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Status |
Public on Mar 31, 2011 |
Title |
wild-type (rifampicin 4 min) |
Sample type |
RNA |
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Source name |
wild-type (rifampicin 4 min)
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Organism |
Shigella sonnei |
Characteristics |
srain: MS390 genome/variation: wild-type
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Treatment protocol |
Half of the samples (200 ml) were taken at OD = 0.8, then proceed to extract protocol. The remaining halves were continued the incubation in the presence of rifampicin (100 microgram per ml) for 4 minutes at 37°C. Then proceed to extract protocol.
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Growth protocol |
Strains were grown in LB medium (37°C, 180 rpm) to OD 600 = 0.8. 400 ml fermentors per strain (wild-type and the deletion mutant of rodZ gene).
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Extracted molecule |
total RNA |
Extraction protocol |
Cells were immediately mixed with 15 ml of 5% acid-phenol in ethanol (Bhagwat et al, Microbiol Methods 55(2): 399), then chilled on ice, centrifuged, and the pelletted before storing at –80°C. Total RNA was extracted using the RNeasy Midi kit (Qiagen), and DNA was removed by digestion with RNase-Free DNase I. RNA quality and concentration was checked with an Agilent bioanalyzer at the University of Florida Gene Expression core before submitting the RNA to Roche Nimblegen in Iceland for analysis.
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Label |
Cy3
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Label protocol |
Conversion of RNA to cDNA and labeling with Cy3 was performed by Roche NimbleGen following their standard operating protocol. See www.nimblegen.com.
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Hybridization protocol |
Hybridization was performed by Roche NimbleGen following their standard operating protocol. See www.nimblegen.com.
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Scan protocol |
Scanning was performed by Roche NimbleGen following their standard operating protocol. See www.nimblegen.com.
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Description |
Wild-type S. sonnei culture. Rifampicin treatment for 4 minutes.
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Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package (Roche NimbleGen, Inc.).
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Submission date |
Mar 24, 2010 |
Last update date |
Mar 31, 2011 |
Contact name |
Jiro Mitobe |
E-mail(s) |
jmitobe@nih.go.jp
|
Phone |
813-5285-1111
|
Fax |
813-5285-1163
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Organization name |
National Institute of Infectious Diseases
|
Department |
Bacteriology
|
Street address |
1-23-1 Toyama
|
City |
Shinjuku |
State/province |
Tokyo |
ZIP/Postal code |
162-8640 |
Country |
Japan |
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Platform ID |
GPL10252 |
Series (1) |
GSE21051 |
Expression analysis of Shigella sonnei MS390 delta-rodZ mutant |
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