geuvadis_rnaseq February 2012

geuvadis_rnaseq@lists.crg.es

4 participants
5 discussions

[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

12 years, 7 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

12 years, 7 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

12 years, 7 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

12 years, 7 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

12 years, 7 months

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geuvadis_rnaseq February 2012