E-GEOD-46281 - RNA-seq analysis of Mycobacterium avium TMC724 vs. M. avium 104 non-coding and coding transcriptome

Status
Released on 23 April 2013, last updated on 12 June 2013
Organism
Mycobacterium avium
Samples (1)
Protocols (4)
Description
Deep sequencing was implemented to study the transcriptional landscape of Mycobacterium avium TMC724. High-resolution transcriptome analysis identified the transcription start points for 652 genes. One third of these coincided with the start codons and therefore belong to leaderless transcripts, whereas the rest of the transcripts had 5' UTRs with the mean length of 83 nt. In addition, the 5' UTRs of 6 genes contained SAM-IV and Ykok types of riboswitches. 87 antisense RNAs and 9 intergenic small RNAs were mapped. Four of the revealed intergenic small RNAs, including igMAV_1034-1035 expressed at a very high level, have no homologs in M. tuberculosis, whilst M. avium lacks several intergenic sRNAs present in M. tuberculosis. Among those, MTS479 and MTS1338 are of special interest due to their possible implication in pathogenesis. Elucidation of differences in the repertoire of intergenic sRNAs between the two mycobacterial species may improve our understanding of mycobacterial diseases pathogenesis. Transcriptional profile of Mycobacterium avium TMC724, grown at 37°C in Dubos broth until mid-logarithmic growth phase
Experiment type
RNA-seq of coding RNA 
Contacts
Dmitriy Ignatov <dima.ignatov@gmail.com>, Alexander Apt, Konstantin Majorov, Sofia Malakho, Tatyana Azhikina, Timofey Skvortsov
MINSEQE
Exp. designProtocolsFactorsProcessedSeq. reads
Files
Investigation descriptionE-GEOD-46281.idf.txt
Sample and data relationshipE-GEOD-46281.sdrf.txt
Processed data (1)E-GEOD-46281.processed.1.zip
Links