Northwestern University Feinberg School of Medicine

Center for Genetic Medicine

Next Generation Sequencing


As the name suggests, NUSeq is primarily a next-gen sequencing core facility. Providing first-class NGS technology to the Northwestern research community is a main focus of the core. In less than two years since the core’s establishment in 2015, NUSeq has grown from an Illumina NextSeq to a fleet of NGS sequencers that spans all major Illumina sequencing technologies from MiSeq to HiSeq 4000. Thousands of sequencing libraries have been constructed and sequenced encompassing all major NGS applications, from RNA-seq to sequencing of CRISPR/Cas9 gene editing products.

Major next-gen sequencers


Illumina HiSeq 4000

5 Billion Single Reads or 10 B Paired-End Reads, Up to 1500 Gbp Sequence Data in <1-3.5 Days, Up to 150 bp in Read Length
12 Human Genomes/96 Exomes/100 Transcriptomes per Run

Illumina NextSeq 500

400 Million Single Reads or 800 M PE Reads, Up to 120 Gbp Sequence Data in 11-29 Hours, Up to 150 bp in Read Length
1 Human Genomes/12 Exomes/16 Transcriptomes per Run

Illumina MiSeq

25 Million Single Reads or 50 M PE Reads, Up to 15 Gbp Sequence Data in 4-56 hours, Up to 300 bp in Read Length
Good for Microbiome 16S rRNA Sequencing, Small Genome, Small RNA Sequencing, Targeted DNA or RNA Sequencing, and Screening of CRISPR/Cas9-Induced Gene Editing Events

Ion Proton

60-80 Million Reads, Up to 10 Gbp Sequence Data in 2-4 Hours, Up to 200 bp in Read Length
Targeted Resequencing


We are constantly evaluating sequencing technology needs for Northwestern researchers. If you have needs for other sequencing platforms, such as the PacBio Sequel or Oxford NanoPore sequencers, please contact us.


NGS projects supported



NUSeq supports all NGS-based research projects. Major types of NGS applications including the following:

RNA Sequencing (Transcriptome analysis)
Whole Genome Sequencing
Whole Exome Sequencing
Mitochondrial DNA Sequencing
DNA Methylation Sequencing
ATAC-Seq
ChIP-Seq

The pie chart below shows the distribution of NGS projects conducted by NUSeq between early 2016 and early 2017. Over 1,000 libraries were constructed and sequenced during this period. All the sequencing was performed on the Core’s NextSeq 500, prior to the installation of the new HiSeq 4000 and MiSeq sequencers. Since the HiSeq and MiSeq become available, new whole genome and microbiome projects have been accepted and performed.

The single-cell RNA-seq projects shown below are based on the use of SMART-seq v4 chemistry. For such projects, single cells can be collected by any single cell preparatory method, including flow cytometry, laser capture microdissection, or free-form microscopic cell collection.



NGS project workflow

To initiate a new NGS project, please call or email Core director Dr. Xinkun “Sequen” Wang at 312-503-3331 or xinkun.wang@northwestern.edu.