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Status
Public on Aug 23, 2007
Title
E. coli O157 Sakai oligonucleotide DNA microarray
Technology type
spotted oligonucleotide
Distribution
non-commercial
Organism
Escherichia coli Manufacturer
Molecular Gene Technics, Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan.
Manufacture protocol
Oligonucleotide probes were prepared for all the protein-coding genes on the O157 Sakai genome (5,447 genes in total). Principles for the probe design were 60-mer in length and two probes for each gene. As for 542 repeated genes, we prepared a single probe for each repeated gene family. Such probes totaled to 151 probes, each having two or more targets of more than 90% sequence identity on the O157 Sakai genome . As for the singleton genes (4905 genes), we were able to design two different 60-mer probes for 4173 genes, but only one 60-mer probe for 725 genes and one 44 or 45-mer probes for 7 genes. In total, 9,620 probes were synthesized (Sigma-Aldrich Japan, Tokyo, Japan), and each probe was spotted onto poly-L-Lysine coated glass slides (SD10011; Matsunami Glass Ind., Osaka, Japan) using SPBIO (Hitachi Software Engineering, Tokyo, Japan).
Support
glass
Coating
other
Contributor(s)
Ogura Y , Tashiro K , Kuhara S , Hayashi T Submission date
May 24, 2007
Last update date
Aug 23, 2007
Contact name
Yoshitoshi Ogura
E-mail(s)
y-ogura@med.miyazaki-u.ac.jp Organization name
University of Miyazaki
Department
Frontier science reserch center
Street address
Kihara 5200
City
Kiyotake
State/province
Miyazaki
ZIP/Postal code
889-1692
Country
Japan
Samples (72)
GSM194758 , GSM194759 , GSM194760 , GSM194761 , GSM194762 , GSM194763
GSM194764 ,
GSM194765 ,
GSM194766 ,
GSM194767 ,
GSM194768 ,
GSM194769 ,
GSM194770 ,
GSM194771 ,
GSM194772 ,
GSM194773 ,
GSM194774 ,
GSM194775 ,
GSM194776 ,
GSM194777 ,
GSM194778 ,
GSM194779 ,
GSM194780 ,
GSM194781 ,
GSM194782 ,
GSM194783 ,
GSM194784 ,
GSM194785 ,
GSM194786 ,
GSM194787 ,
GSM194788 ,
GSM194789 ,
GSM194790 ,
GSM194791 ,
GSM194792 ,
GSM194793 ,
GSM194794 ,
GSM194795 ,
GSM194796 ,
GSM194797 ,
GSM194798 ,
GSM194799 ,
GSM194800 ,
GSM194801 ,
GSM194802 ,
GSM194803 ,
GSM194804 ,
GSM194805 ,
GSM194806 ,
GSM194807 ,
GSM194808 ,
GSM194809 ,
GSM194810 ,
GSM194811 ,
GSM194812 ,
GSM194813 ,
GSM225251 ,
GSM225252 ,
GSM225253 ,
GSM225254 ,
GSM225255 ,
GSM225256 ,
GSM225257 ,
GSM225258 ,
GSM225259 ,
GSM225260 ,
GSM225261 ,
GSM225262 ,
GSM225263 ,
GSM225264 ,
GSM225265 ,
GSM225266 Series (2)
GSE7931 Genomic comparison in Enteroheamorragic E. coli O157 and non-O157 serotypes by comparative genomic hybridization.
GSE8889 Genomic Comparison of the O-antigen Biosynthesis Gene Clusters of E. coli O55 Strains Belonging to Three Lineages.
Data table header descriptions ID SEQUENCE oligonucleotide probe sequence
ORF target ORF
GENOME_ACC oligonucleotide probes were degined based on the genome sequence
SPOT_ID
Data table ID SEQUENCE ORF GENOME_ACC SPOT_ID ECs0001_1
AACGCATTAGCACCACCATTACCACCACCATCACCACCACCATCACCATTACCATTACCA
ECs0001 BA000007.2
ECs0002_1
ATTACCTCGAATCTACTGTCGATATTGCAGAGTCCACCCGCCGTATTGCGGCAAGTCGTA
ECs0002 BA000007.2
ECs0002_2
AACATATCGACTTACGTGTCTGCGGTGTTGCTAACTCGAAGGCTCTGCTCACCAATGTGC
ECs0002 BA000007.2
ECs0003_1
CAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCAC
ECs0003 BA000007.2
ECs0003_2
GCCGCTTAATGACACCCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGACGAATCTCCGG
ECs0003 BA000007.2
ECs0004_1
GAAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTC
ECs0004 BA000007.2
ECs0004_2
GTGCCACGTTTCCTGCATGACGGTCAGTGGTCACCCAAAGCGACTCAGGCGACGTTATCC
ECs0004 BA000007.2
ECs0005_1
AAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAACGCA
ECs0005 BA000007.2
ECs0005_2
TTATTACTGGGATGGCGGTCACTGGCGCGACCACGGCTGGTGGAAACAACATTATGAATG
ECs0005 BA000007.2
ECs0006_1
GAATGCCCGAGGGAAAGATCTGTATCAATTCTGGGGAGATATCATCACCAACAAGCTGAA
ECs0006 BA000007.2
ECs0006_2
AAACGCTTGATTACCAAAGCCCGTTGACCACCACGCGATATACACTGCCGGAGCTGTTAG
ECs0006 BA000007.2
ECs0007_1
ATTTGTTACCCTCGTGGTTATTCTGTTTGCCTTCAGCTCCATCGTTGCCAACTACATTTA
ECs0007 BA000007.2
ECs0007_2
AAATAGCATTCATCCACAGCCAGGCGGTTTAACCTCATTTCAGTCATTGTGTACCAGTCT
ECs0007 BA000007.2
ECs0008_1
CGGGCCGTATCTCAACTGAAGTTGATGCGCGTCTTTCCTATGACACAGAAGCGTCAATTG
ECs0008 BA000007.2
ECs0008_2
CGGAATACCGTAAGTTGATTGATGATGCTGTCGCCTGGGCGAAACAGCAGAGCAACGATC
ECs0008 BA000007.2
ECs0009_1
GCACCAGAAGTGGTTGCTGCATTCAGACCGAAGAGTGCAAGACGCGACGTTAGCGAATAA
ECs0009 BA000007.2
ECs0009_2
CGATCCTTTCGCGTCAGGTGGGTGTGATTCGCAAACAGGCGCTGATCCTTAACTTACCCG
ECs0009 BA000007.2
ECs0010_1
CTGATGCCGAAACTGGGTCTGACCGATGCGCCAAATGCACAGTTCCTTGGTGTCTACCTG
ECs0010 BA000007.2
ECs0010_2
TTAACCTGCACAACGTAGGTTATTTCGCTCTGGACGGTATTATTCTTGCCATGGGCATTT
ECs0010 BA000007.2
ECs0011_1
AACGTAGACATCTCTTTGTCGGCTTTCAGCTTCAATCGTTTTGAAACATCGAGCAAAATG
ECs0011 BA000007.2
9229 830 Kbytes .Supplementary data files not provided
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