workflow  (Amira Pharmaceuticals)

Journal: bioRxiv

Article Title: Biomarker-driven and gene-enhanced viral therapy for malignant peripheral nerve sheath tumor

doi: 10.64898/2026.10.12.758653

Figure Lengend Snippet: A) Schematic representation of the proposed viral silencing mechanism, wherein the host Polycomb Repressive Complex 2 (PRC2) deposits H3K27me3 on host histones associated with viral DNA, reducing RNA polymerase II (RNAPII) transcription. B) Excess total cell H3K27me3 immunoblotting is observed in doxycycline-induced TY5005 (TY/Dox) at 24 hours post-infection (left). Similarly, excess H3K27me3 is observed in the infected PRC2-proficient N0(32.1) at both 12 and 24 hours post-infection (right). C-D) CUT&RUN analysis of H3K27me3 occupancy on the human genome (C) and HSV-1 episome (D) in TY5005 with or without SUZ12 genetic rescue. Y-axes represent total H3K27me3 genomic occupancy, normalized to an E. coli spike-in control and mathematically background-subtracted against matched IgG negative controls (H3K27me3 - IgG). Statistical significance was determined using a Two-Way ANOVA followed by post-hoc pairwise comparisons via estimated marginal means [***: p ≤0.001; ns: not significant]. C) Quantification of H3K27me3 on the human genome confirms successful doxycycline induction of global H3K27me3, with no significant difference observed in host genome deposition between uninfected and infected TY5005/Dox biological replicates. D) H3K27me3 accumulation on the HSV-1 genome was detected specifically after PRC2 rescue, consistent with PRC2-dependent chromatinization of viral DNA. E) Representative track plot visualizing H3K27me3 occupancy across the HSV-1 genome (GU734771.1) for the conditions evaluated in panel D. Robust, widespread H3K27me3 deposition is visible across the viral episome strictly in the TY5005 + Dox + HSV condition. Regions lacking signal correspond to HSV-1 repeat regions that are excluded in multimapping alignment filtering.

Article Snippet: Chromatin cleavage was performed with pAG-MNase (EpiCypher #15-1016), with 0.5 ng E. coli DNA (EpiCypher #18-1401k) per 500,000 nuclei added for spike-in normalization.

Techniques: Western Blot, Infection, Analysis, Control

Journal: Current Protocols

Article Title: A Guide to Enzymatic Targeted Methylation Sequencing Bioinformatics Workflow: Best Practices

doi: 10.1002/cpz1.70464

Figure Lengend Snippet: Input and Output of each stage

Article Snippet: Targeted methylation profiling was performed using the NEBNext EM‐seq Kit combined with the Twist Targeted Methylation Sequencing platform (Twist Bioscience, USA), following the manufacturer's instructions (New England Biolabs, ; “Twist Targeted Methylation Sequencing Protocol | Twist Bioscience,” accessed July 30, 2025).

Techniques: Sequencing, Methylation, Analysis, Control, Tiling

Journal: Current Protocols

Article Title: A Guide to Enzymatic Targeted Methylation Sequencing Bioinformatics Workflow: Best Practices

doi: 10.1002/cpz1.70464

Figure Lengend Snippet: Estimated duration of the complete analysis

Article Snippet: Targeted methylation profiling was performed using the NEBNext EM‐seq Kit combined with the Twist Targeted Methylation Sequencing platform (Twist Bioscience, USA), following the manufacturer's instructions (New England Biolabs, ; “Twist Targeted Methylation Sequencing Protocol | Twist Bioscience,” accessed July 30, 2025).

Techniques: Analysis, QC/EQA/Proficiency, Sequencing, Methylation, Tiling