geuvadis_rnaseq October 2011

geuvadis_rnaseq@lists.crg.es

11 participants
11 discussions

[Geuvadis_rnaseq] Details Geuvadis RNAseq TC Thursday 3rd November

by Gabrielle Anne Bertier

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

12 years, 10 months

[Geuvadis_rnaseq] Geuvadis RNAseq TC Thursday 3rd November

by Gabrielle Anne Bertier

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

12 years, 10 months

[Geuvadis_rnaseq] Next Geuvadis RNAseq TC

by Gabrielle Anne Bertier

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

12 years, 10 months

[Geuvadis_rnaseq] important: contact information for RNA shipment

by Tuuli Lappalainen

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

12 years, 10 months

[Geuvadis_rnaseq] Geuvadis, comments on QC parameters wanted

by Mathias Brännvall

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

12 years, 10 months

[Geuvadis_rnaseq] RE : GEUVADIS Annual Meeting: Call for abstracts

by Gabrielle Anne Bertier

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

12 years, 11 months

[Geuvadis_rnaseq] smallRNA kit

by Esther Lizano

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

12 years, 11 months

[Geuvadis_rnaseq] Geuvadis RNA-seq meeting in Montreal

by Tuuli Lappalainen

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

12 years, 11 months

[Geuvadis_rnaseq] Geuvadis sample allocations

by Tuuli Lappalainen

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

12 years, 11 months

[Geuvadis_rnaseq] GEUVADIS Annual Meeting: Call for abstracts

by Gabrielle Anne Bertier

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

12 years, 11 months

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geuvadis_rnaseq October 2011