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nCounter® ChIP-String Assay

Accurate Differentiation and Quantification of DNA Enriched by ChIP

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.

Product Highlights

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

nCounter ChIP-String Workflow

nCounter ChIP-String Workflow

Chromatin Modifications and Gene Regulation

The DNA of eukaryotic cells interacts with a variety of DNA binding proteins (histones, transcription factors and chromatin regulators) which serve to package the DNA in highly condensed chromatin structures and regulate transcription. Recent studies have shown that chromatin modifications (e.g., methylation and acetylation of key amino acids) are important in gene regulation and are thought to act in concert with chromatin binding proteins. An active area of epigenetic research is in characterizing patterns of chromatin modifications and associated binding proteins to define “chromatin states” which are associated with key transcriptional regulatory functions (initiation, active transcription, repression, etc). Understanding the chromatin state associated with a gene makes it possible to predict whether a gene will be active or repressed. Studies to characterize chromatin state generally involve chromatin immunoprecipitation coupled with a method for sequence-specific quantification of DNA contained in the chromatin.

nCounter® ChIP-String Specifications

  • Specifications
  • Ordering Info


Description Specifications
Maximum number of probes per CodeSet 800
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)

To receive a quote, please fill out the Request Information form.

Ordering Information

Description Quantity / Use Part Number (P/N)
nCounter Custom ChIP-String Assay CIP-P1CS-XXX
nCounter Master Kit
(all reagents, sample cartridges, and consumables necessary for processing 48 or 192 assays)
48 assays
192 assays
nCounter Analysis System
(includes the Prep Station and Digital Analyzer)
1 NCT-SYS-120
Additional nCounter Prep Station 1 NCT-PREP-120
Additional nCounter Digital Analyzer 1 NCT-DIGA-120

To receive a quote, please fill out the Request Information form.

Request Information | E-mail us: info@nanostring.com | Call us: 1 888 358 6266