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The raw data from genotyping experiment processed on 59 samples is given in Additional file 2: Table S1.

Gene expression profiles were generated twice for each sample using standard cartridge format (mouse gene 1.0ST arrays, samples are hybridized separately over 2 days) and using the newer peg format arrays (mouse gene 1.1S T arrays, samples processed on two arrays of 24 samples each).

The average number of samples processed on each day having contamination was 8, ranging from 3 samples to 21 samples.

Blood samples were processed on the day of collection and serum samples were stored at −80 °C in amber glass vials until analysis.

Samples processed on MAXUS4 have been analyzed ex situ and their particle populations have been compared to references obtained under gravity.

Laboratory cross-contamination was investigated in any case where 2 samples processed on the same day grew M. tuberculosis.

Filtered datasets of integration sites were analyzed for cross-contamination between samples processed on the same day and sequenced in the same Illumina run.

The main effect was attributable to subgroups of samples processed on the same day.

All RNA samples processed on Affymetrix microarrays had an RNA integrity number >6.7 and a 260/280 ratio >1.65.

To this end, we analyzed the variability on data set B, where two groups of samples processed on different days were present.

These samples were processed on the same day, typically within 6 hours of sample collection, and stored at -70°C until bioassays were performed.