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Sample GSM1062069 Query DataSets for GSM1062069
Status Public on Apr 19, 2016
Title ΔIP4_OD1.0profile
Sample type RNA
 
Channel 1
Source name ΔIP4
Organism Staphylococcus aureus
Characteristics another strain name: H14msrR*graR*rifR
background strain: deltaIP
genotype: vraS, msrR, graR mutation (replacement), rpoB mutant (selection with 1 mg/liter rifampin)
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 -0.476628863 0.71865494 13895 2.55913307 19680.66667 3.561003934
2 -0.566439234 0.675281419 17779 3.028043872 26898.33333 4.484121416
3 -0.524206026 0.69534168 7257 1.203055195 10080.66667 1.730164077
4 -0.365146267 0.776390157 12186 2.032879627 15068.66667 2.618373776
5 -0.349870479 0.784654539 14586 2.50121415 17983.33333 3.187662884
6 -0.513872865 0.700339874 14216 2.277816774 19548.33333 3.252444789
7 -1.532240197 0.34574009 1118 0.148051348 2497 0.428215738
8 0.079393769 1.056573967 1441 0.211307402 1237.666667 0.199993005
9 -1.120878349 0.459813794 8701 1.501077878 18361.66667 3.264534248
10 0.05608776 1.039642675 1640 0.258218871 1395.666667 0.248372712
11 0.729483727 1.658045649 2596 0.405793054 1338.333333 0.244741786
12 -0.00943383 0.9934823 9254 1.535493495 8642.666667 1.545567038
13 -0.034131055 0.976619809 16679 2.931032709 16314.33333 3.001201371
14 -0.140361766 0.907291617 13485 1.66112334 13575 1.830859351
15 0.440449464 1.357027036 14440 2.242282651 10528.33333 1.652349284
16 -0.267688273 0.830649485 4940 0.87640804 5958.333333 1.055087682
17 -0.075376985 0.949094085 8338 1.444137712 8448.666667 1.521595947
18 -0.253731905 0.83872403 7166 1.208740579 8363 1.441166029
19 -0.259490963 0.835382622 9672 1.66683642 11367.33333 1.995296977
20 -0.193101319 0.874723332 15194 2.227479694 17424.66667 2.54649626

Total number of rows: 3846

Table truncated, full table size 251 Kbytes.




Supplementary file Size Download File type/resource
GSM1062069_04_2012-05-13_532.pair.gz 2.6 Mb (ftp)(http) PAIR
GSM1062069_04_2012-05-13_635.pair.gz 2.6 Mb (ftp)(http) PAIR
Processed data included within Sample table
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