Instrumentation

Quantitative PCR (qPCR) Platforms

QuantStudio™ 12K Flex Real-Time PCR System
According to Applied Biosystems, the newest upgraded All-in-one Real Time PCR system, compatible with TaqMan®. OpenArray® Digital PCR Plates.

Featuring a much higher throughput:

  • With up to 4 arrays, 3,072 reactions per array, can achieve 12,288 reactions in a single run
  • >43,000 reactions (up to 2,304 samples) per work day

More automation:

  • Reduces user error by automated loading (standard deviation <0.25 Ct)
  • Faster, less start-up and hands-on time (<20 minutes loading, 2.5 hours from cDNA/DNA to real time data)
  • Offers much greater flexibility with off-the-shelf and custom-designed assays, and better precision/sensitivity for nucleic acid experiments

 
QuantStudio™ 12K Flex 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


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 (5 M reads per sample)
  • 40 RNA profiling experiments (10 M reads per sample)
  • 30 chip-seq experiments (15 M reads per sample)
  • 12 transcriptome sequencing experiments (40 M reads per sample)
  • 12 exome sequencing experiments (100X on average)
  • 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 60-80 M reads and up to 200 bp read lengths.


Ion Proton Sequencer

NGS Library Prep

Tecan Freedom EVO 100

The Tecan Freedom EVO system is equipped to automate genomic, proteomic, drug discovery and other life science applications. Each platform can be combined with a wide choice of robotic arms, liquid handling tools and application options to cover all genomic automation needs, including DNA extraction, normalization, PCR setup, DNA shearing and NGS sample preparation.

Powered by the intuitive software Freedom EVOware®, Tecan Freedom EVO features:

  • 96- or 384- multichannel pipetting head options
  • Configurable worktable that includes separation and detection devices, shakers and incubators in addition to standard labware carriers
  • Assay-specific setup for PCR, SNP scoring, sequencing and reaction cleanup, as well as library fragment preparation and emPCR enrichment for next-generation sequencing
  • Automated quantification of nucleic acids by integration of Tecan micro plate reader device and dilution of DNA to the perfect concentration
  • Automated preparation of nucleic acid samples with magnetic beads or solid phase extraction by centrifugation or vacuum
  • Fully automated, high-security source and destination barcode identification via Tecan's PosID™ option and standalone barcode readers

Tecan Freedom EVO 100

Fluidigm C1 Single-Cell Auto Prep system

The C1 system is based on innovative microfluidic technology that enables rapid and reliable isolation, processing and profiling of individual cells for genomic analysis. The instrument isolates single cells into individual reaction chambers in an integrated fluidic circuit (IFC) chip. The optically clear IFC enables researchers to automatically stain captured cells and examine them by microscopy for viability, surface markers or reporter genes. After staining, cells are automatically lysed and template is quickly prepared for qPCR and RNA-Seq, or whole-genome amplification and downstream Exome sequencing analysis.

  • The system is expandable: Run new chemistry or applications by modifying existing scripts, or purchase or develop custom applications.
  • The latest collection of new single-cell applications includes mRNA sequencing, epigenetics, DNA sequencing, cell staining and more.

Fluidigm C1 Single-Cell Auto Prep system

 


Quality Control

  • 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 Grid Engine high-performance computing 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)

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 (VM) is a software implementation on the machine that executes programs like a physical machine. We currently have two VM servers:

  • VM server 1 (cslxgenomics01): 4 CPUs and 16 Gs for nonparallel programs.
  • VM server 2 (cslxgenomics02): 2 CPUs and 8 Gs for web portal, LIMS and databases.


Storage/Backup

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

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