The Genomics Core

 

The Genomics Core Laboratory provides current technology in the area of functional genomics for the research community at the Gladstone Institutes and UCSF at reasonable prices.

  • Affymetrix GeneChip Expression Array

    • Conventional human, mouse, rat, yeast, Drosophila, and other model organism arrays
    • Human, mouse, and rat whole transcript arrays covering most well annotated transcripts
    • Human, mouse, and rat exon specific arrays with ~1.5 million probes for detection of splice variants
    • We have robust whole transcript amplification protocols using less than 1ng of total RNA


  • Affymetrix miRNA GeneChips
    • 100 Percent miRBase v15 coverage, all 131 organisms (15,644 probe sets)
    • 2,334 snoRNAs and scaRNAs
    • 2,202 probe sets unique to pre-miRNA hairpins


  • Library Preparation and QC services for Illumina MiSeq, GAIIX and HiSeq 2000 Sequencing Instruments
    • Currently we offer Paired End Genomic DNA library, RNA-Seq library, ChIP-Seq, miRNA-Seq, and Custom Amplicon library preparation and QC for Illumina MiSeq, GAIIX and HiSeq sequencing instruments.
    • Under development are Mate Pair and Fosmid library preparation for Illumina MiSeq, GAIIX and HiSeq sequencing instruments.


At Gladstone we have the Illumina MiSeq sequencer which is suitable for miRNA-Seq, library QC and Custom Amplicon sequencing. 

 

RNA-Seq, ChIP-Seq and Paired-End Genomic libraries are made and QCed at Gladstone but are sent to either the Parnassus or Mission Bay HiSeq laboratories for sequencing.


  • Agilent BioAnalyzer, Nanodrop and QPCR access and services for RNA and DNA samples
    • RNA QC analysis to determine potential RNA degradation and accurate quantification.
    • Illumina library QC analysis to determine potential adapter artifacts and accurate quantification of RNA samples.

 

Genomics Core Director

Robert B. Chadwick, PhD

Gladstone Building Room 209

1650 Owens Street

San Francisco, CA  94158

robert.chadwick@gladstone.ucsf.edu

(415) 734-2799

 

 

Genomics Core Facility Members


Yanxia Hao
Jim McGuire

Linda Ta

 

Contact us at genomics-lab@gladstone.ucsf.edu


Location

J. David Gladstone Institutes

Gladstone Building 2nd Floor

1650 Owens Street

San Francisco, CA 94158

 

Hours of Operation

Monday - Friday

8:30 AM - 4:30 PM

   
   

Visit Our Web Site for More Detailed Information:

http://labs.gladstone.ucsf.edu/genomics/

 

 

 

Contacts

Name Role Phone Email Location
Robert Chadwick
Genomics Core Director
 
(415) 734-2799
 
robert.chadwick@gladstone.ucsf.edu
 
Room 209 Gladstone Building
 
Linda Ta
Senior Research Technologist
 

 
genomics-lab@gladstone.ucsf.edu
 
2nd Floor
 
Jim McGuire
Research Technologist
 

 
genomics-lab@gladstone.ucsf.edu
 
2nd Floor
 
Yanxia Hao
Senior Research Technologist
 

 
genomics-lab@gladstone.ucsf.edu
 
2nd Floor
 

Services

Name Description Price
 

Microarray Services (see under Affymetrix in our service list)
 

These arrays are biotin labeled thus are always a one color design

 

 

Sample Submission Requirements:

 

*All RNA samples must be DNase treated* (for non-miRNA array and sequencing projects)

 

Samples should be submitted at uniform concentration and volume, or handling charges apply.

 

We recommend Qiagen RNAEasy or miRNAEasy kits for RNA isolation.

 

Recommended total RNA: 50ng in 10 ul (5ng/uL) for Gene 1.0 ST arrays, 100ng in 5uL (100ng/uL) for Gene 2.0 ST arrays, 1ug in 10uL (100ng/uL) for miRNA array projects.

We can work with lesser amounts down to 500 pg for non-miRNA array projects, but this requires more expensive reagents.  Unused RNA can be returned upon request.

miRNA-Seq libraries require a minimum of 1ug of total RNA in 5 ul volume or 1 ng of purified miRNA in 5 ul volume.

 

All samples must be submitted in 1.5ml eppendorf tubes

To avoid confusion use "simple" sample names.  Do not use a backslash (/) as part of the sample name

 

Affymetrix arrays must be provided by customer

 

 
*
 

I.M.A.G.E. Consortium Clones

Individual clones and sets of clones from the world's largest public collection of genes are available from the Genomics Core for a small service fee.  You can search for your clone of interest at the following links

https://www.openbiosystems.com/Help/Clone%20Query%20Instructions/

http://mgc.nci.nih.gov/

 

 

 
*
Illumina Library Preparation Services 

For Illumina and Ion Torrrent library preparation services please discuss experimental design with Bob Chadwick at (415) 734-2799 or email at robert.chadwick@gladstone.ucsf.edu

There are multiple methods of library preparation and the experimental approach depends on the sample type and nucleic acid quantity and quality.

 

We offer ChIP-Seq, RNA-Seq, Paired-End Genomic, and miRNA-Seq library prep and QC services.

 

At Gladstone we have the Illumina MiSeq sequencer which is suitable for miRNA-Seq and Custom Amplicon sequencing. 

 

RNA-Seq, ChIP-Seq and Paired-End Genomic libraries are made and QCed at Gladstone but are sent to either the Parnassus or Mission Bay HiSeq laboratories for sequencing.

 

Note we strongly recommend shearing using the Covaris for ChIP-DNA.  Enzymatic and probe based shearing give highly variable results.

 

Quality of the source material for library generation by the Gladstone Genomics Core:

RNA-Seq

High quality total RNA (BioAnalyzer RIN > 7), absorbance ratio 260/280 ~1.8

Chip-Seq

Purified IP DNA with majority of fragments within size range 200 - 500 bp

gDNA-Seq

High quality DNA, single band on agarose gel, absorbance ratio 260/280 ~2
 
*
RNA QC 

The quality of total RNA is pertinent to success of many experiments.  We can check the quantity of RNA on a nanodrop, and the quality on an Agilent Bioanalyzer.  The Agilent 2100 BioAnalyzer is a rapid, high resolution capillary electrophoresis system used to analyze RNA or DNA samples. 


Sample Requirements

Total RNA Nano       50-500ng/uL  (12 samples/chip)

Total RNA Pico        <5ng/uL        (11 samples/chip)

Small RNA              50pg-2ng/uL  (11 samples/chip)

DNA 1000               10-50ng/uL    (12 samples/chip) 

DNA High Sensitivity 300-500pg/uL (11samples/chip)

 
*
Consultation    *
Covaris Access Fee 

Yearly access fee to cover the Covaris S2 service contract

 
*
IMAGE Clone 

I.M.A.G.E. Consortium Clones

Individual clones and sets of clones from the world's largest public collection of genes are available from the Genomics Core for a small service fee.  You can search for your clone of interest at the following links

https://www.openbiosystems.com/Help/Clone%20Query%20Instructions/

http://mgc.nci.nih.gov/

 
*
Ion Torrent Proton Sequencing 

Ion Torrent V3 200 sequencing (single end 200 cycle).

 
*
miRNA Isolation and Purification 

Purification of miRNA from total RNA or non-human tissue or cells.  We are a BSL1 laboratory and can't isolate nucleic acids from human cells or blood.

 
*
Nanodrop 

Access fee per lab/per year

 
*
RNA Isolation 

Isolation of RNA from non-biohazardous cells or tissue.  We cannot isolate RNA from human tissue or blood.

 
*
Rush Service 

We usually can turn most projects around in 2 to 4 weeks.  For rush service we charge $300 per batch of 12 samples.

 
*
Sample Handling Charge 

If your samples need to be concentrated prior to processing, sample handling charges will be applied.

 
*
Affy GeneChip Service: Amplification, Label and Hyb/Stain/Scan (Non-degraded RNA Expression Microarrays) 

This is our routine microarray service

500 pg minimum; NuGEN Pico V2 kit (new)

We require the quality of each RNA to be checked by the Bioanalyzer.

 
*
Agilent Bioanalyzer - Full service 

Charges are per chip.

RNA Concentration Ranges

For the Pico Chip (11 samples on a chip)

   30 pg/ul to 5 ng/ul total RNA concentration range.

For the Nano Chip (12 samples on a chip)

   50 ng/ul to 500 ng/ul total RNA concentration range

 Samples less than 50 ng/ul are diluted and run on Pico Chips

DNA Concentration Ranges

   10-50 ng/ul (12 samples/chip)

   DNA <10ng/ul requires DNA High Sensitivity chips (see below)

 
*
ChIP-Seq Library (NuGen) 

We request that users do their own Chromatin Immunoprecipitation (ChIP).  A minimum of 5 ng of ChIP-DNA is needed to make a library.

Note getting good specificity in the initial ChIP is critical to obtaining good results.  Different antibodies can give highly variable results.

Also, shearing by probe based methods is not recommended.  The Covaris S2 sonicator or Bioruptor give best results. 

The gel image below demonstrates chromatin sheared below 500 bp using the Covaris S2 sonicator at 2 to 12 minutes of shearing.

Better shearing results require 4 or more minutes of shearing.

 

Covaris ChIP Shearing

 

Note your DNA must be sheared to a mean size of 350 bp for Illumina library preps or 200 bp for Ion Torrent library preps.  Please upload a picture of your ChIP-DNA to insure that it is of the correct size. 


ChIP-DNA samples which do not follow our recommended guidelines will be charged for failed library preps.

 

 

 
*
Covaris S2 Sonicator Tubes 

Covaris tubes are sold directly by Covaris or for your convenience are available through the Core. 

Individual Covaris micro tubes (6 x 16 mm) are available for purchase.

 
*
PE150 

Paired end 150 cycle MiSeq run

 
*
Affy GeneChip Service: Amplification, Label and Hyb/Stain/Scan (Degraded RNA Expression Microarrays) 

50 pg minimum; NuGEN FFPE V3 kit (new)

 
*
Agilent Bioanalyzer - Full service (DNA High Sensitivity) 

Charges are per chip.

A minimum concentration of 5 ng/ul is needed to run on the DNA High Sensitive chip.

 
*
Covaris Training 

The Covaris S2 sonicator is used to precisely shear nucleic acids to a specified size.  It works by sending acoustic energy wave packets from a dish-shaped transducer that converges and focuses to a small-localized area. At this focal point the mechanical energy may be controllably focused into the sample of interest without directly contacting the sample.

Although we don't charge a per use fee for this instrument.  We request that each lab contribute a few hundred dollars each year for the service contract.  Labs which don't contribute to the service contract will be removed from the approved user list.

The Covaris training is more productive and cost effective if you use your own samples for the training.  Users must provide or purchase their own tubes for the training.

 

 
*
PE250 

Paired end 250 cycle MiSeq run.

 
*
RNA-Seq Library Preparation 

We can make RNA-Seq libraries from limited amounts of RNA such as those isolated from Laser Capture Microdissected tissue.  However, best results are obtained from non-degraded RNA.  Please check the quality of your isolated RNA prior to submission or fill out a Bioanalyzer QC request form and the Core will run the bioanalyzer for you. 

Note due to the multiple methods of making RNA-Seq libraries it is recommended you discuss experimental strategy with Bob Chadwick prior to designing your experiment.  We strongly recommend random priming for reverse transcription rather than oligo-dT methods which introduce 3' bias in your library.

 
*
Agilent Bioanalyzer - Full service including Training 

Charges are per chip.

RNA >30pg/ul and DNA >50 ng/ul

This is a full service request but training is included.  An appointment with a Core staff member is required.

Training is reserved for frequent users only. 

 
*
Covaris S2 Sonicator Tubes bulk (25 tubes) 

Covaris tubes are sold directly by Covaris or for your convenience are available through the Core.

Covaris micro tubes (6 x 16 mm) are available for purchase in bags of 25 tubes.

 
*
ERCC Spike-In Controls for RNA-Seq Libraries 

Variation in RNA expression data can be attributed to a variety of factors including the quality of the starting material, the level of cellularity and RNA yield, the platform employed, and the person performing the experiment. To control for these sources of variability, a common set of external RNA controls has been developed by the External RNA Controls Consortium (ERCC), an ad-hoc group of academic, private, and public organizations hosted by the National Institute of Standards and Technology (NIST). The controls consist of a set of unlabeled, polyadenylated transcripts designed to be added to an RNA analysis experiment after sample isolation, in order to measure against defined performance criteria.

 

Each Spike-In Mix is ready to be diluted and added to the RNA sample before processing for gene expression measurements.  Spike-In Mix 1 is added to control RNA and Spike-In Mix 2 is added to experimental RNA samples (or vice versa).

http://products.invitrogen.com/ivgn/product/4456739

 

 
*
RNA Sample Amplification (no labeling) 

500 pg minimum; NuGEN Pico V2 kit (new)

 
*
SE50 

Single end 50 cycle MiSeq run.

 
*
Cell Lysate Preparation-amplification only 

Supply sample in lysis buffer with kit

 
*
KAPA QPCR Library Quantification 

Quantitative PCR (qPCR) is inherently well-suited for next-generation sequencing library quantification:

  • qPCR specifically quantifies only PCR-competent DNA molecules,
  • is highly sensitive allowing accurate quantification of low concentration libraries

 We require that all libraries be QC'd by Bioanalyzer and quantified by QPCR prior to MiSeq sequencing.

NOTE: Quantitative PCR (qPCR) is included in the price of library preparations made by the Core.

 
*
Paired-End Genomic Library Preparation 

A minimum of 1 nanogram is needed to make a paired end genomic library.  However, better results will be obtained if you can give us 50 ng or more.

For the initial shearing of the genomic DNA the ideal concentration is 30 ng/ul in a minimum of 25 ul of TE buffer.

 
*
Agilent Bioanalyzer - Equipment and Reagents (Training Required) 

Charges are per chip.

After training, researcher uses Core instrument and reagents to run his/her own RNA or DNA.

 
*
Cell Lysate Preparation-One Direct 

Supply sample in lysis buffer with kit

 
*
Illumina Whole Exome Library Preparation 

The Nextera Rapid Capture Exome library preparation and exome enrichment technology delivers 37 Mb of exonic content and requires as little as 4 Gb of sequencing for ~50X coverage of the exome.

 
*
Agilent Bioanalyzer-Equipment and Reagents (DNA High Sensitivity) 

After training, researcher uses Core instrument and reagents to run his/her own DNA.

Charges are per chip.

A minimum concentration of 5 ng/ul is needed to run on the DNA High Sensitive chip.

 
*
Cell Lysate Preparation-post amplification labeling 

NuGEN One Direct amplified samples for frag/labeling

 
*
Illumina Expanded Whole Exome Library Preparation 

Increase coverage to UTRs and miRNA with Expanded Exome

An expanded whole exome kit is also available for researchers seeking coverage of additional regions. The Nextera Rapid Capture Expanded Whole Exome delivers 62 Mb of genomic content, including exons, untranslated regions (UTRs), and miRNA.

 
*
Extra Data Normalization with RMA 

Additional normalization by RMA or Plier.  This is included for the first experiment.

 
*
miRNA-Seq Library Preparation (Ion Torrent ONLY) 

We do not recommend Illumina sequencing for miRNA-Seq due to severe ligation bias in their protocols.  Ion Torrent sequencing gives much better results.  We only make miRNA-Seq libraries for the Ion Torrent Proton sequencer.

For purification of miRNA we recommend the mirVana kit from Life Tech (Invitrogen) or miRNA-Easy kits from Qiagen.   We recommend starting with 10 micrograms of total RNA and purifying the miRNA with the mirVana kit.  We can make miRNA-Seq libraries from as little as 1 microgram of starting total RNA but a reduced number of miRNA-Seq reads will be obtained.

 
*
C1 Single Cell Library Prep for Illumina Sequencing 

The Fluidigm C1™ Single-Cell Auto Prep System for DNA sequencing enables one workflow to discover genetic variants in heterogeneous samples. Engineered specifically to work with single cells, the C1™ System takes an entirely new approach to streamline cell processing. Based on innovative microfluidic technology at nanoliter-scale reaction volumes, the C1™ System delivers consistent results with the lowest sample requirements.


Key Features:

Highest throughput—Get higher efficiency with parallel sequencing preparation of 96 individual cells
Ultra sensitive—Compatible with as little as 6 pico grams of single-cell DNA input
 
*
miRNA labeling 

miRNA labeling requires  1 ug of total RNA in a maximum volume of 10 ul.   If you use TE to resuspend your RNA use a reduced concentration of EDTA with no more than 0.1 mM of EDTA (ie low TE).

For purification of total RNA which retains the small RNAs we recommend the miRNA-Easy kits from Qiagen.

 
*
DNase Treatment 

We strongly recommend that all RNA samples be DNase treated prior to library creation.  However, we can DNase treat your RNA samples for a small fee.

 
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Service List


Search available services: View: by category alphabetically
Affymetrix (8)
Bioanalyzer (5)
Consultation (1)
Covaris S2 Sonicator (4)
Ion Torrent Proton Sequencing (1)
KAPA QPCR Library Quantification (1)
Library Preparation (9)
MiSeq Sequencing (3)
Service (6)