Ontology highlight
ABSTRACT:
PROVIDER: PRJNA743816 | ENA |
REPOSITORIES: ENA
Similar Datasets
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:We performed the long-read RNA sequencing technique ONT-cappable-seq on RNA samples of T. thermophilus infected with phage P23-45 5 minutes post-infection. Using this approach, we obtained the primary transcriptome at the early infection stage and sequenced it in full-length. Based on this data, we were able to identify viral transcription start sites and termination sites and uncover distinct promoter motifs.
2023-12-12 | GSE215811 | GEO
Project description:Alternative splicing contributes to transcriptomic complexity and plays a role in the regulation of cellular identity and function, but the correct assembly of transcripts of complex loci as well as their quantification based on short-read sequencing is non-trivial. Recent long-read sequencing methods such as those from ONT and PacBio overcome these problems by potentially sequencing full transcripts. The activation of brown adipose tissue e.g., by reduced ambient temperature (cold) exposure, positively affects metabolism by increasing energy expenditure and releasing endocrine factors and has been shown to involve specific alternative splicing events. Here we assessed important features of ONT long read sequencing protocols in relation to Illumina short read sequencing: (i) Alignment characteristics to the reference genome and transcriptome, (ii) Gene and transcript detection and quantification, (iii) Detection of differential gene and transcript expression events, (iv) Transcriptome reannotation and (v) Detection of differential transcript usage events. We find that ONT long-read sequencing is advantageous in terms of transcriptome reassembly, especially when the reads are enriched for full length reads. Illumina sequencing, due to the higher number of counts available, has a higher statistical power for calling differentiall expressed/used features, whereas long-read sequencing has a lower risk of calling false positive events due to the better ability to unambiguously map reads to transcripts. Finally we describe novel transcript isoforms in cold-activated murine iBAT reassembled from ONT long reads.
2023-09-18 | GSE212573 | GEO
Project description:Alternative splicing contributes to transcriptomic complexity and plays a role in the regulation of cellular identity and function, but the correct assembly of transcripts of complex loci as well as their quantification based on short-read sequencing is non-trivial. Recent long-read sequencing methods such as those from ONT and PacBio overcome these problems by potentially sequencing full transcripts. The activation of brown adipose tissue e.g., by reduced ambient temperature (cold) exposure, positively affects metabolism by increasing energy expenditure and releasing endocrine factors and has been shown to involve specific alternative splicing events. Here we assessed important features of ONT long read sequencing protocols in relation to Illumina short read sequencing: (i) Alignment characteristics to the reference genome and transcriptome, (ii) Gene and transcript detection and quantification, (iii) Detection of differential gene and transcript expression events, (iv) Transcriptome reannotation and (v) Detection of differential transcript usage events. We find that ONT long-read sequencing is advantageous in terms of transcriptome reassembly, especially when the reads are enriched for full length reads. Illumina sequencing, due to the higher number of counts available, has a higher statistical power for calling differentiall expressed/used features, whereas long-read sequencing has a lower risk of calling false positive events due to the better ability to unambiguously map reads to transcripts. Finally we describe novel transcript isoforms in cold-activated murine iBAT reassembled from ONT long reads.
2023-09-18 | GSE212572 | GEO
Project description:Alternative splicing contributes to transcriptomic complexity and plays a role in the regulation of cellular identity and function, but the correct assembly of transcripts of complex loci as well as their quantification based on short-read sequencing is non-trivial. Recent long-read sequencing methods such as those from ONT and PacBio overcome these problems by potentially sequencing full transcripts. The activation of brown adipose tissue e.g., by reduced ambient temperature (cold) exposure, positively affects metabolism by increasing energy expenditure and releasing endocrine factors and has been shown to involve specific alternative splicing events. Here we assessed important features of ONT long read sequencing protocols in relation to Illumina short read sequencing: (i) Alignment characteristics to the reference genome and transcriptome, (ii) Gene and transcript detection and quantification, (iii) Detection of differential gene and transcript expression events, (iv) Transcriptome reannotation and (v) Detection of differential transcript usage events. We find that ONT long-read sequencing is advantageous in terms of transcriptome reassembly, especially when the reads are enriched for full length reads. Illumina sequencing, due to the higher number of counts available, has a higher statistical power for calling differentiall expressed/used features, whereas long-read sequencing has a lower risk of calling false positive events due to the better ability to unambiguously map reads to transcripts. Finally we describe novel transcript isoforms in cold-activated murine iBAT reassembled from ONT long reads.
2023-09-18 | GSE212571 | GEO
Project description:Alternative splicing contributes to transcriptomic complexity and plays a role in the regulation of cellular identity and function, but the correct assembly of transcripts of complex loci as well as their quantification based on short-read sequencing is non-trivial. Recent long-read sequencing methods such as those from ONT and PacBio overcome these problems by potentially sequencing full transcripts. The activation of brown adipose tissue e.g., by reduced ambient temperature (cold) exposure, positively affects metabolism by increasing energy expenditure and releasing endocrine factors and has been shown to involve specific alternative splicing events. Here we assessed important features of ONT long read sequencing protocols in relation to Illumina short read sequencing: (i) Alignment characteristics to the reference genome and transcriptome, (ii) Gene and transcript detection and quantification, (iii) Detection of differential gene and transcript expression events, (iv) Transcriptome reannotation and (v) Detection of differential transcript usage events. We find that ONT long-read sequencing is advantageous in terms of transcriptome reassembly, especially when the reads are enriched for full length reads. Illumina sequencing, due to the higher number of counts available, has a higher statistical power for calling differentiall expressed/used features, whereas long-read sequencing has a lower risk of calling false positive events due to the better ability to unambiguously map reads to transcripts. Finally we describe novel transcript isoforms in cold-activated murine iBAT reassembled from ONT long reads.
2023-09-18 | GSE212570 | GEO
Project description:Alternative splicing contributes to transcriptomic complexity and plays a role in the regulation of cellular identity and function, but the correct assembly of transcripts of complex loci as well as their quantification based on short-read sequencing is non-trivial. Recent long-read sequencing methods such as those from ONT and PacBio overcome these problems by potentially sequencing full transcripts. The activation of brown adipose tissue e.g., by reduced ambient temperature (cold) exposure, positively affects metabolism by increasing energy expenditure and releasing endocrine factors and has been shown to involve specific alternative splicing events. Here we assessed important features of ONT long read sequencing protocols in relation to Illumina short read sequencing: (i) Alignment characteristics to the reference genome and transcriptome, (ii) Gene and transcript detection and quantification, (iii) Detection of differential gene and transcript expression events, (iv) Transcriptome reannotation and (v) Detection of differential transcript usage events. We find that ONT long-read sequencing is advantageous in terms of transcriptome reassembly, especially when the reads are enriched for full length reads. Illumina sequencing, due to the higher number of counts available, has a higher statistical power for calling differentiall expressed/used features, whereas long-read sequencing has a lower risk of calling false positive events due to the better ability to unambiguously map reads to transcripts. Finally we describe novel transcript isoforms in cold-activated murine iBAT reassembled from ONT long reads.
2023-09-18 | GSE212569 | GEO
Project description:High throughput RNA sequencing (RNA-seq) using cDNA has played a key role in delineating transcriptome complexity, including alternative transcription initiation, splicing, polyadenylation and base modification. However, the reads derived from current RNA-seq technologies are usually short and deprived of information on modification during reverse transcription, compromising their potential in defining transcriptome complexity. Here we applied a direct RNA sequencing method with ultra-long reads from Oxford Nanopore Technologies (ONT) to study the transcriptome complexity in C. elegans. We sequenced native poly-A tailed mRNAs by generating approximately six million reads from embryos, L1 larvae and young adult animals, with average read lengths ranging from 900 to 1,100 bps across stages. Around half of the reads represent full-length transcripts, judged by the presence of a splicing-leader or their full coverage of an existing transcript. To take advantage of the full-length transcripts in defining transcriptome complexity, we devised a novel algorithm to predict novel isoforms or group them with exiting isoforms using their mapping tracks rather than the existing intron/exon structures, which allowed us to identify roughly 57,000 novel isoforms and recover at least 26,000 out of the 33,500 existing isoforms. Intriguingly, stage-specific expression at the level of gene and isoform demonstrates little correlation. Finally, we observed an elevated level of modification in all bases in the coding region relative to the UTR. Taken together, the ONT long reads are expected to deliver new insights into RNA processing and modification and their underlying biology.
2019-09-10 | GSE130044 | GEO