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ChIP-Seq

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CD Genomics is dedicated to producing high-quality ChIP-seq data sets to help you profiling DNA targets for histone modification, structural proteins, transcription factors, and other DNA-associated proteins at a genome-wide scale.

The Introduction of ChIP-Seq

ChIP-Seq (chromatin immunoprecipitation sequencing), which refers to the binding site analysis, is a way to analyze DNA-protein interactions. The technique combines chromatin immunoprecipitation (ChIP) with NGS to identify where the DNA binds to the associated proteins. It can be used to pinpoint the binding sites of any interested protein throughout the genome. ChIP-seq is often used to determine how transcription factors and other chromatin-related proteins affect phenotypic mechanisms. Determining how proteins interact with DNA to regulate gene expression is essential to fully understand many biological processes and disease states. ChIP-Seq is a valuable tool for discerning and quantifying the specific DNA sequences where proteins bind or epigenetic modifications exist, it has played valuable roles in applications include studies on gene regulation, transcription complex assembly, DNA repair, histone modification, developmental mechanisms, disease progression and modifications.

Applications:

  • Gene regulation
  • Transcription complex assembly
  • DNA repair
  • Histone modification
  • Developmental mechanisms
  • Disease progression

Advantages of ChIP-Seq

  • Exceptionally high quality and high-resolution sequencing: It is possible to acquire millions of sequence tags and rare protein binding sites in the genome, ability to identify novel enrichment sites.
  • Cost-effective: rapid and efficient genome-wide profiling of multiple samples in one run and only use 1/100 of the amount of DNA required for ChIP-chip.
  • Comprehensive analysis: Utilizing widely accepted software and latest programs for motif prediction, peak annotation, functional analysis and data visualization of ChIP-Seq

ChIP-Seq Workflow
A typical ChIP-Seq workflow is shown as follow:

Service Specifications

Sample requirements and preparation

  • Sample type: ChIPed-DNA
  • DNA amount: ≥ 50 ng, DNA concentration: ≥ 10 ng/µl, DNA volume: ≥ 10 μl
  • OD260/280 = 1.8~2.0 without degradation or RNA contamination
Sequencing

  • Illumina HiSeq SE50
  • 150-300 bp insert size range for DNA library preparation
  • ≥10M clean reads (transcription factor), ≥20 M clean reads (histone proteins)
Bioinformatics Analysis

  • Data quality control
  • Alignment to reference genome with mapping statistics
  • Peak calling and annotation
  • Differential peaks annotation
  • Functional analysis of peak-associated genes
  • Motif prediction
  • Pathway analysis
  • Visualization results

Bioinformatics workflow

Deliverables

  • The original sequencing data
  • Experimental results
  • Data analysis report
  • Details in ChIP-Seq for your writing (customization)

At CD Genomics, we provide you with high-quality sequencing and comprehensive bioinformatics analysis for your ChIP-Seq project, enabling accurately screen and determine the protein binding sites in the whole genome. If you have additional requirements or questions, please feel free to contact us.

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45-1 Ramsey Road, Shirley, NY 11967, USA
Tel: 1-631-275-3058
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Email: info@cd-genomics.com