genome bisulfite sequencing  (Azenta)

Journal: bioRxiv

Article Title: Centromeres are hotspots of cytosine methylation epimutations in a filamentous fungus

doi: 10.64898/2026.03.03.709258

Figure Lengend Snippet: Samples taken from the two MA pedigrees for different experiments. A) Ten MA lines were sampled from the two pedigrees. Samples for sequencing were taken after 5, 20, and 40 transfers and DNA methylation was detected using bisulfite sequencing (red circles). B) Three additional MA lines were sampled from both pedigrees and samples were taken after 1, 5, 7, 8, 10, and 15 transfers for Nanopore sequencing and after 5, 8, 10, 20, and 40 transfers for H3K9me3 ChIP-seq.

Article Snippet: For whole genome bisulfite sequencing, DNA samples were sent to Novogene (Cambridge, UK).

Techniques: Sequencing, DNA Methylation Assay, Methylation Sequencing, Nanopore Sequencing, ChIP-sequencing

Journal: bioRxiv

Article Title: Centromeres are hotspots of cytosine methylation epimutations in a filamentous fungus

doi: 10.64898/2026.03.03.709258

Figure Lengend Snippet: Pairwise divergence in cytosine methylation patterns among the MA lines and their ancestors. X-axis shows the number of mitoses separating the two lines that are being compared, and the y-axis shows cytosine methylation divergence. Red line shows a neutral epimutation accumulation model fitted to all data, orange line shows a neutral epimutation accumulation model fitted to data with outlier samples removed, and solid blue line shows a logistic model fitted to all data, and the dotted line shows null model of no increase in divergence. A) The divergence calculated from single cytosines, for CG, CHG, and CHH sequence motifs. B) The divergence calculated for DMRs in different sequence contexts, as in panel A.

Article Snippet: For whole genome bisulfite sequencing, DNA samples were sent to Novogene (Cambridge, UK).

Techniques: Methylation, Sequencing

Journal: BMC Plant Biology

Article Title: Insights into epigenetics suggest a role of DNA methylation in regulating Chinese yam tuber shape

doi: 10.1186/s12870-026-08438-5

Figure Lengend Snippet: Whole-genome DNA methylation analysis of Chinese yam variant F2000 and F60. A Principal component 1 and principal component 2 analyses were performed for each sample. B Methylation level distribution across genetic features including 4 kb upstream of TSS, gene body, and 4 kb downstream of TTS in the three DNA methylation contexts CG, CHG, and CHH. Analyses were performed in biological triplicates for each variant. C Number of DMRs with higher methylation levels in F2000 (hypermethylated) and in F60 (hypomethylated). DMRs were investigated in the three DNA methylation contexts CG, CHG and CHH. Distribution of DMRs upstream in the putative promoter (4 kb of TSS), within the gene body, and down-stream in the putative terminator (4 kb of TTS) were analyzed in DMR-associated genes (q-value ≤ 0.01, methylation difference >|10%|). D Venn analysis of DMR-associated genes split in hyper- and hypomethylated promoters, gene bodies, and terminators. DMR, differentially methylated region; TSS, transcription start site; TTS, transcription termination site

Article Snippet: Prepared DNA samples were sent to Novogene Company (Beijing, China) for low-input whole-genome bisulfite sequencing including the steps of bisulfite treatment and library construction.

Techniques: DNA Methylation Assay, Variant Assay, Methylation