Table 1.
Comparison of Streptavidin conjugated magnetic beads.
Fig 1.
Con A binding assay and cell binding assay.
A, Schematic view of con A binding assay. B, Con A-binding ability was compared between different magnetic beads. Columns indicate mean. Bars indicate SD. Dots indicate individual results of technical replicates. Statistical significance was assessed by one-way ANOVA followed by Turkey’s multiple comparisons test with a single pooled variance. *: P < 0.05. N = 3. C, Schematic view of cell binding assay. D, Cell-binding ability of self-con A-conjugated Dynabeads magnetic beads and BioMag beads with three different kinds of cell types. Columns indicate mean. Dots indicate individual results of technical replicates. Statistical significance was assessed by one-way ANOVA followed by Turkey’s multiple comparisons test with a single pooled variance. *: P < 0.05, **: P < 0.01. N = 3.
Fig 2.
CUT&Tag using BioMag and MyOneT1 beads.
A, Appearance of 1.5 mL tubes containing either BioMag or MyOne T1 on a magnetic stand just after removing the Binding buffer. B, Appearance of 1.5 mL tubes containing either BioMag or MyOne T1 in Antibody buffer 3–5 min after mixing. C, Appearance of 0.2 mL PCR tubes containing either BioMag or MyOne T1 that were bound with cells in Antibody buffer just after mixing (upper) and after ON incubation at 4°C (lower). D, Size distribution of libraries by capillary electrophoresis using Agilent 2100 Bioanalyzer Instrument. E. Electropherogram plots fluorescence intensity versus size (bp) for the sample indicated above. FU: Arbitrary fluorescence unit.
Fig 3.
Sequence results of libraries prepared from CUT&Tag.
A, Distribution of peaks of entire human chromosome 1. Yellow vertical lines indicate statistically significant peaks detected by DROMPA software. B, Distribution of Narrow peaks at gene level in the chromosome 1. Red vertical lines indicate statistically significant peaks detected by DROMPA software. C, Distribution of Broad peaks at gene level in the chromosome 1. Red peaks indicate statistically significant peaks detected by DROMPA software.
Fig 4.
A, Venn diagram for overlap of merged Narrow and Broad peaks between MyOne T1 (T1) and BioMag (BM). Numbers indicate the number of peaks detected. B, Percentage of distribution of H3K4me3 reads in upstream (transcription start site, TSS –5 kb, magenta), genic (blue), downstream (transcription end site, TES +5 kb, green), and intergenic regions (yellow). C, Line plots show read density of T1/BM common or T1 specific narrow peaks from A. D, Distribution of mapped reads at T1 specific peaks and a T1/BM common peak on the chromosome 1 represents read densities for each peak. E, Enrichment profiles of CUT&Tag reads at TSS (0%). F, Heatmap analyses of CUT&Tag reads around H3K4me3 narrow or broad peaks detected using BM or T1 magnetic beads. G, Line plots below heatmaps represent CUT&Tag read density for each corresponding plot in F. H, MA plots show ratio intensities to compare CUT&Tag read densities at T1 and BM peaks (for non-merged single replicate samples). Magenta circles represent log enrichment > 1, grey circles represent log enrichment log enrichment ±1, and blue ones represent low enrichment < -1.