Tailfindr
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB31806 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To identify full-length cap-to-poly(A) mRNA isoforms of CD20 and rule out reverse transcription artifacts which are common in cDNA-seq approaches, long-read Oxford Nanopore direct RNA sequencing was performed on the Raji cell line.
2023-12-08 | GSE243920 | GEO
Project description:Whole-genome bisulfite sequencing (WGBS) is currently the gold standard for DNA methylation (5-methylcytosine, 5mC) profiling, however the destructive nature of sodium bisulfite results in DNA fragmentation and subsequent biases in sequencing data. Such issues have led to the development of bisulfite-free methods for 5mC detection. Nanopore sequencing is a long read non-destructive approach that directly analyzes DNA and RNA fragments in real time. Recently, computational tools have been developed that enable base-resolution detection of 5mC from Oxford Nanopore sequencing data. In this chapter we provide a detailed protocol for preparation, sequencing, read assembly and analysis of genome-wide 5mC using Nanopore sequencing technologies.
2021-12-03 | GSE179673 | GEO
Project description:While numerous studies have described the transcriptomes of EVs in different cellular contexts, these efforts have typically relied on sequencing methods requiring RNA fragmentation, which limits interpretations on the integrity and isoform diversity of EV-encapsulated RNA populations. Furthermore, it has been assumed that mRNA signatures in EVs are likely to be fragmentation products of the cellular mRNA material, and little is known about the extent to which full-length mRNAs are present within EVs. Using Oxford nanopore long-read RNA sequencing, we sought to characterize the full-length polyadenylated (poly-A) transcriptome of EVs released by human chronic myelogenous leukemia K562 cells. We detected 441 and 280 RNAs that were respectively enriched or depleted in EVs. EV-enriched poly-A transcripts consist of a variety of biotypes, including mRNAs, long non-coding RNAs, and pseudogenes. Our analysis revealed that 12.72% of all reads present in EVs corresponded to known full-length transcripts, 65.34% of which were mRNAs. We also observed that for many well-represented coding and non-coding genes, diverse full-length transcript isoforms were present in EV specimens, and these isoforms were reflective-of but often in different ratio compared to cellular samples. Here we report a full-length transcriptome from human EVs, as determined by long-read nanopore sequencing.
2023-09-27 | GSE225471 | GEO
Project description:Oxford Nanopore enables direct RNA sequencing allowing for base calling of RNA modifications. We tested mouse hippocampi RNA samples, using a Nanopore direct RNA-seq protocol that in addition to long poly A selected RNAs allows sequencing also of non-poly A RNAs as well as short RNAs < 200nt (including SINE B2 RNAs and other non poly A non coding RNAs). We provide here as a resource a direct RNA-sequencing dataset generated from mouse brain tissues that includes both mRNAs and non poly A or short non-coding RNAs such as SINEs. Elevated SINE B2 RNA Adenosine to Inosine editing is consistently observed across hippocampal tissues of a mouse model of amyloid beta accumulation compared to hippocampi of wild type animals. Nanopore direct RNA sequencing supports increased RNA modification signals at the sameSINE B2 RNA regions identified by short-read Illumina sequencing in these hippocampi.
2026-03-01 | GSE171312 | GEO
Project description:Cell-free DNA (cfDNA) fragmentation patterns encode biologically and clinically relevant information beyond fragment length, reflecting nuclease activity, chromatin organization, and tissue of origin. Fragmentomics has therefore emerged as a promising strategy to enhance circulating tumor DNA (ctDNA) detection, particularly in cancers with low tumor fractions. However, most existing approaches are optimized for short-read sequencing, limiting their applicability to third-generation platforms. Here, we present FLARE (Fragmentation and Long-read Analysis of Regulatory Epigenetics), an integrated and scalable fragmentomics pipeline specifically optimized for Oxford Nanopore long-read sequencing. FLARE preserves native cfDNA fragment ends and enables the simultaneous analysis of copy number alterations, tumor fraction estimation, methylation-derived signals, fragment length distributions, and 5′ end-motif profiles.
2026-04-01 | GSE317007 | GEO
Project description:Analysis and understanding of transcript functions is greatly helped by knowing the full-length sequence of individual RNAs. New long-read sequencing devices such as Oxford Nanopore and Pacbio have the potential to sequence full-length transcripts, but standard methods lack the ability to capture true RNA 5’ ends and selects for poly-adenylated (pA+) transcripts. We present a method that, by utilizing cap-trapping and 3’ end adapter ligation, can sequence transcripts from the exact 5’ end to 3’ end regardless of whether they are poly-adenylated, with no need for ribosomal RNA depletion. We show that the method can faithfully detect 5’ ends, splice junctions and 3’ ends, has high reproducibility between runs and gene expression estimates from the method correlate well with short-read sequencing methods. We also demonstrate that the method can detect and sequence full-length pA- RNAs, including lncRNAs, promoter upstream transcripts (PROMPTs) and enhancer RNAs. TLDR-seq is therefore useful for the characterization of diverse capped RNA species.
2025-04-09 | GSE289428 | GEO
Project description:Analysis and understanding of transcript functions is greatly helped by knowing the full-length sequence of individual RNAs. New long-read sequencing devices such as Oxford Nanopore and Pacbio have the potential to sequence full-length transcripts, but standard methods lack the ability to capture true RNA 5’ ends and selects for poly-adenylated (pA+) transcripts. We present a method that, by utilizing cap-trapping and 3’ end adapter ligation, can sequence transcripts from the exact 5’ end to 3’ end regardless of whether they are poly-adenylated, with no need for ribosomal RNA depletion. We show that the method can faithfully detect 5’ ends, splice junctions and 3’ ends, has high reproducibility between runs and gene expression estimates from the method correlate well with short-read sequencing methods. We also demonstrate that the method can detect and sequence full-length pA- RNAs, including lncRNAs, promoter upstream transcripts (PROMPTs) and enhancer RNAs. TLDR-seq is therefore useful for the characterization of diverse capped RNA species.
2025-04-09 | GSE279131 | GEO
Project description:This project aims to leverage Oxford Nanopore Technologies (ONT) long-read RNA sequencing to achieve a comprehensive analysis of the human pancreatic cancer transcriptome. Traditional short-read sequencing methods often struggle with accurately reconstructing full-length transcripts and discerning complex splicing events due to their limited read lengths. In contrast, ONT's long-read sequencing can generate reads that span entire RNA molecules, facilitating precise identification of transcript isoforms, alternative splicing patterns, and poly(A) tail length. By applying this technology, we seek to enhance the annotation of the pancreatic cancer transcriptome, uncover novel transcripts, and gain deeper insights into gene expression dynamics. The findings from this study have the potential to advance our understanding of gene regulation and contribute to the development of novel therapeutic strategies.
2025-07-23 | GSE293661 | GEO
Project description:We report that retention of intron 2 which affects expression of CD19 in CART-19 relapsed leukemia occurs in the context of full length CD19 transcript using Oxford Nanopore sequencing technology. By performing Direct RNA sequencing on Reh leukemia cell lines, we showed that intron 2 retention is functionally equivalent to nonsense mutations.
2020-05-19 | GSE136068 | GEO
Project description:Background: Systemic light chain amyloidosis is a protein misfolding disorder characterized by deposition of clonal immunoglobulin light chains in vital organs. To date, little is known about the contribution of light chain constant domain mutations in thermodynamic stability and amyloidogenicity.Methods: In 89 patients, RNA-based full-length light chain repertoire sequencing with Oxford Nanopore was performed, in addition to Illumina sequencing and mass spectrometric detection of light chain protein in serum and amyloid deposits. Computational methods for conservation, free energy calculation, and molecular dynamics simulations were applied to investigate the thermodynamic stability.Results: Monoclonal light chain detection rate was 95.4%, and sequences showed 100% identity with Illumina in all patients. Light chain protein was specifically detectable by mass spectrometry in serum and amyloid deposits. Lambda constant domain mutations were present in 10%, while no kappa constant domain mutations were detected. Fold free energy change and molecular dynamics simulations indicate potential light chain stabilizing or destabilizing effects of detected constant domain mutations.Conclusion: Current findings highlight the importance of routinely implementing full-length light chain sequencing in plasma cell dyscrasias, particularly light chain amyloidosis to account for the potential impact of constant domain mutations on light chain stability and amyloidogenicity.
2026-05-06 | PXD077140 | Pride