ChIP-seq profiles DNA targets of histone modifications, transcription factors and other DNA-associated proteins on a genome-wide scale. It combines the immunospecificity of chromatin immunoprecipitation (ChIP) for recovering specific protein-DNA complexes with the power of NGS for high-throughput sequencing of the DNA. Additionally, because the protein-DNA complexes are recovered from living cells, binding sites can be compared in different cell types, tissues or under different conditions. In ChIP-seq, enriched DNA regions (protein binding sites) are detected as peaks above background reads. Thebioinformatics analyses of these regions can reveal the specific binding motifs of the certain protein. Applications include studies on gene regulation, transcription complex assembly, histone modification, developmental mechanisms and disease processes. Novogene can provide 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 analysisand data visualization.
- Professional bioinformatics:A bioinformatics analysis team composed of Ph.D. scientists entirely for Chip-Seq data analysis.
- 200-400 bp insert DNA library (depending on peak distribution)
- NovaSeq 6000 platform, paired-end 150 bp
- DNA amount:≥ 50 ng, main peak of 100-500 bp
- DNA volume: ≥ 10 μl
- Purity: OD260/280 = 1.8–2.0 without degradation, no protein or RNA contamination
- 22 working days from verification of sample quality without data analysis
Recommended Sequencing Depth
- ≥ 20 M reads
Table. Representative samples showing data quality of Novogene’s ChIP-seq service.
Quality control result of the project: including raw reads, trimmed reads and the raw-to-clean rate.
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.
Figure. Peak width distribution
The x-axis represents the peak width and y-axis represents the peak count.
Figure. Motif prediction results
The base calls as predicted by motif search software. The base calls on the right were the reverse-complementary strands.
|Sample||Raw Reads||Low Quality||Degeneratives||Empty||Too Short||Trimmed||Untrimmed||Clean Reads||Clean Rate (%)|