nCounter® ChIP-String Assay

The nCounter ChIP-String Assay is a read-out method designed to measure dsDNA fragments that have been enriched via various user-defined chromatin immunoprecipitation protocols. Based on NanoString’s molecular barcoding technology, the assay can reliably quantify as few as 5,000 molecules of DNA without the need for amplification. The technology is ideal for validating ChIP-Seq results and screening large sample sets against focused sets of loci involved in chromatin remodeling and gene expression. It also provides a streamlined method for screening ChIP antibodies, optimizing IP protocols, or performing library screening prior to sequencing runs. The nCounter Custom ChIP-String Assay delivers the same level of performance, flexibility, and low hands-on time as other nCounter applications.

Assay Highlights

  • No library prep or amplification required
  • Accurate differentiation and quantification of enriched DNA
  • Excellent correlation with ChIP-Seq results
  • Analyze up to 800 loci in 24 hours with 15 minutes of hands-on time



Maximum number of probes per CodeSet


Recommended size of target region submitted

> 300 bases

Recommended amount of starting material

~10ng unamplified ChIP DNA
~100ng of WGA amplified ChIP DNA or NGS library prepared DNA

Sample type supported

Human genomic DNA prepared by ChIP

Hybridization reaction volume

30 μL

Synthetic spike titration correlation

> 0.95

Linear dynamic range

7 x 10⁵ total counts

nCounter Prep Station throughput

12 samples < 2.5 hours

nCounter Digital Analyzer throughput

12 samples/2.7 hours (up to 108 samples per day unattended running in continuous mode)

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For Research Use Only. Not for use in diagnostic procedures