HIV genotyping by Nanopore
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB25082 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Sequencing was performed to assess the ability of Nanopore direct cDNA and native RNA sequencing to characterise human transcriptomes. Total RNA was extracted from either HAP1 or HEK293 cells, and the polyA+ fraction isolated using oligodT dynabeads. Libraries were prepared using Oxford Nanopore Technologies (ONT) kits according to manufacturers instructions. Samples were then sequenced on ONT R9.4 flow cells to generate fast5 raw reads in the ONT MinKNOW software. Fast5 reads were then base-called using the ONT Albacore software to generate Fastq reads.
2019-03-14 | E-MTAB-7778 | biostudies-arrayexpress
Project description:Rapidly increased studies by third-generation sequencing [Pacific Biosciences (Pacbio) and Oxford Nanopore Technologies (ONT)] have been used in all kinds of research areas. Among them, the plant full-length single-molecule transcriptome studies were most used by Pacbio while ONT was rarely used. Therefore, in this study, we developed ONT RNA-sequencing methods in plants. We performed a detailed evaluation of reads from Pacbio and Nanopore PCR cDNA (ONT Pc) sequencing in plants (Arabidopsis), including the characteristics of raw data and identification of transcripts. We aimed to provide a valuable reference for applications of ONT in plant transcriptome analysis.
2019-12-15 | GSE141641 | GEO
Project description:Purpose: To generate a reference long-read transcriptomic data set for use in developing new analysis pipelines and comparing their performance with existing methods. Synthetic “sequin” RNA standards (Hardwick et al. 2016) were sequenced using the Oxford Nanopore Technologies (ONT) GridION platform.
2020-06-18 | GSE151984 | GEO
Project description:To evaluate targeted MinION next generation sequencing as a diagnostic method for detection of pathogens in human blood and plasma, human blood or plasma samples were spiked with measured amounts of viruses, bacteria, protozoan parasites or tested pathogen-free as negative controls. Nucleic acid was extracted from samples and PCR amplification performed in multiplex primer pools with a procedure described in ArrayExpress experiment submission ID 18379. The PCR products were used for library preparation. The libraries sequenced on an Oxford Nanopore MinION. The passed reads aligned with a custom reference file to determine the identity of the pathogen in the sample.
2024-06-08 | E-MTAB-14011 | biostudies-arrayexpress
Project description:Higher-order chromatin structure arises from the combinatorial physical interactions of many genomic loci. To investigate this aspect of genome architecture we developed Pore-C, which couples chromatin conformation capture with Oxford Nanopore Technologies (ONT) long reads to directly sequence multi-way chromatin contacts without amplification.
2022-05-12 | GSE149117 | GEO
Project description:The Oxford Nanopore (ONT) platform provides portable and rapid genome sequencing, and its ability to natively profile DNA methylation without complex sample processing is attractive for clinical sequencing. We recently demonstrated ONT shallow whole-genome sequencing to detect copy number alterations (CNA) from the circulating tumor DNA (ctDNA) of cancer patients. Here, we show that cell-type and cancer-specific methylation changes can also be detected, as well as cancer-associated fragmentation signatures. This feasibility study suggests that ONT shallow WGS could be a powerful tool for liquid biopsy, especially real-time medical applications.
2022-04-27 | GSE185307 | GEO
Project description:Purpose: The aim of this study is to identify genes that are under the transcriptional control of the epigenetic modifier Smchd1 in mouse neural stem cells. We profiled the transcriptomes of mouse neural stem cells from samples that were either wild-type or contained a null mutation in the epigenetic regulator Smchd1 using Oxford Nanopore Technologies (ONT) direct cDNA sequencing protocol and a PromethION sequencer.
2020-06-18 | GSE151841 | GEO
Project description:The LRGASP challenge encompasses different human, mouse, and manatee samples sequenced using multiple combinations of protocols and platforms. Different challenges will use distinct subsets of the samples for evaluation. The long-read sequencing platforms used in these challenges are the Pacific Biosciences (PacBio) Sequel II, Oxford Nanopore (ONT) MinION and PromethION. Samples will also be sequenced on the Illumina HiSeq 2500. The primary LRGASP library prep protocols are “standard” cDNA sequencing, direct RNA sequencing, R2C2, and CapTrap. Each sample will also include Lexogen SIRV-Set 4 spike-ins. We will also provide simulated PacBio and ONT data as part of the evaluations. This particular study focuses on single strand CAGE sequencing of human iPSCs, defining CAGE peaks from Illumina HiSeq 2500 (SR: 150 cycles) of two biological replicates for use in the LRGASP challenge.
2021-10-27 | GSE185917 | GEO
Project description:To explore in depth and in a quantitative manner the complexity of the HIV-1 splicing landscape we used nanopore long-read cDNA (ONT) sequencing in NL4-3 HIV-1 infected primary CD4+ T cells and transfected/infected HeLa cells. Mean read lengths were between 1286 and 2626 nucleotides with maximum sizes of up to 9182 nucleotides, sufficiently long to span all possible splice junctions and to be assigned to a total of 229 exon combinations. Seventy isoforms were above the threshold of 5 copies in infected T cells and a core of 36 isoforms were found in common in infected T cells, infected HeLa cells and transfected HeLa cells. Quantification of both all viral isoforms as well as splice site (SS) usage were compiled to build “splice trees”, a quantitative representation of the splicing pathways leading to the different viral isoforms. This approach allowed visualizing the complete rewiring of SS usages upon perturbation of SS D2, using over-expression of U1 D2UpEx snRNA in transfected HeLa cells and its impact on viral RNA expression. Furthermore, we produced the first dynamic picture of the cascade of events occuring between 12 and 24 hours of CD4+ T cells HIV-1 infection. In particular, our data highlighted the importance of non-coding exons in viral RNA transcriptome regulation. Altogether, our results show that ONT sequencing allows one to grasp the dynamic of splicing events modulating the viral RNA landscape in infected cells.
2020-08-24 | GSE138423 | GEO
Project description:To explore in depth and in a quantitative manner the complexity of the HIV-1 splicing landscape we used nanopore long-read cDNA (ONT) sequencing in NL4-3 HIV-1 infected primary CD4+ T cells and transfected/infected HeLa cells. Mean read lengths were between 1286 and 2626 nucleotides with maximum sizes of up to 9182 nucleotides, sufficiently long to span all possible splice junctions and to be assigned to a total of 229 exon combinations. Seventy isoforms were above the threshold of 5 copies in infected T cells and a core of 36 isoforms were found in common in infected T cells, infected HeLa cells and transfected HeLa cells. Quantification of both all viral isoforms as well as splice site (SS) usage were compiled to build “splice trees”, a quantitative representation of the splicing pathways leading to the different viral isoforms. This approach allowed visualizing the complete rewiring of SS usages upon perturbation of SS D2, using over-expression of U1 D2UpEx snRNA in transfected HeLa cells and its impact on viral RNA expression. Furthermore, we produced the first dynamic picture of the cascade of events occuring between 12 and 24 hours of CD4+ T cells HIV-1 infection. In particular, our data highlighted the importance of non-coding exons in viral RNA transcriptome regulation. Altogether, our results show that ONT sequencing allows one to grasp the dynamic of splicing events modulating the viral RNA landscape in infected cells.
2020-08-24 | GSE138422 | GEO