Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

34 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: Genomic DNA from 192 meiMIGS-HSBP 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.

INSTRUMENT(S): HiSeq X Ten

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Kyuha Choi

PROVIDER: E-MTAB-10783 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Identifying crossover locations in an Arabidopsis thaliana meiMIGS-HSP70 Col x Ler F2 population using genotyping by sequencing

Project description:Genomic DNA from 96 meiMIGS-HSP70 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.

2023-11-30 | E-MTAB-13415 | biostudies-arrayexpress

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

Project description:Genomic DNA from 96 wild type Col x Ler F2 individual and 96 meiMIGS-HSBP 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.

2022-03-23 | E-MTAB-11586 | 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 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

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) 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 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

Identifying crossover locations in an Arabidopsis thaliana pSPO11-mJ3 Col x Ler F2 population using genotyping by sequencing

Project description:Genomic DNA from 96 pSPO11-mJ3(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.

2023-11-30 | E-MTAB-13413 | 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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data