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Platform GPL8090 Query DataSets for GPL8090
Status Public on May 31, 2009
Title PBI-NRC_Brassica 10K V1.0
Technology type spotted DNA/cDNA
Distribution non-commercial
Organism Brassica napus
Manufacturer Biotechnology Research Institute, National Research Council Canada
Manufacture protocol Protocol for cDNA array fabrication
1) Amplify the insertions with a GeneAmp PCR System 9700 (Applied Biosystems, ABI) using AmpliTaq (ABI);
2) Purify the PCR products using the Biomek FX (Bechman/Coulter) and check the quality through agrose gel electrophoresis;
3) Amplicons were consolidated into 384-well plates, lyophilized, and resuspended in 10 µl of 50% DMSO to a final concentration of 250 ng/µl.
4) The Stratagene SpotReport Alien cDNA Array Validation kit and an in-house Candida albicans ECE1 gene (L17087) were ready in a dilution series. The buffer/blank control was 50% DMSO;
5) Printing the microarray on Corning UltraGAPSTM slides using the VersArray ChipwriterTM Pro microarray printer (Bio-Rad). SMP3 Microspot quill pins (TeleChem) in a 48-pin tool to deposit ~7 nL per spot onto the slide;
Support glass
Coating unknown
 
Description A set of 10,642 PCR primer pairs were designed and corresponding amplicons were produced for preparation of a targeted seed cDNA microarray. cDNA amplicons were printed on Corning UltraGAPS slides with the Chipwriter Pro microarray printer (Bio-Rad). The microarray consists of 12 row × 4 column sub-arrays, and each sub-array has 23 row × 22 column (506) spots. Spots were printed in duplicate side-by-side by columns, and the total number of spots on the microarray is 24288, of which 22,656 spots are cDNA probes. Controls are printed at the beginning and the end of each sub-array. The distance between spot is 185 µm and the spot diameter is 145 µm.
 
Web link http://www.brassicagenomics.ca/
Contributor(s) Xiang D, Datla R, Li F, Cutler A, Malik MR, Krochko JE, Sharma N, Fobert P, Georges F, Selvaraj G, Tsang E, Klassen D, Koh C, Deneault J, Nantel A, Nowak J, Keller W, Bekkaoui F
Citation(s) 18356959
Submission date Jan 18, 2009
Last update date May 31, 2009
Contact name Jitao Zou
E-mail(s) jitao.zou@nrc-cnrc.gc.ca
Phone 1-306-975-5583
URL http://pbi-ibp.nrc-cnrc.gc.ca/ENGLISH/research-officers/zou-j.htm
Organization name Plant Biotechnology Institute, National Research Council Canada
Lab Lipid Biotechnology
Street address 110 Gymnasium Place
City Saskatoon
State/province Saskatchewan
ZIP/Postal code S7N 0W9
Country Canada
 
Samples (24) GSM368747, GSM368748, GSM368749, GSM368750, GSM368751, GSM368752 
Series (1)
GSE14766 Probing the endosperm gene expression landscape in Brassica napus

Data table header descriptions
ID
Note Indicates if probe is cDNA or control
Fiesta ID cDNA ID in the FIESTA database developed at the Plant Biotechnology Institute, National Research Council Canada
GB_ACC Brassica napus GenBank accession
Synonym Locus ID for related Arabidopsis thaliana sequence
Synonym Explanation Specific explanation for Synonym
Description Annotation
Description explanation Specific explanation for Description
GO GO ID
Go explanation Specific explanation for GO
SPOT_ID

Data table
ID Note Fiesta ID GB_ACC Synonym Synonym Explanation Description Description explanation GO Go explanation SPOT_ID
10FGYSUA_UP_001_A03_16OCT2003_031 cDNA 601765 CN728676 AT2G17390;AT4G35450 AKR2 (ANKYRIN REPEAT-CONT...;ankyrin repeat family pro... GO:0005515;GO:0030528;GO:0009507
10FGYSUA_UP_001_A04_16OCT2003_032 cDNA 601564 CN728677 AT1G64850 calcium-binding EF hand f... GO:0005575;GO:0005509;GO:0008150
10FGYSUA_UP_001_A05_16OCT2003_047 cDNA 602388 CN728678 AT3G16250 ferredoxin-related GO:0009055;GO:0006118;GO:0009507
10FGYSUA_UP_001_A06_16OCT2003_048 cDNA 602043 CN728679 AT1G44770 unknown protein GO:0005575;GO:0003674;GO:0008150
10FGYSUA_UP_001_A08_16OCT2003_064 cDNA 601626 CN728680 AT5G07020 proline-rich family prote... GO:0003674;GO:0009535;GO:0008150
10FGYSUA_UP_001_A09_16OCT2003_079 cDNA 602269 CN728681 AT1G13260;AT1G68840;AT1G25560;AT3G25730 RAV2 (REGULATOR OF THE AT...;RAV1 (Related to ABI3/VP1...;AP2 domain-containing tra... GO:0003677;GO:0005634;GO:0006355;GO:0003700;GO:0009507
10FGYSUA_UP_001_A10_16OCT2003_080 cDNA 601593 CN728682 AT5G16840 RNA recognition motif (RR... GO:0008150;GO:0003676
10FGYSUA_UP_001_A12_16OCT2003_096 cDNA 601722 CN728684 AT1G06760;AT2G30620 histone H1, putative;histone H1.2 GO:0005634;GO:0003677;GO:0006334;GO:0000786
10FGYSUA_UP_001_B09_16OCT2003_077 cDNA 602523 CN728691 AT1G12090;AT1G62510;AT4G12500;AT4G12480 pEARLI 1; lipid binding;protease inhibitor/seed s...;ELP (EXTENSIN-LIKE PROTEI... GO:0050832;GO:0008289;GO:0012505;GO:0006869
10FGYSUA_UP_001_B10_16OCT2003_078 cDNA 602064 CN728692 AT2G37420 kinesin motor protein-rel... GO:0007018;GO:0005875;GO:0003777;GO:0009507
10FGYSUA_UP_001_C03_16OCT2003_027 cDNA 601868 CN728696 AT3G04600 tRNA synthetase class I (... GO:0005524;GO:0006436;GO:0005829;GO:0006418;GO:0004812
10FGYSUA_UP_001_C04_16OCT2003_028 cDNA 601602 CN728697 AT1G20010;AT1G75780;AT2G29550;AT4G20890;AT5G62690;AT5G23860;AT5G62700;AT5G44340;AT5G12250 TUB8 (tubulin beta-8);TUB2 (Tubulin beta-2); st...;TUB1 (tubulin beta-1 chai...;TUB4 (tubulin beta-4 chai...;TUB5 (tubulin beta-5 chai...;TUB9 (tubulin beta-9 chai...;TUB7 (tubulin beta-7 chai...;TUB3 (Tubulin beta-3); st...;TUB6 (BETA-6 TUBULIN) GO:0051258;GO:0007018;GO:0005874;GO:0043234;GO:0007017;GO:0005198
10FGYSUA_UP_001_C05_16OCT2003_043 cDNA 601898 CN728698 AT1G47128 cysteine proteinase (RD21... GO:0012505;GO:0009414;GO:0008234
10FGYSUA_UP_001_C08_16OCT2003_060 cDNA 602574 CN728701 AT4G15955;AT4G15960 epoxide hydrolase, putati...;catalytic/ hydrolase GO:0005575;GO:0016787;GO:0006725;GO:0004301;GO:0005739;GO:0003824
10FGYSUA_UP_001_C09_16OCT2003_075 cDNA 602203 CN728702 AT5G45950 GDSL-motif lipase/hydrola... GO:0012505;GO:0016789;GO:0006629
10FGYSUA_UP_001_C10_16OCT2003_076 cDNA 602234 CN728703 AT2G39220;AT3G54950 PLA IIIA/PLP7 (Patatin-li...;PLA IIB/PLP6 (Patatin-lik... GO:0045735;GO:0051707;GO:0006629
10FGYSUA_UP_001_C11_16OCT2003_091 cDNA 601832 CN728704 AT2G27920;AT2G27900 unknown protein;SCPL51; serine carboxypep... GO:0005575;GO:0003674;GO:0012505;GO:0004185;GO:0006508;GO:0005739;GO:0008150
10FGYSUA_UP_001_D01_16OCT2003_009 cDNA 601524 CN728706 AT2G17200;AT2G17190 ubiquitin family protein GO:0003674;GO:0006512
10FGYSUA_UP_001_D02_16OCT2003_010 cDNA 602290 CN728707 AT1G20620;AT1G20630;AT4G35090 CAT3 (CATALASE 3); catala...;CAT1 (CATALASE 1); catala...;CAT2 (CATALASE 2); catala... GO:0004096;GO:0005739
10FGYSUA_UP_001_D03_16OCT2003_025 cDNA 601871 CN728708 AT4G00940 Dof-type zinc finger doma... GO:0003677;GO:0005634;GO:0003700;GO:0045449

Total number of rows: 10642

Table truncated, full table size 1618 Kbytes.




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Supplementary file Size Download File type/resource
GPL8090.gal.gz 726.0 Kb (ftp)(http) GAL

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