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Sample GSM1062064 Query DataSets for GSM1062064
Status Public on Apr 19, 2016
Title ΔIP5_VCM 10mg/L_OD2.0
Sample type RNA
 
Channel 1
Source name ΔIP5_V10_OD2
Organism Staphylococcus aureus
Characteristics another strain name: H14msrR*graR*rifR-fdh2*
background strain: deltaIP
genotype: vraS, msrR, graR mutation (replacement), rpoB mutant (selection with 1 mg/liter rifampin), fdh2 mutation (replacement)
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 ΔIP5_OD2
Organism Staphylococcus aureus
Characteristics another strain name: H14msrR*graR*rifR-fdh2*
background strain: deltaIP
genotype: vraS, msrR, graR mutation (replacement), rpoB mutant (selection with 1 mg/liter rifampin), fdh2 mutation (replacement)
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 0.035442786 1.024871324 9476 1.833171034 8479 1.788684092
2 -0.151902488 0.900062763 14661 3.149143594 14443 3.498804442
3 0.102737646 1.073809181 7005 1.328174669 5997 1.23688146
4 0.169861644 1.124950595 10151 1.860573969 8418 1.65391616
5 0.003976063 1.002759798 14190 2.937273652 12778 2.929189679
6 0.09957079 1.071454651 15059 2.917309949 12898 2.722756344
7 -0.02785363 0.980878515 283 0.047953268 256 0.04888808
8 0.298600686 1.229950868 1014 0.192410461 769 0.156437518
9 -0.126210998 0.916234633 11731 2.398409452 12179 2.617680411
10 -0.272640749 0.827802925 1611 0.300034191 1762 0.362446402
11 -0.010000463 0.993092176 1441 0.274242963 1296 0.276150562
12 -0.115602627 0.922996686 4940 0.989455771 4698 1.072003601
13 0.037362606 1.026236046 11798 2.525011187 10760 2.460458484
14 0.059492354 1.04209901 9459 1.490093065 8400 1.429895865
15 0.09773839 1.070094636 13910 2.468761363 12090 2.307049563
16 0.038260871 1.026875211 1038 0.194507843 946 0.189417215
17 0.033333828 1.023374243 8735 1.662409611 7904 1.624439566
18 0.044243984 1.031142687 9800 1.878794277 8751 1.82205072
19 0.140991042 1.102662316 9138 1.726603426 7515 1.565849672
20 0.132327241 1.096060353 10312 2.022181627 8484 1.844954633

Total number of rows: 3846

Table truncated, full table size 231 Kbytes.




Supplementary file Size Download File type/resource
GSM1062064_12_2012-05-13_532.pair.gz 2.6 Mb (ftp)(http) PAIR
GSM1062064_12_2012-05-13_635.pair.gz 2.6 Mb (ftp)(http) PAIR
Processed data included within Sample table
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