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Platform GPL7395 Query DataSets for GPL7395
Status Public on Sep 28, 2009
Title MGAC_Ecoli_v1.0
Technology type spotted oligonucleotide
Distribution custom-commercial
Organism Escherichia coli
Manufacturer GEM (Genome Encyclopedia of Microbes)
Manufacture protocol Oligonucleotide microarrays were fabricated by which both E. coli B REL606 and K-12 MG1655 could be tested for the synthesis of both common and unique mRNAs. Probes (70-mers) were designed by Array Designer (Premier Biosoft International) and cross-hybridization was checked by BLASTN. A total of 4,819 probes were synthesized by Illumina. The probes represented 3,762 genes that shared over 80-mer of sequence in the two E. coli strains, 382 genes found uniquely in REL606, and 534 genes unique to MG1655. The other probes were positive and negative controls. The probes were spotted in duplicate onto a GAPSII glass slide (Corning Inc.) by Digital Genomics in Seoul, Korea.
Support glass
Coating aminosilane
 
 
Web link http://www.gem.re.kr
Contributor(s) Kim JF, Yoon S, Jeong H, Yu D
Submission date Sep 29, 2008
Last update date Sep 28, 2009
Contact name Sung Ho Yoon
Organization name Konkuk University
Department Department of Bioscience and Biotechnology
Street address 120 Neungdong-ro, Gwangjin-gu
City Seoul
ZIP/Postal code 05029
Country South Korea
 
Samples (30) GSM325748, GSM325750, GSM325753, GSM325755, GSM325756, GSM325759 
Series (2)
GSE13011 Transcriptomic differences between E. coli B REL606 and K-12 MG1655
GSE47589 Transcriptome analysis of Escherichia coli C strains (wt and PKH5000, a butanol-tolerant mutant) after 1-butanol treatment

Data table header descriptions
ID
PROBE_CLASS The microarray was designed both for E. coli B REL606 (B) and E. coli K-12 MG1655 (K); CS (the probe sequence matches perfectly the target gene of B and K, no cross hybridization with other genes. In other words, this probe detects only one gene of each genome.), CX (the probe can detect more than one gene of each genome (60~69 out of 70 probe sequence matches to other genes when the probe sequence is aligned with the those of all genes in B and K.), BS (the probe matches perfectly to only B gene without cross-hybridization.), BX: the probe matches perfectly to only B gene with possible cross-hybridization with K genes.), KS (the probe matches perfectly to only K gene without cross-hybridization.), KX (the probe matches perfectly to only K gene with possible cross-hybridization with B genes.), NC (non-coding RNA), EN (randomized negative control), EP (positive control)
SEQUENCE Sequence of the 70-mer probe
B_ORF Unique ORF ID of E. coli B REL606 represented by the probe sequence
K_ORF Unique ORF ID of E. coli K-12 MG1655 represented by the probe sequence
B_ORF_CROSS Possible cross hybridization of the probe with other B ORF (number of matched region/number of aligned region)
K_ORF_CROSS Possible cross hybridization of the probe with other K ORF (number of matched region/number of aligned region)
GENE_NAME Gene name
GENE_DISC Description of the gene
ORF locus tag
SPOT_ID E. coli B REL606 ORF

Data table
ID PROBE_CLASS SEQUENCE B_ORF K_ORF B_ORF_CROSS K_ORF_CROSS GENE_NAME GENE_DISC ORF SPOT_ID
CB0027 CS GGATCTAAAGCAGGTGCCGGGGATGGGCAATTCGCTGGTGGAACGTAATCTGGCGGTATTAACCCTGTAA ECB_00394 b0442 - - ybaV hypothetical protein b0442 E. coli B REL606 ECB_00394
CB0028 CS GAGTCATATCCTCTGAAAAGAAAATGTCCCACAGGTACAGATAGAGTTGCTGCTTATCATACTCACGGTG ECB_00448 b0497 - - rhsD rhsD element protein b0497 E. coli B REL606 ECB_00448
CB0112 CS TCTCGACAACATTATCTGGTTTGATCATCTGTCAACCGACGTGATCCATCAGGTGGTGGATAAATTCATC ECB_00887 b0882 - - clpA ATPase and specificity subunit of ClpA-ClpP ATP-dependent serine protease, chaperone activity b0882 E. coli B REL606 ECB_00887
CB0281 CS TGTCTTTGACATTACTTGAACAAGGTGTTTATTTTCCGGGGAATGACGAACCAATTAAATTACTCATCGG ECB_02764 b2934 - - cmtB predicted mannitol-specific enzyme IIA component of PTS b2934 E. coli B REL606 ECB_02764
CB0321 CS CATATTGAACAACTGGGTTATCACAAAGGCATTGATTTACTGGCGTGGTGGATGCAGCGAACCGATCTCA ECB_02850 b2981 - - yghO predicted DNA-binding transcriptional regulator b2981 E. coli B REL606 ECB_02850
CB0428 CS CATTGCGATGGCGCTAAATGTACTGGGTAAACAATTCGATAAACTGCTTAATGTTACGCTGTGTTATCCG ECB_03748 b3862 - - yihG predicted endonuclease b3862 E. coli B REL606 ECB_03748
CB0438 CS TCCGCTGATTCATTTGAAGGATTTAACCGTACAAAGAAATGGCTATTTATATGCGACAGTTTATTCGACA ECB_03933 b4061 - - yjcC transcriptional repressor of Zn transport system b4061 E. coli B REL606 ECB_03933
CB0439 CS ATGATAGAACAGATAACTGATTATGTTATTGATAATGTCTTCCGCGATCTGGGCGATTACCTGGCAACAC ECB_03933 b4061 - - yjcC transcriptional repressor of Zn transport system b4061 E. coli B REL606 ECB_03933
CC0001 CS CTAAAGTTCTTCACCCCCGCACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATAC ECB_00002 b0002 - - thrA bifunctional aspartokinase I/homeserine dehydrogenase I b0002 E. coli B REL606 ECB_00002
CC0002 CS ATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTAT ECB_00003 b0003 - - thrB homoserine kinase b0003 E. coli B REL606 ECB_00003
CC0003 CS TGGAAGAGTTGTTCCGCCGCAAAATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAAC ECB_00004 b0004 - - thrC threonine synthase b0004 E. coli B REL606 ECB_00004
CC0004 CS GCTGCGGAAATTACGTTAGTCCCGTCAGTAAAATTACAGATAGGCGATCGTGATAATCGTGGCTATTACT ECB_00005 b0005 - - yaaX hypothetical protein b0005 E. coli B REL606 ECB_00005
CC0005 CS ATTAATCTGGCGTCAGATGAGTATTTTAAATCGGTGAAGCCGAAGAAATTGAATGCCGAGATTATCAAGC ECB_00006 b0006 - - yaaA hypothetical protein b0006 E. coli B REL606 ECB_00006
CC0006 CS AAAAGTCTTAAAAATAGCATTCATCCACAGCCAGGCGGTTTAACCTCATTTCAGTCATTGTGTACCAGTC ECB_00007 b0007 - - yaaJ predicted transporter b0007 E. coli B REL606 ECB_00007
CC0007 CS GACAAACTGGCAGTAAATATTGGTCTGGAAATCCTGAAACTGGTTCCGGGCCGTATCTCAACTGAAGTTG ECB_00008 b0008 - - talB transaldolase B b0008 E. coli B REL606 ECB_00008
CC0008 CS ATGAATACTTTACGTATTGGCTTAGTTTCCATCTCTGATCGCGCATCCAGCGGCGTTTATCAGGATAAAG ECB_00009 b0009 - - mogA molybdenum cofactor biosynthesis protein b0009 E. coli B REL606 ECB_00009
CC0009 CS CAAATGCACAGTTCCTTGGTGTCTACCTGGGTCTGTGGGGCGTATTTACGCTGTTTATGTTCTTCGGCAC ECB_00010 b0010 - - yaaH conserved inner membrane protein associated with acetate transport b0010 E. coli B REL606 ECB_00010
CC0012 CS CGTAACGAAACCAACGATCTGGCGCTGAAACTTCCTGTTTGTCGCATTGTGAAACGCATACAACTCTCTG ECB_00013 b0013 - - yaaI hypothetical protein b0013 E. coli B REL606 ECB_00013
CC0013 CS CGAAGATGAAATCCAGAAAATGGTACGCGACGCAGAAGCTAACGCCGAAGCTGACCGTAAGTTTGAAGAG ECB_00014 b0014 - - dnaK molecular chaperone DnaK b0014 E. coli B REL606 ECB_00014
CC0014 CS CAAAGATCCGTGCAACAAATGTCATGGTCATGGTCGTGTTGAGCGCAGCAAAACGCTGTCCGTTAAAATC ECB_00015 b0015 - - dnaJ chaperone Hsp40, co-chaperone with DnaK b0015 E. coli B REL606 ECB_00015

Total number of rows: 4721

Table truncated, full table size 794 Kbytes.




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