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Sample GSM194761 Query DataSets for GSM194761
Status Public on Aug 23, 2007
Title O157 no.3 (strain 980706) replicate 2
Sample type genomic
 
Channel 1
Source name Genomic DNA from O157 strain 980706
Organism Escherichia coli
Characteristics Enteroheamorragic E. coli
Growth protocol Cells were grown to the stationary phase at 37ºC in Luria-Bertani medium.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was purified using the Genomic-tip 100/G and Genomic DNA buffer set (Qiagen) according to the manufacturer's instruction.
Label Cy3
Label protocol First, 3 µg of genomic DNA was labeled with aminoallyl-modified dUTP (Sigma) using the Bioprime DNA Labeling System (Invitrogen). DNAs were not sheared or digested by restriction enzymes prior to the labeling. The aminoallyl-labeled DNA was purified by Microcon YM-30 (Millipore), dried in a speed-vac, and resuspended in 10 µl of 50 mM NaHCO3. After adding 10 µl of dimethyl sulfoxide solution containing Cy3 or Cy5 monofunctional reactive dye (Amersham), the sample was incubated at room temperature in the dark for 1 h to allow the dye to couple with DNA. The fluorescently labeled DNA was finally purified by the Qiaquick PCR purification kit (Qiagen) into 30 µl elution buffer provided by the manufacturer.
 
Channel 2
Source name O157 strain Sakai
Organism Escherichia coli
Characteristics Enteroheamorragic E. coli
Growth protocol Cells were grown to the stationary phase at 37ºC in Luria-Bertani medium.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was purified using the Genomic-tip 100/G and Genomic DNA buffer set (Qiagen) according to the manufacturer's instruction.
Label Cy5
Label protocol First, 3 µg of genomic DNA was labeled with aminoallyl-modified dUTP (Sigma) using the Bioprime DNA Labeling System (Invitrogen). DNAs were not sheared or digested by restriction enzymes prior to the labeling. The aminoallyl-labeled DNA was purified by Microcon YM-30 (Millipore), dried in a speed-vac, and resuspended in 10 µl of 50 mM NaHCO3. After adding 10 µl of dimethyl sulfoxide solution containing Cy3 or Cy5 monofunctional reactive dye (Amersham), the sample was incubated at room temperature in the dark for 1 h to allow the dye to couple with DNA. The fluorescently labeled DNA was finally purified by the Qiaquick PCR purification kit (Qiagen) into 30 µl elution buffer provided by the manufacturer.
 
 
Hybridization protocol The Cy5-labeled and the Cy3-labeled DNA preparations (15 µl for each) were mixed with a 90-µl hybridization solution containing 6.4 x SSC, 0.64 % sodium dodecyl sulfate (SDS), and 1.3 mg/ml yeast tRNA. After incubation at 96ºC for 2 min, the denatured sample was applied to a microarray slide and incubated on an ArrayBooster hybridization apparatus (Advalytix AG, Brunnthal, Germany) at 50ºC for 16 h. The slide was then washed twice in 2x SSC/0.2% SDS at room temperature for 10 min, twice in 0.2x SSC/0.2% SDS at 50ºC for 5 min, and twice in 0.2x SSC at room temperature for 10 min. Finally, the slide was briefly rinsed with ethanol and dried by centrifugation.
Scan protocol Scanned with a FLA-8000 scanner (Fuji Photofilm, Tokyo, Japan). The obtained data were analyzed by the ArrayVision 8.0 software (Imaging Research).
Description none
Data processing Spots with reference signal intensities lower than the local background (LBG) plus 5 standard deviations or with some spotting abnormalities were removed from analysis. Signal intensities of other spots were corrected by subtracting the LBG.
 
Submission date May 28, 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
 
Platform ID GPL5329
Series (1)
GSE7931 Genomic comparison in Enteroheamorragic E. coli O157 and non-O157 serotypes by comparative genomic hybridization.

Data table header descriptions
ID_REF
VALUE log2 ratio (Cy3/Cy5)

Data table
ID_REF VALUE
ECs0001_1 0.617713109
ECs0002_1 0.399970929
ECs0002_2 0.515385254
ECs0003_1 0.375125972
ECs0003_2 0.474381543
ECs0004_1 0.815444118
ECs0004_2 0.678939722
ECs0005_1 0.434107869
ECs0005_2 0.471012157
ECs0006_1 0.858677057
ECs0006_2 0.549371189
ECs0007_1 0.368561616
ECs0007_2 0.473690847
ECs0008_1
ECs0008_2 0.699894656
ECs0009_1 0.467965974
ECs0009_2 0.348389604
ECs0010_1 0.62027718
ECs0010_2 0.591369617
ECs0011_1 0.826755174

Total number of rows: 9229

Table truncated, full table size 196 Kbytes.




Supplementary file Size Download File type/resource
GSM194761.txt.gz 168.1 Kb (ftp)(http) TXT
Processed data included within Sample table

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