consortium for Genomic Research on All Salmon Project
Introduction
Salmonids are the most widely studied group of fish and in the last few years genomics technologies have begun to contribute to this rich biology. The first salmonid microarrays appeared in 2004 and since then several dozen studies have demonstrated the utility of genomic approaches. The widespread use of the Genomics Research on Atlantic Salmon Project (GRASP) 16K array and greatly expanded genome resources has led to the development of a 32K cDNA microarray (Feb 08) and a 22K 70mer oligo array (Sept 08). These arrays were designed to have the largest gene/transcript representation possible with lowest redundancy. Below we provide some of the procedures used in the development of arrays however individual labs may have to experiment to achieve optimal results. Some preliminary control experiments using oligo arrays show the effects of distance from the polyA tail, the effects of mismatches and cross-species hybridization specificity. At the bottom of this page are some useful papers.GRASP microarrays have been used in cross species applications for most salmonids (Salmoninae), whitefish (Coregoninae) and even rainbow smelt(Osmerus mordax). Features are based on Atlantic salmon and rainbow trout clones.
As a service to the scientific community, we have made the GRASP microarrays available on a not-for-profit basis. We ask for the cost of replacement and provide no warranties. Please read the "usage agreement" for details. We have distributed these arrays to many labs around the world and have contributed to many successful scientific studies. The Annotation files are provided for a list of transcripts on the arrays. Please note that annotation is conservative (less than 1e-08 to swissprot) and is based on EST assemblies containing the clone or oligo represented on the array.
For more details see von Schalburg et al 2005, Koop et al 2008.
Usage and Reimbursement
Usage Agreement -updated Jan 08
Reimbursement Details
Microarrays
cGRASP 32K (Salmonid) cDNA Companion Files
| GRASP array Release Date 02/08 | ||
| Methods: | Feature Identification <-- Read me first! | |
| Feature Selection | ||
| Help: | Coming soon. | |
| Annotation files: | Select the batch number corresponding to your array from the list below | |
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| arrayBatch Numbers: | |
| IB019 only | |
| IE007 - onwards |
cGRASP 44K Salmonid Oligo Array; Release Date: 11/09
| cGRASP Oligo Array - based on 500K ESTs Atlantic Salmon and 250K ESTs Oncorhynchus mykiss (Koop et. al, 2008) | ||
| Design Files and Ordering (eArray best viewed in Internet Explorer web browser): | Agilent eArray | |
| For availability or other questions, contact bkoop@uvic.ca | ||
| Annotation files: | ||
| 44K Salmonid GAL file (11/09) (updated very soon) | Download | |
| 44K Salmonid annotation file (08/11) (preliminary version: 0.2) | Download | |
| 44K Salmonid GEML1 file (02/10) | Download | |
| 44K Salmonid GEML2 file (02/10) | Download | |
Agilent 44K (Atlantic Salmon) Oligo Array; Release Date; ~06/08
| NonGRASP array - based on unknown number of ESTs and contig assembly date; estimated pre2008 GeneIndex Rel3.0 | ||
| Agilent DNA Microarrays Web Site | ||
| Annotation files: | ||
| Agilent 44K (Atlantic Salmon) GAL file | Download | GRASP Annotation file(08/09) | Download |
| Combined Annotation (GRASP & Agilent) |
Download | |
| Agilent annotation files obtained directly from Agilent | ||
Protocols
Genisphere Array 50 Protocol Revised version 5
Invitrogen Indirect cDNA Labeling System version 3
Tecan Hybridization Protocol
Publications
Key cGRASP 32k Array Paper
A salmonid EST genomic study: genes, duplications, phylogeny and microarrays. Koop et al., BMC Genomics 2008 Nov 17;9:545
Key GRASP 16k Array Paper
Fish and Chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray.
BMC Genomics. 2005 Sep 15;6(1):126 [Epub ahead of print]
Key 3.7k Array and EST paper
Development and application of a salmonid EST database and cDNA microarry: datamining and interspecific hybridization characteristics.
Genome Research. 2004 14:478-490.
Support
| email: | Dr. B.F. Koop |
| telephone: | 250-472-4072 |
Other cGrasp Projects
- SFU GRASP site, Physical and genetic maps, BAC ends
- EST Database Project
- EST BLAST Database
- Genome Sciences Centre Salmon Page
- Norwegian Salmon Genome Project
Acknowledgments
| Funded by: | Genome BC |
| Genome Canada | |
| NSERC |