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Sample GSM1062065 Query DataSets for GSM1062065
Status Public on Apr 19, 2016
Title Mu50_VCM 10mg/L_OD2.0
Sample type RNA
 
Channel 1
Source name Mu50_V10_OD2
Organism Staphylococcus aureus
Characteristics strain: Mu50
genotype (compare to deltaip）: vraS, msrR, graR, rpoB, fdh2 mutation
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 Mu50_OD2
Organism Staphylococcus aureus
Characteristics strain: Mu50
genotype (compare to deltaip）: vraS, msrR, graR, rpoB, fdh2 mutation
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 -0.217105446 0.86028975 8980 1.547749572 9213.333333 1.799102653
2 0.126351472 1.091529765 14565 2.63521158 12110 2.414237031
3 -0.206323248 0.866743341 5741 0.876259463 6267 1.01097917
4 -0.240348745 0.846540652 8976 1.365943444 9501.333333 1.613559184
5 -0.014335421 0.990112648 15262 2.647296462 13969.66667 2.673732598
6 0.04916657 1.034667035 20062 3.434160082 17813.66667 3.319096837
7 -0.078055906 0.94733336 482 0.074486377 538 0.078627419
8 0.437616855 1.354365243 907 0.153322452 859.3333333 0.113206133
9 0.203161595 1.151218431 14765 2.561012021 11393.33333 2.224609989
10 -0.089666611 0.939739887 1325 0.234061303 1380.333333 0.249070307
11 -0.123942978 0.917676152 1733 0.303143675 1846 0.330338404
12 -0.037237286 0.974519335 4642 0.659320042 4352.666667 0.676559221
13 0.024589533 1.017190246 15183 2.442912816 13426.66667 2.401628236
14 0.030742672 1.021537859 15146 2.345548616 13442 2.296095633
15 0.030505735 1.021370103 18156 2.960889753 16605 2.898939125
16 0.332614592 1.259293522 2332 0.433887587 1931.333333 0.344548415
17 0.107097027 1.077058811 9636 1.646544937 7895.666667 1.528741904
18 0.079415199 1.056589662 13058 2.238882701 11091.66667 2.118970857
19 -0.006891508 0.995234562 11614 1.766464281 10540.33333 1.774922565
20 -0.13301538 0.911923444 15961 2.51422683 16320.33333 2.757059101

Total number of rows: 3846

Table truncated, full table size 250 Kbytes.




Supplementary file Size Download File type/resource
GSM1062065_2011-01-13_6_Slot25_532.pair.gz 2.7 Mb (ftp)(http) PAIR
GSM1062065_2011-01-13_6_Slot25_635.pair.gz 2.7 Mb (ftp)(http) PAIR
Processed data included within Sample table
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