Cells were collected by centrifugation at 4,500rpm for 5 minutes at room temperature prior to storage in the -80 degree freezer.
Growth protocol
Bifidobacterium breve UCC2003 was grown in filtered reinforced clostridial medium (RCM; Oxoid Ltd.) and subcultured in modified Rogosa medium. Bifidobacterial cultures were incubated at 37°C, anaerobically in a modular, atmosphere-controlled system (Davidson and Hardy, Belfast, Ireland) to an optical density OD600 of 0.7.
Extracted molecule
genomic DNA
Extraction protocol
Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).RNA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).
Label
cy3
Label protocol
Labelling was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).
Channel 2
Source name
B. breve strain grown in modified Rogosa until OD.600 of 0.7
Cells were collected by centrifugation at 4,500rpm for 5 minutes at room temperature prior to storage in the -80 degree freezer.
Growth protocol
Bifidobacterium breve UCC2003 was grown in filtered reinforced clostridial medium (RCM; Oxoid Ltd.) and subcultured in modified Rogosa medium. Bifidobacterial cultures were incubated at 37°C, anaerobically in a modular, atmosphere-controlled system (Davidson and Hardy, Belfast, Ireland) to an optical density OD600 of 0.7.
Extracted molecule
genomic DNA
Extraction protocol
Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).RNA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).
Label
cy5
Label protocol
Labelling was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).
Hybridization protocol
Labelled total gDNA was hybridised as described in the Agilent manual Two-Color Microarray-Based Gene Expression Analysis (v4.0) (publication no. G4140-90050) to the B. breve UCC2003 microarray slides overnight at 65 °C.
Scan protocol
Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).
Description
CGH array
Data processing
Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5).
