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Sample GSM1062055 Query DataSets for GSM1062055
Status Public on Apr 19, 2016
Title ΔIP3_VCM 10mg/L_OD1.0
Sample type RNA
 
Channel 1
Source name ΔIP3_V10_OD1
Organism Staphylococcus aureus
Characteristics another strain name: H14msrR*graR*
background strain: deltaIP
genotype: vraS, msrR, graR 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 ΔIP3_OD1
Organism Staphylococcus aureus
Characteristics another strain name: H14msrR*graR*
background strain: deltaIP
genotype: vraS, msrR, graR 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 0.347884985 1.272693469 10853 1.956713179 8172 1.537458332
2 0.452384359 1.368299794 20080 4.133461936 14656.33333 3.020874485
3 -0.110497376 0.926268671 5790 1.072056109 6204 1.157392171
4 -0.154734093 0.898297925 8278 1.35112973 9002 1.504099801
5 -0.213797889 0.862264334 12660 2.217648108 14169.33333 2.571888946
6 -0.122830198 0.918384248 15501 2.360807068 17161 2.570609277
7 -0.596632084 0.661295925 826 0.124161205 1375.666667 0.187754378
8 -0.070601073 0.952241181 1425 0.133676918 1103.666667 0.140381366
9 -0.910596315 0.531965167 11775 2.160337347 22276.33333 4.06105039
10 0.597131846 1.512706235 1016 0.182271158 787 0.120493427
11 0.562884591 1.477219888 2097 0.382209661 1489.666667 0.258735794
12 0.329640642 1.256700307 4890 0.847067268 3664 0.674040791
13 0.065396915 1.046372779 11346 2.023799743 10669 1.934109701
14 -0.491945852 0.711065393 11393 1.696156659 16258 2.385373661
15 0.147721298 1.107818317 11287 1.768750381 9892 1.596606911
16 -0.729360437 0.603171247 2464 0.406332353 3754 0.673660017
17 0.329586552 1.256653191 9021 1.698696962 7000.666667 1.351762741
18 0.315802711 1.24470401 9189 1.621917168 6969.666667 1.303054505
19 0.058279763 1.041223489 5596 0.885000844 5314 0.849962427
20 -0.098267958 0.934153826 12798 1.701604255 13412 1.821546096

Total number of rows: 3846

Table truncated, full table size 251 Kbytes.




Supplementary file Size Download File type/resource
GSM1062055_04_2011-01-21_532_No_ID_Slot_17.pair.gz 2.7 Mb (ftp)(http) PAIR
GSM1062055_04_2011-01-21_635_No_ID_Slot_17.pair.gz 2.7 Mb (ftp)(http) PAIR
Processed data included within Sample table
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