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cGRASP

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

batch number
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.
von Schalburg KR, Rise ML, Cooper GA, Brown GD, Gibbs RA, Nelson CC, Davidson WS, Koop BF.
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.
Rise, ML., K. vonSchalburg, GD Brown, RH Devlin, MA Mawer, N Kuipers, M Busby, M Beetz-Sargent, R Alberto, AR Gibbs, P Hunt, R Shukin, JA Zeznik, C Nelson, SRM Jones, D Smailus, S. Jones, J Schein, M Marra, WS Davidson & BF Koop.
Genome Research. 2004 14:478-490.

Support

email: Dr. B.F. Koop
telephone:  250-472-4072

Other cGrasp Projects

Acknowledgments

Thank you to all participants

Funded by: Genome BC
Genome Canada
NSERC


Last update: August 14, 2009.