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Sample GSM111424 Query DataSets for GSM111424
Status Public on Jun 01, 2006
Title biological rep3 sample b IAA
Sample type RNA
 
Source name Escherichia coli K12 growing in exponential growth phase
Organism Escherichia coli K-12
Characteristics Genotype: wild type strain MG1655
Age: 5 days old liquid colture, 4-times subcultivated
Treatment protocol Exponentially growing E. coli K-12 (MG1655) cultures (OD600 = 0.6) was treated with an IAA solution to a final concentration of 0.5 mM. After two hours (OD600 = 1.2) different cell batches were aliquoted, frozen in liquid nitrogen for 5 min and stored at –80 °C for use in experiments.
Growth protocol E.coli cells were grown aerobically at 37 °C in M9 minimal medium containing: 20 mg l-1 uracil, 1 mg l-1 thiamine, 0.4 % L-arabinose as carbon source, and supplemented with 40 mg l-1 casein acid hydrolysate.
Extracted molecule total RNA
Extraction protocol Total RNA was purified from cells grown in M9 arabinose medium using the RNeasy Mini-Kit from QIAGEN by following the manufacturer’s instructions.
Label 33P
Label protocol 33P-labelled probes were prepared using E. coli gene-specific primers (Sigma-Genosys) following the protocol provided by the manufacturer, except that the reaction mixture contained 40 mCi of [a-33P]dCTP (1,000 to 3,000 Ci mmol-1;Amersham Pharmacia), and 200 U of Superscript II (Promega) in 30 ml volume. Unincorporated-radiolabelled nucleotides were removed by applying the reaction mixture to a Sephadex G-25 gel filtration spin column.
 
Hybridization protocol After incubation for 2 h at 65 °C, the pre-hybridisation solution was replaced with 3 ml of hybridisation buffer containing the denatured radioactively labelled cDNA probes. Filter hybridisations were carried out for 16 h in a hybridisation oven. The filters were then washed three times, for 5 min each, at room temperature and then three times at 65 °C of warmed wash solution.
Scan protocol The exposed phosphorimager screens were scanned at 100 mm resolution using a STORM 445 PhosphorImager (Molecular Dynamics).
Description Gene expression data from late exponentially growing E. coli cells
Data processing The signal intensities were measured by Image-Quant (version 3.0) software (Molecular Dynamics). Background values were measured in the surrounding region of the four corner grids containing E. coli genomic DNA, as a positive control, and empty spots. To avoid extreme intensity ratio for genes close to or below the detection limit, signal intensity values corresponding to a signal-to-background (S/B) ratio < 2.0 were scaled up to a value corresponding to the normalised background means.
 
Submission date May 30, 2006
Last update date May 31, 2006
Contact name Roberto Defez
E-mail(s) [email protected]
Phone +390816132440
Fax +390816132706
URL http://www.igb.cnr.it
Organization name National Research Council
Department Institute of Genetics and Biophysics
Lab Microbial Biotechnology
Street address via Castellino 111
City Napoli
ZIP/Postal code 80131
Country Italy
 
Platform ID GPL189
Series (1)
GSE4941 Expression data from untreated and IAA treated cells

Data table header descriptions
ID_REF Spot number
VALUE Image-Quant-calculated Signal intensity
Raw_Data

Data table
ID_REF VALUE Raw_Data
385 440.4833946 57.11
481 491.0799814 63.67
577 1030.828326 133.65
673 8432.275974 1093.27
9 1521.522663 197.27
105 1704.781032 221.03
201 994.8091095 128.98
297 646.6490598 83.84
393 2489.028126 322.71
489 612.9437116 79.47
585 1399.350417 181.43
681 645.2607388 83.66
17 769.1298216 99.72
113 1996.328437 258.83
209 808.5427116 104.83
305 1082.119073 140.3
401 968.5081398 125.57
497 1195.035846 154.94
593 1220.719784 158.27
689 1433.364281 185.84

Total number of rows: 4314

Table truncated, full table size 96 Kbytes.




Supplementary data files not provided

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