ChIP-seq (Chromatin Immunoprecipitation Sequencing) is a method that combines the DNA linked proteome information obtained from IP with next-generation sequencing.
Most commonly, ChIP-seq is used to identify regions of the genome that are targeted by transcription factors or analyze histone/chromatin modifications. ChIP-seq can also be used in conjunction with other methods to provide insight into how the functional mechanics of the regulatory genome give rise to expression and protein production.
Real-world applications of ChIP-Seq
ChIP-seq experiments have been used to:
- Investigate chromatin remodeling as a direct result of prolonged drug use (Loh et al., 2017)
- Analyze chromatin structural components in breast cancer cell lines (Shimbo, Takaku and Wade, 2015)
- Utilize transcription factor binding sites to identify potential disease-causing loci (Tehranchi et al., 2016).
These are just a few ways that recent studies have utilized ChIP-seq. Protocols for chromatin immunoprecipitation are constantly being updated but the experimental design and subsequent sequencing specifics (such as correct library preparation and sequencing configuration) play an important role for downstream analysis purposes. We suggest discussing your experiment with experienced scientists before carrying out the immunoprecipitation.
ChIP-Seq workflow – How we can help
Step 1: ChIP assay
The ChIP assay is only the first step and there are various modifications being utilized in order to optimize protocols for specific experimental needs. We offer free experimental design consultation (i.e. sample size determination) and protocol tips.
Step 2: ChIP Sequencing
After ChIP, IPed DNA can be sent for sequencing. During this step, one of our Ph.D. level scientists can help you determine sequencing specifics such as correct library preparation kits and sequencing coverage needed for your experiment.
Step 3: ChIP-seq Data analysis
We offer bioinformatic support from a team of highly knowledgeable and experienced scientists. Why worry about data storage and hassle with parsing through large sequencing files? We take your data, analyze it according to your experimental specifications and deliver a concise report along with graphics and spreadsheets that are all available in one easy to access location.
Basic analysis of ChIP data includes:
- ChIP QC
- Peak annotation
- Differential peak annotation
- Interactive representation of results
- Comprehensive report and visualization of data
- Project and results discussion
Contact us for an estimate and free consultation!