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Status
Public on Nov 10, 2005
Title
Rhodopseudomonas palustris whole genome microarray
Technology type
spotted DNA/cDNA
Distribution
non-commercial
Organism
Rhodopseudomonas palustris Manufacturer
Environmental Sciences Division, Oak Ridge National Laboratory
Manufacture protocol
PCR primers for 4508 out of 4836 predicted ORFs of the Rhodopseudomonas palustris chromosome were designed using the PRIMEGENS software. Each gene was amplified 16 times in parallel 100 µl reactions in 96 well plates. All of the amplified products were pooled and purified using a Biomek F/X Automated Workstation (Beckman). All the amplified products were analyzed on 1.5% agarose gels, and were considered correct if the PCR reactions contained a single product of the expected size. Of the 4508 total predicted genes, 4350 ORFs were correctly amplified, which represents approximately 90% of the genome. Specific 50-mer oligonucleotide probes (385 ORFs) were synthesized for the genes that were not amplified. In total, the PCR amplicons and oligo probes represented 98% of the total predicted gene content of Rhodopseudomonas palustris. The purified PCR products were diluted in 50% DMSO to a minimum concentration of 50 ng/µl. Probes were then printed onto Corning UltraGAPS coated slides (Corning, Corning, NY) with a BioRobotics Microgrid II printer (Genomic Solutions, Ann Arbor, MI) as recommended by the manufacturer, and were UV cross-linked to the surfaces of slides (Statagene UV Crosslinker; Stratagene, La Jolla, CA). Each slide was printed with probes representing two copies of the genome.
Support
glass
Contributor(s)
Oda Y , Wu L , Liu X , Yan T , Zhou J , Harwood CS Submission date
Jul 28, 2005
Last update date
Nov 10, 2005
Contact name
Yasuhiro Oda
E-mail(s)
yasuhiro@uw.edu Organization name
University of Washington
Department
Department of Microbiology
Lab
Harwood
Street address
Box 357242, 1705 N.E. Pacific Street, HSB K-354
City
Seattle
State/province
WA
ZIP/Postal code
98195-7242
Country
USA
Samples (93)
GSM66690 , GSM66691 , GSM66692 , GSM66693 , GSM66694 , GSM66695
GSM66705 ,
GSM66707 ,
GSM66709 ,
GSM66711 ,
GSM66713 ,
GSM66715 ,
GSM66716 ,
GSM66717 ,
GSM66719 ,
GSM66721 ,
GSM66722 ,
GSM66724 ,
GSM66725 ,
GSM66726 ,
GSM66728 ,
GSM66729 ,
GSM66730 ,
GSM66731 ,
GSM66732 ,
GSM66733 ,
GSM66734 ,
GSM66738 ,
GSM66740 ,
GSM66741 ,
GSM66745 ,
GSM66746 ,
GSM66747 ,
GSM66749 ,
GSM66750 ,
GSM66751 ,
GSM66753 ,
GSM66755 ,
GSM66757 ,
GSM66759 ,
GSM66773 ,
GSM66775 ,
GSM66777 ,
GSM66778 ,
GSM66779 ,
GSM66780 ,
GSM66781 ,
GSM66783 ,
GSM66784 ,
GSM66786 ,
GSM98700 ,
GSM98701 ,
GSM98702 ,
GSM98703 ,
GSM98704 ,
GSM98705 ,
GSM98706 ,
GSM98707 ,
GSM98708 ,
GSM98709 ,
GSM98710 ,
GSM98711 ,
GSM98712 ,
GSM98713 ,
GSM98715 ,
GSM98716 ,
GSM155188 ,
GSM155199 ,
GSM155246 ,
GSM155247 ,
GSM155250 ,
GSM155258 ,
GSM155260 ,
GSM155261 ,
GSM155262 ,
GSM798761 ,
GSM798762 ,
GSM798763 ,
GSM798764 ,
GSM798765 ,
GSM798766 ,
GSM798767 ,
GSM798768 ,
GSM799898 ,
GSM799899 ,
GSM799900 ,
GSM800076 ,
GSM800316 ,
GSM800317 ,
GSM800318 ,
GSM800319 ,
GSM800320 ,
GSM800321 Series (4)
GSE3030 Functional genomic analysis of three nitrogenase isozymes in the photosynthetic bacterium Rhodopseudomonas palustris
GSE4320 Regulation of uptake hydrogenase and effects of hydrogen utilization on gene expression in Rhodopseudomonas palustris
GSE6742 FixK, a universal regulator of microaerobic growth, controls photosynthesis in Rhodopseudomonas palustris
GSE32292 How post-translational modification of nitrogenase is circumvented in Rhodopseudomonas palustris strains that produce hydrogen gas constitutively
Data table header descriptions ID
Array ID Rhodopseudomonas palustris microarray ID number
RPA Rhodopseudomonas palustris (RPA) gene ID number
ORF SPOT_ID Annotation Rhodopseudomonas palustris gene annotation
Data table ID Array ID RPA ORF SPOT_ID Annotation 1
or1526
RPA0797
RPA0797
uraI dihydroorotate dehydrogenase 883955:885049 forward MW:39178
2
or4470
RPA2455
RPA2455
CDS Peptidase M23/M37 2789329:2790699 reverse MW:49615
3
or4045
RPA3027
RPA3027
kup1 potassium uptake protein Kup 3427479:3429341 reverse MW:67621
4
or0390
RPA4062
RPA4062
CDS conserved hypothetical protein 4594774:4596105 forward MW:48441
5
or2984
RPA2605
RPA2605
queA S-adenosylmethionine tRNA ribosyltransferase 2962252:2963346 forward MW:39147
6
or7032
RPA3893
RPA3893
CDS putative carboxylesterase 4395182:4396705 reverse MW:55018
7
or2925
RPA2538
RPA2538
CDS putative acyl-CoA carboxylase, beta chain 2877195:2878850 forward MW:59093
8
or2858
RPA2463
RPA2463
nifS1 putative cysteine desulfurase, nifS homolog 2801091:2802263 forward MW:40148
9
or6159
RPA0139
RPA0139
CDS methyl-accepting chemotaxis receptor/sensory transducer 157930:160131 reverse MW:77029
10
or2327
RPA1789
RPA1789
CDS putative branched-chain amino acid transport system substrate-binding protein 2004817:2005974 forward MW:40884
11
or4243
RPA2785
RPA2785
CDS possible flavodoxin oxidoreductase 3158421:3159758 reverse MW:48822
12
or5536
RPA0952
RPA0952
dxs 1-D-deoxyxylulose 5-phosphate synthase 1052203:1054128 reverse MW:68804
13
or0094
RPA3634
RPA3634
tal putative Transaldolase Phosphoglucose isomerase 4094709:4097633 forward MW:104202
14
or6426
RPA4644
RPA4644
cbbP phosphoribulokinase (phosphopentokinase) (PRK) 5228833:5229708 reverse MW:33245
15
or0184
RPA3760
RPA3760
hpcC 5-carboxy-2-hydroxymuconate semialdehyde dehydrogenase 4255103:4256644 forward MW:54556
16
or2319
RPA1782
RPA1782
CDS TrapT family, dctP subunit, C4-dicarboxylate periplasmic binding protein 1997376:1998386 forward MW:37078
17
or2126
RPA1536
RPA1536
ppsR2 transcriptional regulator PpsR2; Fis family 1703829:1705223 forward MW:50792
18
or1160
RPA0271
RPA0271
tesB acyl-CoA thioesterase II 299186:300061 forward MW:33221
19
or1017
RPA0072
RPA0072
folC putative folylpolyglutamate synthase / dihydrofolate synthase 77980:79308 forward MW:47349
20
or2478
RPA1975
RPA1975
CDS periplasmic mannitol-binding protein, SmoM; possible Trap-T transport system, dctP subunit 2224485:2225576 forward MW:40120
11520 1010 Kbytes .Supplementary data files not provided
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