Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1140741 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30026461_1.fastq.gz | Fastqsanger.gz | |||
| SRR30026462_1.fastq.gz | Fastqsanger.gz | |||
| SRR30026463_1.fastq.gz | Fastqsanger.gz | |||
| SRR30026464_1.fastq.gz | Fastqsanger.gz | |||
| SRR30026465_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 9 |
Similar Datasets
Project description:Antimicrobial resistance (AMR) arises from complex genetic and regulatory changes, including single mutations, gene acquisitions or cumulative effects. Advancements in genomics and proteomics facilitate more comprehensive understanding of the mechanisms behind antimicrobial resistance. In this study, 74 clinically obtained Klebsiella pneumoniae isolates with increased meropenem and/or imipenem MICs were characterized by broth microdilution and PCR to check for the presence of carbapenemase genes. Subsequently, a representative subset of 15 isolates was selected for whole genome sequencing (WGS) by Illumina and Nanopore sequencing, and proteomic analysis by liquid chromatography-mass spectrometry (LC-MS/MS) to investigate the mechanisms underlying the differences in carbapenem susceptibility of Klebsiella pneumoniae isolates. Identical techniques were applied to characterize 4 mutants obtained after sequential meropenem exposure. We demonstrated that in clinically obtained isolates, increased copy numbers of blaOXA-48 containing plasmids, combined with OmpK36 loss, contributed to high carbapenem MICs without involvement of OmpK35 or other porins or efflux systems. In the meropenem exposed mutants, increased copy numbers of blaCTX-M-15 or blaOXA-48 containing plasmids, combined with OmpK36 loss was demonstrated. The OmpK36 loss resulted from the insertion of IS1 transposable elements or partial deletion of the ompK36 gene. Additionally, we identified two mutations, C59A and C58A, in the DNA coding the copA antisense RNA of IncFII plasmids and multiple mutations of an IncR plasmid, associated with increased plasmid copy numbers. This study demonstrates that by combining WGS and LC-MS/MS, the effect of genomic changes on protein expression related to antibiotic resistance and the mechanisms behind antibiotic resistance can be elucidated.
2025-06-06 | PXD061983 | Pride
Project description:We used the nanopore Cas9 targeted sequencing (nCATS) strategy to specifically sequence 125 L1HS-containing loci in parallel and measure their DNA methylation levels using nanopore long-read sequencing. Each targeted locus is sequenced at high coverage (~45X) with unambiguously mapped reads spanning the entire L1 element, as well as its flanking sequences over several kilobases. The genome-wide profile of L1 methylation was also assessed by bs-ATLAS-seq in the same cell lines (E-MTAB-10895).
2023-09-22 | E-MTAB-12247 | biostudies-arrayexpress
Project description:Antibiotic resistance is exacerbated by the exchange of antibiotic resistance genes (ARGs) between microbes from diverse habitats. Plasmids are important ARGs mobile elements and are spread by horizontal gene transfer (HGT). In this study, we demonstrated the presence of multi-resistant plasmids from inhalable particulate matter (PM) and its effect on gene horizontal transfer. Three transferable multi-resistant plasmids were identified from PM in a hospital, using conjugative mating assays and nanopore sequencing. pTAir-3 contained 26 horizontal transfer elements and 10 ARGs. Importantly pTAir-5 harbored carbapenem resistance gene (blaOXA) which shows homology to plasmids from human and pig commensal bacteria, thus indicating that PM is a media for antibiotic resistant plasmid spread. In addition, 125 μg/mL PM2.5 and PM10 significantly increased the conjugative transfer rate by 110% and 30%, respectively, and augmented reactive oxygen species (ROS) levels. Underlying mechanisms were revealed by identifying the upregulated expressional levels of genes related to ROS, SOS, cell membranes, pilus generation, and transposition via genome-wide RNA sequencing. The study highlights the airborne spread of multi-resistant plasmids and the impact of inhalable PM on the horizontal transfer of antibiotic resistance.
2022-10-31 | GSE159850 | GEO
Project description:Nanopore sequencing for plasmids and chromosomes
| PRJNA558442 | ENA
Project description:Nanopore RNA sequencing of polyA+ chromatin associated RNA of Naive CD4+ T cells to identify novel chromatin associated RNAs containing TEs.
2021-10-20 | E-MTAB-10797 | biostudies-arrayexpress
Project description:Microsatellites are short tandem repeats (STRs) of a motif of 1 to 6 nucleotides that are ubiquitous in almost all genomes and widely used in many biomedical applications. However, despite the development of next-generation sequencing (NGS) over the past two decades with new technologies coming to the market, accurately sequencing and genotyping STRs, particularly homopolymers, are still very challenging today due to several technical limitations. This leads in many cases to erroneous allele calls and difficulty in correctly identifying the genuine allele distribution in a sample. In the present study, we assessed several second and third NGS approaches in their capability to correctly determine the length of microsatellites using plasmids containing A/T homopolymers, AC/TG or AT/TA dinucleotide STRs of variable length. Standard PCR-free and PCR-containing, single Unique Molecular Index (UMI) and dual UMI ‘duplex sequencing’ protocols were evaluated using Illumina short-read sequencing, and two PCR-free protocols using PacBio and nanopore long-read sequencing. Several bioinformatics algorithms were developed to correctly identify microsatellite alleles from sequencing data, including four and two modes for generating standard and combined consensus alleles, respectively. We provided a detailed analysis and comparison of these approaches and made several recommendations for the accurate determination of microsatellite allele length.
2025-02-27 | GSE286310 | GEO
Project description:Microsatellites are short tandem repeats (STRs) of a motif of 1 to 6 nucleotides that are ubiquitous in almost all genomes and widely used in many biomedical applications. However, despite the development of next-generation sequencing (NGS) over the past two decades with new technologies coming to the market, accurately sequencing and genotyping STRs, particularly homopolymers, are still very challenging today due to several technical limitations. This leads in many cases to erroneous allele calls and difficulty in correctly identifying the genuine allele distribution in a sample. In the present study, we assessed several second and third NGS approaches in their capability to correctly determine the length of microsatellites using plasmids containing A/T homopolymers, AC/TG or AT/TA dinucleotide STRs of variable length. Standard PCR-free and PCR-containing, single Unique Molecular Index (UMI) and dual UMI ‘duplex sequencing’ protocols were evaluated using Illumina short-read sequencing, and two PCR-free protocols using PacBio and nanopore long-read sequencing. Several bioinformatics algorithms were developed to correctly identify microsatellite alleles from sequencing data, including four and two modes for generating standard and combined consensus alleles, respectively. We provided a detailed analysis and comparison of these approaches and made several recommendations for the accurate determination of microsatellite allele length.
2025-02-27 | GSE286309 | GEO
Project description:Microsatellites are short tandem repeats (STRs) of a motif of 1 to 6 nucleotides that are ubiquitous in almost all genomes and widely used in many biomedical applications. However, despite the development of next-generation sequencing (NGS) over the past two decades with new technologies coming to the market, accurately sequencing and genotyping STRs, particularly homopolymers, are still very challenging today due to several technical limitations. This leads in many cases to erroneous allele calls and difficulty in correctly identifying the genuine allele distribution in a sample. In the present study, we assessed several second and third NGS approaches in their capability to correctly determine the length of microsatellites using plasmids containing A/T homopolymers, AC/TG or AT/TA dinucleotide STRs of variable length. Standard PCR-free and PCR-containing, single Unique Molecular Index (UMI) and dual UMI ‘duplex sequencing’ protocols were evaluated using Illumina short-read sequencing, and two PCR-free protocols using PacBio and nanopore long-read sequencing. Several bioinformatics algorithms were developed to correctly identify microsatellite alleles from sequencing data, including four and two modes for generating standard and combined consensus alleles, respectively. We provided a detailed analysis and comparison of these approaches and made several recommendations for the accurate determination of microsatellite allele length.
2025-02-27 | GSE286306 | GEO
Project description:Microsatellites are short tandem repeats (STRs) of a motif of 1 to 6 nucleotides that are ubiquitous in almost all genomes and widely used in many biomedical applications. However, despite the development of next-generation sequencing (NGS) over the past two decades with new technologies coming to the market, accurately sequencing and genotyping STRs, particularly homopolymers, are still very challenging today due to several technical limitations. This leads in many cases to erroneous allele calls and difficulty in correctly identifying the genuine allele distribution in a sample. In the present study, we assessed several second and third NGS approaches in their capability to correctly determine the length of microsatellites using plasmids containing A/T homopolymers, AC/TG or AT/TA dinucleotide STRs of variable length. Standard PCR-free and PCR-containing, single Unique Molecular Index (UMI) and dual UMI ‘duplex sequencing’ protocols were evaluated using Illumina short-read sequencing, and two PCR-free protocols using PacBio and nanopore long-read sequencing. Several bioinformatics algorithms were developed to correctly identify microsatellite alleles from sequencing data, including four and two modes for generating standard and combined consensus alleles, respectively. We provided a detailed analysis and comparison of these approaches and made several recommendations for the accurate determination of microsatellite allele length.
2025-02-27 | GSE286308 | GEO