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Platform GPL4028 Query DataSets for GPL4028
Status Public on Jul 03, 2007
Title ORNL-ESD Geobacter metallireducens 70mer oligo-array
Technology type spotted oligonucleotide
Distribution non-commercial
Organism Geobacter metallireducens GS-15
Manufacturer Microbial Ecology and Functional Genomics Laboratory, Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN
Manufacture protocol All 70mer oligonucleotides were commercially synthesized without modification by MWG Biotech Inc. (High Point, NC). The concentration of oligonucleotides was adjusted to 100 pmol/µl. Oligonucleotide probes were prepared in 50% vol/vol DMSO (Sigma-Aldrich, St. Louis, MO) and spotted onto UltraGAPS glass slides (Corning Life Sciences, Corning, NY) using a BioRobotics Microgrid II microarrayer (Genomic Solutions, Ann Arbor, MI). Each oligonucleotide probe had two replicates on a single slide. After printing, the oligonucleotide probes were fixed onto the slides by UV cross-linking (600 mJ of energy) according to the protocol of the manufacturer of the UltraGAPS glass slides (Corning Life Science, Corning. NY).
Support glass
Coating aminosilane
 
Description In total, 4129 probes were designed based on an early version of the gene model (2003) and printed on the microarray, among which 3727 probes have 1 perfect match with one single ORF; 98 probes have more than 1 perfect matches with more than 1 ORFs; 261 probes have at least 1 perfect match with the genome, but not with an ORF; and 43 probes have no perfect match with the genome.
 
Web link http://img.jgi.doe.gov/cgi-bin/m/main.cgi?page=taxonDetail&taxon_oid=625610000
Contributor(s) He Q, He Z, Zhou J
Submission date Jul 21, 2006
Last update date Jul 03, 2007
Contact name Qiang He
E-mail(s) qianghe@utk.edu
Phone 865-974-6067
Fax 865-974-2669
Organization name The University of Tennessee
Department Civil and Environmental Engineering
Lab Environmental Biotechnology
Street address 57A Perkins Hall
City Knoxville
State/province TN
ZIP/Postal code 37996-2010
Country USA
 
Samples (12) GSM122727, GSM123332, GSM123333, GSM123455, GSM123456, GSM123457 
Series (1)
GSE5401 Aromatics Degradation in Geobacter metallireducens

Data table header descriptions
ID
Meta Row Meta_Row of a spot on the microarray grid
Meta Column Meta_Column of a spot on the microarray grid
Row Row of a spot on the microarray grid
Column Column of a spot on the microarray grid
Probe ID Unique identification of the oligonucleotide probe
SEQUENCE The sequence of the 70mer oligonucleotide probe
GENOME_MATCH_NO The number of sequences in the whole genome that have matches with a probe
ORF_MATCH_NO The number of ORFs in the whole genome that have matches with a probe
ORF ORF identification according to GeneBank
GENOME ACC The accession No. of the whole genome sequence
GENOME_ACC GenBank genome accession number
SPOT_ID
Annotation Functional annotation

Data table
ID Meta Row Meta Column Row Column Probe ID SEQUENCE GENOME_MATCH_NO ORF_MATCH_NO ORF GENOME ACC GENOME_ACC SPOT_ID Annotation
1 1 1 1 1 Gm_10_C4 GCGGAATAATGCTCAGAGAGCGAAGCAAGCGGAATGTTGTAACGCAACTTGATGGGACTGCATTGCGGCT 1 1 Gmet_2540 gi|78221228|ref|NC_007517.1| NC_007517.1 ATP-binding region, ATPase-like
2 1 1 1 2 Gm_10_G6 ATCTGGGGCTTTCTTGGGACCAGGTGAAGGAAATCGACAAGCGCTCACTCACAGAGCGGGTCGGCACCGT 14 14 Gmet_0323, Gmet_0443, Gmet_0800, Gmet_1185, Gmet_1310, Gmet_1977, Gmet_2166, Gmet_2284, Gmet_2376, Gmet_2515, Gmet_2840, Gmet_3102, Gmet_3396, Gmet_3527 IS204/IS1001/IS1096/IS1165 transposase
3 1 1 1 3 Gm_10_C10 GCCGGTCCCAGATGTTCGAGGGGCACGCCGACTGGCAGCAGATCGCCGAGATGAAGCAGAGCGTGAAAAT 1 1 Gmet_2561 gi|78221228|ref|NC_007517.1| NC_007517.1 Dihydrouridine synthase TIM-barrel protein nifR3
4 1 1 1 4 Gm_10_G12 CATATCCAGCCACCCTCCAGCCTGGTGTGGCAACGACGCTTTCCGCCCTGAGCATCAACTGCTCAAAGCC 1 1 Gmet_1195 gi|78221228|ref|NC_007517.1| NC_007517.1 Peptidase S8 and S53, subtilisin, kexin, sedolisin
5 1 1 1 5 Gm_22_C4 GGACTCCATTTCAGAAAATGGTGCGCCCTTAGTGGAGATTGACGAGATCGGAGCAGAGCATGCTCTGGGG 1 1 Gmet_2800 gi|78221228|ref|NC_007517.1| NC_007517.1 hypothetical protein Gmet_2800
6 1 1 1 6 Gm_22_G6 GTGTCGGAAAGAAGGAAAACGTGGGGGTCATTGCCGAGCTTGCCAAGGTGCTTGGCGGAGAGTTGGGGGC 1 1 Gmet_3301 gi|78221228|ref|NC_007517.1| NC_007517.1 Electron transfer flavoprotein, alpha subunit
7 1 1 1 7 Gm_22_C10 TCGTTCAACTACGCAACCGTCAGCCCGTTAATCGGTCCACAGGGGGACAAGACCGGCGCCAAGGGGTATG 1 1 Gmet_3303 gi|78221228|ref|NC_007517.1| NC_007517.1 hypothetical protein Gmet_3303
8 1 1 1 8 Gm_22_G12 TACGCTTCGGACGGGAGGCTCCATGAAACAACGTGTAACTGCACTGGTGGCGCTTGCGGCGCTGTTGCCT 1 0 unknown
9 1 1 1 9 Gm_34_C4 GCGACATCATCCTCAAGCCCTACCAGGAGGACGACGTGCTGGCCAAGGTGGAAAAGTTCCTGAACGCCGC 1 1 Gmet_3117 gi|78221228|ref|NC_007517.1| NC_007517.1 response regulator receiver domain protein (CheY-like)
10 1 1 1 10 Gm_34_G6 GGTACGACTTGAGGTGATGGGCATCGACAAGTATCGACGATCGGTTTCCTTTGTCTGGTTGGGGGATCGG 1 1 Gmet_3053 gi|78221228|ref|NC_007517.1| NC_007517.1 SNase-like nuclease
11 1 1 1 11 Gm_34_C10 GTTCACCGAGATGACCAACCCGGAGACCGGCATCTTCTCCCAGGGGGAGGAATTCGTCCGCAAGATCCTG 1 1 Gmet_3111 gi|78221228|ref|NC_007517.1| NC_007517.1 Flagellar motor switch protein FliG
12 1 1 1 12 Gm_34_G12 CGGCATCGGCAACGATGGGCAGGTGGAACTGGTTTCCGGGAACCTCAAGGAAAACGACCAGGTGATCATC 1 1 Gmet_3038 gi|78221228|ref|NC_007517.1| NC_007517.1 Secretion protein HlyD
13 1 1 1 13 null null
14 1 1 1 14 null null
15 1 1 1 15 null null
16 1 1 1 16 null null
17 1 1 2 1 Gm_10_A4 TCCGATGAGATTCTGCGTAATCTGCCCGGCCTCACCATCCACGATGTCATGCTCCTCCCCCTGGACCGCT 1 1 Gmet_2580 gi|78221228|ref|NC_007517.1| NC_007517.1 Excinuclease ABC, A subunit
18 1 1 2 2 Gm_10_E6 TCCGTTGAGTTTTACCCACCTGGAAAAGATTTATGACTTCGAGACGTTCCTGCCGGCGGCCGGGAGTGGG 1 1 Gmet_2603 gi|78221228|ref|NC_007517.1| NC_007517.1 transcriptional modulator of MazE/toxin, MazF
19 1 1 2 3 Gm_10_A10 GTGGCCACCGATATCGCCGCCCGGGGGATTGATGTCTCCCAGGTGTCCCACGTCATCAACTACGACATCC 1 1 Gmet_2573 gi|78221228|ref|NC_007517.1| NC_007517.1 ATP-dependent RNA helicase RhlE
20 1 1 2 4 Gm_10_E12 TCTGGGACGTCCTCTCCACGGACATCGAGGGGCCGGTGGAGCTCATCTGGGAGGATAGCGAACACTCGAA 1 1 Gmet_2617 gi|78221228|ref|NC_007517.1| NC_007517.1 Barstar

Total number of rows: 9216

Table truncated, full table size 1477 Kbytes.






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