geuvadis_rnaseq

geuvadis_rnaseq@lists.crg.es

97 discussions

by Gabrielle Anne Bertier

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

12 years, 8 months

[Geuvadis_rnaseq] IMPORTANT: Geuvadis RNAseq cell line delivery info

by Tuuli Lappalainen

Dear all, I would need the Geuvadis RNAseq partner labs to *confirm their shipping address by December 21st *for delivery of the 500 cell lines from ECACC in mid-January. Also, make sure that you have *space in your freezers* for these samples. I will give ECACC the delivery info that was used for shipping the RNA samples, but I need you to confirm that the the information of your lab (below) is the one that should be used for this shipment. Apologies for the tight schedule here. If you need further information about the shipment, please be in touch with the ECACC logistics team: hpacultures(a)hpa.org.uk . They say that they know the customs etc. regulations of these kinds of shipments. You will of course be notified when the samples are on the way. Happy holidays to all of you, Tuuli *Shipping address list: * BARCELONA Esther Lizano Centre for Genomic Regulation (CRG) Genes and Disease Programme C/ Dr. Aiguader, 88 08003 Barcelona, Spain Tel. +34 933 160 233 esther.lizano(a)crg.es BERLIN Marc Sultan Max Planck Institute for Molecular Genetics Ihnestr. 63 - 73 D-14195 Berlin Germany +49 40 8413 1349 sultan(a)molgen.mpg.de KIEL Melanie Friskovec Universitätsklinikum Schleswig-Holstein, Campus Kiel Institut für Klinische Molekularbiologie Sequenzierung Arnold-Heller-Str. 14 24105 Kiel Tel.: +49-(0)431-597-1235 m.friskovec(a)ikmb.uni-kiel.de LEIDEN Dr. Peter A.C. 't Hoen Leiden University Medical Center Department of Human Genetics Postzone S4-P Einthovenweg 20 2333 ZC Leiden Phone number: +31715269421 P.A.C._t_Hoen(a)lumc.nl MUNICH PD Dr. Tim Strom Helmholtz Zentrum München Institut für Humangenetik Ingolstädter Landstraße 1 85764 Neuherberg Germany Tel.: +49 (0)89 3187 3296 TimStrom(a)helmholtz-muenchen.de UPPSALA Att: Ulrika Liljedahl UPPSALA UNIVERSITY, DEPT OF MED SCI (EORI: SE2021002932) ENTRANCE 70 3RD FLR RES DEPT 2 AKADEMISKA SJUKHUSET 751 85 UPPSALA SWEDEN Tel: +46 (0)18- 611 49 34 Ulrika.Liljedahl(a)medsci.uu.se -- 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, 9 months

[Geuvadis_rnaseq] Geuvadis RNAseq kit deliveries: update

by Tuuli Lappalainen

Dear all, Manolis has been in touch with Illumina regarding the problems of mRNA kit deliveries to the labs. They are doing their best to deliver the kits as soon as possible but can't promise when this will happen. This is really unfortunate, but let's wait still until the beginning of January. If the labs are still missing the kits then, we'll come up with a Plan B. *Please send me an update **before the Christmas holidays (by Dec 22) **whether you have received the mRNA and miRNA kits or not. * 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, 9 months

[Geuvadis_rnaseq] GEUVADIS mRNA

by Tim M Strom

There are currently 2 version 2 mRNA Kits: RS-122-2001 with 2*12 Indexes and FC-122-2001 with 2*6 Indexes. Illumina can corrently deliver FC-122-2001 but not RS-122-2001. I fact, we have FC-122-2001 available. Is it ok when we use FC-122-2001? Regards Tim -- Tim M. Strom, MD Tel: +49 89 3187 3296 Institute of Human Genetics Fax: +49 89 3187 3297 http://ihg.helmholtz-muenchen.de Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) Ingolstädter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir´in Bärbel Brumme-Bothe Geschäftsführer: Prof. Dr. Günther Wess und Dr. Nikolaus Blum Registergericht: Amtsgericht München HRB 6466 USt-IdNr: DE 129521671

12 years, 9 months

[Geuvadis_rnaseq] RNAseq Analysis Regular TCs

by Gabrielle Anne Bertier

Dear all, As suggested by Tuuli, we will set up a regular time for the Geuvadis RNAseq analysis group TCs, and try to have the first call before Christmas. Please fill in the doodle<http://www.doodle.com/bc2ewnuc4rtsu4u6> and mark whether the suggested times of the week are good for you in general (even if you can't participate on this particular week). Full doodle link: http://www.doodle.com/bc2ewnuc4rtsu4u6 On the agenda: - progress of sequencing, the kit issue - further specifications on sequencing protocols if needed - low-level analysis pipeline(s) to use: anyone who wants to do mapping-quantification-normalization of this dataset should send a brief summary of their methods to geuvadis_rna_analysis(a)lists.crg.es<mailto:geuvadis_rna_analysis@lists.crg.es?subject=Mapping-quantification-normalization%20method%20summary> before the call. So far are on the RNA_analysis list: (if you want to be added do the list please just send me an email) esther.lizano(a)crg.es gmicha(a)gmail.com mgut(a)pcb.ub.es olof.karlberg(a)medsci.uu.se P.A.C._t_Hoen(a)lumc.nl p.rosenstiel(a)mucosa.de roderic.guigo(a)crg.cat rodericguigo(a)gmail.com sultan(a)molgen.mpg.de Tuuli.Lappalainen(a)unige.ch Kind regards, Tuuli & Gabrielle

12 years, 9 months

[Geuvadis_rnaseq] GEUVADIS Action Points

by Gabrielle Anne Bertier

Dear all, You'll find attached a series of Action Points that stemmed out of our lively discussions during the Annual Meeting. Note that the slides of all presentations are accessible from our website intranet in the 'Documents - Annual Meeting 2011 Toulouse' section. Don't hesitate to contact me in case of any doubt, 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<mailto:gabrielle.bertier@crg.es> web: www.geuvadis.eu

12 years, 9 months

[Geuvadis_rnaseq] Kit delivery

by Marc Sultan

Dear Tuuli, dear all, I want to inform you, that we just got the information from Illumina that they are not able to meet the original ship date (05/12) of both the smallRNA and the mRNA TrueSeq kits due to a kit component that is on backorder. They can't commit to a new ship date yet! This will make it hard to have samples processed this year here. Best regards, Marc ------------------------------------------------------------------- Dr. Marc Sultan Dept. Vertebrate Genomics Max Planck Institute for Molecular Genetics Ihnestr. 63-73 14195 Berlin Germany Tel.+49308413-1349 Mob. +49 175 585 3465 Fax +49308413-1128 sultan(a)molgen.mpg.de

12 years, 9 months

[Geuvadis_rnaseq] Geuvadis RNAseq summary from Toulouse

by Tuuli Lappalainen

Dear all, Here's a brief summary of Geuvadis RNAseq discussions from Toulouse. It was very nice to meet most of the people who are contributing to the data production and analysis, lots of interesting discussions and ideas! The slides that I presented are attached. A couple of things from the discussions that I'd like to highlight: - Everyone who wants to do RNAseq data analysis should join the analysis group mailing list (geuvadis_rna_analysis(a)lists.crg.es) *now* by emailing Gabrielle (gabrielle.bertier(a)crg.eu). - Only Geneva and Barcelona have received the mRNA prep kits. Manolis is in touch with Illumina to speed things up. - The fastq files will be shared by the partners uploading them to the ftp site, and Natalja will then reposit everything to ENA. She will send instructions for the ftp upload. - The first mRNAseq results will be ready from Geneva very soon, and can be used for testing. - Most labs have pipelines for low-level data processing (mapping, quantification, etc). We can use a couple of different methods according to the needs of different analyses, but should avoid unnecessary redundancy. - The analysis group will have regular calls every 1 or 2 weeks, and the whole RNAseq group every 3 or 4 weeks. We'll schedule a call before Christmas. 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, 9 months

[Geuvadis_rnaseq] availability of TruSeq kit

by P.A.C._t_Hoen＠lumc.nl

Dear all We have ordered the TruSeq RNA Sample Prep Kit v2 already 2 months ago but it has not been delivered due to high demand / production problems. Are other people experiencing the same? We heard that it may come in before the end of the year but even that is not certain. Best wishes Peter Dr. Peter A.C. 't Hoen Center for Human and Clinical Genetics Leiden University Medical Center Postal zone S4-P PO Box 9600 2300 RC Leiden The Netherlands phone: +31-71-5269421 fax: +31-71-5268285 e-mail: p.a.c.hoen(a)lumc.nl

12 years, 9 months

[Geuvadis_rnaseq] GEUVADIS Annual Meeting final Guide and Interim Report

by Gabrielle Anne Bertier

Dear all, You'll find attached the final guide for the Annual Meeting, including the agenda and all useful information for attendees. I also attach the finalised Interim Report which was sent to our Scientific Advisory Board as well as to our EU project Officer. For any enquiry please don't hesitate to contact me, Looking forward to see you in Toulouse for those who'll be there, 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<mailto:gabrielle.bertier@crg.es> web: www.geuvadis.eu

12 years, 9 months

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