The price for sequencing can range from $3.50-15.00 per reaction, based largely on the number of reactions per order. It can also be influence by any additional prep, purification or special conditions used for each reaction. Please contact one of our knowledgeable sales representatives for a personalized price quote.
What payment methods are accepted?
We accept single-use and blanket PO numbers, as well as all major credit cards. We will not process sequencing requests until current billing information is confirmed.
What is the turnaround time for sequencing results?
Sequencing turnaround is usually 24 hours or less. In most cases, if samples are received by 5pm results will be available online the next day by 10am Monday through Friday and by 12pm on Saturday. Occasionally additional turnaround time may be required if reactions use special "Large Template" conditions or need to be repeated due to poor initial results.
What read length can I expect?
For plasmid templates we strive to produce an overall read length of 1000bp, with 800-900bp being high quality base calls.
For PCR products we strive for a full read of the amplified fragment, with a short tail to confirm PCR stop.
Obviously there are a number of factors (DNA quality, template/primer compatibility, contaminants, difficult regions, etc.) that will shorten the overall read length. If reactions do not meet the target read length, we work diligently to troubleshoot and produce the longest read possible.
For smaller orders (1-23 samples) please use 1.5mL pop cap epi tubes. Screw cap tubes and 8-tube strips are more time consuming and can be difficult to label and keep track of. For large orders (24+ samples) please use 96-well plates with samples arranged in the vertical orientation. We recommend using strip lids to cap plates as they prevent leakage and cross-contamination, especially during overnight shipping.
How should I label the tubes?
To ensure efficient and accurate processing of your order, please label the top of sample tubes with a name matching all or a key part of the corresponding sample name listed on the order form. We recommend using names that are at least somewhat unique so they can be easily distinguished from other orders.
For example, customer John Smith submitting an order of three templates to be sequenced with the same custom forward primer might label his sample tubes JS-1, JS-2, JS-3 and JS-For.
How do I send my samples?
Southern California customers in San Diego, Orange County, and Los Angeles can contact us to request a sample pickup and our courier will retrieve them.
All others customers can overnight samples to:
Retrogen, Inc. Sequencing Department 6645 Nancy Ridge Dr. San Diego, CA 92121
When sending samples overnight, we do not recommend using Dry Ice as this greatly increases the shipping costs.
How do Southern California customers schedule a pickup?
Please have your pickup scheduled and have your samples in the designated pickup location by 11am for the first pickup. Our courier will pick up your samples between 11am and 1pm. For the second pickup have your samples ready by 3:00 pm and we will pick them up between 3pm and 5pm.
North San Diego County (North of Hwy 56)
Please have your pickup scheduled by 1pm and have your samples in the designated pickup location by 1:30 pm. Our courier will pick up your samples between 1:30-2:30pm and you will receive your results the following morning as usual.
San Diego (South of Hwy 52)
Please have your pickup scheduled and have your samples in the designated pickup location by 1:30pm. Our courier will pick up your samples between 1:30-3:30pm and you will receive your results the following morning as usual.
Orange County
Please have your pick up scheduled, electronically or by telephone by 2pm, and have your samples in the designated pickup location by 3pm. Our courier 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 pick up scheduled, electronically or by telephone by 12pm, and have your samples in the designated pickup location by 1pm. Our courier will pick up your samples around 1pm and you will receive your results the following morning as usual. (Please note: Our Los Angeles pickup service area is limited to South of Burbank and West of Azusa. We currently do not offer pickup service in the Diamond Bar, Pomona, or Claremont areas.)
What types of DNA templates can be sequenced?
Most of the sequencing we do is from plasmids and PCR products. We can also sequence from BAC DNA, cosmids, phage supernatants and bacterial clones, sent either as colonies or in glycerol stocks. Please inquire about any additional preparation/purification services that may be needed.
What Universal Primers does Retrogen provide?
A complete list of no-charge universal primers we offer for sequencing can be found at the link below.
Using a spectrophotometer is the easiest way to measure your DNA concentration. We suggest noting the 260/280 and 260/230 wavelength ratios to increase accuracy.
You may alternately estimate your DNA concetration by running some of your sample on a gel with a known concentration marker. This tends to be less accurate so please indicate "estimated concentration" on the order form submitted with samples.
Once the samples arrive, we can determine a more accurate DNA concentration using a spectrophotometer.
How close to the region of interest can I design my sequencing primer?
It can be difficult to ensure consistent sequencing signal intensity within the first 50bp after the sequencing primer, and reliable results generally start between 20-40bp. Because of this we suggest leaving at least a 75-100bp buffer between the end of the sequencing primer and the beginning of the region of interest.
Can Retrogen help me design sequencing primers for my templates?
We offer a wide range of primer design and synthesis services. Currently we only design and synthesize primers needed for sequencing reactions.
Given a vector map or reference sequence with the region of interest highlighted, we can design primers to initiate new sequencing reactions. If consensus sequence verification is needed over the length of a long insert, we can take initial sequencing results and elongate the read via primer walking. Please inquire about pricing for primer design and synthesis customized for your individual projects.
How long will my sequencing samples be stored?
We keep sequencing templates and primers in freezer storage for four weeks, and then rotate them to room temperature storage for an additional 2 months. For large projects over an extended period of time, we can store sequencing primers for up to one year in freezer storage.
If you know you will need to use templates or primers for additional sequencing, please note this in the comments section of the original order form. Within 3-6 months simply reference the order number the samples were originally sent with for efficient processing of future orders.
How can I view my sequencing results?
No later than 10am the next day your sequencing results will be posted to your Retrogen dnaLIMS account. A confirmation email will be sent to the address listed for your account to alert you that results are available.
Simply login to your account, navigate to "Download DNA Results" and click the order number for your recent sequencing projects. From there you will have access to download both the text sequence (.seq) and chromat (.ab1) files for each reaction. You will also be able to do an initial analysis of your data using our in-browser sequencing viewer.
A number of free software programs are available for viewing trace or chromatogram files. Please click the link below to download and install the necessary software.
Upon request we can email your results directly or ship results on a CD (additional charge applies for shipment).
How long are sequencing results stored?
We will maintain the text, chromat, phd, qual, and fasta files for your data posted to your account for at least 6 months. After that point we will periodically archive data and post only the text files.
We strongly recommend you download all sequencing results within the first week they are posted online to ensure there is no loss of data. Under rare circumstances upon request, we can re-extract and reprocess archived sequencing data (additional charge may apply).
What if my sequencing results fail?
We have a troubleshooting guide that can help you determine why a reaction may have failed. If you still have questions please call our technical support or email sequencing@retrogen.com. An experienced sequencing specialist will assist you troubleshoot the failed reactions and work with you to get the longest read possible.
What is your repeat policy for poor results?
We will independently repeat a portion of an order in an attempt to troubleshoot poor quality data or if we think the initial results can be improved. Please call our sequencing department or email sequencing@retrogen.com to discuss any reactions you think should be repeated.
Why do redo reactions give better data than the initial reactions?
Because our sequencing process is largely automated, the chance for human error is very low. That said, sometimes mistakes happen.
When sequencing reactions fail to yield high quality data, we begin to troubleshoot the most likely cause. We will independently enter redo/rerun reactions if we believe better data can be obtained from the reaction.
The major reason we get better results is that we almost never run redo reactions using the same sequencing conditions as the initial reactions. Usually simple adjustments such as changing template and primer volume, adding stabalizing reagents, or modifying thermal cycling conditions will lead to much improved data.
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