geuvadis_rnaseq

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97 discussions

[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

14 years, 1 month

[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

14 years, 1 month

[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

14 years, 1 month

[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

14 years, 2 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

14 years, 2 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

14 years, 2 months

[Geuvadis_rnaseq] Geuvadis mRNAseq kit

by Tuuli Lappalainen

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

14 years, 2 months

[Geuvadis_rnaseq] Geuvadis RNAseq and 1000 Genomes

by Tuuli Lappalainen

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

14 years, 2 months

[Geuvadis_rnaseq] Geuvadis RNAseq and 1000 Genomes

by Gabrielle Anne Bertier

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>

14 years, 2 months

[Geuvadis_rnaseq] Geuvadis mRNAseq kit

by Gabrielle Anne Bertier

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>

14 years, 2 months

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