ChIP-sequencing, also known as ChIP-Seq or ChIP-seq, is a method used to analyze protein interactions with DNA. It combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. ChIP-seq 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. This epigenetic information is complementary to genotype and expression analysis.
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ChIP-seq Data Analysis Workflow:
Sample requirements
• DNA amount quantified by Qubit 2.0: ≥ 100ng; minimum 10 ng
• DNA concentration: ≥1 ng/μL
• Total volume: ≥10 μL
• Purity: OD260/280= 1.8-2.0 without degradation or RNA contamination
Bioinformatics for ChIP Sequencing
Standard Analysis:
a.Raw data QC and clean up
b.Alignment to a reference with mapping statistics
c.Peaking calling with or without control samples
d.Gene assignment and peak annotation
e.Pathway Analysis
f. Final project report (HTML) with analysis methods, publication-ready graphics, and references
Advanced Analysis:
h.Motif analysis
i.clustering and visualization
Turnaround time
~3-4 weeks depending on project requirements, one additional week for data analysis