Transcriptome analysis of TB cohorts

Assessment of the transcriptome of TST and monocytes from patients in cohort 1 (active and latent TB) was performed by RNA-Seq. cDNA libraries were generated using the KAPA Hyperprep kit (Roche), and sequencing was performed on the Illumina Nextseq using the Nextseq 500 High Output 75 cycle kit (Illumina) according to manufacturers’ instructions, giving 15-20 million 41bp paired end- reads per sample. Mapping and generation of read counts per transcript were done using Kallisto (72 (link)). The R/Bioconductor package tximport was used to import the mapped counts data and summarize the transcript-level data into gene level data (73 (link)).
The TST transcriptome from active TB cohort 2 was derived directly from the data repository E-MTAB-3254 (ArrayExpress), and transcriptional profiling of individuals with cured TB was performed by microarray, as previously described (5 (link)).