GEO DataSets

(Submitter supplied) Two wide type strains of Bacillus subtilis, S-2 and 312, were selected to study their genic differences treated by L-alanine through comparative transcriptomics analysis. The spores of B. subtilis S-2 were selected because of their high germination potential to L-alanine. The spores of B. subtilis 312 without a response to L-alanine were used as the control. The spores with or without L-alanine (100 mm) pretreatment were both cultured in the synthetic medium for 9 h, and then collected for sequencing.

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29318

8 Samples

Download data: TXT

(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) Antibiotics have dose-dependent effects on exposed bacteria. The medicinal use of antibiotics relies on their growth-inhibitory activities at sufficient concentrations. At subinhibitory concentrations, exposure effects vary widely among different antibiotics and bacteria. Bacillus subtilis responds to bacteriostatic translation inhibitors by mobilizing a population of cells (MOB-Mobilized Bacillus) to spread across a surface. more...

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19910

20 Samples

Download data: CSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL28092

6 Samples

Download data: BIGWIG, TXT

(Submitter supplied) Ribosome pausing slows down translation and can affect protein synthesis. Improving translation efficiency can therefore be of commercial value. Here, we investigated the occurrence of ribosome pausing during amylase secretion by the industrial production organism Bacillus subtilis under semi fed-batch fermentation conditions. We first assessed our ribosome profiling setup by inducing ribosome stalling at isoleucine codons using the antibiotic mupirocin, and found a pause preference for isoleucine codons preceded by E and P site codons with guanosine residues in their first nucleotide position. more...

Organism:

Bacillus subtilis

Type:

Other

Platform:

GPL28092

4 Samples

Download data: BIGWIG, TXT

(Submitter supplied) Ribosome pausing slows down translation and can affect protein synthesis. Improving translation efficiency can therefore be of commercial value. Here, we investigated the occurrence of ribosome pausing during amylase secretion by the industrial production organism Bacillus subtilis under semi fed-batch fermentation conditions. We first assessed our ribosome profiling setup by inducing ribosome stalling at isoleucine codons using the antibiotic mupirocin, and found a pause preference for isoleucine codons preceded by E and P site codons with guanosine residues in their first nucleotide position. more...

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28092

2 Samples

Download data: BIGWIG, TXT

(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) The transcriptional control of sporulation in Bacillus subtilis is reasonably well understood, but its translational control is underexplored. Here, we use RNA-seq, ribosome profiling and fluorescence microscopy to study the translational dynamics of B. subtilis sporulation. We identify two events of translation silencing and describe spatiotemporal changes in subcellular localization of ribosomes during sporulation. more...

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24109

64 Samples

Download data

(Submitter supplied) Translational control during the intricate process of sporulation in Bacillus subtilis as a response to nutrient limitation is still underexplored. Here, we employed a comprehensive approach including RNA-seq, ribosome profiling and fluorescence microscopy to dissect the translational landscape of B. subtilis during sporulation. We identified two events of translation silencing and described the spatiotemporal changes in the subcellular location of translational machinery during sporulation. more...

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24109

32 Samples

Download data: XLSX

(Submitter supplied) Translational control during the intricate process of sporulation in Bacillus subtilis as a response to nutrient limitation is still underexplored. Here, we employed a comprehensive approach including RNA-seq, ribosome profiling and fluorescence microscopy to dissect the translational landscape of B. subtilis during sporulation. We identified two events of translation silencing and described the spatiotemporal changes in the subcellular location of translational machinery during sporulation. more...

Organism:

Bacillus subtilis

Type:

Other

Platform:

GPL24109

32 Samples

Download data: XLSX

(Submitter supplied) Objective: to compare and contrast the effects of exogenous application of strigolatone analogue rac-dGR24, on gene expression in bacillus subtilis. The experiment compared the effects on three genotypes: wild type and two mutant lines, a ∆rsbQ and RsbQS96A.

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30886

18 Samples

Download data: XLSX

(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) N-terminal coding sequences (NCS) are key regulatory elements for fine-tuning gene expression during translation initiation, the rate-limiting step of translation. However, due to complex combinatory effects of NCS biophysical factors and endogenous regulation, designing NCS remains challenging. Herein, we implemented multi-view learning strategy for model-driven generation of synthetic NCS for Saccharomyces cerevisiae and Bacillus subtilis, which are model microorganisms widely used in the laboratory and industry.

Organism:

Saccharomyces cerevisiae; Bacillus subtilis

Type:

Other

Platforms:

GPL27812 GPL30886

4 Samples

Download data: CSV

(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