Resources

Sequencing FAQs

What is the price for sequencing?
We offer highly competitive prices. Discounts are available for large orders. Please call for a quote.

What payment methods are accepted?
We accept PO numbers as well as all major credit cards.

What is the turnaround time?
Sequencing results are available the day after we receive your samples. Your results will be online by 10:00 am Monday through Friday and by 12:00 pm on Saturday. Additional turnaround time may be required if your reactions need to be repeated.

What read length will I get?
800-1000bp

How do I order sequencing online?
Click here http://www.retrogen.com/pdf/EnteringRetrieving.pdf to download the instructions for ordering online.

What tubes should I use?
Smaller orders should use 1.5mL epi Eppendorf tubes. Screw cap tubes are more time consuming so pop caps should be used. Tube strips, while convenient, are hard to label and keep track of, so for large orders (24+ samples) use 96-well plates. We recommend using strip lids to cap plates as they prevent leakage and cross contamination – especially for plates shipped overnight.

How should I label the tubes?
The label on the tubes should match the name listed on the order form. It is advisable to have names that are at least somewhat unique so they can be distinguished from other orders. Labeling the tops of the tubes is preferable but not required.

How do I send my samples?
San Diego customers can request a sample pickup and our courier will retrieve them. Others can overnight them to:
Retrogen, Inc.
Sequencing Department
6645 Nancy Ridge Dr.
San Diego, CA 92121
We do not recommend using Dry Ice as this greatly increases the shipping costs.

How do San Diego County, Orange County, and Los Angeles County customers schedule a pickup?
You can call, email, or request a pickup through our LIMS System or our website at http://www.retrogen.com/index/pickup_request2.htm

La Jolla / Sorrento Valley
Please have your pickup scheduled and have your samples in the appropriate pickup location by 11:00 am for the first pickup. We will pick up your samples between 11:00 am and 1:00 pm. For the second pickup have your samples ready by 3:00 pm and we will pick them up between 3:00 pm and 5:00 pm.

North San Diego County (North of Hwy 56)
Please have your pickup scheduled, electronically or by telephone, by 1:00 pm and have your samples in the appropriate pickup location by 1:30 pm. We will pick up your samples between 1:30 and 2:30 and you will receive your results the following morning as usual.

San Diego (South of Hwy 52)
Please have your pickup scheduled, electronically or by telephone and have your samples in the appropriate pickup location by 1:30 pm. We will pick up your samples between 1:30 - 3:30 and you will receive your results the following morning.

Orange County
Please have your pick up scheduled, electronically or by telephone by 2:00 pm, and have your samples in the appropriate pick up location by 3:00 pm. We will pick up your samples around 3:00 pm and you will receive your results the following morning as usual.

Los Angeles County
Please have your pickup scheduled, electronically or by telephone by 12:00 pm, and have your samples in the appropriate pickup location by 1:00 pm. We will pick up your samples around 1:00 pm and you will receive your results the following morning as usual. (Please note: Los Angeles pickup area is limited to south of Burbank).

Riverside/San Bernardino
Please have your pickup scheduled, electronically or by telephone by 11:00 am, and have your samples in the appropriate pickup location by 12:00 pm. We will pick up your samples around 12:00 pm and you will receive your results the following morning as usual.

Can I send my samples on a Saturday?
Retrogen is closed on weekends so samples mailed on Friday will be delivered to us Monday.

How much DNA template/primer do I need to send? What concentration should it be at?
Please click here http://www.retrogen.com/site/submissionrequirements for detailed information.

Can Retrogen prep my DNA for me?
Yes. Please call for a quote.

What universal priming sites are there in my vector?
Contact the vendor who supplied the vector. If you email a text file with the sequence of the cloning region we can check it for binding sites for universal primers.

What primers can Retrogen provide?
The following universal primers are available at no extra charge:

Primer NameSequence
AOX1-For GAC TGG TTC CAA TTG ACA AGC
AOX1-Rev GCA AAT GGC ATT CTG ACA TCC
BGHrev TAG AAG GCA CAG TCG AGG
CMV-F CGC AAA TGG GCG GTA GGC GTG
DON1-F TCG CGT TAA CGC TAG CAT GGA TCT C
DON2-R GTA ACA TCA GAG ATT TTG AGA CAC
EGFP-C ATG GTC CTG CTG GAG TTC
EGFP-N CGT CGC CGT CCA GCT CGA CCA G
GLprimer1 TGT ATC TTA TGG TAC TGT AAC TG
GLprimer2 CTT TAT GTT TTT GGC GTC TTC C
M13-40 GTT TTC CCA GTC ACG AC
M13F GTT TTC CCA GTC ACG ACG TTG TA
M13F-20 GTA AAA CGA CGG CCA GT
M13R CAG GAA ACA GCT ATG ACC
Sp6 ATT TAG GTG ACA CTA TAG
T3 ATT AAC CCT CAC TAA AGG GA
T7 TAA TAC GAC TCA CTA TAG GG
T7term GCT AGT TAT TGC TCA GCG G
pBADf ATG CCA TAG CAT TTT TAT CC
pBADr GAT TTA ATC TGT ATC AGG
pGEX3 CCG GGA GCT GCA TGT GTC AGA GG
pGEX5 GGG CTG GCA AGC CAC GTT TGG TG
pTriplEx3 ACT CAC TAT AGG GCG AAT TG
pTriplEx5 CTC GGG AAG CGC GCC ATT GTG TTG GT

How do I design primers?
They are usually 18-25bp. Annealing temperature should be 50-65º, ideally 55-60 º. Primers that can self-hybridize should be avoided. Also primers should be very site-specific to your binding site. Primers with homology to alternate sites, especially at their 3’ ends can cause multiple signals.

Can Retrogen make/design primers for me?
We can design and/or synthesize your primers for you. Call for a quote.

If Retrogen synthesizes my primer can it be used again for future sequencing orders?
Yes. If you plan on reusing primers synthesized by Retrogen you should ask us for its tracking number. Referring to the primer by this number will make it easy for us to locate.

If Retrogen synthesizes my primer will it be sent to me after being used for the sequencing order?
We will send your primers upon request only. A shipping charge will apply.

Can I use the same primers I used to amplify my PCR product to sequence it?
Yes.

If I send primers and template DNA premixed how much of each should I use?
DNA DNA PrimerTotal Vol.2X DNA 2X Primer 2X Total Vol.
PCR product DNA 50ng 10pmoles 10uL 100ng 20pmoles 20uL
Single stranded plasmid 250ng 10pmoles 10uL 500ng 20pmoles 20uL
Double stranded plasmid 300ng 10pmoles 10uL 600ng 20pmoles 20uL
BAC 2000ng 10pmoles 10uL 4000ng 20pmoles 20uL

We recommend 2x amount of DNA in case we need to repeat the reactions.


Example 1: If your PCR template and primer are at the concentration of 20ng/uL and 10pmol/uL, respectively, you need to add 2.5uL of PCR template and 1uL of primer to the 1.5mL epi tube, and add 6.5ul of H2O to bring the total volume of 10uL.

Example 2: If your Plasmid template and primer are at the concentration of 200ng/uL and 10pmol/uL, respectively, you need to add 2.5uL of PCR template and 1uL of primer to the 1.5mL epi tube, and add 6.5ul of H2O to bring the total volume of 10uL.

How long do you keep my DNA/primers?
Samples are stored in our freezer for at least a month.

Can I get my DNA/primers back?
Yes, but shipping charges will apply so we advise you aliquot a portion of your sample for us and keep the rest.

How close to the primer can I get sequence?
Sequence usually appears about 25-30 bases from the primer.

Can you sequence genomic DNA?
Directly sequencing genomic DNA is not very practical. Contact our technical support for help with your genomic sequencing projects.

Do you have special conditions for GC rich/secondary structure/siRNA/etc.?
Yes. Be sure to note on your order any known issues so we can use conditions optimized for your sample. An additional charge will apply. For Special Sequencing pricing, please contact our sales dept.

My template is XX% GC, is that GC rich?
Templates that are 70%+ should be sequenced with our GC rich conditions. Also when sequencing through small regions (30-40bp) of very high GC content (80%+) our GC rich conditions can improve the results.

What is FDA quality sequencing?
It is designing additional primers for reactions to generate overlapping sequences so you can be confident that every base has been called with 100% accuracy.

How will I receive my data?
Your data will be posted to our website: http://sequencing.retrogen.com You will be given login information and instructions for signing in and downloading your results.

How will I know when my data is ready?
You will receive an email notifying you when the results are ready.

How do I view the chromatograms?
You will need a program to view the chromatograms. You can find links to download a free program here: http://sequencing.retrogen.com/cgi-bin/dna/tools.cgi

Why did my reaction fail/give poor results?
We have a troubleshooting guide that can aid you in determining why a reaction may have failed. If you still have questions please call our technical support or email sequencing@retrogen.com

Can you repeat my reactions?
We may repeat a portion of an order in an attempt to troubleshoot or if we think the results can be improved. Call or email sequencing@retrogen.com to discuss any reactions you think should be repeated. Our full repeat policy can be found here: http://www.retrogen.com/index/seq_quality_assurance2.htm