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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.  

ChIP-Seq (chromatin immunoprecipitation sequencing) is the genome-wide study of DNA-protein interactions and is used primarily to determine how transcription factors and other chromatin-associated proteins influence phenotype-affecting mechanisms. Determining how proteins interact with DNA to regulate gene expression is essential for fully understanding many biological processes and disease states. Genomic regions that interact with the protein of interest are identified and quantified by the power of high-throughput sequencing of the enriched DNA that is co-immunoprecipitated with that protein. The enriched DNA regions are detected as peaks above background reads, and bioinformatics analyses of these regions can reveal binding motifs. A typical ChIP-Seq workflow is shown in Figure 1.

Schematic  workflow of ChIP-Seq process Figure 1. Schematic workflow of ChIP-Seq process.

For a complete and decent ChIP-seq, the quality of the immunoprecipitation is important, and input DNA is the appropriate comparison to ChIPed DNA, not an IgG control pulldown, and a reference NON-pulldown gene is also essential. It is important to use properly size fragmented DNA as the starting material, larger DNA fragments will result in greatly reduced yields and poor sequencing performance.

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, and disease progression.

Sequencing Strategy and Recommended Sequencing Depth

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

Data Analysis

ChIP-Seq
  1. Data quality control
  2. Alignment to reference genome with mapping statistics
  3. Peak calling and annotation
  4. Differential peaks annotation
  5. Functional analysis of peak-associated genes
  6. Motif prediction
  7. Pathway analysis
  8. Visualization results

Sample Requirements

  1. Sample type: ChIPed-DNA
  2. DNA amount and quality: ≥ 50 ng, DNA concentration: ≥ 10 ng/µl, OD260/280 = 1.8~2.0 without degradation or RNA contamination

Key Features and Advantages

  • 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.
  • Extraordinary informatics expertise and comprehensive bioinformatics solution: Utilizing widely accepted software and latest programs for motif prediction, peak annotation, functional analysis and data visualization.

CD Genomics a professional ChIP-Seq provider. 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. The sequencing strategy is determined in close collaboration between the customer and our product specialist.

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