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Services

ChIP-Seq

Overview

Chromatin Immunoprecipitation Sequencing (ChIP-Seq) provides genome-wide profiling of DNA targets for histone modification, transcription factors, and other DNA-associated proteins. It combines the selectivity of chromatin immuno-precipitation (ChIP) to recover specific protein-DNA complexes, with the power of next-generation sequencing (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 and tissues, or under different conditions. At Novogene, we provide high-quality sequencing and comprehensive bioinformatics solutions for your ChIP-Seq projects.

Service Specifications

Applications

  • Applications range from transcriptional regulation to developmental pathways to disease mechanisms and beyond.

Advantages

  • Cost-effective: Rapid and efficient genome-wide profiling of multiple samples, using only 1/100 of the amount of DNA required for ChIP-chip.
  • Unsurpassed data quality: We guarantee that ≥ 80% of bases have a sequencing quality score ≥ Q30, exceeding Illumina’s official guarantee of ≥ 75%.
  • 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.

Sample Requirements

Sample Type Required Amount Fragment size Purity
Enriched DNA Sample
≥50 ng (Concentration ≥2ng/μL)
100 bp~500bp
OD260/280=1.8-2.0

Sequencing Parameter and Analysis

Platform Illumina Novaseq 6000
Read length Pair-end 150
Recommended Sequencing Depth ≥20 million read pairs per sample for the species with reference genome
Standard Data Analysis
Data quality control
Mapping onto reference genome
Peak calling
Motif prediction
Peak annotation and functional analysis of peak-associated genes
Summary of differential peaks and functional analysis of differential peak related genes
Visualization of ChIP-seq data

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Project Workflow

E6 Protein Expressed by High-Risk HPV Activates Super-Enhancers of the EGFR and c-MET Oncogenes by Destabilizing the Histone Demethylase KDM5C

Background:

Cervical cancer is one of the most common gynecological tumors, which seriously threatens women’s health. Infection by the high-risk (HR) types of HPV, HPV-16 and HPV-18, is the major cause of anogenital carcinomas in women and men, as well as a fraction of head and neck cancer. As a noncanonical function, HR HPV E6 plays an important role in regulating certain oncogene expression, such as EGFR and c-MET. However, the molecular mechanisms underlying the upregulation of these two proto-oncogenes are unknown. An emerging role in proto-oncogene activation is the abnormal epigenetic modifications. Previous studies have shown that HR HPV E6 interacts with both histone methyltransferases and acetyltransferases. Moreover, the generation and activation of super-enhancers can be a persistent regulatory element that drives the uncontrolled proliferation in cancer cells. A number of super-enhancers have been identified in various types of cancer, but it has not been reported in cervical carcinomas. It was demonstrated that the presence of HPV16 E6 is sufficient to upregulate the EGFR and c-MET super-enhancers, further elevating the expression of these two protooncogenes.


Figure 1 Distribution of MAPQ


Figure 2 Plots of strand cross correlation


Figure 3 Distance distribution of peaks to TSS


Figure 4 Motif analysis


Figure 5 Peak distribution in functional gene region


Figure 6 GO enrichment


Figure 7 KEGG enrichment scatter