GEO DataSets

(Submitter supplied) To identify the effect of additional deletion of rel and mprA in the aa3 mutant strain lacking the aa3 cytochrome c oxidase of the respiratory electron transport chain of Mycobacterium smegmatis MC2 155, we constructed the aa3 rel double mutant and aa3 mprA double mutant and profiled the transcriptomes of the aa3 mutant, aa3 mprA double mutant and aa3 rel double mutant strains. Our comparative RNA sequencing analysis revealed that expression of most ribosomal proteins was induced in the aa3 rel double mutant and aa3 mprA double mutant relative to the aa3 mutant.

Organism:

Mycolicibacterium smegmatis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28556

6 Samples

Download data: TXT

(Submitter supplied) The gene expression during early (30min) and late (210 minutes) infection of Mycobacteriophage Adephagia was analyzed, as well as in a Adephagia lysogen.

Organism:

Mycolicibacterium smegmatis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26314

3 Samples

Download data: BEDGRAPH

(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) Mycobacterium tuberculosis (Mtb) is a bacterial pathogen that causes tuberculosis (TB), an infectious disease that inflicts major health and economic costs around the world. Mtb encounters diverse environments during its lifecycle and responds to these changes by reprogramming its transcriptional output. However, the mechanisms and regulation of Mtb transcription remains poorly understood. In this work, we simultaneously determine the 5' and 3' ends of individual RNA molecules in Mtb cells using the SEnd-seq method, which enables us to profile the Mtb transcriptome at high resolution. more...

Organism:

Mycolicibacterium smegmatis; Mycobacterium tuberculosis

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL27507 GPL28556 GPL22688

69 Samples

Download data: WIG

(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:

Mycolicibacterium smegmatis MC2 155; Mycobacterium tuberculosis H37Rv

Type:

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

Platforms:

GPL26169 GPL32938

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) The study was conducted to identify transcriptome changes in M. smegmatis during adaptation to low temperatures.

Organism:

Mycolicibacterium smegmatis

Type:

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

Platforms:

GPL28556 GPL28938

16 Samples

Download data: BIGWIG, CSV

(Submitter supplied) Analysis of changes in gene expression in MSMEG_1415 knockout strains with or without arginine treatment.

Organism:

Mycolicibacterium smegmatis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26255

4 Samples

Download data: TXT

(Submitter supplied) The quantification of transcriptome through RNA sequencing (RNA-seq) has widely been used to characterize all patterns of genes in a certain period. However, although many experimental protocols have recently been developed, RNA-seq is still a challenging technology in application. It is necessary to develop an easy and versatile RNA-seq method available in a wide range from single cell RNA to bulk RNA. more...

Organism:

Mycolicibacterium smegmatis; Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL24247 GPL28556

80 Samples

Download data: TXT

(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) We calculated transcriptome-wide mRNA half-life using RNAseq to characterize the mRNA stability in log phase and hypoxia, as well as the impact of RNase E on mRNA degradation.

Organism:

Mycolicibacterium smegmatis

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL25202

96 Samples

Download data: TXT

(Submitter supplied) Cytochrome bd (CydAB), a high-affinity oxidase that performs terminal oxygen reduction in cellular respiration, is used by various bacteria to grow in hypoxic environments, form nonreplicating persister cells, or resist antimicrobial killing. It is thought that oxygen concentration solely determines the usage of CydAB in bacteria, with the tradeoff being that CydAB-containing respiratory chains generate less ATP than those containing low-affinity proton-pumping cytochrome oxidases, as CydAB does not pump protons when generating a proton motive force (PMF). more...

Organism:

Mycolicibacterium smegmatis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26210

24 Samples

Download data: TSV

(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:

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

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL32962 GPL32963

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) The second messenger, cyclic-AMP (cAMP) is conserved across all taxa of life. It is involved in propagating the signal from environmental stimuli and converting it into a response. In bacteria such as M. tuberculosis (Mtb), P. aeruginosa, V. cholerae and B. pertussis, cAMP has been implicated in virulence, regulation of metabolism and gene expression. Cyclic AMP signalling in mycobacteria is especially complex – with 16 enzymes that produce cAMP in Mtb alone. more...

Organism:

Mycolicibacterium smegmatis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28938

6 Samples

Download data: CSV

(Submitter supplied) Our comparative RNA sequencing analysis of the wild-type strain of M. smegmatis and its isogenic crp2 (MSMEG_0539) mutant strain lacking the cAMP receptor protein 2 revealed Crp2 regulon in the M. smegmatis

Organism:

Mycolicibacterium smegmatis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28938

6 Samples

Download data: TXT

(Submitter supplied) To identify the SigB and SigE regulons in Mycobacterium smegmatis MC2 155, we constructed the sigB and sigE mutant strains and profiled the transcriptomes of the wild-type and mutant strains. Differentially expressed genes were identified pair-wisely by means of the DEGseq package in R language. 110 and 271 genes are differentially expressed in the sigB and sigE mutant strains relative to the wild-type strain, respectively.

Organism:

Mycolicibacterium smegmatis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28556

9 Samples

Download data: TXT

(Submitter supplied) We have shown that elevated levels of wild-type M. tuberculosis PknK (PknK Mtb), but not phosphorylation-defective PknKMtb, in Mycobacterium smegmatis cause significant retardation of growth rate and altered colony morphology (Malhotra et al., 2012). LIX79 (WT PknK) and LIX80 (PknK K55M mutant) M. smegmatis strains will be grown in LB and induced with 0.2% acetamide for the induction of wild type or phosphorylation defective pknK gene. more...

Organism:

Mycolicibacterium smegmatis

Type:

Expression profiling by array

Platform:

GPL30399

8 Samples

Download data: TXT