Dear all,
Please note that the TC will take place this Thursday 3rd November at 15.00. CET
Details for call-in :
Calling from Spain 902 125 136
Other countries +34 91 495 18 99
Participants' Pin-code: 764989*
Agenda:
> - go through practicalities of sequencing and fix a deadline for data submission
> - the Iberian cells from Coriell are now available - should we order them?
> - setup of the wiki and the analysis group
Kind regards,
Gabrielle
Dear all,
Please note that the TC will take place this Thursday 3rd November at 15.00. CET
Details for call-in will come asap.
Agenda:
> - go through practicalities of sequencing and fix a deadline for data submission
> - the Iberian cells from Coriell are now available - should we order them?
> - setup of the wiki and the analysis group
Best, Gabrielle
> -----Original Message-----
> From: Gabrielle Anne Bertier
> Sent: jueves, 27 de octubre de 2011 11:47
> To: 'geuvadis_rnaseq(a)lists.crg.es'
> Cc: 'geuvadis_wpl(a)lists.crg.es'
> Subject: Next Geuvadis RNAseq TC
>
> Dear all,
> At the request of Tuuli, please fill-in the doodle to schedule the next RNAseq TC:
> http://www.doodle.com/kf9raqz9wii6srft
>
> Agenda:
> - go through practicalities of sequencing and fix a deadline for data submission
> - the Iberian cells from Coriell are now available - should we order them?
> - setup of the wiki and the analysis group
>
> Kind regards,
> Gabrielle
>
>
> Gabrielle Bertier
> Scientific Project Manager
> International Collaboration Office
> CRG, Center for Genomic Regulation
> Carrer Dr. Aiguader, 88
> 08003 Barcelona, España
> Tel: +34933160374
> Mobile: +34639960656
> email: gabrielle.bertier(a)crg.es
> web: www.geuvadis.eu
>
>
>
--
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
Dear all,
At the request of Tuuli, please fill-in the doodle to schedule the next RNAseq TC:
http://www.doodle.com/kf9raqz9wii6srft
Agenda:
- go through practicalities of sequencing and fix a deadline for data submission
- the Iberian cells from Coriell are now available - should we order them?
- setup of the wiki and the analysis group
Kind regards,
Gabrielle
Gabrielle Bertier
Scientific Project Manager
International Collaboration Office
CRG, Center for Genomic Regulation
Carrer Dr. Aiguader, 88
08003 Barcelona, España
Tel: +34933160374
Mobile: +34639960656
email: gabrielle.bertier(a)crg.es
web: www.geuvadis.eu
Dear all,
We will be shipping the RNA samples in 2 weeks time, so you will be
receiving them during the week starting on November 7. In order to do
this, I will need you to *fill in the commercial invoice draft and send
it back to me **by November 1st**. *
In addition to the contact details of the person who'll be receiving the
samples and the shipping address, it is absolutely critical that you
make sure that the text is compatible with the customs regulations of
your country. Please check this with people from your department who
have experience of international shipping of biological samples.
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 Geuvadis partners,
I have here attached the draft for the survey of sequence data quality
control in WP2 (D2.2/T2.1) . It covers parameters that we (Uppsala) have
identified ourselves and now we would like to have input from all of you
to see if there are more things that should be included and/or if there
are questions that are not clear.
So, I kindly ask each partner to go through the survey and give any
feedback to me before *7 November*.
Please note that you don't have to answer /*all*/ the questions now,
just the questions: i) ; ii) and 44 since the survey will be
circulated at a later stage for D2.2.
This information is also in the survey so please feel free to send it to
the person in your organisation you see fit.
Thank you in advance and best regards
Mathias
--
_____________________________________________
Mathias Brännvall, PhD
Project coordinator
Dept. of Medical Sciences, sect. Molecular Medicine,
Uppsala University
phone:+46-18-6114934
e-mail: Mathias.Brannvall(a)medsci.uu.se
Dear all,
Here is the right link for the abstract submission:
https://docs.google.com/spreadsheet/viewform?formkey=dGlKMEtmVDFSenFwU2dKN2…
Thanks very much Terry for pointing this out, and sorry for the mistake.
Best,
Gabrielle.
________________________________________
De : Gabrielle Anne Bertier
Date d'envoi : vendredi 7 octobre 2011 13:10
À : geuvadis_partners(a)lists.crg.es
Cc : geuvadis_rnaseq(a)lists.crg.es; geuvadis_exome(a)lists.crg.es; geuvadis_wpl(a)lists.crg.es
Objet : GEUVADIS Annual Meeting: Call for abstracts
Dear all,
As the date for our first Annual Meeting is approaching, please find below important information regarding its organisation:
1. Registration: Please complete the registration form<https://docs.google.com/spreadsheet/viewform?formkey=dDFkdktiQ1Y0RzhCSkR0aG…> before next Monday October 10th.
2. Interim Report: As decided by the Management Committee, all PIs should prepare a very short scientific and financial report to be submitted to the SAB and the EU Officer. You'll receive a specific email with instructions.
3. Call for abstracts: The Management Committee has decided to open a call for abstracts<https://spreadsheets.google.com/spreadsheet/viewform?formkey=dDFkdktiQ1Y0Rz…> for the Meeting. This call is open to the whole GEUVADIS community. The 2 best abstracts will be selected for oral presentation on 28th November afternoon. The 5 next ones will be selected for posters presentation. Abstracts submission deadline: Sunday October 30th.
4. Presentations and posters:
a. All WPL should prepare a 20 mins presentation highlighting main results from the project.
b. All posters made quoting GEUVADIS should be brought to the Meeting.
5. Practical information: all the information is accessible on our intranet dedicated page. Please don't hesitate to let me know if you have troubles entering the intranet. Information on accommodation will be delivered next week, after the registration deadline
For any enquiry please let me know.
Kind regards,
Gabrielle
--> Registration form full link: https://docs.google.com/spreadsheet/viewform?formkey=dDFkdktiQ1Y0RzhCSkR0aG…
--> Abstract submission full link: https://spreadsheets.google.com/spreadsheet/viewform?formkey=dDFkdktiQ1Y0Rz…
Gabrielle Bertier
Scientific Project Manager
International Collaboration 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
Dear all,
For the small RNA sequencing of the Geuvadis samples, we suggest using the
latest Illumina sample prep kit for HiSeq: TruSeq Sm RNA Sample Prep.
Each kit is enough to prepare 24 small RNA libraries but there are four
different catalog numbers depending on how many different indexes you
want to use:
TruSeq Sm RNA Sample Prep (Indexes 1-12), Catalog#: RS-200-0012
TruSeq Sm RNA Sample Prep (Indexes 13-24), Catalog#: RS-200-0024
TruSeq Sm RNA Sample Prep (Indexes 25-36), Catalog#: RS-200-0036
TruSeq Sm RNA Sample Prep (Indexes 37-48), Catalog#: RS-200-0048
If you have any questions regarding the protocol, don't hesitate to
contact me.
Best regards,
Esther
Dear all,
Since many of us involved in the Geuvadis RNA-seq project will be
attending the ICHG in Montreal next week, Peter suggested that we could
meet there, especially since I've never met many of you. So, we'll be
having an informal lunchtime meeting on Thursday, and everyone is
welcome to join - let's meet on *Thu 13th at 12:40* at the meeting point
of the convention centre.
I hope to see you in Montreal!
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,
Mathias suggested that we could adjust the sample counts in different
labs to multiplies to 12, 24 or 48. Would that make the sample
processing easier in your lab?
Below are the sample allocations:
- the original allocation is what we have agreed on
- we also agreed that in addition to that, 5 samples would be
sequenced in every lab. However, there are 18 cell lines out of the
total 500 that we haven't been able to obtain/grow, so the second
column contains the counts adjusted by these numbers.
- the third column has the suggested adjustment to even numbers.
It would be a bit less sequencing for most of the labs, and a
bit more for Geneva.
Please let me know as soon as possible if you think we should adjust the
allocations. For most of the labs the numbers would change only little.
best regards,
Tuuli
original +duplicates -dropoffs adjusted
UNIGE 130 130 157
CRG 100 102 96
MPIMG 70 73 72
HMGU 50 53 48
UU 50 53 48
LUMC 50 53 48
ICMB 50 53 48
total 500 517 517
--
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,
As the date for our first Annual Meeting is approaching, please find below important information regarding its organisation:
1. Registration: Please complete the registration form<https://docs.google.com/spreadsheet/viewform?formkey=dDFkdktiQ1Y0RzhCSkR0aG…> before next Monday October 10th.
2. Interim Report: As decided by the Management Committee, all PIs should prepare a very short scientific and financial report to be submitted to the SAB and the EU Officer. You'll receive a specific email with instructions.
3. Call for abstracts: The Management Committee has decided to open a call for abstracts<https://spreadsheets.google.com/spreadsheet/viewform?formkey=dDFkdktiQ1Y0Rz…> for the Meeting. This call is open to the whole GEUVADIS community. The 2 best abstracts will be selected for oral presentation on 28th November afternoon. The 5 next ones will be selected for posters presentation. Abstracts submission deadline: Sunday October 30th.
4. Presentations and posters:
a. All WPL should prepare a 20 mins presentation highlighting main results from the project.
b. All posters made quoting GEUVADIS should be brought to the Meeting.
5. Practical information: all the information is accessible on our intranet dedicated page. Please don't hesitate to let me know if you have troubles entering the intranet. Information on accommodation will be delivered next week, after the registration deadline
For any enquiry please let me know.
Kind regards,
Gabrielle
--> Registration form full link: https://docs.google.com/spreadsheet/viewform?formkey=dDFkdktiQ1Y0RzhCSkR0aG…
--> Abstract submission full link: https://spreadsheets.google.com/spreadsheet/viewform?formkey=dDFkdktiQ1Y0Rz…
Gabrielle Bertier
Scientific Project Manager
International Collaboration 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