OHSU

DNA Sequencing

We perform DNA sequencing & fragment analysis with our state-of-the-art, 48-capillary ABI 3730xL. Several levels of service are available to match your research needs and finances. We have a "break-even" fee structure, i.e., charge what it costs to provide the service. Please send me feedback on the data quality, length of read, and turnaround time.

We will email your data (traces and plain text-files of base calls) as soon as they are available.

Full Service (A-mode)

cadillac service

A-mode is most appropriate for new clients, clients with few samples, new projects, and troublesome templates. We take your template and use either your custom primer or one of our common primers and give you an edited sequence data file ready for use. Further data processing and analysis (blast, orf prediction, primer design, etc.: just ask) is available and usually free.

Full-service samples have highest priority. It is most appropriate for new projects and troublesome templates. We will troubleshoot difficult to sequence templates and determine a course of action.

Sample preparation


Hybrid Service (B-mode)

Hybrid Service

B-mode is most appropriate for clients seeking high priority, accurate sequencing, and ready to use sequencing data. It is economical, but does requires some skill with purification and quantification of template DNA. You save some money by quantifying your own template. We add the primer (either one of our "common" primers, on-hand in the lab, or your custom primer) and other reagents for cycle sequencing. Cycles are modified for the type of template: e.g., high G-C content or large templates. We do troubleshoot the sequencing results, and edit your data. Priority right after our Cadillac service.

Sample preparation


Scooter Service (C-mode)

Scooter (C-mode)

C-mode is most appropriate for those clients who want to save some money but are experienced clients with proven sample preparation systems, and easy to sequence templates. Sample preparation is the same as for B-mode samples, but you edit your own sequence data, ... so wear your helmet! Turnaround time is usually 1-2 days from receipt of samples.

Please note: any samples requiring troubleshooting or extra reagents will not be able to use C-mode. We are happy to sequence difficult templates, but they are "bumped up" to the B or A level depending on the extra reagents and/or bench time.

Further data processing and analysis is available on a fee-for-service basis. 

Sample preparation


"Do-it-yourself" Service (D-mode)

Do-it-your-self (D-mode) sequencing service.

You can really save some money by doing the cycle sequencing reactions yourself.

This mode is appropriate for experienced clients with proven sample preparation systems and high-throughput needs. D-mode is not for samples that require troubleshooting, additional reagents, special cycling, data processing or analysis: use B-mode for those.

Sample preparation


House Primers

Core Lab "Common" Primers
Primer name Sequence (5' to 3')
M13/pUC(-21) F TGT AAA ACG ACG GCC AGT
M13/pUC RP CAG GAA ACA GCT ATG ACC
SP6 TAT TTA GGT GAC ACT ATA G
T3 ATT AAC CCT CAC TAA AGG GA
T7 promoter TAA TAC GAC TCA CTA TAG GG
T7 terminator GCT AGT TAT TGC TCA GCG G
pGEX-5' GGG CTG GCA AGC CAC GTT TGG TG
pGEX-3' CCG GGA GCT GCA TGT GTC AGA GG
pQE9-F115 TAT GAG AGG ATC GCA TCA CCA T
pQE9-R348 TTG GGA TAT ATC AAC GGT GGT A


If you design your own primer, be sure to use data of known, high quality, i.e., phred-value >30.
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Fragment Analysis

Fragment analysis (AFLP)

Amplified fragment length polymorphism (AmFLP) analysis is a mapping technique that uses selective amplification to generate a set of labeled fragments of varying and characteristic sizes; also known as a "fingerprint". We have installed the GeneMapper software from Applied Biosystems for performing fragment analsysis on our 48-capillary ABI3730. Multiplexed samples are simple to run: you give us the dye-labelled DNA fragments and we give you a printout with the fragment sizes calculated. For multiples of 48, the charge is $2.60 per well. For non-multiples, $3 per well.

Sample preparation