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
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
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
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
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
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
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
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
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
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