Nucleosome spike-ins for quantitative ChIP-Seq

Chromatin immunoprecipitation (ChIP) is a powerful and widely used approach to understanding chromatin regulation. However, ChIP experiments have numerous sources of technical challenges that can be avoided by using SNAP-ChIP® Spike-In Controls:

  • Ensure antibody specificity
  • Normalize ChIP data
  • Test antibody enrichment
  • Monitor technical variation

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Sample Normalization & Antibody Profiling for ChIP (SNAP-ChIP) spike-in controls provide a powerful new tool to generate highly reliable ChIP-seq data

What are SNAP-ChIP® Spike-in Controls?

SNAP-ChIP spike-in controls are panels of recombinant nucleosomes carrying widely studied histone post-translational modifications (PTMs), each denoted by a unique DNA barcode.

SNAP-ChIP spike-in control panels are compatible with both native and cross-linked workflows. Simply spike-in the panel of interest prior to IP.

The nucleosomal DNA barcodes on the spike-ins can then be detected by qPCR or NGS and used to quantify antibody performance and normalize samples for reliable cross-experimental comparisons (Grzybowski et al. 2015).

Use SNAP-ChIP Spike-Ins To Control Your ChIP Experiment

Ensure Antibody Specificity

Our findings (Shah et al. 2018) and several publications (including Lamet al. 2019) have found that:

  • Histone peptide arrays used for antibody validation do not predict specificity in ChIP (Shah et al. Mol. Cell 2018).
  • Antibody specificity can vary significantly between production lots (see our blog).
  • The use of highly cited antibodies does not guarantee quality results (Shah et al. Mol. Cell 2018 and Lam et al. Nat. Comm.2019).
  • Shah et al. and Lam et al. both found that many ChIP-grade antibodies cross-react, leading to incorrect biological interpretations (see figure

Only by validating with SNAP-ChIP spike-in controls can scientists correctly identify and avoid cross-reactive antibodies which would confound their results.

Monitor Technical Viability

Our spike-in controls will make sure you never sequence another failed ChIP experiment again.

  • Seamlessly integrate into native and cross-linked ChIP workflows.
  • Serve as positive (on-target) and negative (off-target) controls.
  • Monitor technical variability in antibody specificity / efficiency across replicates.
  • qPCR of DNA barcodes provides a valuable STOP / GO step prior to expensive sequencing

Normalize Between Experiments

SNAP-ChIP spike-in controls can also be used to normalize between experiments (Grzybowski et al. 2015, Shah et al. 2018, and Lam et al. 2019).

Some methods use exogenous chromatin (e.g. Drosophila) for normalization. However, these approaches are problematic because they are heterogeneous, poorly defined, and inconsistent between lots.

SNAP-ChIP spike-ins provide a homogeneous defined control and are consistent from lot to lot. EpiCypher is currently working to create more robust and streamlined SNAP-ChIP workflows for ChIP normalization.

Interested in SNAP-ChIP Spike-in Controls?

SNAP-ChIP® Spike-In Control Panel

Defined controls for superior ChIP. We offer panels for a variety of histone PTMs, including lysine methylation and acylation.

SNAP-ChIP® Certified Antibodies

These antibodies have been validated using SNAP-ChIP spike-ins and have best-in-class specificity and target enrichment.

SNAP-ChIP® Validation Service

Let the experts help! With SNAP-ChIP Validation Services, EpiCypher will help find the best antibody for your ChIP-seq studies.

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