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12 results for “Oxford Nanopore Technologies”
Supplementary dataset to publication: Oxford nanopore technologies - a valuable tool to generate whole-genome sequencing data for in silico serotyping and the detection of genetic markers in Salmonella, Thomas et al 2023
<p>Bacteria of the genus <em>Salmonella</em> pose a major risk to livestock, the food economy, and public health. <em>Salmonella</em> infections are one of the leading causes of food poisoning. The identification of serovars of <em>Salmonella</em> achieved by their diverse surface antigens is essential to gain information on their epidemiological context. Traditionally, slide agglutination has been used for serotyping. In recent years, whole-genome sequencing (WGS) followed by <em>in silico</em> serotyping has been established as an alternative method for serotyping and the detection of genetic markers for <em>Salmonella</em>. Until now, WGS data generated with Illumina sequencing are used to validate <em>in silico</em> serotyping methods. Oxford Nanopore Technologies (ONT) opens the possibility to sequence ultra-long reads and has frequently been used for bacterial sequencing. In this study, ONT sequencing data of 28 <em>Salmonella</em> strains of different serovars with epidemiological relevance in humans, food, and animals were taken to investigate the performance of the <em>in silico</em> serotyping tools SISTR and SeqSero2 compared to traditional slide agglutination tests. Moreover, the detection of genetic markers for resistance against antimicrobial agents, virulence, and plasmids was studied by comparing WGS data based on ONT with WGS data based on Illumina. Based on the ONT data from flow cell version R9.4.1, <em>in silico</em> serotyping achieved an accuracy of 96.4 and 92% for the tools SISTR and SeqSero2, respectively. Highly similar sets of genetic markers comparing both sequencing technologies were identified. Taking the ongoing improvement of basecalling and flow cells into account, ONT data can be used for <em>Salmonella in silico</em> serotyping and genetic marker detection.</p>
Hieracium alpinun PAI33838 (2n = 2x = 18) Oxford Nanopore Technology sequences library
<p>Sample 1 000 000 reads (trimmed).</p>
Sequencing of individual barcoded cDNAs on Pacific Biosciences and Oxford Nanopore technologies reveals platform-specific error patterns (repository for Genome Research paper, 2022)
<p>Simulated ONT and PacBio RNA-Seq data for "Sequencing of individual barcoded cDNAs on Pacific Biosciences and Oxford Nanopore technologies reveals platform-specific error patterns" paper (Mikheenko et al., Genome Research, 2022). All details can be found in the Methods section of the paper.</p> <p><strong>PacBio.simulated_uniform_coverage.fasta.gz</strong> and <strong>ONT.simulated_uniform_coverage.fasta.gz files</strong> were used in Supplemental Note “Benchmarking of the read-to-isoform assignment algorithm”.</p> <p><strong>ONT.simulated_real_expression.fasta.gz</strong> file and all GTF files were used in the Section "Splice site correction improves transcript discovery precision". <strong>mouse.gencode.M26.spatial.15percent.reduced.gtf</strong> was used as the annotation file for all tools. <strong>mouse.gencode.M26.spatial.15percent.expressed.gtf </strong>contains the set of all expressed isoforms. <strong>mouse.gencode.M26.spatial.15percent.expressed_kept.gtf</strong> contains those of the isoforms that are in presented in the annotation file ("known" transcripts), <strong>mouse.gencode.M26.spatial.15percent.reduced.gtf</strong> contains expressed isoforms that were removed from the annotation ("novel" transcripts).</p>
Matched Oxford Nanopore Technologies and Bisulfite Sequencing of the GM24385 Cell Line
<p>One of the most widespread genomic modifications is 5-methylcytosine (5mC), which most frequently occurs at <a href="https://en.wikipedia.org/wiki/CpG_site">CpG</a> dinucleotides. Compared to whole-genome bisulfite sequencing, the traditional method of 5mC detection, nanopore technology can offer many advantages such as simplicity of sample prep and subsequent analysis.</p> <p>In order to demonstrate the utility and convenience of Oxford Nanopore Technologies’ sequencing platform for performing detection and analysis of 5mC, we have sequenced the HG002 Genome in a Bottle Sample GM24385 with both traditional bisulfite sequencing and using nanopore sequencing. Both technologies, old and new, were applied to the same sample from a single DNA extraction.</p> <p><em>Bisulfite sequencing</em></p> <p>Bisulfite sequencing was performed by a commercial provider and processed with the commonly used <a href="https://www.bioinformatics.babraham.ac.uk/projects/bismark/">bismark</a> package to obtain the proportion of reads displaying methylation at CpG sites throughout the whole genome. </p> <p><em>Nanopore sequencing</em></p> <p>Nanopore sequencing was performed using the same sample of GM24385 material sent for bisulfite sequencing. Sequencing was performed on the MinION platform, across multiple flowcells, as part of ongoing platform development activities. The sequencing was not performed explicitly for the analysis presented here; we are making available all sequencing runs undertaken with this sample for the benefit of the community.</p> <p><em>Data Access</em></p> <p>Data is available as part of the Registry of Open Data on AWS: https://registry.opendata.aws/ont-open-data/. This dataset can be accessed through the S3 prefix:</p> <blockquote> <p>s3://ont-open-data/gm24385_mod_2021.09/</p> </blockquote> <p><em>Further Information</em></p> <ul> <li>https://labs.epi2me.io/gm24385-5mc/</li> <li>https://labs.epi2me.io/gm24385-5mc-remora</li> </ul>
CircRNAs full-length sequencing in the human and mouse brain samples using Oxford Nanopore Technology
GEO Series GSE127059. Homo sapiens; Mus musculus. 8 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Pore-C: Combination of chromatin capture assay and Oxford Nanopore Technology long read sequencing.
GEO Series GSE149117. Homo sapiens. 5 samples. Type: Other.
scNanoATAC-seq: Long-read Single-cell ATAC-seq by Oxford Nanopore Technologies Sequencing
GEO Series GSE194024. Mus musculus; Homo sapiens. 17 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
scNanoATAC-seq: Long-read Single-cell ATAC-seq by Oxford Nanopore Technologies Sequencing [DataSet1: scNanoATAC-seq]
GEO Series GSE194022. Mus musculus; Homo sapiens. 7 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
scNanoATAC-seq: Long-read Single-cell ATAC-seq by Oxford Nanopore Technologies Sequencing [DATASet2: bulkATAC-seq]
GEO Series GSE194023. Mus musculus; Homo sapiens. 10 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Oxford Nanopore Technology (ONT) long-read data of NCIH2170 cell line
GEO Series GSE293274. Homo sapiens. 2 samples. Type: Other.
Scanning and Mining of High Fecundity Genes by Oxford Nanopore Technologies (ONT) in Sheep (Ovis aries) Pituitary
GEO Series GSE275684. Ovis aries. 6 samples. Type: Expression profiling by high throughput sequencing.
RNA quality control by CCR4 safeguards chromatin integrity and centromere function in Arabidopsis [Oxford Nanopore Technology Direct RNA Sequencing]
GEO Series GSE274200. Arabidopsis thaliana. 4 samples. Type: Expression profiling by high throughput sequencing.
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