NUSeq (genomic services)

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Mission

The NUSeq Core Facility provides state-of-the-art genomics instrumentation, bioinformatics, and technological expertise to support genome and biomedical research at the Feinberg School of Medicine and Northwestern University. Major technologies provided encompass next-generation sequencing (NGS), including single cell sequencing and spatial profiling, microarray, high-throughput nucleic acid extraction, cell line authentication, quantitative and digital PCR, and Sanger sequencing (via a partnership). Major project applications include gene expression profiling, gene mutation/structural variation detection, epigenomics, DNA-protein interaction, 3D genome and DNA accessibility, and metagenomics. The Core provides data analysis and bioinformatics services for genomics data generated in-house or externally. 

NUSeq strives to adopt and provide the latest genomics technologies for the FSM and Northwestern communities. For example, the Core has been providing single cell sequencing and spatial biology services (with partner cores) since 2017 and 2021, respectively. With more technologies becoming available, the Core now offers multiple platforms for both single cell and spatial services (see below). NUSeq’s bioinformatics and data mining capabilities grow as part of the Core’s technology acquisitions.

As the only genomics research facility at Northwestern, NUSeq currently provides 90 genomics services to all groups at FSM/Northwestern on both the Evanston and Chicago campuses, as well as to Northwestern affiliates and external institutions. The Core’s highly trained lab and bioinformatics staff support each project at every step, from experimental design to advanced data mining. Initial project consultation is provided free of charge.

Services Offered

• Short Read Sequencing on Multiple Platforms (Illumina NovaSeq X Plus/NextSeq/MiSeq, Element AVITI, and Complete Genomics DNBSEQ-G400)
  
  • RNA-seq, from standard to ultra-low input
  • DNA-seq, from whole genome, exome, to gene panel sequencing
  • DNA methyl-seq
  • ChIP-seq
  • ATAC-seq
  • Microbiome/metagenome sequencing
  • Single cell sequencing
  • Spatial transcriptomics
  • Multiomics
• Long Read Sequencing on Oxford Nanopore (MinION and PromethION) and PacBio Revio Platforms
  
  • Whole genome sequencing, including structural variant detection, copy number variant analysis, phasing, and de novo assembly
  • Full-length RNA transcript sequencing to detect alternative splicing isoforms and fusion transcripts, at the levels of bulk, single cell, and spatial transcriptomics
  • Epigenetics with native methylation detection
  • Microbiome and metagenomics
• Single Cell DNA, RNA, Chromatin Accessibility, Methylation, and Multiomic Sequencing on Multiple Platforms (10x Genomics, Parse, etc.)
  • Cell atlasing to uncover cell-to-cell heterogeneity in a tissue or organism
  • Discovery of new cell types
  • Identification of new disease cellular markers
  • Establishment of cell development trajectory
• Spatial Transcriptomics on Multiple Platforms (10x Visium HD, Xenium In Situ, Stereo-seq)
  
  • Profiling of spatiotemporal gene expression
  • Spatial organization of tissue development
  • Cell neighborhood analysis
  • New disease biomarker discovery
  • Integrated analysis with single cell sequencing
• Microarray
  • Illumina BeadChip for genotyping and epigenomics (methylation) analyses
• Bioinformatics and Data Mining
  • Experimental Design
  • NGS Data Analysis
  • Single Cell Sequencing Data Analysis
  • Spatial/In Situ Profiling
  • Illumina Genotyping and Methylation Microarray Data Analysis
  • Advanced or Customized Data Mining
• Human Cell Line Authentication
• High-Throughput DNA/RNA Extraction
• DNA/RNA Concentration Measurement and QC
• Real-time Quantitative PCR (Equipment Use)
• Digital Droplet PCR (Equipment Use)
• NanoString nCounter (Targeted gene analysis at pathway level)