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Sample GSM1062063 Query DataSets for GSM1062063
Status Public on Apr 19, 2016
Title ΔIP4_VCM 10mg/L_OD2.0
Sample type RNA
 
Channel 1
Source name ΔIP4_V10_OD2
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 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 ΔIP4_OD2
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 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 0.001684197 1.001168078 6677 1.538021495 6431.333333 1.536227062
2 0.026154244 1.018294064 13376 3.271065886 12792.33333 3.212299867
3 -0.073670933 0.950217095 5745 1.35002743 5845 1.420756833
4 0.025188488 1.017612635 8878 2.104668431 8405.666667 2.068241254
5 -0.015642644 0.989215915 13572 3.145535962 13261 3.179827491
6 0.018625154 1.012993667 15026 3.330883691 14313.33333 3.288158455
7 0.113021939 1.081491209 418 0.076496619 392.6666667 0.070732539
8 0.379098132 1.300528606 1075 0.205900341 817.6666667 0.158320502
9 -0.162647359 0.893384198 12134 2.761493727 13107 3.091048324
10 0.100498532 1.072143884 2422 0.493322078 2204.333333 0.460126747
11 -0.034384086 0.976448536 1812 0.388307747 1800.666667 0.397673541
12 -0.021013742 0.985539949 4483 0.976884158 4296.666667 0.991217209
13 0.095023347 1.068082693 12289 2.813879549 11118 2.634514694
14 0.092173157 1.06597467 11384 2.439703014 10406.66667 2.288706367
15 0.048060194 1.033873872 15398 3.625280675 14499.66667 3.506501879
16 0.138698648 1.100911615 1024 0.201842089 909.6666667 0.183340866
17 0.042262001 1.02972707 7884 1.748596062 7340 1.698116047
18 0.093089632 1.066652048 9681 2.104073016 8764.333333 1.972595487
19 0.033710045 1.023641147 7331 1.526759982 6912 1.49149923
20 0.03946344 1.027731526 9546 2.120699846 8977.333333 2.063476493

Total number of rows: 3846

Table truncated, full table size 250 Kbytes.




Supplementary file Size Download File type/resource
GSM1062063_2011-01-13_5_Slot22_532.pair.gz 2.7 Mb (ftp)(http) PAIR
GSM1062063_2011-01-13_5_Slot22_635.pair.gz 2.7 Mb (ftp)(http) PAIR
Processed data included within Sample table
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