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Sample GSM1230411 Query DataSets for GSM1230411
Status Public on Mar 31, 2014
Title ΔIP_rpoBmutant
Sample type RNA
 
Channel 1
Source name ΔIP_rpoB(R512P)
Organism Staphylococcus aureus
Characteristics background strain: ΔIP
genotype/variation: rpoB mutation (R512P)
mic_van: 2
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
Organism Staphylococcus aureus
Characteristics background strain: ΔIP
genotype/variation: wild-type
mic_van: 0.5
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
Description Sample 1
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 Sep 12, 2013
Last update date Mar 31, 2014
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)
GSE50826 A Single Amino-Acid Substitution of RNA Polymerase ß subunit Confers A Novel Class of VISA phenotype on hVISA Strain Mu3

Data table header descriptions
ID_REF
VALUE normalized log2 ratio test/reference

Data table
ID_REF VALUE
1 0.134774887
2 0.460715623
3 1.233558446
4 1.094404835
5 0.535593313
6 0.288528894
7 0.418628123
8 0.596436568
9 -0.032224859
10 -0.70453564
11 -0.527192122
12 -0.813865912
13 -0.364059709
14 -0.405448995
15 -0.314455356
16 -1.593161197
17 -0.094010228
18 -0.286728789
19 -0.315215242
20 -0.137064798

Total number of rows: 3846

Table truncated, full table size 64 Kbytes.




Supplementary file Size Download File type/resource
GSM1230411_120224_IP_rpoB_R512P_.txt.gz 80.9 Kb (ftp)(http) TXT
GSM1230411_12_No_ID_Slot_19_2012-02-24_532.pair.gz 2.7 Mb (ftp)(http) PAIR
GSM1230411_12_No_ID_Slot_19_2012-02-24_635.pair.gz 2.7 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file
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