Major Resources
Community Resources
Community resources are shared via this Daphnia Genomics Consortium (DGC) website.
Genomics Resources
Daphnia genome data can be explored and downloaded from wFleaBase: Waterflea Genome Database and the JGI Daphnia Genome Portal.
Bioinformatic Resources
Open-source web-portals for Daphnia pulex genome data, analysis results and bioinformatic tools.
Daphnia informatics |
URL address |
|---|---|
wFleaBase |
http://wFleaBase.org/ |
JGI Genome Portal |
http://www.jgi.doe.gov/Daphnia/ |
PASA Database |
http://wfleabase.org/genome/Daphnia_pulex/current/pasa/ |
ESTPiper |
http://cas-bioinfo.cas.unt.edu/estpiper/ |
Superfamily |
http://supfam.org/ |
Cado |
http://omics.informatics.indiana.edu/lab/CADO/precalculated/DpulInterPro/ |
OrthoDB |
http://cegg.unige.ch/orthodb |
miROrtho |
http://cegg.unige.ch/mirortho/ |
DGC Web Portal |
http://daphnia.cgb.indiana.edu/ |
Scaffold Dotplot |
http://cancer.informatics.indiana.edu/cgi-bin/jeochoi/daphnia/tandemduplicategene/index.cgi |
MGEScan-LTR |
http://darwin.informatics.indiana.edu/cgi-bin/evolution/daphnia_ltr.pl/ |
DGC Wiki Portal |
https://wiki.cgb.indiana.edu/display/DGC/Home |
NIH Model Organisms |
http://www.nih.gov/science/models/ |
NCBI UniGene |
http://www.ncbi.nlm.nih.gov/UniGene/UGOrg.cgi?TAXID=6669/ |
euGenes Arthropods |
http://arthropods.eugenes.org/arthropods/ |
Companion papers for the genome sequence |
http://www.biomedcentral.com/series/Daphnia
. |
Contact: Don Gilbert
BAC & Fosmid Libraries
Clones from large insert genomic DNA libraries that were sequenced to produce version 1 of the Daphnia pulex draft genome sequence assembly are archived at the Hubbard Center for Genome Studies, University of New Hampshire.
Contact: W. Kelley Thomas
cDNA Libraries
Thirty seven cDNA libraries were created from animals challenged by ecological conditions to discover and annotate the transcribed genome. Over 200,000 arrayed cDNA clones are archived at The Center for Genomics and Bioinformatics, Indiana University.
Contact: John Colbourne
Microarrays
Four types of microarrays for Daphnia pulex have been produced at The Center for Genomics and Bioinformatics, Indiana University
Contact: John Colbourne
QTL Resources
Large genetic mapping panels are being produced and genotyped at University of Notre Dame for rapid placement of Quantitative Trait Loci on the genome.
Contact: Michael Pfrender
Other Resources
Other shared resources include protocols for Daphnia biology and genomic studies.
Contact : John Colbourne