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Stem Cell Genomics and Microscopy Core: Instruments and Services

 

BIOINFORMATICS

ROSALIND - Fast Genomics Data Analysis - OnRamp

 

Rosalind Analytics

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Check the Video to see How it Works

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, scRNA-seq, Total RNA-seq, ChiP-seq, and Small RNA-seq.

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

Pricing:

Inside rate: 

$32 per unit 

Outside rate: 

Custom quote - Contact e6molina@ucsd.edu

Please inquire with Dr. Elsa Molina for more information.

DIGITAL SPATIAL PROFILING

GeoMx Digital Spatial Profiler - NanoString

Instrument:

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GeoMx Digital Spatial Profiler

The GeoMx Digital Spatial Profiler (DSP) provides morphological context in spatial transcriptomics and spatial proteomics experiments from just one slide.
 
For Capability: The GeoMx DSP workflow seamlessly integrates with current histology or genomics workflows to help researchers obtain robust and reproducible spatial multiomics data quickly. Whole tissue sections, FFPE or fresh frozen, can be imaged and stained for RNA or protein.

 

Internal Price
First Slide: $1,000 
Extra Slides: $325
External Price
First Slide: $2,000
Extra Slides: $650.

GENE EXPRESSION

nCounter MAX Analysis System - NanoString

 

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nCounter® MAX Analysis System

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

  • $540 per cartridge

Outside User Rates

  • $1080 per cartridge

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

Stem Cell Characterization Panel

Please inquire with Dr. Elsa Molina for more information.

MICROSCOPY

Confocal Microscope LSM 780 - Zeiss

 

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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.

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

 

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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.

Keyence Fluorescence Microscope Bz-X Series

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Keyence BZ-X800 Fluorescence Microscope

VIdeo overview of the system

Capability: 

Fluorescence observation can be performed anywhere in the lab just by closing the front panel to create a built-in darkroom. Exposure time can be individually adjusted while overlaying images in real time on one screen. A fully-motorized setup allows the user to control the XY/Z-axis stage, aperture stop, phase contrast rings, neutral density filter, monochrome/color camera switching, shutter speed, filter turret, and lens turret. The large, fully-motorized XY stage allows for rapid scanning and observation of slides, dishes, and multi-well plates. This allows researchers to observe their samples faster and more efficiently, leading to quicker results. The Navigation and Stage View functions facilitate the simultaneous observation of multiple samples, without ever losing sight of areas of interest. The cooled monochrome CCD enables highly-sensitive imaging of weak fluorescent signals, which allows for accurate brightness quantification for applications measuring protein expression. Additionally, a color filter allows one-click transition between monochrome and high-resolution color observation. Unlike a color camera, the color filter is not attached to the CCD, which can lead to distortions during fluorescence viewing. Quickly capture a wide-area image of an entire tissue section just by specifying its outer edges. All fields-of-view will be automatically captured and merged together to create a seamless, high-resolution image of up to 50,000 x 50,000 pixels. XY stitching can be combined with the Z-stack function to create fully focused images of thick or unevenly cut sections.  Overview of the BZ-X800/BZ-X8101-5BZ-X800 User’s ManualGetting Started1Multi-dimensional time lapsePerform time-lapse experiments with bright field, phase contrast, and fluorescence samples by specifying the capture settings and interval time. By using the Multi-point function, up to 99 different areas of interest can be captured in a given interval, each with unique capture settings such as magnification, exposure time, etc. This drastically improves the efficiency of time-lapse experiments, allowing for multiple samples to be observed simultaneously throughout the duration of the experiment. Capture and analyze multiple samples simultaneously and collectively by the image cytometer function. Easy and direct captures can be made with the same condition to multiple wells.Analysis conditions can be specified easily by referring to images. Since many samples can be analyzed simultaneously, more reliable statistical data can be acquired effectively. The chronological change of a living cell can be confirmed by combination with the time lapse.

Pricing:

  • Self service : $30 per hour

Please inquire with Dr. Elsa Molina for more information.

SAMPLE QC

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): $3 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.

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):

  • $1.00 per sample (tubes included/ reagents not included)
  • $3.00 per sample (all included)

Self service (outside user rate):

  • $2.00 per sample (tubes included/ reagents not included)
  • $6.00 per sample (all 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.

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.

SAMPLE SHEARING & ISOLATION

Covaris E220 Focused-ultrasonicator - Covaris

 

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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.

SEQUENCING

MiSeq - illumina

 

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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 (Reagents not Included):

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.

SINGLE-CELL LIBRARY PREPARATION

Chromium X - 10x Genomics


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10x Chromium Controller 

Download Technology Brochure 

Capability:

Chromium X makes single-cell analysis easy, reliable, and scalable thanks to its proprietary Next GEM technology. The key to this technology is the ability to generate hundreds of thousands of single-cell partitions, each containing an identifying barcode for downstream analysis. Combined with an innovative reagent delivery system and turnkey software analysis tools, we enable the discovery of previously inaccessible biological information. In addition, the Chromium X features fully integrated, automated system support in the 10x Genomics Cloud, complete with temperature control and improved access to support.

Pricing:

Inside User rate (reagents not included):

$60 per sample 

Outside User rate (reagents not included):

$120 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.

C1 Single-Cell Auto Prep System - Fluidigm

 

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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.

THERMOCYCLER

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.

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.

TRAINING & FULL-SERVICE

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.