Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SNPore

ABSTRACT: Forensic Nanopore SNP sequencing

PROVIDER: PRJEB18110 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR1742661.fastq.gz	Fastqsanger.gz
	ERR1742881.fastq.gz	Fastqsanger.gz
	ERR1742677.fastq.gz	Fastqsanger.gz
	ERR1744029.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

Forensic Tri-allelic SNP sequencing

Project description:Forensic tri-allelic SNP genotyping using nanopore sequencing

| PRJEB25630 | ENA

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

Identifying crossover locations from leaves of Arabidopsis thaliana Col x Ler F1 plants (WT and recq4) using Nanopore-seq and COmapper

Project description:We sequenced DNA from the leaves of ten Col x Ler F1 hybrid plants (WT and recq4) using Nanopore long-read sequencing and identified crossover sites with COmapper. These data were used as a negative control for COmapper, as no crossover sites were expected to be detected. For nanopore sequencing of gDNA from leaves, leaves from 10 5-week-old plants 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-14381 | 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

LoRTIS: A long read method for analysis of large transposon mutant libraries

Project description:Transposon insertion site sequencing (TIS) is a powerful method for associating genotype to phenotype. However, all TIS methods described to date use short nucleotide sequence reads which cannot uniquely determine the locations of transposon insertions within repeating genomic sequences where the repeat units are longer than the sequence read length. To overcome this limitation, we have developed a TIS method using Oxford Nanopore sequencing technology that generates and uses long nucleotide sequence reads; we have called this method LoRTIS (Long Read Transposon Insertion-site Sequencing). This experiment data contains sequence files generated using Nanopore and Illumina platforms. Biotin1308.fastq.gz and Biotin2508.fastq.gz are fastq files generated from nanopore technology. Rep1-Tn.fastq.gz and Rep1-Tn.fastq.gz are fastq files generated using Illumina platform. In this study, we have compared the efficiency of two methods in identification of transposon insertion sites.

2022-05-30 | E-MTAB-11351 | biostudies-arrayexpress

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

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

Methylome profiling of human glioblastoma using Illumina 450K microarrays for the GlioTeX panel

Project description:Genome-wide methylation profiles were generated as part of a multi-omics characterization (SNP array, WES, RNA-seq, cDNA microarray) of a panel of gliomasphere cell lines and matched parental tumors. See https://www.ncbi.nlm.nih.gov/pubmed/27571888 about the GlioTeX panel. Methylation profiling data in this record come from tumour samples. SNP array (ArrayExpress E-MTAB-4804), cDNA microarray (ArrayExpress E-MTAB-4803), WES and RNAseq (European Genome-Phenome Archive EGAS00001001871) have been published before. In addition, for the current project we compare 450K methylation data to nanopore sequencing based methylation profiles. These sequencing data will be accessible via European Genome-Phenome Archive (EGAS00001002213). Please also refer to https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5795/files/E-MTAB05795.additional.1.zip for further information on the background of this multi-omics study.

2017-06-24 | E-MTAB-5797 | biostudies-arrayexpress

Proteomic Genotyping: Using Mass Spectrometry to Infer SNP Genotypes in Pigmented and Non-Pigmented Hair

Project description:Proteomic genotyping is the use of genetically variant peptides (GVPs), detected in a forensic protein sample, to infer the genotype of corresponding non-synonymous SNP alleles in the donor’s genome. This process does not depend on the presence of accessible or useable DNA in a sample. This makes proteomic genotyping an attractive alternative for analysis of problematic forensic samples, such as hair shafts, degraded bones or teeth, fingermarks, or sexual assault evidence. To demonstrate the concept in hair shafts, we developed an optimized sample processing protocol that could be used with high effectiveness on single hairs. This allows us to determine if the detected profiles of genetically variant peptides are robust and result in a consistent profile of inferred SNP alleles regardless of the chemical or biological history of the sample. Several real world scenarios have been evaluated. Here we include a study of four European subjects that had both pigmented and non-pigmented (or gray and non-gray) hair shafts. We tested whether (a) protein profiles change as a result of the loss of pigmentation and (b) these changes were reflected in the inferred genotype derived from detection of genetically variant peptides. Using this information, we can determine whether the resulting GVP profiles are more dependent on the biological context of pigmentation status or the underlying genotype.

2020-05-27 | PXD016156 | Pride

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