Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

62 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole-genome resequencing of BC1 populations from Arabidopsis (Col x Ler) x Col crosses (wild type)

ABSTRACT: This experiment aims at analyzing crossover distribution in male and female meiosis, in the Arabidopsis. Wild-type Col plant was crossed with Ler plant to produce F1 hybrid. Then, the F1 hybrid was crossed as female or as male with wild-type Col to generate two BC1 populations. Leaf samples from plants of the obtained BC1 populations were used for DNA purification and library preparation for Illumina sequencing (HiSeq 3000 2x150 bp), performed by the Max Planck-Genome-centre Cologne, Germany (https://mpgc.mpipz.mpg.de/home/) and Novogene.

INSTRUMENT(S): Illumina HiSeq 3000

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Qichao Lian

PROVIDER: E-MTAB-11254 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Whole-genome resequencing of BC1 populations from Arabidopsis (Col x Ler) x Col crosses (wild type, HEI10oe, zyp1, and zyp1 HEI10oe)

Project description:This experiment aims at analyzing crossover distribution in male and female meiosis, in the Arabidopsis HEI10oe, zyp1, and zyp1 HEI10oe compared to wild type. Plants double heterozygous of zyp1-1+/- HEI10oe (Col) were crossed with zyp1-6+/- mutant plants (Ler) to generate zyp1-1/zyp1-6 HEI10oe heterozygous, HEI10oe heterozygous, zyp1-1/zyp1-6 and wild type in Col/Ler hybrid background, and then crossed as male or as female with wild-type Col. Backcross populations were grown in the greenhouse (16 h day/8 h night) for 3 weeks and 4 days in the dark, 100-150mg leave samples from plants from the 8 obtained BC1 populations were used for DNA purification and library preparation for Illumina sequencing (HiSeq 3000 2x150 bp), performed by the Max Planck-Genome-centre Cologne, Germany (https://mpgc.mpipz.mpg.de/home/).

2022-09-08 | E-MTAB-11696 | biostudies-arrayexpress

Whole-genome resequencing of BC1 populations from Arabidopsis (Col x Ler) x Col crosses (wild type and zyp1)

Project description:This experiment aims at analyzing crossover distribution in male and female meiosis, in the Arabidopsis zyp1 mutant compared to wild type. Plants heterozygous for the zyp1-1 mutation (Col) were crossed as female with plants heterozygous for the zyp1-6 mutation (Ler). Wild type and zyp1-1/zyp-6 plants were selected among the F1s, and crossed as male or as female with wild-type Col. Leaf samples from plants from the four obtained BC1 populations were used for DNA purification and library preparation for Illumina sequencing (HiSeq 3000 2x150 bp), performed by the Max Planck-Genome-centre Cologne, Germany (https://mpgc.mpipz.mpg.de/home/).

2021-02-26 | E-MTAB-9593 | biostudies-arrayexpress

Whole-genome resequencing of F1* populations from Arabidopsis Col

Project description:This experiment aims at analyzing crossover distribution in female and male meiosis, in the Arabidopsis pure Col. Wild-type Col seeds were subjected to EMS mutagenesis, and four independent M2 plants were crossed to produce two independent F1*, which were heterozygous for a set of EMS mutations. Then, the two F1* plants were reciprocally crossed to generate two F1 populations. Leaf samples from plants from the obtained F1 populations were used for DNA purification and library preparation for Illumina sequencing (HiSeq 3000 2x150 bp), performed by the Max Planck-Genome-centre Cologne, Germany (https://mpgc.mpipz.mpg.de/home/).

2022-06-14 | E-MTAB-11249 | biostudies-arrayexpress

Whole-genome resequencing of F1 populations from Arabidopsis Col

Project description:This experiment aims at analyzing crossover distribution in male and female meiosis, in the Arabidopsis pure Col. Wild-type Col seeds were subjected to EMS mutagenesis, and four independent M2 plants were crossed to produce two independent F1*, which were heterozygous for a set of EMS mutations. Then, the two F1* plants were reciprocally crossed to generate two F1 populations. Leaf samples from plants from the obtained F1 populations were used for DNA purification and library preparation for Illumina sequencing (HiSeq 3000 2x150 bp), performed by the Max Planck-Genome-centre Cologne, Germany (https://mpgc.mpipz.mpg.de/home/).

2022-06-14 | E-MTAB-11250 | biostudies-arrayexpress

Whole-genome resequencing of BC1 populations from Arabidopsis (Col x Ler) x Col crosses (wild type and hei10+/-)

Project description:This experiment aims at analyzing crossover distribution in male and female meiosis, in the Arabidopsis hei10+/- compared to wild type. Plants heterozygous for the hei10-2 mutation (Col-0) were crossed as females with Ler as males. Wild-type and hei10+/- plants were selected among the F1s and crossed as female or as male with wild-type Col-0. Leaf samples from the four back-crossed populations were used for DNA purification and library preparation for Illumina sequencing (NextSeq 2000 2×150 base pairs [bp]), performed at the Max Planck-Genome-center (https://mpgc.mpipz.mpg.de/home/).

2024-09-23 | E-MTAB-14423 | biostudies-arrayexpress

Whole-genome resequencing of BC1 populations from Arabidopsis (Col x Ler) x Col crosses (wild type and heip1)

Project description:This experiment aims at analyzing crossover distribution in male and female meiosis, in the Arabidopsis heip1 compared to wild type. Plants heterozygous for the heip1-4 mutation (Col.0) were crossed as females with plants heterozygous for the heip1-5 mutation (Ler). Wild-type and heip1-4/heip1-5 plants were selected among the F1s and crossed as male or as female with wild-type Col.0. Leaf samples from the four back-crossed populations were used for DNA purification and library preparation for Illumina sequencing (HiSeq 3000 2 × 150 base pairs [bp]), performed at the Max Planck-Genome-center (https://mpgc.mpipz.mpg.de/home/).

2023-05-12 | E-MTAB-12838 | biostudies-arrayexpress

Whole-genome resequencing of BC1 populations from Arabidopsis (Col x Ler) x Col crosses (wild type and mlh1)

Project description:This experiment aims at analyzing crossover distribution in female and male meiosis, in the Arabidopsis mlh1 compared to wild type. Plants heterozygous for the mlh1-2 mutation (Col-0) were crossed as females with plants heterozygous for the mlh1-3 mutation (Ler). Wild-type and mlh1-2/mlh1-3 plants were selected among the F1s and crossed as female or as male with wild-type Col-0. Leaf samples from the four back-crossed populations were used for DNA purification and library preparation for Illumina sequencing (NextSeq 2000 2×150 base pairs [bp]), performed at the Max Planck-Genome-center (https://mpgc.mpipz.mpg.de/home/).

2024-09-23 | E-MTAB-14422 | biostudies-arrayexpress

Whole-genome resequencing of BC1 populations from Arabidopsis (Col x Ler) x Col crosses (scep1)

Project description:This experiment aims at analyzing crossover distribution in female and male meiosis, in the Arabidopsis scep1 compared to wild type. The heterozygous scep1-1+/- plants were crossed with heterozygous scep1-7+/- plants to produce scep1-1/scep1-7 heteroallelic homozygous mutant. These plants were backcrossed as male or female with wild-type Col to generate the sequencing populations. Leaf samples from the back-crossed population were used for DNA purification and library preparation for Illumina sequencing (HiSeq 3000 2 × 150 base pairs [bp]), performed at the Max Planck-Genome-center (https://mpgc.mpipz.mpg.de/home/).

2023-08-24 | E-MTAB-12985 | 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

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