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Items: 15

1.

High-resolution analysis of the pneumococcal transcriptome under a wide range of infection-relevant conditions

(Submitter supplied) Streptococcus pneumoniae is an opportunistic human pathogen that typically colonizes the nasopharyngeal passage and causes lethal disease in other host niches such as the lung or the meninges. How pneumococcal genes are expressed and regulated at the different stages of its life cycle, as commensal or as pathogen, has not been entirely described. To chart the transcriptional responses of S. pneumoniae, we quantified the transcriptome under 22 different infection-relevant conditions. more...
Organism:
Streptococcus pneumoniae D39
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24384
34 Samples
Download data: TXT
Series
Accession:
GSE108031
ID:
200108031
2.

The response of Streptococcus pneumoniae to antibiotic stress on the transcriptome of a competence negative strain

(Submitter supplied) The aim of this study is to identify the rapid (RR) and adaptative (AR) response of S. pneumoniae to aztreonam and clavulanic acid stress on transcriptional level Streptococcus pneumoniae is able to acquire antibiotic resistance by activation of competence and subsequent DNA uptake. Several antibiotics induce competence by disrupting protein-quality control or perturbing DNA replication. Here, we demonstrate that aztreonam (AZT) and clavulanic acid (CLA) also promote competence. more...
Organism:
Streptococcus pneumoniae D39
Type:
Expression profiling by array
Platform:
GPL22631
5 Samples
Download data: TXT
Series
Accession:
GSE111562
ID:
200111562
3.

Transcriptomic comparison of wild-type and ptvR deletion mutant of Streptococcus pneumoniae D39

(Submitter supplied) Reversible or phenotypic tolerance to antibiotics within microbial populations has been implicated in treatment failure of chronic infections and development of persister cells. However, the molecular mechanisms regulating phenotypic drug tolerance are largely unknown. In this study, we identified a four-gene operon in Streptococcus pneumoniae that contributes to phenotypic tolerance to vancomycin (ptv). more...
Organism:
Streptococcus pneumoniae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23152
2 Samples
Download data: TXT
Series
Accession:
GSE95709
ID:
200095709
4.

IPTG-induced CRISPRi repression of firefly luciferase in Streptococcus pneumoniae

(Submitter supplied) Genome-wide screens have discovered a large set of essential genes in the human pathogen Streptococcus pneumoniae. However, the function of many essential genes is still unknown, hampering vaccine and drug development programs. Based on results from transposon-sequencing (Tn-Seq), we refined the list of essential genes in S. pneumoniae serotype 2 strain D39. Next, we created a knockdown library targeting all 391 potentially essential genes using CRISPR interference (CRISPRi). more...
Organism:
Streptococcus pneumoniae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18183
6 Samples
Download data: TXT
Series
Accession:
GSE89763
ID:
200089763
5.

Time-resolved dual RNA-seq reveals extensive rewiring of lung epithelial and pneumococcal transcriptomes during early infection

(Submitter supplied) BACKGROUND: Streptococcus pneumoniae, the pneumococcus, is the main etiological agent of pneumonia. Pneumococcal infection is initiated by bacterial adherence to lung epithelial cells. The exact transcriptional changes occurring in both host and microbe during infection are unknown. Here, we developed a time-resolved infection model of human lung alveolar epithelial cells by S. pneumoniae and assess the resulting transcriptome changes in both organisms simultaneously by using dual RNA-seq. more...
Organism:
Streptococcus pneumoniae D39; Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21685
18 Samples
Download data: XLSX
Series
Accession:
GSE79595
ID:
200079595
6.

Transcriptome and/or marker frequency analysis of S. pneumoniae (control vs. HPUra/Kanamycin/Ciprofloxacin/Hydroxyurea/Rifampicin)

(Submitter supplied) Pneumococcal bacteriocins (pneumocins) are antibacterial toxins that mediate intra- and interspecies competition within the human host. What triggers pneumocin expression is poorly understood. Using RNA-sequencing, we mapped the regulon of the pneumocin cluster (blp) of Streptococcus pneumoniae D39 and show that several antibiotics activate the blp-genes. Real-time gene expression measurements showed that while the promoter driving expression of the two-component regulatory system blpS/H was constitutive, the remaining blp-promoters (e.g. more...
Organism:
Streptococcus pneumoniae
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL18183
16 Samples
Download data: TXT
7.

Transcriptome and marker frequency analysis of E. coli (control vs. Trimethoprim) and S. pneumoniae (control vs. HPUra/Kanamycin)

(Submitter supplied) We show that treatment with HPUra (for S. pneumoniae) and trimethoprim (for E. coli) leads to a skewed gene dosage profile (increase around the origin of replication), which is also propagated to the transcriptome level. Kanamycin, however, does not have this effect. In case of S. pneumoniae this shift in gene dosage distribution leads to the population-wide activation of competence.
Organism:
Escherichia coli; Streptococcus pneumoniae
Type:
Genome variation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL14548 GPL18183
18 Samples
Download data: TXT
Series
Accession:
GSE54199
ID:
200054199
8.

B. subtilis response to rotten meat volatiles.

(Submitter supplied) To find a promoter upregulated in the presence of rotten meat, we exposed B. subtilis 168 to the volatiles of rotten meat (mixed beef/pork) and performed a microarray comparing it to B. subtilis which was not exposed to the meat. The results where used to build iGEM Groningen 2012s Food Warden, a spoiled meat detector. Find more information at: 2012.igem.org/Team:Groningen
Organism:
Bacillus subtilis; Bacillus subtilis subsp. subtilis str. 168
Type:
Expression profiling by array
Platform:
GPL17671
4 Samples
Download data: TXT
Series
Accession:
GSE50538
ID:
200050538
9.

The response of Streptococcus pneumoniae to replication stress on the transcriptome of a wild-type strain

(Submitter supplied) The aim of this study is to identify the response of S. pneumoniae to HPUra-induced replication stress on transcriptional level in a wild type strain.
Organism:
Streptococcus pneumoniae D39
Type:
Expression profiling by array
Platform:
GPL11484
12 Samples
Download data: TXT
Series
Accession:
GSE46002
ID:
200046002
10.

Single cell fitness of B. subtilis correlates with the ability to adapt to various stresses.

(Submitter supplied) How cells dynamically respond to fluctuating environmental conditions depends on the architecture and noise of the underlying genetic circuits. Most work characterizing stress pathways in the model bacterium Bacillus subtilis has been performed on bulk cultures using ensemble assays. However, investigating the single cell response to stress is important since noise might generate significant phenotypic heterogeneity. more...
Organism:
Bacillus subtilis
Type:
Expression profiling by array
Platform:
GPL5957
3 Samples
Download data: TXT
Series
Accession:
GSE33506
ID:
200033506
11.

Chromosome segregation in Streptococcus pneumoniae

(Submitter supplied) Segregation of replicated chromosomes during cell division is an essential process in all organisms. Chromosome segregation is promoted by the action of the DNA-binding ParB protein in the rod-shaped model bacterium Bacillus subtilis. How oval shaped bacteria, such as the human pathogen Streptococcus pneumoniae, efficiently segregate their chromosomes is poorly understood. Here, we show that the pneumococcal homolog of ParB is enriched at four centromere-like DNA sequences (parS sites) that are present near the origin of replication.
Organism:
Streptococcus pneumoniae D39; Streptococcus pneumoniae
Type:
Genome binding/occupancy profiling by array
Platform:
GPL11484
1 Sample
Download data: TXT
Series
Accession:
GSE26839
ID:
200026839
12.

Subpopulation array data, Veening et al.

(Submitter supplied) The transcriptome profiles of sporulating vs non-sporulating cells, within an isogenic culture were compared. Keywords: isogenic subpopulation comparison Bacillus subtilis sporulation
Organism:
Bacillus subtilis
Type:
Expression profiling by array
Platform:
GPL6031
1 Sample
Download data: TXT, XLS
Series
Accession:
GSE9266
ID:
200009266
13.

Secretion stress caused by overexpression of heterologous α-amylase in Bacillus subtilis

(Submitter supplied) Transcriptome analysis was used to investigate the global stress response of the Gram-positive bacterium Bacillus subtilis caused by overproduction of the well-secreted AmyQ α-amylase from Bacillus amyloliquefaciens. Analyses of the control and overproducing strains were carried out at the end of exponential growth and in stationary phase, when protein secretion from B. subtilis is optimal. Among the genes that showed increased expression were htrA and htrB, which are part of the CssRS regulon that responds to high-level protein secretion and heat stress. more...
Organism:
Bacillus subtilis subsp. subtilis str. 168; Bacillus subtilis
Type:
Expression profiling by array
Platform:
GPL188
18 Samples
Download data
Series
Accession:
GSE8014
ID:
200008014
14.

Bacillus subtilis 168 4K Oligo Array

(Submitter supplied) 12pins spotting with Telechem 946MP3 pins spotsize 90-100 um Protocol: Oligo spotted on ArrayIt Superamine slides in duplicates
Organism:
Bacillus subtilis
9 Series
173 Samples
Download data: TXT
Platform
Accession:
GPL6031
ID:
100006031
15.

Subpopulation array data, Veening et al.

Organism:
Bacillus subtilis
Source name:
Endospore fraction (channel 1) Vegetative cell fraction (channel 2)
Platform:
GPL6031
Series:
GSE9266
Download data: TXT
Sample
Accession:
GSM235080
ID:
300235080
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