NEBNext Ultrashear® FFPE DNA Library Prep Kit
Product informationCode | Name | Size | Quantity | Price | |
---|---|---|---|---|---|
E6655S |
NEBNext UltraShear FFPE DNA Library Prep Kit |
24 assays | - | Unavailable in your region | |
E6655L |
NEBNext UltraShear FFPE DNA Library Prep Kit |
96 assays | - | Unavailable in your region |
NEBNext Ultrashear® FFPE DNA Library Prep Kit
Catalog #E6655
Product Introduction
FFPE DNA poses many challenges for library preparation, including low input amounts and highly variable damage from fixation, storage, and extraction methods. Regions of interest are often enriched using hybrid capture-based approaches, and these workflows require a high input of diverse, uniform DNA library.
The NEBNext Ultrashear™ FFPE DNA Library Prep Kit incorporates enzymatic fragmentation of FFPE DNA using NEBNext UltraShear, a new enzyme mix optimized for use with FFPE DNA that increases library yields and quality, while improving scalability and ease of use. The kit also repairs damage to DNA caused by the FFPE process and includes reagents and a protocol optimized for library prep of FFPE DNA. The workflow is streamlined and user-friendly, with minimal hands-on time, and the kit improves yields and quality of libraries from a range of FFPE DNA sample input (5-250 ng) and quality.
View or download extensive performance data in our Data Supplement.
- Includes specialized enzymatic fragmentation and FFPE DNA repair reagents, plus optimized library prep reagents and protocol
- Increased library yields
- Improved sequencing metrics
- Greater sensitivity of somatic variant calling
- 5-250 ng input range
- Automation-friendly workflow
For FFPE DNA library prep without enzymatic fragmentation, the NEBNext FFPE DNA Library Prep Kit (NEB #E6650) is available.
- Product Information
- Protocols, Manuals & Usage
- Tools & Resources
- FAQs & Troubleshooting
- Citations & Technical Literature
- Quality, Safety & Legal
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Product Information
Description
View or download extensive performance data in our Data Supplement.
FFPE DNA is often compromised in quality and quantity and is challenging for library prep and sequencing, including in target enrichment workflows that require high amounts of library input. The NEBNext UltraShear FFPE DNA Library Prep Kit addresses these challenges and improves ease of workflow and scalability:
- Repairs FFPE-induced damage using the NEBNext FFPE DNA Repair Mix v2
- Incorporates specialized enzymatic DNA fragmentation using NEBNext UltraShear
- Uses NEBNext Ultra II library prep reagents in a protocol optimized for FFPE DNA
- Robustly amplifies libraries using NEBNext MSTC™ FFPE Master Mix
- High library yields, sufficient for input into target enrichment workflows
- User-friendly workflow with minimal hands-on time and multiple safe stopping points
The NEBNext UltraShear FFPE DNA Library Prep Kit reduces damage from deamination and oxidation due to the fixation, storage, and extraction process for FFPE DNA samples, thereby reducing false positive variant calls.
The combination of specialized enzymatic FFPE DNA fragmentation and repair with optimized reagents and protocols provides superior performance with this challenging sample type.
For FFPE DNA library prep without enzymatic fragmentation, the NEBNext FFPE DNA Library Prep Kit (NEB #E6650) is available.
- This product is related to the following categories:
- FFPE DNA Products,
- Next Generation Sequencing Library Preparation Products,
Kit Components
Kit Components
The following reagents are supplied with this product:
Properties & Usage
Materials Required but not Supplied
- 80% Ethanol
- Nuclease-free Water
- 0.1X TE (1 mM Tris-HCl, pH 8.0, 0.1 mM EDTA)
- DNase-, RNase-free PCR strip tubes
- NEBNext Multiplex Oligos for Illumina® (www.neb.com/oligos)
- Magnetic rack/stand (NEB #S1515S, Alpaqua® cat. #A001322, or equivalent)
- Thermal cycler
- Agilent® Bioanalyzer® or TapeStation® and associated reagents and consumables
- Adaptor Dilution Buffer NEB #B1430S or NEBNext Unique Dual Index UMI Adaptor Dilution Buffer supplied with NEBNext Unique Dual Index UMI Adaptor DNA Sets (NEB #E7395/E7874/E7876/E7878)
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Protocols, Manuals & Usage
Protocols
Manuals
Tools & Resources
Selection Charts
FAQs & Troubleshooting
FAQs
- What sample types can I use with the NEBNext UltraShear FFPE DNA Library Prep Kit?
- How much starting material is required for the NEBNext UltraShear FFPE DNA Library Prep Kit?
- When preparing samples using the NEBNext UltraShear FFPE DNA Library Prep Kit, can my input DNA be in EDTA-containing solutions?
- Do I really need to vortex the NEBNext UltraShear enzyme mix before use?
- What fragmentation time should be used with the NEBNext UltraShear FFPE DNA Library Prep Kit for FFPE DNA samples?
- Is size selection recommended?
- What are the safe stopping points in this protocol?
- Which NEBNext Multiplex Oligos can be used with the NEBNext UltraShear FFPE DNA Library Prep Kit?
- What input amount (nanograms) is recommended for standard versus target enrichment library prep with FFPE DNA samples?
- Can I use this NEBNext kit with adaptors and primers from vendors other than NEB?
- Will treating my DNA with the FFPE DNA Repair Mix v2 as part of the NEBNext UltraShear FFPE DNA Library Prep Kit hurt my downstream reaction?
- Does the FFPE DNA Repair v2 Mix repair DNA-protein crosslinks?
- Does the FFPE DNA Repair v2 Mix fix blocked 3′ ends?
- Can the FFPE DNA Repair v2 Mix repair damage in both single- and double-stranded DNA? Or, does it require double stranded DNA as a template?
- If I had a DNA template with mutation sites (i.e. 8-oxoguanine or deaminated cytosines) that are directly adjacent to each other on opposite strands would treatment with the FFPE DNA Repair v2 Mix cause a double strand nick/break?
- What gap lengths can be repaired with the FFPE DNA Repair v2 Mix?
- Can I fragment my gDNA sample with NEBNext UltraShear® in buffers other than 1X TE (10mM Tris pH 8.0, 1mM EDTA)?
Citations & Technical Literature
Citations
Quality, Safety & Legal
Quality Assurance Statement
Quality Control tests are performed on each new lot of NEB product to meet the specifications designated for it. Specifications and individual lot data from the tests that are performed for this particular product can be found and downloaded on the Product Specification Sheet, Certificate of Analysis, data card or product manual. Further information regarding NEB product quality can be found here.Specifications
The Specification sheet is a document that includes the storage temperature, shelf life and the specifications designated for the product. The following file naming structure is used to name these document files: [Product Number]_[Size]_[Version]Certificate Of Analysis
The Certificate of Analysis (COA) is a signed document that includes the storage temperature, expiration date and quality controls for an individual lot. The following file naming structure is used to name these document files: [Product Number]_[Size]_[Version]_[Lot Number]Safety DataSheets
The following is a list of Safety Data Sheet (SDS) that apply to this product to help you use it safely.NEBNext® FFPE DNA Repair Mix v2
NEBNext® Thermolabile Proteinase K
NEBNext® Ultra II End Prep Enzyme Mix
NEBNext® Ultra™ II Ligation Master Mix
NEBNext® Ligation Enhancer
Legal and Disclaimers
Products and content are covered by one or more patents, trademarks and/or copyrights owned or controlled by New England Biolabs, Inc (NEB). The use of trademark symbols does not necessarily indicate that the name is trademarked in the country where it is being read; it indicates where the content was originally developed. The use of this product may require the buyer to obtain additional third-party intellectual property rights for certain applications. For more information, please email busdev@neb.com.This product is intended for research purposes only. This product is not intended to be used for therapeutic or diagnostic purposes in humans or animals.
New England Biolabs (NEB) is committed to practicing ethical science – we believe it is our job as researchers to ask the important questions that when answered will help preserve our quality of life and the world that we live in. However, this research should always be done in safe and ethical manner. Learn more.
The supporting documents available for this product can be downloaded below.