Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Tissues adaptive sampling

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

PROVIDER: PRJEB78709 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR14747340.fastq.gz	Fastqsanger.gz
	ERR14747353.fastq.gz	Fastqsanger.gz
	ERR14747356.fastq.gz	Fastqsanger.gz
	ERR14747360.fastq.gz	Fastqsanger.gz
	ERR14747362.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Plasmodium adaptive sampling

Project description:Assessment of Nanopore adaptive sampling for Plasmodium whole-genome sequencing

| PRJEB57715 | ENA

Nanopore adaptive sampling with carrier DNA

Project description:Nanopore adaptive sampling with carrier DNA

| PRJEB59467 | ENA

Evaluation of adaptive sampling methods on Nanopore

Project description:Evaluation of adaptive sampling methods on Nanopore

| PRJEB73272 | ENA

Nanopore Adaptive Sampling for pneumococcal surveillance

Project description:Nanopore Adaptive Sampling for pneumococcal surveillance using serotyping

| PRJEB72455 | ENA

Adaptive sampling and chromosome sorting Y chromosome data

Project description:Y chromosome chromosome sorting and adaptive sampling data

| PRJEB58141 | 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

Analysis of the Elements Involved in the Enrichment of a Panel of Genomic Regions by Nanopore Sequencing Using Adaptive Sampling

Project description:DNA sequencing using nanopore technologies with the affordable MinION device is useful for the identification and characterization of structural variants, long haplotypes, sequencing of repetitive regions and identification of epigenetic modifications. The main limitation of this approach is the low coverage obtained, which might be avoided by adaptive sampling, a computationally controlled method of enrichment for targeted genomic regions. This study dissects the factors involved in the enrichment by adaptive sampling of a panel of 18 human genome regions containing 20 genes implicated in breast cancer sequenced in 16 patients with familial breast cancer negative for NGS screening. An average coverage of 2.0x was obtained for the whole genome and 5.1x for selected regions. Sequencing time was the main factor improving coverage. The selection of long reads (>1 Kb) did not improve the enrichment. The length of the selected region, which in our study ranged from 126 to 565 Kb, did not play a significant role in enrichment. However, the region containing PMS2 showed significantly lower coverage, which could be explained by the high number of PMS2 pseudogenes (N = 14), which were also enriched. Our study shows new evidence of enrichment obtained by adaptive sampling in a panel of genomic regions and shows parameters, the relevance of sequencing time and the role of pseudogenes, that improve the enrichment yield with no library reloading or GPU use, data useful for a more efficient application of this procedure in future studies.

| EGAS00001007375 | EGA

SARS-CoV-2

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

| PRJNA930601 | ENA

Project description:Adaptive sampling nanopore long-read sequencing of 22Rv1 cell

| PRJNA1158791 | ENA

Project description:Species identification of mammalian scat using nanopore adaptive sampling

| PRJNA1026962 | ENA