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:

OpenArray NT Cycler System


Next-Generation Sequencing

Illumina NextSeq 500

From Illumina, Illumina’s NextSeq 500 is the first desktop high-throughput sequencing system that can perform Whole-Genome Sequencing, Exome Sequencing and RNA-Seq. With tunable output and industry-leading data quality, the NextSeq Series offers the perfect combination of high-throughput sequencing, flexibility, and accuracy, all at a cost that makes it just right for your lab. New NextSeq reagents enable up to 500 M sequencing reads and 2x150 bp read lengths.

In a single run, NextSeq 500 can sequence up to:

  • 80 small RNA Sequencing experiments (5M reads per sample)
  • 40 RNA profiling experiments (10M reads per sample)
  • 30 Chip-seq experiments (15M reads per sample)
  • 12 Transcriptome Sequencing experiments (40M reads per sample)
  • 12 Exome sequencing experiments (90% reads at >20X)
  • One human whole genome sequencing (>30X coverage)

Illumina NextSeq 500

Illumina MiSeq

From Illumina, the MiSeq desktop sequencer allows you to access more focused applications such as microbiome (bacterial and fungal) amplicon sequencing, metagenomics, small genome sequencing, starting at 10 ng DNA. New MiSeq reagents enable up to 25 M sequencing reads and 2x300 bp read lengths.

Illumina MiSeq

Ion Proton™ Sequencer

The Genomics Core now offers new applications for targeted Exome and RNA sequencing with rapid turnaround times using an Ion Proton Sequencer. These sequencers deliver faster results and less expensive data than current next-generation sequencing machines. With current reagents, the Proton can deliver 60-80M reads and up to 200 bp read lengths.

Ion Proton™ Sequencer


Quality Control (QC)

  • Invitrogen E-Gel
  • Advanced Analytical Fragment Analyzer
  • Agilent Bioanalyzer
  • Invitrogen Qubit

Invitrogen E-Gel

Advanced Analytical Fragment Analyzer

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.




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.

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

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