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Identifying crossover locations in an Arabidopsis thaliana recq4ab Col x recq4a Ler F2 population using genotyping by sequencing

ABSTRACT: Identifying crossover locations in an Arabidopsis thaliana recq4ab Col x recq4a Ler F2 population using genotyping by sequencing

PROVIDER: PRJEB60451 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR10969800_1.fastq.gz	Fastqsanger.gz
	ERR10969800_2.fastq.gz	Fastqsanger.gz
	ERR10969801_1.fastq.gz	Fastqsanger.gz
	ERR10969801_2.fastq.gz	Fastqsanger.gz
	ERR10969802_1.fastq.gz	Fastqsanger.gz

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Identifying crossover locations in an Arabidopsis thaliana recq4ab Col x recq4a Ler F2 population using genotyping by sequencing

Project description:Genomic DNA from 96 recq4ab Col x recq4a 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. These data can be compared to a set of wild type control libraries available at E-MTAB-10168.

2023-03-14 | E-MTAB-12726 | biostudies-arrayexpress

Identifying crossover locations in an Arabidopsis thaliana pJ3-J3(G155R) recq4ab Col x recq4a Ler F2 population using genotyping by sequencing

Project description:Identifying crossover locations in an Arabidopsis thaliana pJ3-J3(G155R) recq4ab Col x recq4a Ler F2 population using genotyping by sequencing

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Identifying crossover locations in an Arabidopsis thaliana pJ3-J3(G155R) recq4ab Col x recq4a Ler F2 population using genotyping by sequencing

Project description:Genomic DNA from 96 pJ3-J3(G155R) recq4ab Col x recq4a 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. These data can be compared to a set of wild type control libraries available at E-MTAB-10168.

2023-03-14 | E-MTAB-12697 | biostudies-arrayexpress

Whole-genome resequencing of F2 CSL_Chr4/5_C hybrids populations from Arabidopsis (Col x Ler, wild type and recq4ab figl1 mutants)

Project description:This experiment aims at analyzing crossover distribution in the Arabidopsis recq4ab figl1 compared to wild type. CSL_Chr4_C and CSL_Chr5_C populations were produced through successive crosses as: A first cross was done between recq4ab figl1+/- Col plants and parental homozygote CSLs with Chr4 and Chr5 pure Ler, respectively. The resulting plant was then backcrossed to the parental CSLs for Chr4 and Chr5. From the resultant BC1 plants, we selected the recq4ab figl1 +/- and we identified the lines with pure Ler Chr4 (or Chr5, respectively). The offspring from the selfing of the selected plant was crossed with Col recq4ab figl1 +/-. Among the resultant plants, we selected wild-type and recq4ab figl1 individuals as the parents of the populations used for recombination and QTL analyses. Leaf samples from the self-crossed population were used for DNA purification and library preparation for Illumina sequencing (HiSeq 3000 2 × 150 bp), performed at the Max Planck-Genome-center (https://mpgc.mpipz.mpg.de/home/).

2024-05-21 | E-MTAB-13656 | biostudies-arrayexpress

Whole-genome resequencing of F2 CSL_Chr2/5_L hybrids populations from Arabidopsis (Col x Ler, wild type and recq4ab figl1 mutants)

Project description:This experiment aims at analyzing crossover distribution in the Arabidopsis recq4ab figl1 compared to wild type. CSL_Chr2_L and CSL_Chr5_L populations were produced through successive crosses as: A first cross was done between recq4ab figl1+/- Ler plants and parental homozygote CSLs with Chr2 and Chr5 pure Col, respectively. The resulting plant was then backcrossed to the parental CSLs for Chr2 and Chr5. From the resultant BC1 plants, we selected the recq4ab figl1 +/- and we identified the lines with pure Col Chr4 (or Chr5, respectively). The offspring from the selfing of the selected plant was crossed with Ler recq4ab figl1 +/-. Among the resultant plants, we selected wild-type and recq4ab figl1 individuals as the parents of the populations used for recombination and QTL analyses. Leaf samples from the self-crossed population were used for DNA purification and library preparation for Illumina sequencing (HiSeq 3000 2 × 150 bp), performed at the Max Planck-Genome-center (https://mpgc.mpipz.mpg.de/home/).

2024-05-21 | E-MTAB-13657 | biostudies-arrayexpress

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 genotyping by sequencing.

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

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

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

| PRJEB79144 | ENA

Whole-genome resequencing of F2 full hybrids populations from Arabidopsis (Col x Ler, wild type and recq4ab figl1 mutants)

Project description:This experiment aims at analyzing crossover distribution in the Arabidopsis recq4ab figl1 compared to wild type. Hybrid lines were obtained through the crossing of Col plants bearing the recq4a, recq4b, and figl1 mutations and Ler plants bearing the recq4a and figl1 mutations. F1 plants either wild type or mutants were selected and F2 seeds were obtained by selfing. Leaf samples from the F2 plants were used for DNA purification and library preparation for Illumina sequencing (HiSeq 3000 2 × 150 bp), performed at the Max Planck-Genome-center (https://mpgc.mpipz.mpg.de/home/).

2024-05-21 | E-MTAB-13653 | biostudies-arrayexpress

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

Project description:Genomic DNA from 192 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). 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.

2016-06-11 | E-MTAB-4657 | biostudies-arrayexpress

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