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

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

PROVIDER: PRJEB79391 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR13601540.fastq.gz	Fastqsanger.gz
	ERR13601541.fastq.gz	Fastqsanger.gz

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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 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 in an Arabidopsis thaliana recq4 Col x recq4 Ler F2 population using Nanopore-seq and COmapper

Project description:Identifying crossover locations in an Arabidopsis thaliana recq4 Col x recq4 Ler F2 population using Nanopore-seq and COmapper

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Identifying crossover locations from bulked seedlings of Arabidopsis thaliana Col x Ler F2 plants (HEI10-mRFP1) using Nanopore-seq and COmapper

Project description:Identifying crossover locations from bulked seedlings of Arabidopsis thaliana Col x Ler F2 plants (HEI10-mRFP1) using Nanopore-seq and COmapper

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

Project description:Identifying crossover locations from pollen of Arabidopsis thaliana Col x Ler F1 plants (WT) using Nanopore-seq and COmapper

| PRJEB88886 | 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:Identifying crossover locations from bulked seedlings of Arabidopsis thaliana Col x Ler F2 plants (WT and recq4) using Nanopore-seq and COmapper

| PRJEB79133 | ENA

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

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

| PRJEB79145 | ENA

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

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

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Identifying crossover locations in Arabidopsis thaliana asy1/+ Col × Ler F2 populations using genotyping-by-sequencing

Project description:Identifying crossover locations in Arabidopsis thaliana asy1/+ Col × Ler F2 populations using genotyping-by-sequencing

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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

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