The RPCI Genomics Shared Resource offers investigators a full spectrum of services including access to RPCI BAC and shRNA libraries, SNP genotyping (targeted and global), methylation (targeted and global), copy number and expression (gene and miRNA), and Sanger and next generation sequencing (NGS). The state-of-the-art facility houses an Illumina iScan, HiSeq2000 and MiSeq systems, Ion Torrent Protons and PGMs, Sequenom MassARRAY MALDI-TOF MS, ABI7900HT Sequence Detection Systems, Caliper Sciclone NGS workstation and GenePix laser scanner for high throughput studies and sample processing. miRNA activity can be measured using NGS or the Exiqon miRNA RT-PCR panels for compromised RNA samples (serum). Similarly, the methylation content of intact or compromised DNA samples can be quantitated using Sequenom EpiTYPER (targeted assays) or the Illumina humanmethylation450 BeadChip (global). The GSR also provides full service gene expression analysis using qPCR and the Illumina BeadChips, and performs sequence capture (RainDance, SureSelect, HaloPlex) and sample library preparations (TruSeq, Ion AmpliSeq) for Illumina MiSeq/HiSeq2000, and Ion Torrent PGM/Proton NGS.
The RPCI Genomics Shared Resource has approximately 3,300 sq. ft of space in the Genetics and Pharmacology building, immediately adjacent to several other core facilities and the Center for Personalized Medicine. This is divided into eight well-equipped labs of approximately 400 sq. ft. each, including dedicated areas for the shRNA resource, microarray analysis, next-generation sequencing and genotyping. Also included are a computer/informatics suite and a linear equipment room with a built-in temperature alarm system and a diesel-powered generator that protects all freezers and refrigerators in the event of a power outage. The separate shRNA, microarray and NGS spaces are designed to efficiently process samples for high throughput sample preparations and analyses. The layout minimizes cross-contamination between samples/reactions and houses other supporting instrumentation: BioRad thermalcyclers, Tecan EVO Freedom 200 liquid handler, Illumina iScan, HiSeq2000(2) and MiSeq (2), Ion Torrent Proton (4) and PGM (2), ABI 7900HT SDS (2), Matrix liquid handling dispenser, Caliper Sciclone NGS workstation and Sequenom MassARRAY.
Gene Modulation Services
Sequence-validated human and mouse shRNA libraries in virus vectors are available through Gene Modulation Services which is part of the Genomics Shared Resource. The shRNA library permits rapid, cost-efficient, loss of-function genetic screens and rapid tests for genetic interactions to be performed in mammalian cells. Each shRNA construct has been sequence verified and cloned into a retroviral vector to ensure a match to the target gene. Each gene is represented by a target set that consists of an average of 3-5 individual constructs or clones targeting different regions of the gene sequence. In addition, the resource has the Human Cancer Retroviral Library. The Expression Arrest™ Human Cancer shRNAmir Retroviral Library targets all cancer related genes, including known tumor suppressor genes with multiple shRNAmir constructs per gene. The library contains over 2311 shRNAmir constructs targeting 967 cancer related genes. Additionally, the libraries have an incorporated DNA “bar-coding” system, by which each RNA molecule has been tagged with a unique 60 nucleotide DNA sequence. This facilitates shRNA validation and gene identification after library screens.