Frequently Asked Questions

1. What if my DNA concentration is too low? If your DNA concentration is lower than what we recommend on our website please be sure that you bring it up to the proper concentration before submitting for sequencing. There are several methods you may consider for concentrating your DNA including the use of a speed vac or ethanol precipitation. Please be advised that the success of your sequencing reaction is heavily dependent on the purity and concentration of your DNA so please adjust your protocols and concentrations accordingly.

2. What is the current turnaround time? Our turnaround time is approximately 1-2 business days but we are frequently able to give 24-hour turn-around M-Th. Samples are sequenced on a first come first served basis so turnaround time can vary depending on current workload, when you submit your samples, and how many samples you have. We typically start setting up sequencing reactions by noon so submitting your samples in the morning will give you the quickest turnaround time.

3. Which universal primers does the UCDNA Sequencing Facility provide? We provide the following universal primers free of charge: M13-21, M13-R, T7Promotor, T7Terminator, T3, and SP6.

4. How does cycle sequencing differ from PCR? Cycle sequencing is a much more stringent protocol than PCR in that it uses only one primer for extension and therefore is a linear extension rather than an exponential extension. This means that the growth of the product is linear and not exponential as in a PCR reaction.

5. If my primer worked for PCR why didn’t it work for sequencing? Again, because sequencing is a linear amplification and more stringent than PCR, if the primer does not anneal very efficiently and accurately, you could end up with either very weak and noisy data or, in some cases, no data at all. In a PCR reaction, there are two primers at work generating a product that grows exponentially so even if the primer/primers are not very efficient there are many more opportunities for the reaction to “go” and you should still end up with a product. So, be forewarned, even if the band looks great on your gel, your PCR product might not sequence well, if at all!

6. How do I interpret my sequence data? First and foremost, even the best sequence data can contain up to a 2% error rate so you must look at the electropherogram for your sequence! You are responsible for manual editing of your sequences so accurate sequence data can only be determined from the electropherogram. This is critically important to the integrity and validity of your sequence! Please do not rely on your text file. Visit our software downloads page for freeware sequence viewing software if needed.

7. How do I interpret the ambiguous bases in my data? The letters used for ambiguities are called IUB codes. The IUPAC-IUB codes are used to define multiple nucleotide possibilities in one position. The table below indicates the definitions:

Code

Represents

Complement

A

Adenine

T

G

Guanine

C

C

Cytosine

G

T

Thymine

A

Y

Pyrimidine (C or T)

R

R

Purine (A or G)

Y

W

weak (A or T)

W

S

strong (G or C)

S

K

keto (T or G)

M

M

amino (C or A)

K

D

A, G, T (not C)

H

V

A, C, G (not T)

B

H

A, C, T (not G)

D

B

C, G, T (not A)

V

X/N

any base

X/N

-

Gap

-

8. What if I want a sequence run again? If your sequence fails due to an error on our part, we will automatically re-run the sequence free of charge. However, if you ask us to re-run a sequence and the results are the same as the first time, then we will have to charge you for the additional reaction. If the results are different from the first time, then we will not charge you.

**COVID-19 Update Jan 25 2021**

California's Statewide December stay-at-home order does not affect UC Davis Phase 2X research so UCDNA Sequencing will continue its normal services.

UCDNA Sequencing is available to receive DNA sequencing samples and fragment analysis runs during specific drop-off times on specific days. Runs and turn-around time on data will vary, depending on sample volume. Current turn-around time is approximately 2-3 days.

DNA Sample Drop-Off Schedule:

Storer Hall: Mon, Wed & Fri until 12pm

VM3B Annex: Mon, Wed & Fri until 11am

UCDMC: By request only

If this schedule does not work for you, please contact us 530-754-9259 and we will arrange another time for you to drop off your samples.

Sample Drop-off Instructions:

Storer Hall is locked and requires authorized access and COVID testing to enter the building so we have provided a FedEx envelope taped to the front doors of Storer Hall for sample drop-off. Place your samples in a clean Ziploc with your order number on it, drop them off in the envelope during our scheduled drop-off times and email DNAdivas@ucdavis.edu that they are there.

The VM3B annex appears to be unlocked now so you may drop samples off on any day of the week. We will pick up samples on Mondays, Wednesdays and Fridays at 11am.

If you have a 96-well plate or fragment analysis samples, you will need to schedule a time to drop off to us in person on Monday, Wednesday or Friday at Storer Hall. We will arrange to meet you at the front or back door of Storer Hall to receive your samples. Please wear your PPE, including mask and gloves.

To minimize any exposure, please exercise caution and refrain from placing orders if you or anyone in your lab has recently been ill. 

Shipping Instructions :

Our receiving department is open M-F so you can ship to us any day during the week. Please email DNAdivas@ucdavis.edu to let us know how many samples you will be sending and when.

Thank you from the UCDNA Sequencing Staff

 

 
 
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