DMD Duchenne muscular dystrophy DGC Dystrophin-associated glycoprotein complex NMJ Neuromuscular junction VSN Variance stabilization and normalization RT-PCR Reverse transcription followed by polymerase chain reaction RT performed the microarray hybridisations, analysed the microarrays and wrote the draft of the paper.
Data in SEDM are presented for 100 microarray hybridisations with the additional 5 hybridisations provided by extra replicates for some of the 19 conditions as described above.
This approach confirmed the data from the microarray hybridisations, indicating that the CysR regulon consists of at least seven transcription units, by name cysIXHDNYZ, fpr2, ssuR, cg1514-cg4005, cg2810, cg3138-39, and 3372-75.
We also thank Dr Kate Gould for performing the microarray hybridisations and all the team at BμG@S (Bacterial Microarray Group at St George's, University of London) for their assistance.
GB printed the microarrays, supervised the microarray hybridisations and helped with the data analysis.
All 7 ORFs showed more than one band in the DNA of wild strain compared to the single band of strain Rm 1021, confirming that the higher intensity of the microarray hybridisation of the wild strain was indeed due to a duplication of the ORF.
The procedure for the microarray hybridisation and the subsequent analysis has been previously described by us (Chaturvedi et al, 2007).
The microarray hybridisations were done for the 12 samples (three scion/rootstock combinations with four biological replicates) by the Plateforme Biopuces, Institut National des Sciences Appliquées, Toulouse, France according to the manufacturer's instructions.
These results suggest that other sources of variation (e.g. day-to-day variation, labelling, chip-batches) are of greater influence on the total variation of microarray hybridisations rather than the RNA amplification itself.
WL participated in the study design, carried out microarray hybridisation, performed the statistical analysis, developed the analysis workflow, generated the new chip definition, carried out the laboratory validation experiments, performed the expression analysis of FOX genes, and drafted the manuscript.
