User:Etchevers/Notebook/Conference notes/2008/10/30

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Notes for discussion with Claude and Sophie

Recall that Mathieu and he have carried out array hybridization using two sorts of Affymetrix arrays - custom, with high density spotting in all potential ESTs and "known" transcripts in the three genomic areas associated with HSCR, but also with a wishlist of our favorite developmental genes, and on the U133 Plus 2.0 chips.

Three-way comparison of hNCC with microdissected adult enteric neurons and glia. Working from some known pathways, could not get him to be specific about which (this is not just coyness from me because of online consignation to my notebook). Hopes to get insight into cell differentiation and specificity of function. Rather vague.

Claude then launched into discussion of how Stan had made an oral commitment to pay for all the "global" gene chips and expects it to be covered by ANR / ERARE grants that included transcriptomics aspects to them. The bill from Curie amounts to 43000 euros. I said that I was under the impression that the work with Curie was collaborative. Claude countered that the collaboration consisted of getting the protocol for linear amplification right, and they shared the cost of materials equally. That otherwise, all the global chip stuff was a service run by Jean-Paul Thiery at the time heading Curie Transfert. I looked this up just now and see there is some justification for calling it "Curie Transfert". It does say, though, "Pour plus d'informations sur la réalisation d'un projet, d'un devis expérimental, merci de contacter David Gentien." And neither the group nor Stanislas certainly saw a quote before Claude signed his name to this commitment.

It wouldn't be an issue if Claude had not made the insinuation that he would hold any sort of publication of data from these chips hostage to getting them paid for, first. I sort of understand this reasoning - anyone he hopes to get money from certainly won't give it after publication. And he seems incapable of raising any sort of money on a future project that he could use to pay for them, either, despite making some noises on principle about how that is unethical in his view. So he's broke, and expects us all to chip in to bail him out because there was a general engagement to support the project.

This is bad news for Sophie, of course, to whom a "second or third author position" is already granted, generously, by Claude. In a few years, when something will actually come out of it. I pressed Claude numerous times during the talk to know any sort of genes we could assess either by qPCR or by HIS, but he was loath to give any whatsoever. Meanwhile, he is occupied in the short term by providing a list to Anna of candidate genes in the three genomic regions to sequence.

We then discussed briefly, if not constructively, what Sophie has done with the bit of data Claude did release to her, concerning the comparison between hNCC that had been immediately isolated (+8h) versus three to five weeks in vitro. She used the RankProd Bioconductor R package after Isabelle had applied GCRMA filtering across the board. Claude is hung up on filtering and estimates it necessary to apply a whole bunch of different filters. Then he asked if a LIMMA (Linear Models for Microarrays) file was available. Possibly, but to what end? We said the differences were minimal and likely to be integrated into another paper.

In addition, Claude would like us to refer any eventual "stagiaires" who would like to work with differential expression of gene networks, eg. magisteres a l'ENS. Overall, a useless meeting.

  • Heather 09:31, 3 November 2008 (EST):

The unilateral contract that Claude signed is discussed here, too.

  • Heather 06:07, 4 November 2008 (EST):