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Platform GPL6531 Query DataSets for GPL6531
Status Public on Mar 04, 2008
Title GBC_ FOAR03-S1-0002
Technology type spotted oligonucleotide
Distribution custom-commercial
Organism Arabidopsis thaliana
Manufacturer Opern Array-Ready Oligo Set v1, printed at the GenomeBC Gene Array Facility at The Prostate Centre, Vancouver BC, Canada
Manufacture protocol The Arabidopsis Genome Oligo Set Version 1.0 (Operon Biotechnologies, Huntsville, AL, USA) consists of 26090 70mer oligonucleotides (http://operon.com/arrays/oligosets_arabidopsis.php). As positive controls, we included oligos for twelve housekeeping genes (Operon). As negative controls, we synthesized four oligonucleotides specific for human genes with no similarity to any Arabidopsis gene and included twelve oligonucleotides with no similarity to any Arabidopsis gene (Operon). We used a PCR amplified green fluorescent protein (GFP) cDNA (Invitrogen, Carlsbad, CA, USA) as an orientation marker. Oligonucleotides were resuspended in 384 well flat bottom plates (Nunc, Rochester, NY, USA) to a concentration of 100 mM in 3 x SSC. Oligos were printed on MicroGrid II robots using Microspot 10k pins (Biorobotics, Huntington, UK) depositing approximately 0.5 nl (0.0075 pmole) of each oligo onto EZ rays aminosilane slides (Apogent Discoveries, Hudson, NH, USA). The pitch of the grid used for this library was 0.2 mm. Oligos were UV cross linked at 3000 x 100 μJ using a UV Stratalinker 2400 (Stratagene, La Jolla, CA, USA). We spotted single spots for the 26090 target oligonucleotides; in addition, each subgrid contained six replicate spots of each of the four human negative controls, three spots of equally distributed Operon negative controls, a single spot of each of the twelve house keeping controls, and GFP marker on each corner of the subgrid. The location of each oligo is given in this platform file.
 
 
Contributor(s) Ehlting J, Zeznik J, Ellis BE, Douglas C, Bohlmann J
Submission date Feb 26, 2008
Last update date Mar 04, 2008
Contact name Juergen Ehlting
E-mail(s) je@uvic.ca
Organization name University of British Columbia
Department Michael Smith Laboratories
Lab Bohlmann lab
Street address 321 - 2185 East Mall
City Vancouver
State/province BC
ZIP/Postal code V6T 1Z4
Country Canada
 
Samples (75) GSM268403, GSM269468, GSM269470, GSM269472, GSM269473, GSM269474 
Series (2)
GSE10681 Diamond Back Moth treatment
GSE62287 Transcriptional responses of Arabidopsis thaliana to chewing and sucking insect herbivores

Data table header descriptions
ID
OLIGO_ID identifies the oligo spotted. Non-control spots are identical to oligo ID’s from Operon
LOCUS Arabidopsis Genome Initiative locus identifier targeted by the oligo
DESCRIPTION TAIR Arabidopsis gene annotation
GB_ACC GeneBank accession used for oligo design
UNIGENE UniGene identifier
META_ROW pin head identifier, defines sub-grid row position
META_COLUMN pin head identifier, defines sub-grid column position
ROW defines the row position within a subgrid
COLUMN defines the column position within a subgrid
SPOT_ID spot identifier

Data table
ID OLIGO_ID LOCUS DESCRIPTION GB_ACC UNIGENE META_ROW META_COLUMN ROW COLUMN SPOT_ID
1 GFP_marker green fluorescence protein from Aequorea victoria, PCR product of cds spotted U17997 1 1 1 1 --CONTROL: GFP_marker
2 A025180_01 At5g41510 F-box family protein, contains Pfam:PF00646 F-box domain AB005233 8335 1 1 1 2
3 A025204_01 At5g52320 member of CYP96A AB019226 8905 1 1 1 3
4 A025138_01 At5g53090 oxidoreductase, putative, similar to forever young oxidoreductase (FEY3) GI:12004621 from (Arabidopsis thaliana) AB025622 7141 1 1 1 4
5 A025162_01 At3g27710 zinc finger protein-related, contains similarity to zinc finger proteins and Pfam domain, PF01485: IBR domain AB018114 8027 1 1 1 5
6 A025186_01 At5g43610 sucrose transporter-related / sucrose-proton symporter-related, similar to sucrose-proton symporter SUC1 (Arabidopsis thaliana) GI:407094, sucrose transporter (Arabidopsis thaliana) GI:12057172; contains Pfam profile PF00083: major facilitator superfamily AB016875 8618 1 1 1 6
7 A025210_01 At5g37410 hypothetical protein, contains Pfam PF04510: Family of unknown function (DUF577); common family comprised of At5g37410, At5g37400, At5g37920, At5g37460, At5g37650, At5g37470, At5g37420, At5g37430 AP000607 9051 1 1 1 7
8 A025512_01 At1g63360 disease resistance protein (CC-NBS-LRR class), putative, domain signature CC-NBS-LRR exists, suggestive of a disease resistance protein. AC008047 14995 1 1 1 8
9 A025536_01 At1g22000 F-box family protein, contains F-box domain Pfam:PF00646 AC069252 15607 1 1 1 9
10 A025560_01 At1g51820 leucine-rich repeat protein kinase, putative, similar to light repressible receptor protein kinase GI:1321686 from (Arabidopsis thaliana); contains leucine rich repeat (LRR) domains, Pfam:PF00560; contains protein kinase domain, Pfam:PF00069 AC015448 16057 1 1 1 10
11 A025584_01 At1g63330 At1g62590 pentatricopeptide (PPR) repeat-containing protein, contains Pfam profile PF01535: PPR repeat AC005698 16351 1 1 1 11
12 human_control_02_H002751_01 4803 Nerve growth factor, beta polypeptide X52599 2561 1 1 1 12 --CONTROL: human_control_02_H002751_01
13 A025518_01 none AC068602 15077 1 1 1 13
14 A025542_01 At1g29310 protein transport protein sec61, putative, similar to PfSec61 (Plasmodium falciparum) GI:3057044; contains Pfam profile PF00344: eubacterial secY protein AC021043 15797 1 1 1 14
15 A025566_01 At1g13460 serine/threonine protein phosphatase 2A (PP2A) regulatory subunit B', putative, similar to SWISS-PROT:Q28653 serine/threonine protein phosphatase 2A, 56 kDa regulatory subunit, delta isoform (PP2A, B subunit, B' delta isoform, PP2A, B subunit, B56 delta i AC011810 16128 1 1 1 15
16 A025590_01 none AC007534 16414 1 1 1 16
17 A025892_01 At3g54590 AB022782 Arabidopsis thaliana mRNA for hydroxyproline-rich glycoprotein, complete cds AB022782 22895 1 1 1 17
18 A025916_01 At1g02305 cathepsin B-like cysteine protease, putative, similar to cathepsin B-like cysteine proteinase (Nicotiana rustica) GI:609175; contains Pfam profile PF00112: Papain family cysteine protease AY039887 23486 1 1 1 18
19 A025940_01 At5g66690 UDP-glucoronosyl/UDP-glucosyl transferase family protein, contains Pfam profile: PF00201 UDP-glucoronosyl and UDP-glucosyl transferase AB018119 24024 1 1 1 19
20 A025964_01 At3g20130 member of CYP705A AP000383 24546 1 1 1 20

Total number of rows: 28800

Table truncated, full table size 4187 Kbytes.




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