GESR Instruments and Services
The GESR has partnered with the Institute for Genome Sciences: Genomics Resource Center at UMD through the Mid-Atlantic Shared Resources Consortium, which provides access to additional instruments including the Illumina HiSeq 4000 and Pacific Biosciences RS II. This partnership provides users of the GESR with internal pricing, which is discounted relative to outside users, which greatly facilitates research. Through this partnership, the GESR has generated next-generation sequence data for numerous PIs both within Lombardi and from the larger GU community.
Agilent Bioanalyzer 2100 (lab-on-a-chip) is used to perform DNA and RNA quality control tests prior to analysis of samples by microarray, NGS, NanoString and RT-PCR. The instrument provides a microfluidics-based platform for sizing, quantification and quality control of RNA, DNA, proteins and cells.
Three microarray platforms (Affymetrix, Agilent, and Illumina) are used for mRNA/miRNA expression profiling, SNP genotyping, CNV analysis and DNA methylation analysis. The Affymetrix system includes GeneChip scanner 3000 7G-Plus that allows scanning high-density microarrays. The Agilent system is a high-resolution scanner that scans Agilent SurePrint G3 microarrays. The Illumina system offers a cost-effective alternative to Affymetrix and Agilent microarray systems.
Next generation sequencing including whole genome sequencing (WGS), whole exome sequencing (WES), RNA-seq, miRNA-seq and targeted sequencing is offered using a new Illumina NextSeq 550 the GESR acquired in 2018, Illumina MiSeq available at LCCC, acific Biosciences (PacBio) at Children’s National Medical Center (CNMC) and HiSeq at the University of Maryland (UMD).
Three Real-Time PCR (RT-PCR) instruments are used for mRNA/miRNA profiling and SNP genotyping with TaqMan probes:
- A new QuantStudio RT-PCR with OpenArray block and Accufill System that the GESR acquired in 2016
- A 7900 HT RT-PCR system with a 96-well block and SDS 2.4 software that is compatible with the ABI TaqMan Low Density Array (TLDA)
- A 96-well StepOnePlus RT-PCR
The GESR uses a liquid handling robotic system (Biomek NXp) capable of performing a wide range of tasks, including assay preparation by transferring samples and reagents from tubes to 96- or 384-well plates (e.g., DNA plating and assay preparation for SNP genotyping).
A NanoString nCounter acquired in 2017 allows direct, digital quantification of nucleic acids and protein without amplification. Its highly multiplexed multi-analyte assays enables analysis of up to 800 targets in a single reaction, on a single system, with a single data output. It allows direct analysis of tissue, cell and blood lysates, single cell and FFPE samples.