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Platform GPL17407 Query DataSets for GPL17407
Status Public on Sep 27, 2013
Title OUHSC Neisseria gonorrhoeae 12K
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Neisseria gonorrhoeae FA 1090
Manufacturer CombiMatrix
Manufacture protocol The present studies were done using a custom 12K microarray designed by CombiMatrix Corporation (Mukilteo, WA). Probe lengths were 34-35 bp with each ORF having 4-5 probes; representing 1916 genes identified in the NCBI annotation of the N. gonorrhoeae FA1090 genome. Controls on the array included: no oligo and negative control-bacterial probes, factory probes, and three Arabidopsis thaliana genes as positive controls. Probes also were designed in intergenic regions to include both the sense and antisense strand. Experimental and control probe sets were distributed randomly across the microarray.
 
 
Submission date Jul 03, 2013
Last update date Sep 27, 2013
Contact name Lydgia Jackson
E-mail(s) lydgia-jackson@ouhsc.edu
Organization name OUHSC
Department Micorbiology and Immunology
Lab David Dyer
Street address 975 NE 10th Street
City Oklahoma City
State/province OK
ZIP/Postal code 73104
Country USA
 
Samples (18) GSM1180323, GSM1180324, GSM1180325, GSM1180326, GSM1180327, GSM1180328 
Series (1)
GSE48526 Control of RNA stability by NrrF, an iron-regulated small RNA in Neisseria gonorrhoeae.

Data table header descriptions
ID
ORF ORF Name
Probe Comment
GeneID

Data table
ID ORF Probe Comment GeneID
NGO0001 NGO0001 putative chromosomal replication protein (DnaA)\ Context:(NC_002946)+[159-1715]\ Notes:Best Blastp Hit: emb|CAB83845.1| (AL162753) putative chromosomal replication initiator protein [Neisseria meningitidis] COG0593 ATPase involved in DNA replication GeneID:3283049
NGO0002 NGO0002 DNA polymerase III subunit beta\ Context:(NC_002946)+[1795-2898]\ Notes:binds the polymerase to DNA and acts as a sliding clamp GeneID:3283050
NGO0003 NGO0003 polyphosphate kinase\ Context:(NC_002946)-[3047-5104]\ Notes:catalyzes the reversible transfer of the terminal phosphate of ATP to form a long chain polyphosphate GeneID:3283051
NGO0004 NGO0004 hypothetical protein\ Context:(NC_002946)-[5273-5716]\ Notes:Best Blastp Hit: pir||D81974 probable periplasmic protein NMA0556 [imported] - Neisseria meningitidis (group A strain Z2491) >gi|7379295|emb|CAB83849.1| (AL162753) putative periplasmic protein [Neisseria meningitidis] GeneID:3283052
NGO0006 NGO0006 leucyl-tRNA synthetase\ Context:(NC_002946)+[6500-9136]\ Notes:leucine--tRNA ligase; LeuRS; class-I aminoacyl-tRNA synthetase; charges leucine by linking carboxyl group to alpha-phosphate of ATP and then transfers aminoacyl-adenylate to its tRNA; due to the large number of codons that tRNA(Leu) recognizes; the leucyl-tRNA synthetase does not recognize the anticodon loop of the tRNA; but instead recognition is dependent on a conserved discriminator base A37 and a long arm; an editing domain hydrolyzes misformed products; in Methanothermobacter thermautotrophicus this enzyme associates with prolyl-tRNA synthetase GeneID:3283053
NGO0007 NGO0007 putative type II restriction endonuclease\ Context:(NC_002946)+[9365-10294]\ Notes:Best Blastp Hit: possibly phase variable - 8A residue homopolymer repeat in the coding sequence (ON) COG0338 Site-specific DNA methylase dam GeneID:3283054
NGO0008 NGO0008 putative modification methylase\ Context:(NC_002946)+[10394-11071]\ Notes:Best Blastp Hit: sp|P09358|MT22_STRPN modification methylase DpnII 2 (adenine-specific methyltransferase DpnII 2) (M.DPNII 2) >gi|6978344|gb|AAA88581.2| (M14339) DNA adenine methyltransferase [Streptococcus pneumoniae] COG0863 Adenine-specific DNA methylase GeneID:3283055
NGO0009 NGO0009 hypothetical protein\ Context:(NC_002946)+[11091-11546]\ Notes:Best Blastp Hit: sp|P54298|LUXM_VIBHA LUXM protein >gi|487037|pir||S37349 luxM protein - Vibrio harveyi >gi|295433|gb|AAC36807.1| (L13940) Lux M [Vibrio harveyi] GeneID:3283056
NGO0010 NGO0010 hypothetical protein\ Context:(NC_002946)-[12107-12307]\ Notes:Best Blastp Hit: gb|AAF42226.1| (AE002539) hypothetical protein [Neisseria meningitidis MC58] GeneID:3283057
NGO0011 NGO0011 hypothetical protein\ Context:(NC_002946)-[12417-12728]\ Notes:Best Blastp Hit: pir||B81975 probable DNA-binding protein NMA0564 [imported] - Neisseria meningitidis (group A strain Z2491) >gi|7379301|emb|CAB83856.1| (AL162753) putative DNA-binding protein [Neisseria meningitidis] GeneID:3283058
NGO0015 NGO0015 hypothetical protein\ Context:(NC_002946)+[13341-13625]\ Notes:Best Blastp Hit: emb|CAB83858.1| (AL162753) hypothetical protein NMA0567 [Neisseria meningitidis] GeneID:3283059
NGO0016 NGO0016 preprotein translocase subunit SecG\ Context:(NC_002946)-[14081-14431]\ Notes:SecG; Best Blastp Hit: pir||F81031 protein-export membrane protein SecG NMB1888 [imported] - Neisseria meningitidis (group B strain MD58; group A strain Z2491) >gi|7227147|gb|AAF42222.1| (AE002538) protein-export membrane protein SecG [Neisseria meningitidis MC58] >gi|7379305|emb|CAB83860.1| (AL162753) putative protein-export integral membrane protein [Neisseria meningitidis] GeneID:3283060
NGO0017 NGO0017 triosephosphate isomerase\ Context:(NC_002946)-[14438-15211]\ Notes:Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate GeneID:3283061
NGO0018 NGO0018 hypothetical protein\ Context:(NC_002946)+[15370-15897]\ Notes:Best Blastp Hit: pir||H81975 hypothetical protein NMA0571 [imported] - Neisseria meningitidis (group A strain Z2491) >gi|7379307|emb|CAB83862.1| (AL162753) hypothetical protein NMA0571 [Neisseria meningitidis] COG1956 GAF domain-containing proteins GeneID:3283062
NGO0019 NGO0019 putative protein-L-isoaspartate O-methyltransferase\ Context:(NC_002946)+[16000-16656]\ Notes:PimT; Best Blastp Hit: gb|AAF42219.1| (AE002538) protein-L-isoaspartate O-methyltransferase [Neisseria meningitidis MC58] GeneID:3283075
NGO0020 NGO0020 hypothetical protein\ Context:(NC_002946)+[16737-17060]\ Notes:Best Blastp Hit: emb|CAB83864.1| (AL162753) hypothetical protein NMA0573 [Neisseria meningitidis] GeneID:3283063
NGO0021 NGO0021 putative TonB-dependent receptor protein; iron related\ Context:(NC_002946)-[17323-19500]\ Notes:Best Blastp Hit: pir||D81976 probable ferric siderophore receptor protein NMA0575 [imported] - Neisseria meningitidis (group A strain Z2491) >gi|7379311|emb|CAB83866.1| (AL162753) putative ferric siderophore receptor protein [Neisseria meningitidis] COG1629 Outer membrane receptor proteins; mostly Fe GeneID:3283064
NGO0022 NGO0022 hypothetical protein\ Context:(NC_002946)-[19763-20086]\ Notes:Best Blastp Hit: pir||E81976 hypothetical protein NMA0576 [imported] - Neisseria meningitidis (group A strain Z2491) >gi|7379312|emb|CAB83867.1| (AL162753) hypothetical protein NMA0576 [Neisseria meningitidis] COG0662 Mannose-6-phosphate isomerase GeneID:3283065
NGO0023 NGO0023 putative ABC transporter; periplasmic binding protein;iron related\ Context:(NC_002946)-[20119-21090]\ Notes:Best Blastp Hit: gb|AAF42214.1| (AE002538) ABC transporter; periplasmic solute-binding protein; putative [Neisseria meningitidis MC58] COG0614 Ferrichrome-binding periplasmic proteins GeneID:3283066
NGO0024 NGO0024 hypothetical protein\ Context:(NC_002946)-[21087-21251]\ Notes: GeneID:3283067

Total number of rows: 1916

Table truncated, full table size 529 Kbytes.




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