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

Service info

  • Category:Bioinformatics
  • Skills:NextFlow, R, Python, TF/biology, statistics
  • Inquire: Email us