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Identifying crossover locations in an Arabidopsis thaliana wild type Col x Ler F2 and meiMIGS-PPX1-PPX2 Col x Ler F2 population using genotyping by sequencing

ABSTRACT: Identifying crossover locations in an Arabidopsis thaliana wild type Col x Ler F2 and meiMIGS-PPX1-PPX2 Col x Ler F2 population using genotyping by sequencing

PROVIDER: PRJEB43381 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR5385260_1.fastq.gz	Fastqsanger.gz
	ERR5385260_2.fastq.gz	Fastqsanger.gz
	ERR5385270_1.fastq.gz	Fastqsanger.gz
	ERR5385270_2.fastq.gz	Fastqsanger.gz
	ERR5385280_1.fastq.gz	Fastqsanger.gz

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Identifying crossover locations in an Arabidopsis thaliana wild type Col x Ler F2 and meiMIGS-PPX1-PPX2 Col x Ler F2 population using genotyping by sequencing

Project description:Genomic DNA from 144 wild type Col x Ler F2 individual and 96 meiMIGS-PPX1-PPX2 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 37°C 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 can 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: 385–98. 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: 2183–202.

2021-03-12 | E-MTAB-10168 | biostudies-arrayexpress

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Project description:Genomic DNA from 96 meiMIGS-PPX1-PPX2 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 37°C 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 can 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: 385–98. 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: 2183–202.

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