M. tuberculosis mycP1-eccE1 deletion mutant
The M. tuberculosis delta mycP1-eccE1 mutant was grown in 10mL 7H9 broth to OD600 0.8. Bacteria were harvested by centrifugation and DNA was extracted using the QIAmp UCP pathogen kit (Qiagen) as described previously (Avanzi, Del Pozo et al. 2016). DNA was quantified using the Qubit dsDNA HS Assay Kit and the Qubit 2.0 Fluorometer (Thermo Fisher Sc.). Ilumina libraries were prepared using the Kapa Hyper prep kit as described (Avanzi et al. 2016). Briefly, 1g of extracted DNA was sonicated to obtain 400 bp long fragments with the S220 Covaris (Covaris) using the manufacturer's protocol and purified using 1.8X AMPure beads (ThermoFisher Sc.) and eluted in 50L of Tris-HCl 10mM. Sequencing libraries were synthesized with the Kapa Hyper prep kit (Kapa Biosystems) according to the manufacturers instructions and an adapter stock of 15M of PentAdaptersTM (PentaBase) were used to barcode the library. After the final amplification step, libraries were then quantified using Qubit dsDNA BR Assay Kit (Thermo Fisher Sc) and the fragment size was assessed on a Fragment Analyzer (Advanced Analytical Technologies).