cofactor genomics award of a Illumina run

Discussions of Grants and Awards in Genomics Education
cshaffer
Posts: 211
Joined: Sun Feb 04, 2007 10:29 pm
Location: Washington University in St Louis
Contact:

cofactor genomics award of a Illumina run

Postby cshaffer » Mon May 04, 2009 1:37 pm

Dear colleagues,
Cofactor Genomics is planning to donate a Illumina run to the undergraduate class/group who comes up with the best project - ~700Mb of new DNA sequence! Applications are due by the end of May. You can read all about if at http://www.cofactorgenomics.com/classroom.php . Should we put in a proposal? Your thoughts?
Cheers, Sally

PS One of the directors of Cofactor Genomics is a Bio 4342 alum, Ryan Richt – he’s the one with the spiky hair who shows up in some class pictures....completed both a BA and an MBA at Wash U while working at the Genome Sequencing Center.
Last edited by cshaffer on Wed May 06, 2009 3:24 pm, edited 1 time in total.

drevie
Posts: 67
Joined: Sun Feb 04, 2007 10:23 pm
Location: California Lutheran University, Thousand Oaks, CA

Postby drevie » Tue May 05, 2009 12:26 pm

I think a project for this would be great.

That amount of sequence is a huge overkill for a prokaryote (it would be almost 500X coverage for one that I have worked on). One possibility is another Drosophila or related insect, but it looks like there would be only about 3-4X coverage. 700 Mb of sequence seems better suited to a eukaryote with a smaller genome size.

Although the sequences can run 7 or 8 samples at once, it looks like they are offering one channel?

cshaffer
Posts: 211
Joined: Sun Feb 04, 2007 10:29 pm
Location: Washington University in St Louis
Contact:

posting message from Yuying Gosser

Postby cshaffer » Wed May 06, 2009 12:03 pm

Dear Dr. Elgin,

We would like to participate in this project. If you write
the proposal, please include the CCNY team.
Thank you.

Yuying

cshaffer
Posts: 211
Joined: Sun Feb 04, 2007 10:29 pm
Location: Washington University in St Louis
Contact:

posting message from Eric Spana

Postby cshaffer » Wed May 06, 2009 12:05 pm

Hi Sally-
My first thought is a Dmel cell line like S2, or Kc or some other--it may be underway from the modencode project though. A professor here at Duke (David MacAlpine) has some CGH data for cell lines that is pretty interesting. I can check with him to see if there is any sequencing on the horizon. The selective pressure on cells in culture could be pretty interesting.

eric

cshaffer
Posts: 211
Joined: Sun Feb 04, 2007 10:29 pm
Location: Washington University in St Louis
Contact:

message from Eric Spana

Postby cshaffer » Wed May 06, 2009 2:28 pm

Hi Sally-

I checked with David MacAlpine, and he's submitting a grant to sequence a bunch of Dmel cell lines, so that doesn't seem like an avenue worth pursuing for that company's grant.

Eric

cjones
Posts: 99
Joined: Sun Feb 04, 2007 10:19 pm
Location: Moravian College, Bethlehem PA
Contact:

Postby cjones » Wed May 13, 2009 12:51 am

How much depth of coverage should we aim for? If we can find a good organism, I think we should go for it, indubitably. It would be quite a feather in the group's cap, great for our students' sense of ownership, and a great proof of the ability of undergraduates to contribute independently to the research community.

Given Dennis's estimate of 3-4X coverage for Drosophila (which, lord knows, there's more than enough of being done right now), if we want 10X coverage that suggests a genome size of roughly 50MB. According to an online database of genome sizes <http://www.genomesize.com/> there aren't a whole lot of animals with genomes that small. (One more fortunate thing in the choice of Drosophila all those decades ago!)

Even the common planarian Dugesia tigrina has a genome apparently 20 times the size of D. melanogaster's!

I'd advocate for some pest species like gypsy moth or woolly adelgid, but these also have genome sizes larger than the fruit fly. Nasonia is already being done, but perhaps some other parasitic wasp?
Chris Jones
Assoc. Prof. of Biology
Moravian College
Bethlehem PA

cjones
Posts: 99
Joined: Sun Feb 04, 2007 10:19 pm
Location: Moravian College, Bethlehem PA
Contact:

Postby cjones » Wed Jun 17, 2009 2:40 pm

It appears that no one has sequenced firefly genomes. Definitely up there on the "cool" scale, and there are lots of other insect genomes out there to compare it with. No idea of genome size, though, so coverage could be pretty thin in the end -- but mightn't partial success argue well for additional funding to continue or complete the project?
Chris Jones

Assoc. Prof. of Biology

Moravian College

Bethlehem PA


Return to “Funding Opportunities”

Who is online

Users browsing this forum: No registered users and 1 guest