Transcriptomic changes associated with deletion of Rv3143 from Mycobacterium tuberculosis H37Rv in relation to wild-type strain grown in 7H9/OADC medium

RNA-Seq results accompanying submission of a manuscript: "The orphan response regulator Rv3143 modulates the activity of the NADH dehydrogenase complex (Nuo) in Mycobacterium tuberculosis via protein-protein interactions" describing the function of the Rv3143 "orphan" response regulator of the two-component signal transduction systems family, which enable mycobacterial cells to quickly adapt and adequately respond to adverse environmental conditions encountered at various stages of host infection. We identified the Rv3143 protein as an interaction partner for NADH dehydrogenase complex involved in oxidative phosphorylation. We propose that the regulatory protein Rv3143 is a component of the complex and modulates its activity. Overall design: Next generation sequencing results are provided in three independent biological replicates for each strain growing in standard 7H9/10% OADC medium. The effect of Rv3143 removal on M. tuberculosis transcriptome was analysed on 7H9/10% OADC medium. The bacteria were grown to mid-logarythmic phase of growth, when they were collected and total RNA was isolated. The resulting RNA was subjected to ribodepletion with RiboZero Bacteria kit (Illumina, San Diego, CA, USA) and used for preparation of sequencing libraries,generated with a KAPA-stranded RNA Seq kit according to the manufacturer's protocol (Roche Diagnostics, Rotkreuz, Switzerland). The resulting adapter-ligated, PCR-amplified cDNA libraries were subjected to sequencing on a NextSeq500 sequencer using the NextSeq500/550 v.2 sequencing kit (Illumina, San Diego, CA, USA), and approximately 5 to 10 million paired-end reads were sequenced for each sample.