A wide breadth of sequencing applications

MiSeq applications include targeted gene, small genome, and amplicon sequencing, 16S metagenomics, and more

MiSeq Applications & Methods

Get a detailed genome view of the smallest organisms. Small genome sequencing provides comprehensive analysis of microbial or viral genomes for public health, epidemiology, and disease studies. Sequence up to 24 small genomes per MiSeq run.

Estimated Cost Per Sample: $98*

*Small whole-genome sequencing on the MiSeq System estimated cost per sample calculated 2016, based on 5 Mb genome, 50-100X coverage, 2 x 300 bp read length, Nextera XT Library Prep Kit, MiSeq Reagent v3 600-cycle kit

Targeted resequencing focuses time, expenses, and analysis on sequencing only a subset of genes or genome regions of research interest. Amplicon sequencing, the ultra-deep sequencing of PCR amplicons, enables cost-effective analysis of up to hundreds of target genomic regions in one assay. Sequence up to 96 samples and 1536 amplicons or more in a single MiSeq run.

Sequencing the 16S ribosomal RNA (rRNA) gene is a culture-free method to identify and compare bacteria from complex microbiomes or environments that are difficult to study. Our demonstrated protocol for 16S rRNA sequencing can help take the guess work out of your experiments. Multiplexing lets you sequence up to 96 samples per MiSeq run.

See how other researchers are using the MiSeq System to power their metagenomics studies:

Estimated Cost Per Sample: $18*

*16S rRNA sequencing on the MiSeq System estimated cost per sample calculated 2016, based on 96 samples, 2 x 300 bp read length, Nextera XT index primers, MiSeq Reagent v3 600-cycle kit

NGS is Fueling Species Research in Australia

High-throughput sequencing is paving the way to support agriculture, aquaculture, biodiversity, and conservation studies at the Deakin Genomics Center

Read Interview
Gene Expression Analysis with Targeted RNA-Seq

Targeted RNA sequencing (RNA-Seq) focuses on specific transcripts of interest, used to analyze gene expression and identify fusion genes.

Application Note

TruSeq Targeted RNA Expression Solution for the MiSeq System

Researcher Interviews

Cancer Pathways in Pediatric Leukemia
Uncovering Effect of CNV Linked to Schizophrenia

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Targeted Gene Panels

Targeted gene sequencing panels contain defined probe sets focused on specific genes of interest. Both predesigned and custom panels are available.

Researcher Interviews

Seeking Out Dyslipidemia Variants with LipidSeq
NGS Proves Invaluable for Biomarker Discovery

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De Novo Sequencing

De novo sequencing with next-generation sequencing (NGS) enables fast, accurate characterization of species without a reference genome.

Application Note

TELLSeq: Bringing Speed and Accuracy to Long-Range Sequencing

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miRNA & Small RNA Analysis

Isolate and sequence small RNA species, such as microRNA, to study the role of noncoding RNA in gene silencing and posttranscriptional regulation.

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DNA-Protein Interaction Analysis with ChIP-Seq

Combining chromatin immunoprecipitation (ChIP) assays with sequencing, ChIP-Seq is a powerful method for genome-wide surveys of gene regulation.

Researcher Interview

Surveying the Chromatin Landscape with NGS

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Quality Control

Perform quality control (QC) applications for bioproduction studies, or assess the quality of a sequencing library before committing it to a full-scale run.

Researcher Interview

Using NGS for Biological QC in BioPharma Production

Learn More: Library QC
Illumina Methods Guide

Methods Guide

Access the information you need—from BeadChip arrays to library preparation for genome, transcriptome, or epigenome studies to sequencer selection, analysis, and support—all in one place. Select the best tools for your lab with our comprehensive guide designed specifically for research applications.

Access Guide