Genomics Facility

• Illumina Next-Generation Sequencing (NextSeq 2000 and MiSeq)
  
  • Gene Expression Analysis: Lexogen QuantSeq
  • 3’ mRNA-Seq library prep kit is used to generate Illumina-compatible libraries
  • Transcriptome analysis applications: RNA-seq, RNA-IP-seq, small RNA-seq
  • Genome sequencing, Exome and Amplicon sequencing
    • ChIP-seq
  • BCR and TCR immune repertoire profiling
    • Targeted sequencing
  • Single cell gene expression analysis, single cell immune profiling, scATAC-Seq
  • NanoString nCounter platform: Multiplexed digital quantification of nucleic acids without sample amplification.
  • Other applications: miRNA, SNPs and CNV.
    
    
• Single-cell analysis system
  
  • 10x Genomics Chromium Controller: The chromium system uses GemCode technology to enable thousands of micro-reactions in parallel. A two-step partitioning process allows thousands of single cells and their transcripts to be uniquely barcoded and then pooled for downstream processing and library preparation for single cell gene expression analysis, immune repertoire profiling and epigenetic studies. In addition, feature barcoding technology using specific oligonucleotide sequences to identify cell surface proteins and CRISPR alterations can be done simultaneously.
    
    
• Spatial platforms:
  
  • Nanostring GeoMx Digital Spatial Profiler provides morphological context in spatial transcriptomics and proteomics from just one tissue slide. It seamlessly integrates current histology and genomics workflows and has the capacity to simultaneously detect more than 20,000 RNA transcripts or 140 protein targets using barcoded RNA probes or antibodies. At the same time, fluorescently labeled morphological markers are added for easy selection of biologically relevant areas of interest.
  • Nanostring CosMx Spatial Molecular Imager allows rapid quantification and visualization of up to 1,000 RNA and 64 protein analytes at single cell and subcellular resolution. Applications include definition of cell types, cell states, tissue microenvironment phenotypes and gene expression networks within a single cell context.
    
    
• Digital PCR
  • The QX200 Droplet Digital PCR system enables absolute quantification of targets by partitioning a qPCR reaction into millions of picoliter-sized droplets. Each droplet contains either 0 or 1 molecule of interest. Every droplet is measured for fluorescence to generate a negative or positive signal, providing a true digital result.
    
    
• Capillary DNA sequencing
• 16-panel microsatellite analysis
• HLA typing
• KIR allele genotyping
• C. bovis Detection
• qPCR services using Taqman assays
• SNP genotyping analysis

Additional Services

• RNA and DNA preparation and quality control for all services
• NGS library preparation
• qPCR: primer selection through data extraction
• qRCR for library quantification purposes
• Experimental consultation and project troubleshooting

• Illumina NextSeq 2000
• Illumina NextSeq1000
• Oxford Nanopore Technologies Long-read Sequencer
• 10x Genomics Chromium Controller
• NanoString GeoMx Digital Spatial Profiler
• NanoString CosMx single cell Digital Spatial Profiler (June 2023)
• NanoString nCounter Analysis System
• Thermofisher SeqStudio
• Covaris High Performance Ultrasonicator
• GE Healthcare Bioscience ImageQuant LAS4010
• Agilent TapeStation
• Agilent 2100 Bioanalyzer
• Integra Assist Plus liquid handler