Direct urine sample N. gonorrhoeae Nanopore sequencing
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB35173 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Whole genome sequencing of Neisseria gonorrhoeae using Oxford Nanopore
| PRJNA504608 | ENA
Project description:transcription profiles of two groups each containing 5 strains of Disseminated gonorrhoeae (DG) and Undisseminated (superficial) gonorrhoeae (UG) were compared. An additional set of comparisons was done between 4 strains from group one Disseminated gonorrhoeae (DG) and another 4 strains from the same group.
2012-06-15 | E-MEXP-3254 | biostudies-arrayexpress
Project description:Neisseria gonorrhoeae, the etiologic agent of gonorrhea, is frequently asymptomatic in women, often leading to chronic infections. One factor contributing to this may be biofilm formation. N. gonorrhoeae can form biofilms over glass and plastic surfaces. There is also evidence that biofilm formation may occur during natural cervical infection. To further study the mechanism of this biofilm formation, transcriptional profiles of N. gonorrhoeae biofilm were compared to planktonic profiles. Biofilm RNA was extracted from N. gonorrhoeae 1291 grown for 48 hours in continuous flow chambers over glass. Planktonic RNA was extracted from the biofilm runoff. When biofilm was compared to planktonic growth, 3.8 % of the genome was differentially regulated. Genes highly up-regulated in biofilm included aniA, norB, and ccp, which play critical roles in anaerobic metabolism and oxidative stress tolerance. Down-regulated genes included the nuo gene cluster (NADH dehydrogenase) and the cytochrome bcI complex, which are involved in aerobic respiration and are thought to contribute to endogenous oxidative stress. Furthermore, we determined that aniA, ccp, and norB insertional mutants are attenuated for biofilm formation over glass and transformed human cervical epithelial cells (THCEC). This data suggests that biofilm formation could minimize oxidative stress during cervical infection and allow N. gonorrhoeae to maintain a nitric oxide steady state that may be anti-inflammatory.
2009-02-27 | GSE14815 | GEO
Project description:State-of-the-art algorithms for m6A detection and quantification via nanopore direct RNA sequencing have been continuously developed, little is known about their capacities and limitations, which makes a comprehensive assessment in urgent need. Therefore, we performed comprehensive benchmarking of 10 computational tools relying on current-based and base-calling “errors” strategies for m6A detection by nanopore sequencing.
2023-03-01 | GSE195618 | GEO
Project description:Purpose: The goal of this study was the identification of target genes of the Neisseria gonorrhoeae sRNAs NgncR_237, NgncR_162 and NgncR_163. Methods: RNA was isolated from N. gonorrhoeae using the miRNeasy Micro Kit (Qiagen). Enrichment of mRNA was done using the Universal Ribodepletion Kit followed by Next Ultra Directional Library Preparation Kit for Illumina (NEB). The cDNA was sequenced on Illumina HiSeq 3000 platform with 100 bp paired end reads. Adapters from Fastq sequences were removed using cutadapt version 1.2.1. Only reads exceeding a mean base quality 5 within all sliding windows of 5 bp were mapped to the genome of strain N. gonorrhoeae MS11 (reference genome ASM15685v2). Annotation of non-coding RNAs was according to Remmele et al.(2014). Read mapping was conducted using Bowtie2 v2.1.0. DeSEQ2 version 1.6.2 was used to identify differentially regulated transcripts. Results: N. gonorrhoeae genes were identified which were upregulated or downregulated upon induced expression of sRNAs NgncR_237, NgncR_162 and NgncR_163. Conclusions: sRNA NgncR_237, NgncR_162 and NgncR_163 are involved in the regulation of genes involved in type IV pilus biogenesis, energy metabolism and transport processes.
2021-07-28 | GSE177032 | GEO
Project description:Droplet-based single-cell sequencing techniques have provided unprecedented insight into cellular heterogeneities within tissues. However, these approaches only allow for the measurement of the distal parts of a transcript following short-read sequencing. Therefore, splicing and sequence diversity information is lost for the majority of the transcript. The application of long-read Nanopore sequencing to droplet-based methods is challenging because of the low base-calling accuracy currently associated with Nanopore sequencing. Although several approaches that use additional short-read sequencing to error-correct the barcode and UMI sequences have been developed, these techniques are limited by the requirement to sequence a library using both short- and long-read sequencing. Here we introduce a novel approach termed single-cell Barcode UMI Correction sequencing (scBUC-seq) to efficiently error-correct barcode and UMI oligonucleotide sequences synthesized by using blocks of dimeric nucleotides. The method can be applied to correct both short-read and long-read sequencing, thereby allowing users to recover more reads per cell that permits direct single-cell Nanopore sequencing for the first time. We illustrate our method by using species-mixing experiments to evaluate barcode assignment accuracy and multiple myeloma cell lines to evaluate differential isoform usage and Ewing’s sarcoma cells to demonstrate Ig fusion transcript analysis.
2021-01-31 | GSE162053 | GEO
Project description:comparison of RNA expression profiles from Neisseria gonorrhoeae strain WHO Z grown in presence of DMSO vs PBT2
2020-03-10 | GSE146622 | GEO
Project description:Hfq is an RNA chaperone, which functions as a pleiotropic regulator for RNA metabolism in bacteria. To characterize the role of Hfq in pathogenicity of Neisseria gonorrhoeae we generated a N. gonorrhoeae hfq mutant, MS11hfq.Transcriptional analysis using a custom-made N. gonorrhoeae microarray revealed that 369 open reading frames were differentially regulated in MS11hfq compared to the wild-type (wt) strain (202 were upregulated, 167 were downregulated).
2009-09-15 | GSE16046 | GEO