ChIP-Seq

Interplay between DNA and its interacting proteins

ChIP-Seq is used primarily to determine how proteins interact with DNA to regulate gene expression with the intent to elucidate the complex circuitry of genetic regulatory networks, genetic pathways and epigenetic mechanisms in living cells. The approach enables thorough examination of the genome-wide distribution of chromatin-binding proteins and histone modifications in any genome with a known sequence, giving insights into gene regulation events that play a role in various diseases and biological pathways, such as development and cancer progression.

Library preparation and sequencing

Library Preparation and Sequencing Service

Our ChIP-seq workflow begins with immunoprecipitated (IP) DNA samples. Despite the often low quantities of DNA generated by IP, our high-performance library preparation techniques enable the creation of high-quality libraries from even picogram amounts of DNA.

ChIP-seq experiments typically include matched controls (such as input, IgG, or untagged strains) to facilitate background subtraction and ensure more accurate peak identification. Both IP samples and controls are processed in parallel to maintain consistency.

Sequencing is conducted on the Illumina platform using 150bp paired-end reads, ensuring comprehensive and reliable data for your research needs.

Bioinformatics analysis

Our analysis services enable the discovery of novel transcription factor binding sites, identification of genes regulated by known transcription factors and co-regulators, direct comparison of regulatory events in different cell states (e.g., normal vs. disease), and investigation of drug effects and other stimuli on regulatory pathways.

Standard bioinformatics analysis:

• Trimming: Removal of low-quality bases and adapters to ensure high-quality data.
• Reads Alignment: Alignment of reads to the reference genome and selection of uniquely mapping reads.
• Quality Control: Assessment of contaminants using proprietary scripts and evaluation of how well the signal in the ChIP-seq sample can be differentiated from the background distribution of reads in the control sample (bamFingerprinting).
• Peak Detection: Identification of significant peaks representing binding sites.
• Peak Annotation: Identification of potential associations of ChIP regions with functionally important genomic regions. This analysis provides statistics on ChIP enrichment at important genome features such as specific chromosomes, promoters, gene bodies, or exons, and infers genes most likely to be regulated by a binding factor.

Advanced bioinformatics analysis:

• Differential Binding Analysis: Identification of sites that are differentially bound between two sample groups. This includes overlapping and merging peak sets, counting sequencing reads overlapping intervals in peak sets, and identifying statistically significantly differentially bound sites based on evidence of binding affinity (measured by differences in read densities).
  

KEY DELIVERABLES

• Raw Sequencing Data: raw reads generated by the sequencing platform in FASTQ format.
• Quality Control Reports: detailed HTML reports on read quality and preprocessing steps.
• Annotated Peak Lists: Detailed lists of identified peaks with annotations.
• Differential Binding Reports: Comprehensive reports on differentially bound sites between sample groups.
• Quality Control Metrics: Detailed quality control metrics and visualizations.
• Genome Browser Tracks: Files for visualization in genome browsers, allowing easy exploration of the data.

Our ChIP-seq services provide the comprehensive data and analysis you need to advance your research in gene regulation and epigenetics.

We provide full support on study design to ensure correct sequencing and bioinformatics strategies are used to meet your project goals. Our expert will consult with you about your specific requirements.