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Platform GPL6358 Query DataSets for GPL6358
Status Public on Feb 11, 2008
Title MSU/JMT Exiguobacterium sibiricum 70mer array v. 1.0
Technology type spotted oligonucleotide
Distribution non-commercial
Organism Exiguobacterium sibiricum 255-15
Manufacturer oligonucleotides were commercially synthesized without modification by MWG Biotech Inc. (High Point, NC), Dr. Zhou from University of Oklahoma spotted the oligos into arrays
Manufacture protocol The design criteria of the 70 mer probes were as follows: (i) 85% sequence similarity, 18-base stretch, and -35 kcal/mol free energy for gene-specific probes; and (ii) 96% sequence similarity, 55-base stretch, and -90 kcal/mol free energy for group-specific probes. Based on those criteria, 2931 CDS had gene-specific probes; 25 CDS were covered by six group-specific probes; no qualified probes were selected for 22 CDS. In addition, 10 human and 10 Arabidopsis probes were designed as controls. All designed oligonucleotides were commercially synthesized without modification by MWG Biotech Inc. (High Point, NC). The concentration of oligonucleotides was adjusted to 100 pmol µl-1. Oligonucleotide probes prepared in 50% DMSO (Sigma Chemical Co., MO) were spotted onto UltraGAPS glass slides (Corning Life Science, NY) using a Microgrid II robotic arrayer (Genomic Solutions Inc., MI). Each oligonucleotide probe had two spots on a single slide. Additionally, six different concentrations (5~300 ng µl-1) of genomic DNA were also spotted (four duplicates on a single slide) as positive controls. After printing, the oligonucleotide probes were fixed onto the slide by UV cross-linking at 600 mJ of energy (Corning Life Science, NY). The oligo design information provided in the supplementary file.
Support glass
Coating polysine
 
 
Submission date Jan 10, 2008
Last update date Feb 11, 2008
Contact name Debora Frigi Rodrigues
E-mail(s) rodri257@msu.edu
Fax 517-353-2917
Organization name Michigan State University
Department Microbiology and Molecular Genetics
Lab Center for Microbial Ecology
Street address 540 Plant and Soil Science Bldg.
City East Lansing
State/province MI
ZIP/Postal code 48824
Country USA
 
Samples (36) GSM256115, GSM256116, GSM256117, GSM256118, GSM256119, GSM256120 
Series (1)
GSE10133 Architecture of thermal adaptation in Exiguobacterium sibiricum strain 255-15: A genome and transcriptome approach

Data table header descriptions
ID Contains the information about the gene location in the genome sequence used to design the oligonucleotides: microorganism_contig_gene number, also if it is a control oligo or blank spot
Description Gene Description
Gene name Gene name
COGs description Gene symbol defined by COGs (Cluster of orthologs Groups)
SEQUENCE The sequence of the oligonucleotides used in the array
GenBank accession Genome GenBank accession numbers used to design oligonucleotide probe, annotation also available in http://genome.ornl.gov/microbial/exig/
SPOT_ID
CLONE_ID

Data table
ID Description Gene name COGs description SEQUENCE GenBank accession SPOT_ID CLONE_ID
exig_226_1 hypothetical AGGGATTAAAATGCCTGTTCGTGAAGAAATGAGATATGGGGACATAAAAAAAGTAGTAGGGTCTGAGAAA AADW02000001 to AADW02000051 ExigDRAFT_0001
exig_232_2 hypothetical ATCGGTATTCGCTGCGATTGATACGTCATCTATGCAAAAAGCACTTGACGAGGATTTGAAGAGTACACAT AADW02000001 to AADW02000051 ExigDRAFT_0002
exig_232_3 membrane protein, putative Predicted membrane protein COG3759 CCAACACCTCAATTCTTTTCAAACAAGGGCTTCCGGCCATCATTGCTTTTTTACTCGTCTTATTCGTCTG AADW02000001 to AADW02000051 ExigDRAFT_0003
exig_232_4 similar to proteins Predicted small secreted protein COG5584 CGCATACGAGTCACGTGACTACCAAAGCTACAAAGGTGGCATCTCGGTCCTTGAAGGTGACGATGAAAAA AADW02000001 to AADW02000051 ExigDRAFT_0004
exig_232_5 deblocking aminopeptidase, M42 family [EC:3.4.11.-] Cellulase M and related proteins FrvX CAGGAGATAAAACGGAATTCGGTCAGCTTGGTCAAGGACCGTTGTTACGTATTAAAGACAGCGTCATGAT AADW02000001 to AADW02000051 ExigDRAFT_0005
exig_232_6 conserved hypothetical protein Predicted membrane protein putative toxin regulator PfoR GCCGCACAAATGATCGGTTTCGGTGTCATCAGTTATCGCGATAACGGGATTGGGGGTTTCATTGCCCAAG AADW02000001 to AADW02000051 ExigDRAFT_0006
exig_232_7 hypothetical GTTAAGCATCTTTTTGAACGATTTGTTGGTTTTGTCGGCATGACAAGCTGTCTCCGGTACGGCTATTCGT AADW02000001 to AADW02000051 ExigDRAFT_0007
exig_234_10 glyoxylase family protein Lactoylglutathione lyase and related lyases GloA ACTTTGACGATCCGGGAACCTATCACTTTTATTTCGGCAATGAATCGGGTAAACCTGGAACAATCATCAC AADW02000001 to AADW02000051 ExigDRAFT_0010
exig_234_11 ATPas ABC-type uncharacterized transport system ATPase component COG4152 CAAAAGGAAATCAGCAAAAAATCCAGCTGATTTCTGCCGTCCTACATAAACCCGACTTATTAATCCTCGA AADW02000001 to AADW02000051 ExigDRAFT_0011
exig_234_12 ABC transporter (permease) (Na+ exclusion) KO: K01992 ABC-2 type transport system permease protein ABC-type Na+ efflux pump permease component NatB TGATGGTCGTGTTCCTTGTCGGATTCAGCAACATCGAGCGGATCATCGACTGGTTCTCGGGAGACGATCC AADW02000001 to AADW02000051 ExigDRAFT_0012
exig_234_8 hypothetical CCCAGTTTTACATCGGTCATGAAACCGTCGTGACCTGGTGCCTCATCATCGACAGCATGTGGTTGATCCG AADW02000001 to AADW02000051 ExigDRAFT_0008
exig_234_9 phospholipase/carboxylesterase family protein Predicted esterase COG0400 TGATTTTCGAACAGGCAGGGGCTACGGTCGATGTGACCTGGTCGAACCATGGTCATCAGCTCATCATGCC AADW02000001 to AADW02000051 ExigDRAFT_0009
exig_238_13 hypothetical CAAACAAATGAAGTTCCTCGATGTAGCAAAAACGCATGCTCCAGTAGGACGTGAGAAGCTTCGTGAGGCG AADW02000001 to AADW02000051 ExigDRAFT_0013
exig_238_14 hypothetical ACAGGATCGAATCATTTTAAAATTGTTGGTTATAAAGACGGGGTCCAAATTACAAACAAAAAAGAAGGCA AADW02000001 to AADW02000051 ExigDRAFT_0014
exig_238_15 hypothetical TCCCAGCACTACTCATGACTACTTTCATTTCTTCAAACGTCATTCATGCAGAAGAACCATCAATCGATCC AADW02000001 to AADW02000051 ExigDRAFT_0015
exig_238_16 hypothetical Uncharacterized distant relative of cell wall-associated hydrolases COG3863 AGGACCGGTTTTAAAAAAAGGAGATATTTTAGTTAGCAATGCTACATCTTCTTATGGTTTGACGGGGCAT AADW02000001 to AADW02000051 ExigDRAFT_0016
exig_242_17 Bacterial regulatory protein, MarR Transcriptional regulators MarR GAACTCAACCGACTGTTTGAAGGGACCGCGACACGAAGTGAATTTTTCATTTTACGCAGTCTGTCCGAAA AADW02000001 to AADW02000051 ExigDRAFT_0017
exig_242_18 GGDEF Response regulator containing a CheY-like receiver domain and a GGDEF domain PleD ACAAATGGATGCCGCTGTCGTGTCAACAATCGTCATCGGAGTGTTAATCCTGACGATTGCCGTCGTCCGT AADW02000001 to AADW02000051 ExigDRAFT_0018
exig_242_19 transcriptional regulator, TetR family Transcriptional regulator AcrR CAAAGCGGTCACGTGACCGTATTACAAAAGAATTATTTCGTTTGCTGGACAGTCATCCTTTTTCGACGAT AADW02000001 to AADW02000051 ExigDRAFT_0019
exig_242_20 multidrug resistance protein A Multidrug resistance efflux pump EmrA AAAGTCTCACTGTCACAAGAAAAATCACTCGACATTCGACCTGGTATGAATGTGACCGTCCGCATTCATA AADW02000001 to AADW02000051 ExigDRAFT_0020

Total number of rows: 2961

Table truncated, full table size 602 Kbytes.




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Supplementary file Size Download File type/resource
GPL6358.txt.gz 107.5 Kb (ftp)(http) TXT

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