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Stem Cell Genomics and Microscopy Core: Instruments and Services

 

10x Chromium Controller - 10x Genomics


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10x Chromium Controller 

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Capability:

The Chromium Controller rapidly and efficiently combines large partition numbers with a massively diverse barcode library to generate >100,000 barcode-containing partitions in a matter of minutes. The Chromium Controller fits on a standard laboratory bench and allows a user to run any Chromium Solution, from genome to single cell analysis.

Pricing:

Inside User rate (reagents not included):

$50 per sample 

Outside User rate (reagents not included):

$100 per sample

*Inside users include UC San Diego, Salk Institute for Biological Studies, Sanford Burnham Prebys Medical Discovery Institute, and La Jolla Institute for Immunology.

Note: Reagents for the Single Cell Gene Expression Profiling Assay (3'RNA) are available for purchase. Please inquire with Dr. Elsa Molina for more information.

Please inquire with Dr. Elsa Molina for more information.

TapeStation 2200 - Agilent

 

tape station

TapeStation 2200 - Agilent

Capability:

DNA, RNA, protein, and Genomic DNA Qualification and Quantification

Pricing:

Tape Station (Reagents and consumables not included)

  • Self service (inside* user rate): $2.50 per sample
  • Self service (outside user rate): $6 per sample
*Inside users include UC San Diego, Salk Institute for Biological Studies, Sanford Burnham Prebys Medical Discovery Institute, and La Jolla Institute for Immunology.

Note: Some consumables are also available for purchase. Please inquire with Dr. Elsa Molina for more information.

Protocols:

Please inquire with Dr. Elsa Molina for more information.

ROSALIND - Fast Genomics Data Analysis - OnRamp

 

Rosalind Analytics

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Capability:

The ROSALIND™ platform provides a biologist-friendly experience with instant results to visualize, interpret and discover more in your data. ROSALIND™ offers researchers, biologists and life scientists' solutions to analyze their own data without needing prior bioinformatics experience. ROSALIND is intended to speed up and simplify the process of genomic data analysis from experiment setup and QC to interactive data visualization and interpretation. 

Experiment Types:

NanoString assays, RNA-seq, ChiP-seq, and Small RNA-seq. 

For other assays, please submit a request at e6molina@ucsd.edu

Pricing:

Inside rate: 

$40 per unit 

Outside rate: 

Custom quote - Contact e6molina@ucsd.edu

Please inquire with Dr. Elsa Molina for more information.

Thermal Cycler C1000 Touch 96w - Bio-Rad

 

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Thermal Cycler C1000 Touch 96w - Bio-Rad

Capability: 

96-well fast reaction module to perform cDNA synthesis or to run PCR reactions in plate and tube formats. Quickly and easily identify optimal annealing temperatures by using the programmable temperature gradient.

Pricing:

Free of charge

Please inquire with Dr. Elsa Molina for more information.

Olympus FV1000 Confocal

Instrument: 

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Olympus FV1000 Confocal

Schedule Type: 

Microscopes

Capability:

This model features the world's first twin scan system. This system enables time-resolved spectroscopy of living intercellular contents and also makes it possible to analyze objects down to a 2nm wavelength resolution.

Pricing:

$40

Covaris E220 Focused-ultrasonicator - Covaris

 

covaris

Covaris E220 Focused- ultrasonicator 

Capability:

DNA Fragmentation, Chromatin Shearing

Pricing:

Covaris E220

  • Self service (inside* user rate): $35 per hour (minimum 1 hour)
  • Self service (outside user rate): $70 per hour (minimum 1 hour)
Covaris E220
  • Self service (inside* user rate): Full plate $100
  • Self service (outside user rate): Full plate $200

Microtubes [ 130uL PN 520052; 320uL, 500uL PN 500452]

  • Self service (inside* user rate): $5 each
  • Self service (outside user rate): $10.50 each

Reagents and consumables not included. 

*Inside users include UC San Diego, Salk Institute for Biological Studies, Sanford Burnham Prebys Medical Discovery Institute, and La Jolla Institute for Immunology.

Protocols:

Please inquire with Dr. Elsa Molina for more information.

Biomark HD - Fluidigm

 

biomark

Biomark - Fluidigm

Capability:

Gene Expression, Single-Cell Gene Expression, SNP Genotyping, Copy Number Variation, Sample Quantification for Sequencing

High-throughput qPCR
96 assays by 96 samples =  9,216 reactions
48 assays by 48 samples = 2,304 reactions
*Protocols for TaqMan and EvaGreen available. Not compatible with SYBRGreen.

Pricing:

  • Self service (inside* user rate): $300
  • Self service (outside user rate): $600

Reagents and consumables not included. 

*Inside users include UC San Diego, Salk Institute for Biological Studies, Sanford Burnham Prebys Medical Discovery Institute, and La Jolla Institute for Immunology.

Protocols:

Please inquire with Dr. Elsa Molina for more information.

C1 Single-Cell Auto Prep System - Fluidigm

 

c1

Fluidigm C1

Capability:

The automated solution for single-cell genomics research. The innovative C1 system carefully isolates single cells into individual reaction chambers in the exclusive Fluidigm integrated fluidic circuit (IFC). The optically clear IFC lets you automatically stain captured cells and examine them by microscopy for viability, surface markers or reporter genes. After staining, cells are automatically lysed, and the template is quickly prepared for qPCR or sequencing analysis—all in as little as four hours. Provides pre-amped cDNA, total RNA-seq libraries, full-length mRNA-seq from single cells.

Pricing:

C1 Fluidigm

  • Self service (inside* user rate): $600
  • Self service (outside user rate): $1,200

C1 Fluidigm-Failed Run/Insufficient Load

  • Self service (inside* user rate): $75
  • Self service (outside user rate): $150

Reagents and consumables not included. 

*Inside users include UC San Diego, Salk Institute for Biological Studies, Sanford Burnham Prebys Medical Discovery Institute, and La Jolla Institute for Immunology.

Protocols:

Please inquire with Dr. Elsa Molina for more information.

MiSeq - illumina

 

miseq illumina

MiSeq - illumina

Capability: 

Highly multiplexed amplicon sequencing, Targeted Resequencing, Small Genome Sequencing, De Novo sequencing, CHiP Seq, Small RNA Sequencing, Library QC for HiSeq

*MiSeq not recommended for deep sequencing or sequencing of large genomes. For deep sequencing on the HiSeq, please contact the UCSD IGM Genomics Center

Pricing:

MiSeq 50, 100 and 150 cycles

  • Self service (inside* user rate): $200
  • Self service (outside user rate): $375

MiSeq 300 cycles

  • Self service (inside* user rate): $255
  • Self service (outside user rate): $375

MiSeq 500 and 600 cycles

  • Self service (inside* user rate): $295
  • Self service (outside user rate): $375

MiSeq Nano and Micro

  • Self service (inside* user rate): $200
  • Self service (outside user rate): $375

*Inside users include UC San Diego, Salk Institute for Biological Studies, Sanford Burnham Prebys Medical Discovery Institute, and La Jolla Institute for Immunology.

Protocols:

Please inquire with Dr. Elsa Molina for more information.

NanoDrop 2000 Spectrophotometer - Thermo Fisher Scientific

 

Nano Drop

NanoDrop 2000 - UV-Vis Spectrophotometer

Capability: 

Measure concentration and purity of DNA, RNA or protein samples.

Pricing:

  • Free of charge
Please inquire with Dr. Elsa Molina for more information.

nCounter MAX Analysis System - NanoString

 

Capability: Detect and quantify RNA, DNA, and protein from the same sample in as little as 15 minutes and up to 770 targets with the nCounter MAX.

Pricing:

Inside* User Rates

  • 12 to 35 samples: $32 per sample
  • 36 samples or more: $29 per sample

Outside User Rates

  • 12 to 35 samples: $65 per sample
  • 36 samples or more: $59 per sample

*Inside users include UC San Diego, Salk Institute for Biological Studies, Sanford Burnham Prebys Medical Discovery Institute, and La Jolla Institute for Immunology.

Please inquire with Dr. Elsa Molina for more information.

Confocal Laser Scanning Biological Microscope FV1000 FluoView with Two-Photon - Olympus

 

olympus fv1000

Confocal Laser Scanning Biological Microscope FV1000 FluoView with Two-photon - Olympus

Capability: 

The Olympus FluoView FV1000 opens new frontiers in live cell imaging with advanced technologies that provide improved sensitivity and high scan speeds for imaging live organisms with minimal specimen damage.

The innovative, Olympus-developed SIM Scanner incorporates two independent, fully synchronized laser scanners in a single compact design for simultaneous laser stimulation and confocal observation. Rapid cellular reactions that occur during or immediately following laser stimulation may now be captured without a time lag. Such studies of rapid cellular responses can provide important insight into how various cellular mechanisms operate. This makes the FV1000 ideal for such advanced techniques as FRAP, FLIP, uncaging, photoactivation and photoconversion.

Pricing:

  • Self service (inside* user rate): $45 per hour
  • Self service (outside user rate): $90 per hour

*Inside users include UC San Diego, Salk Institute for Biological Studies, Sanford Burnham Prebys Medical Discovery Institute, and La Jolla Institute for Immunology.

Please inquire with Dr. Elsa Molina for more information.

ProFlex 3x32-well PCR System - Thermo Fisher Scientific

 

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ProFlex 3x32-well PCR System

User Guide

Capability: 

The ProFlex™ 3x32-Well PCR System is the latest in line of Applied Biosystems® thermal cyclers. The instrument allows you to run three experiments at once, access the system remotely (and conveniently) through a mobile app, and optimize your PCR quickly and efficiently with better-than-gradient VeriFlex™ blocks.

Pricing:

Free of Charge

Please inquire with Dr. Elsa Molina for more information.

Qubit 3.0 Fluorometer - Thermo Fisher Scientific

 

qubit

Qubit 3.0 Fluorometer

Capability: 

Powerful, dual-core processor quickly and accurately quantifies DNA, RNA, and protein, in <5 seconds per sample. Uses as little as 1 μL of sample.

Pricing

FREE of charge (if reagents and Qubit tubes are not included)

Self service (inside* user rate):

  • $1.50 per sample (tubes included/ reagents not included)
  • $4.00 per sample (reagents included)

Self service (outside user rate):

  • $3.00 per sample (tubes included/ reagents not included)
  • $8.00 per sample (reagents included)

*Inside users include UC San Diego, Salk Institute for Biological Studies, Sanford Burnham Prebys Medical Discovery Institute, and La Jolla Institute for Immunology.

Note: Some consumables are also available for purchase. Please inquire with Dr. Elsa Molina for more information.

Protocols:

Please inquire with Dr. Elsa Molina for more information.

Confocal Microscope LSM 780 - Zeiss

 

zeiss lsm 710

Zeiss LSM 780 Confocal Microscope

Capability:

The new illumination and detection design of the LSM 780 confocal microscope brings complete freedom to your fluorescence microscopy. You work with up to ten dyes and use continuous spectral detection across the complete wavelength range. LSM 780 enables confocal microscopy for a wide variety of applications.With the inverse Axio Observer from Carl Zeiss, LSM 780 offers you unrivalled confocal microscopy in cell and developmental biology. Upright stands such as Axio Imager or Axio Examiner offer you have all the equipment you need to record neurobiological, physiological and developmental relationships to an exceptional standard.

Objectives:

10x, 20x, 40x, 60x, and 100x

Pricing:

  • Self service (inside* user rate): $30 per hour
  • Self service (outside user rate): $60 per hour

*Inside users include UC San Diego, Salk Institute for Biological Studies, Sanford Burnham Prebys Medical Discovery Institute, and La Jolla Institute for Immunology.

Please inquire with Dr. Elsa Molina for more information.

Training and Technical Assistance

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Pricing:

  • Training (inside* user rate): $55 per hour (minimum 1 hour) in addition to instrument run charge
  • Training (outside user rate): $110 per hour (minimum 1 hour) in addition to instrument run charge
  • Labor for full service
    • Inside* user rate: $95 per hour in addition to instrument run charge
    • Outside user rate: $190 per hour in addition to instrument run charge 

*Inside users include UC San Diego, Salk Institute for Biological Studies, Sanford Burnham Prebys Medical Discovery Institute, and La Jolla Institute for Immunology.

Please contact Dr. Elsa Molina for further training information.