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:

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

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:

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

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:

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

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) The classical bordetellae (Bordetella pertussis, B. parapertussis, and B. bronchiseptica) are obligate aerobes that use only oxygen as their terminal electron acceptor for electron transport-coupled oxidative phosphorylation. Therefore, access to oxygen is critical for these bacteria to survive. To better understand how B. bronchiseptica changes its gene regulation when faced with different levels of oxygen, we grew liquid cultures of B. more...

Organism:

Bordetella bronchiseptica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34533

12 Samples

Download data: TSV

(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) NTHi infection of Normal Human Nasal Epithelia (NHNE) for 14 days

Organism:

Haemophilus influenzae; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL25730

28 Samples

Download data: TXT

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

Organism:

Phaseolus vulgaris; Xanthomonas citri pv. fuscans

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL33255

17 Samples

Download data: SF

(Submitter supplied) To investigate the bacterial functions involved in seed contamination during their formation, we sequenced bacterial mRNA at 24, 35 and 42 days after pollination (DAP). Gene expression was compared between the different stages.

Organism:

Xanthomonas citri pv. fuscans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33255

17 Samples

Download data: SF

(Submitter supplied) The transcriptome of the wild type strain and ΔzntR of Vibrio parahaemolyticus was compared by RNA sequencing analysis. The data revealed that some genes, such as zntA, were significantly differentially expressed in the mutant.

Organism:

Vibrio parahaemolyticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34522

6 Samples

Download data: TXT

(Submitter supplied) RNA helicases—central enzymes in RNA metabolism— often feature intrinsically disordered regions (IDRs) that enable phase separation and complex interactions with other proteins and/or RNA molecules. IDRs are varied and fast evolving, which makes their function hard to predict. In the bacterial pathogen Pseudomonas aeruginosa, two non-redundant RNA helicases, RhlE1 and RhlE2, share a conserved REC catalytic core but have different C-terminal extensions (CTEs) composed of IDRs of diverse length and amino acid composition. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26913

36 Samples

Download data: XLSX

(Submitter supplied) Bacteria are major drivers of organic matter decomposition and play crucial roles in global nutrient cycling. Although the degradation of dead fungal biomass (necromass) is increasingly recognized as an important contributor to soil carbon (C) and nitrogen (N) cycling, the genes and metabolic pathways involved in necromass degradation are under characterized. In particular, how bacteria degrade necromass containing different quantities of melanin, which largely control rates of necromass decomposition in situ, is largely unknown. more...

Organism:

Chitinophaga pinensis; Serratia marcescens; Cellvibrio japonicus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34520 GPL34518 GPL34519

48 Samples

Download data: CSV, XLSX

(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:

Arabidopsis thaliana; Danio rerio; Escherichia coli; synthetic construct

Type:

Other; Expression profiling by high throughput sequencing

4 related Platforms

60 Samples

Download data: BW

(Submitter supplied) Pseudomonas aeruginosa (PA) is an opportunistic pathogen frequently isolated from cutaneous chronic wounds. How PA, in the presence of oxidative stress (OS), colonizes chronic wounds and forms a biofilm is still unknown. The purpose of this study is to investigate the changes in gene expression seen when PA is challenged with the high levels of OS present in chronic wounds. We used a biofilm-forming PA strain isolated from the chronic wounds of our murine model (RPA) and performed a qPCR to obtain gene expression patterns as RPA developed a biofilm in vitro in the presence of high levels of OS, and then compared the findings in vivo, in our mouse model of chronic wounds. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33271

18 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) Small non-coding RNAs (sRNAs) are pivotal regulators of post-transcriptional activities and various cellular processes in bacteria. This study highlighted a framework for understanding novel identified sRNA functions at gene expression and phenotypical levels and provides insights into sRNome assemblies in bacteria.

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19430

32 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:

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