GEO DataSets

(Submitter supplied) Like other functional RNAs, ribozymes contain a conserved catalytic center supported by peripheral domains that vary among ribozyme sub-families. To understand how core-peripheral interactions contribute to ribozyme fitness, we compared the cleavage kinetics of all single base substitutions at 152 sites across the Bacillus subtilis glmS ribozyme by high-throughput sequencing (ClvSeq). The in vitro activity map mirrored phylogenetic sequence conservation in glmS ribozymes, indicating that biological fitness reports all biochemically important positions. more...

Organism:

Bacillus subtilis

Type:

Other

Platform:

GPL29318

12 Samples

Download data: TXT

(Submitter supplied) In a previous study we used RNA-seq to identify cellular stresses related to the overexpression of xylanase XynA, and found that upregulation of the CtsR regulon improves the yield of XynA production in B. subtilis. In this study, we compared the transcriptomes of B. subtilis cells overexpressing either the xylanase XynA or the heterologous amylase AmyM, to identify general and enzyme-specific stress responses. more...

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL28092

16 Samples

Download data: FASTA, GFF3, XLSX

(Submitter supplied) Protein synthesis is a major energy-consuming process of the cell, which requires controlled production and turnover of ribosomes. While the last years have seen major advances in our understanding of ribosome biogenesis, structural insight into the degradation of ribosomes has been lacking. Here we present native structures of two distinct small ribosomal 30S subunit degradation intermediates associated with the 3’ to 5’ exonuclease, RNase R. more...

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21373

9 Samples

Download data: BEDGRAPH

(Submitter supplied) Transcriptional pausing aids gene regulation by cellular RNA polymerases (RNAPs). In many bacteria, a surface-exposed domain inserted into the catalytic trigger loop (TL) of RNAP, called SI3 in Escherichia coli, modulates pausing and is essential for growth. Here we describe a viable E. coli strain lacking SI3 enabled by a suppressor TL substitution (β'Ala941→Thr; ∆SI3*). ∆SI3* increased transcription rate in vitro relative to ∆SI3, possibly explaining its viability, but retained both positive and negative effects of ∆SI3 on pausing. more...

Organism:

Bacillus subtilis; Escherichia coli

Type:

Other

Platform:

GPL33390

2 Samples

Download data: TXT

(Submitter supplied) Bacterial cell envelope is the first and the major line of defense against threats from the environment. Because of its crucial roles in bacterial cell life, cell envelope is a prime target for numerous antibiotics. In this study, by treating Gram-positive model strain Bacillus subtilis with numbers of cell wall targeted antibiotics, we aimed to obtain a global comprehensive transcriptional profile of cell envelope stress response in B. more...

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29318

27 Samples

Download data: BW, TSV, XLSX

(Submitter supplied) PNPase is the primary RNA turnover enzyme in Bacillus subtilis and plays a crucial role in regulating gene expression. To investigate the life activities that PNPase participated in Bacillus subtilis 9407, RNA immunoprecipitation-sequencing (RIP-seq) analysis was performed to pinpoint the direct RNA targets of PNPase using 6×his-tagged PNPase (PNPase group) and PNPaseD493A (D493A group) constructs that were driven by the IPTG-induced Pgrac promoter. more...

Organism:

Bacillus subtilis

Type:

Other

Platform:

GPL30886

3 Samples

Download data: TSV

(Submitter supplied) Using transcriptomics, we studied the spatiotemporal dynamics of B. subtilis swarming colonies on soft-agar surface and identified functional subpopulations.

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30886 GPL29318

317 Samples

Download data: CSV

(Submitter supplied) M3-Seq is a single-cell RNA-sequencing platform for bacteria that pairs combinatorial cell indexing with post hoc rRNA depletion. We use M3-Seq to profile hundreds of thousands of bacterial cells and reveal rare populations of bacteria that include bet-hedging strategies, prophage induction, and phage-infected cells in E. coli and B. subtilis.

Organism:

Pseudomonas aeruginosa; Bacillus subtilis; Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL33391 GPL33390

4 Samples

Download data: CSV

(Submitter supplied) Here we use Structure-seq2 to probe the in vivo RNA structurome of B. subtilis grown at four different temperatures. We show that increases in reactivity with increasing temperature follow non-monotonic trends. Focusing on subregions of the transcriptome led to the discovery of two novel RNA thermometers that control expression of glpF and glpT.

Organism:

Bacillus subtilis

Type:

Other

Platform:

GPL32426

24 Samples

Download data: TXT

(Submitter supplied) Analysis of B. subtilis biofilm metabolism at gene expression level. The hypothesis tested in the present study was that extracellular pH and environmental buffer influence the biofilm development. Results provide important information of the response of biofilms to changes in extracellular pH.

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29515

24 Samples

Download data: XLSX

(Submitter supplied) Regulation of gene activity during the cell cycle is fundamental to bacterial replication but is challenging to study in unperturbed, asynchronous bacterial populations. Using single cell RNA-sequencing of heterogeneous Staphylococcus aureus populations, we uncovered a global gene expression pattern dominated by chromosomal position. We show that this pattern results from the effect of DNA replication on gene expression, and in Escherichia coli, changes under different growth rates and modes of replication. more...

Organism:

Bacillus subtilis; Escherichia coli; Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24034 GPL24109 GPL21222

88 Samples

Download data: TXT

(Submitter supplied) To identify RoxS targets and do the comparison with RoxS targets identified by pulsed SILAC experiment

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19910

6 Samples

Download data: TXT

(Submitter supplied) We used one of the RNA-DNA proximity ligation approaches, RedC, for the analysis of an RNA-DNA interactome of microbial cells. We assess the distribution of main RNA types — mRNA, tRNA and rRNA — along the genomes of E.coli, B.subtilis, and thermophilic archaea T. adornatum.

Organism:

Escherichia coli; Bacillus subtilis; Thermofilum adornatum

Type:

Other

Platforms:

GPL32512 GPL30886 GPL25368

6 Samples

Download data: TSV

(Submitter supplied) The microbiome has revealed itself as a key player in health and disease. To better understand its role, in addition to microbial diversity, it is important to understand species-specific activity and gene expression. While metatranscriptomics investigates mRNA abundance2, it does not inform about faster post-transcriptional regulation3. Although prokaryotic translation is a common target for antibiotics, a direct measurement of microbiome ribosome dynamics remains inaccessible. more...

Organism:

Listeria monocytogenes; Saccharomyces cerevisiae; Salmonella enterica; Parabacteroides merdae; Escherichia coli; Synechocystis sp. PCC 6803; Staphylococcus aureus; Bacillus amyloliquefaciens; Lactiplantibacillus plantarum; Cryptococcus neoformans; Caulobacter vibrioides; Enterococcus faecalis; Bacillus subtilis; Limosilactobacillus reuteri; Limosilactobacillus fermentum; human feces metagenome; Segatella copri; Alistipes finegoldii; Hoylesella timonensis; compost metagenome

Type:

Other

17 related Platforms

199 Samples

Download data: BEDGRAPH, TXT, XLSX

(Submitter supplied) To explore the effects of different stress conditions on Bacillus subtilis str.168, a selection of conditions were applied to the organism and RNA-seq data gathered. A matrix of gene counts was produced as a basis for further analysis into the transcription profiles of Bacillus subtilis str.168.

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30886

54 Samples

Download data: TSV

(Submitter supplied) We examined the effect of high-level expression of the commercially important endo-1,4-β-xylanase XynA on the B. subtilis transcriptome using RNA-seq. Rather unexpectedly, we found a reduced expression of several protein chaperones, including ClpC, ClpE and ClpX, was downregulated when XynA was overproduced. Expression of these proteins is controlled by the transcriptional repressor CtsR. CtsR levels are directly controlled by regulated proteolysis, involving ClpC and its cognate protease ClpP. more...

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28092

8 Samples

Download data: TXT

(Submitter supplied) Clonal bacterial populations rely on transcriptional variation across individual cells to commit to specialized states that increase the population’s fitness. Such heterogeneous gene expression is implicated in fundamental microbial processes including sporulation, cell communication, detoxification, substrate utilization, competence, biofilm formation, and motility1. To identify specialized cell states and determine the processes by which they develop, isogenic bacterial populations need to be studied at the single cell level2,3. more...

Organism:

Bacillus subtilis; Escherichia coli; Clostridium perfringens

Type:

Expression profiling by high throughput sequencing

4 related Platforms

8 Samples

Download data: H5

(Submitter supplied) Bacillus subtilis has been extensively used as a model for molecular studies on biofilm formation. These studies encompassed the development of complex macro-colonies on agar, the formation of pellicles at the air-liquid interface, and lately the formation of submerged architectural biofilms at the solid-liquid interface. Beside similarities, these multicellular communities also display considerable heterogeneity at the structural, chemical and biological levels. more...

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28092

27 Samples

Download data: CSV

(Submitter supplied) In this work we conducted Term-seq on Wild Type B. subtilis, and strains compromosing all logical mutations in all combinations of the genes that encode for NusA, NusG, and Rho, where we developed the first transcription termination atlas. We used this atlas to find that Rho can stimulate intrinsic termination in B. subtilis and we recapitulated this finding in vitro to dissect the mechanism.

Organism:

Bacillus subtilis

Type:

Other

Platforms:

GPL30886 GPL24109

32 Samples

Download data: BEDGRAPH

(Submitter supplied) Characterization of the putative genetic determinants of the VBNC state in a known spore-forming Gram-positive organism Bacillus subtilis 168. The VBNC state was induced under osmotic stress and aminoglycoside treatment. The transcriptome landscape of VBNC cells was compared to the viable, antibiotic sensitive B. subtilis cells and to the viable cells with no antibiotic treatment.

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28092

9 Samples

Download data: TXT