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Poster Full Abstracts - Techniques and Functional Genomics
Poster board number is above title. The first author is the presenter
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interface to these data enables users to perform arbitrary and complex queries across the data either via a web or a programming interface. Queries and sets
of results can be saved for use in further queries or for feeding to analysis programs. A sophisticated list upload and analysis facility enables users to work
with many genes at a time. FlyMine loads data from over 30 different sources, including mRNA expression data from BDGP, interactions, pathways and
RNA_seq expression data from the modENCODE (www.modencode.org) project. We will describe the data and analysis available through FlyMine, with a
focus on new and soon-to-be available features. These include a Genomic Region Search, which allows users to search for features mapped to particular
genomic regions, new analysis widgets, in particular providing statistical enrichment analysis and interaction visualisation, new export formats and
developments to web services. In addition, FlyMine is entering an exciting new phase of development which allows users to easily view and query data from
other model organisms. An NHGRI-funded initiative to deploy the software FlyMine is built with (InterMine) at several major model organism databases
(MODs) is well under way with InterMine already up and running for SGD (yeast) and RGD (rat), with ZFIN (zebrafish), MGI (mouse) and WormBase
(worm) in development. Through this collaboration researchers will be able to see relevant information from another model organism without leaving
FlyMine and transfer a list of genes for further analysis. Further information and documentation can be found on the FlyMine website (www.flymine.org).
865A
The TRiP: The Transgenic RNAi Project at Harvard Medical School.
D. Yang-Zhou
1
, L. Holderbaum
1
, J. Ni
1,4
, L. Liu
1,4
, S. Kondo
1,5
, R. Tao
1
, L. Jiang
1
,
Y. Hu
1
, R. Sopko
1
, A. Miller
1
, S. Randklev
1
, M. Foos
1
, S. Ball
1
, B. McElvany
1
, I. Flockhart
1
, S. Mohr
1
, N. Perrimon
1,2
, L. Perkins
1,3
. 1) Dept. of Genetics,
HMS, Boston, MA; 2) HHMI; 3) MGH, Boston, MA; 4) Tsinghua, China; 5) DGRC, Japan.
The
Drosophila
Transgenic RNAi Project (TRiP) started in 2006. The initial goals of the TRiP, funded by NIH/NIGMS in 2008, were to improve
in vivo
transgenic RNAi methods and generate RNAi stocks for the community. We have optimized vectors, the VALIUM series, for introducing RNAi into the
genome. The first generation of vectors, VALIUM1 and VALIUM10 proved effective for transgenic RNAi (Ni et al., 2008. Nature Methods; Ni et al., 2009.
Genetics). The second generation of the TRiP vectors, VALIUM20 and VALIUM22, expresses short hairpins through the microRNA pathway. Data have
shown that small hairpin RNAs (shRNAs) are much better reagents than long double stranded RNAs (dsRNAs) as they are more effective in somatic tissues
and work in the male and female germlines (Ni et al., 2011; unpublished results). We have generated >6,000 fly stocks (including 3,000 shRNA stocks) that
are openly available from the BDSC. The TRiP reagents are extremely popular, as evidenced by the high volume of TRiP stocks requested from the BDSC
and the growing number of research citations. With NIH funding from our recent successful competing application, we will continue to generate shRNA
stocks. Our goal is to generate at least 1 fully validated, transgenic line for each fly gene. In addition, we are generating a digital “Red Book” for all the
RNAi lines generated at the TRiP. To create this community resource, we will perform a number of validation experiments, including qPCR, collect
community information on existing stocks, and make this information available and searchable online. The community is invited to review the list of
available TRiP stocks, and/or contribute to the RNAi "Red Book" on our website (http://www.flyrnai.org/TRiP-HOME.html). The TRiP is also accepting
nominations of any gene(s) of interest that are not yet available.
866B
Metabolomic characterization of
Sod1
null flies using Liquid Chromatography/Mass Spectrometry.
Jose M Knee, Thomas J.S. Merritt. Department of
Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada.
Mass spectrometry is a powerful and fast developing tool in metabolomics, providing researchers with a highly sensitive and accurate method for
quantification of a broad array of small molecule metabolites. The field is, however, still in its infancy and well-established methods and protocols are not
broadly available. We are developing such protocols for liquid chromatography/mass spectrometry (LC/MS) using oxidative stress and cytosolic superoxide
dismutase gene (
Sod1
) in
Drosophila melanogaster
as a model system. SOD1 is involved in reactive oxygen species scavenging and Sod1 mutants
accumulate both ROS and products of ROS damage. Our initial work is targeting these “known” metabolites to allow us to develop and optimize sample
preparation and chromatography protocols. Using known standards, fly homogenates, and spiked-homogenates, we are investigating different
homogenization buffers, filtering and sample clean-up techniques and chromatography formats including both C18 and Hydrophilic Interaction Liquid
Chromatography (HILIC). Subsequent work will use these protocols to expand our investigation to a broader, currently unknown, suite of metabolites. This
combination of targeted and discovery metabolomics is allowing us to develop methods and protocols while investigation both SOD1 function, oxidative
stress in general, and biological networks and their response to genetic alterations.