Core Laboratories

DNA Laboratory

The DNA Laboratory at ASU supports a variety of techniques useful to molecular biologists. The laboratory is open to both on- and off-campus researchers. 

Contact

DNA Lab

Arizona State University, School of Life Sciences

PO Box 874501

Tempe, AZ 85287-4501

PH: 480-965-8520  Fax: 480-965-6899

 

DNA Lab techniques and equipment

DNA sequencing is run as a service. Laboratories may submit samples along with a sequencing request form. Sequencing reactions are usually run in our lab. However, we will run at significantly reduced cost sequencing reactions — run and purified in other laboratories. We maintain a stock of common plasmid primers accessible through a link on the sequencing form. We use an Applied Biosystems 3730 capillary sequencer. Read lengths are routinely 800–900bp. Turnaround time is 24–48 hours. As of December 2007 we will also provide plasmid and PCR product purifications in a 96 well format.

Fragment analysis, which includes microsatellites, AFLP, or STR applications, can also be run on the 3730 sequencer. This is our primary platform for fragment analysis. If interested in using dyes incompatible with the 3730, we maintain an ABI 377 gel sequencer. Dye-labeled samples are normally generated in respective laboratories and delivered to our lab for analysis. Contact us before submitting samples.

Microarray slides can be scanned using an Agilent scanner. We do not manufacture microarrays. We do have the equipment to complete all other aspects of microarray analysis. Files generated from the scanner are processed using either Agilent’s Feature Extraction or Axon’s GenePix Pro 6.0 software. Statistical analysis, gene filtering and gene clustering can be accomplished with Agilent’s Genespring software. Normally we instruct users on the techniques and software. However, we will provide microarray hybridization and analysis to laboratories that provide us the RNA. Contact us for more information.

Real time PCR in the DNA lab is run on an ABI7900HT thermocycler using a 384 well format. Samples are usually set up in respective laboratories. We provide training on the software and help in experimental setup. Primers and probes can be designed using ABI Primer Express software available in the lab.

The Agilent 2100 Bioanalyzer is a type of capillary electrophoresis unit capable of separating RNA, DNA or protein in lieu of gel electrophoresis. Samples may be submitted as a service request or you can be trained how to use the instrument. We routinely run RNA samples only, so please contact us before planning to submit any other samples. Any RNA submitted for microarray analysis will be checked on the bioanalyzer for integrity before beginning the labeling reactions.

Single Pass Sequencing for non-profit customers

  • $3.85/sequencing reaction for PCR or plasmid
  • $3.12/sequencing reaction in a 48 or more quantity
  • $ .73/already reacted and purified sample
  • $52.45/plate for reacted and purified 96 well plates

Single Pass Sequencing for for-profit customers

  • $6.10/sequencing reaction for PCR or plasmid
  • $5.00/sequencing reaction in a 48 or 96 well plate or tube strips
  • $1.15/ already reacted and purified sample
  • $68.85/plate for reacted samples. We will purify.

Rerun policy

We’ll rerun, at no cost, any sample giving suboptimal sequence, for whatever reason. Just let us know on the sequence submission sheet that this is a repeat. We can often help if sequencing isn’t going as well as you’d like. Talk to us.

Special conditions

If you have a high GC content or known secondary structure, let us know on your sheet. We offer more primers than are listed on the submission form. We can alter our reactions for you. Check the link at the bottom of the form.

Fragment Analysis

  • $52.45/plate of 96
  • $26.22/plate of 48 or fewer

Size standards are available.

Plasmid Preparations

$100/96 well plate. Plasmids purified when accompanying a sequencing order.

PCR Purifications

$50/96 well plate. PCR purified when accompanying a sequencing order. We can purify individual samples at $1.00/sample.

Bioanalyzer RNA Runs, DNA1000, DNA12000

$30/chip (12 samples). Please call about other chip types.

Real time PCR

  • $15/run, including plate and optical cover
  • $10/run with your plate and cover

Submitting Sequencing Samples

Purity and quantitation of the DNA template and primer dictate the quality of the sequencing results. The templates should be purified and quantified before submitting for sequencing. We can quantify templates for you, especially off campus customers; however this may delay the return of your data.

Optimal amounts for templates and primers are as follows:

  • Single stranded DNA 100-200 ng
  • Double stranded DNA (plasmids) 150-200 ng
  • PCR products 10-30 ng (10ng for templates <500bp; 30ng for >1kb)
  • BAC or Cosmid DNA 500 ng

The amount of primer required for all of the above is 20 ng, except BAC and Cosmid which need 100 ng primer.

Mix the template and primer at above amount and bring the volume to 6 ul with dd H2O. For off campus customers we recommend drying the sample prior to shipment to avoid possible loss.

If you prefer that we set up reactions for you, submit sufficient template and primer in separate tubes.

Results

Sequencing
We routinely deliver data by email. For large projects or regular customers we can also create an FTP folder.

Text files open with word or notepad. To open electropherogram files, use the programs at the following links:

Fragment analysis

We can deliver data by email or by disk. To open the data files, use programs at one of the following links:

​DNA Sequencing Forms

DNA sequencing form 1 (PDF)
DNA sequencing form 2 (PDF)

Sequencing Primers

The following primers can be added by the DNA Lab.

  • T3 5’CAA TTA ACC CTC ACT AAA GGG 3’
  • T7 5’ TAA TAC GAC TCA CTA TAG GG 3’
  • SP6 5’TAT TTA GGT GAC ACT ATA G 3’
  • SP6* 5’GAT TTA GGT GAC ACT ATA G 3’
  • M13F 5’ GTT GTA AAA CGA CGG CCA GT 3’
  • M13R 5’AGG AAA CAG CTA TGA CCA TG 3’
  • M13R (–23) 5’AGC GGA TAA CAA TTT CAC ACA GG’
  • T7 terminator 5’ GCT AGT TAT TGC TCA GCG G 3’
  • BGH-R 5’ TAG AAG GCA CAG TCG AGG C 3’

 

Electron Microscopy (EM) Laboratory

The Electron Microscopy Laboratory is one of two core imaging laboratories located in ASU School of Life Sciences. It is also part of ASU Research Technical Services, which is administered by the College of Liberal Arts and Sciences.

The lab provides training and service for both on-campus and off-campus researchers who may require electron microscopy. Please refer to our website for a list of microscopes and associated instruments currently available for use in the lab.

Goldwater Environmental Laboratory

The Goldwater Environmental Laboratory (GEL) is a shared-use facility available to all research staff, faculty and students. The facility encompasses seven laboratories and is part of the College of Liberal Arts and Sciences Research Technical Services group. 

Proteomics and Protein Chemistry Lab

Services provided by the Proteomics and Protein Chemistry facility include molecular mass determinations by MALDI-TOF mass spectrometry, protein sequencing by automated Edman degradation, solid phase peptide synthesis, and amino acid analysis. Graduate students and postdoctoral researchers are encouraged to use the facility, and training students is provided free-of-charge.

WM Keck Bioimaging Laboratory

The Keck Bioimaging Lab, housed in the School of Life Sciences, provides training, consultation and use of various light-based microscope systems. It hosts a range of microscopy instrumentation including epi-fluorescent, laser scanning confocal and multi-photon systems. This multi-user facility is part of the Liberal Arts and Sciences Research Technical Services group and is available to all research staff, faculty and students. Please see the website for a complete list of equipment.

WM Keck Environmental Biogeochemistry Lab

This Keck Lab was established in 2004 by faculty from ASU’s departments of Chemistry, Geological Sciences and School of Life Sciences with the intent to get scientists directly involved in all aspects of isotope ratio measurements. Research groups interested in using these facilities need to provide at least one person who will be trained to prepare and set up samples for analysis.