Stem Cell Genomics Core

Welcome!

 

The UC San Diego Stem Cell Genomics Core is a self-service genomics facility located at the Sanford Consortium for Regenerative Medicine. We provide state of the art equipment as well as guidance to promote the advancement of genomics research and to increase the level of control and expertise in researchers’ projects.
The Stem Cell Genomics Core's mission is to promote cutting-edge technologies and make them available to every scientist, as well as to provide advice and encourage collaborative efforts between labs and disciplines. 

 

Sanford Consortium for Regenerative Medicine
2880 Torrey Pines Scenic Drive 
La Jolla, CA 92037
USA

Leadership

Elsa Molina, Ph.D.

Email: e6molina@ucsd.edu | Office phone: (+1) 858-246-1446 | LinkedIn profile

 

 About the core

  • The Stem Cell Genomics Core is a self-service genomics facility offering state of the art equipment and cutting-edge technology.
  • Full-service and training options are available for some instruments.
  • Access to these instruments is open to UC San Diego users as well as off-campus researchers and private companies


Please, contact 
Dr. Elsa Molina (e6molina@ucsd.edu) for further information or questions.

 

Seminars & Symposia

Seminars are open to everyone and lunch is provided

2019

  • January 10th, 12:30pm - NanoCellect/ WOLF Cell Sorter
  • January 17th, 12:30pm - OnRamp Bioinformatics/ Rosalind platform (Sequencing data analysis tool for biologists)
  • February 07th, 12:30pm - Chemometec/ NucleoCounter NC-200
  • February 21st, 12:30pm - Thermo Fisher Scientific/ Single-Cell Analysis
  • March 07th, 12:30pm - Fluidigm/ Invited speaker: Dr Douglas Galasko, Professor of Neurosciences at UCSD
  • March 14th, 12:30pm - NanoString
  • March 28th, 12:30pm - 10x Genomics/ Single-cell sequencing
  • April 04th, 12:30pm - IDT/ CRISPR 
  • April 11th, 12:30pm - Thermo Fisher Scientific/ 3D cell culture presentation 
  • April 25th, 12:30pm - IDT/ NGS
  • April 29th, 12pm - Bionano Genomics/ Long-read sequencing technology
  • May 08th, New Technologies Symposium - FlowJo and SeqGeq Technologies
  • May 23rd, 12:30pm - Takara/ SMARTer single-cell and low-input DNA library preparation
  • June 13th, 12:30pm - Agilent
  • July 11th, 12:30pm - ABclonal/ Antibodies for chromatin remodeling and RNA binding protein
  • July 25th, 12:30pm - Molecular InstrumentsIn situ imaging of DNA, RNA, and proteins
  • September 05th, 12:30pm - Active Motif/ New & Notable Epigenomic Tools & Techniques
  • September 12th, 12:30pm - Qiagen/ Power of Unique Molecular Indexes for Studying Gene Regulation
  • September 26th, 12:30pm - OnRamp Bioinformatics/ Rosalind platform (Sequencing data analysis tool for biologists)
  • October 24th, 12:30pm - Takara/ Full-length transcriptomics and Epigenetic Profiling using ICELL8 single-cell technology
  • November 07th, 12:30pm - AgilentTargeted RNA Sequencing: Easier, Faster, Less Sample
  • November 14th, 12:30pm - LexogenAdvances in RNA-Seq Experiment Pipeline

 

 

 Equipment & Services

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10x Chromium Controller - 10x Genomics

NEW!

 

 

  • 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. You can capture as few as 500 cells and up to 10,000. The rule of thumb is to start with 2x the initial cell number to get around half the desired cell number out.

 > Check the instrument webpage here

 > 10x kits & solutions here

  

  • Pricing

Inside rate (reagents not included)

$50 per sample 

Outside rate (reagents not included)

$100 per sample

 

  • Links

 > 10x kits & solutions here

 > 3'V3 protocol

 > Training videos

 

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ROSALIND - Fast Genomics Data Analysis - OnRamp

NEW!

 

 

  • 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 your request at e6molina@ucsd.edu

  > Check video how it works here

  > Create your free account!

 

  • Pricing

  > Account fees

  > Unit fees via the Genomics Core

Inside rate 

$40 per unit 

Outside rate 

Custom quote

 

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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.

  > Check the instrument webpage here 

 

  • Pricing

  > Here

 

  • Links

  > Gene expression panels
  > Literature 
  > Workshops & Events

 

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Biomark HD - Fluidigm 

   

  • Capability: Gene Expression, Single-Cell Gene Expression, SNP Genotyping, Copy Number Variation, Sample Quantification for Sequencing, High-throughput qPCR, digital PCR
    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.

   Check the instrument webpage here

 

  • Pricing 

  > Here

 

  • Links

  Protocols  

  

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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. 
    Gene Expression
    Genetic Analysis
    Epigenetics
    Immune Profiling
    Multiomics

   Check the instrument webpage here

 

  • Pricing 

  > Here

 

  • Links

  > Protocols    


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

             

  • Capability: 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.

   Check the instrument webpage here

 

  • Pricing

  > Here

 

  • Links

   Protocols

 

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Confocal Microscope LSM 780 - Zeiss

                     

  • 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

  > Check the instrument webpage here

 

  • Pricing

  > Here

 

  • Links

   Protocols

 

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Covaris E220 Focused-ultrasonicator - Covaris

                        

 

  • Capability: The Covaris E220 is a targeted ultrasound device designed for the treatment of samples of many biological and chemical applications, including DNA and shear chromatin tissue homogenization, cell lysis, dissolution compound, and micronization particles. The use of acoustic energy (Adaptive Focused Acoustics ™) allows processing of 1-96 samples with precision and accuracy to samples of variable volumes.

DNA shearing
RNA fragmentation
Chromatin shearing
DNA and RNA extraction from FFPE tissues
Protein extraction
DBS DNA extraction
Microbe extraction for MALDI-TOF analysis

Check the instrument webpage here 

 

  • Pricing

> Here

 

  • Links

Protocols
User manual
Literature

           

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MiSeq - illumina 

  • Capability: Miseq is dedicated to small genome, amplicon and targeted gene panel sequencing such as: 

Highly Multiplexed Amplicon Sequencing
Targeted Resequencing 
Small Genome Sequencing
De Novo Sequencing
CHiP Seq
Small RNA Sequencing
Library QC for HiSeq

 Check the instrument webpage here 

 

  • Pricing

 > Here

 

  • Links

  Protocols 
 >  Library preparation kits
 >  MiSeq support



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NanoDrop 2000 Spectrophotometer - Thermo Fisher Scientific

 

                          

 

  • Capability: Quantify and assess purity of DNA, RNA, Protein and more. Spectrophotometer with patented sample retention technology that measure sample volumes as small as 0.5μL.

 Check the instrument webpage here

 

  • Pricing

FREE of charge 

 

  • Links

  User manual

 

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ProFlex 3x32-well PCR System - Thermo Fisher Scientific

                    

  • 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.

   Check the instrument webpage here

 

  • Pricing

FREE of charge

 

  • Links

  > User guide

 

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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 by using as little as 1 μL of sample. 

  > Check the instrument webpage here

 

  • Pricing

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

 

  • Links

  > Protocols

 

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TapeStation 2200 - Agilent           


       

 

  • Capability: DNA, RNA, protein, and genomic DNA qualification and quantification.

  > Check the instrument webpage here

 

  • Pricing

 > Here

 

  • Links

  > User guide & Protocols
  > DNA ScreenTape & Reagents
  > RNA ScreenTape & Reagents

 

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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.

   Check the instrument webpage here

 

  • Pricing

FREE of charge 

 

  • Links

  > User guide

 

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Training & Technical Assistance

 

  • Reservation & Info: Please contact Elsa Molina at e6molina@ucsd.edu

  • Pricing

 > Here

 

 

Core Location & Hours of Operation

Sanford Consortium for Regenerative Medicine
2880 Torrey Pines Scenic Drive
La Jolla, CA 92037 

The Stem Cell Genomics Core is open 24/7 for registered and trained users.

Training and full-service hours are from 9am-5pm, Monday - Friday.

 

Links & Resources

UC San Diego Stem Cell Genomics Core

UC San Diego Human Embryonic Stem Cell Core Facility

UC San Diego Stem Cell Program

Sanford Consortium for Regenerative Medicine

 

Contacts

Name Role Phone Email Location
Elsa Molina, Ph.D.
Director, Stem Cell Genomics Core
 
858-246-1446
 
e6molina@ucsd.edu
 
SCRM Room 1318
 
Jake Banfield-Weir
Manager, UC San Diego Stem Cell Program
 
858-822-3197
 
jbanfieldweir@ucsd.edu
 
SCRM Room 3314
 

Map


https://www.google.com/maps/@32.8884224,-117.2430848,15z