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Sample GSM1062052 Query DataSets for GSM1062052
Status Public on Apr 19, 2016
Title ΔIP_VCM 10mg/L_OD1.0
Sample type RNA
 
Channel 1
Source name ΔIP_V10_OD1
Organism Staphylococcus aureus
Characteristics strain: deltaIP
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 ΔIP_OD1
Organism Staphylococcus aureus
Characteristics strain: deltaIP
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 Cy3 intensity

Data table
ID_REF VALUE PRE_VALUE CH1_S CH1_normS CH2_S CH2_normS
1 0.039522375 1.027773511 19161.66667 3.507574496 17664.66667 3.412789353
2 0.42299074 1.340703986 25599 5.841377264 19508.33333 4.356947787
3 0.246419911 1.186259722 12677.66667 2.176937434 9051 1.835127159
4 -0.115192014 0.923259422 11487 1.915581773 10717.33333 2.074803384
5 -0.217170205 0.860251135 14592 2.628153047 15290 3.055099774
6 0.07701848 1.054835829 14517.66667 2.507509154 12841.33333 2.377155843
7 -1.169907091 0.444449962 1724.333333 0.272972172 3238 0.614179762
8 -0.582659522 0.667731719 626.6666667 0.103535672 817.6666667 0.155055794
9 -0.472391943 0.720768595 13053 2.508646694 16151.66667 3.480516093
10 -0.270549741 0.829003593 1269.333333 0.221876586 1272.333333 0.26764249
11 0.304566188 1.235047208 1561 0.27189901 1067 0.220152727
12 0.133913599 1.097266222 6040.666667 1.024729995 4778.666667 0.933893684
13 -0.194487333 0.873883378 10960.66667 1.986111967 10783.33333 2.272742584
14 -0.494344404 0.709884194 11328.33333 1.582040621 14047.33333 2.228589726
15 0.078183061 1.055687663 10586 1.839809697 9177.666667 1.742759493
16 -1.269929166 0.414680133 4969.333333 0.93987559 10115.33333 2.266507403
17 0.515135883 1.429128739 14177 2.842426014 8597.666667 1.988922297
18 0.176776662 1.130355567 9627.333333 1.622339063 7405.333333 1.435246669
19 -0.09387039 0.937005623 7489.666667 1.209165097 6888 1.290456607
20 -0.18279028 0.880997433 12357.66667 1.890641557 12021.66667 2.146023912

Total number of rows: 3846

Table truncated, full table size 269 Kbytes.




Supplementary file Size Download File type/resource
GSM1062052_01_2011-01-21_532_No_ID_Slot_8.pair.gz 2.7 Mb (ftp)(http) PAIR
GSM1062052_01_2011-01-21_635_No_ID_Slot_8.pair.gz 2.7 Mb (ftp)(http) PAIR
Processed data included within Sample table
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