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.
    • 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  5th Floor

1650 Owens Street

San Francisco, CA  94158

genomics-core@gladstone.ucsf.edu

 

 

Genomics Core Facility Members

 

Yanxia Hao
Jim McGuire

Linda Ta

 

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

 

Location

J. David Gladstone Institutes

Gladstone Building 5th 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
 

 
genomics-core@gladstone.ucsf.edu
 
5thFloor Gladstone Building
 
Linda Ta
Senior Research Technologist
 

 
genomics-core@gladstone.ucsf.edu
 
5th Floor
 
Jim McGuire
Research Technologist
 

 
genomics-core@gladstone.ucsf.edu
 
5th Floor
 
Yanxia Hao
Senior Research Technologist
 

 
genomics-core@gladstone.ucsf.edu
 
5th Floor
 

Services

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

This is our routine and most frequently used 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.

Full service runs are done by core personnel after samples are dropped off.

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 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.

 

 
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 (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.

 
SE50 (V2) 

Single end 50 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)

For requests with fewer than 10 samples, the user is financially responsible for the cost of the remainder of the kit, as the core does not have high demand for it.

 
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 Access Fee 

Yearly access fee to cover the Covaris S2 service contract.

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

 
PE150 (V2) 

Paired end 150 cycle MiSeq run.

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

 
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. 

 
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.

 
RNA Sample Amplification (no labeling) 

500 pg minimum; NuGEN Pico V2 kit (new)

 
Cell Lysate Preparation-amplification only 

Supply sample in lysis buffer with kit

 
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.

 
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 (stranded Clontech) 

Clontech stranded RNA-Seq library preparation and QC.

A minimum of 100 ng good quality total RNA is needed for a Clontech RNA-Seq library prep.  This method is recommended only for comparison studies such as wildtype vs knockout, treated vs control, normal vs tumor etc.

Note, we don't recommend comparing RNA-Seq expression data made using different library preparation methods, particularly if they use different cDNA methods (i.e. steric selection against RiboRNA or rRNA depletion and random priming versus oligo-dT priming).

We recommend Qiagen RNAEasy or Qiagen RNAEasy micro (small volume elution) kits for RNA isolation.  All RNA samples should be on-column DNase treated. 

 
Sample Handling Charge 

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

Charges are per hour.

 
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

 
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). This service is provided for RNA seq libraries made by the Core.

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

 

 
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.

 
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

 
Nanodrop 

Access fee per lab/per year

 
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.

 
Extra Data Normalization with RMA 

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

 
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.

 
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 EDTA).

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

For requests with fewer than 8 samples, the user is financially responsible for the remainder of the reagent kit, as the core does not have high demand for it.

 
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.

 
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/

 
miRNA-Seq Library Preparation 

For purification of miRNA, we recommend the mirVana kit from Life Tech (Thermo Fisher) or miRNeasy 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 for the Qiagen miRNeasy 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 miRNAs with the mirVana kit. 

 
C1 Single Cell Library Prep for Illumina Sequencing 

The C1 system isolates single cells into individual reaction chambers in Fluidigm's exclusive 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 template is quickly prepared for qPCR or sequencing analysis.

Depending on the Chip type 96 to 800 single cells can be isolated and prepared for analysis.

 

   
   
 
DNase Treatment 

We strongly recommend that all RNA samples be DNase treated prior to library creation.  DNase treatment can be done on isolated RNA.

Pricing is per sample.  Bioanalyzer QC recommended after treatment.

 

Service List


Search available services: View: by category alphabetically
Affymetrix (8)
Bioanalyzer (5)
Consultation (1)
Covaris S2 Sonicator (4)
KAPA QPCR Library Quantification (1)
Library Preparation (7)
MiSeq Sequencing (5)
Service (6)