GEO DataSets

(Submitter supplied) This study investigates the RNA targets and cleavage sites of endogenous Cas9 in the food-borne pathogen Campylobacter jejuni. Direct RNA binding targets of Cas9 in C. jejuni strain NCTC11168 were determined using RIP-seq. The Cleavage sites were then predicted in the RNA targets by comparing total transcriptome data from WT and deletion (cas9, crRNA3, tracrRNA, CRISPR-tracrRNA) strains. PAMs for the CjeCas9 were enriched using the PAM-SCANR platform, which operates through a GFP reporter gene. more...

Organism:

Escherichia coli K-12; Campylobacter jejuni

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL19974 GPL19168

13 Samples

Download data: TXT, WIG, XLSX

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

Organism:

Campylobacter jejuni subsp. jejuni CG8421

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL29024 GPL29023

10 Samples

Download data: WIG

(Submitter supplied) Differential RNA sequencing using terminator exonuclease (TEX) to identify processed versus unprocessed transcripts in Campylobacter jejuni strain CG84-21

Organism:

Campylobacter jejuni subsp. jejuni CG8421

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29024

4 Samples

Download data: WIG

(Submitter supplied) RIP-seq analysis to identify CjCas9 bound RNAs using co-immunoprecipitation and sequencing in CG84-21.

Organism:

Campylobacter jejuni subsp. jejuni CG8421

Type:

Other

Platform:

GPL29023

6 Samples

Download data: WIG

(Submitter supplied) Neisseria meningitidis, a commensal β-proteobacterium of the human nasopharynx, constitutes a worldwide leading cause of sepsis and epidemic meningitis. The molecular basis for their "accidental" pathogenicity is still not fully understood. Here, we show that knock-out strains lacking the Cas9 protein are impaired in the adhesion to human nasopharyngeal cells which constitutes a central step in the pathogenesis of invasive meningococcal disease. more...

Organism:

Neisseria meningitidis 8013

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24628

8 Samples

Download data: WIG

(Submitter supplied) Objective: We previously showed that Campylobacter jejuni Cas9 was necessary for full virulence and efficient induction of human cell stress followed by cell death, but no virulence mechanism could be unravelled then. Therefore, we carried out global genome-wide transcriptomics, using RNA samples extracted from cells infected by a wild-type C. jejuni strain and the corresponding cas9 deletion strain. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL22654

33 Samples

Download data: CEL

(Submitter supplied) The species Campylobacter jejuni is naturally competent for DNA uptake; nevertheless, nonnaturally transformable strains do exist. For a subset of strains we previously showed that a periplasmic DNase, encoded by dns, inhibits natural transformation in C. jejuni. In the present study, genetic factors coding for DNase activity in absence of dns were identified. DNA arrays indicated that nonnaturally transformable dns-negative strains contain putative DNA/RNA non-specific endonucleases encoded by CJE0566 and CJE1441 of strain RM1221. more...

Organism:

Campylobacter jejuni

Type:

Genome variation profiling by array

Platform:

GPL6315

29 Samples

Download data: GPR

(Submitter supplied) CRISPR-mediated gene activation (CRISPRa) is a promising therapeutic gene editing strategy without inducing DNA double-strand breaks (DSBs). However, in vivo implementation of these CRISPRa systems remains a challenge. Here, we report a compact and robust miniCas9 activator (termed miniCAFE) for in vivo activation of endogenous target genes. The system relies on recruitment of an engineered minimal nuclease-null Cas9 from Campylobacter jejuni and potent transcriptional activators to a target locus by a single guide RNA. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing

Platforms:

GPL20795 GPL23227 GPL24676

26 Samples

Download data: XLSX

(Submitter supplied) A major challenge for RNA-seq analysis of gene expression is to achieve sufficient coverage of informative non-ribosomal transcripts. In eukaryotic samples, this is typically achieved by selective oligo(dT)-priming of messenger RNAs to exclude ribosomal RNA (rRNA) during cDNA synthesis. However, this strategy is not compatible with prokaryotes in which functional transcripts are generally not polyadenylated. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; Bacteroides thetaiotaomicron VPI-5482

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28278 GPL20056

40 Samples

Download data: CSV, WIG

(Submitter supplied) Argonaute proteins are programmable nucleases that are found in both eukaryotes and prokaryotes and provide defense against invading genetic elements. Although some prokaryotic Argonautes (pAgos) were shown to recognize RNA targets in vitro, the majority of studied pAgos have strict specificity toward DNA, which limits their practical use in RNA-centric applications. Here, we describe a unique pAgo nuclease, KmAgo, from the mesophilic bacterium Kurthia massiliensis that can be programmed with either DNA or RNA guides and can precisely cleave both DNA and RNA targets. more...

Organism:

Escherichia coli

Type:

Other

Platform:

GPL18133

2 Samples

Download data: BEDGRAPH

(Submitter supplied) Programmable RNA-targeting tools provide the unique opportunity to study RNA regulation and control gene expression in an endogenous environment. However, the temporal control over these systems is lacking, rendering studies on the temporal control of regulation challenging. Here, we report the development of a small molecule-controllable RNA effector system to overcome this challenge.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20301

2 Samples

Download data: CSV