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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

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

PROVIDER: PRJEB91059 | ENA |

REPOSITORIES: ENA

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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).

2024-08-19 | E-MTAB-14381 | biostudies-arrayexpress

Identifying crossover locations in an Arabidopsis thaliana HEI10-mRFP1 Col x Ler F2 population using genotyping by sequencing

Project description:Identifying crossover locations in an Arabidopsis thaliana HEI10-mRFP1 Col x Ler F2 population using genotyping by sequencing

| PRJEB91044 | ENA

Identifying crossover locations in an Arabidopsis thaliana HEI10-mRFP1 Col x Ler F2 population using genotyping by sequencing

Project description:Identifying crossover locations in an Arabidopsis thaliana HEI10-mRFP1 Col x Ler F2 population using genotyping by sequencing

| PRJEB91045 | ENA

Identifying crossover locations in an Arabidopsis thaliana HEI10-mRFP1 Col x Ler F2 population using genotyping by sequencing

Project description:Identifying crossover locations in an Arabidopsis thaliana HEI10-mRFP1 Col x Ler F2 population using genotyping by sequencing

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Whole-genome resequencing of BC1 populations from Arabidopsis (Col x Ler) x Col crosses (wild type and hei10+/-)

Project description:This experiment aims at analyzing crossover distribution in male and female meiosis, in the Arabidopsis hei10+/- compared to wild type. Plants heterozygous for the hei10-2 mutation (Col-0) were crossed as females with Ler as males. Wild-type and hei10+/- plants were selected among the F1s and crossed as female or as male with wild-type Col-0. Leaf samples from the four back-crossed populations were used for DNA purification and library preparation for Illumina sequencing (NextSeq 2000 2×150 base pairs [bp]), performed at the Max Planck-Genome-center (https://mpgc.mpipz.mpg.de/home/).

2024-09-23 | E-MTAB-14423 | 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: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 in an Arabidopsis thaliana HEI10 Col x Ler F2 population using genotyping by sequencing.

Project description:Genomic DNA from 192 HEI10 Col x Ler F2 individuals was extracted using CTAB and used to generate sequencing libraries as described (Rowan et al; Yelina et al), with the following modifications. DNA was extracted from 3 rosette leaves of 5 week old plants and 150 ng of DNA used as input for each library. DNA shearing was carried out for 20 minutes at 37C with 0.4U of DNA Shearase (Zymo research). The barcoded adapters used for library construction are listed in Rowan et al. Each set of 96 libraries was sequenced on one lane of an Illumina NextSeq500 instrument (300-cycle Mid Output run). Sequencing data was analysed to identify crossovers as previously reported, using the TIGER pipeline (Rowan et al; Yelina et al). These data should be compared to a set of wild type control libraries available at E-MTAB-4657. Rowan BA, Patel V, Weigel D, Schneeberger K. Rapid and Inexpensive Whole-Genome Genotyping-by-Sequencing for Crossover Localization and Fine-Scale Genetic Mapping. G3 (Bethesda). 2015;5: 38598. Yelina NE, Lambing C, Hardcastle TJ, Zhao X, Santos B, Henderson IR. DNA methylation epigenetically silences crossover hot spots and controls chromosomal domains of meiotic recombination in Arabidopsis. Genes Dev. 2015;29: 2183202.

2016-08-05 | E-MTAB-4967 | biostudies-arrayexpress

Identifying crossover locations in an Arabidopsis thaliana HEI10 Col x Ler F2 population using genotyping by sequencing.

Project description:Identifying crossover locations in an Arabidopsis thaliana HEI10 Col x Ler F2 population using genotyping by sequencing.

| PRJEB14931 | ENA

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

| PRJEB79391 | ENA