Development of Sinorhizobium meliloti pilot macroarrays for transcriptome analysis.
In order to prepare for whole-genome expression analysis in Sinorhizobium meliloti, pilot DNA macroarrays were designed for 34 genes of known regulation. The experimental parameters assessed were the length of the PCR products, the influence of a tag at the 5' end of the primers, and the method of RNA labeling. Variance and principal-component analysis showed that the most important nonbiological parameter was the labeling method. The sizes of PCR products were also found to be important, whereas the influence of 5' tags was minimal. The variability between replicated spots on a membrane was found to be low. These experimental procedures were validated by analyzing the effects of microaerobic conditions on gene expression.
Bergès
Hélène
H
Laboratoire de Biologie Moléculaire des Relations Plantes-Microorganismes, UMR215 CNRS-INRA, 31326 Castanet-Tolosan Cedex, France.
Lauber
Emmanuelle
E
Liebe
Carine
C
Batut
Jacques
J
Kahn
Daniel
D
de Bruijn
Frans J
FJ
Ampe
Frédéric
F
D000704:Analysis of Variance; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D015342:DNA Probes; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010100:Oxygen / Q000494:pharmacology; D016133:Polymerase Chain Reaction; D012329:RNA, Bacterial / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016962:Sinorhizobium meliloti / Q000235:genetics / Q000254:growth & development / Q000378:metabolism*; D014158:Transcription, Genetic
D001426:Bacterial Proteins; D015342:DNA Probes; D012329:RNA, Bacterial; D012333:RNA, Messenger; D010100:Oxygen