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Sample GSM526117 Query DataSets for GSM526117
Status Public on Mar 31, 2011
Title wild-type (rifampicin 4 min)
Sample type RNA
 
Source name wild-type (rifampicin 4 min)
Organism Shigella sonnei
Characteristics srain: MS390
genome/variation: wild-type
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.
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).
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.
Label Cy3
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.
 
Hybridization protocol Hybridization was performed by Roche NimbleGen following their standard operating protocol. See www.nimblegen.com.
Scan protocol Scanning was performed by Roche NimbleGen following their standard operating protocol. See www.nimblegen.com.
Description Wild-type S. sonnei culture. Rifampicin treatment for 4 minutes.
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.).
 
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
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
 
Platform ID GPL10252
Series (1)
GSE21051 Expression analysis of Shigella sonnei MS390 delta-rodZ mutant

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
SSON_0001 1760.05
SSON_0002 1099.77
SSON_0003 671.86
SSON_0004 391.19
SSON_0005 473.43
SSON_0006 97.38
SSON_0007 1360.47
SSON_0009 7931.78
SSON_0010 118.60
SSON_0011 63.51
SSON_0012 94.53
SSON_0013 61.55
SSON_0014 4725.49
SSON_0015 789.47
SSON_0016 117.63
SSON_0017 4892.70
SSON_0018 952.09
SSON_0019 3809.37
SSON_0020 6713.71
SSON_0021 85.68

Total number of rows: 4467

Table truncated, full table size 74 Kbytes.




Supplementary file Size Download File type/resource
GSM526117_27109702_532.pair.gz 968.8 Kb (ftp)(http) PAIR
GSM526117_27109702_532_RMA.calls.gz 47.7 Kb (ftp)(http) CALLS
GSM526117_27109702_532_calls.txt.gz 384.0 Kb (ftp)(http) TXT
GSM526117_27109702_532_norm_RMA.pair.gz 1006.6 Kb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file

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