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BGI Genomics Co
sequencing data
Sequencing Data, supplied by BGI Genomics Co, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/genome+sequence+data/sequencing+data/pmc11971355-236-9-14
Average 90 stars, based on 1 article reviews
Sequencing Data, supplied by BGI Genomics Co, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/genome+sequence+data/sequencing+data/pmc11971355-236-9-14
Average 90 stars, based on 1 article reviews
sequencing data - by Bioz Stars,
2026-10
90/100 stars
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1) Product Images from "Accurate cross-species 5mC detection for Oxford Nanopore sequencing in plants with DeepPlant"
Article Title: Accurate cross-species 5mC detection for Oxford Nanopore sequencing in plants with DeepPlant
Journal: Nature Communications
doi: 10.1038/s41467-025-58576-x
Figure Legend Snippet: CHH methylation sites, particularly those with high-methylation levels (≥90%), are rare in plants. This figure presents the statistics on high-methylation CHH sites from previously published bisulfite sequencing (BS-seq) datasets , – and those generated in this study. a Ratios of high-methylation CHH sites among quantified CHH motifs (≥5 read coverage) (left panel) and the number of covered 9-mer contexts (right panel) in BS-seq datasets from ten plant species. Only 9-mers observed at three or more high-methylation CHH sites were considered. Species other than A. thaliana and O. sativa were selected based on high CHH methylation ratios reported in previous studies , . b Ratios of high-methylation CHH sites in BS-seq datasets sequenced for this study, including A. thaliana , O. sativa , and species with abundant high-methylation CHH sites identified in ( a ), as well as Glycine max and Marchantia polymorpha . c Number of covered 9-mer contexts (top) and heatmap of context abundance (bottom) grouped by CHH motifs in nanopore datasets from six plant species. In the top panel, the top line of each bar corresponds to the number (36,864) of all possible 9-mer sequences centered with a CHH motif. A 9-mer was considered covered if present in 50 or more positive training samples and had at least an equal number of negative samples. “Mixed” refers to combined samples from S. miltiorrhiza , R. communis , and S. tuberosum . Source data are provided as a Source Data file.
Techniques Used: Methylation, Methylation Sequencing, Generated
Figure Legend Snippet: Quantitative evaluation of CHH methylation detection by DeepPlant and Dorado
Techniques Used: Methylation, Sequencing
![a Circos plot illustrating DeepPlant CHH methylation profiling in centromeric regions and 100 kb intervals upstream and downstream in O. sativa . From outer to inner: ideograms of centromere (center box) and neighboring regions (two terminal boxes); histograms of normalized sequencing coverage across 100 bp bins (gray, normalized against mean genomic coverage); histograms of CHH methylation frequencies (blue) across 100 bp bins. b Comparison of CHH motif coverage ratios across different genomic regions between BS-seq, DeepPlant, and Dorado profiling. To be noticed, the same nanopore dataset was used for DeepPlant and Dorado profiling, and the coverage difference between DeepPlant and Dorado derived from the distinct read filters they applied. DeepPlant applies three thresholds for screening high-quality alignments, including MAPQ ≥ 20, primary alignment length/read length ≥80%, and mapping identity ≥80% by default. Only CHH motifs with a minimum read coverage of 10 were regarded as quantified. TE transposable element, CDS non-TE protein-coding sequences. c Read coverage and CHH methylation frequencies in the centromeric regions of Chr1, comparing whole-genome BS-seq data, DeepPlant, and Dorado analysis on Nanopore data. d Boxplot illustrating CHH methylation frequencies on the forward (+) and reverse (−) strands in protein-coding and transposable element (TE) regions. The center line represents the median; each box shows the first and third quartiles; minima represents the larger between Q1−1.5×IQR and the minimum observed value; maxima represents the smaller between Q3 + 1.5×IQR and the maximum observed value. e Violin plot displaying strand-specific CHH methylation status across various TE types and non-TE protein-coding regions. The annotation of TEs and protein-coding regions was acquired from T2T-NIP . Source data of ( c , d ) are provided in Zenodo [10.5281/zenodo.15062213]. Source data of the other panels are provided as a Source Data file.](https://pub-med-central-images-cdn.bioz.com/pub_med_central_ids_ending_with_1355/pmc11971355/pmc11971355__41467_2025_58576_Fig3_HTML.jpg "... neighboring regions (two terminal boxes); histograms of normalized sequencing coverage across 100 bp bins (gray, normalized against ...")
Figure Legend Snippet: a Circos plot illustrating DeepPlant CHH methylation profiling in centromeric regions and 100 kb intervals upstream and downstream in O. sativa . From outer to inner: ideograms of centromere (center box) and neighboring regions (two terminal boxes); histograms of normalized sequencing coverage across 100 bp bins (gray, normalized against mean genomic coverage); histograms of CHH methylation frequencies (blue) across 100 bp bins. b Comparison of CHH motif coverage ratios across different genomic regions between BS-seq, DeepPlant, and Dorado profiling. To be noticed, the same nanopore dataset was used for DeepPlant and Dorado profiling, and the coverage difference between DeepPlant and Dorado derived from the distinct read filters they applied. DeepPlant applies three thresholds for screening high-quality alignments, including MAPQ ≥ 20, primary alignment length/read length ≥80%, and mapping identity ≥80% by default. Only CHH motifs with a minimum read coverage of 10 were regarded as quantified. TE transposable element, CDS non-TE protein-coding sequences. c Read coverage and CHH methylation frequencies in the centromeric regions of Chr1, comparing whole-genome BS-seq data, DeepPlant, and Dorado analysis on Nanopore data. d Boxplot illustrating CHH methylation frequencies on the forward (+) and reverse (−) strands in protein-coding and transposable element (TE) regions. The center line represents the median; each box shows the first and third quartiles; minima represents the larger between Q1−1.5×IQR and the minimum observed value; maxima represents the smaller between Q3 + 1.5×IQR and the maximum observed value. e Violin plot displaying strand-specific CHH methylation status across various TE types and non-TE protein-coding regions. The annotation of TEs and protein-coding regions was acquired from T2T-NIP . Source data of ( c , d ) are provided in Zenodo [10.5281/zenodo.15062213]. Source data of the other panels are provided as a Source Data file.
Techniques Used: Methylation, Sequencing, Comparison, Derivative Assay
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