ChIP-qPCR Service

Chromatin Immunoprecipitation followed by quantitative PCR (ChIP-qPCR) is a sensitive and cost-effective method to measure protein–DNA interactions at defined genomic regions. It is ideal for validating genome-wide findings (e.g., from ChIP-seq), monitoring known regulatory elements, or assessing locus-specific chromatin changes across treatments or time points. CD BioSciences's ChIP-qPCR Service offers end-to-end support for targeted chromatin profiling—covering antibody validation, primer design, immunoprecipitation, qPCR detection, and data interpretation.

Introduction to ChIP-qPCR

ChIP-qPCR combines chromatin immunoprecipitation with real-time quantitative PCR to measure enrichment of a DNA-associated target at specific genomic loci. Briefly, cells or tissues are crosslinked to preserve protein–DNA interactions, chromatin is fragmented, and target-associated complexes are immunoprecipitated using a ChIP-grade antibody (histone modification, transcription factor, Pol II, or chromatin regulator). The recovered DNA is then quantified by qPCR using locus-specific primers.

Compared to ChIP-seq, ChIP-qPCR is faster, lower cost, and ideal for targeted questions, including peak validation, locus comparisons, pilot optimization, antibody screening, and time-course studies.

Fig.1 ChIP‒qPCR confirmed that ATF2 can activate HSPH1 expression by binding to its promoter. (Xu, X., et al., 2023)

Features of ChIP-qPCR

1. Locus-specific quantification of protein binding or histone modification enrichment
2. Fast and cost-effective alternative to ChIP-seq for targeted studies
3. High sensitivity for low-abundance targets and subtle chromatin changes
4. Ideal for small-scale screens (antibody tests, perturbation panels, time courses)
5. Direct comparability across conditions (treatments, developmental stages, cell states)
6. Flexible target scope including histone marks, TFs, Pol II, and co-regulators

Our Services

CD BioSciences provides an end-to-end ChIP-qPCR service to support hypothesis-driven, locus-specific chromatin validation and mechanistic studies. From sample processing and immunoprecipitation to qPCR detection and result interpretation, our standardized workflow is designed to deliver reliable enrichment measurements with strong reproducibility.

Project Design & Target Planning

1. Define target protein/histone mark and experimental conditions
2. Select loci (candidate regulatory elements, peak regions, negative regions, reference loci)
3. Determine controls (Input, IgG/isotype, optional positive control loci)

Sample Preparation

1. Crosslinking of cells or tissue (optimized fixation conditions)
2. Nuclei isolation as needed (especially for tissues)
3. Chromatin fragmentation (sonication-based shearing)
4. Input DNA reserved for normalization and QC

Immunoprecipitation (ChIP)

1. Immunoprecipitation with client-selected or CD BioSciences-recommended antibodies
2. Protein A/G magnetic bead capture
3. Parallel processing of IgG/isotype controls (and optional spike-in strategy upon request)

DNA Recovery & Purification

1. Crosslink reversal
2. RNase/proteinase digestion
3. DNA purification (column-based or equivalent validated method)
4. Quantification and quality checks prior to qPCR

Primer Design & qPCR

1. Custom primer design and in silico screening (or user-provided primers)
2. Primer validation for efficiency/specificity (as applicable)
3. SYBR Green–based qPCR with technical replicates
4. Melt-curve and amplification QC for every reaction set

Data Analysis & Reporting

1. Standard outputs: Percent Input and Fold Enrichment (relative to IgG and/or reference loci)
2. Normalization to Input DNA and reference regions
3. Optional comparisons across treatments/conditions/time points
4. Deliverables include summary plots, QC metrics, primer information, and interpretation notes

Supported Sample Types

1. Cultured cells
2. Fresh or fresh-frozen tissues
3. Primary cells and stem cells

1. Low-input samples (project-dependent; feasibility assessed by target and loci)
2. Other sample types

Our Advantages

1. Precise Locus-Specific Detection: Quantify enrichment at defined promoters, enhancers, and regulatory elements with high specificity.
2. Rapid Turnaround for Validation: Ideal for quick confirmation of ChIP-seq findings and targeted mechanistic studies.
3. Custom Primer Support: Primer design, validation strategy, and qPCR optimization integrated into the workflow.
4. Flexible Targeting: Compatible with histone modifications, transcription factors, Pol II, and chromatin regulators.
5. Low Sample Requirement: Typically effective with ~10⁵–10⁶ cells depending on target abundance and locus accessibility.
6. Reliable Controls and Replication: Input normalization, negative IP controls, and technical replicates to support confident conclusions.

Validate chromatin findings and monitor regulatory loci with high precision. CD BioSciences' ChIP-qPCR service delivers targeted, reproducible results to accelerate chromatin biology and transcription research. Contact us to design your custom ChIP-qPCR study—or combine it with ChIP-seq validation for streamlined confirmation and follow-up.

Reference

1. Xu, X., et al. (2023). Increased ATF2 expression predicts poor prognosis and inhibits sorafenib-induced ferroptosis in gastric cancer. Redox biology, 59, 102564.