GEO DataSets

(Submitter supplied) Mycofactocin is a redox cofactor essential for the alcohol metabolism of Mycobacteria. While the biosynthesis of mycofactocin is well established, the mftG gene, which encodes an oxidoreductase of the glucose-methanol-choline superfamily remained functionally uncharacterized. Here, we show that MftG enzymes strictly require mft biosynthetic genes, and are found in 75% of organisms harboring these genes. more...

Organism:

Mycolicibacterium smegmatis MC2 155

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28006

12 Samples

Download data: XLSX

(Submitter supplied) Background: Mtb's cell wall comprises peptidoglycan, arabinogalactan, and mycolic acids linked to capsule proteins and polysaccharides by noncovalent bonds. Cell division requires extensive remodeling by inserting cell wall-building subunits, which require multiple enzymes to ensure precision and accuracy during the addition and conjugation of biomolecules to the cell wall. Approximately 35% of division and cell wall cluster operon genes are involved in cell wall biosynthesis, 22% in cell division, and 43% are still unstudied. more...

Organism:

Mycolicibacterium smegmatis MC2 155

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27707

4 Samples

Download data: TXT

(Submitter supplied) RNA-Seq results accompanying submission of a manuscript: "Depletion of CCA-adding enzyme in Mycobacterium tuberculosis leads to polyadenylation of transcripts and precursor tRNAs" describing the function of the Rv3907c gene product as a CCA-adding enzyme in Mycobacterium tuberculosis.

Organism:

Mycobacterium tuberculosis H37Rv; Mycolicibacterium smegmatis MC2 155

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL32938 GPL26169

24 Samples

Download data: TXT

(Submitter supplied) Mycobacterium smegmatis respond to various environmental stimuli via ESX systems. We probed the transcriptional response to nitrogen addition to the medium using a series of ESX-1 knockout mutants.

Organism:

Mycolicibacterium smegmatis MC2 155

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28006

48 Samples

Download data: TSV, TXT

(Submitter supplied) Regulation of Mycobacterium smegmatis gene expression by treatment with sodium citrate.

Organism:

Mycolicibacterium smegmatis MC2 155

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26152

4 Samples

Download data: XLSX

(Submitter supplied) To examine the role of the essential transcription factor CarD in regulating gene expression in Mycobacterium smegmatis, we performed

Organism:

Mycolicibacterium smegmatis MC2 155

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28006

16 Samples

Download data: CSV

(Submitter supplied) RNA-seq of Mycobacteriophage Island3 infection of Mycolicibacterium smegmatis mc2155, Mycolicibacterium smegmatis mc2155(Butters), and Mycolicibacterium smegmatis mc2155(Buttersgp57r) to assess the impact of Butters lysogen and specifically Buttersgp57r on transcript levels of island3 during infection.

Organism:

Mycobacterium phage Butters; Mycobacterium phage Island3; Mycolicibacterium smegmatis MC2 155

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL32963 GPL32962

18 Samples

Download data: CSV, TXT

(Submitter supplied) A study was conducted to analyse the membrane fraction transcriptome of active and dormant (ovoid) M. smegmatis cells.

Organism:

Mycolicibacterium smegmatis MC2 155

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26152 GPL28007

6 Samples

Download data: TXT

(Submitter supplied) In the present study, we sought to explore the role of Lsr2 as a regulator of transcription in the saprophytic species, M. smegmatis. We used RNA-seq to compare the global transcription profiles of Δlsr2 and wild-type M. smegmatis strains in an attempt to decode Lsr2 regulatory network under optimal conditions or during hypoxia. We show that Lsr2 binds AT-rich regions and mainly acts as a gene repressor, either directly by binding promoter regions or indirectly through DNA-loop formation.

Organism:

Mycolicibacterium smegmatis MC2 155

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29895

11 Samples

Download data: BEDGRAPH, GFF, TXT

(Submitter supplied) To gain molecular insight into the role of Rv2872 in increased vancomycin resistance, change of the intracellular amino acids content and cell wall structure, the transcriptome of Rv2872 overexpression M. smegmatis was assessed through RNA-Seq analysis. The transcriptome data showed that the transcription of four genes involved in peptidoglycan synthesis was significantly lower in the MS_Rv2872 overexpression strain . more...

Organism:

Mycolicibacterium smegmatis MC2 155

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24510

2 Samples

Download data: TXT

(Submitter supplied) Expression profiling in LepA knock-out in M. smegmatis

Organism:

Mycolicibacterium smegmatis MC2 155

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26152

9 Samples

Download data: TSV

(Submitter supplied) To understand how GreA may affect gene expression at the transcriptional level, we performed whole-transcriptome RNA-seq analyses. To examine whether GreA binds to specific chromosomal regions, we performed chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) and then sought to verify the binding mode of GreA. ChIP-seq experiments were performed by using M. smegmatis strains producing GreA proteins fused with two repeats of the FLAG epitope (FLAG2). more...

Organism:

Mycolicibacterium smegmatis MC2 155

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL28006 GPL28007

10 Samples

Download data: BED, BW, TXT

(Submitter supplied) ROS can damage cellular components and is a key player in many cellular signaling. Tuberculosis remains a major global public health concern largely due to the ability of its causative agent-Mycobacterium tuberculosis (Mtb) to subvert ROS toxicity. DNA methylation deficiency was previously shown to attenuate the Mtb virulence. But the role of DNA methyltransferase in Mycobacteria survival and the link with ROS are unknown. more...

Organism:

Mycolicibacterium smegmatis MC2 155

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27707

6 Samples

Download data: TXT

(Submitter supplied) The goal of this sequencing project was to measure transcription levels of several Cluster A actinobacteriophages during lysogeny in order to study which genes contribute to lysogeny and superinfection immunity.

Organism:

Mycolicibacterium smegmatis MC2 155

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25917

3 Samples

Download data: BEDGRAPH

(Submitter supplied) We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mycobacterium smegmatis C2 155. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of Mycobacterium smegmatis C2 155. We find that amino acids synthesis and degradation genes, genes that are expressed.The ratio of gene expression based on transcriptome substantiate an enhanced TCA cycle. more...

Organism:

Mycolicibacterium smegmatis MC2 155

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24382

2 Samples

Download data: TXT

(Submitter supplied) The non-pathogenic bacterium Mycobacterium smegmatis mc2155 has been widely used as a model organism in mycobacterial research, yet a detailed study about its transcription landscape remains to be established. Here we report the transcriptome, expression profiles and transcriptional structures through growth-phase-dependent RNA sequencing (RNA-seq) as well as other related experiments. We found: (1) 2,139 transcriptional start sites (TSSs) in the genome-wide scale, of which eight samples were randomly selected and further verified by 5'-RACE; (2) 2,233 independent monocistronic or polycistronic mRNAs in the transcriptome within the operon/sub-operon structures which are classified into five groups; (3) 47.50% (1016/2139) genes were transcribed into leaderless mRNAs, with the TSSs of 41.3% (883/2139) mRNAs overlapping with the first base of the annotated start codon. more...

Organism:

Mycolicibacterium smegmatis MC2 155

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23958

6 Samples

Download data: TXT

(Submitter supplied) The goal of this sequencing project was to measure transcription levels of several Cluster N actinobacteriophages during different stages of their lifecycle, including lysogeny, early infection (30 minutes), and late infection (2 hours 30 minutes), in order to study which genes contribute to superinfection exclusion.

Organism:

Mycobacterium phage Butters; Mycolicibacterium smegmatis MC2 155; Mycobacterium phage Charlie; Mycobacterium phage MichelleMyBell; Mycobacterium phage Phrann; Mycobacterium phage Redi; Mycobacterium phage Xerxes; Mycobacterium phage Panchino; Mycobacterium phage Xeno

Type:

Expression profiling by high throughput sequencing

8 related Platforms

12 Samples

Download data: BEDGRAPH

(Submitter supplied) Mycobacteria are known to be non-spore forming but very hardy: the bacilli can for instance survive starvation in zero-nutrient saline in a non-replicating state. Recently we reported that mycobacteria in fact can undergo cellular differentiation when exposed to different starvation conditions. The presence of traces of nutrients triggers the development of a new, ‘small resting cell’ form (SMRCs). Saline shock-starved large resting cells (LARCs), which did not show cell size or surface changes when observed by scanning electron microscopy, remodeled their internal structure to the septated, multi-nucleoided cells seen during differentiation to SMRCs. Here we conduct RNA-seq to gain greater insights into whether starvation elicited a distinct developmental pathway. Comparative transcriptome analysis of SMRC and LARC development revealed largely overlapping sets of differentially expressed regulatory and metabolic genes. These transcriptome data are consistent with a mycobacterial starvation-induced differentiation program in which at first septated, multi-nuceloided cells are generated. Under zero-nutrient conditions bacteria terminate development at this stage as LARCs. In the presence of traces of a carbon source, these multi-nucleoided cells continue differentiation into mono-nuleoided SMRCs.

Organism:

Mycolicibacterium smegmatis MC2 155

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20580

30 Samples

Download data: TXT

(Submitter supplied) Several temperate actinobacteriophages have been identified that lack integration machinery and instead have genes with predicted partitioning functions. The goal of this sequencing project was to measure transcription levels of these extrachromosomal phages during different stages of their lifecycle, including lysogeny, early infection (30 minutes), and late infection (2 hours 30 minutes), in order to study which genes contribute to extrachromosomal stability.

Organism:

Mycolicibacterium smegmatis MC2 155

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21573

7 Samples

Download data: BEDGRAPH

(Submitter supplied) To identify the genes with napM-dependent differential expression, the gene expression profiles of the wild-type M. smegmatis strain and the napM-deleted strains were compared. For this case, the genes with fold changes exceeding 2 (P < 0.05) were considered significant. Strikingly, 156 genes were found to be differentially expressed in the absence of napM. Among these genes,121 were upregulated and 35 were downregulated.

Organism:

Mycolicibacterium smegmatis MC2 155

Type:

Expression profiling by array

Platform:

GPL21792

6 Samples

Download data: TXT