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Sample GSM1062059 Query DataSets for GSM1062059
Status Public on Apr 19, 2016
Title ΔIP_VCM 10mg/L_OD2.0
Sample type RNA
 
Channel 1
Source name ΔIP_V10_OD2
Organism Staphylococcus aureus
Characteristics strain: deltaIP
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 ΔIP_OD2
Organism Staphylococcus aureus
Characteristics strain: deltaIP
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 -0.174538107 0.886051152 11678 2.092595821 12149.66667 2.36170995
2 -0.08734015 0.941256514 16990 3.787163159 17040.33333 4.02351867
3 -0.088365675 0.94058767 5846 1.107546513 5753 1.177504818
4 0.061699597 1.043694583 7068 1.319647872 6236.333333 1.264400423
5 -0.025853183 0.982239548 11227 2.121747389 10305.33333 2.160111953
6 0.057499216 1.040660304 10805 1.87824768 9470 1.804861464
7 -0.167649452 0.890292031 1141 0.210120479 1214.333333 0.236012985
8 0.2825944 1.216380337 4445 0.665397199 3433.666667 0.547030546
9 0.090897661 1.065032651 20851 4.270360313 18745.33333 4.009605065
10 0.130035913 1.094320942 634 0.117292607 547 0.107183005
11 0.121581826 1.087927054 618 0.106704671 534.3333333 0.098080722
12 -0.071239942 0.951819594 2326 0.415279993 2261.333333 0.43630116
13 -0.012078233 0.991662954 8531 1.555743184 7870.333333 1.568822529
14 -0.003861382 0.997327073 14386 2.473411113 13324.33333 2.48004008
15 0.051721056 1.036500675 9427 1.867497709 8388.666667 1.80173323
16 -0.061547363 0.958235812 603 0.108522157 567.3333333 0.113252036
17 0.013040253 1.009079788 11798 2.274150933 10789.33333 2.253687925
18 0.087025666 1.062178083 11499 2.026113016 10010.33333 1.907507836
19 0.042471508 1.029876617 9966 1.693192843 8748 1.644073489
20 0.082523902 1.058868844 15717 2.516051707 13841 2.376169363

Total number of rows: 3846

Table truncated, full table size 250 Kbytes.




Supplementary file Size Download File type/resource
GSM1062059_2011-01-13_1_Slot10_532.pair.gz 2.7 Mb (ftp)(http) PAIR
GSM1062059_2011-01-13_1_Slot10_635.pair.gz 2.7 Mb (ftp)(http) PAIR
Processed data included within Sample table
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