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Identifying crossover locations in Arabidopsis thaliana wild type and taf4b Col × Bur F2 populations using genotyping-by-sequencing

ABSTRACT: Identifying crossover locations in Arabidopsis thaliana wild type and taf4b Col × Bur F2 populations using genotyping-by-sequencing

PROVIDER: PRJEB33249 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3403630_1.fastq.gz	Fastqsanger.gz
	ERR3403630_2.fastq.gz	Fastqsanger.gz
	ERR3403640_1.fastq.gz	Fastqsanger.gz
	ERR3403640_2.fastq.gz	Fastqsanger.gz
	ERR3403650_1.fastq.gz	Fastqsanger.gz

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Identifying crossover locations in Arabidopsis thaliana wild type and taf4b Col × Bur F2 populations using genotyping-by-sequencing

Project description:Genomic DNA from 180 Col/Bur F2 individuals, and 186 taf4b/Bur F2 individuals, was extracted by CTAB and used to generate sequencing libraries as previously described (Ziolkowski et al, 2017 Genes & Dev). Sequencing data was analysed to identify crossovers using the TIGER pipeline as previously described (Rowan et al, 2015 G3 (Bethesda); Yelina et al, 2015 Genes & Dev).

2019-12-31 | E-MTAB-8099 | 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

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 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 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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RNA-seq of Bur, Col and taf4b Arabidopsis thaliana meiocytes

Project description:Purified meiocytes from Col, Bur and taf4b Arabidopsis thaliana plants were extracted as previously described (Walker at al, 2018 Nat. Genet.), and cDNA used to produce libraries.

2019-12-31 | E-MTAB-7870 | biostudies-arrayexpress

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

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.

2020-12-14 | E-MTAB-9621 | biostudies-arrayexpress

Identifying crossover locations in Arabidopsis thaliana wild-type Col x Ler F2 populations using genotyping by sequencing

Project description:Identifying crossover locations in Arabidopsis thaliana wild-type Col x Ler F2 populations using genotyping by sequencing

| PRJEB25431 | ENA

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 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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