GEO DataSets

(Submitter supplied) Current methods for R-loop mapping need to perform DNA:RNA immunoprecipitation for each sample individually, with consequent limitations in throughput. Here, we develop and validate mDRIP-seq, a multi-sample barcoding and pooling method for R-loop mapping. We show mDRIP-seq performs equivalently as conventional methods, but with the merits of high throughput and cost-efficiency. We also show the simplicity of mDRIP-seq for relative and absolute quantitation of genomic R-loop fractions for multiple samples. more...

Organism:

Escherichia coli; Homo sapiens; Mus musculus

Type:

Other

Platforms:

GPL24676 GPL24247 GPL25368

6 Samples

Download data: BW

(Submitter supplied) Bacteria respond to changes in their external environment like temperature by changing the transcription of their genes, but we know little about how these regulatory patterns evolve. We used RNA-seq to study the transcriptional response of a shift from 37°C to 15°C in wild-type Escherichia coli, Salmonella enterica, Citrobacter rodentium, Enterobacter cloacae, Klebsiella pneumoniae, and Serratia marcescens, as well as ∆rpoS strains of E. more...

Organism:

Citrobacter rodentium; Serratia marcescens; Salmonella enterica; Enterobacter cloacae; Escherichia coli; Klebsiella pneumoniae

Type:

Expression profiling by high throughput sequencing

6 related Platforms

64 Samples

Download data: TXT

(Submitter supplied) Current methods for R-loop profiling need to perform experiments for each sample individually, with consequent limitations in throughput. Here, based on the barcoding strategy, we develop mDRIP-seq, a high-throughput method showing equivalent performance as conventional methods, but with merits of 7-fold less cost and 6-fold less hand-on time per sample. We also show the simplicity and effectiveness of mDRIP-seq for relative and absolute quantitation of genomic R-loop fractions for multiple samples. more...

Organism:

Escherichia coli; Arabidopsis thaliana; Mus musculus; Oryza sativa; Saccharomyces cerevisiae; Homo sapiens

Type:

Other; Expression profiling by high throughput sequencing

6 related Platforms

384 Samples

Download data: BW, TXT

(Submitter supplied) Current methods for R-loop mapping need to perform DNA:RNA immunoprecipitation for each sample individually, with consequent limitations in throughput. Here, we develop and validate mDRIP-seq, a multi-sample barcoding and pooling method for R-loop mapping. We show mDRIP-seq performs equivalently as conventional methods, but with the merits of high throughput and cost-efficiency. We also show the simplicity of mDRIP-seq for relative and absolute quantitation of genomic R-loop fractions for multiple samples. more...

Organism:

Saccharomyces cerevisiae; Escherichia coli; Arabidopsis thaliana; Oryza sativa; Homo sapiens; Mus musculus

Type:

Other

6 related Platforms

356 Samples

Download data: BW

(Submitter supplied) Purpose: Searching for sRNAs in Salmonella pullorum by RNA sequencing and exploring their functions.Methods: High-throughput sequencing of RNA extracted from Salmonella pullorum under normal growth conditions to detect newly discovered sRNAs, followed by experiments to verify their functions.Results: The proportion of Clean Reads of this sequencing was >65%, and the base Q30s were all above 85%, indicating that the sequencing quality is good and can be used for subsequent analysis. more...

Organism:

Salmonella enterica subsp. enterica serovar Pullorum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL34564

3 Samples

Download data: XLSX

(Submitter supplied) Fimbriae are important virulence traits that promote bacterial adhernece to surfaces. Here, we assessed whether fimbriae modulate gene expression using microarrays. We used microarrays to compare gene expression in wild-type of fimbrial deletion strains of EHEC

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

3 Samples

Download data: CEL, CHP

(Submitter supplied) All elongator tRNAs harbor 5-methyluridine at position 54 and pseudouridine at position 55 in the T arm, which are generated by the enzymes TrmA and TruB, respectively. Escherichia coli TrmA and TruB have both been shown to act as tRNA chaperones, and strains lacking trmA or truB are outcompeted by wildtype. Here, we investigate how TrmA and TruB contribute to cellular fitness. Deletion of trmA and truB in E. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21433

12 Samples

Download data: CSV, TXT

(Submitter supplied) The R-loop is a common chromatin feature presented from prokaryotic to eukaryotic genomes and has been revealed to be involved in multiple cellular processes. Here, we developed a novel R-loop profiling technique, ULI-ssDRIP-seq, to decte global R-loops from a limited number of cells. Based on this method, we profiled the R-loop landscapes during parental-to-zygotic transition and early development regulatory in zebrafish, and revealed a series of important characters of R-loops.

Organism:

Escherichia coli; synthetic construct; Arabidopsis thaliana; Danio rerio

Type:

Other; Expression profiling by high throughput sequencing

4 related Platforms

60 Samples

Download data: BW

(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) 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:

Expression profiling by high throughput sequencing

Platform:

GPL34485

6 Samples

Download data: XLS

(Submitter supplied) The dataset contains small RNAs that associated with HrAgo1 during heterologous expression in E. coli. The goal of the study was to determine what type of small RNAs associate with HrAgo1 and from what RNA transcripts these small RNAs are derived

Organism:

Escherichia coli

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL25368

1 Sample

Download data: XLSX

(Submitter supplied) The ability of bacteria to sense and respond to mechanical forces has important implications for pathogens during the in vivo infection process, as they experience wide fluid shear fluctuations in the host. However, relatively little is known about how mechanical forces encountered in the infected host drive microbial pathogenesis. We previously demonstrated an inverse relationship between fluid shear-induced responses of classic gastrointestinal disease-causing Salmonella Typhimurium (x3339) and systemic multidrug resistant (MDR) S. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. D23580

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24393

6 Samples

Download data: XLSX

(Submitter supplied) Bacteria often evolve antibiotic resistance through mutagenesis. However, the processes causing the mutagenesis have not been fully resolved. Here we found that a broad range of ribosome-targeting antibiotics caused mutations through an underexplored pathway. Focusing on the clinically important aminoglycoside gentamicin, we found that the translation inhibitor caused genome-wide premature stalling of RNA polymerase (RNAP) in a loci-dependent manner. more...

Organism:

Escherichia coli

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25368

12 Samples

Download data: BED, TXT

(Submitter supplied) Protein production by the ribosomes is fundamental to life and proper assembly of the ribosome is required for protein production. The RNA, which is post-transcriptionally modified, provides the platform for ribosome assembly. Thus, a complete understanding of ribosome assembly requires the determination of the RNA post-transcriptional modifications in all the ribosome assembly intermediates and on each pathway. more...

Organism:

Escherichia coli

Type:

Other

Platform:

GPL16085

3 Samples

Download data: CSV

(Submitter supplied) Polyamines, crucial molecules involved in cell proliferation and growth, play a pivotal role in cancer development and progression. Within the tumor microenvironment, macrophages, key components of the immune system, exhibit a complex relationship with polyamines. Evidence suggests that polyamines can modulate macrophage polarization, influencing their functional phenotypes. Here, we detected the gene DNA methylation changes in spermine-stimulated human macrophages isolated from PBMCs and TAMs.

Organism:

Campylobacter jejuni; Francisella tularensis subsp. novicida; Yersinia pestis; Staphylococcus aureus; Mycobacterium avium subsp. paratuberculosis; Cowpox virus; Escherichia coli O157:H7; Francisella tularensis subsp. mediasiatica; Paslahepevirus balayani; Leptospira interrogans; Rickettsia typhi; Mycobacterium tuberculosis variant bovis; Mycobacterium tuberculosis; Mycobacterium tuberculosis variant microti; Mycobacterium canetti; Orthohantavirus seoulense; Yersinia enterocolitica; Toxoplasma gondii; Salmonella enterica subsp. enterica serovar Typhimurium; Mammarenavirus choriomeningitidis; Orthohantavirus puumalaense; Yersinia pseudotuberculosis; Rickettsia prowazekii; Bartonella quintana; Mycobacterium avium; Homo sapiens; Streptobacillus moniliformis; Bartonella henselae; Francisella tularensis subsp. tularensis; Francisella tularensis subsp. holarctica

Type:

Methylation profiling by array

Platform:

GPL21445

4 Samples

Download data: IDAT, TXT

(Submitter supplied) Purpose: To elucidate the survival strategies in egg white of Salmonella Pullorum, a host-restricted pathogen with vertical transmission capability. Methods: The logarithmic-phase wild-type and Δfim mutant strains were inoculated into LB medium and egg white (final concentration 80%) and statically cultured at 42°C for 6 hours. RNA samples were then extracted for sequencing. Three biological replicates were carried out per sample. more...

Organism:

Salmonella enterica subsp. enterica serovar Pullorum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34216

12 Samples

Download data: TXT

(Submitter supplied) The deposited microarray data were generated in a study that integrated the gene expression profiles and metabolic responses of Caco2 cells incubated with Bifidobacterium infantis subsp. infantis and Salmonella enterica subsp. enterica sv. Typhimurium. The aim of this study was to investigate the interaction of B. infantis, S. Typhimurium, and host cells (Caco2) in the course of infection to understand the molecular mechanics of probiotic-pathogen-host interactions.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. LT2; Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL570 GPL34454

36 Samples

Download data: CEL

(Submitter supplied) Multiple immune pathways in humans conjugate ubiquitin-like proteins to virus and host molecules as a means of antiviral defense. Here we studied an anti-phage defense system in bacteria, comprising a ubiquitin-like protein, ubiquitin-conjugating enzymes E1 and E2, and a deubiquitinase. We show that during phage infection, this system specifically conjugates the ubiquitin-like protein to the phage central tail fiber, a protein at the tip of the tail that is essential for tail assembly as well as for recognition of the target host receptor. more...

Organism:

Escherichia coli; Caulobacter sp. Root343

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34341 GPL32081

12 Samples

Download data: XLSX

(Submitter supplied) RNA-protein interactions are fundamental for bacterial homeostasis. However, we lack a system-wide understanding of their dynamics upon environmental perturbation. In this study, we have characterised the dynamics of 91% of the Escherichia coli proteome and the RNA-interaction properties of 271 RNA-binding proteins (RBPs) at different growth phases. We find that 68% of RBPs differentially bind RNA across growth phases and reveal novel RBP functions for proteins like the chaperone HtpG, a new tRNA-binding protein. more...

Organism:

Escherichia coli

Type:

Other

Platform:

GPL16085

8 Samples

Download data: BEDGRAPH

(Submitter supplied) Here, we treated Escherichia coli strain TO114 expressing a halotolerant cyanobacterium Halothece sp. PCC7418-derived NhaC Na+/H+ antiporter (H2569) with salt stress (0.4 M NaCl) and performed RNA sequencing analysis.

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25368

3 Samples

Download data: XLSX