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Platform GPL9307 Query DataSets for GPL9307
Status Public on Sep 09, 2010
Title CombiMatrix_Prokaryotic_4x2K_design 6809
Technology type in situ oligonucleotide
Distribution custom-commercial
Organisms Bacteria; Archaea
Manufacturer CombiMatrix Corporation
Manufacture protocol The custom oligonucleotide microarray is synthesized on a semiconductor using an electrochemical synthesis process. Each oligonucleotide probe (spot) is synthesized on a platinum electrode that is independently controlled by the synthesizer’s computer. Synthesis is based on established phosphoramidite chemistry and occurs at thousands of sites simultaneously according to a computer algorithm that activates only specified electrodes. Since physical photolithographic masks, mechanical micromirrors, or inkjet technologies are not involved in the process, all probes can be easily changed without extra time or cost.
The oligonucleotides are synthesized in a proprietary porous reaction layer that coats the surface of the semiconductor, and acts to covalently attach the oligonucleotide to the surface of the chip.
 
Description Prokaryotic (bacteria and archaea) microorganisms known to be present in aquatic and soil habitats of the Northern Hemisphere.
 
Submission date Sep 28, 2009
Last update date Sep 09, 2010
Contact name Maria Smit
E-mail(s) smitm@ebs.ogi.edu
Phone 425-923-6433
Organization name Oregon Health and Science University
Department Environmental and Biomolecular Systems
Lab Simon
Street address 20000 NW Walker Rd
City Beaverton
State/province OR
ZIP/Postal code 97006
Country USA
 
Samples (64) GSM456951, GSM456952, GSM456953, GSM456954, GSM456955, GSM456956 
Series (1)
GSE18303 Gene Expression in Prokaryotic Microbial Assemblages Across Salinity Gradients in the Columbia River Coastal Margin

Data table header descriptions
ID number of each unique feature
Probe # number of each unique probe (unique sequence)
ORGANISM organism name
Phylum organism taxonomic classification
IMG_Gene_Identifier unique gene object identifier from the Integrated Microbial Genomes (IMG) database from the DOE Joint Genome Institute (JGI) (http://img.jgi.doe.gov/cgi-bin/pub/main.cgi)
Name full annotation, containing gene name, microorganism name, genome accession number, gene accession number, and position of the probe within the gene
Function 'C', carbon fixation; 'N', nitrogen metabolism; 'HK', housekeeping gene; 'L', light perception
SEQUENCE probe sequence
Computer_ID unique computer-generated ID

Data table
ID Probe # ORGANISM Phylum IMG_Gene_Identifier Name Function SEQUENCE Computer_ID
1 1510 delta proteobacterium MLMS-1 Deltaproteobacteria 639154072 Iron-containing alcohol dehydrogenase [delta proteobacterium MLMS-1 unfinished sequence: NZ_AAQF01000025] (-)|639154072_1044_1078 HK TATTCCCAAAATCGCCGCCAATGTCTACGGGATCG a0f3c9b5bf4c9f9e83482038d4da2548
2 1591 Pelobacter carbinolicus DSM 2380 Deltaproteobacteria 637749630 nitrogen fixation protein nifU [Pelobacter carbinolicus DSM 2380: NC_007498] (-)|637749630_41_75 N ATCCTCGCAATGTTGGTGAAGTCGAAGATCCGGAC de1d0fd14ba8255a840ff05909137f5c
3 1851 Vibrio angustum S14 Gammaproteobacteria 639017687 nitrogen regulatory protein P-II (IMGterm) [Vibrio angustum S14 unfinished sequence: NZ_AAOJ01000005] (+)|639017687_63_98 N TGATGTCGGTGTAGAAGGTATGACAGTCTCGGAAGT 46b9610a7a5e14363bea362218ebcc28
4 2015 Opitutaceae bacterium TAV2 Verrucomicrobia 641182817 nitrogenase molybdenum-iron protein beta chain [Opitutaceae bacterium TAV2 unfinished sequence: NZ_ABEA01000244] (+)|641182817_1430_1464 N TCATCGACCAGATCACGAGCGCCCTCTTCGACAAG 318fed581f725bc62fc1f648471ea9af
5 96 Roseobacter denitrificans OCh 114 Alphaproteobacteria 639637445 assimilatory nitrate reductase (NADH) alpha subunit apoprotein (EC 1.7.1.1) (IMGterm) [Roseobacter denitrificans OCh 114: NC_008209] (-)strand|639637445_2425_2459 N GGTCGAAATACGTTGTTGGCTGCCGTTGAGAATGG 36c1c87e168c8175cd71ac86c9aac572
6 763 Methanosarcina acetivorans str. C2A EuArch 638178768 nitrogenase, subunit beta [Methanosarcina acetivorans str. C2A: AE010299] (+)strand|638178768_257_291 N AAGCTCTCGTCAACCTTACAACCGTATACCAGCCT 5fdfb8ba298c6f9c35d5e947fcc70170
7 206 Limnobacter sp. MED105 Betaproteobacteria 641169298 assimilatory nitrite reductase (NAD(P)H) small subunit (EC 1.7.1.4) (IMGterm) [Limnobacter sp. MED105, unfinished sequence: NZ_ABCT01000008] (+)strand|641169298_39_73 N AATGGAATGGATCAACATTTGCGCAGTGGAAGACA 79841e5434e8353786dc89580c97ad25
8 519 Nitrobacter sp. Nb-311A Alphaproteobacteria 638923405 nitrate reductase, beta subunit [Nitrobacter sp. Nb-311A, unfinished sequence: NZ_AAMY01000031] (-)strand|638923405_18_52 N GCGCAGAAGTCTCCCGGTTTTCCAGTTCGTGAAGA d7da5f0abc7569066a8262c9a25c642b
9 1498 Methylococcus capsulatus str. Bath Gammaproteobacteria 637170145 hydroxylamine oxydoreductase [Methylococcus capsulatus str. Bath: NC_002977] (-)|637170145_1001_1035 N CCACCTGTCAATACTGCCATTTCGAGTTCAACGGC 3f373f0353dee57365d6df6533384247
10 690 Methanococcus maripaludis C5 EuArch 640166164 Nitrogenase [Methanococcus maripaludis C5: NC_009135] (+)strand|640166164_964_999 N ACAGTGGCAATCTACGGTGACCCATCAATAACAGTA 4e26166e734289ba95837d76b4fd235b
11 1455 Psychrobacter sp. PRwf-1 Gammaproteobacteria 640598619 carbonic anhydrase [Psychrobacter sp. PRwf-1: NC_009524] (+)|640598619_301_335 C GATACCCGTTTGGTTGTGGTACTTGGCCATTCAAA 4dfb78d7054f7485b57ffbc2bd438498
12 956 Mycobacterium avium 104 Actinobacteria 639734663 respiratory nitrate reductase alpha subunit apoprotein (IMGterm) [Mycobacterium avium 104: NC_008595] (+)strand|639734663_3070_3104 N AACATCGAGAACCTCAAGCCGTTCCACACGCTGAC 141c587390e54badce2919e0bc271aac
13 757 Methanococcus maripaludis C5 EuArch 640165836 nitrogenase reductase related protein [Methanococcus maripaludis C5: NC_009135] (+)strand|640165836_32_67 N TCATGGATTATTTGGGCGGCAGACCTTTTGTCATGG 6cd669501692551bfaa131a54b3d8bb4
14 1710 Sagittula stellata E-37 Alphaproteobacteria 640644780 nitrogen regulation protein ntrY [Sagittula stellata E-37 unfinished sequence: NZ_AAYA01000010] (-)|640644780_1792_1826 N ATGATCGGGCAGGCCTTCACCAACCTGATCAAGAA 66122573b5d7f524205f3eebfe0902f7
15 972 Salinispora arenicola CNS-205 Actinobacteria 641269718 respiratory nitrate reductase alpha subunit apoprotein (IMGterm) [Salinispora arenicola CNS-205: NC_009953] (+)strand|641269718_3290_3324 N ACTCGATGTACCACGACAACGAATTGATGTTGGCG 45f875296ebea34a60e9f2c294b79d97
16 1857 Vibrio sp. MED222 Gammaproteobacteria 638942170 nitrogen regulatory protein P-II (IMGterm) [Vibrio sp. MED222 unfinished sequence: NZ_AAND01000038] (-)|638942170_53_87 N AAGCGCTCTCTGATGTGGGTATTGAAGGTATGACG ca160e5f46d69bafee746dfcecbfbe0f
17 725 Methanospirillum hungatei JF-1 EuArch 637896430 nitrogenase iron protein subunit NifH (EC 1.18.6.1) (IMGterm) [Methanospirillum hungatei JF-1: NC_007796] (-)strand|637896430_97_131 N ATGCAGATTGGGTGTGATCCGAAACGTGATAGTAC c82e069ccf92c530bdfcf682a90937e5
18 849 Beggiatoa sp. SS Gammaproteobacteria 641095191 periplasmic nitrate reductase subunit NapB (IMGterm) [Beggiatoa sp. SS, unfinished sequence: NZ_ABBY01000294] (-)strand|641095191_369_403 N TCAAGTCGATGCCCAGCCGCTGATAGATAACACCT 98b06a62175fc0a42e3355e795ddff1f
19 1502 Pelodictyon luteolum DSM 273 Chlorobi 637769702 hydroxylamine reductase [Pelodictyon luteolum DSM 273: NC_007512] (-)|637769702_686_720 N GCATCCTGATTTCGGGTCACGACCTCCGCGATATG 5563860506531a655b3cb49f13b90584
20 1478 Magnetospirillum magnetotacticum MS-1 Alphaproteobacteria 638371705 Carbonic anhydrases/acetyltransferases isoleucine patch superfamily [Magnetospirillum magnetotacticum MS-1 unfinished sequence: NZ_AAAP01003557] (+)|638371705_610_644 C CGCACCGCCTATTTCGCCCTGATGATCTTGCTGAT 6539b7d18d1821e25b0f43d9f0cf8ecc

Total number of rows: 2240

Table truncated, full table size 575 Kbytes.




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