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

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

PROVIDER: PRJEB79133 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR13510232.fastq.gz	Fastqsanger.gz
	ERR13510233.fastq.gz	Fastqsanger.gz

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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).

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

Project description:Genomic DNA from 39 recq4 Col x Ler F2 individuals was extracted using the CTAB method. Equal amounts of DNA from these 39 plants were pooled 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).

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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 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

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Identifying crossover locations in an Arabidopsis thaliana recq4 Ler x recq4 Col/Ler backcross F1 population using genotyping by sequencing for male-specific crossover map

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

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

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