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MetabolomicsFIRST-seq: a nanopore-based cDNA sequencing platform for RNA modification and structure profiling

This repository contains the LC-MS/MS raw data for the RNA quantifications obtained from in vivo DMS probed RNAs from E.coli and MDA-MB231 cell lines.

2026-04-26 | MTBLS14382 | MetaboLights
TranscriptomicsNanopore sequencing reveals endogenous NMD-targeted isoforms in human cells
Nonsense-mediated mRNA decay (NMD) is a eukaryotic, translation-dependent degradation pathway that targets mRNAs with premature termination codons and also regulates the expression of some mRNAs that encode full-length proteins. Although many genes express NMD-sensitive transcripts, identifying them...
2021-07-20 | E-MTAB-10452 | biostudies-arrayexpress
GenomicsNanopore sequencing of B. thetaiotaomicron hankyphages
We identified hankyphage prophages within B. thetaiotaomicron isolates gathered from French hospitals. We extracted genomic DNA from an overnight culture from a single colony of each strain and sequenced them using Nanopore sequencing using the Plasmidsaurus platform. This long-read approach helped ...
ORGANISM(S): Bacteroides thetaiotaomicron 
2025-01-24 | E-MTAB-14724 | biostudies-arrayexpress
TranscriptomicsComparative analysis of single-cell and spatial Nanopore long-read methods
Alternative splicing significantly contributes to transcriptome complexity and has critical implications for cellular functions. Recent advancements in single-cell isolation and capture techniques have enabled high-throughput quantification of gene expression at single-cell resolution. Long-read seq...
ORGANISM(S): Mus musculus 
2025-08-26 | E-MTAB-15190 | biostudies-arrayexpress
TranscriptomicsNanopore native RNA-seq for genome-wide identification of transcription units and transcriptional termination sites in the phytopathogen Dickeya dadantii 3937
In this study, based on Nanopore direct RNA-seq where native RNAs are sequenced directly as near full-length transcripts in the 3' to 5' direction, transcription units of the phytopathogen Dickeya dadantii 3937 were validated and transcriptional termination sites were determined. Briefly, D. dadanti...
ORGANISM(S): Dickeya dadantii 3937 
2022-01-01 | E-MTAB-10482 | biostudies-arrayexpress
GenomicsOxford nanopore sequencing data from the Arabidopsis thaliana accessions Ler-0, Cvi-0 and Tanz-1
Oxford nanopore sequencing data from the Arabidopsis thaliana accessions Ler-0, Cvi-0 and Tanz-1
ORGANISM(S): Arabidopsis thaliana 
2022-08-06 | E-MTAB-12009 | biostudies-arrayexpress
GenomicsIdentifying crossover locations in an Arabidopsis thaliana Col x Ler F2 population using Nanopore-seq and COmapper
Genomic DNA from 55 wild type Col x Ler F2 individuals was extracted using the CTAB method. Equal amounts of DNA from these 55 plants were pooled into two groups (pool 1 = 4 plants; pool 2 = 51 plants), and nine micrograms of gDNA from each pool was used to generate Nanopore sequencing libraries wit...
ORGANISM(S): Arabidopsis thaliana 
2024-09-02 | E-MTAB-14367 | biostudies-arrayexpress
TranscriptomicsOxford Nanopore sequencing of poly(A)+ RNA from two Trypanosoma brucei strains
EATRO1125 bloodstream forms grown to about 5 x 10e5 per ml. Lister 427 procyclic forms at no more than 2 million per ml. Direct nanopore sequencing on cells approaching their expiration date.
ORGANISM(S): Trypanosoma brucei brucei 
2020-07-16 | E-MTAB-9319 | biostudies-arrayexpress
GenomicsNanopore sequencing data of rolling-circle amplification products from apoptotic cells and its relative gDNA control
Nanopore sequencing data of rolling-circle amplification (RCA) products performed on hES cells, treated with 2mJ UV-C to induce apoptosis. The experimental conditions were designed to characterize circular DNA forms generated during apoptosis. gDNA from untreated and UV-treated cells are used as con...
ORGANISM(S): Homo sapiens 
2026-04-30 | E-MTAB-16581 | biostudies-arrayexpress
TranscriptomicsComparative evaluation of Oxford Nanopore Technologies’ adaptive sampling and the Twist long-read PGx panel for pharmacogenomic profiling
We used targeted long-read Oxford Nanopore Technologies sequencing enriching for a panel of 1036 pharmacogenes extracted from the PharmGKB database. The enrichment was performed using ONT's adaptive sampling feature, enabling in silico enrichment without physically capturing the fragments of interes...
ORGANISM(S): Homo sapiens 
2025-12-30 | E-MTAB-15248 | biostudies-arrayexpress
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