geuvadis_rnaseq

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97 discussions

[Geuvadis_rnaseq] Geuvadis miRNAseq update

by Tuuli Lappalainen

Dear all, This email contains further guidelines for miRNA seq. The partner labs should now *move forward with miRNAseq* as with mRNAseq, without further waiting for additional instructions. - the coverage is minimum 3M *total* production reads (from a good-quality experiment) - You should follow the protocol of the TruSeq Sm RNA Sample Prep kit with parameters that work in your lab. We are doing the optional ethanol precipitation step after the gel, but we don't require everyone to do this if all works well without it. - 36bp single-end sequencing, fragment size 145-160 bp - there was a typo in the guidelines: the Cluster generation kit will of course be TruSeq *SR* Cluster Kit v3, not PE - deadline for both miRNAseq and mRNAseq data is February 15 The updated sequencing guidelines document is enclosed. ** Don't hesitate to ask if you have any questions, and see you soon in Toulouse. 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 pilot data release

by Tuuli Lappalainen

Dear all, As you probably know, the Geuvadis pilot data (5 CEU individuals, RNAseq in 7 labs) is stored in EBI. The release date of these data is approaching, so we need to decide *whether we let the pilot data go public or ask for an extension*. Last spring it was decided that publishing a paper of the pilot data is not worth the effort, and at the moment the data has a release deadline at the end of this year. Our suggestion is that we release the data - what's your opinion on this? We can also ask for an extension e.g. until the main paper is out, but from our part we don't see any problem releasing the data now since we have no use for it. Philip and Matthias, would you need to keep e.g. the Solid data private because of the strand-specific project? I don't have access to the data submitted by the other labs, so EBI will be in touch with the owners of these data if any changes in the release date are needed. Have a nice weekend, 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 RNAseq - final guidelines and sample sheets

by Tuuli Lappalainen

Dear all, Here is the final version of the sequencing guidelines for the Geuvadis project, and the sample lists for mRNA and miRNA sequencing. Please download the sample sheet for your lab, and make sure that the guidelines are followed in your lab as closely as possible. The samples were shipped yesterday, and are either on the way or just arrived (except for Barcelona that will receive the samples next week). We decided to send the samples with their real IDs, instead of anonymous pseudo-IDs as was discussed on the call. Everything should now be in order to start mRNAseq - finally! With miRNAseq we will wait until Barcelona sees that these samples work well. We agreed that the deadline for sequencing is February 15th, and I will give instructions about data submission later. Please let me know if anything is unclear, and see you soon in Toulouse! 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 RNAseq analysis group

by Tuuli Lappalainen

Dear all, We now have a mailing list for the Geuvadis RNAseq Analysis Group:geuvadis_rna_analysis@lists.crg.es . You can join by emailing Gabrielle (gabrielle.bertier(a)crg.eu). Everyone who would like to participate in the RNAseq data analysis is invited to join - this will be a huge dataset with possibilities to analyze all kinds of cool things. It's important that we have many people with different areas of expertise contributing to the analysis, so that we can get as much as possible out of the data. PI's please see if there are members of your lab that are not on this RNAseq mailing list, but who could be involved the analysis group. The members of the analysis group will be listed in our wiki - please go and add your interests and areas of expertise in "Partners and contact info -> Analysis group" . I hope to meet many of you in Toulouse as well. 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 RNAseq Minutes

by Tuuli Lappalainen

Dear all, Enclosed are the Minutes of this afternoon's TC. Action items copypasted below. best regards, Tuuli *Action items* -*Tuuli* will take care of the RNA sample shipments (7/14 November) and inform the contact persons from each lab when the samples are shipped -*Esther* from Barcelona will email Tuuli further specifications of the miRNAseq protocol, including the minimum coverage per sample and how exactly that is defined -*Tuuli* will send the final version of the sequencing guidelines to all the labs by November 10 -*Gabrielle* will set up a mailing list for the analysis group -After the labs have received the samples, there is one major action item for *all partners*: sequencing! -- 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 sequencing guidelines draft

by Tuuli Lappalainen

Dear all, Enclosed please find a document that summarizes the sequencing guidelines for the Geuvadis RNAseq project. It is still a draft, and on tomorrow's TC we should discuss and agree on the remaining suggestions and open questions that are indicated in the document. 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] 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

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