Arabidopsis thaliana methylation pattern analysis based on ONT sequence reads

Schilbert H, Kleinbölting N, Weisshaar B, Pucker B (2021)
Bielefeld University.

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OA GK_050B11.vcf.gz 183.65 MB
OA GK_082G09.vcf.gz 185.46 MB
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Abstract / Bemerkung
We sequenced the genomes of 14 Arabidopsis thaliana GABI-Kat T-DNA insertion lines (Col-0 background), which eluded flanking sequence tag-based attempts to fully characterize their insertion alleles, with Oxford Nanopore Technologies (ONT) long reads. Detailed information about each line, e.g. their T-DNA insertion site(s), have been described by Pucker et al. (BMC Genomics (2021) 22:599; https://doi.org/10.1186/s12864-021-07877-8). The DNA that has been sequenced is derived from a mixtures of tissues as expected for DNA extracted from young plantlets. For 11 of the datasets from these lines, we called 5mC methylation patterns with the tool Megalodon v.2.2.9 provided by ONT (https://github.com/nanoporetech/megalodon/). Results of this analysis are available per line as individual VCF files. We are sharing unfiltered output files to grant full control over the down-stream analysis steps and to accelerate the research in epigenomics. We identified between 706,254 and 1,020,654 positions per line where at least 80% of 5 or more reads support a methylation site. The following datasets are available and the file names reveal the respective GK line: 1. GK_040A12.vcf 2. GK_050B11.vcf 3. GK_082G09.vcf 4. GK_290G05.vcf 5. GK_399C06.vcf 6. GK_410B07.vcf 7. GK_430F05.vcf 8. GK_433E06.vcf 9. GK_654A12.vcf 10. GK_767D12.vcf 11. GK_909H04.vcf
Stichworte
long read sequencing; ONT; methylation; plant epigenomics; GABI-Kat; Megalodon
Erscheinungsjahr
2021
Page URI
https://pub.uni-bielefeld.de/record/2956654

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Schilbert H, Kleinbölting N, Weisshaar B, Pucker B. Arabidopsis thaliana methylation pattern analysis based on ONT sequence reads. Bielefeld University; 2021.
Schilbert, H., Kleinbölting, N., Weisshaar, B., & Pucker, B. (2021). Arabidopsis thaliana methylation pattern analysis based on ONT sequence reads. Bielefeld University. https://doi.org/10.4119/unibi/2956654
Schilbert, H., Kleinbölting, N., Weisshaar, B., and Pucker, B. (2021). Arabidopsis thaliana methylation pattern analysis based on ONT sequence reads. Bielefeld University.
Schilbert, H., et al., 2021. Arabidopsis thaliana methylation pattern analysis based on ONT sequence reads, Bielefeld University.
H. Schilbert, et al., Arabidopsis thaliana methylation pattern analysis based on ONT sequence reads, Bielefeld University, 2021.
Schilbert, H., Kleinbölting, N., Weisshaar, B., Pucker, B.: Arabidopsis thaliana methylation pattern analysis based on ONT sequence reads. Bielefeld University (2021).
Schilbert, Hanna, Kleinbölting, Nils, Weisshaar, Bernd, and Pucker, Boas. Arabidopsis thaliana methylation pattern analysis based on ONT sequence reads. Bielefeld University, 2021.
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