 1 Rue Michel-Servet Geneva 1211 Switzerland

13 years, 10 months

[Geuvadis_rnaseq] Important - Please read & respond!

by Thomas Giger

Hello, This e-mail contains important information that affects the design of the RNAseq experiment which is done within the Geuvadis consortium. The time point at which the Iberian samples (IBS) would be available to us has shifted back to the end of 2011. Initially, those samples should have been available to us in the beginning of 2011 - but now this has changed (http://www.1000genomes.org/about). This means that we would have to wait for those samples until the end of the year (or potentially longer) until we could start with the sequencing. We've discussed this here in Geneva and concluded that this should not be a reason to delay data generation. We therefore suggest that we should analyze an African population (YRI) instead of the IBS population. This means that we will of course have less power for detecting regulatory variation among Europeans but it opens up the possibility to look at differences between continental populations. Unless you express disagreement with this change within the next 10 days - we will go ahead and analyze the YRI instead of the IBS population. Kindest regards, Thomas ------------------------------------------------------------------------ Thomas Giger, Ph.D. Department of Genetic Medicine and Development University of Geneva Medical School 1 Rue Michel-Servet Geneva 1211 Switzerland

13 years, 11 months

[Geuvadis_rnaseq] Publication recommendation: RNA-sequence analysis of human B-cells

by Gabrielle Anne Bertier

Dear all, Please note that the attached publication (also deposited in our intranet) may be of high significance for you. RNA-sequence analysis of human B-cells. Jonathan M. Toung, Michael Morley, Mingyao Li, et al. Genome Res. published online May 2, 2011 Access the most recent version at doi:10.1101/gr.116335.110 Many thanks to Esther Lizano. Best regards, Gabrielle 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(a)crg.es<mailto:gabrielle.bertier@crg.es> web: www.geuvadis.eu

14 years

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