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 (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 60-80 M reads and up to 200 bp read lengths.


Ion Proton Sequencer


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.

Android app on Google Play