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

epMotion 5075tc
According to Eppendorf, the new epMotion 5075tc automated liquid handling system provides a precise, accurate alternative to time-consuming manual pipetting and liquid handling tasks. The combination of accelerated operational speed, new software and hardware features and an increased number of work table positions make the systems ideal for simple and flexible laboratory use across a wide range of liquid handling applications. With the integrated 2D ThermoMixer module, the epMotion® 5075tc is the one of the most flexible automated pipetting systems. In addition, novel features such as a new CleanCap option, including UV light decontamination and a HEPA filter for purified air, offer new standards of decontamination and sample safety. This is supported even further by an optical sensor that checks labware, liquid levels and tip counts and type at the start of each cycle, hugely decreasing any risk of error during the run.

  • Up to 15 work table positions for more complex NGS protocols
  • Automatic recognize, exchange, transport plates and labware (stacking of up to five plates)
  • Free-jet pipetting: no tubes/wires, no air bubbles to minimize cross contamination
  • Excellent pipetting precision: <2% CV at 1 microliter
  • 8 channel pipetting with volume range 1-1000 microliter
  • IOS 8655 compliance calibrated, with automatic calibration reminder

epMotion 5075tc

10X Chromium
Designed for automatic and efficient parallel partitioning and molecular barcoding, the new Chromium platform unlocks critical long-range genomics and cell-by-cell gene expression information.

The system supports the following applications:

  • Single cell 3' counting for single cell transcriptomics, which performs deep profiling of complex cell populations (up to 70,000 cells) with high-throughput digital gene expression on a cell-by-cell basis.
  • Long range DNA genome/exome sequencing, which provides long-range information for phasing structural variant detection and copy number determination on a genome/exome-wide scale. This enables identification of critical variants and discovery of key alterations, including those located at low-complexity and repetitive regions previously missed with short-read sequencing, inheritable disorders as well as in cancer.
  • De novo sequencing, which builds true diploid de novo assemblies with >10 Mb scaffold size and long-range accuracy by unlocking sample-specific sequence and producing diploid genome structure for human and non-human genomes for agricultural and environmental applications.

10X Chromium

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

Formulatrix Mantis
With as low as 6 µL dead volume, the Mantis noncontact liquid dispenser is perfect for low-input genomics applications. The user-friendly software allows for quick setup and accurate dispensing into 96-, 384-, or 1536-well plates. Combined with single-cell isolation methods (such as FACS), the Mantis offers a robust and flexible solution for standard or custom single-cell genomics applications.

Formulatrix Mantis


Quality Control

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.