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Sample GSM1230415 Query DataSets for GSM1230415
Status Public on Mar 31, 2014
Title ΔIP vs Mu3
Sample type RNA
 
Channel 1
Source name ΔIP
Organism Staphylococcus aureus
Characteristics background strain: ΔIP
genotype/variation: wild-type
mic_van: 0.5
Extracted molecule total RNA
Extraction protocol See reference:
Neoh HM, et al.: Mutated response regulator graR is responsible for phenotypic conversion of Staphylococcus aureus from heterogeneous vancomycin-intermediate resistance to vancomycin-intermediate resistance. Antimicrob Agents Chemother. 2008 Jan;52(1):45-53.
Label Cy3
Label protocol SuperScript Indirect cDNA Labeling System (Invitrogen Life Technologies, Carlsbad, California).
 
Channel 2
Source name Mu3
Organism Staphylococcus aureus
Characteristics background strain: Mu3
genotype/variation: wild-type
mic_van: 2
Extracted molecule total RNA
Extraction protocol See reference:
Neoh HM, et al.: Mutated response regulator graR is responsible for phenotypic conversion of Staphylococcus aureus from heterogeneous vancomycin-intermediate resistance to vancomycin-intermediate resistance. Antimicrob Agents Chemother. 2008 Jan;52(1):45-53.
Label Cy5
Label protocol SuperScript Indirect cDNA Labeling System (Invitrogen Life Technologies, Carlsbad, California).
 
 
Hybridization protocol Labeled samples were hybridized onto the microarray at 50°C for 16-20 hr. After hybridization, the arrays were washed in the following buffers, and dry by spin slide.
2X SSC/0.05% SDS, for 15 min
0.2X SSC/0.05% SDS, for 15 min
0.5X SSC, for 3 min
0.2X SSC, for 3 min
Scan protocol Nimblegen MS200
Description Sample 5
Data processing Software: NimbleScan
Algorithm: Robust Multi-Array Analysis (Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Biostatistics. 2003 Apr;4(2):249-64 (PMID 12925520)).
Normalize: global normalization
 
Submission date Sep 12, 2013
Last update date Mar 31, 2014
Contact name tomomi hishinuma
Organization name juntendo university
Street address 2-1-1,Hongo
City Bunkyo-Ku
State/province Tokyo
ZIP/Postal code 113-8421
Country Japan
 
Platform ID GPL16176
Series (1)
GSE50826 A Single Amino-Acid Substitution of RNA Polymerase ß subunit Confers A Novel Class of VISA phenotype on hVISA Strain Mu3

Data table header descriptions
ID_REF
VALUE normalized log2 ratio test/reference

Data table
ID_REF VALUE
1 0.17128956
2 1.214292754
3 -0.201629869
4 -0.250523314
5 -0.40873879
6 -0.119272419
7 0.870185188
8 0.780933223
9 1.194399255
10 0.421954618
11 -0.682006763
12 0.185018943
13 -0.373113142
14 -0.143622573
15 -0.462740214
16 0.965570305
17 -0.904332467
18 -0.731718694
19 -1.008534143
20 0.756329461

Total number of rows: 3846

Table truncated, full table size 64 Kbytes.




Supplementary file Size Download File type/resource
GSM1230415_02june_2013-07-04_532_422080.pair.gz 2.7 Mb (ftp)(http) PAIR
GSM1230415_02june_2013-07-04_635_422080.pair.gz 2.7 Mb (ftp)(http) PAIR
GSM1230415_130704_parent.txt.gz 109.3 Kb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file
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