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Sample GSM1062053 Query DataSets for GSM1062053
Status Public on Apr 19, 2016
Title ΔIP1_VCM 10mg/L_OD1.0
Sample type RNA
 
Channel 1
Source name ΔIP1_V10_OD1
Organism Staphylococcus aureus
Characteristics another strain name: H14
background strain: deltaIP
genotype: vraS 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 ΔIP1_OD1
Organism Staphylococcus aureus
Characteristics another strain name: H14
background strain: deltaIP
genotype: vraS 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 -0.252479127 0.83945266 11146 2.268993043 14020.33333 2.70294342
2 0.076008481 1.05409762 17944 4.21235259 18181.66667 3.996169339
3 0.007690481 1.005344868 8409 1.579340697 8863.333333 1.570944207
4 -0.360458058 0.778917233 8316 1.57082774 11378.33333 2.016681201
5 -0.533044253 0.691094904 11077 2.35654493 16638 3.409871662
6 -0.592943407 0.662988887 11286 1.951701885 18111.33333 2.94379276
7 -0.787588902 0.579311455 755 0.150102118 1544.666667 0.259104349
8 -0.091321653 0.938662447 696 0.153673065 956 0.163714938
9 -0.609480906 0.65543249 9287 1.96691084 15056.66667 3.000935826
10 -0.219871592 0.858641857 1049 0.224734388 1468 0.261732393
11 0.508368299 1.422440492 1841 0.386191458 1541.666667 0.271499202
12 -0.278126597 0.824661181 5293 1.064373752 7090 1.290680071
13 -0.39255725 0.761778117 10777 2.084528943 14823.66667 2.736399087
14 -0.249458024 0.841212374 12721 2.253741819 15752.33333 2.67915914
15 -0.242110626 0.845507452 9954 1.889326589 12386.66667 2.234547532
16 -2.072456046 0.237754401 2083 0.434480515 9353.666667 1.827434162
17 0.328399463 1.255619607 8643 1.679901258 7423.333333 1.337906201
18 -0.099758027 0.933189495 6906 1.379856687 8007.333333 1.478645756
19 -0.381968678 0.767389708 5439 0.996399999 7736.666667 1.298427628
20 -0.33136462 0.794784355 9697 1.691777943 12913.66667 2.128599955

Total number of rows: 3846

Table truncated, full table size 251 Kbytes.




Supplementary file Size Download File type/resource
GSM1062053_02_2011-01-21_532_327941.pair.gz 2.7 Mb (ftp)(http) PAIR
GSM1062053_02_2011-01-21_635_327941.pair.gz 2.7 Mb (ftp)(http) PAIR
Processed data included within Sample table
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