FAQ (Frequently afsked questions)
DNA Sequencing
How do I submit samples to Baseclear?
Sample requirements (amount, concentration, etc.) are described on our specific orderforms, which can be downloaded from our ordering section (which can be found in the top left corner, or click here). We prefer that samples are send in our special Baseclear vials which can be found in our Baseboxes. Send your samples to Baseclear in a sufficient stamped envelope to our visiting address, or bring the samples yourself to Baseclear (Einsteinweg 5, 2333CC Leiden).
What is a Basebox, and how do I use it?
A Basebox is a convenient method to send your samples to Baseclear. Each Basebox contains 15 Baseclear vials, 15 closing caps and 15 labelling stickers, and can be ordered for free by clicking on the special Basebox button on the right, or click here.
Print out the desired orderform from our website, follow the instructions on the orderform, and send your samples (and if necessary your primers) in the Basebox to Baseclear in a padded envelop together with the orderform.
The client is responsible for sending the Basebox to Baseclear, so make sure you stamp the envelope sufficient!
What is the difference between Quick Shot sequencing and Full Sequencing?
Quick Shot sequencing is the most cost-effective option in our sequencing services. The customer premixes DNA and primer and BaseClear performs the DNA sequencing reaction. No manual editing of data is done, reruns are only performed upon request.
Full sequencing means full service and high quality. This option guarantees the best sequencing results when it comes to read length, quality of data and customer wishes. DNA concentration will be measured prior to the sequencing reaction, in order to obtain optimal results. Poor sequence runs that do not meet our quality standards are reviewed manually. Failed runs are repeated at no additional charge. Primers can be chosen from our standard primer list, send with the order or ordered in advance (additional costs).
How long does it take to receive results?
Baseclear provides Quick Shot sequencing results within 2 working days, and Full sequencing results within 1 working day. In addition, for both services we have a 24-hour sequencing option (please use our 24 hour sequencing form then): If samples are delivered before 10 a.m., results are reported the next day before 10 a.m..
What is the read length of the sequencing options?
For our Sequencing short option, read length is up to 550 bp. For our Sequencing long option, read length is up to 1000 bp. The long and short sequencing options are available for both Full sequencing and Quick Shot sequencing.
What are the criteria for primer design?
Please note that the first 50 basepairs after the primer are not optimal sequenced. For this reason, we advice to develop a primer at least 100 bp upstream of the region of interest, in order to obtain optimal results.
What kind of machines are used?
DNA Sequencing reactions are performed on the ABI3730 (Applied Biosystems).
Does Baseclear also offer a primer walking service?
Yes, primer walking is the same as our project sequencing service. For this service, the price is calculated as price per basepair. This service includes design and synthesis of all necessary primers, optimal sequencing reaction (if necessary under specific conditions, e.g. in case of GC-rich DNA), assembly and manual editing of the sequence data and comparison to a reference sequence if requested. The customer will be informed regularly about the progress and extensive advice is given for special projects.
If you want to sequence more than 10.000 basepairs, it might be more beneficial to use our next generation sequencing technology.
I have a lot of samples, should I send all samples in single tubes?
No, for routine sequencing analysis of large numbers of samples (over 60 samples), it is more cost efficient to send in your samples in a plate (High Throughput sequencing). Our state-of-the-art robotics guarantee fast and accurate results. Especially for our Quick Shot service, this could be a real cost advantage.
For our Full Sequencing service however, only a single primer can be used for the entire plate. Therefore, when Full sequencing is required with multiple primers, we advice to send in the single samples.
For our HT sequencing option, samples can be submitted in regular 96- or 384-well plates.
We also offer our HT sequencing opton in half plate format (up to 48 samples).
I have samples that cannot be sequenced easily by straightforward normal sequencing, is this possible at Baseclear?
As a specialist in DNA sequencing, BaseClear has developed special efficient protocols for sequencing samples that cannot be sequenced easily by normal sequencing, such as large construct sequencing (BAC, PAC, cosmid or lambda DNA, etc.), genomic sequencing (< 5 Mb) and siRNA sequencing.
For each of these sequencing options, there are special order forms which can be found in the ordering section.
Note: some parts of the genome are almost impossible to read through, due to high stability regions, secondary structures, mispriming of primers, etc. Also certain siRNA inserts are almost impossible to read through, due to the high stability of the hairpin structure.
Where do the abbreviations in my results stand for?
You can find a list with all abbreviations here.
I have a question regarding DNA sequencing which is not answered in this FAQ, what should I do?
We will be happy to answer all your questions. Please fill in our contact form (button on the left top of the screen, or click here), or send an email to info@baseclear.com. We will answer your questions as soon as possible, but at least within 3 working days. Most questions will be answered the same day! You can also call us at number +31 (0)71 523 3917.
Related pages:
