Ontology highlight
ABSTRACT:
PROVIDER: PRJNA609320 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR11198163_subreads.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
Similar Datasets
Project description:New tools for improved long-read transcript assembly and coalescence with its short-read counterpart are required. Using our short- and long-read measurements from different cell lines with spiked-in standards, we systematically compared key parameters and biases in the read alignment and assembly of transcripts. We report a cDNA synthesis artifact in long-read datasets that impacts the identity and quantitation of assembled transcripts. We developed a computational pipeline to strand long-read cDNA libraries that markedly improves assembly of transcripts from long-reads. Incorporating stranded long-reads in a new hybrid assembly approach, we demonstrate its efficacy for improved characterization of challenging lncRNA transcripts. Our workflow can be applied to a wide range of transcriptomics datasets for superior demarcation of transcript ends and refined isoform structure, which can enable better differential gene expression analyses and molecular manipulations of transcripts.
2023-10-14 | GSE215357 | GEO
Project description:New tools for improved long-read transcript assembly and coalescence with its short-read counterpart are required. Using our short- and long-read measurements from different cell lines with spiked-in standards, we systematically compared key parameters and biases in the read alignment and assembly of transcripts. We report a cDNA synthesis artifact in long-read datasets that impacts the identity and quantitation of assembled transcripts. We developed a computational pipeline to strand long-read cDNA libraries that markedly improves assembly of transcripts from long-reads. Incorporating stranded long-reads in a new hybrid assembly approach, we demonstrate its efficacy for improved characterization of challenging lncRNA transcripts. Our workflow can be applied to a wide range of transcriptomics datasets for superior demarcation of transcript ends and refined isoform structure, which can enable better differential gene expression analyses and molecular manipulations of transcripts.
2023-10-14 | GSE215355 | GEO
Project description:In order to polish a long-read genome assembly, short-read illumina data was obtained from Heterodera schachtii cysts (Woensdrecht population from IRS, the Netherlands). Cysts where obtained from infected plant material. Nematodes were cleaned using a sucrose gradient centrifugation step. Thereafter DNA was extracted and used for library preparation and sequencing by Illumina NextSeq500.
2023-11-03 | E-MTAB-13472 | biostudies-arrayexpress
Project description:Short-read RNA sequencing (RNAseq) remains a cornerstone for transcriptome profiling, but is limited in reconstructing full-length transcripts and capturing transcript diversity. While long-read RNAseq spans entire transcripts and resolves complex structures, this technology is hindered by its high error rates. In parallel, noncoding RNA transcripts remain underrepresented in current references. Here, we present HyDRA (Hybrid de novo RNA Assembly), a pipeline that integrates the accuracy of short reads with the structural resolution of long reads to produce more complete de novo transcriptome assemblies. Benchmarking showed HyDRA to outperform existing methods by up to 40%. Using the HyDRA human ovarian metatranscriptome, we identified >50,000 high-confidence long noncoding RNAs, most of which have not been previously detected using traditional methods. Although long-read RNAseq is advancing, the vast availability of short reads ensures HyDRA’s ongoing role in capturing high-confidence, cell-type specific transcripts and advancing our understanding of transcriptomic complexity and the noncoding genome.
2026-04-06 | GSE327033 | GEO
Project description:a chromosome-level nuclear genome and organelle genomes of the alpine snow alga Chloromonas typhlos were sequenced and assembled by integrating short- and long-read sequencing and proteogenomic strategy
| PXD056928 |
Project description:Nanopore long-read sequencing was used to generate a complete assembly of the Arabidopsis centromeres.
2021-04-02 | E-MTAB-10272 | biostudies-arrayexpress
Project description:<p class='ql-align-justify'>Megasphaera hexanoica KCCM 43214T, isolated from cow rumen, is capable of producing medium-chain carboxylic acids such as n-caproate and n-caprylate. In this study, we present a high-quality genome assembly, along with intracellular metabolomic profiling and pangenomic analysis. Illumina sequencing generated 2.3 Mbp from 15,293,634 reads with a GC content of 49.5%, while PacBio HiFi sequencing produced 331.5 Mbp across 45,266 reads, with an average read length of 7,323 bp and a HiFi read N50 of 8,214 bp. Hybrid assembly of short and long reads resulted in a single 2.88 Mbp contig, containing 2,075-2,083 unique genes. A genome-scale metabolic model was constructed, to evaluate its metabolic capabilities under specific growth conditions. Intracellular metabolomic analysis of cells grown in fructose medium and lactate medium revealed key metabolic activities associated with chain elongation. Pangenomic analysis across nine annotated genomes identified 6,721 orthologous gene using OrthoMCL, emphasizing the genetic and functional diversity within the Megasphaera genus. This dataset offers valuable insights into the metabolism and biotechnological potential of M. hexanoica KCCM 43214T.</p>
2026-04-03 | MTBLS14019 | MetaboLights
Project description:Accurate annotation of transcript isoforms is crucial to understand gene functions, but automated methods for reconstructing full-length transcripts from RNA sequencing (RNA-seq) data remain imprecise. We developed Bookend, a software package for transcript assembly that incorporates data from different RNA-seq techniques, with a focus on identifying and utilizing RNA 5′ and 3′ ends. Through end-guided assembly with Bookend we demonstrate that correct modeling of transcript start and end sites is essential for precise transcript assembly. Furthermore, we discovered that utilization of end-labeled reads present in full-length single-cell RNA-seq (scRNA-seq) datasets dramatically improves the precision of transcript assembly in single cells. Finally, we show that hybrid assembly across short-read, long-read, and end-capture RNA-seq datasets from Arabidopsis, as well as meta-assembly of RNA-seq from single mouse embryonic stem cells (mESCs) can produce end-to-end transcript annotations of comparable quality to reference annotations in these model organisms.
2022-01-08 | GSE189482 | GEO
Project description:The accuracy of methods for assembling transcripts from short-read RNA sequencing data is limited by the lack of long-range information. Here we introduce Ladder-seq, an approach that separates transcripts according to their lengths prior to sequencing and uses the additional information to improve the quantification and assembly of transcripts. Using simulated data, we demonstrate that a kallisto algorithm extended to process Ladder-seq data quantifies transcripts of complex genes with substantially higher accuracy than conventional kallisto. For reference-based assembly, a modified StringTie2 algorithm reconstructs a single transcript with 30.8% higher precision than its conventional counterpart and is >30% more sensitive for complex genes. For de novo assembly, a modified Trinity algorithm correctly assembles 78% more transcripts than conventional Trinity, while improving precision by 78%. In experimental data, Ladder-seq reveals 40% more genes harboring isoform switches compared with conventional RNA-seq and unveils widespread changes in isoform usage upon m6A depletion by Mettl14 knock-out.
2021-10-11 | GSE158985 | GEO