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Series GSE2430

Query DataSets for GSE2430

Status

Public on May 10, 2006

Title

Azithromycin-treated PAO1 vs untreated PAO1

Organism

Pseudomonas aeruginosa

Experiment type

Expression profiling by array

Summary

Experimental Design

Type of experiment:
In order to evaluate the influence of subinhibitory concentrations of the macrolide antibiotic Azithromycin (AZM) on the global Pseudomonas aeruginosa gene expression, we performed a comparative gene expression analysis of AZM-treated versus untreated P. aeruginosa PAO1 cultures.

Experimental factors:
P. aeruginosa PAO1 cultures with and without addition of 2 µg/ ml AZM were grown until early stationary phase. Total RNA was extracted when the cultures reached an OD600 of 2.8.

The transcriptomes of the untreated cultures were taken as reference values. Both of the AFFYMETRIX Chips of AZM-treated PAO1 (GSM45590, GSM45591) were compared with each of the two chips of the untreated PAO1 (GSM45588, GSM45589).

Hybridization procedures and parameters:
Hybridization of the probes was carried out according to the manufacturer’s “Expression Analysis Protocol (p. 25: Modified Fluidic Protocol for P. aeruginosa cDNA Assay)”, see http://www.affymetrix.com:

Hybridization for 16 h at 50°C and 60 rpm.

- Post Hyb Wash 1: 10 cycles of 2 mixes/cycle with Wash Buffer A at 25°C
- Post Hyb Wash 2: 4 cycles of 15 mixes/cycle with Wash Buffer B at 50°C
- Stain: Stain the probe array for 10 minutes in Streptavidin Solution Mix at 25°C
- Post Stain Wash: 10 cycles of 4 mixes/cycle with Wash Buffer A at 30°C
- 2nd Stain Wash: Stain the probe array for 10 minutes in antibody solution at
25°C
- 3rd Stain Wash: Stain the probe array for 10 minutes in SAPE solution at 25°C
- Final Wash: 15 cycles of 4 mixes/cycle with Wash Buffer A at 30°C. The
holding temperature is 25°C.

Measurement of data and specifications:
Data transformation and selection procedures:
· The entire signals were scaled to 150 (4% capped median); scaling factors of the arrays were within 3.4 fold of each other, as the % genes called present were in the range of 23.7% and 38.1% for three arrays (GSM455889, GSM45589, GSM45591) and 74,4% for one array (GSM45590).
The background levels (Average Background) were similar for all arrays (in a range of 47.20 and 55.64). The Q scores were comparable (in a range of 2.38 and 2.81).
The Average Signals of the four arrays were similar (between 187.8 and 228.7).
· Scanning hardware: AFFYMETRIX Scanner; software: AFFYMETRIX MAS 5 (Statistical Algorithms Reference Guide, http://www.affymetrix.com/support/technical/technotes/statistical_reference_guide.pdf), MICRO DB 3 and DMT 3
· Image analysis software: AFFYMETRIX MAS 5

Data selection:
· Threshold of Signal Log ratio: -1/1; change is I (increased), MI (marginally increased), D (decreased), MD (marginally decreased); change p-value >0.999 or <0.001; only genes that are present (Detection=P) in at least one of the compared chipsets.
· Only following genes were considered: Minimal threshold of regulation ±2 fold; minimal change p-values of 0.999 and 0.001, respectively; minimal difference of signal intensities of 200.
· The final gene expression data table used by the authors to make their conclusions after data selection and transformation will be published as supplementary data.
Keywords: other

Contributor(s)

Nalca Y, Jaensch L, Bredenbruch F, Geffers R, Buer J, Haussler S, Jansch L

Citation(s)

16641435

Submission date

Mar 22, 2005

Last update date

Jul 06, 2016

Contact name

Yusuf Nalca

E-mail(s)

yna@gbf.de