Project description:Modest target sequencing yield improvements using Nanopore adaptive sampling to reduce human DNA contamination from clinical tissue samples

| PRJEB78709 | ENA

SARS-CoV-2

Project description:Nanopore adaptive sampling with carrier DNA (NASCarD)

| PRJNA930601 | ENA

Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples

Project description:Oxford Nanopore sequence data from adaptive sampling experiments using a synthetic bacterial mock community.

| PRJEB44844 | ENA

Adaptive sampling and chromosome sorting Y chromosome data

Project description:Y chromosome chromosome sorting and adaptive sampling data

| PRJEB58141 | ENA

Single-molecule simultaneous profiling of DNA methylation and DNA-protein interactions with Nanopore-DamID

Project description:We present Nanopore-DamID, a method to simultaneously detect cytosine methylation and DNA-protein interactions from single molecules, via selective sequencing of adenine-labelled DNA. Assaying LaminB1 and CTCF binding with Nanopore-DamID, we identify escape from LAD-associated repression of hypomethylated promoters amidst generalised hypermethylation of LaminB1-associated regulatory elements. We detect novel CTCF binding sites in highly repetitive regions, and allele-specific CTCF binding to imprinted genes and the active X chromosome. Nanopore-DamID highlights the importance of DNA methylation to transcription factor activity.

2025-05-15 | GSE203109 | GEO

NASCarD (Nanopore Adaptive Sampling with Carrier DNA): A Rapid, PCR-Free Method for SARS-CoV-2 Whole-Genome Sequencing in Clinical Samples.

Project description:Whole-genome sequencing (WGS) represents the main technology for SARS-CoV-2 lineage characterization in diagnostic laboratories worldwide. The rapid, near-full-length sequencing of the viral genome is commonly enabled by high-throughput sequencing of PCR amplicons derived from cDNA molecules. Here, we present a new approach called NASCarD (Nanopore Adaptive Sampling with Carrier DNA), which allows a low amount of nucleic acids to be sequenced while selectively enriching for sequences of interest, hence limiting the production of non-target sequences. Using COVID-19 positive samples available during the omicron wave, we demonstrate how the method may lead to >99% genome completeness of the SARS-CoV-2 genome sequences within 7 h of sequencing at a competitive cost. The new approach may have applications beyond SARS-CoV-2 sequencing for other DNA or RNA pathogens in clinical samples.

| S-EPMC10818518 | biostudies-literature

CDCA7-associated global aberrant DNA hypomethylation translates to localized, tissue-specific transcriptional responses [ONT adaptive sampling]

Project description:CDCA7-associated global aberrant DNA hypomethylation translates to localized, tissue-specific transcriptional responses [ONT adaptive sampling]

| PRJNA1043620 | ENA

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