geuvadis_rnaseq

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97 discussions

[Geuvadis_rnaseq] Geuvadis RNAseq poster for Biology of Genomes

by Tuuli Lappalainen

Dear all, Enclosed please find a draft of the Geuvadis RNAseq poster that I'll be presenting next week at the Biology of Genomes meeting in Cold Spring Harbor. Small changes are still possible until Thursday, so comments are welcome. I think we managed to put together some pretty cool results in a very short time - my special thanks go to Micha, Marc F, Jean and Manny for contributing results and figures for the poster. 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

[Geuvadis_rnaseq] Geuvadis RNAseq next analysis group meeting - fill the doodle

by Tuuli Lappalainen

Dear all, The next Geuvadis analysis group meeting will take place in Barcelona in late June or early July. If you'd be interested in attending, please fill the Doodle to find the best time for the 2-day meeting: http://www.doodle.com/z7a3mq92b9syz9xg 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, 1 month

[Geuvadis_rnaseq] Geuvadis RNAseq analysis group meeting

by Tuuli Lappalainen

Dear all, We will have a face-to-face meeting for the Geuvadis RNAseq analysis group in Geneva on April 16-17. The goal of the meeting is to present first results and plan future analyses. Everyone involved in the project is welcome to attend, and we hope that especially those who plan to contribute to data analysis will be able to come. *If you would like to attend the meeting, please fill out the following registration form by March 16*: https://docs.google.com/spreadsheet/viewform?formkey=dE1vZEV3ZmlubFBZUkxHMk… The preliminary schedule can be found in: https://docs.google.com/document/d/1xzm154L2ZD8qEgl9E4cKsoeuAhCLJZ4c6ZXiM3U… Practicalities: - Everyone should book their own flights - We will arrange and pay lunch and coffee on the 16th and 17th, and a dinner on the 16th - For accommodation, we can recommend two hotels listed below. If you want to stay in either of them, you can make your own reservation or we can do it for you - just fill in the relevant information in the registration form. You can also stay elsewhere and arrange it yourself. 1. Hotel du Midi ~190 CHF + breakfast = ~ 220 CHF Place Chevelu 4, 1201 Geneva - phone +41 22 544 15 00 webpage: http://www.hotel-du-midi.ch/ 2**. Hotel "Bel'Espérance" single CHF 125, double CHF 150, breakfast included Rue de la Vallée 1, 1204 Geneva phone +41 22 818 37 37 webpage: http://www.hotel-bel-esperance.ch/ Don't hesitate to ask me or our admin assistant Ancilla Stefani (Ancilla.Stefani(a)unige.ch) if you have any questions. 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, 2 months

[Geuvadis_rnaseq] Geuvadis RNAseq activities for the mid-term report

by Tuuli Lappalainen

Dear all, We are collecting information for the mid-term report for the Geuvadis WP4 (RNAseq). Thus, could you please send me information by March 14 of all your presentations, publications, grants, etc that acknowledge Geuvadis or are otherwise relevant to the RNAseq project. 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, 2 months

[Geuvadis_rnaseq] Geuvadis RNAseq abstract for Biology of Genomes

by Tuuli Lappalainen

Dear all, Here is the Geuvadis RNAseq draft for the abstract for the Biology of Genomes meeting. Please *comment and give your author and affiliation info by Tuesday Feb 21*. Regarding the author list: The length limitation includes author & affiliation info, so we need to keep it very short for this abstract. We suggest the following: - analysis people with major contribution: Tuuli Lappalainen, Michael Sammeth, Natalja Kurbatova, Tim Strom, Peter t' Hoen, Matthias Barann, Marc Sultan, Esther Lizano, Manuel Rivas. If someone else feels that they should be included, we can try to squeeze in an additional name or two. - One PI per institute - *Kiel and Berlin, please indicate who*: Alvis Brazma, Ann-Christine Syvanen, Thomas Meitinger, Gert-Jan van Ommen, Philip Rosenstiel */* Stefan Schreiber, Ralf Sudbrak */* Hans Lehrach, Ivo Gut, Xavier Estivill, Emmanouil T Dermitzakis - and last: "on behalf of the Geuvadis Consortium" *Everyone on the author list: please reply to this email with your name and affiliation info. *Due to length limitations, please include only your Geuvadis partner affiliation and use abbreviations when possible. best regards, Tuuli Author information example: First name: Tuuli Middle initial: Last name: Lappalainen Email: tuuli.lappalainen(a)unige.ch Affiliation name: University of Geneva Department: Dept of Genetic Medicine and Development Street: R. Michel Servet 1 City : Geneva Postal code: 1211 4 Country: Switzerland -- 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, 3 months

[Geuvadis_rnaseq] Geuvadis RNAseq TC Minutes

by Tuuli Lappalainen

Hello all, Please find the Geuvadis RNAseq TC minutes enclosed. Action items: -All the labs with miRNA data (everyone except Leiden, Uppsala?) should upload 3 fastq files (preferably of different read counts; before any trimming) to the ftp site, to /upload/geuvadis/wp4_rnaseq/main_project/working/miRNA_QC. Then everyone should analyze these files using their standard methods to make sure that the data from different labs is of comparable quality. These analyses need to be done asap. -UNIGE will finish the details of invoicing the cell & RNA costs -Tuuli will write and send around an abstract for Biology of Genomes 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, 3 months

[Geuvadis_rnaseq] it works now

by Tuuli Lappalainen

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 -------- Original Message -------- Subject: RE: Rut, it seems that they cannot connect to the call can you double check ? I´m in a meeting... Date: Tue, 14 Feb 2012 16:09:07 +0100 From: Rut Carbonell Garcia <rut.carbonell(a)crg.eu> To: Esther Lizano <Esther.Lizano(a)crg.eu>, Gabrielle Anne Bertier <gabrielle.bertier(a)crg.eu> CC: Tuuli Lappalainen <Tuuli.Lappalainen(a)unige.ch> Try it now please *De:*Esther Lizano *Enviado el:* martes, 14 de febrero de 2012 16:06 *Para:* Gabrielle Anne Bertier *CC:* Tuuli Lappalainen; Rut Carbonell Garcia *Asunto:* Re: Rut, it seems that they cannot connect to the call can you double check ? I´m in a meeting... the problem is the pin code, it says invalid. could we use the coordinator pin? On 2/14/12 4:04 PM, Gabrielle Anne Bertier wrote: *_14th of February at 4-5pm, 15 ppl_* Spain 902 125 136 Other countries +34 91 495 18 99 Participants' Pin-code: 764989* *From:*geuvadis_rnaseq-bounces@lists.crg.es <mailto:geuvadis_rnaseq-bounces@lists.crg.es> [mailto:geuvadis_rnaseq-bounces@lists.crg.es] *On Behalf Of *Tuuli Lappalainen *Sent:* Tuesday, February 14, 2012 4:02 PM *Cc:* geuvadis_rnaseq(a)lists.crg.es <mailto:geuvadis_rnaseq@lists.crg.es>; geuvadis_rna_analysis(a)lists.crg.es <mailto:geuvadis_rna_analysis@lists.crg.es> *Subject:* Re: [Geuvadis_rnaseq] [Geuvadis_rna_analysis] Geuvadis RNAseq TC today at 4pm These were the codes that I got from Gabrielle, I hope that she can fix this! 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> On 2/14/12 4:01 PM, M.Sammeth wrote: invalid code 764989* On Tue, Feb 14, 2012 at 3:46 PM, Tuuli Lappalainen <Tuuli.Lappalainen(a)unige.ch <mailto:Tuuli.Lappalainen@unige.ch>> wrote: Sorry - here's the attachment. 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 <tel:%2B41-%280%2922-3795550> tuuli.lappalainen(a)unige.ch <mailto:tuuli.lappalainen@unige.ch> On 2/14/12 3:45 PM, Tuuli Lappalainen wrote: Dear all, Here is a slide of small RNA quality analysis to discuss on the call. 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 <tel:%2B41-%280%2922-3795550> tuuli.lappalainen(a)unige.ch <mailto:tuuli.lappalainen@unige.ch> On 2/14/12 12:37 PM, Tuuli Lappalainen wrote: Here are the call details Spain 902 125 136 Other countries +34 91 495 18 99 Participants' Pin-code: 764989* 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 <tel:%2B41-%280%2922-3795550> tuuli.lappalainen(a)unige.ch <mailto:tuuli.lappalainen@unige.ch> On 2/14/12 9:18 AM, Tuuli Lappalainen wrote: Dear all, As a reminder, we have a Geuvadis RNAseq TC today (14th) at 4 PM. On the agenda: - update on sequencing progress - miRNA quality - RNAseq meetings April 16-17 in Geneva, future meetings? - cell line & RNA extraction costs - abstract for Biology of Genomes meeting at Cold Spring Harbor - collaborations best regards, Tuuli _______________________________________________ Geuvadis_rna_analysis mailing list Geuvadis_rna_analysis(a)lists.crg.es <mailto:Geuvadis_rna_analysis@lists.crg.es> http://davinci.crg.es/mailman/listinfo/geuvadis_rna_analysis _______________________________________________ Geuvadis_rnaseq mailing list Geuvadis_rnaseq(a)lists.crg.es <mailto:Geuvadis_rnaseq@lists.crg.es> http://davinci.crg.es/mailman/listinfo/geuvadis_rnaseq _______________________________________________ Geuvadis_rnaseq mailing list Geuvadis_rnaseq(a)lists.crg.es <mailto:Geuvadis_rnaseq@lists.crg.es> http://davinci.crg.es/mailman/listinfo/geuvadis_rnaseq -- Dr. Michael Sammeth, Functional Bioinformatics Phone: +34-934-020-580, http://www.cnag.eu Centre Nacional d'Anàlisi Genòmica (CNAG), PCB Baldiri Reixac 4-6, Room 02A8, 08028 Barcelona

13 years, 3 months

[Geuvadis_rnaseq] Geuvadis RNAseq TC today at 4pm

by Tuuli Lappalainen

Dear all, As a reminder, we have a Geuvadis RNAseq TC today (14th) at 4 PM. On the agenda: - update on sequencing progress - miRNA quality - RNAseq meetings April 16-17 in Geneva, future meetings? - cell line & RNA extraction costs - abstract for Biology of Genomes meeting at Cold Spring Harbor - collaborations 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, 3 months

[Geuvadis_rnaseq] Geuvadis RNAseq analysis group face-to-face meeting

by Tuuli Lappalainen

Dear all, The Geuvadis RNAseq analysis group is planning to have a face-to-face meeting in April. Please *fill in the Doodle by the end of the week* (Feb 12) if you think you would like to attend**so that we can fix the date of the meeting: *http://www.doodle.com/24a4i3n8bkynhpwx* The goal of the meeting is to present first results as well as plan and decide on future analyses. The 1.5-day meeting will probably take place in Geneva. 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, 3 months

Re: [Geuvadis_rnaseq] [Geuvadis_rna_analysis] GEUVADIS RNAseq TC

by Tuuli Lappalainen

Dear all, Let's have the Geuvadis RNAseq TC on *Tuesday 14th of February at 4-5pm*, this**time seemed to be good for most people. I will send a reminder with a more detailed agenda later. best regards, Tuuli Lappalainen 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 On 1/16/12 3:20 PM, Gabrielle Anne Bertier wrote: > > Dear all, at the request of Tuuli, please fill in this doodle > <http://www.doodle.com/ccm7dkvtngwwquqt> for the next GEUVADIS RNAseq TC. > > _Preliminary agenda:_ > > - update on sequencing progress > > - preliminary QC/analysis results > > - analysis plans > > - analysis group meeting in the spring > > Kind regards, > > Gabrielle > > http://www.doodle.com/ccm7dkvtngwwquqt > > > > _______________________________________________ > Geuvadis_rna_analysis mailing list > Geuvadis_rna_analysis(a)lists.crg.es > http://davinci.crg.es/mailman/listinfo/geuvadis_rna_analysis

13 years, 4 months

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