Project name: Rhodopseudomonas palustris

Description: We used transcriptome analysis to identify genes that were differentially expressed between wild-type (CGA010) and hupV mutant cells (CGA009) grown photoheterotrophically with malate under nitrogen-fixing conditions. We also compared the transcriptome of a hupS mutant with that of the wild type.Keywords: Genetic modificationOverall design: RNA was isolated from various Rhodopseudomonas palustris strains that were grown to the mid-logarithmic phase of growth. Fluorescently labeled cDNA was prepared by direct incorporation of either Cy3-dCTP or Cy5-dCTP during a first-strand reverse transcription reaction. The hybridization mixtures containing the two labeled cDNA samples to be compared were applied to microarray slides that had been covered with Lifterslips (Erie Scientific Company, Portsmouth, NH). The slides were assembled with hybridization chambers (Corning, Corning, NY) and submerged in a 65ºC water bath. After 14-16 h of hybridization, the slides were washed and scanned with a ScanArray 4000XL scanner (PerkinElmer, Boston, MA). Images (Cy3 and Cy5) were captured as TIFF files and were analyzed with the image processing software ImaGene version 5.6 (BioDiscovery, Inc., El Segundo, CA). The software package lcDNA was used for data normalization and assessment of the statistical confidence intervals of gene expression. Duplicate calibration experiments and three comparative experiments using RNA from three separately grown cultures (three biological replicates) with duplicate slides for each (10 slides in total) were used to generate each data set.

Data type: Transcriptome or Gene expression

Sample scope: Multiisolate

Relevance: Industrial

Release date: 2006-11-03

Last updated: 2006-03-01