Product Class: Kit

NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads

Product Introduction

Even more from less, for DNA
 
Are you challenged with trying to obtain higher library yields using ever-decreasing input amounts? Each component in the NEBNext Ultra II DNA Library Prep Kit from NEB has been reformulated, resulting in a several-fold increase in library yield with as little as 500 picograms of input DNA. These advances deliver unprecedented performance, while enabling lower inputs and fewer PCR cycles.

  • Get more of what you need, with the highest library yields
  • Use to generate high quality libraries from a broad range of input amounts, from 500 pg to 1 µg
  • Prepare libraries from ALL your samples, including GC-rich DNA and FFPE DNA samples
  • Improve yields and quality for target enrichment applications
  • Save time with streamlined workflows, reduced hands-on time and automation compatibility, and enjoy the flexibility of kit or module formats
  • Enjoy the flexibility and reliability of the gold standard SPRIselect® size selection and clean-up beads, supplied in just the amounts you need

Note: If your input DNA has not already been sheared, we recommend the NEBNext Ultra II FS DNA Library Prep Kit for Illumina, which fragments, end repairs, and dA-tails DNA, all in a single tube with no cleanups or transfers. This kit is available with and without sample purification beads..

Bioz Badge Exists : True
Catalog # Size Concentration
E7103S 24 reactions
E7103L 96 reactions

Product Information

Description

[squirrel thumbnail] Download the NEBNext® for DNA Library Prep Brochure for the Illumina® Platform

The NEBNext Ultra II DNA Library Prep with Sample Purification Beads contains the enzymes, buffers and purification beads required to convert a broad range of DNA input amounts into indexed libraries for next-generation sequencing on the Illumina platform. The fast, user-friendly workflow has minimal hands-on time and, for added convenience, this kit contains NEBNext Sample Purification Beads (SPRIselect® beads from Beckman Coulter) for size selection and enzyme reaction cleanup.

Advantages
  • Get more of what you need, with the highest library yields 
  • Use to generate high quality libraries  even when you have only limited amounts of DNA, with inputs as low as 500 pg
  • Prepare libraries from ALL of your samples, including GC-rich targets  and FFPE DNA samples 
  • Improve yields and quality for target enrichment applications
  • Save time with streamlined workflows, reduced hands-on time and automation compatibility, and enjoy the flexibility of kit or module formats
  • Enjoy the flexibility and reliability of the gold standard SPRIselect size selection and clean-up beads, supplied in just the amounts you need

To learn more about how NEBNext Ultra II addresses lower input amounts and challenging sample types, download our technical note.

For use with NEBNext Multiplex Oligos for Illumina (Unique Dual Index UMI Adaptors DNA Set 1) (NEB #E7395), refer to the Protocols tab for UMI Adaptors-specific guidance.

 

Figure 1: NEBNext Ultra II produces the highest library yields and conversion rates from a broad range of input amounts

Bar graphs comparing yield and rates of conversion for NEBNext® Ultra™ II DNA Library Prep Kit
A: Libraries were prepared from Human NA19240 genomic DNA using the input amounts and numbers of PCR cycles shown. Manufacturers’ recommendations were followed, with the exception that size selection was omitted.

B: Libraries were prepared from Human NA19240 genomic DNA using the input amounts and library prep kits shown without an amplification step, following manufacturers' recommendations. qPCR was used to quantitate adaptor-ligated molecules, and quantitation values were then normalized to the conversion rate for Ultra II. The Ultra II Kit produces the highest rate of conversion to adaptor-ligated molecules, for a broad range of input amounts.

Figure 2: NEBNext Ultra II provides uniform GC coverage for microbial genomic DNA over a broad range of GC composition and input amounts

Graphs of GC coverage for microbial genomic DNA over a broad range of GC composition and input amounts
Libraries were made using 500 pg, 1 ng and 100 ng of the genomic DNAs shown and the Ultra II DNA Library Prep Kit and sequenced on an Illumina MiSeq®. Reads were mapped using Bowtie 2.2.4 and GC coverage information was calculated using Picard's CollectGCBiasMetrics (v1.117). Expected normalized coverage of 1.0 is indicated by the horizontal grey line, the number of 100 bp regions at each GC% is indicated by the vertical grey bars, and the colored lines represent the normalized coverage for each library.

Figure 3: NEBNext Ultra II provides superior yields in PCR-free workflows

Bar graphs comparing PCR-free yield for NEBNext® Ultra™ II 
Libraries were generated from 100 ng of Human NA19240 genomic DNA using the library prep kits shown, following manufacturers' recommendations, and with no amplification step. Library yields were determined by qPCR using the NEBNext Library Quant Kit for Illumina. The NEBNext Ultra II Kit produces the highest yields.

Figure 4: NEBNext Ultra II provides superior yields for target enrichment applications

Bar graphs comparing yields for Niblegen and SureSelect 
For Nimblegen® enrichment, libraries were prepared with 100 ng of Human HG02922 genomic DNA, using NEBNext Ultra II with the NEBNext Adaptor and index primers, or the Kapa Library Preparation Kit Illumina Platforms with the SeqCap® Adapter Kit (Roche). Target enrichment was performed with NimbleGen SeqCap Human Exome v3.

For SureSelectXT enrichment, libraries were prepared with 200 ng of Human HG02922 genomic DNA, using NEBNext Ultra II or Kapa Hyper with the NEBNext Adaptor and index primers, or the SureSelectXT Reagent Kit, Illumina (ILM) platforms with Herculase® II Fusion DNA Polymerase. Target enrichment was performed with SureSelect® Human All Exon V6.

Manufacturers’ recommendations were followed, including use of the recommended number of PCR cycles for pre- and post-capture. NEBNext Ultra II libraries resulted in the highest post-capture yields for both enrichment workflows.
This product is related to the following categories:
Analysis of DNA Methylation by Bisulfite Conversion,
DNA Library Prep for Illumina,
Automation for NEBNext® NGS Library Prep,
DNA Methylation Analysis,

Kit Components

Kit Components

The following reagents are supplied with this product:

NEB # Component Name Component # Stored at (°C) Amount Concentration
  • NEB # Stored at (°C)
    E7103S Multi-temperature
    Component Name Component # Stored at (°C) Amount Concentration
    NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® E7645S -20 1 x 24 reactions Not Applicable
    NEBNext® Ultra II End Prep Enzyme Mix E7646AVIAL -20 1 x 0.072 ml Not Applicable
    NEBNext® Ultra II End Prep Reaction Buffer E7647AVIAL -20 1 x 0.168 ml Not Applicable
    NEBNext® Ultra™ II Ligation Master Mix E7648AVIAL -20 1 x 0.72 ml Not Applicable
    NEBNext® Ligation Enhancer E7374AVIAL -20 1 x 0.024 ml Not Applicable
    NEBNext® Ultra II Q5® Master Mix E7649AVIAL -20 1 x 0.6 ml Not Applicable
    NEBNext® Sample Purification Beads E7104S 25 1 x 4 ml Not Applicable
    NEBNext® Sample Purification Beads E7104SVIAL 25 1 x 4 ml Not Applicable
  • NEB # Stored at (°C)
    E7103L Multi-temperature
    Component Name Component # Stored at (°C) Amount Concentration
    NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® E7645L -20 1 x 96 reactions Not Applicable
    NEBNext® Ultra II End Prep Enzyme Mix E7646AAVIAL -20 1 x 0.288 ml Not Applicable
    NEBNext® Ultra II End Prep Reaction Buffer E7647AAVIAL -20 1 x 0.672 ml Not Applicable
    NEBNext® Ultra™ II Ligation Master Mix E7648AAVIAL -20 3 x 0.96 ml Not Applicable
    NEBNext® Ligation Enhancer E7374AAVIAL -20 1 x 0.096 ml Not Applicable
    NEBNext® Ultra II Q5® Master Mix E7649AAVIAL -20 2 x 1.2 ml Not Applicable
    NEBNext® Sample Purification Beads E7104L 25 1 x 16 ml Not Applicable
    NEBNext® Sample Purification Beads E7104SVIAL 25 4 x 4 ml Not Applicable

Properties & Usage

Materials Required but not Supplied

  • 80% Ethanol (freshly prepared) 
  • Nuclease-free Water 
  • 0.1X TE (1 mM Tris-HCl, pH 8.0, 0.1 mM EDTA) 
  • DNA LoBind Tubes (Eppendorf #022431021) 

  • NEBNext Multiplex Oligos for Illumina (for a full list, visit www.neb.com/oligos)

  • Magnetic rack or plate (e.g., NEBNext® Magnetic Separation Rack (NEB #S1515S), Alpaqua ® 96S Super Magnet Plate (#A001322), or equivalent)
  • PCR Machine
Optional:
  • 10 mM Tris-HCl, pH 8.0 or 
  • Tris/NaCl, pH 8.0 (10 mM Tris, 10 mM NaCl)
    (for adaptor dilution of DNA input ≤ 100 ng)

Storage Temperature:
Package 1: NEBNext Ultra II DNA Library Prep Kit for Illumina - Store at -20°C
Package 2: NEBNext Sample Purification Beads - Store at Room Temperature. Do not freeze.

FAQs & Troubleshooting

FAQs

  1. For what type of sample prep/library construction can I use the NEBNext Ultra II DNA Library Prep kit for Illumina?
  2. What type and how much starting material do I need to use when preparing libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina?
  3. Is size selection required and what is the recommended method?
  4. Can I use the NEBNext Ultra II DNA Library Prep Kit for Illumina reagents for preparing libraries for sequencing on the Ion Torrent PGM or Proton?
  5. Can NEB provide any of the reagents for the cluster generation step or the actual sequencing run?
  6. Are these reagents available in a customized format, larger format or 96 well formats?
  7. I am currently using Agencourt Ampure XP beads. Will the NEBNext Sample Purification Beads be a suitable replacement?
  8. Can I use this NEBNext kit with adaptors and primers from other vendors than NEB?
  9. What do I do if I see a precipitate in the Ultra II End Prep Reaction Buffer?
  10. Does the kit include adaptor and primers?

Tech Tips

When removing the supernatant from the magnetic beads during cleanup, itis important not to disturb the pellet. Find these and other helpfultips for optimizing the size selection and clean up steps in thisprotocol video.
 
Size Selection and Cleanup with NEBNext Ultra

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.

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.

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.

Licenses

This product is licensed for research and commercial use from Bio-Rad Laboratories, Inc., under U.S. Pat. Nos. 6,627,424, 7,541,170, 7,670,808, 7,666,645, and corresponding patents in other countries. No rights are granted for use of the product for Digital PCR or real-time PCR applications, with the exception of quantification in Next Generation Sequencing workflows.

For additional information or to inquire about commercial use, please contact busdev@neb.com.

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