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Status
Public on Jun 15, 2009
Title
JCVI Synechococcus sp. WH 8102 19K v1.0
Technology type
mixed spotted oligonucleotide/cDNA
Distribution
non-commercial
Organism
Parasynechococcus marenigrum WH 8102 Manufacturer
J. Craig Venter Institute
Manufacture protocol
Primers were designed to yield 2142 PCR amplicons of approximately 800 base pairs, and 70-mer oligonucleotides were designed for another 389 genes that were less than 200 base pairs in length or could not be amplified by PCR. PCR amplicons and oligonucleotides were suspended in 50% DMSO and spotted onto Corning UltraGAPS slides using an Intelligent Automation Systems arrayer. Each gene is represented six times on the array. Negative controls include 50% DMSO / 50% DI water and air. A mixture of PCR amplicons, Arabidopsis spike-in controls, and Arabidopsis 70-mer oligonucleotides were used as positive controls. Slides were air dried for at least 30 minutes after printing. DNA was irreversibly cross-linked to the slides with 250 mJ/cm^2 UV energy by using a Stratagene Stratalinker. Slides were stored at room temperature in a dessicator.
Support
glass
Coating
aminosilane
Contributor(s)
Paulsen I , Palenik B , Phillippy K , Johnson DA Submission date
Oct 08, 2008
Last update date
Jun 15, 2009
Contact name
Ian Paulsen
E-mail(s)
ipaulsen@cbms.mq.edu.au Organization name
Macquarie University
Department
Department of Chemistry and Biomolecular Sciences
Street address
Macquarie University
City
Sydney
State/province
NSW
ZIP/Postal code
2109
Country
Australia
Samples (21)
GSM329374 , GSM329375 , GSM329387 , GSM329389 , GSM329391 , GSM329392
GSM329393 ,
GSM348485 ,
GSM348486 ,
GSM461228 ,
GSM461229 ,
GSM982627 ,
GSM982628 ,
GSM982629 ,
GSM982630 ,
GSM982631 ,
GSM982632 ,
GSM982633 ,
GSM982634 ,
GSM982635 ,
GSM982636 Series (4)
GSE13170 Microarray analysis of phosphate regulation in Synechococcus sp. WH8102
GSE13910 Gene expression response to copper toxicity between coastal and open ocean strains of marine Synechococcus
GSE18511 PtrA is required for coordinate regulation of gene expression during phosphate depletion in a marine Synechococcus
GSE39972 Ni Deprivation in Synechococcus WH8102
Data table header descriptions ID row feature coordinate within tiff image
column feature coordinate within tiff image
meta_row feature coordinate within tiff image
meta_column feature coordinate within tiff image
sub_row feature coordinate within tiff image
sub_column feature coordinate within tiff image
block feature coordinate within tiff image
feat_name feature name
ORF Open reading frame designator
SPOT_ID description gene product or control feature description
GENOME_ACC Genome accession number
SEQUENCE sequence of spotted 70mer oligonucleotide if applicable
Data table ID row column meta_row meta_column sub_row sub_column block feat_name ORF SPOT_ID description GENOME_ACC SEQUENCE 1
1
1
1
1
1
1
1
A12g14610a_219
positional_control
positional_control
NC_003071
TTGTCCTTACACACATTTTTCCTAATATTGTTTCGTATCGGTAGCTTTGCCATTGTTGATATATTTTTTT
2
1
2
1
1
1
2
1
or2725
SYNW1998 conserved hypothetical protein
NC_005070
3
1
3
1
1
1
3
1
or3438
SYNW1153 possible 33kD chaperonin, heat shock protein HSP33
NC_005070
4
1
4
1
1
1
4
1
or2115
SYNW0476 conserved hypothetical protein
NC_005070
ATTGCCCCCAGGCCTGCTGACGCACCCAGCAACGTCCACCCCGGCATTGGATCAATTGAAACGGTGGCAG
5
1
5
1
1
1
5
1
or0684
SYNW1862 cytochrome c oxidase subunit I
NC_005070
6
1
6
1
1
1
6
1
or1639
SYNW0754 conserved hypothetical
NC_005070
7
1
7
1
1
1
7
1
or2085
SYNW0522 hypothetical
NC_005070
GGGATTGCACCAACTGTCGCTGCAGCACCAGAGCAGAAGCCTGATCACCGTTGTTCCAGAACTGGGCAGC
8
1
8
1
1
1
8
1
or1462
SYNW0494 ATP synthase subunit alpha
NC_005070
9
1
9
1
1
1
9
1
or1539
SYNW0609 putative ribose 5-phosphate isomerase A
NC_005070
10
1
10
1
1
1
10
1
or3620
SYNW0894 conserved hypothetical
NC_005070
11
1
11
1
1
1
11
1
or0786
SYNW2027 putative bifunctional enzyme; pantothenate synthetase/cytidylate kinase
NC_005070
12
1
12
1
1
1
12
1
or0646
SYNW1798 putative iron ABC transporter
NC_005070
13
1
13
1
1
1
13
1
or3599
SYNW1383 conserved hypothetical
NC_005070
14
1
14
1
1
1
14
1
NULL
50% DMSO 50% DI water
50% DMSO 50% DI water
NULL
15
1
15
1
1
1
15
1
or1092
SYNW2501 putative chloride channel
NC_005070
16
1
16
1
1
1
16
1
or2200
SYNW0348 Staphylococcal nuclease homologue
NC_005070
17
1
17
1
1
1
17
1
A12g14610a_219
positional_control
positional_control
NC_003071
TTGTCCTTACACACATTTTTCCTAATATTGTTTCGTATCGGTAGCTTTGCCATTGTTGATATATTTTTTT
18
1
18
1
1
1
18
1
or2725
SYNW1998 conserved hypothetical protein
NC_005070
19
1
19
1
1
1
19
1
or3438
SYNW1153 possible 33kD chaperonin, heat shock protein HSP33
NC_005070
20
1
20
1
1
1
20
1
or2115
SYNW0476 conserved hypothetical protein
NC_005070
ATTGCCCCCAGGCCTGCTGACGCACCCAGCAACGTCCACCCCGGCATTGGATCAATTGAAACGGTGGCAG
19200 1765 Kbytes .Supplementary data files not provided
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