The Rush University Genomics and Microbiome Core Facility (GMCF) is a 2000+ square foot laboratory performing nucleic acid extractions (BSL2) from a wide range of sample types, next-generation sequencing library preparation for DNA and RNA sequencing, targeted amplicon sequencing, microbiome sequencing, and quantitative analysis of targets for gene expression, absolute quantification, and genotyping analyses.
The GMCF is also the site of the Regional Innovative Public Health Laboratory (RIPHL) – part of a collaboration with the Chicago Department of Public Health (CDPH). RIPHL’s current focus is on whole genome sequencing (WGS) for SARS-CoV-2 and provides flexible, advanced molecular laboratory capacity to CDPH, including: WGS for a range of pathogens of public health importance; biobanking of clinical specimens positive for SARS-CoV-2 and other pathogens of public health importance; and bioinformatics, large-volume data management, and genomic epidemiologic support.
The facility is equipped with ancillary equipment for molecular biology work, including 96- and 384-well thermocyclers, real-time PCR instruments, a gel-doc station, a plate reader, a plate sealer, biosafety cabinets, bead-beating devices, barcode scanners, refrigerators and freezers, and a refrigerated centrifuge. The facility also has a Qiagen QIAcuity digital PCR instrument (4x96 plate throughput) and a 384-well real-time PCR (Thermofisher) for high-throughput quantitative PCR analyses. The facility maintains a Maxwell RSC48 purification instrument for automated DNA and RNA extractions and a MaxPrep pre-processing device for nucleic acid extractions (Promega), an Agilent TapeStation4150 device for automated nucleic acid quality inspection, a Blue PippinPrep automated DNA size selection device, a VIAFLO96 semi-automated pipettor and two Opentrons OT2 instruments for semi-automated liquid handling. In addition, the facility has two IDOT2.0 non-contact liquid handling devices.
Access to an Illumina MiSeq and 10x Chromium device are provided through nearby laboratories within Rush University. The facility maintains two small Illumina sequencers (Illumina MiniSeq and iSeq) and an Oxford Nanopore MinION device, with big data sequencing performed at external sequencing facilities using NovaSeq6000 instruments. The GMCF has extensive experience in the preparation of samples for whole genome sequencing, including that of the SARS-CoV-2 virus, shotgun metagenome library preparation, RNAseq library preparation, amplicon-based NGS library preparation, and deep sequencing and bioinformatics analyses.