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Platform GPL2716 Query DataSets for GPL2716
Status Public on Aug 05, 2005
Title GRASP 16K version 2
Technology type spotted DNA/cDNA
Distribution non-commercial
Organisms Osmerus mordax; Oncorhynchus mykiss; Salmo salar; Coregonus clupeaformis; Oncorhynchus tshawytscha
Manufacturer The Prostate Centre at Vancouver General Hospital, Gene Array Facility
Manufacture protocol Clones were robotically rearrayed from daughter glycerol stock 384-well plates into 96-well plates pre-filled with 7% glycerol in LB + ampicillin, incubated overnight at 37°C, and checked for uniform optical density. Plasmid inserts were PCR amplified in a Tetrad PTC-200 thermocycler (MJ Research) using 1 ul overnight culture, 0.2 mM M13/pUC forward primer (5'-CCCAGTCACGACGTTGTAAAACG-3'), 0.2 mM M13/pUC reverse primer (5'-AGCGGATAACAATTTCACACAGG-3'), 2 mM MgCl2, 10 mM Tris-HCl, 50 mM KCl, 250 mM dNTPs, 1U AmpliTaq (Perkin Elmer), and nuclease-free H2O (Gibco) to 100 ul. PCR conditions were: 2 min for 95°C; then 35 cycles of 95°C for 30 sec, 60°C for 45 sec, 72°C for 3 min; followed by 72°C for 7 min. Five ul of each PCR product were run on a 1% agarose gel to assess yield and quality. PCR products were robotically cleaned (Qiagen) and consolidated into 384-well plates, lyophilized by speed-Vac, and resuspended in 20 ul 3X SSC. Each purified PCR product concentration was determined and diluted to give a final concentration of 400ng/uL.
All cDNAs were printed as single spots on EZ Rays aminosilane slides (Matrix/Apogent Discoveries) with the Biorobotics Microgrid II microarray printer (Genomic Solutions). Microspot™ 10K quill pins (Biorobotics) in a 48 pin tool were used to deposit approximately 0.5 nl (0.2 ng cDNA) per spot onto the slide. The slides were crosslinked in a UV Stratalinker 2400 (Stratagene) at 300 mJ.
Support glass
Coating aminosilane
 
Description The microarrays have a 4-by-12 metagrid layout with 19 X19 spot subgrid, each spot having an approximate diameter and pitch of 100 um and 0.20 mm, respectively. A 280 bp GFP (green fluorescent protein) cDNA was amplified from a GFP clone (Clontech) using the primers (5'-GAAACATTCTTGGACACAAATTGG-3') and (5'-GCAGCTGTTACAAACTCAAGAAGG-3') and printed in each subgrid corner to assist in gridding. Six exogenous genome (Arabidopsis) cDNAs were amplified from the following clones kindly provided by The Arabidopsis Information Resource: rubisco activase [GenBank:T41667], protochlorophyllide reductase precursor [GenBank:R30630], chlorophyll a/b-binding protein CP29 [GenBank:N65746], PSII oxygen-evolving complex protein 2 [GenBank:H36167], tonoplast intrinsic protein root-specific RB7 [GenBank:AA067532] and ferredoxin (2Fe_2S) precursor [GenBank:W43249] and spotted in quadruplicate on each microarray. Also, a ubiquitin normalizer serially diluted (50 pg, 5 pg, 500 fg, 50 fg, 5 fg, 0.05 fg and 0.005 fg) was applied to the array. Spot morphology was assessed by visual inspection, SYBR® Green 1
(Molecular Probes) staining or hybridization with labeled non-specific probe.
 
Web link http://web.uvic.ca/cbr/grasp
Contributor(s) von Schalburg KR, Rise ML, Cooper GA, Brown GD, Gibbs RA, Leong J, Nelson CC, Zeznik J, Shukin B, Dangerfield B, Le Bihan S, Davidson WS, Koop BF, Wardroper A
Citation(s) 18282602
Submission date Aug 03, 2005
Last update date Apr 05, 2013
Contact name Ben F Koop
E-mail(s) bkoop@uvic.ca
Phone (250) 472-4067
Organization name The University of Victoria
Department Biology
Lab Centre for Biomedical Research
Street address PO Box 3020 STN CSC
City Victoria
State/province BC
ZIP/Postal code V8W 3N5
Country Canada
 
Samples (1235) GSM88265, GSM88266, GSM88267, GSM88268, GSM88269, GSM88270 
Series (33)
GSE3857 Atlantic Salmon Amoebic Gill Disease Study
GSE6416 Toxicogenomic responses in rainbow trout hepatocytes exposed to model chemicals and a synthetic mixture
GSE8309 Differences found in expression of cell surface & ECM components during development of the rainbow trout ovary & testis.
Relations
Alternative to GPL10770

Data table header descriptions
ID
GB_ACC GenBank accession number
SPOT_ID Concatenation of [meta row][ meta column][row][ column] from geneID file
ORGANISM Organism
SEQUENCE Sequence

Data table
ID GB_ACC SPOT_ID ORGANISM SEQUENCE
01010101 U17997 GFP
01010102 Blank Well
01010103 Blank Well
01010104 Blank Well
01010105 Blank Well
01010106 Blank Well
01010107 Blank Well
01010108 Blank Well
01010109 Blank Well
01010110 CA054869 Salmo salar ATATATTTATTCCCTTGGCAAGTCATTTTTAACTGTTGGGCACATTTTTTACTTGTTTGTGTGTGTGTGGTCTCCCACAGTATAAATGGTAAAAAGTCTATAAAAAAATGACTTCAAATGTCAAACGACATCTTCCAAGTGCTAATAGAGTACCTTCAACTGAGGGCCAATGCAGTCAAAAACGTGAATTACCTGTGTTTTAAATTTCCACACTATGAGGTTGGAATAATACTGTGAAATTATGATAATGTCCTTTACGTATAAGAGCAGTTTGAAAAGACCGTCTGAAATTTCAGCCTTTTTATGTAGGATGGAGTTTTGGGCTTCCATGGTGACATCACCATGTGGTAAATTAGTTAATAGACCAATAAGAAAGAGTTCCGAACCTCTCTGCCAATAACAGTTCATTTTCTGTTTTTGCCTAAAGCACTCTCAGACAGTCCTAGCAAATGTCTTGATTAAGAAATTGCTCTTTGATAAAAAAAGCTATTTGTTTCCTTTTCACTATTTTAATTGAAGTACCTTACTCTGTTTTCATTGTTACTCATAAATGATTTGATATTTAGATAAAAATGGCTGCATTGGTCCTTTAAATATCCTTCACAAACAGTGTCACACAAGAGACATATAGGCACAAACACAGAGTGCATCAAGGCATAAACACAGACCATGTAATACTCCCCTCCTGGTGTTGTGCAATTTGGACTGTGTTGTTAGTCTCTCTGATGACAGTGGTTGAACCATTTCGTTGCCCTATAC
01010111 CB490276 Oncorhynchus mykiss CTTGGCCCGAACAGACTGCTGGGTCTCAAGGCGCTGCAGATATCCATAGATATCCTTTATATATTCAGAGCACAGTTGTGGCAGGTCTGAATCCCCTTCATCAATGTCTTCTACAGCAAGCAGAGCTTCTGAGAACGCCTGGCACAATTCCTCTTCCTTCATGGACACGTTAGCATACACTTCAGGCTGAGGAACTTTAGGCCAAACAGCTGCGGGCTGGTCTTGTTGGTTCATAGATTGTTTGGTTGAGGCCTTGGCAGGAACGGTCTTCTTGAACGGCACCGCTTTGCAAGCATTGGGAAAGTTGGACAGCTCTCCAAGCACAGCCCTTCCTGCTCCAGCTACGTTTGCTTTTCCCATTAGTGTTGGGTTGTCTGCGTTCCTTAACGCAGAACCAACTTCTAATGACATCGTC
01010112 CA769480 Salmo salar GCTACAGCAGTAGGACACGTCCATATCGTAGTGACACAATATGCAAAGTGTGAAAAGGCTGCAATCAAGCACGTTCAAAATGGATAAAAATAACATTTTCAGAAACAATTTTTATGTTAAGGTAGAGTCGATGCACATGGCCACGGTAAAATTCACCTTGTCTGTTTCAACCATCCCCCCAAAAAGTTAAAGAAAAAATGTCATTTCAGAGCACTTTTGGTTAGCAAGTTTTGCAATGATTCAATCGTTCATTCATTGATTATAAGAAGTAATTTGTGATGATTTGTCAGTATATGCAGCTTGCAATGTGGTGGATCACCAGGTCCTGTAGCAGGACACAGGTGGAGATCAGCCCAGGTAGAGGAGGGTGATAGGGGAGAGAGGGGGGTTTGGAGAGTTAAGGGAGGCAGGGTCATAGCGGGAGTTGAAAGGTGGGGATAGAGATGGGGGACATGGGGAAGGGGGGGCTGATTTCGAGGCTTTGTCCTCATTTCTTCTTGGGTTTTGCTTCCAGAGGCAGTCCAATATCTTTCCCACGCAGCTTCAAACCGATTGCTCTCTCAATTTTGCCCATGACCTGATTGTTGGGAATTGCTTTTCCACACTCATAGTCTGCGATGACCTG
01010113 CA063502 Salmo salar AAGTAGGCAAGTGAATGGTCGAGGACAGGCAAAAGGTCAAAACCAGTTCAGAGTCCAGGAGGCACAGAGTGGCAGGCAGGCTTGAGGTCAAGGCAGGCAGAATGGTCAGGCAGGCGGGTACAGAGTCCAGAATAGGCAAGGGTCAAAACCGGGAGGATTAGAAAAAGGAGAATAGCAAAGGCAGGAGTACGGGAAAAAACGCTGGTTGACGTGGAACATACAACACGAACTGGCACAGAGAGACAGGAAACACAGGGATAAATACACTGGGGAAAACAAGCGACACCTGGAGGGGGTGGAGACAATAACAAGATCAGGTGAAACAGATCAGGGTGTGACACTGTATACAAATGTATTTTTAAAATATTTATTAGATCCCAGAACAGCAGTCTTGACATTGTAATTTGTGCTTACCTATGGCTAACCTTGTGGTTTGATCCCCGACCAAGTCATACCAAAGGCTTTAAAAATGAGACCTGATGCGTCTCTACTTGGCTCTCAGCATCAAGGAGATGCGCTAGACTTGTGTCCTGTCTAGAGGGTGTACTTGTAAATCATGCTGCTTTTCGCTACAGAAGCAGGAGATAGGCTCCTGCTTCTATGAGCCTTTCTGGCTTGTACAAGGTTACTTACTATGGCTTATTACAAACCTTCCATATACATACACTGTTATGTAAGAGCTGGCATAAACTGATTGATCTTCATGATCCCAAGTCTTAAAACAGTATTTTATGTTT
01010114 CB512130 Salmo salar CAAATACTATTTGTTTTCAAGGACAATTTTATGATTGAATAATATAATCTACGAGTTGAGTTGCAATGTAGTTTACTGGGTGTCATAACATCAATAAAAATAGTAATATTGTCCAAAGTTGCTCAACATTCTCCACTTATGATGACCCTCGAATCACACTCAAATATAGCCAAATACGTGTTATGAATAAAATACATTTAGCGTAACCTTCTTTGATCACAAGAAACACAGAATGGTGACAACCACTCAGTTCTAAAATACATGATTTTATGCCTTGCCTTTTTTGTTACAGACCAACTTAATATGCTAATGATAACAAGTGACTCAGAGCACGTGAGAAACATATTATACTGTATTAGTCCACTACATCAGGTCAAATTGGAATTATGAAGGGTAATAATGTCAAACTCCCAACACTGAACGGCAAAGACAGAAATGAAACATTACAATAACAATGTATTTGAAAAAAATCCTAACAGAAAAACAATAGTAAGATAAATGAAGGTGTGATATTCTACACATCATACAATACATATAGCCATTGAAAATTGTTTTGGCTGAAGTTGTAGAAAAGTAGATTACAAAAAAAAAAACCTTCCTTGAAAAAAATGTATAATTCCTCTTCCAAGTAAGAATACACACAATAGTAAATAAATGTAAATGGCTTGTTGGCCATCTGCCCAAACCTGAAGTCATACAGTTTGGTGGCATGACTA
01010115 CA044918 Salmo salar GAAAACCTCAGCATTCACTGTGGTGAGAAGATCACTATGGACCATGAGTTGATTTTCAATAAGATTGTGAGGAGCAATCGGGGGGGTTGGTGTTGTGAGAATAACCTCCTCTTTGCTTGGGTGCTAAAAGAGATGGGTTATAATCCAGTAACACTGGGTTCAAGAGTCTACAACAACACCATCAACCAGTTCGGCCCAAAAGACTCTCACCTCATCAACAAGGTAGTTATTGATGGGACTGCTTACATTGCAGATGTGAGCTTTGGGGCATCCTCCCAAATATGGTACCCTCTTGAGCTCGTCTCCGGGAAGGACCAGCCACAATCCCCTGGTGTCTTCCGTCTCATACAAGATGGAGACCTGTGGACCCTGGAGAAGACTGGTCGAAAGCCTCTGGTTCTCAATGAGGCCTTTACCAACTCACCTCTAGTAGACAAGAGCCCAACCAAGAAGATCTACGGCTTCACCCTGGTTCCCCGTGGGGTTGATAATTTCCTAGAGACTTCCCACTGCCTTCAGACAGATCCAAAGTCTCTATTCACCAACAAGTCCATCTGCTCACTGCAGACTGCTACAGGATTCAGAGCTCTAATTGGCTGGACCTTCAGTGAGGTCACCTACAACAACCAGGAGGGTTTTGATGTTTTGGATATGAAAGACATATCTGATGATGATGTTGATAAAGTGCTGAAGGAAATGTTTAATGTG
01010116 CB512117 Salmo salar ACTTTATTCAGGATGGAAAAAAAGTAGATTAAGTCAGTTAAGTAGCACTGCTCGGACTTCCAAAAAGCAACACCAGACATGTACTGTACATACAATCCAAGGAGCAGCCTTGTGTGGATGAAAACCGTTCACTGTGCTTCCTGTTTCTGGCACACATGAGAGACGAGACCATCTAAACAAAAGAAAGTGCCAAGGGGGGAAGAACATGGAATCACATTGGTACAAATAAGCCATGTAGTGAAGTTAAGGACTTTTCAAATGTACAGAAATTATTAATTAATTTAGAAAACAAATTACCTATGGTATTGATTATGGTTACAACTTGAACAAGGTCATTCTAGTCTAGTGTGATTTCAGAATGCTTGGATGAGCCATGGTTTAATTGAGTCCAATTAACCCACAATCTTGCTATCCAATGAGCCAGTGGCTCCCACTTCTCAGACTGGCTTACATGCCACATAATACAGCACCCCCAGGGTGGGTAAACAAAGGTTACATGGGGTTGGACTCACTGGAGTATAAGCGTGATCAGATGGGTTCATTAGATTAAAGATTACCATTGCCTTTGGCAGCATTCCCAAACCCAAGTCTAAAAGTACCCCTCATGATAACTGGACACCAATCCATCTCTGTTCATTTCCCTACAAACTGCAAAACAAAGGTGATGTCCAATAAGTGGTTAACATTCACCTTANAACAGACTCAGCATATGACGTTGCCACGAACAGAAAATATGCAACGCAAGATTACACTCCTCAAATGTANGCACATGTGCTCTTCATGCTGCTACAACATGATCACTGCTGGACAAA
01010117 CB505689 Salmo salar TTTTTAAGAGTCAACAAACTTTTATTGAAATAAATACAAAAGCAACAAATGAGAACGTGAGAAACTCAAAAGCAACAAATATCTGCAACATTTCTCATCTTTTTACATATGGTCTATTGTAGAAAAAAAACAATAGATTTCTCATTTGTGACAATAAAAATTATAGAACAAAATAGAAACACTATTCACATTTAACGGTTGTCAAAAACTACAAAACAAGCAAAGTGACCAAACCTAAAATTGGTATTAGAATGTCAAAGTTTGGTCTCAGAATCATCAATAGTGAAGTACACTCCATTTACTTTTTAAATAACAAATTATATATTAAAGCATGGGTTTTAAAGGAATGTGACAGTTCATTGACCAAGACTGTCTGAGTGTGGATCACAGGGCCAGATAATACACCATCTAGATTAATCCCATAAACCCCCCCCCCATTGGCACCATCCCAATAAACAAACAAGAGCAGAATACCTTTAACAATTATTTTTTTTAACACAATAACAGAATTGTACAATCTTATGCTTTAAAAAAACATGACCACATCACATTAGCTGATTTTAAATAAATTGACAGATCATTCCTAGAATTATAATTTCAGAGTACGCAACCAATCAATTCATATTTAGAGTCACTGCTAGAGCAGCTCAAGACATTGGCAGCAATTGACAATTAGTGTCTGTCAAATGGACGTACATACATTTGAAAAGTACTTAGAACATTTCATATATAAATATTGATTGTATAGTATTTGTCACATATAATTATCC
01010118 CA050278 Salmo salar GGTTTCCTTTATTTAATTGGGTTTTTATAACGTCAGATAATTGAATCAGCACAAGTACGGGCACCCAGGAATGACGGGGCACCCATGGGTAGCTGTGGCGCGACCACAACCCCACCAGCGGCCGTGAACCTGTTGGGAACAGCATACACAGCAGCATGGCACCAGAGTCACTCCAGACGGCACCAGACCCTCGGGGCCTGAGGACCAGAACCACAGGCTGCTGAACCTGCCATCTCCTCAGCCTGGGTCAGACTCGGACACTGGGTGGCATCTAGGAACAGGAGGAGCCCCCCTGCTCACTTACTGCTTCACTCACTGACACACACAGCAATGGAGGGAAACAGGAGTGGAGGTTCAGAGAAAGAAAGAGGGGATAATGGTGGGTTGGGTAAGATAAAAGAATCCCAGGGGTTGTACTGTGTTTATCAGTGATTCTCCCTCAAAGCGAAGACTTGTTTGCACACTTCAGTGTGTTCAAAACTGTGTGTTTATAAAAAGGTGTGTCCAGTATGATGTGCGTTGGATTTTTATGGAATGAGGCATGTATTATGATTATGATGTTATGTGAAAGTAAGTGTTACTGTGTTTGTGTGTGTGTGTGGAGGGGGCGGTGCTCATGGCTGTTTCCTGTGAGAGAATAGCAGGTCAGAGGTGAGAGGTCAGCGTCTA
01010119 U17997 GFP
01010201 CA053075 Salmo salar GTGAAATGATTGCGGTGACAAGTGATACAGTACTTATTCAAGGATGAAAAAAGACTGCGTAAAAGGTAGTTACTGAGAAACAGCATATGCTTTTTGTTTGAAGTACATTTAGAGCGATGCTACTGAAATATAGATTATACTTATACAGTAGCCATCTCAATTCAGAAGTCACGCCAAGGCCATTTGTGGTGACAGCTGCTCCAGTCTCTGAAGTGTGACACTATTCTAACAGGCCATTGAGCATGGTTTTCCTAATAAGGGACATAGTCAAGCATCAGAACTGTTTTGCCCAAGCTGTATACTACACATTTTCAAATCAAATACAGTAGAATTGTACAAAACATTCCATTAAACCAATGGCATGTTACAGCTTTAGACCAGGCACTTGCTTCTAGATAACATTGTTTCTCTCTCTCTCTCTCTCTCTCTTATGAATGCTATGGTCCAAAATTGGTACATTAATGACCTGGCACTTACTTTACATATACACATTCTATAACTCGGAAATGCAATGCTTTGTCAGTGATGATTAAAACAAAATCCCCATTACAAGTCTTAGTAGCAAACAAAATGTGTTATTTTTGGTTGACTATTCCGAGTCAGTAATAGACAAATCATATTCAGCAGTGTAAACTGTATGGTCATTACTGATCAACTGGGATTGGCATCTACAGTATACGGGCACATGGTGGAGTCAAAGACTAGCAGGAGTAATAGTAAGCAGAG

Total number of rows: 17328

Table truncated, full table size 10438 Kbytes.






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