CUT&RUN (Cleavage Under Targets and Release Using Nuclease) is a chromatin profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing. Unlike ChIP (chromatin immunoprecipitation), which fragments and solubilizes total chromatin, CUT&RUN is performed in situ, allowing for both quantitative high-resolution chromatin mapping and probing of the local chromatin environment. In CUT&RUN, DNA in the starting cells are initially intact, allowing protein-DNA interactions to be maintained in their natural state. CUT&RUN yields precise transcription factor profiles while avoiding crosslinking and solubilization issues, and requires less sequencing depth then ChIP-Seq.
Our standard service includes alignment of short reads to an appropriate genome, data quality control and normalization, peak calling and visualization, as well as motif discovery.
- Quality control of raw sequencing reads
- Alignment to standard reference genome and mapping to appropriate gene annotations
- Alignment to spike-in genome (optional)
- Filter on quality, sort and index alignments
- Duplicate read marking
- Create bedGraph files and bigWig coverage files
- Peak calling (SEACR, MACS2), followed by Consensus peak merging and reporting
- Library complexity
- Fragment-based and peak-based quality control
- Heatmap peak analysis
- Genome browser session
Extended services are available, which supplement our standard/fixed workflow described above:
- Acquiring data from 3rd party services, such as ArrayExpress or GEO
- Iterative customization of results and plots for presentations, publications, grants, etc...
- Batch correction and modeling
- Integration with other data