SNAP-ChIP™ Spike-In Controls
Great Experiments Require Great Controls
Chromatin immunoprecipitation (ChIP) is a powerful and widely used approach to understanding chromatin regulation. However, ChIP experiments have numerous sources of technical challenges:
- Antibody cross-reactivity
- Variation between replicates
- Ill-defined normalization resources
Introducing SNAP-ChIP Spike-In Controls
Sample Normalization and Antibody Profiling for ChIP (SNAP-ChIP) Spike-In Controls provide a powerful new tool to generate highly reliable ChIP-seq data.
This technology uses a pool of recombinant nucleosomes carrying widely studied histone post-translational modifications (PTMs), each denoted by unique DNA barcodes.
SNAP-ChIP Spike-Ins 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. Nat Protoc 2019).
Essential Controls for Every ChIP Experiment
Ensure Antibody Specificity
Our findings and several publications 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.
- 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 Variability
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. Mol Cell 2015, Shah et al. Mol. Cell 2018, and Lam et al. Nat. Comm. 2019).
- Traditional methods for ChIP-seq normalization use exogenous chromatin spike-ins (e.g. Drosophila).
- 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.
Available to Order Online
SNAP-ChIP™ Spike-In Panels
EpiCypher SNAP-ChIP Panels are sold as a single tube which contains a mixture of DNA-barcoded recombinant nucleosomes with unique PTMs. Panel sets are focused around the most widely studied, disease-implicated histone PTMs. This enables flexibility in experimental design and allows users to characterize antibody specificity for their target of interest relative to the most likely cross-reactive species. SNAP-ChIP Panels are also available for studies of:
Lysine methylation: K-MetStat Panel
Lysine acetylation: K-AcylStat Panel
Oncogenic histone mutations: OncoStat Panel
(Coming Soon) Arginine methylation: R-MetStat Panel
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SNAP-ChIP™ Certified Antibodies
Antibody selection is the single most important decision a researcher must make when designing a ChIP experiment, but rigorous antibody validation is costly and time-consuming. At EpiCypher, we recognize this challenge and have embarked on a massive effort to analyze and identify the highest performing ChIP antibodies.
SNAP-ChIP Certified Antibodies are best-in-class antibodies that have been rigorously validated using EpiCypher’s SNAP-ChIP spike-in technology. Custom antibody screening services available
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