H3K4me3 Antibody, SNAP-Certified™ for CUT&RUN and CUT&Tag

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Figure 2: CUT&RUN genome-wide enrichment
CUT&RUN was performed as described in Figure 4. Sequence reads were aligned to 18,793 annotated transcription start sites (TSSs ± 2 kbp). Signal enrichment was sorted from highest to lowest (top to bottom) relative to the H3K4me3 - 500k cells reaction (all gene rows aligned). High, medium, and low intensity are shown in red, yellow, and blue, respectively. H3K4me3 antibodies produced the expected enrichment pattern, which was consistent between 500k and 50k cells and greater than the IgG negative control.

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Figure 3: H3K4me3 CUT&RUN representative browser tracks
CUT&RUN was performed as described in Figure 4. Gene browser shots were generated using the Integrative Genomics Viewer (IGV, Broad Institute). H3K4me3 antibody tracks display sharp peaks at gene promoters, consistent with the biological function of this PTM. Similar results in peak structure and location were observed for both 500k and 50k cell inputs.

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Figure 4: CUT&RUN methods
CUT&RUN was performed on 500k and 50k K562 cells with the SNAP-CUTANA™ K-MetStat Panel (EpiCypher 19-1002) spiked-in prior to the addition of 0.5 µg of either IgG negative control (EpiCypher 13-0042) or H3K4me3 antibodies. The experiment was performed using the CUTANA™ ChIC/CUT&RUN Kit v3 (EpiCypher 14-1048). Library preparation was performed with 5 ng of CUT&RUN enriched DNA (or the total amount recovered if less than 5 ng) using the CUTANA™ CUT&RUN Library Prep Kit (EpiCypher 14-1001/14-1002). Both kit protocols were adapted for high throughput Tecan liquid handling. Libraries were run on an Illumina NextSeq2000 with paired-end sequencing (2x50 bp). Sample sequencing depth was 3.5 million reads (IgG 500k cell input), 4.0 million reads (IgG 50k cell input), 5.6 million reads (H3K4me3 500k cell input), and 2.8 million reads (H3K4me3 50k cell input). Data were aligned to the hg19 genome using Bowtie2. Data were filtered to remove duplicates, multi-aligned reads, and ENCODE DAC Exclusion List regions.

(Click to enlarge)

Figure 6: CUT&Tag genome-wide enrichment
CUT&Tag was performed as described in Figure 8. Sequence reads were aligned to 18,793 annotated transcription start sites (TSSs ± 2 kbp). Signal enrichment was sorted from highest to lowest (top to bottom) relative to the H3K4me3 - 100k nuclei reaction (all gene rows aligned). High, medium, and low intensity are shown in red, yellow, and blue, respectively. H3K4me3 antibodies produced the expected enrichment pattern, which was consistent between 100k and 10k nuclei and greater than the IgG negative control.

(Click to enlarge)

Figure 7: H3K4me3 CUT&Tag representative browser tracks
CUT&Tag was performed as described in Figure 8. Gene browser shots were generated using the Integrative Genomics Viewer (IGV, Broad Institute). H3K4me3 antibody tracks display sharp peaks at gene promoters, consistent with the biological function of this PTM. Similar results in peak structure and location were observed for both 100k and 10k nuclei inputs.

(Click to enlarge)

Figure 8: CUT&Tag methods
CUT&Tag was performed on 100k and 10k K562 nuclei with the SNAP-CUTANA™ K-MetStat Panel (EpiCypher 19-1002) spiked-in prior to the addition of 0.5 µg of either IgG negative control (EpiCypher 13-0042) or H3K4me3 antibodies. The experiment was performed using the CUTANA™ CUT&Tag Kit v1 (EpiCypher 14-1102/14-1103). Libraries were run on an Illumina NextSeq2000 with paired-end sequencing (2x50 bp). Sample sequencing depth was 1.3 million reads (IgG 100k nuclei input), 2.0 million reads (IgG 10k nuclei input), 6.9 million reads (H3K4me3 100k nuclei input), and 10.6 million reads (H3K4me3 10k nuclei input). Data were aligned to the hg19 genome using Bowtie2. Data were filtered to remove duplicates, multi-aligned reads, and ENCODE DAC Exclusion List regions.