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Sequencing
Microarrays Popular Genomics Applications

NGS library prep methods

An extensive collection of published techniques for preparing sequencing libraries

Sequencing Library Preparation Methods

Sequencing Method Explorer

Use this interactive tool to explore experimental NGS library prep methods compiled from the scientific literature. The tool includes a subset of methods from the sequencing methods review articles and posters below. New methods will be added as they become available.

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Sequencing Method Explorer

Sequencing Method Posters

View illustrated schematics of DNA, RNA, and single-cell library preparation techniques that are compatible with SBS technology. Also see brief diagrams of Illumina library preparation kit protocols.

For All You Seq—DNA

This poster includes NGS methods for analyzing:

  • DNA variants
  • Low levels of DNA
  • Epigenetics
  • DNA–protein interactions
  • Protein–protein interactions
Download Poster
For All You Seq—RNA

This poster includes a comprehensive set of NGS methods for analyzing:

  • RNA transcription
  • RNA–protein interactions
  • Low levels of RNA
  • RNA modifications
  • RNA structure
Download Poster
For All You Seq—Single-Cell

This poster includes a comprehensive set of NGS-based single-cell analysis methods for:

  • Low-level RNA detection
  • Low-level DNA detection
  • Integrated DNA and RNA analysis
Download Poster
Sequencing Methods Posters
DNA and RNA Methods Reviews

Compare a Broad Range of Methods

Explore the world's largest collection of NGS library preparation techniques. These methods, compiled from the scientific literature, demonstrate the wide range of scientific questions you can address with Illumina sequencing by synthesis (SBS) technology.

These comprehensive review articles describe the various NGS methods, with pros and cons, publication summaries, and references.

Access DNA Methods ReviewAccess RNA Methods Review

Method of the Week

ATAC-Seq

Assay for transposase-accessible chromatin using sequencing (ATAC-Seq) is a protocol that utilizes the Epicentre Tn5 transposome. In this method, DNA is incubated with Tn5 transposome, which performs adaptor ligation and fragmentation of open chromatin regions. Deep sequencing of the purified regions provides base-pair resolution of nucleosome-free regions in the genome.

Pros
  • Two-step protocol with no adaptor ligation steps, gel purification, or crosslink reversal
  • Very high signal to noise ratio compared to FAIRE-Seq
Cons:
  • During mechanical sample processing, bound chromatin regions might open and be tagged by the transposome
References:
Most Recent References:
  1. Allum F., Shao X., Guenard F., Simon M. M., Busche S., et al. (2015) Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants. Nat Commun 6: 7211
  2. Chen C. W., Koche R. P., Sinha A. U., Deshpande A. J., Zhu N., et al. (2015) DOT1L inhibits SIRT1-mediated epigenetic silencing to maintain leukemic gene expression in MLL-rearranged leukemia. Nat Med 21: 335-343
  3. Davie K., Jacobs J., Atkins M., Potier D., Christiaens V., et al. (2015) Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling. PLoS Genet 11: e1004994
  4. Gehrke A. R., Schneider I., de la Calle-Mustienes E., Tena J. J., Gomez-Marin C., et al. (2015) Deep conservation of wrist and digit enhancers in fish. Proc Natl Acad Sci U S A 112: 803-808
  5. Kearns N. A., Pham H., Tabak B., Genga R. M., Silverstein N. J., et al. (2015) Functional annotation of native enhancers with a Cas9-histone demethylase fusion. Nat Methods 12: 401-403
  6. Maza I., Caspi I., Zviran A., Chomsky E., Rais Y., et al. (2015) Transient acquisition of pluripotency during somatic cell transdifferentiation with iPSC reprogramming factors. Nat Biotechnol 33: 769-774
  7. Qu K., Zaba L. C., Giresi P. G., Li R., Longmire M., et al. (2015) Individuality and variation of personal regulomes in primary human T cells. Cell Syst 1: 51-61
  8. Sammons M. A., Zhu J., Drake A. M. and Berger S. L. (2015) TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity. Genome Res 25: 179-188
  9. Sazonova O., Zhao Y., Nurnberg S., Miller C., Pjanic M., et al. (2015) Characterization of TCF21 Downstream Target Regions Identifies a Transcriptional Network Linking Multiple Independent Coronary Artery Disease Loci. PLoS Genet 11: e1005202
  10. Scharer C. D., Choi N. M., Barwick B. G., Majumder P., Lohsen S., et al. (2015) Genome-wide CIITA-binding profile identifies sequence preferences that dictate function versus recruitment. Nucleic Acids Res 43: 3128-3142
  11. Schmidl C., Rendeiro A. F., Sheffield N. C. and Bock C. (2015) ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors. Nat Methods
  12. Tomazou E. M., Sheffield N. C., Schmidl C., Schuster M., Schonegger A., et al. (2015) Epigenome mapping reveals distinct modes of gene regulation and widespread enhancer reprogramming by the oncogenic fusion protein EWS-FLI1. Cell Rep 10: 1082-1095
  13. Umansky K. B., Gruenbaum-Cohen Y., Tsoory M., Feldmesser E., Goldenberg D., et al. (2015) Runx1 Transcription Factor Is Required for Myoblasts Proliferation during Muscle Regeneration. PLoS Genet 11: e1005457
Explore Sequencing Methods

SBS Technology

Learn more about the advantages of sequencing by synthesis, how it works, and the many ways you can leverage sequencing technology to help answer your research questions.

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Illumina NGS Methods Guide

All the information you need, from library preparation to sequencer selection to analysis. Select the best tools for your lab.

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Additional Resources

Custom NGS Protocols
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Generate custom sequencing protocols tailored to your Illumina instrument and experimental requirements.

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Library Prep and Array Kit Selector
Library Prep and Array Kit Selector

Find the right kit for your lab, study, and application.

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Latest Genome Sequencer
Latest Genome Sequencer

Scalable throughput and flexibility for virtually any genome, sequencing method, and scale of project with the NovaSeq Series.

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