Spores for S. lividans TK21 were generated on Mannitol-Soy flour or R5 agar Cultures for genomic DNA preparation were performed in YEME medium with 0.5% glycine supplement at 30°C until early stationary phase (refer to T Kieser, MJ Bibb, MJ Buttner, KF Chater, DA Hopwood: Practical Streptomyces Genetics: The John Innes Foundation, Norwich, UK; 2000).
Extracted molecule
genomic DNA
Extraction protocol
Genomic DNA (gDNA) extraction was carried out using Kirby mix procedure as described elsewhere (T Kieser, MJ Bibb, MJ Buttner, KF Chater, DA Hopwood: Practical Streptomyces Genetics: The John Innes Foundation, Norwich, UK; 2000). About 500 µl of 20 µg/µl gDNA was sonicated briefly for 30-40 sec for shearing them to ~500 bp average size (confirmed by gel electrophoresis).
Label
Cy5
Label protocol
The DNA was labeled with Label IT® Cy5 Labeling Kit (Mirus Bio Corp., Madison, WI) according to suppliers instructions.
Spores for S. coelicolor M145 were generated on Mannitol-Soy flour or R5 agar Cultures for genomic DNA preparation were performed in YEME medium with 0.5% glycine supplement at 30°C until early stationary phase (refer to T Kieser, MJ Bibb, MJ Buttner, KF Chater, DA Hopwood: Practical Streptomyces Genetics: The John Innes Foundation, Norwich, UK; 2000).
Extracted molecule
genomic DNA
Extraction protocol
Genomic DNA (gDNA) extraction was carried out using Kirby mix procedure as described elsewhere (T Kieser, MJ Bibb, MJ Buttner, KF Chater, DA Hopwood: Practical Streptomyces Genetics: The John Innes Foundation, Norwich, UK; 2000). About 500 µl of 20 µg/µl gDNA was sonicated briefly for 30-40 sec for shearing them to ~500 bp average size (confirmed by gel electrophoresis).
Label
Cy3
Label protocol
The DNA was labeled with Label IT® Cy3 Labeling Kit (Mirus Bio Corp., Madison, WI) according to suppliers instructions.
Hybridization protocol
Samples containing ~500 ng each of Cy3 and Cy5 labeled gDNA from S. coelicolor M145 and S. lividans TK21 respectively were hybridized to a whole-genome S. coelicolor microarray as described previously (S Mehra, W Lian, KP Jayapal, SP Charaniya, DH Sherman, WS Hu: A framework to analyze multiple time series data: a case study with Streptomyces coelicolor. J Ind Microbiol Biotechnol 2006, 33:159-72).
Scan protocol
Hybridizations were carried out in triplicate for ~16 hr at 50°C; arrays were washed and scanned using ScanArray5000 (Perkin Elmer, Wellesley, MA). Images were analyzed using GenePix (Axon Instruments, Union City, CA) to obtain raw intensity data for each spot. The median fluorescence intensity from each spot was used for all subsequent analysis.
Description
No additional description
Data processing
Raw relative intensity values for each spot were first normalized by scaling one of the gDNA channel signal intensities by a normalization factor to set the total intensity from both channels as equal. Log2 hybridization signal ratios were then calculated from normalized intensities as log2[gDNASliv/gDNAScoe] and values were averaged using the median from triplicate experiments.
