EpiNext CUT&LUNCH Library Preparation Kit

The EpiNext™ CUT&LUNCH Library Preparation Kit is a complete set of optimized reagents designed for, in a fast manner, highly sensitive CUT&LUNCH applications, including preparations of DNA library from low input samples to profile interactions between proteins and DNA via next generation sequencing using Illumina platforms. The kit has the following advantages and features:

• High sensitivity and flexibility: Can be used for both non-barcoded (singleplexed) and barcoded (multiplexed) DNA library preparation. The amount of input DNA can be as low as 1 ng with a range from 1 to 100 ng.
• Extremely fast and streamlined procedure: The procedure from enriched DNA to ready-to-use library is about only 1 hr. No clean-up is required between each step, and all reactions take place in the same tube before PCR, thereby saving time and preventing handling errors as well as loss of valuable samples.
• The most convenient for use: Contains all required components for each step of DNA library preparation, which are sufficient for end polishing, ligation, clean-up, size selection, and library amplification, thereby allowing the library preparation to be the most convenient with reliable and consistent results.
• Minimized bias: Ultra HiFi amplification enables researchers to reproducibly achieve high yields of DNA library with minimal sequence bias and low error rates.
  
  
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CUT&LUNCH peak profiles are consistent with ENCODE ChIP-seq profiles. CUT&LUNCH: Peak scores are plotted in the bar graph for 0.1 million MCF-7 cells. ENCODE ChIP-Seq: Peak scores are plotted in the bar graph for 5 million cells. A: H3K4me3 (active regions), B: H3K9me3 (silenced regions).

 

Background Information
DNA library preparation is a critical step for next generation sequencing (NGS). For generating accurate sequencing data in NGS, the prepared library DNA should be sufficient in yield and of high quality. Also, as NGS technology is continuously improving, DNA library preparation is required to be optimized accordingly. The amount of DNA enriched by CUT&LUNCH from low input cells or from low abundant target protein is often at low or sub-nanogram levels, which causes insufficient DNA library yields by using currently available library preparation methods. In addition, the currently used library preparation methods are time-consuming. To address this issue, EpigenTek developed the EpiNext™ CUT&LUNCH Library Preparation Kit, specifically suitable for use with the CUT&LUNCH assay.

Principle & Procedure
This kit contains all reagents required at each step of the workflow for carrying out successful DNA library preparation with use of enriched DNA from the CUT&LUNCH assay. In the library preparation, the end repair/dA tailing (end polishing) of the enriched DNA is performed simultaneously. Adaptors are then ligated to both ends of the polished DNA fragments for amplification and sequencing. Ligated fragments are size selected and purified with MQ beads, which allows quick and precise size selection of DNA. Size-selected DNA fragments are amplified with a high-fidelity PCR mix that ensures maximum yields from minimum amounts of starting material and provides highly accurate amplification of library DNA with low error rates and minimum bias.