GEO DataSets

(Submitter supplied) We used microarrays to study the changes in whole-genome expression profiles accompanying the evolution of one bacterial population propagated in glucose minimal medium for 20,000 generations.

Organism:

Escherichia coli; Escherichia coli B str. REL606

Type:

Expression profiling by array

Platform:

GPL3154

18 Samples

Download data

(Submitter supplied) We used trimethylpsoralen intercalation to map supercoiling across the E. coli chromosome. We treated E. coli cells with trimethylpsoralen and exposed them to UV light. Psoralen enters cells, intercalates between DNA base pairs, and crosslinks the two strands of DNA at a rate proportional to the local superhelical density. We then fragmented DNA and hybridized crosslinked and non-crosslinked DNA fragments separately to tiling microarrays.

Organism:

Escherichia coli; Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platform:

GPL8585

14 Samples

Download data: CEL, TXT

(Submitter supplied) E. coli RNA was hybridized to tiling arrays to study the pattern of gene expression across the chromosome.

Organism:

Escherichia coli; Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by genome tiling array

Platform:

GPL8585

2 Samples

Download data: CEL, TXT

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

Organism:

Streptococcus pneumoniae R6

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL21444 GPL18733

14 Samples

Download data: TXT, XLSX

(Submitter supplied) We studied the response to increased DNA-supercoiling in Streptococcus pneumoniae by using seconeolitsine (SCN), a DNA topoisomerase I inhibitor. A homeostatic transcriptional response allowing recovering of supercoiling density was observed in cells treated with subinhibitory SCN concentrations. Supercoiling increases up to 40.7% (6 µM SCN) and 72.9% (8 µM SCN) were reverted to 8.5% and 44.1%, respectively. more...

Organism:

Streptococcus pneumoniae R6

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21444

6 Samples

Download data: XLSX

(Submitter supplied) We studied the response to increased DNA-supercoiling in Streptococcus pneumoniae by using seconeolitsine (SCN), a DNA topoisomerase I inhibitor. A homeostatic transcriptional response allowing recovering of supercoiling density was observed in cells treated with subinhibitory SCN concentrations. Supercoiling increases up to 40.7% (6 µM SCN) and 72.9% (8 µM SCN) were reverted to 8.5% and 44.1%, respectively. more...

Organism:

Streptococcus pneumoniae R6

Type:

Expression profiling by array

Platform:

GPL18733

8 Samples

Download data: TXT, XLSX

(Submitter supplied) DNA supercoiling is essential for life because it controls critical processes, including transcription, replication and recombination. Current methods to measure DNA supercoiling in vivo are laborious and unable to examine single cells. Here we report a method for high-throughput measurement of bacterial DNA supercoiling in vivo. Fluorescent Evaluation of DNA Supercoiling (FEDS) utilizes a plasmid harboring the gene for a green fluorescent protein transcribed by a discovered promoter that responds exclusively to DNA supercoiling, and the gene for a red fluorescent protein transcribed by a constitutive promoter as internal standard. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27471

11 Samples

Download data: TXT

(Submitter supplied) This study aims to explore whether and how positive and negative supercoiling contribute to the three-dimensional (3D) organization of the bacterial genome. We used recently published Escherichia coli GapR ChIP-seq and TopoI ChIP-seq (also called EcTopoI-seq) data, which marks positive and negative supercoiling sites, respectively, to study how supercoiling correlates with the spatial contact maps obtained from chromosome conformation capture sequencing (Hi-C and 5C). more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platform:

GPL21117

2 Samples

Download data: MATRIX

(Submitter supplied) The most basic level of transcription regulation in Streptococcus pneumoniae is the organization of its chromosome in topological domains. In response to drugs that caused DNA-relaxation, a global transcriptional response was observed. Separate domains were identified depending of the transcription of their genes: up-regulated (U), down-regulated (D), non-regulated (N), and flanking (F). We show here that these distinct domains have different expression and conservation tendencies. more...

Organism:

Streptococcus pneumoniae R6

Type:

Genome variation profiling by array

Platform:

GPL18733

2 Samples

Download data: TXT

(Submitter supplied) The cyanobacterium Synechococcus elongatus PCC 7942 exhibits oscillations in mRNA transcript abundance with 24-hour periodicity under continuous light conditions. The mechanism underlying these oscillations remains elusive – neither cis nor trans-factors controlling circadian gene expression phase have been identified. Here we show that the topological status of the chromosome is highly correlated with circadian gene expression state. more...

Organism:

Synechococcus elongatus PCC 7942 = FACHB-805

Type:

Expression profiling by array

Platform:

GPL9534

23 Samples

Download data: GPR

(Submitter supplied) For Staphylococcus aureus it was shown previously that aminocoumarinecoumarin antibiotics such as novobiocin lead to immediate down-regulation of recA expression and thereby inhibition of the SOS response, the mutation frequency and the recombination capacity. Aminocoumarinecoumarin function by inhibition of the ATPase activity of the gyrase subunit B. Here we analysed the global impact of the DNA relaxing agent novobiocin on gene expression in S. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by array

Platform:

GPL1339

6 Samples

Download data: CEL, CHP

(Submitter supplied) We obtained RNA polymerase II profiles across the genome of S.cerevisiae cells harbouring Top1-AID and Top2-AID tagged proteins. Cells were treated with anauxin analog (IAA) to induce degradation of Top1-AID and Top2-AID. This allowed us to compare RNAPII in absence of Top1 and Top2 activity to the control condition (absence of IAA treatment).

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL19756

4 Samples

Download data: BW

(Submitter supplied) We analyed the nucleosome positions by using 2 concentrations of micrococcal nuclease of haploid yeast strains that were grown in galactose containing synthetic complete media. Strains contained AID-tags at the endogeous TOP1 and TOP2 genes. One strain contained OsTIR1 and these cells were either untreated or treated for 60 min with 500 uM auxin.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21656

11 Samples

Download data: TXT

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

Organism:

Caenorhabditis elegans

Type:

Other

Platform:

GPL22765

27 Samples

Download data: BW

(Submitter supplied) We developed an efficient method to map DNA supercoils that quantifies genome-wide incorporation of biotinylated psoralen using high throughput DNA sequencing and applied it to C. elegans. We discovered that GC-rich regions flanked by sharp GC/AT boundaries delineate the extent of negative supercoiling at transcription start sites, the regions of DNA accessibility and the positioning of nucleosomes. more...

Organism:

Caenorhabditis elegans

Type:

Other

Platform:

GPL22765

7 Samples

Download data: BW

(Submitter supplied) We developed an efficient method to map DNA supercoils that quantifies genome-wide incorporation of biotinylated psoralen using high throughput DNA sequencing and applied it to C. elegans. We discovered that GC-rich regions flanked by sharp GC/AT boundaries delineate the extent of negative supercoiling at transcription start sites, the regions of DNA accessibility and the positioning of nucleosomes. more...

Organism:

Caenorhabditis elegans

Type:

Other

Platform:

GPL22765

20 Samples

Download data: BW

(Submitter supplied) Quantification of circadian gene expression in WT Synechocystis sp. PCC 6803 cells

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL15867

12 Samples

Download data: TXT

(Submitter supplied) To investigate the relationship between RNA polymerase binding and transcription ChIP-seq on the common house-keeping SigmaD and RNA polymerase beta subunit were coupled with RNA-seq at various growth phases of Escherichia coli in rich media.

Organism:

Escherichia coli

Type:

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

Platform:

GPL21433

40 Samples

Download data: BED, TXT