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 MicroArrays

    • 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.
    • miRNA-Seq Library Preparation (Ion Torrent ONLY)

 

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.

The Core is aware that sometimes it not possible to get good quality RNA and DNA, and we are willing to work with researchers to process difficult samples.  In fact, the Core has had considerable success with generating sequencing and microarray data from less than ideal samples.  However, investigators are responsible for all costs associated with failed reactions due to poor quality or degraded starting material. 

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 or by appointment.

   
   

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
Consultation    *
Covaris Access Fee 

Yearly access fee to cover the Covaris S2 service contract.

Permits all members of lab access for one year: "Trained users only"

 
*
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

 
*
PE75 (V3) 

Paired end 75 cycle MiSeq run (or SE150) with V3 chemistry.

Before libraries are run on the MiSeq they will require Kapa qPCR and Bioanalyzer analysis.

 
*
RNA Isolation 

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

 
*
Rush Service 

After samples are received by the Core, turn around time for most projects is usually 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.

Charges are per hour.

 
*
Training on MiSeq Sequencer 

Training on the Illumina MiSeq sequencer.  Users must purchase their own reagents from Illumina.

Service is available to Gladstone researchers ONLY.

 

We strongly recommend  libraries be quantified by Kapa qPCR and evaluated by the bioanalyzer before running the MiSeq.

 
*
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)

Please check the quality of your isolated DNase treated RNA prior to submission or select a Bioanalyzer QC request to have the Core run the Bioanalyzer for you.  All RNA quality must be checked by Bioanalyzer.

 

 

 
*
Agilent Bioanalyzer - Full service 

The bioanlyzer is used to check the quality of RNA and DNA.

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 (V2) 

Paired end 150 cycle MiSeq run.

Before libraries are run on the MiSeq they will require Kapa qPCR and Bioanalyzer analysis.

 
*
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.  11 samples 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 (V2) 

Paired end 250 cycle MiSeq run.

Before libraries are run on the MiSeq they will require Kapa qPCR and Bioanalyzer analysis.

 
*
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 DNase treated RNA prior to submission or select a Bioanalyzer QC request and the Core will run the Bioanalyzer for you.  All RNA quality must be checked by Bioanalyzer.

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.

No shipping charge, tubes are pickuped at 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 (V2) 

Single end 50 cycle MiSeq run.

Before libraries are run on the MiSeq they will require Kapa qPCR and Bioanalyzer analysis.

 
*
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

Pooling (if necessary) and submission to the a UCSF sequencing lab is included in the qPCR price.

We require that all libraries be QC'd by Bioanalyzer (additional service if done by the Core) and quantified by qPCR prior to MiSeq sequencing.

NOTE: Bioanalyzer QC, qPCR, pooling and submission to a UCSF sequencing lab is included in the price of all libraries made by the Gladstone 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.  For best results the small RNAs should be isolated from the total RNA.  The mirVana kit includes reagents for isolating the small RNAs but the for the Qiagen RNAEasy kit an additional RNeasy MinElute Cleanup Kit is required (thus the Qiagen method is twice as expensive).

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.

 
*

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 (5)
Service (6)