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Notes for Group meeting 6 avril 2009
No loupe with camera available – only microscopes for mitoses in karyotyping over at the IFB building.
Point sur la myopie:
Jackie has 96 samples all ready, migrate DNA on gel for quality check. Patrick and Francois wanted a population overview for Maria Martinez made by Sylvain. Will see about it on his return from vacation tomorrow. Controls – Berangère has 8 since last week, one today. Presentation to interns as well.
New resident in ophthalmology has been requested by Patrick to participate 1d/week in collection of controls. Will also see Francois. Pierre-Julien. If could get 10/week would be nice.
Have paid for keratoconus? Not clear yet – MyEuropia is managed by INSERM. Out of 34K, there is 25K for “fonctionnement”
Faire le point pour les comptes avec Pauline – lesquels budgets et quelles dates limites? pour la prochaine fois.
Reusing analyses from myopia families with Weihua ? only if need further data after case-control studies, to use PDT or TDT to detect same loci (if available) that come out of the analysis. 40 controls so far available. Wellcome / Affymetrix controls available but pbs of stratification and perhaps Affy platform. Trying to replicate Sandrine’s data using MERLIN (DOS) and Genehunter (Unix).
If we did want the Wellcome Trust data need to apply for it now. But the controls according to Patrick are not very appropriate, and may well have mild myopia. Compare these two sets to our own controls, because maybe the Affy and Wellcome would be exploitable even if diluted by the 25% mildly myopic general population.
Wellcome is homogeneous and English population as opposed to the Affy data. Weihua will apply for access; Matthias has access to dbGAP already.
Keratoconus – Matthias says problem with dbGAP – password to retrieve genotypes is a general one for INSERM and can not create a specific project. How did Maria get the password? Matthias had requested it 6 months. I will call with Matthias tomorrow to get this sorted. None of the cleaned up data needed to be removed as the DNA was of good quality.
Comparative studies of KC and normal corneas. Two or three more coming in and then re-test pure elutions on Nano chips Agilent rather than the dilutions on the Pico chips which gave unsatisfactory RINs. Even if they remain unsatisfactory, Matthias will go to Genoscope to do the arrays anyhow.
Immunofluorescence with Anais on Steph’s project – lots of background staining still. Look over with Jackie.
Review with Nicolas on ChIP non-enrichment of qPCR amplicons is due to poor choice of amplicons. Patrick – check IP in cell lines that express lymphoblasts. Antibody problems? There are other antibodies available from a friend of Patricks. Possibly mix different antisera like siRNAs or like a meta-pAb.
Patrick wants to make sure to find consensus sequence in chromatin IP’d after sequencing.
--Heather 10:53, 6 April 2009 (EDT)