Product Class: Kit

NEBNext® Primers for Epigenetics (Unique Dual Index Set 3)


Catalog #E3404

Product Introduction

NEBNext® Primers for Epigenetics (Unique Dual Index Set 3) includes 96 unique pairs of i5 and i7 index primers optimized for NEBNext epigenetics workflows, including NEBNext E5hmC-seq™, with Illumina® sequencing. The primers enable incorporation of unique index pairs during library amplification and have been designed to minimize index hopping.

  • Optimized for the NEBNext epigenetics workflows, including E5hmC-seq
  • Addresses the “barcode hopping” issue seen with some Illumina sequencing instruments
  • Increases sample identification specificity with unique dual index primer pairs

Product Information

Description

Indices are incorporated during PCR using these Unique Dual Index primer pairs that have been optimized for NEBNext epigenetics workflows, including E5hmC-seq. These primers enable multiplexing and have been designed to minimize index hopping. They are supplied as premixed i5 and i7 8-base index primers in 96 wells of a plate that has a pierceable foil seal for easy, single use.

The index sequences from the NEBNext Primers for Epigenetics (Unique Dual Index Set 3) (NEB #E3404S) and the 24-reaction NEBNext Primers for Epigenetics (Unique Dual Index Set 2B) (NEB #E3392S) are compatible, and can be combined to multiplex up to 120 reactions.

Please refer to the NEBNext Enzymatic 5hmC-seq Kit manual (NEB #E3350) for use of the NEBNext Primers for Epigenetics.

This product is related to the following categories:
Enzymatic Conversion for DNA Methylation Analysis,
Hydroxymethylation Detection and Analysis,
Methylome Analysis Products,
NEBNext® Multiplex Oligos (Adaptors & Primers) Products,
DNA Methylation Analysis,
Next Generation Sequencing Library Preparation Products,

Kit Components

Kit Components

The following reagents are supplied with this product:

NEB # Component Name Component # Stored at (°C) Amount Concentration
  • E3404S     -20    
      NEBNext® Primers for Epigenetics (Unique Dual Index Set 3) E3404AVIAL -20 1 x 5 μl/well 10 µM

Properties & Usage

Protocols, Manuals & Usage

Manuals

The Product Manual includes details for how to use the product, as well as details of its formulation and quality controls.

Usage & Guidelines

Tools & Resources

Selection Charts

Web Tools

FAQs & Troubleshooting

FAQs

  1. Are Sample Sheets available for use with the NEBNext® Primers for Epigenetics?
  2. Are dual-indexed libraries compatible with single end sequencing?
  3. What is provided in the NEBNext® Primers for Epigenetics?
  4. Can the NEBNext® Primers for Epigenetics be used to address “index hopping” with Illumina® patterned flow cells?
  5. How many indices are available with the 24 reaction or 96 reaction size of the NEBNext® Primers for Epigenetics?
  6. Are the NEBNext® Primers for Epigenetics the same as NEBNext® Multiplex Oligos for Illumina®?
  7. Are the NEBNext® Primers for Epigenetics validated for the E5hmC-seq™ workflow?
  8. What is the concentration of the Index Primers in NEBNext® Primers for Epigenetics?
  9. How many reactions worth of primer are in each well for the NEBNext® Primers for Epigenetics?
  10. Can I use the 96-well primer plate supplied with the NEBNext® Primers for Epigenetics to do my PCR reactions?
  11. Do I need to spike in custom sequencing primers when sequencing libraries made with NEBNext® Primers for Epigenetics on Illumina® sequencing instruments?
  12. Can I perform single read runs and still get both index sequences? Can I run both single read and paired-end recipes with dual-indexed libraries?
  13. What sequences need to be trimmed for NEBNext libraries that are sequenced on an Illumina instrument?
  14. What is the difference between NEBNext® Primers for Epigenetics and NEBNext LV Unique Dual Index Primers?
  15. Are Sample Sheets available for use with the NEBNext® LV Unique Dual Index Primers Sets 1-5?
  16. Are libraries that have been dual indexed using the NEBNext® LV Unique Dual Index Primers compatible with single-end sequencing?
  17. How many primer pairs are available in the NEBNext® LV Unique Dual Index Primer Pairs Sets 1-5?
  18. Can the NEBNext® LV Unique Dual Index Primers be used to address “index hopping” with Illumina® patterned flow cells?
  19. Are the NEBNext® LV Unique Dual Index Primers the same as NEBNext Multiplex Oligos for Illumina®?
  20. Are the NEBNext® LV Unique Dual Index Primers validated for the EM-seq™ v2 or E5hmC-seq™ workflows?
  21. What is the concentration of the Index Primers in NEBNext® LV Unique Dual Index Primers?
  22. How many reactions’ worth of primer are in each well of the NEBNext® LV Unique Dual Index Primers?
  23. Can I use the 96-well primer plate supplied with the NEBNext LV Unique Dual Index Primers to do my PCR reactions
  24. Do I need to spike in custom sequencing primers when sequencing libraries made with NEBNext® LV Unique Dual Index Primers on Illumina® sequencing instruments?

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]

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.

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