imaris spot detection plug in  (Oxford Instruments)

Journal: bioRxiv

Article Title: Direct measurement of sub-kilobase chromatin structure reveals that linker histone H1 broadly compacts chromatin, with differential impact amongst epigenetic states

doi: 10.64898/2025.12.19.695525

Figure Lengend Snippet: Nucleosome-nucleosome contacts as measured by Micro-C in epigenetic regions defined by published WT K562 ChIP datasets in a) scr-CTRL b) and H1-low conditions . Two biological replicates shown each. c) Ratio of N/N+odd contacts and N/N+even nucleosome contacts in epigenetic state regions. Error bar: standard deviation between biological replicates, n=2. d) Capillary electrophoresis (TapeStation) traces of the fragment size distribution produced by MNase titration with different amounts of enzyme. The estimated fragment length of the mononucleosome peak is indicated. e) Micro-C contact probability curves for the libraries obtained from the MNase titration in (d) . f-g) RICC-seq FLDs from irradiated cells and matched gDNA controls in h-i) j-k) scr-CTRL cells and H1-low cells, subset by histone mark gapped peaks. 1 biological replicate shown.

Article Snippet: Genomic DNA control plugs were equilibrated in 0.5 M Tris-HCl pH 8 on ice (three 15-min exchanges, then +400 μL Tris) and irradiated identically, followed by the same washes. ssDNA was eluted by incubating plugs in 0.1 N NaOH (200 μL, 15 min), neutralized with 1 M Tris-HCl pH 7.5 (100 μL) + 2 mM EDTA (RT, ∼4 h), and purified with the Zymo RNA Clean & Concentrator-5 kit (R1016) using modified speeds (binds at 3,800 RCF; washes at 10,000 RCF); columns were loaded with 600 μL RNA Binding Buffer then 900 μL absolute ethanol and eluted twice in 10 μL 10 mM Tris pH 8 (total ∼18 μL).

Techniques: Standard Deviation, Electrophoresis, Produced, Titration, Irradiation

Journal: bioRxiv

Article Title: Direct measurement of sub-kilobase chromatin structure reveals that linker histone H1 broadly compacts chromatin, with differential impact amongst epigenetic states

doi: 10.64898/2025.12.19.695525

Figure Lengend Snippet: a) ATAC-seq accessibility signal over Cut&Tag H3K27me3 peaks +/- 5 kb around peak centers shown with a bin size of 100 bp. b) RICC-seq FLD plot over downregulated vs unchanging H3K27me3 peaks in H1-low vs scr-CTRL. n= 1 biological replicate shown as ratio over subset genomic DNA control. Signal normalized to mononucleosome peak. c) RICC-seq FLD plot over unchanging ATAC-seq peaks and genome-wide smoothed (30 nt rolling average). n=1 biological replicate shown corrected by biological replicate-specific correction factor and ratio over similarly subset and corrected sample-matched genomic DNA control. Signal normalized to mononucleosome peak. d) RICC-seq FLD plot over upregulated ATAC-seq peaks and genome-wide, as in (c). e) RICC-seq FLD plot over upregulated ATAC-seq peaks, H3K27me3, and H3K27ac, as in (c).

Article Snippet: Genomic DNA control plugs were equilibrated in 0.5 M Tris-HCl pH 8 on ice (three 15-min exchanges, then +400 μL Tris) and irradiated identically, followed by the same washes. ssDNA was eluted by incubating plugs in 0.1 N NaOH (200 μL, 15 min), neutralized with 1 M Tris-HCl pH 7.5 (100 μL) + 2 mM EDTA (RT, ∼4 h), and purified with the Zymo RNA Clean & Concentrator-5 kit (R1016) using modified speeds (binds at 3,800 RCF; washes at 10,000 RCF); columns were loaded with 600 μL RNA Binding Buffer then 900 μL absolute ethanol and eluted twice in 10 μL 10 mM Tris pH 8 (total ∼18 μL).

Techniques: Control, Genome Wide