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
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 this week if you don't
agree with using this kit - 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
Dear all,
I would like to ask your opinion on potential collaboration in the
future between the Geuvadis RNA sequencing project and the 1000 Genomes
Consortium.
There will be a 1000g project meeting in Montreal in mid-November that I
will attend - me and Manolis belong to the 1000g analysis group. In the
Phase 1 of the project there is now increasing interest to analyze
functional consequences of the discovered variants, also in the
regulatory context.
There's no doubt that the Geuvadis dataset will be hugely valuable in
annotating regulatory variation, which is of interest to many people.
The vast majority of the work will naturally happen within the Geuvadis
framework. However, the really unique property of our dataset is the
combination of genome and transcriptome sequence data, and in my opinion
the expertise that the 1000g people have in analyzing genome sequence
might help us to get the most out of our data, benefiting us all.
So, what would you think of exploring the possibilities for
collaboration? We suggest that I will let relevant people from the 1000g
consortium to know about Geuvadis, and discuss if there would be joint
interests - open the door a little bit, so to say. It goes without
saying all external collaborations would be conditional to full
acceptance by the partners and all due credit to the Geuvadis project.
Please let me know what you think by early October.
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
FYI, from Tuuli
-------- Original Message --------
Dear all,
I would like to ask your opinion on potential collaboration in the
future between the Geuvadis RNA sequencing project and the 1000 Genomes
Consortium.
There will be a 1000g project meeting in Montreal in mid-November that I
will attend - me and Manolis belong to the 1000g analysis group. In the
Phase 1 of the project there is now increasing interest to analyze
functional consequences of the discovered variants, also in the
regulatory context.
There's no doubt that the Geuvadis dataset will be hugely valuable in
annotating regulatory variation, which is of interest to many people.
The vast majority of the work will naturally happen within the Geuvadis
framework. However, the really unique property of our dataset is the
combination of genome and transcriptome sequence data, and in my opinion
the expertise that the 1000g people have in analyzing genome sequence
might help us to get the most out of our data, benefiting us all.
So, what would you think of exploring the possibilities for
collaboration? We suggest that I will let relevant people from the 1000g
consortium to know about Geuvadis, and discuss if there would be joint
interests - open the door a little bit, so to say. It goes without
saying all external collaborations would be conditional to full
acceptance by the partners and all due credit to the Geuvadis project.
Please let me know what you think by early October.
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<mailto:tuuli.lappalainen@unige.ch>
FYI, from Tuuli Lappalainen
-------- Original Message --------
Subject:
Geuvadis mRNAseq kit
Date:
Tue, 27 Sep 2011 10:29:00 +0200
From:
Tuuli Lappalainen <Tuuli.Lappalainen(a)unige.ch><mailto:Tuuli.Lappalainen@unige.ch>
To:
geuvadis_rnaseq(a)lists.crg.es<mailto:geuvadis_rnaseq@lists.crg.es> <geuvadis_rnaseq(a)lists.crg.es><mailto:geuvadis_rnaseq@lists.crg.es>
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 this week if you don't
agree with using this kit - 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<mailto:tuuli.lappalainen@unige.ch>