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Sample GSM1062062 Query DataSets for GSM1062062
Status Public on Apr 19, 2016
Title ΔIP3_VCM 10mg/L_OD2.0
Sample type RNA
 
Channel 1
Source name ΔIP3_V10_OD2
Organism Staphylococcus aureus
Characteristics another strain name: H14msrR*graR*
background strain: deltaIP
genotype: vraS, msrR, graR mutation (replacement)
growth: up to OD2.0
treatment: 10min with vancomycin 10mg/L
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 ΔIP3_OD2
Organism Staphylococcus aureus
Characteristics another strain name: H14msrR*graR*
background strain: deltaIP
genotype: vraS, msrR, graR mutation (replacement)
growth: up to OD2.0
treatment: none
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 09, 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 -0.152509074 0.899684408 5467 1.038636026 5939.666667 1.154444844
2 -0.259390836 0.835440602 10990 2.474415265 12643.66667 2.961808727
3 -0.378082919 0.769459384 5249 1.033519168 6597.666667 1.343175728
4 -0.195983428 0.872977619 6725 1.290761944 7500 1.478573925
5 -0.203624302 0.868366333 11266 2.179185448 12259 2.509523187
6 -0.20484708 0.867630648 12707 2.306553403 13987.33333 2.658450816
7 -0.175671643 0.885355248 954 0.165278491 1068.333333 0.186680421
8 0.574138708 1.488788388 1948 0.363531772 1355 0.244179613
9 -0.414778433 0.75013469 16949 3.386059907 21152.33333 4.513935898
10 -0.212855631 0.862827682 1348 0.255149621 1560.666667 0.2957133
11 -0.111443429 0.925661466 1048 0.191294048 1158.333333 0.206656596
12 -0.114256027 0.923858606 3581 0.677490559 3809.333333 0.733327107
13 -0.048975691 0.966622384 10670 2.063803832 10650.33333 2.135067287
14 -0.098433162 0.934046862 13018 2.175517319 13312.66667 2.329130805
15 -0.070020862 0.952624222 10935 1.999654902 11049.66667 2.099101466
16 0.084561706 1.060365551 542 0.099968875 533.3333333 0.094277747
17 0.109706253 1.079008517 7980 1.674370705 7216.333333 1.55176783
18 0.070672213 1.050205905 10921 1.915594815 9994 1.824018324
19 0.016187836 1.01128374 8025 1.356113745 7753.333333 1.340982448
20 0.024170907 1.016895131 14957 2.341401466 14027.33333 2.30250042

Total number of rows: 3846

Table truncated, full table size 251 Kbytes.




Supplementary file Size Download File type/resource
GSM1062062_2011-01-13_4_Slot19_532.pair.gz 2.7 Mb (ftp)(http) PAIR
GSM1062062_2011-01-13_4_Slot19_635.pair.gz 2.7 Mb (ftp)(http) PAIR
Processed data included within Sample table
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