ChIP-on-chip Service

ChIP-on-chip (also known as ChIP-chip) combines chromatin immunoprecipitation (ChIP) with a DNA microarray ("chip") to study protein–DNA interactions in vivo. It enables researchers to profile, on a genome-wide basis, where a DNA-binding protein (or a chromatin-associated factor) binds across the genome—often referred to as the cistrome, i.e., the sum of binding sites for a given factor under specific biological conditions.

CD BioSciences' ChIP-on-chip Service provides an end-to-end workflow—from chromatin preparation and immunoprecipitation to array hybridization and bioinformatic interpretation—helping you identify enriched binding regions, compare chromatin states across conditions, and translate array signals into actionable regulatory insights.

Introduction to ChIP-on-chip

ChIP-on-chip integrates ChIP enrichment with microarray-based detection. After crosslinking to capture protein–DNA interactions in living cells, chromatin is fragmented and immunoprecipitated using a target-specific antibody (e.g., transcription factor, Pol II, histone variant, or histone modification). The recovered DNA (and matched input DNA) is labeled and hybridized to a microarray containing probes that represent genomic regions of interest (e.g., promoter arrays, tiling arrays, CpG/regulatory arrays, or custom designs). Enrichment is then computed from probe intensities to reveal binding/modification landscapes within the array's coverage.

Fig.1 Workflow overview of a ChIP-on-chip experiment. (Wikipedia)

What you get biologically: ChIP-on-chip can define a factor's cistrome—the genome-wide set of cis-acting targets/binding sites (often contextualized by cell type, treatment, and time).

Features of ChIP- on-chip

1. Genome-wide, in vivo mapping of protein–DNA interactions (array-defined coverage)
2. Identifies a factor's cistrome (the sum of binding sites) under specific conditions
3. Works with transcription factors, chromatin regulators, and histone marks/modifications
4. Tiling arrays support higher-resolution profiling within covered regions
5. Standardized microarray readout enables strong cross-sample comparability
6. Well-suited for comparative designs (treatment vs control, time-course, perturbations)

Our Services

CD BioSciences provides a complete ChIP-on-chip (ChIP-chip) service for researchers who need robust, array-based genome-wide chromatin profiling and interpretable binding/enrichment results.

Wet-lab Portion of The Workflow

1. Crosslinking (capture in vivo interactions): Protein of interest (POI) is cross-linked to DNA—commonly using gentle formaldehyde fixation, reversible with heat.
2. Cell lysis & chromatin fragmentation: Cells are lysed, and DNA is sheared by sonication or micrococcal nuclease to produce double-stranded chromatin fragments (often ≤ ~1 kb).
3. Immunoprecipitation (ChIP enrichment): POI–DNA complexes are enriched using a POI-specific antibody (native protein) or tag-based strategy (e.g., FLAG/HA), with physical separation via beads/solid supports.
4. Reverse crosslinking & DNA purification: Crosslinks are reversed (often by heating) and DNA is purified for downstream processing.
5. Amplification & denaturation (as needed): DNA may be amplified and denatured to prepare single-stranded material for labeling/hybridization.
6. Fluorescent labeling & microarray hybridization: Single-stranded DNA fragments are labeled with a fluorescent tag (e.g., Cy5/Alexa dyes) and applied to the microarray; complementary sequences hybridize to probes on the chip.

Dry-lab Portion of The Workflow

1. Array scanning & raw image acquisition: After hybridization, the array is illuminated and fluorescence signals are captured as a raw image (often false-color encoded).
2. Image-to-signal conversion (feature extraction): The raw image is converted into numerical probe-level intensity values suitable for analysis.
3. Background correction & QC: Address nonspecific binding and technical noise introduced during readout; evaluate hybridization/scanning performance as part of QC.
4. Normalization using control signals: Normalize fluorescence signals using control-derived signals (from the same or a second chip) to distinguish properly hybridized probes from nonspecific signals and reduce technical bias.
5. Enriched region detection (peak/enrichment calling): Apply numerical/statistical tests to identify POI-enriched regions; commonly described approaches include median percentile rank, single-array error, and sliding-window methods.
6. Downstream interpretation: For transcription factors, enriched regions can be further analyzed for motifs/patterns and used for functional annotation of regulatory elements.

Supported Sample Types

1. Cultured Cells
2. Fresh-Frozen Tissue
3. Primary Cells

1. Xenograft or Organoid-Derived Samples
2. Time-Course or Drug-Treated Samples
3. Epitope-Tagged Cell Models

Our Advantages

1. Workflow clarity: wet-lab + dry-lab packaged as one integrated service
2. Strong cross-sample comparability using standardized array designs
3. Cistrome-oriented outputs for transcription factors and chromatin regulators
4. Actionable interpretation: annotated enriched regions to support follow-up validation

Define cistromes and compare protein–DNA interaction landscapes with a proven microarray-based approach. CD BioSciences' ChIP-on-chip service provides a standardized wet-lab and dry-lab workflow to deliver interpretable enrichment maps and condition-to-condition insights. Contact us to discuss your target, sample type, and array strategy.