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Platform GPL11088 Query DataSets for GPL11088
Status Public on Oct 28, 2010
Title Synechocystis sp. strain PCC 6803 12K full genome array version 4
Technology type spotted DNA/cDNA
Distribution non-commercial
Organism Synechocystis sp. PCC 6803
Manufacturer Robert Burnap Oklahoma State University, Lou Sherman Purdue University
Manufacture protocol Construction and Preparation of Synechocystis Spotted Microarrays: 3168 genes or putative ORFs of Synechocystis sp. PCC6803 were PCR amplified in two stages. Primary amplification was achieved using gene-specific up-stream and down-stream primers modified with adaptamer sequences and genomic DNA template. Secondary amplification was achieved using adaptamer primers and individual primary PCR product templates. The quality of the PCR products was determined by agarose gel electrophoresis. The PCR products were purified using Millipore Multi-screen plates and resuspended in Micro Spotting buffer (TeleChem; Sunnyvale, CA) to a concentration of 500ng/ul. Each probe was then printed (spotted) in triplicate onto TeleChem SuperAmine substrates at room temperature and 50% relative humidity using a GeneMachines Omnigrid 100 (Genomic Solutions; Ann Arbor, MI) robot fitted with 4x4 TeleChem SMP4 pins. After printing, each slide was rehydrated by holding the slide with the array side down over a container of steaming water for 1 s and snap-dried on a warm hot plate. Printed slides were baked at 80°C for 1 h and then subjected to a UV-cross-linking at a dose of 1500 mJ cm2. Slides with immobilized probes were then stored in slide holders and placed in a desiccator at room temperature.
Support glass
Coating aminosilane
 
 
Submission date Oct 21, 2010
Last update date Oct 28, 2010
Contact name Tina Summerfield
E-mail(s) tina.summerfield@otago.ac.nz
Phone +64 3 4797578
Fax +64 3 479 7853
URL http://www.botany.otago.ac.nz/people/summerfield.html
Organization name University of Otago
Department Botany
Street address 464 Great King Street
City Dunedin
ZIP/Postal code 9014
Country New Zealand
 
Samples (12) GSM611733, GSM611952, GSM611953, GSM611954, GSM611955, GSM611956 
Series (1)
GSE24882 Gene expression under low O2 in Synechocystis sp. PCC 6803 wild type and hik31 mutant

Data table header descriptions
ID
Block spot block number
Row spot row number
Column spot column number
SPOT ID
GENE_SYMBOL name of the gene represented by the spot/feature
TOP_BLAST_HIT GenBank Top Blast Hit Accession Number
ORF
SPOT_ID spot identifier
CyanoBase Cyanobase Gene Information Link
LEFT left location of gene on chromosome
RIGHT Right location of gene on chromosome
LENGTH_AA Number of amino acids in protein
DIRECTION Direction of gene on chromosome (d=direct, c=complement)
KEGG KEGG Gene Information Link
PATHWAYS KEGG Pathways Link
EC KEGG EC Number Link
GENE_DESC description of the gene represented by the spot/feature
GO_MOL_FUNCTION Gene ontology consortium molecular function
GO_BIO_PROCESS Gene ontology consortium biological association
GO_CELL_COMPONENT Gene ontology consortium cellular component association

Data table
ID Block Row Column SPOT ID GENE_SYMBOL TOP_BLAST_HIT ORF SPOT_ID CyanoBase LEFT RIGHT LENGTH_AA DIRECTION KEGG PATHWAYS EC GENE_DESC GO_MOL_FUNCTION GO_BIO_PROCESS GO_CELL_COMPONENT
1 1 1 1 slr0335 apcE Q02907APCE_SYNY4 slr0335 slr0335 2292188 2294878 896 d slr0335 slr0335 phycobilisome core-membrane linker polypeptide Phycobilisome LCM core-membrane linker polypeptide|IEA|GO:0006118//Phycobilisome LCM core-membrane linker polypeptide|IEA|GO:0015979// Phycobilisome LCM core-membrane linker polypeptide|IEA|GO:0009503//Phycobilisome LCM core-membrane linker polypeptide|IEA|GO:0030089//
2 1 1 2 bad spot --bad spot
3 1 1 3 bad spot --bad spot
4 1 1 4 sll1124 plpA, hik3 ZP_00106627.1 sll1124 sll1124 862262 866377 1371 c sll1124 sll1124 2.7.3.- two-component sensor histidine kinase, phytochrome-like protein Sensory transduction histidine kinase|IEA|GO:0000155//Sensory transduction histidine kinase|IEA|GO:0004871//Sensory transduction histidine kinase|IEA|GO:0005524//Sensory transduction histidine kinase|IEA|GO:0008020//Sensory transduction histidine kinase|IEA|GO:0008020//Sensory transduction histidine kinase|IEA|GO:0016301//Sensory transduction histidine kinase|IEA|GO:0016301//Sensory transduction histidine kinase|IEA|GO:0016740// Sensory transduction histidine kinase|IEA|GO:0000160//Sensory transduction histidine kinase|IEA|GO:0006355//Sensory transduction histidine kinase|IEA|GO:0007165//Sensory transduction histidine kinase|IEA|GO:0007600//Sensory transduction histidine kinase|IEA|GO:0009585// Sensory transduction histidine kinase|IEA|GO:0016020//
5 1 1 5 slr2104 hik22 NP_616936.1 slr2104 slr2104 1572849 1575701 950 d slr2104 slr2104 2.7.3.- two-component hybrid sensor and regulator Sensory transduction histidine kinase|IEA|GO:0000155//Sensory transduction histidine kinase|IEA|GO:0000156//Sensory transduction histidine kinase|IEA|GO:0003677//Sensory transduction histidine kinase|IEA|GO:0004871//Sensory transduction histidine kinase|IEA|GO:0005524//Sensory transduction histidine kinase|IEA|GO:0016301//Sensory transduction histidine kinase|IEA|GO:0016301//Sensory transduction histidine kinase|IEA|GO:0016740// Sensory transduction histidine kinase|IEA|GO:0000160//Sensory transduction histidine kinase|IEA|GO:0006355//Sensory transduction histidine kinase|IEA|GO:0007165//Sensory transduction histidine kinase|IEA|GO:0007600// Sensory transduction histidine kinase|IEA|GO:0016020//
6 1 1 6 slr0152 NP_683094.1 slr0152 slr0152 2182063 2183958 631 d slr0152 slr0152 serine/threonine protein kinase Serine/threonine protein kinase|IEA|GO:0004672//Serine/threonine protein kinase|IEA|GO:0004674//Serine/threonine protein kinase|IEA|GO:0004674//Serine/threonine protein kinase|IEA|GO:0005524//Serine/threonine protein kinase|IEA|GO:0005524//Serine/threonine protein kinase|IEA|GO:0016740// Serine/threonine protein kinase|IEA|GO:0006468//
7 1 1 7 bad spot --bad spot
8 1 1 8 sll0199 petE 1JXDA sll0199 sll0199 2525827 2526207 126 c sll0199 sll0199 plastocyanin Plastocyanin precursor|IEA|GO:0005489//Plastocyanin precursor|IEA|GO:0005489//Plastocyanin precursor|IEA|GO:0005507//Plastocyanin precursor|IEA|GO:0005507// Plastocyanin precursor|IEA|GO:0006118//Plastocyanin precursor|IEA|GO:0006118//Plastocyanin precursor|IEA|GO:0006118//
9 1 1 9 sll1005 NP_484556.1 sll1005 sll1005 516088 516897 269 c sll1005 sll1005 MazG protein homolog
10 1 1 10 slr1214 NP_441708.1 slr1214 slr1214 901197 902315 372 d slr1214 slr1214 two-component response regulator PatA subfamily PATA protein|IEA|GO:0000156//PATA protein|IEA|GO:0003677// PATA protein|IEA|GO:0000160//PATA protein|IEA|GO:0006355//PATA protein|IEA|GO:0007600//
11 1 1 11 sll1229 hik41 NP_809971.1 sll1229 sll1229 1663554 1664690 378 c sll1229 sll1229 two-component hybrid sensor and regulator Regulatory components of sensory transduction system|IEA|GO:0000155//Regulatory components of sensory transduction system|IEA|GO:0000156//Regulatory components of sensory transduction system|IEA|GO:0003677//Regulatory components of sensory transduction system|IEA|GO:0005524//Regulatory components of sensory transduction system|IEA|GO:0016301//Regulatory components of sensory transduction system|IEA|GO:0016301//Regulatory components of sensory transduction system|IEA|GO:0016740// Regulatory components of sensory transduction system|IEA|GO:0000160//Regulatory components of sensory transduction system|IEA|GO:0006355//Regulatory components of sensory transduction system|IEA|GO:0007165//Regulatory components of sensory transduction system|IEA|GO:0007600// Regulatory components of sensory transduction system|IEA|GO:0016020//
12 1 1 12 sll0750 hik8, sasA ZP_00109603.1 sll0750 sll0750 2421536 2422687 383 c sll0750 sll0750 two-component sensor histidine kinase, KaiC-interacting protein, involved in circadian rhythm Sensory transduction histidine kinase|IEA|GO:0000155//Sensory transduction histidine kinase|IEA|GO:0005524//Sensory transduction histidine kinase|IEA|GO:0016301//Sensory transduction histidine kinase|IEA|GO:0016301//Sensory transduction histidine kinase|IEA|GO:0016740// Sensory transduction histidine kinase|IEA|GO:0007165//Sensory transduction histidine kinase|IEA|GO:0007600// Sensory transduction histidine kinase|IEA|GO:0016020//
13 1 1 13 bad spot --bad spot
14 1 1 14 sll1382 petF, fdx NP_486959.1 sll1382 sll1382 1831561 1831929 122 c sll1382 sll1382 ferredoxin, petF-like protein Ferredoxin|IEA|GO:0005489// Ferredoxin|IEA|GO:0006118//
15 1 1 15 slr1759 hik14 CAA65047.1 slr1759 slr1759 533086 537474 1462 d slr1759 slr1759 2.7.3.- two-component hybrid sensor and regulator Sensory transduction histidine kinase|IEA|GO:0000155//Sensory transduction histidine kinase|IEA|GO:0000156//Sensory transduction histidine kinase|IEA|GO:0003677//Sensory transduction histidine kinase|IEA|GO:0004871//Sensory transduction histidine kinase|IEA|GO:0005524//Sensory transduction histidine kinase|IEA|GO:0016301//Sensory transduction histidine kinase|IEA|GO:0016301//Sensory transduction histidine kinase|IEA|GO:0016740// Sensory transduction histidine kinase|IEA|GO:0000160//Sensory transduction histidine kinase|IEA|GO:0006355//Sensory transduction histidine kinase|IEA|GO:0007165//Sensory transduction histidine kinase|IEA|GO:0007600// Sensory transduction histidine kinase|IEA|GO:0016020//
16 1 1 16 bad spot --bad spot
17 1 2 1 slr1969 hik24 ZP_00073210.1 slr1969 slr1969 1777729 1779981 750 d slr1969 slr1969 two-component sensor histidine kinase Sensory transduction histidine kinase|IEA|GO:0000155//Sensory transduction histidine kinase|IEA|GO:0000156//Sensory transduction histidine kinase|IEA|GO:0003677//Sensory transduction histidine kinase|IEA|GO:0005524//Sensory transduction histidine kinase|IEA|GO:0008020//Sensory transduction histidine kinase|IEA|GO:0016301//Sensory transduction histidine kinase|IEA|GO:0016301//Sensory transduction histidine kinase|IEA|GO:0016740// Sensory transduction histidine kinase|IEA|GO:0000160//Sensory transduction histidine kinase|IEA|GO:0006355//Sensory transduction histidine kinase|IEA|GO:0007165//Sensory transduction histidine kinase|IEA|GO:0007600// Sensory transduction histidine kinase|IEA|GO:0016020//
18 1 2 2 slr0484 hik26 NP_484374.1 slr0484 slr0484 2618067 2620094 675 d slr0484 slr0484 two-component sensor histidine kinase Sensory transduction histidine kinase|IEA|GO:0000155//Sensory transduction histidine kinase|IEA|GO:0005524//Sensory transduction histidine kinase|IEA|GO:0016301//Sensory transduction histidine kinase|IEA|GO:0016301//Sensory transduction histidine kinase|IEA|GO:0016740// Sensory transduction histidine kinase|IEA|GO:0007165//Sensory transduction histidine kinase|IEA|GO:0007600// Sensory transduction histidine kinase|IEA|GO:0016020//
19 1 2 3 bad spot --bad spot
20 1 2 4 ssl0020 petF P00243FER_SYNY4 ssl0020 ssl0020 2484890 2485183 97 c ssl0020 ssl0020 ferredoxin I, essential for growth

Total number of rows: 12288

Table truncated, full table size 2611 Kbytes.




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