Technologies
Breakthroughs in modern biomedical research are largely driven by rapidly evolving genomics technologies. The NUSeq Core is a state-of-the-art core facility that provides genomics and bioinformatics support to investigators at Northwestern University, affiliated institutions, and external academic and commercial institutions. The major technologies available at the core are listed 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.
Complete Genomics DNBSEQ-T1+
- Low to intermediate throughput, quick turnaround time
- Multiple flow cell types for flexibility, including
- FCS (small): 400-500 million reads per flow cell, distributed across 2 lanes
- FCL (large): 1,500 million reads per flow cell, 4 lanes
- Read length available: 1x100, 2x150, and 2x300 bases. The specific read length required by STOmics Stereo-seq is also available.
- Visit the Complete Genomics DNBSEQ-T1+ page for more technical specifications.
Illumina NextSeq 500
- Intermediate throughput, quick turnaround time
- 130 or 400 million reads from one flow cell depending on sequencing mode, no separable lanes
- Read length available: 1x75, 1x150, and 2x75 bases
- Visit the Illumina NextSeq 550 page for more technical specifications.
Illumina MiSeq
- Low throughput, quick turnaround time
- 1, 4, 15, to 25 million reads from one flow cell with throughput depending on flow cell type, no separable lanes
- Read length available: 2x150, 2x250, and 2x300 bases
- Visit the Illumina MiSeq 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 unravele 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
- Read length: Typically in the 15-20 kb range
- Read accuracy: Q30
- Data throughput: 90 Gb data per SMRT cell
- Generates methylation (5mC at CpG sites) data from native DNA simultaneously
- 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 detecton 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.
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 (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.
Stereo-Seq (STOmics)
- Sequencing based, whole transcriptome analysis
- Spot size and pitch: Each transcript capture spot is 0.22 µm in diameter, with spot center-to-center distance of 0.5 µm
- Tissue capture area size: ranging from 5 mm x 5 mm to custom-designed chips as large as 13 cm x 13 cm
- Sample type: FFPE and fresh frozen tissues
- Visit our Spatial Transcriptomics page for service details.