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

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

PROVIDER: PRJEB60015 | ENA |

REPOSITORIES: ENA

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Identifying crossover locations in an Arabidopsis thaliana pJ3-J3(G155R) Col/Ler x Ler backcross F1 population using genotyping by sequencing for female-specific crossover map

Project description:Genomic DNA from 96 pJ3-J3(G155R) Col/Ler x Ler backcross F1 population 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.

2023-03-14 | E-MTAB-12692 | biostudies-arrayexpress

Identifying crossover locations in an Arabidopsis thaliana Ler x pJ3-J3(G155R) Col/Ler backcross F1 population using genotyping by sequencing for male-specific crossover map

Project description:Genomic DNA from 96 Ler x pJ3-J3(G155R) Col/Ler backcross F1 population 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.

2023-03-14 | E-MTAB-12694 | biostudies-arrayexpress

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

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

2023-03-14 | E-MTAB-12663 | 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: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

Identifying crossover locations in an Arabidopsis thaliana pJ3-mJ3 (G155R) x Ler F2 population using genotyping by sequencing

Project description:Genomic DNA from 96 pJ3-mJ3 (G155R) x Ler F2 individuals (1-48: pJ3-mJ3 #2 x Ler F2; 49-96: pJ3-mJ3 #3 x Ler F2)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.

2023-11-30 | E-MTAB-13414 | biostudies-arrayexpress

Identifying crossover locations in an Arabidopsis thaliana pJ3-J3(G155R) Col/Ler x Ler backcross F1 population using genotyping by sequencing for female-specific crossover map

Project description:Identifying crossover locations in an Arabidopsis thaliana pJ3-J3(G155R) Col/Ler x Ler backcross F1 population using genotyping by sequencing for female-specific crossover map

| PRJEB60335 | ENA

Identifying crossover locations in an Arabidopsis thaliana Ler x pJ3-J3(G155R) Col/Ler backcross F1 population using genotyping by sequencing for male-specific crossover map

Project description:Identifying crossover locations in an Arabidopsis thaliana Ler x pJ3-J3(G155R) Col/Ler backcross F1 population using genotyping by sequencing for male-specific crossover map

| PRJEB60367 | ENA

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

| PRJEB60434 | ENA

Identifying crossover locations in an Arabidopsis thaliana pJ3-mJ3 (G155R) x Ler F2 population using genotyping by sequencing

Project description:Identifying crossover locations in an Arabidopsis thaliana pJ3-mJ3 (G155R) x Ler F2 population using genotyping by sequencing

| PRJEB67394 | ENA

Identifying crossover locations in an Arabidopsis thaliana j3-1 Col x j3-5 Ler F2 population using genotyping by sequencing

Project description:Genomic DNA from 96 j3-1 Col x j3-5 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.

2023-11-30 | E-MTAB-13412 | biostudies-arrayexpress

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