GEO DataSets

(Submitter supplied) RNC-seq experiment of the simulated acetylation mutant S1K247Q of S1 protein

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26592

6 Samples

Download data: TXT

(Submitter supplied) RNA-seq experiment of the simulated acetylation mutant S1K247Q of S1 protein

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26592

6 Samples

Download data: TXT

(Submitter supplied) Microbial physiology plays a pivotal role in construction of a superior microbial cell factory for efficient production of desired products. Here we identified pcnB repression through genome-scale CRISPRi modulation combining fluorescence-activated cell sorting (FACS) and next-generation sequencing (NGS), which confers improved physiology for free fatty acids (FFAs) overproduction in Escherichia coli. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platform:

GPL26592

5 Samples

Download data: XLSX

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

Organism:

Pseudomonas aeruginosa PAO1; Escherichia coli str. K-12 substr. MG1655; Staphylococcus aureus

Type:

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

Platforms:

GPL28916 GPL27158 GPL26592

21 Samples

Download data: NARROWPEAK, TXT, XLSX

(Submitter supplied) Biofilms are heterogeneous bacterial communities featured by high persister prevalence, responsible for antibiotic tolerance. However, the mechanisms underlying persister formation within biofilms remained ambiguous. Here, by developing and utilizing a ribosomal RNA depleted bacterial single-cell RNA-seq method, RiboD-mSPLiT, we resolved biofilm heterogeneity and discovered pdeI as a marker gene for persister subgroup within biofilms. more...

Organism:

Staphylococcus aureus; Escherichia coli str. K-12 substr. MG1655; Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL27158 GPL26592 GPL28916

14 Samples

Download data: TXT, XLSX

(Submitter supplied) Biofilms are heterogeneous bacterial communities featured by high persister prevalence, responsible for antibiotic tolerance. However, the mechanisms underlying persister formation within biofilms remained ambiguous. Here, by developing and utilizing a ribosomal RNA depleted bacterial single-cell RNA-seq method, RiboD-mSPLiT, we resolved biofilm heterogeneity and discovered pdeI as a marker gene for persister subgroup within biofilms. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26592

1 Sample

Download data: TXT, XLSX

(Submitter supplied) Biofilms are heterogeneous bacterial communities featured by high persister prevalence, responsible for antibiotic tolerance. However, the mechanisms underlying persister formation within biofilms remained ambiguous. Here, by developing and utilizing a ribosomal RNA depleted bacterial single-cell RNA-seq method, RiboD-mSPLiT, we resolved biofilm heterogeneity and discovered pdeI as a marker gene for persister subgroup within biofilms. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26592

6 Samples

Download data: NARROWPEAK

(Submitter supplied) Our focus of this study is to determine the differential expression of genes related to uptake and degradation of nitrogenous compounds in E. coli colonizing the mouse intestine as compared to E. coli grown in minimal medium in vitro. We colonized CD-1 male mice with E. coli MG1655 StrR wild type and extracted the total RNA from mouse cecal mucus (GSE217743). We also colonized CD-1 male mice with E. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26592

10 Samples

Download data: WIG

(Submitter supplied) Elucidating genome-scale regulatory networks requires a comprehensive collection of gene expression profiles, yet measuring gene expression responses for every transcription factor (TF)-gene pair in living prokaryotic cells remains challenging. Here, we develop pooled promoter responses to TF perturbation sequencing (PPTP-seq) via CRISPR interference to address this challenge. Using PPTP-seq, we systematically measure the activity of 1372 Escherichia coli promoters under single knockdown of 183 TF genes, illustrating more than 200,000 possible TF-gene responses in one experiment. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platform:

GPL26592

112 Samples

Download data: CSV

(Submitter supplied) Antibiotic binding sites are located in important domains of essential enzymes and have been extensively studied in the context of resistance mutations, however their study is limited by positive selection. Using multiplex genome engineering1 to overcome this constraint, we generate and characterize a collection of 760 single residue mutants encompassing the entire rifampicin binding site of E. coli RNA polymerase (RNAP). more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26592

4 Samples

Download data: BEDGRAPH

(Submitter supplied) Antimicrobial resistance (AMR) is a global health crisis that is predicted to worsen. While improper antibiotic usage is an established driver, less is known on the impacts of metal supplements. Here, we probe the impact of zinc (Zn) on AMR. In conflict settings where diarrhea disease cases are high, Zn, which is associated with weapons of war, is given as a supplement for diarrhea treatment prior to antibiotics such as ciprofloxacin. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26592

3 Samples

Download data: XLSX

(Submitter supplied) Our focus of this study is to determine the gene expression changes in E. coli colonizing the mouse intestine as compared to E. coli grown in minimal medium in vitro. We colonized CD-1 male mice with E. coli MG1655 StrR wild type and extracted the total RNA from mouse cecal mucus. We also extracted E. coli MG1655 StrR RNA from in vitro culture and sequenced and compared to determine the genes important for E. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26592

5 Samples

Download data: WIG

(Submitter supplied) Cold shock adaptability is a key survival skill of gut bacteria of warm-blooded animals. Escherichia coli cold shock responses are controlled by a complex multi-gene, timely-ordered transcriptional program. We investigated its underlying mechanisms. Having identified short-term, cold shock repressed genes, we show that their responsiveness is unrelated to their transcription factors or global regulators, while their single-cell protein numbers’ variability increases after cold shock. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24659 GPL26592

15 Samples

Download data: CSV

(Submitter supplied) Sequencing technologies, in particular RNASeq, have become critical tools in the design, build, test, learn cycle for synthetic biology. They provide a better understanding of synthetic designs and they help identify ways to improve and select designs. While this data is beneficial to design, its collection and analysis is a complex, multi-step process that has implications both on discovery and reproducibility of experiments. more...

Organism:

Escherichia coli str. K-12 substr. MG1655; Bacillus subtilis subsp. subtilis str. 168

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26592 GPL30358

1344 Samples

Download data: CSV

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

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL26592 GPL21117

8 Samples

Download data

(Submitter supplied) The study investigates how varying target expression levels influences self-targeting and defense using Cas13a. We see how immunity is activated only over a target transcription threshold, which is variable between targets. A gRNA library targeting transcripts from the whole coding genome of E. coli MG1655 confirms the importance of the transcription threshold in determining immunity and shows that most of the cellular transcripts do not induce cytotoxicity.

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26592

4 Samples

Download data: CSV

(Submitter supplied) The robustness and sensitivity of gene networks to environmental changes is critical for cell survival. How gene networks produce specific, chronologically ordered responses to genome-wide perturbations, while robustly maintaining homeostasis, remains an open question. We analysed if short- and mid-term genome-wide responses to shifts in RNA polymerase (RNAP) concentration are influenced by the known topology and logic of the transcription factor network (TFN) of Escherichia coli. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26592

12 Samples

Download data: CSV

(Submitter supplied) This SuperSeries is composed of the following SubSeries: GSE178278 [poor media] GSE178279 [rich media] GSE197447 [poor media time lapse]

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17439 GPL24659 GPL26592

36 Samples

Download data

(Submitter supplied) Substrains in Escherichia coli K-12 MG1655 can possess various swimming motility, which is mostly resulted from different expression levels of flhDC. Here, we studied the swimming motility of two MG1655 substrains, CY562 and CY570. Our results showed that CY562 had no insertion at the promoter region of flhDC and possessed no swimming motility. In contrast, CY570 had an IS-element insertion at the promoter region of flhDC and showed a hyper-motile phenotype. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26592

4 Samples

Download data: TXT

(Submitter supplied) Bacteriophage P1 along with λ and T4 phages are among the best described bacterial viruses in molecular biology. For years, P1 features as well as its life cycle have been studied and its complete genome was published. Undeciphered phenomenon of improved P1vir lytic development in the absence of DksA protein in cell engaged us to more holistic experimental approach. Bacterial wild type and dksA strains were cultured to OD600 = 0.2. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26592

18 Samples

Download data: CSV, TXT