DNA Technologies: Frequently Asked Questions

Where do I start?

You can find out more about Getting Started in the Core; this page has information on billing, data storage & distribution, scheduling, equipment & training, bulletins, research support, seed grants, and more.

Which sequencing technologies do I need to consider for my project?

The table below shows the range of outputs from the sequencing platforms currently available in the Core. The choice of platform depends on the required data output – contact us to discuss your options.

Sequencing Platforms HiSeq3000 HiSeq2500 – High Output HiSeq2500 – Rapid Output MiSeq PacBio RS II
Sequencing Output per Lane average 104 Gb up to 36 Gb up to 45 Gb up to 15 Gb 500 Mb to 1 Gb  (official estimate after titration; potentially up to 1.2 Gb very dependent on library type, DNA quality, library titration)
Passing Reads per Lane
in Millions
average 340 M up to 200 M up to 170 M up to 17 M (v2)  up to 25 M (v3) 20-60 K
Read Length up to 2x 150bp up to 2x 100bp up to 2x 250bp up to 2x 300bp average 9-12kb, N50 up to 17kb
Typical Sequencing Format
SR (single reads), PE (paired end reads)
SR50, PE100, PE150 SR50, PE100 SR100, PE150, PE250 SR50, PE75 (v3), PE150, PE250, PE300 (v3) 1-1.5kb (CCS), 2kb, 5kb, 10kb, 20kb, 30kb

How should I provide DNA and RNA?  — Sample Submissions

Quality and quantity of DNA and RNA is critical for high quality sequencing output. Please make sure your DNA is not degraded and is free of RNA contamination. RNA samples should always be assessed on the Bioanalyzer for the absence of gDNA contamination (can be removed with DNAseI treatment followed by a clean-up) and degradation. Preferentially determine the quantity of your DNA and RNA samples using fluorometry (e.g. Qubit or a plate reader).  The purity of your samples should be assessed via spectrophotometry (e.g. Nanodrop). The Sample Requirements page provides a comprehensive table with requirements and metrics for sample QC, library preps, or library submissions.  Please see the Library Prep Page for details on the library prep processes.  For submission information, including submission forms and shipping details, please visit the Sample Submission & Scheduling page. If you are submitting DNA for PacBio libraries, please follow the PacBio Guidelines for Shipping and Handling.
The  Real-time PCR core can carry out DNA as well as RNA extractions for you.

What type of library services are available through the Core?

We make libraries for sequencing with Illumina and PacBio instruments. Illumina libraries include genomic DNA, RNA-seq, ChIP-seq, micro RNA, small RNA, Methyl-seq, and RRBS. We carry out real-time quantitative PCR to accurately measure the concentration of sequence-able library molecules to achieve optimal sequencing output.

How many indexes are available for my libraries?

We currently stock adapters with 96 different indices. Bioo Scientific offers NEXTflex HT barocde sets for up to 384 samples. If you are planning to use homebrew versions of indexed adapters please consult with us first, as  incorrectly designed adapters may cause sequencing failures.

Can I submit a library I made?

Certainly. Please provide a Bioanalyzer trace (we can run this QC for you), library prep methods, and index sequences used. We will check the quantity of your libraries using real-time PCR (included in the sequencing price).  The Sample Requirements page provides all the details.  We suggest to submit your library in at least 15 ul volume at a minimum concentration of 10 nM.  Depending on sequencing platform, we can work with less library (down to 1 nM).  However, at low concentrations the quantification becomes less reproducible, the library becomes less stable, and relatively larger amounts of the library get lost sticking to the tube. The best buffer to ​store and ​submit libraries is 10 mM Tris​/0.01% Tween-20 ph=8.0 or 8.4​, but EB buffer is sufficient. Please use 1.5 ml low-retention tubes (e.g. Eppendorf ​​DNA LoBind). If you do not provide a Bioanalyzer profile of your library, we will carry out the QC for a fee.
Please note that libraries for the HiSeq3000/Hiseq4000  have some more stringent requirements.

What is the price associated with genotyping and sequencing?

Please check our Prices page for the complete list of pricing for genotyping and sequencing.

Can I use Core facility equipment if I do not have access in my lab?

Several pieces of equipment are available for use during normal working hours for a nominal ‘instrument use’ fee. Please see the Shared Equipment page. To be able to use these instruments you will need to be trained first by Core staff (subject to a ‘training &usage fee’, good for one year). Your PI will need to create an account with the Genome Center and supply a DaFIS # or PO for billing. Visit our login site and follow the instructions for “Creating an Account.”  Also visit here to learn more about the Training and Use of Core Facility Equipment. To schedule a time for instrument training, please email the responsible staff member.

When can I expect to get my data?

Work in the Core is performed on a “first come, first served” basis. HiSeq sequencing data will typically be delivered within about four to six weeks, while MiSeq has a 5-8 day turnaround time. The turnaround time can fluctuate and is dependent on the number of customer samples in the queue and the read lengths requested.

Where and how can I get my data?

Following analysis of each run, users have access to parsed output through the SLIMS server. A SLIMS account will be created for you on your first run, with information about how to set up and access your account distributed via email (you may receives this email before your actual files are available). The main SLIMS page can be reached here.

Sanger DNA Sequencing and Genotyping Services at UC Davis

The DNA Technologies and Expression Analysis Cores do not offer Sanger DNA Sequencing, but these services are available on campus. See the UC DNA Sequencing Facility or the CAES Genomics Facility for more information. There are multiple other service facilities that may be of interest, including the Veterinary Genetics Laboratory, CCM Mouse Biology Program, and Real-time PCR Research and Diagnostics Core Facility. If we missed out any UC Davis facilities that you would like us to list here, please contact us.

Information above is current as of March 2015