Technology Highlights

Breakthroughs in modern biomedical research are largely driven by rapidly advancing genomics technologies. The NUSeq Core is a state-of-the-art facility that provides genomics and bioinformatics support to investigators at Northwestern University, affiliated institutions, and external academic and industrial organizations. Highlights of the major technologies and capabilities available through the Core are presented below:

Short Read Sequencing

Applications: Whole Genome/Exome Sequencing, Gene Panel Sequencing, RNA-Seq (incl. Single Cell RNA-Seq), ChIP-Seq, Methyl-Seq, Microbiome Sequencing

With the power to sequence millions to hundreds of millions of DNA fragments simultaneously in a matter of hours or few days, NGS has been the major driving force in life science and medicine in the last decade. The sequences (or reads) generated from the DNA molecules can be used to assemble new genomes, while more often they are used for mutation or variation detection, differential gene expression analysis, detection of protein-DNA interaction, epigenomics, and environmental microbial diversity profiling.

Northwestern investigators continually pioneer new strategies to solve their research questions with NGS. To meet the sequencing needs of our users, NUSeq maintains a fleet of major NGS systems, summarized below. If your project requires a different NGS platform, please notify us as we are constantly working to build our capacity.

Illumina NovaSeq X Plus

Top data throughput, cost effective
Three flow cell types at different throughput levels:
- 25B flow cell: 2,000-2,500 million* reads per lane, 8 lanes per flow cell. Read length available: 2x150 bases. Sequencing on this flow cell is the most cost effective among all NUSeq sequencers at <$3 per Gbp
- 10B: 900-1,000 million reads per lane, 8 lanes per flow cell. Read length available: 2x50 and 2x150 bases
- 1.5B: 600-700 million reads per lane, 2 lanes per flow cell. Read length available: 2x50 and 2x150 bases
Visit the Illumina NovaSeq X Plus Specifications page for more technical specifications.

Element AVITI

Intermediate throughput, quick turnaround time
Read length and output:
- 2x75 bases: 400-500 million reads in Medium Output mode, or 800-1,000 million reads High Output, per flow cell. Each flow cell has 2 lanes
- 2x150 bases: 400-500 million reads in Medium Output mode, or 800-1,000 million reads High Output, per flow cell. Each flow cell has 2 lanes
- 2x300 bases: 100 million reads in Medium Output mode, or 300 million reads High Output, per flow cell. Each flow cell has 2 lanes
Accuracy: Equivalent to other short read sequencing platforms. UltraQ mode achieves Q50 accuracy in 70% of reads, and Q40 in 90% of reads, for applications that require highest accuracy possible
Visit the Element Biosciences AVITI page for more technical specifications.

Illumina MiSeq i100 Plus

Low throughput, quick turnaround time
5, 25, 50, to 100 million reads from one flow cell with throughput depending on flow cell type, no separable lanes
Read length available: 2x300 and 2x500 bases
Visit the Illumina MiSeq i100 page for more technical specifications.

Long Read Sequencing

Applications: Full-Length Transcript Profiling (at both bulk and single cell levels), Splicing Isoform Detection, Fusion Transcript Detection, Whole Genome Assembly, Haplotype Resolution, Structural Variant Detection, DNA Repeat Expansion Determination, Native Methylation Calling, Metagenomics

Long read sequencing technologies overcome challenges and limitations of short-read sequencing, and enable investigators to resolve complex genomic regions, accurately assemble genomes, identify structural variants, and unravel gene alternative splicing isoforms. Below are two currently available long read sequencing platforms available at NUSeq, both of which have seen significant advancements in recent years and continue to improve on accuracy and throughput.

PacBio Revio HiFi Long Read Sequencer

(Sep'26 Update) Multi-use SMRT cell significantly lowers sequencing costs
Read length: Typically in the 15-20 kb range
Read accuracy: Q30-Q40+
Data throughput: Up to 120 Gb data per SMRT cell (or per acquisition with the multi-use SMRT cell) with the latest SPRQ chemistry
Native epigenetic detection: 5hmC, 5mC, and 6mA calling at no additional costs
Visit the PacBio Revio page for more technical specifications.

Oxford Nanopore Long Read Sequencer

Read length: 10-100 kb for long-read sequencing, and 100-300 kb for ultra-long read sequencing mode. 4 Mbp is the current record
Read accuracy: Q20-Q30+
Data throughput:
- PromethION: We see typically 50-100 Gb data per flow cell
- MinION: We see typically 10-20 Gb data per flow cell
Simultaneous detection of epigenetic modifications with primary sequence
Visit the Oxford Nanopore Technologies PromethION and MinION page for more technical specifications.

Single-Cell Sequencing

Applications: Single-Cell RNA-Seq, Single Cell ATAC-Seq, Single-Cell DNA-Seq, Single-Cell Methyl-Seq, Single-Cell Multi-Omics

Single cell sequencing offers unprecedented opportunities to study cell-to-cell variation, identify/visualize different cell types/identities in a population, and infer cellular developmental trajectories. NUSeq offers multiple single-cell sequencing platforms, including 10x Genomics, Illumina, and Parse Biosciences, to meet the increasing needs for single cell sequencing, As listed above, besides transcriptome, single cell sequencing increasingly encompasses genome, exome, and epigenome of individual cells. While most single cell sequencing projects analyze large numbers of cells, the Core also offers a low-throughput option for teams who need to sequence small numbers of cells at greater depth.

10x Genomics Chromium

Target cell number: 500-20,000 cells/nuclei in each sample
Input type: Freshly prepared single-cell (or nucleus) suspension, fixed cells (or nuclei), cryopreserved cells, and FFPE embedded tissues
Available assays: 3’ and 5' gene expression, immune repertoire profiling, chromatin accessibility, multiome (i.e., simultaneous chromatin accessibility and gene expression from the same set of nuclei)

Illumina PIP-Seq

Target cell number: 100-100,000 cells in each sample
Input type: Single-cell (or nucleus) suspension prepared from fresh or cryopreserved cells, or nuclei isolated from fresh or frozen mammalian tissues. Fresh and DSP-methanol-fixed cells or nuclei are compatible
Available assays: 3’ gene expression

Parse Evercode

Target cell number: 10,000-1,000,000 cells in each sample
Input type: Fixed single-cell or -nucleus suspension
Available assays: Whole transcriptome, TCR profiling, CRISPR detection, gene capture

Other single cell platforms are also available, e.g., those from Bioskryb Genomics for integrated genome/transcriptome analysis and Scale Biosciences (now part of 10x Genomics) for single cell methylation studies. Visit our Single-Cell Sequencing page for more service details on the aforementioned platforms.

Spatial Genomics

Applications: Spatially Resolved Transcriptomics, Tissue Neighborhood Analysis, Tumor Microenvironment Analysis, Cell-Cell Interaction Inference, Spatial Cell Atlasing

Spatial context is important for cells to carry out their functions. For diseased conditions, pathologists examine tissue sections to look for microenvironments where cells turn abnormal. Spatial genomics provides a “map” of gene activity in morphology-preserved tissues, often with subcellular resolution. This state-of-the-art technology enables us to investigate gene expression in the context of tissue structure to shed light on functional diversity and heterogeneity in regions of interest. Depending on technical approaches employed, spatial resolution of gene transcripts in tissue sections is achieved using a sequencing-based workflow or in situ hybridization.

Atera In Situ from 10x Genomics

Atera (10x Genomics, upcoming early 2027)

In situ hybridization based, whole transcriptome analysis
Resolution: 200 nm
Tissue image area size: >500 mm² per slide (standard glass slide compatible, please contact NUSeq for recommendations)
Sample type: FFPE and fresh frozen tissues
Allow optional tissue section staining, e.g., H&E, following an Atera instrument run
Visit our Spatial Transcriptomics page for service details.

Visium HD sequencer

Visium HD (10x Genomics)

Next-gen sequencing based, whole transcriptome
Resolution: 2 µm
Tissue capture area size: 6.5 x 6.5 mm (each Visium slide has two capture areas)
Sample type: FFPE and fresh frozen tissues
Enables integration of spatial gene expression data with bright-field and fluorescence microscope images
Visit our Spatial Transcriptomics page for service details.

xenium sequencer

Xenium (10x Genomics)

In situ hybridization based, targeted analysis
Resolution: 200 nm
Tissue image area size: 10.45 x 22.45 mm
Sample type: FFPE and fresh frozen tissues
Allows immunofluorescence, H&E staining, or Visium whole transcriptome analysis on the same tissue section
Visit our Spatial Transcriptomics page for service details.