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ChIP-Seq

Service Overview
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ChIP-Seq ServiceChIP-Seq provides genome-wide profiling of DNA targets for histone modification, transcription factors, and other DNA-associated proteins; it combines the selectivity of chromatin immunoprecipitation (ChIP) for recovering specific protein-DNA complexes with the power of NGS for high-throughput sequencing of the recovered DNA. Additionally, because the protein-DNA complexes are recovered from living cells, binding sites can be compared in different cell types or tissues, or under different conditions.

In ChIP-Seq, enriched DNA regions (protein binding sites) are detected as peaks above background reads, and bioinformatics analyses of these regions can reveal binding motifs. Applications include studies on gene regulation, transcription complex assembly, histone modification, developmental mechanisms, and disease processes. At Novogene, we can provide you with high quality sequencing and comprehensive bioinformatics analysis for your ChIP-Seq project.

Novogene also provides sequencing service and bioinformatics analysis on other kinds of IP-sequencing. Please contact us for more information.

The Novogene Advantage

  • Cost-effective: rapid and efficient genome-wide profiling of multiple samples, using only 1/100 of the amount of DNA required for ChIP-chip.
  • Comprehensive analysis: expert bioinformatics analyses utilizing widely accepted MACS2 software and latest programs for motif prediction, peak annotation, functional analysis and data visualization.
  • Professional bioinformatics: all PhD team for Chip-Seq data analysis.

Project Workflow

chip seq service project workflow

Sequencing Strategy

  • 100~350 bp insert DNA library (depending on peak distribution)
  • HiSeq platform, single-end 50 bp

Sample Requirements

  • DNA amount ≥ 50 ng, main peak in 100~500 bp
  • OD260/280 ≥ 1.8~2.0 without degradation or RNA contamination

Turnaround Time

  • 15 working days from verification of sample quality without data analysis

Recommended Sequencing Depth

  • ≥ 20 M reads

Analysis Pipeline

chip seq service analysis pipeline


Table. Representative samples showing data quality of Novogene’s ChIP-seq service.
Sample Raw ReadsLow QualityDegenerativesEmptyToo ShortTrimmedUntrimmedClean ReadsClean Rate (%)
Sample 1216186314322076820791420703080208680642157114499.78
Input Control303007902169210383255888869766294041613027392799.91

Quality control result of the project: including raw reads, trimmed reads and the raw-to-clean rate.

Strand cross-correlation evaluation curve

Figure. Strand cross-correlation evaluation curve

The x-axis represents the distance (nt) between forward strand and reverse strand and the y-axis represents the Pearson Correlation Coefficient.

Chip Seq Peaks

Figure. Peak width distribution

The x-axis represents the Peak width and y-axis represents the peak count.

Motif prediction results

Figure. Motif prediction results

The base calls as predicted by motif search software. The base calls on the right were the reverse-complementary strands.

  Whole Genome Sequencing on HiSeq X (Human/ Animal/ Plant)
  Whole Exome Sequencing
  mRNA-Seq
  LncRNA Sequencing
  Small RNA Sequencing
  Whole Genome Bisulfite Sequencing
  ChIP-Seq
  Animal & Plant Re-Sequencing
  Genotyping by Sequencing
  de novo Sequencing
  Pan-genome Sequencing
  Metagenomic Sequencing
  Single-cell DNA Sequencing
  Single-cell RNA Sequencing
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  Others- please specify
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