Stem Cell Genomics & Microscopy Core
- Instruments and Services
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Stem Cell Genomics and Microscopy Core: Instruments and Services
BIOINFORMATICS
ROSALIND - Fast Genomics Data Analysis - OnRamp
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, 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.
CUSTOM IMAGING SOLUTIONS
GENE EXPRESSION
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.
Biomark HD - 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.
MICROSCOPY
Confocal Microscope LSM 780 - Zeiss
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
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.
SAMPLE QC
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
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
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
NanoDrop 2000 - UV-Vis Spectrophotometer
Capability:
Measure concentration and purity of DNA, RNA or protein samples.
Pricing:
- Free of charge
SAMPLE SHEARING & ISOLATION
Covaris E220 Focused-ultrasonicator - 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)
- 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
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.SINGLE-CELL LIBRARY PREPARATION
10x Chromium Controller - 10x Genomics
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 sampleOutside 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.
C1 Single-Cell Auto Prep System - Fluidigm
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
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
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
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.
