GEO DataSets

(Submitter supplied) Pathogenic allele silencing is a promising treatment for genetic hereditary diseases. However, the concern about the specificity of present RNA-knockdown strategies has limited their in vivo applications. Here a TaqTth-hpRNA system consisting of a small, chimeric protein (TaqTth) and hairpin-RNA probe (hpRNA) is provided. The TaqTth-hpRNA showed a high-specific knockdown against targeted mRNA with minimal flanking sequence-motif requirement and less cell viability damage, then was applied to mutant APPswe mRNA silencing without altering the wild-type APP mRNA in Alzheimer’s disease. more...

Organism:

Escherichia coli BL21

Type:

Other

Platform:

GPL34578

2 Samples

Download data: TXT

(Submitter supplied) Symbiotic interactions between humans and our communities of resident gut microbes (microbiota) play many roles in health and disease. Some gut bacteria utilize mucus as a nutrient source and can under certain conditions damage the protective barrier it forms, increasing disease susceptibility. We investigated how Ruminococcus torques—a known mucin-degrader that remains poorly studied despite its implication in inflammatory bowel diseases (IBDs)— degrades mucin glycoproteins or their component O-linked glycans to understand its effects on the availability of mucin-derived nutrients for other bacteria. more...

Organism:

[Ruminococcus] torques VIII-239

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34352

6 Samples

Download data: GFF, XLSX

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

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24659

22 Samples

Download data: TXT

(Submitter supplied) The Proline-rich Antimicrobial Peptide (PrAMP) apidaecin (Api) inhibits translation by binding in the ribosomal nascent peptide exit tunnel, trapping release factors RF1 or RF2, and arresting ribosomes at stop codons. To explore the extent of sequence variations of the native 18-amino acid Api that allows it to preserve its activity, we screened a library of synthetic mutant Api genes expressed in bacterial cells, resulting in nearly 350,000 peptide variants with multiple substitutions. more...

Organism:

Escherichia coli

Type:

Other

Platform:

GPL16085

7 Samples

Download data: TXT, XLSX

(Submitter supplied) The flagellar motor is a powerful macromolecular machine used to propel bacteria through various environments. Flagellar motility of the alpha-proteobacterium Sinorhizobium meliloti is nearly abolished in the absence of the transcriptional regulator LdtR, which is involved in peptidoglycan remodeling. We report that LdtR does not regulate motility gene transcription. Remarkably, the motility defects of the DldtR mutant can be restored by secondary mutations in the motility gene motA or a previously uncharacterized gene in the flagellar regulon, which we named motS. more...

Organism:

Sinorhizobium meliloti RU11/001

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34034

6 Samples

Download data: XLSX

(Submitter supplied) Lactococcus lactis is a lactic acid bacterium of major importance for food fermentation and biotechnological applications. The ability to manipulate its genome quickly and easily through competence for DNA transformation would accelerate its general use as a platform for a variety of applications. Natural transformation in this species requires the activation of the master regulator ComX. However, the growth conditions that lead to spontaneous transformation, as well as the regulators that control ComX production, are unknown. more...

Organism:

Lactococcus lactis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34188

6 Samples

Download data: TXT, XLSX

(Submitter supplied) We have developed the vaccine candidate BCGΔBCG1419c, by deletion of BCG1419c in BCG Pasteur ATCC 35734, which improved control of tuberculosis (TB) in preclinical models. Here, we compared the transcriptomes of BCG and BCGΔBCG1419c during planktonic growth.

Organism:

Mycobacterium tuberculosis variant bovis BCG

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34031

6 Samples

Download data: TXT

(Submitter supplied) Microbes able to convert gaseous one-carbon (C1) waste feedstocks are increasingly important to transition to the sustainable production of renewable chemicals and fuels. Acetogens are interesting biocatalysts since gas fermentation using Clostridium autoethanogenum has been commercialised. However, most acetogen strains need complex nutrients, display slow growth, and are not robust for bioreactor fermentations. more...

Organism:

Clostridium autoethanogenum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24458

15 Samples

Download data: 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; 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:

Mus musculus; Oryza sativa; Saccharomyces cerevisiae; Homo sapiens; 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) Tuberculosis (TB) is an ancient disease caused by the intracellular bacterial pathogen Mycobacterium tuberculosis (Mtb). The rise of antimicrobial resistance (AMR) threatens to bring Mtb to the forefront of bacterial pathogens as the current treatments are increasingly becoming ineffective. Understanding the development of AMR and the virulence processes of Mtb is crucial for the identification of new drug targets and the rational design of anti-TB treatments. more...

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Genome variation profiling by high throughput sequencing

Platform:

GPL34550

5 Samples

Download data: XLSX

(Submitter supplied) The ability to sense and respond to host defenses is essential for pathogen survival. Some mechanisms involve two-component systems (TCS) that respond to host molecules, such as antimicrobial peptides (AMPs) and activate specific gene regulatory pathways to aid in survival. Alongside TCSs, bacteria coordinate cell division proteins, chaperones, cell wall sortases and secretory translocons at discrete locations within the cytoplasmic membrane, referred to as functional membrane microdomains (FMMs). more...

Organism:

Streptococcus pyogenes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24880

9 Samples

Download data: XLSX

(Submitter supplied) The ability to sense and respond to host defenses is essential for pathogen survival. Some mechanisms involve two-component systems (TCS) that respond to host molecules, such as antimicrobial peptides (AMPs) and activate specific gene regulatory pathways to aid in survival. Alongside TCSs, bacteria coordinate cell division proteins, chaperones, cell wall sortases and secretory translocons at discrete locations within the cytoplasmic membrane, referred to as functional membrane microdomains (FMMs). more...

Organism:

Streptococcus pyogenes

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL28678

6 Samples

Download data: WIG

(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