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Sample GSM185051 Query DataSets for GSM185051
Status Public on May 01, 2007
Title KT2440(pCAR1deltaORF70)_succinate_rep2
Sample type RNA
 
Source name KT2440(pCAR1delta0RF70)_succinate
Organism Pseudomonas putida
Characteristics Pseudomonas putida KT2440(pCAR1deltaORF70)
Growth protocol 100 ml of Nitrogen-plus Mineral Medium-4 supplemented with 1.0 mg ml-1 sodium succinate was inoculated by overnight culture in Luria broth to obtain initial optical densities at 600 nm (OD600) of 0.05. Cultures were incubated at 30˚C in a rotating shaker at 120 rpm to exponential phase.
Extracted molecule total RNA
Extraction protocol A total of 1 × 10^9 cells were mixed with RNA Protect Bacteria reagent (Qiagen, Valencia, CA) as recommended by the manufacturer. Total RNA was extracted using the RNeasy Midi kit (Qiagen). The eluted RNA was treated with RQ1 RNase-free DNase (Promega, Madison, WI) at 37˚C for 1 h. After the inactivation of the DNase by the addition of the stop reagent, and subsequent incubation at 65˚C for 15 min, RNA samples were again purified with the RNeasy Mini column according to the manufacturer’s clean-up protocol (Qiagen).
Label Cy3
Label protocol Samples were labeled by Nimblegen Systems, Inc.
www.nimblegen.com
 
Hybridization protocol Hybridization was performed by Nimblegen Systems, Inc.
www.nimblegen.com
Scan protocol Scan was performed by Nimblegen Systems, Inc.
www.nimblegen.com
Description Exponential phase
Data processing Microarray data analysis was performed using the robust multi-array average (RMA) method (Irizarry et al., 2003) based on log2 values of absolute signal intensities for PM probes only.
 
Submission date Apr 27, 2007
Last update date May 01, 2007
Contact name Masatoshi Miyakoshi
E-mail(s) mmiyakoshi@ige.tohoku.ac.jp
Organization name Tohoku University
Department Department of Environmental Life Sciences
Lab Laboratory of Microbial Genetics
Street address Aoba-ku, Katahira, 2-1-1
City Sendai
State/province Miyagi
ZIP/Postal code 980-8577
Country Japan
 
Platform ID GPL5128
Series (1)
GSE7650 Transcriptional network between pCAR1 and KT2440 chromosome

Data table header descriptions
ID_REF
VALUE Normalized log2 signal data.

Data table
ID_REF VALUE
PPUT041000000001 6.472513
PPUT041000000002 7.042947
PPUT041000000003 6.493084
PPUT041000000004 7.188569
PPUT041000000005 6.208432
PPUT041000000006 7.228023
PPUT041000000007 6.429608
PPUT041000000008 8.490264
PPUT041000000009 6.265903
PPUT041000000010 6.140338
PPUT041000000011 6.870017
PPUT041000000012 6.536662
PPUT041000000013 6.635635
PPUT041000000014 6.389833
PPUT041000000015 6.151744
PPUT041000000016 6.574202
PPUT041000000017 5.762403
PPUT041000000018 6.514178
PPUT041000000019 6.333827
PPUT041000000020 6.201312

Total number of rows: 5561

Table truncated, full table size 140 Kbytes.




Supplementary file Size Download File type/resource
GSM185051.pair.gz 1.6 Mb (ftp)(http) PAIR

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