Instrumentation

Quantitative PCR (qPCR) Platforms

Traditional 96/384 well qPCR (ViiA™ 7 Real-Time PCR System)
According to Life Technologies™, the system has been designed to improve researcher productivity for research that includes how gene expression changes in response to pharmacological agents and how genetic variation influences response to treatments for disease. The system simplifies real-time PCR applications, which are all integrated and accessible from a touch screen. The system provides the sensitivity to detect a single copy of starting genetic material and offers enhanced multiplexing flexibility.

 
ViiA 7 Real Time PCR System

 

 

 

High-Throughput Nanofluidic Single-cell qPCR (BioMark™ HD System)
According to Fluidigm®, the BioMark HD System is the newest real-time PCR system developed by Fluidigm. With enhanced productivity, increased reliability and a smaller footprint, the BioMark HD System provides everything the original BioMark delivered and more.


BioMark HD System

 

 

 

OpenArray® NT Cycler System
The OpenArray Real-Time PCR System provides PCR-based genotyping, gene expression, and microRNA analysis of hundreds to thousands of samples and assays per day. Researchers can analyze up to 144 samples on a single OpenArray® Plate. Three OpenArray Plates can be cycled and imaged simultaneously on the OpenArray Real-Time PCR Instrument, providing high-throughput results. (Source: gene-quantification.info/)


OpenArray NT Cycler System

 

Next-Generation Sequencing

Illumina Genome Analyzer IIx (GAIIx)
Using a massively parallel sequencing approach, the Illumina Genome Analyzer (GA) generates gigabases of high-quality sequence data for each sample. The system uses Illumina sequencing technology and novel reversible terminator chemistry, optimized to achieve unprecedented levels of cost-effectiveness and throughput. More information describing this instrument and its application is available at: http://www.illumina.com/systems/genome_analyzer_iix.ilmn and  http://www.illumina.com/applications/sequencing.ilmn.

Sequencing applications including, but not limited to:

  • RNA-Seq
  • ChIP-Seq
  • Exome
  • Bacteria/fungi


Illumina Genome Analyzer IIx

 

 

 

cBot Cluster Generation System
The core’s cBot system is the next generation of workflow improvements for Illumina sequencing. According to the Illumina website, cBot is a revolutionary automated system that creates clonal clusters from single molecule DNA templates, preparing them for sequencing by synthesis.

 

 

 

Paired-End Module
A simple modification to the standard single-read DNA library preparation facilitates reading both the forward and reverse template strands of each cluster during one paired-end read. In addition to sequence information, both reads contain long-range positional information, allowing for highly precise alignment of reads.

 

 

 

Ion Torrent™ Personal Genome Machine (PGM) Sequencer and Ion Proton™ Sequencer
The Genomics Core now offers new applications for microbiome profiling, RNA sequencing for transcriptome analyses, and targeted resequencing with rapid turnaround times using both a brand-new Ion Torrent Personal Genome Machine and an Ion Proton Sequencer. These sequencers deliver better, faster and less expensive data than current next-generation sequencing machines.


Ion Torrent Personal Genome
Machine Sequencer


Ion Proton Sequencer

 

Microarray Platforms

Illumina iScan System
According to the Illumina website,the iScan System is a leading-edge, dedicated array scanner that supports rapid, sensitive and accurate imaging of Illumina's array-based genetic analysis products. The system features a high signal-to-noise ratio, high sensitivity and high sample throughput.


Illumina iScan

 

 

Affymetrix GeneChip® System
A pioneer in genetic analysis, Affymetrix introduced highly parallel genetic assays to the marketplace by commercializing the first DNA microarray in the late 1980s. (Source: Department of Biosciences and Nutrition at Novum, KI South Campus Huddinge)


Affymetrix GeneChip

 

Quality Control (QC)

  • Invitrogen E-Gel
  • Agilent Bioanalyzer
  • Invitrogen Qubit

Invitrogen E-Gel

Agilent Bioanalyzer

Invitrogen Qubit

 

Informatics Infrastructure

Cedars-Sinai uses a Sun high-performance computing (HPC) grid to analyze next-generation sequencing and for other computational research.

THE QUEUE

NODE

CPU

Genomics queue

4 nodes

4 x 16 CPUs (per node)

Development queue

4 nodes

4 x 16 CPUs (per node)

LargeMem queue

4 nodes

4 x 24 CPUs (per node)

All/Short/Long/MatLab queue

370 nodes

370 x 2 CPUs (per node)

 

Virtual Machine Servers
A virtual machine or VM is a software implementation on the machine that executes programs like a physical machine. We currently have 3 VM servers:
1. VM server 1 (cslxgenomics01): 4 CPUs and 16Gs for nonparallel programs.
2. VM server 2 (cslxgenomics02): 2 CPUs and 8Gs for web portal, LIMS and databases.
3. VM server 1 (cslxgenomics01): 4 CPUs and 16Gs. It is the 2009 Windows server.

Storage/Backup
The Genomics Core has several layers (levels) of storage devices (fast storage, slower storage). The core has access to 200TB plus.