Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nanopore metagenomics

ABSTRACT: Nanopore metagenomics

PROVIDER: PRJNA479723 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7499264_1.fastq.gz	Fastqsanger.gz
	SRR7497945_1.fastq.gz	Fastqsanger.gz
	SRR7497167_1.fastq.gz	Fastqsanger.gz
	SRR7500591_1.fastq.gz	Fastqsanger.gz
	SRR7503035_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 11

Similar Datasets

Mosquito metagenomics

Project description:Nanopore metagenomics of a mosquito

| PRJEB82460 | ENA

Nanopore sequencing of B. thetaiotaomicron hankyphages

Project description: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 the assembly of the phages and determination of the hankyphage ends. We also improved the annotation of the reference hankyphage (hankyphage p00 from P. dorei HM719) using a structural prediction approach and annotated our B. thetaiotaomicron hankyphages using this new annotation. In this project we upload the genomic raw reads of nanopore sequencing of our hankyphage-bearing B. thetaiotaomicron collection (jmh strains) and the processed assembled hankyphages.

2025-01-24 | E-MTAB-14724 | biostudies-arrayexpress

Qilian Mt. glacier melting water Nanopore metagenomics sequencing

Project description:Rapid in-field MinION Nanopore glacier melting water metagenomics sequencing at Qilian Mountain

| PRJEB36071 | ENA

Targeted nanopore resequencing and methylation analysis of LINE-1 retrotransposons

Project description:We used the nanopore Cas9 targeted sequencing (nCATS) strategy to specifically sequence 125 L1HS-containing loci in parallel and measure their DNA methylation levels using nanopore long-read sequencing. Each targeted locus is sequenced at high coverage (~45X) with unambiguously mapped reads spanning the entire L1 element, as well as its flanking sequences over several kilobases. The genome-wide profile of L1 methylation was also assessed by bs-ATLAS-seq in the same cell lines (E-MTAB-10895).

2023-09-22 | E-MTAB-12247 | biostudies-arrayexpress

Assembly of the Arabidopsis (Col-0) centromeres using Oxford Nanopore Technology long-read DNA sequencing.

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

Identifying crossover locations in an Arabidopsis thaliana Col x Ler F2 population using Nanopore-seq and COmapper

Project description: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 with the Ligation Sequencing Kit V14 (Nanopore, SQK-LSK114). The libraries were sequenced independently using PromethION (BGI, Hong Kong).

2024-09-02 | E-MTAB-14367 | biostudies-arrayexpress

Oxford nanopore sequencing data from the Arabidopsis thaliana accessions Ler-0, Cvi-0 and Tanz-1

Project description:Oxford nanopore sequencing data from the Arabidopsis thaliana accessions Ler-0, Cvi-0 and Tanz-1

2022-08-06 | E-MTAB-12009 | biostudies-arrayexpress

Comparative analysis of 43 distinct RNA modifications by nanopore tRNA sequencing

Project description:Transfer RNAs are the fundamental adapter molecules of protein synthesis and the most abundant and heterogeneous class of noncoding RNA molecules in cells. The study of tRNA repertoires remains challenging, complicated by the presence of dozens of post transcriptional modifications. Nanopore sequencing is an emerging technology with promise for both tRNA sequencing and the detection of RNA modifications; however, such studies have been limited by the throughput and accuracy of direct RNA sequencing methods. Moreover, detection of the complete set of tRNA modifications by nanopore sequencing remains challenging. Here we show that recent updates to nanopore direct RNA sequencing chemistry (RNA004) combined with our own optimizations to tRNA sequencing protocols and analysis workflows enable high throughput coverage of tRNA molecules and characterization of nanopore signals produced by 43 distinct RNA modifications. We share best practices and protocols for nanopore sequencing of tRNA and further report successful detection of low abundance mitochondrial and viral tRNAs, providing proof of concept for use of nanopore sequencing to study tRNA populations in the context of infection and organelle biology. This work provides a roadmap to guide future efforts towards de novo detection of RNA modifications across multiple organisms using nanopore sequencing.

2025-12-01 | GSE272876 | GEO

Xdrop - Oxford Nanopore long read seqeuncing of HepG2 genetic modified clones

Project description:This dataset contains Xdrop followed by oxford nanopore long read sequencing performed in target tRNA gene deletion (t8) and intergenic region deletion (i50) clones in HepG2 . By applying de novo assembly based approach to Xdrop-LRS data, we identified Cas9-induced on-target genomic alteration.

2022-09-16 | E-MTAB-11327 | biostudies-arrayexpress

Identifying crossover locations from bulked seedlings of Arabidopsis thaliana Col x Ler F2 plants (WT and recq4) using Nanopore-seq and COmapper

Project description:We sequenced DNA from a bulk of Col x Ler F2 hybrid plants (WT and recq4) using Nanopore long-read sequencing and identified crossover sites with COmapper. For nanopore sequencing of gDNA from 1,000 pooled seedlings, 10-day-old seedlings were ground in liquid nitrogen using a mortar and pestle. The ground tissue was resuspended in four volumes of CTAB buffer (1% [w/v] CTAB, 50 mM Tris-HCl pH 8.0, 0.7 M NaCl, 10 mM EDTA) and incubated at 65°C for 30 min. Following chloroform extraction, isopropanol precipitation and removal of RNAs as above, the gDNA pellet was resuspended in 150 μl TE (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA) buffer and gDNA was quantified using a Qubit dsDNA Broad Range assay kit (Thermo Fisher, Q32853). Nine micrograms of gDNA from pollen or seedlings was used to construct a nanopore long-read sequencing library using a Ligation Sequencing Kit V14 (Nanopore, SQK-LSK114). The libraries were sequenced using a PromethION platform (BGI, Hong Kong).

2024-08-19 | E-MTAB-14368 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data