Journal: Advanced Science

Article Title: Accounting for ALA Natural Mutations Enhances the Efficiency of Graphene Oxide Nanopriming in Bar ‐Modified Arabidopsis

doi: 10.1002/advs.202500058

Figure Lengend Snippet: Genome‐wide DNA methylation analysis in WT and GM seeds before and after GO treatments. a) Circos plots show the methylation levels across different chromosomes for WT and GM seeds before and after GO exposure. The colored sections on the outer ring represent different chromosomes. The concentric rings from outer to inner illustrate untreated samples, 0.75 mg‐C/L GO‐treated samples, and 1.5 mg‐C/L GO‐treated samples. Whole‐genome methylation levels were calculated as mean values within 100 kb windows for each chromosome. The color gradient from cyan to red indicates the methylation percentages, whereas the innermost ring represents gene density. b) Whole‐genome methylation levels in CG, CHG, and CHH contexts for WT and GM seeds after various GO exposures (sample size n = 3). Data are presented as means ± SD, with gray and red dots depicting individual data points in the WT and GM groups. Three biological replicates were included for each treatment. Independent sample two‐sided t ‐tests were performed: * indicates significant differences within the same genotype relative to the condition without GO, and # indicates significant differences between GM and WT under the same treatment. Significant differences are marked with p values. c) Differential methylation regions at promoter regions and gene bodies of key genes (Figure ) are represented by a color gradient showing Log 2 FC in methylation levels. Triangles and circles indicate CG and CHH methylation, respectively. No differential methylation was observed in the CHG context. Regions without differential methylation are blank. d) Dot plots of differential methylation for ALA metabolism‐related genes compare promoter and gene body methylation across conditions. Blue and red dots denote different comparisons, as indicated in the legend. Dots with circles indicate methylation levels with |Log 2 FC| >10.

Article Snippet: Library construction was performed using an MGIEasy whole‐genome bisulfite library preparation kit (MGI).

Techniques: Genome Wide, DNA Methylation Assay, Methylation

Journal: bioRxiv

Article Title: Low-cost and highly efficient generation of near-complete bacterial pathogen genomes by TELL-Seq

doi: 10.1101/2024.08.17.608388

Figure Lengend Snippet: (a) Distribution of TELL-Seq assembly quality indicators under different sequencing depth for clinical and standard strains. (b) Correlation between assemble quality indicators and GC-content, min mappability and genome size.

Article Snippet: TELL-seq libraries were constructed using a TELL-Seq Microbial Library Prep Kit (Universal Sequencing Technology).

Techniques: Sequencing

Journal: Genome Biology

Article Title: Genomic variant benchmark: if you cannot measure it, you cannot improve it

doi: 10.1186/s13059-023-03061-1

Figure Lengend Snippet: Comparing different whole genome sequencing technologies

Article Snippet: Tell-seq , Universal Sequencing Technology , TELL-Seq Library Prep Kit , 100 k range information , 5ng g , $ i + Illumina cost , 3 + Illumina run.

Techniques: Sequencing, Binding Assay