10x mnase buffer  (New England Biolabs)

Journal: iScience

Article Title: Simulating cell-free chromatin using preclinical cancer models for liquid biopsy applications

doi: 10.1016/j.isci.2025.114113

Figure Lengend Snippet: MNase treatment of media from preclinical models reproducibly generates nucleosomal distributions from cfChromatin (A) HCT116-conditioned media without (left) or with (right) MNase treatment shows enrichment for mono- and oligo-nucleosome-sized cfDNA fragments. LM, lower marker; UM, upper marker. (B) MNase treatment generates significantly different proportions of mono-, di-, and tri-cell-free nucleosomes compared to no nuclease treatment, reproducible across various 2D and organoid culture models (CAMA-1 and MCF7 = breast adenocarcinoma, HCT116 = colorectal carcinoma, A549 = lung adenocarcinoma, SU-DHL-6 = diffuse large B cell lymphoma, BPTO.95 and DCBPTO.66 = breast cancer patient-derived tumor organoids, BXTO.64 = breast cancer patient-derived xenograft-derived organoid). Paired t test for fragments (<200 bp, p = 1.53 × 10 −7 ; 200–400 bp, p = 5.05 × 10 −4 ; 400–600 bp, p = 1.44 × 10 −3 ; >600 bp, p = 6.07 × 10 −8 ). Results from (B) are extracted from the BioAnalyzer traces shown in B. (C) HCT116 (top) and CAMA-1 (bottom) media samples were treated with a fixed concentration of MNase over a 0- to 30-min time course. The proportion of mononucleosome-sized fragments increases with digestion time, with a small fraction of mononucleosomes at earlier time points relative to later.

Article Snippet: MNase & MNase buffer (included) , New England Biolabs , Cat# M0247S.

Techniques: Marker, Derivative Assay, Concentration Assay

Journal: iScience

Article Title: Simulating cell-free chromatin using preclinical cancer models for liquid biopsy applications

doi: 10.1016/j.isci.2025.114113

Figure Lengend Snippet: Simulated cfChromatin reflects chromosomal variation and nucleosome profiles associated with gene expression and chromatin accessibility patterns (A) PCA of cfMNase-seq samples across various sample types and MNase digestion times ( n = 21) and samples from three external MNase-seq datasets for HCT116 ( n = 4) and MCF7 ( n = 8). The PCA was performed over 10,000 bp bins genome-wide. A visual representation of the 10,000 bp bin size is shown in A. Clusters were identified using k -means clustering. A silhouette score was calculated to validate clustering; cluster 1 (bottom right) had an average silhouette score of 0.92, cluster 2 (middle left) 0.94, and cluster 3 (top middle) 0.96. (B) Analysis of the association between cfMNase-seq coverage and gene expression around the TSS. Composite cfMNase-seq coverage profiles at TSSs falling within five FPKM levels shown for CAMA-1 (30-min digestion). Coverage is shown as average GC-corrected fragment midpoint coverage. The complementary analysis for all other models, information on the FPKM subsets, and coverage profiles across MNase digestion times are shown in . (C) Normalized central coverage metric from cfMNase-seq coverage profiles across different gene expression levels (Spearman correlation ρ = −0.85, p = 3.5 × 10 −16 ), shown for all samples with a 30-min digestion time. (D) Composite cfMNase-seq coverage profiles (mean ±95% confidence interval) at 6,260 sites with enriched chromatin accessibility for A549, shown for A549 and the average of BPTO.95, CAMA-1, DCBPTO.66, HCT116, MCF7, and SU-DHL-6 grouped together (all 30-min digestions). The complementary results for other model-specific enriched open chromatin sites are shown in D. (E) Normalized central coverage metric from cfMNase-seq coverage profiles across sites of enriched chromatin accessibility for each model (specific) compared to the average across the rest (others) (paired Wilcoxon signed-rank test p = 0.063).

Article Snippet: MNase & MNase buffer (included) , New England Biolabs , Cat# M0247S.

Techniques: Gene Expression, Genome Wide