Table 1.

Transcriptome profiling and validation techniques used for Mtb sputum transcriptomics

Comparative transcriptomics of SMtb	RNA profiling method	Validation	#Transcript	Reference
SMtb vs culture with 7H10 agar /7H9 broth/Dubos a	Microarray	qRT-PCR	516	[29]
SMtb vs culture	Microarray	qRT-PCR	557	[89]
SMtb vs MAF/Mtb	qRT-PCR		2179	[90]
SMtb vs Exponential phase of liquid culture	Dual RNA seq	Nano String	198	[91]
SMtb vs Stationary phase of liquid culture	Dual RNA seq	Nano String	392	[91]
Sputum vs MGIT 460 culture	Microarray	qRT-PCR	1083	[92]
SMtb at Day 3 vs SMtb at day0 treatment	Microarray	qRT-PCR	109	[92]
SMtb at Day7/14 vs day 0 treatment	Microarray	qRT-PCR	39	[92]
Lipid rich Dubos brothb vs Dextrose rich Dubos brothb	RNA seq	qRT-PCR	–	[60]
SMtb/ BAL-Mtb vs 7H9/ DTAc culture	qRT-PCR		–	[93]
SMtb before Rx vs SMtb after Rx	qRT-PCR	qRT-PCR	2411	[94]
Sputum Mtb vS culture H37Rv	Microarray	qRT-PCR	–	[95]

^a7H10 agar with oleic acid-albumin-dextrose-catalase supplement or in 7H9 broth with albumin-dextrose-catalase supplement, 0.2% glycerol and 0.05% Tween-80. Hypoxic (non-replicating persistence) cultures M. tuberculosis strains H37Rv and CH were grown in Dubos Tween albumin broth. ^bDubos broth (Difco), without glycerol, containing 0.5% albumin, supplemented with either 0.2% dextrose or a lipid mixture (oleic acid, palmitic acid, stearic acid, at final concentration of 0.001% each, plus 0.01% cholesterol). ^c7H9 media (0.05% Tween 80, 0.2% glycerol, 10% ADC supplement)/ DTA: Dubos Tween albumin; for the NRP-2 model was grown in 100 mL Dubos Tween albumin (DTA). SMtb sputum-derived M. tuberculosis, Mtb Mycobacterium tuberculosis, vs versus, Rx treatment, MAF Mycobacterium africanum, L4 Lineage 4, qRT-PCR Real-Time Quantitative Reverse Transcription PCR, RNA seq RNA-sequencing, DTA Dubos Tween, BAL Broncho alveolar lavage