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Sample GSM1062068 Query DataSets for GSM1062068
Status Public on Apr 19, 2016
Title ΔIP3_OD1.0profile
Sample type RNA
 
Channel 1
Source name ΔIP3
Organism Staphylococcus aureus
Characteristics another strain name: H14msrR*graR*
background strain: deltaIP
genotype: vraS, msrR, graR mutation (replacement)
growth: up to OD1.0
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 ΔIP
Organism Staphylococcus aureus
Characteristics strain: deltaIP
genotype: wild
growth: up to OD1.0
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
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 Jan 10, 2013
Last update date Apr 19, 2016
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)
GSE43643 Complete Genetic Reconstitution of VISA Phenotype of Mu50 in Vancomycin-Susceptible Staphylococcus aureus.

Data table header descriptions
ID_REF
VALUE normalized log2 ratio test/reference
PRE_VALUE ratio (normalized data)
CH1_S Cy3 intensity
CH1_normS Normalized Cy3 intensity
CH2_S Cy5 intensity
CH2_normS Normalized Cy5 intensity

Data table
ID_REF VALUE PRE_VALUE CH1_S CH1_normS CH2_S CH2_normS
1 -0.198795979 0.871277397 15421 2.936674873 17518.33333 3.370539491
2 -0.249377524 0.841259313 20884 4.354275586 25899 5.175901793
3 -0.555928378 0.680219195 5697 1.051146531 8109.333333 1.5453056
4 -0.253260845 0.838997929 12159 2.302444046 14084.33333 2.74427858
5 -0.168982387 0.889469853 15855 3.309221481 17809.66667 3.720442544
6 -0.101803975 0.931867037 18329 3.348825424 19365 3.593673014
7 0.048003566 1.033833291 2177 0.384239434 2050.666667 0.37166479
8 -0.1450651 0.904338569 1034 0.1934734 1011.666667 0.213939123
9 -0.798399071 0.574986875 10247 1.996218267 17823.66667 3.471763191
10 0.300548497 1.23161257 1541 0.315285997 1195 0.255994462
11 0.553516296 1.46765848 1778 0.319221664 1119 0.217504051
12 0.339106167 1.264972628 9863 1.941607263 7454.666667 1.534900614
13 0.219809788 1.164580032 16645 3.278400012 13836.33333 2.815092069
14 -0.166650937 0.890908431 10248 1.635691681 10682 1.835981817
15 0.177414954 1.130855782 11853 2.0571356 10049.66667 1.819096328
16 0.17097779 1.125821254 6174 1.167583273 5342.666667 1.037094715
17 -0.009321749 0.993559486 7372 1.366314171 6840.666667 1.37517098
18 -0.043031687 0.970613152 9594 1.746335043 9320 1.799208099
19 -0.216010615 0.860942854 8423 1.62776351 9242.333333 1.890675442
20 -0.282384969 0.822230635 12204 2.133000687 13606.66667 2.594163481

Total number of rows: 3846

Table truncated, full table size 250 Kbytes.




Supplementary file Size Download File type/resource
GSM1062068_03_2012-05-13_532.pair.gz 2.6 Mb (ftp)(http) PAIR
GSM1062068_03_2012-05-13_635.pair.gz 2.6 Mb (ftp)(http) PAIR
Processed data included within Sample table
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