CUTANA™ ChIC/CUT&RUN Kit

For Targeted Release of Genomic Fragments into Solution

Quickstart Guide User Manual Data sheet Product Sheet Video

Product Description

ChIC and CUT&RUN have revolutionized the study of chromatin regulation by enabling targeted release of genomic fragments into solution. CUTANA™ CUT&RUN kits, reagents, and assay services map histone PTMs and chromatin-interacting proteins with high resolution, at a fraction of the time and cost of standard ChIP-seq experiments.

Dramatically reduced background
High resolution genomic mapping for histone PTMs and chromatin-associated proteins
Small number of cells and only 3-8 million sequencing reads per sample needed
Streamlined and cost saving workflow

Kit Description

The CUTANA™ ChIC/CUT&RUN Kit enables streamlined chromatin profiling of histone post-translational modifications (PTMs) and chromatin associated proteins while providing increased throughput and reproducibility with multi-channel pipetting. Positive (H3K4me3) and negative (IgG) control antibodies are included to pair with SNAP-CUTANA™ spike-in controls for assay optimization and continuous monitoring (Figure 1). E. coli DNA is included for data normalization. The kit is compatible with a variety of inputs including cells or nuclei derived from native, cryopreserved, or cross-linked samples. While it is recommended to start with 500,000 cells, comparable data can be generated using as few as 5,000 cells. The inclusion of controls, as well as compatibility with diverse target types, sample inputs, and low cell numbers, make this kit the go-to solution for chromatin mapping experiments.

DNA for use in this kit can be easily purified with the CUTANA™ DNA Purification Kit.

Figure 1: SNAP-CUTANA™ K-MetStat Spike-in Controls. DNA-barcoded designer nucleosomes (dNucs) representing 16 different K-methyl PTM states: mono-, di-, and tri-methylation at H3K4, H3K9, H3K27, H3K36, and H4K20, as well as unmodified control, were spiked into CUT&RUN samples prior to the addition of the control antibodies provided with the kit (IgG, H3K4me3). Instances of each spike-in barcode were counted and normalized from raw fastq files. Barcodes for IgG (top; normalized to the sum of total reads) and H3K4me3 (bottom; normalized to on-target) antibodies provided with this kit are shown. The spike-ins confirmed optimal experimental conditions (H3K4me3 antibody specifically recovered the target dNuc, while IgG showed no preferential enrichment).

Validation Data

Fig.2. CUT&RUN DNA Fragment Size Distribution Analysis. CUT&RUN was performed using the CUTANA ChIC/CUT&RUN Kit starting with 500,000 K562 cells. CUT&RUN DNA isolated from IgG Negative Control (13-0042k) and H3K4me3 Positive Control (13-0041k) antibodies was used to prepare paired-end Illumina sequencing libraries. Library DNA was analyzed by Agilent Tapestation®. This analysis confirmed that mononucleosomes were predominantly enriched in CUT&RUN (~300 bp peak represents 150 bp nucleosomes + sequencing adapters).

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Figure 3: CUT&RUN genome-wide heatmaps. CUT&RUN data was generated using the CUTANA ChIC/CUT&RUN Kit with 500,000 K-562 cells. Three replicates (“Rep”) of IgG (left) and H3K4me3 (right) antibodies are shown in a heatmap. CUT&RUN signal (from an average of 5.9 million paired-end reads) aligned to the transcription start site (TSS, +/- 2kb) are presented for 18,793 genes. High and low signal are ranked by intensity (top to bottom) and reflected by red and blue colors, respectively. Gene rows in each heatmap are aligned and sorted.