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Sample GSM1062056 Query DataSets for GSM1062056
Status Public on Apr 19, 2016
Title ΔIP4_VCM 10mg/L_OD1.0
Sample type RNA
 
Channel 1
Source name ΔIP4_V10_OD1
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
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_OD1
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
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 -0.254570851 0.838236442 9008 1.658653512 10184.66667 1.978741831
2 -0.027800618 0.980914558 15763 3.457219556 14911.33333 3.524485927
3 -0.38774839 0.764321549 4808 0.864063507 5652.333333 1.130497378
4 -0.410143247 0.752548649 7722 1.364854065 9535.333333 1.813642304
5 -0.356715094 0.780940699 11751 2.235820521 14093.33333 2.862983737
6 -0.25610772 0.837343964 13720 2.108422541 15470 2.517988582
7 -0.311806692 0.805632231 752 0.1195961 804.6666667 0.148449994
8 0.298926892 1.230229002 638 0.100959416 486.3333333 0.082065547
9 -0.218771095 0.859297084 10193 1.974042075 11081 2.297275425
10 0.963471865 1.949996947 1715 0.308477734 807.3333333 0.158193957
11 1.769798549 3.410063368 2294 0.467114654 733.6666667 0.136981224
12 -0.195292763 0.873395642 5026 0.938577237 5313 1.07463009
13 -0.151013908 0.900617298 10900 2.173554407 11174.66667 2.413405132
14 -0.10906322 0.927189915 12793 2.022361297 12848 2.181172663
15 -0.148343383 0.902285944 12387 2.381343506 12787.33333 2.639233739
16 -1.115730819 0.461457338 3154 0.523416153 6097.666667 1.134267699
17 -0.049896627 0.966005543 6584 1.386926788 6485.666667 1.435733777
18 -0.147944545 0.902535419 6321 1.208726868 6513.666667 1.339256989
19 -0.309488438 0.806927835 4900 0.751798366 5532.666667 0.931679802
20 -0.143289829 0.905452065 9866 1.526942565 9510.333333 1.686386971

Total number of rows: 3846

Table truncated, full table size 251 Kbytes.




Supplementary file Size Download File type/resource
GSM1062056_05_2011-01-21_532_No_ID_Slot_20.pair.gz 2.7 Mb (ftp)(http) PAIR
GSM1062056_05_2011-01-21_635_No_ID_Slot_20.pair.gz 2.7 Mb (ftp)(http) PAIR
Processed data included within Sample table
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