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Sample GSM1062057 Query DataSets for GSM1062057
Status Public on Apr 19, 2016
Title ΔIP5_VCM 10mg/L_OD1.0
Sample type RNA
 
Channel 1
Source name ΔIP5_OD1
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 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 Cy3
Label protocol SuperScript Indirect cDNA Labeling System (Invitrogen Life Technologies, Carlsbad, California).
 
Channel 2
Source name ΔIP5_V10_OD1
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 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 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 -0.249182375 0.841373115 8499 1.807875217 6923 1.521097604
2 -0.35755918 0.780483923 20096 3.661007533 13310 2.857357522
3 -0.001942582 0.998654411 4014 0.716344115 3813 0.71538021
4 -0.040635555 0.972226555 7469 1.375863756 6957 1.33765128
5 -0.12781091 0.915219116 14875 2.600105914 12548 2.379666635
6 -0.159782738 0.895159867 19156 3.295657218 15634 2.950140078
7 -0.384903675 0.76583013 1367 0.112848039 1045 0.086422428
8 1.031154739 2.04365935 1541 0.146597048 1960 0.299594428
9 0.201897486 1.15021016 15506 3.9145601 17225 4.502566799
10 -0.504098243 0.705100963 1928 0.272285578 1394 0.191988823
11 -0.158175299 0.896157803 2115 0.300172787 1861 0.269002185
12 -0.286139932 0.820093363 5388 1.188558521 4170 0.974728955
13 -0.286486286 0.819896504 12937 2.710593421 10472 2.22240607
14 0.075699472 1.053871868 8384 1.151821726 8448 1.213872514
15 -0.153992965 0.898759509 16433 2.625891851 14268 2.360045271
16 -0.822807608 0.56534067 3703 0.665836722 2267 0.376424578
17 0.110078076 1.079286644 5785 1.296375911 5964 1.399161206
18 -0.15947439 0.895351211 8047 1.424933132 6910 1.275815605
19 0.081181378 1.057883954 5059 0.874555553 5072 0.925178287
20 -0.078004577 0.947367065 10016 1.140711795 7897 1.080672785

Total number of rows: 3846

Table truncated, full table size 234 Kbytes.




Supplementary file Size Download File type/resource
GSM1062057_2011-07-08_09v_No_ID_Slot_21_532.pair.gz 2.8 Mb (ftp)(http) PAIR
GSM1062057_2011-07-08_09v_No_ID_Slot_21_635.pair.gz 2.7 Mb (ftp)(http) PAIR
Processed data included within Sample table
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