{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Kyuha Choi"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["genotyping by high throughput sequencing"],"organism":["Arabidopsis thaliana"],"species":["Arabidopsis thaliana"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15280"],"description":["Genomic DNA from 96 pJ3-mJ3 (G155R) 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."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - CTAB","Library Construction - Ultra™ II DNA Library Prep Kit for Illumina®","Growth Protocol - long day conditions (16 hr light), 20 degrees Celcius","Sample Collection - 3 rosette leaves of 5 week old plants","Sequencing - Illumina HiSeq instrument"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Kyuha Choi"],"additional_accession":[]},"is_claimable":false,"name":"Identifying crossover locations in an Arabidopsis thaliana pJ3-mJ3 (G155R) x Ler F2 population using genotyping by sequencing","description":"Genomic DNA from 96 pJ3-mJ3 (G155R) 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.","dates":{"release":"2025-07-19T00:00:00Z","modification":"2025-06-25T21:28:34.855Z","creation":"2025-06-25T21:28:34.855Z"},"accession":"E-MTAB-15280","cross_references":{"ENA":["ERP174056"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0002771","EFO_0005518","EFO_0004184"]}}