Hi Thomas et al.

I’ll join. Petr is on holidays but has sent his comments on the topic list which I cc below.

Bw GJ

I would say the random design is preferred.

2. How long are the library prep / sequencer queue up times in the different labs (once you receive the RNA samples - how long do you think will it take you to analyze them?).
If some labs expect to have much larger delays, we could make arrangements that those labs get samples earlier than other labs.
This would also mean that we would all use the protocol that is used at the time point when the first lab starts to analyze samples.

3-4 months

3. Which other samples (other than the 500 1KGP European samples) should be analyzed by RNAseq?

Disease related samples for which we are also analyzing exomes, e.g. intestinal expression profiles for IBD

4. Specifications for the small RNA protocol.

We suggest 36 cycles single end sequencing aiming for at least 3 million reads per sample.

Prof dr GertJan B. van Ommen
Head, Department of Human Genetics
Center for Human and Clinical Genetics
Leiden University Medical Center
Director, Center For Medical Systems Biology
Visiting address: Building 2, Zone S-4-P, Room S04-046
Einthovenweg 20
P.O.Box 9600, 2300 RC Leiden NL
Tel +31-71-526 9401 / 9400
Fax +31-71-526 8285
Email gjvo@lumc.nl
Website: <http://www.humgen.nl>; <http://www.cmsb.nl>
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From: geuvadis_rnaseq-bounces@lists.crg.es [mailto:geuvadis_rnaseq-bounces@lists.crg.es] On Behalf Of Thomas Giger
Sent: vrijdag 6 mei 2011 10:38
To: geuvadis_rnaseq@lists.crg.es
Subject: [Geuvadis_rnaseq] Geuvadis RNAseq TC 11am - local Access numbers

Dear All,

please find attached to this message the local Access numbers for joining the TC at 11am.

cheers,

Thomas

Begin forwarded message:

From: Thomas Giger <Thomas.Giger@unige.ch>

Date: April 26, 2011 11:27:49 AM GMT+02:00

To: geuvadis_rnaseq@lists.crg.es, Manolis Dermitzakis <Emmanouil.Dermitzakis@unige.ch>

Subject: [Geuvadis_rnaseq] Geuvadis RNAseq TC details

Dear All,

thank you for having filled in the doodle.

The Geuvadis RNAseq phone conference will take place on May 6 from 11am - 12pm CEST.

To participate in this call you have to do the following:

- if you call in from Switzerland dial: +41 58 262 07 22

- otherwise from other countries please find enclosed the list with the "local access numbers for teleconferences" and dial the number corresponding to your country.

Then enter the PIN: 611683

In case you need assistance during the call - dial "OO" (nil nil) to get in touch with an operator.

I have written down the following points that should be discussed:

1. As of now we made plans that the different labs analyze samples from one particular population (as listed in the workflow document that I've sent around on April 7).
It would be a better experimental design if the samples were randomly distributed among the different labs. Since there is still time to react - do we want to switch the strategy?

2. How long are the library prep / sequencer queue up times in the different labs (once you receive the RNA samples - how long do you think will it take you to analyze them?).
If some labs expect to have much larger delays, we could make arrangements that those labs get samples earlier than other labs.
This would also mean that we would all use the protocol that is used at the time point when the first lab starts to analyze samples.

3. Which other samples (other than the 500 1KGP European samples) should be analyzed by RNAseq?

4. Specifications for the small RNA protocol.

If you already know now, that you would like to have additional things discussed - please let me know and I can make sure that we don't forget about.

Looking forward to talk to you soon,

Thomas