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DNA used in the microarray hybridisations was extracted from 5 ml of an overnight culture (18 h) of MRSA252 using the Edge Biosystems Bacterial Genomic DNA purification kit according to manufacturer's instructions.

Total RNA for use in the microarray hybridisations was extracted as described for the cDNA library construction above.

A loop design, in which consecutive moult stages were compared via dual channel microarray hybridisations, was employed for the analysis.

Amplified and fluorescently labelled cRNA (complimentary RNA) for microarray hybridisations was prepared in accordance with the Two-Color Microarray-Based Gene Expression Analysis - Low Input Quick Amp Labelling Protocol v6.6 (Agilent Technologies, USA).

Microarray hybridisations were performed for each of the five basal and luminal samples, hybridising each against universal reference cDNA.

Microarray hybridisations were conducted as previously described [67] with 5 µg Cy5-labelled cDNA derived from amplified M. tuberculosis RNA against 2 µg Cy3-labelled M. tuberculosis H37Rv genomic DNA.

Altogether, 18 microarray hybridisations were performed.

Microarray hybridisations were performed by the VIB MicroArrays Facility (http://www.microarrays.be).be

Microarray hybridisations were performed in SureHyb hybridisation chambers in a DNA Microarray Hybridisation Oven (Agilent Technologies).

Microarray hybridisations were performed in a Lucidea semi-automated system (GE Healthcare), without a pre-hybridisation step.

Nine microarray hybridisations were carried out in total as part of this design.