Major Applications


Illumina NextSeq 550: allows for analysis of mid-sized genome re-sequencing or transcriptome sequencing projects​

NextSeq 550  (run duration: 8-30 hours)

The NextSeq uses a 4 lane flow cell that is clustered with a single library pool, the flow cell has two run types High Output (NX-HO) and Mid Output (NX-MO).  The High Output flow cell can produce 360-400 million reads per run with read lengths up to 150 bp, single or paired end, while the Mid Output flow cell can produce 117-130 million reads per run with read lengths up to 150 bp, single or paired end.  

Illumina MiSeq: allows for more targeted sequencing of smaller genomes and amplicons

MiSeq  (run duration: 8-50 hours)

Uses a single lane flow cell and can produce 15-25 million reads per run with read lengths up to 300 bp, single or paired end. This sequencing system is good for metagenomic studies. MiSeq runs can also serve as a way of quality checking library preparations prior to running on the NextSeq or HiSeq.

MiSeq has a smaller output flow cell producing 1 million (MiSeq Nano) or 4 million (MiSeq Micro) reads, which can be used for sequencing library QC and small amplicon sequencing projects.


Applications and Recommended Run Types

1.  Whole Genome Sequencing and Re-Sequencing (DNA-seq):

  •      Genome re-sequencing: mutant identification, evolutionary comparisons, disease tissue sequencing: 
    •      Single read 100 (SR100) or paired end 100 (PE 100)
  •      De novo genome assembly for new unsequenced species:
    •      ​PE100 or PE150

2.  Expression/Transcriptome Analysis (RNA-seq):

  •      De novo transcriptome analysis in an unsequenced or unannotated genome:
    •      ​PE100 or PE150
  •      RNA-seq to study comparative transcriptomics in model genomes (e.g. sequenced and annotated genomes):
    •      ​SR50 or SR100
  •      Small RNA transcriptomics:
    •      ​SR50

3.  Epigenomics and Gene Regulation:

  •      Chromatin immunoprecipitation sequencing (ChIP-seq) to identify transcription factor interaction sites:
    •      ​SR50 or SR100
  •      Methylated DNA sequencing to identify methylated regions of the genome:
    •     ​SR100, PE100 or PE150 depending on the extent of annotation of the reference genome

4.  Metagenomics, Amplicon, or Targeted Gene Sequencing:

  •       MiSeq
    • V2 and V3 reagents produce 15-20 million reads - good for Metagenomic or Targeted Gene sequencing projects
    • Micro reagents produce 4 million reads ​- Nano reagents produce 1 million reads
      • good for QC of custom library preps or small scale amplicon sequencing projects

Note: Users can download the Illumina Sequencing Coverage Calculator to estimate the number of lanes of sequencing required for your experiment. 

CMADP Events

Ralph N. Adams Lectureship
KU Chemistry Dept.

Robert Kennedy, Ph.D.
Hobart H. Willard Distinguished University Professor and Chair of Chemistry
Professor of Pharmacology
University of Michigan

"The Nanoliter Lab: Droplet Microfluidics for Screening and Sensing"
Friday, September 6, 2019 at 4:00pm
Integrated Science Building, Room 1154

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