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Novel strategies for chromatin immunoprecipitation (ChIP) with low input samples.
Standard ChIP workflows require a starting sample quantity of around 106 to 107 cells, below which the assay is hindered by high background binding, poor enrichment efficiencies and loss of enriched library complexity.
Improving enrichment efficiency and sample loss
To counter this, several adjustments to the ChIP workflow have been proposed for low input samples to increase enrichment efficiency1 and minimize sample loss2.
Platform choice and downstream sample processing
In addition to the assay itself, the choice and optimization of downstream processing (ie sequencing, array, or PCR) and bioinformatic analysis are also important.
The Abcam high-sensitivity ChIP assay
Embarking on ChIP with low sample input quantities can be a daunting prospect. Our high-sensitivity ChIP kit (ab185913) has been developed specifically for this application:
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2. Dirks, R. Genome-wide epigenomic profiling for biomarker discovery. Clinical Epigenetics. 8, 122. (2016).
3. Cejas, P. Chromatin Immunoprecipitation from fixed clinical tissues reveals tumor-specific enhancer profiles. Nature Medicine. 22, 685. (2016).
4. Reverberi, R. Factors affecting the antigen-antibody reaction. Blood transfusion. 5, 227. (2007).
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6. Xiong, X. A scalable epitope tagging approach for high throughput ChIP-Seq analysis. ACS Synth biol . (2017, Feb 19).
7. ENCODE. (n.d.). ENCODE Platform Comparison. Retrieved from https://genome.ucsc.edu/ENCODE/platform_characterization.html
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9. Bolduc, N. Preparation of low-input and ligation-free librarIes using template-switching technology. In Current protocols in molecular biology (Vol. Unit 7.26). Wiley & Sons. (2016).
10. Kidder, B. ChIP-Seq: Technical considerations for obtaining high quality data. Nature Immunology. 12, 918. (2011).
11. Stelloo, S. Androgen receptor profiling predicts prostate cancer outcome. EMBO Mol Med. 7, 1450. (2015).