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Sample GSM1062054 Query DataSets for GSM1062054
Status Public on Apr 19, 2016
Title ΔIP2_VCM 10mg/L_OD1.0
Sample type RNA
 
Channel 1
Source name ΔIP2_V10_OD1
Organism Staphylococcus aureus
Characteristics another strain name: H14msrR*
background strain: deltaIP
genotype: vraS, msrR mutation (replacement)
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 ΔIP2_OD1
Organism Staphylococcus aureus
Characteristics another strain name: H14msrR*
background strain: deltaIP
genotype: vraS, msrR mutation (replacement)
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 -0.156823176 0.896998094 11857 2.194187629 12248.33333 2.446145253
2 0.324312292 1.252067457 19977 4.511567553 16010.66667 3.603294318
3 0.037166245 1.026096378 9903 1.631877231 7647.666667 1.590374224
4 -0.293705733 0.815803876 8989 1.62270683 10327 1.989089384
5 -0.446257389 0.733944365 13472 2.522180589 16892.66667 3.436473813
6 -0.580839922 0.668574427 13122 2.252117864 18826 3.368537254
7 -1.419779512 0.373769431 852 0.141958698 2043.666667 0.379802857
8 -0.012262551 0.991536268 665 0.12350121 691.3333333 0.124555413
9 0.185941889 1.137559406 12719 2.288930534 11031.33333 2.012141539
10 -0.197735152 0.87191829 1333 0.252063247 1401 0.289090445
11 0.624159479 1.541312588 2252 0.376938194 1368.666667 0.244556618
12 -0.350485255 0.784320245 6136 1.041668176 7378.333333 1.328115884
13 -0.425998221 0.744323545 11692 2.203053028 14724.33333 2.95980564
14 -0.271722263 0.82833011 11510 1.98990885 13439.66667 2.402313795
15 -0.337232534 0.791558272 10871 1.972062958 12618 2.491368011
16 -1.129452059 0.457089296 2933 0.547621023 5888.666667 1.198061357
17 0.340336056 1.266051469 9481 1.868556885 7162 1.475893303
18 -0.11932209 0.920620141 8586 1.551973375 8855 1.685791247
19 -0.321008515 0.800510086 6084 1.080286168 7162.333333 1.34949726
20 -0.335917203 0.792280279 9997 1.820917017 11915 2.2983243

Total number of rows: 3846

Table truncated, full table size 250 Kbytes.




Supplementary file Size Download File type/resource
GSM1062054_03_2011-01-21_532_327844.pair.gz 2.7 Mb (ftp)(http) PAIR
GSM1062054_03_2011-01-21_635_327844.pair.gz 2.7 Mb (ftp)(http) PAIR
Processed data included within Sample table
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