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Frequently Asked Questions About Our Products And Services

The right answers to frequently asked questions

Find the answers to all our products and services by clicking the links below.

Custom DNA Sequencing

Products & Services

What are Tube Labels - when / why do I need it?

Tube Labels are free barcode labels used for error free labelling and identification of your samples and primers in tubes for all kind of Eurofins Sequencing services. They allow fast processing your sequencing order. You can track the usage status, the usage date as well as the user of the lables under "Kits & Labels".

Tube Labels can be ordered online and are free of charge.

What are TubeSeq Labels?

TubeSeq Labels - formerly known as Prepaid Barcodes - are barcode labels to prepay for our TubeSeq Service. They can also be used to pay for the primer synthesis ordered along with any DNA sequencing service. 

TubeSeq Labels can be shared with colleagues. You can track the usage status, the usage date as well as the user of the lables under "Kits & Labels".

They can be ordered online in any quantity, starting from 50 labels. 

What are unpaid barcodes?

With SupremeRun, payment is conveniently by bill. Please request unpaid DNA barcodes for secure labelling of your DNA samples by contacting our Customer Care team.
Yellow primer barcodes are also unpaid barcodes and are used to identify your own primers.

You must activate and customise all unpaid barcodes in your account under Barcode Management GATC using a batch and BIN number.

What are SupremeRun barcodes?

SupremeRun barcodes are prepaid barcodes for the SupremeRun tube service. With prepaid barcodes, you deposit a certain amount for sequencing in advance. In addition, the DNA sample is automatically assigned to the online order. The advantage for you is straightforward handling. You will receive only one bill and can conveniently monitor your barcode stock via the Barcode Management System, and transfer barcodes to or from colleagues.

When should I use primer barcodes?

With SupremeRun, you can send your own primers separately in a tube. Please use yellow primer barcodes for this. They are used to identify the primers and to link to the online order. Primer barcodes can be requested free of charge at our Customer Care team and must be activated and customised by you with a batch and BIN number in your account und Barcode Management GATC.

What are PlateSeq Kits resp. PlateSeq Coupons?

PlateSeq Kits and PlateSeq Coupons are the prepaid solutions for our PlateSeq service.

Each PlateSeq Kit comes with a 96well plate and the appropriate seals in a metallic sample box. For each template type we offer the perfect PlateSeq Kit.

PlateSeq Coupons are code numbers provided electronically in your online account. You can use them:

  • For additional prepaid sequencing runs in addition to one of our PlateSeq Kits 
  • As alternative to the PlateSeq Kits for plasmid DNA, purified PCR products or premixed samples for immediate use.

Prepaid solutions reduce your administrative efforts and additionally help you to save your budget. 

What is NightXpress?

With NightXpress your individual samples are sequenced overnight in our laboratory. We offer this service to customers with NightXpress GATC collection points or LIGHTrun tube NXP barcodes.

Please note that PCR products with PCR purification are processed during the day. Your SupremeRun tube results will be available the following working day between 8 and 11 am.

GATC collection points with a NightXpress pick-up service are available in many European towns and cities, and so NightXpress sequencing of SupremeRun samples is possible. 

(*Please note that timely delivery of your samples to the laboratory is required for NightXpress processing. Unfortunately, we cannot accept any liability for the transportation of samples).

How long will my sequencing data be stored?

We will keep your data 100 days after finishing your reads in your personal account. During this time, you can download and save your data.

How long do you store samples and primers?

For the Eurofins Services, all DNA samples and synthesised primers are stored for 4 weeks. During this time it is possible to use the DNA and primer for further reactions.

If using SupremeRun services, we keep your DNA samples and primers for 10 calendar days from the date of arrival in the laboratory. 

Premixed samples (DNA mixed with the primer), pre-cycled samples for the Ready2Load service and enclosed primers will be discarded three days after the order is finished and the data submitted.

 

Can I send shRNA constructs or other DNA templates with probable secondary structures?

Yes, we accept templates with more difficult sequence structures with our TubeSeq Service and PlateSeq Service in combination with the Power Read Upgrade. 

Can you sequence phage or genomic DNA?

Please contact our Customer Support to get the best recommendation for your request.

How to order

How can I order your DNA sequencing service?

Please use our online shop for every Custom DNA Sequencing product and service. In the order menu you find all links to the respective sequencing order pages. 

For Mix2Seq you only need to place an online order for the Mix2Seq Kit and no further online order when sending your Mix2Seq samples.

You will find all necessary information regarding sample preparation for each sequencing service under in the sample submission tab of the respective service.

Where should I send my sequencing samples?

Eurofins Genomics and GATC has already installed hundreds of DropBoxes respective Collection Points in Europe for free sample pick-up. Your nearest DropBox location with pick-up time is displayed in your account when you are logged in.

In case there is no DropBox near you, you can of course send your samples by post or arrange for them to be delivered by another delivery company. Please send Sanger sequencing samples to the addresss which is shown to you during checkout.

Options for sending sequencing material are available under sample shipment.

 

Can I order more than one read per sample?

Yes, indepenent on the sample type, up to 8 reactions per sample can be specified with our TubeSeq Service. For the PlateSeq Service up to 4 reactions per sample (= per well) are possible across one 96well plate.

 

How many plates per order can I send?

Up to 15 plates can be uploaded / specified at once and saved in you cart. There is no limitation on the number of plates per order you can checkout.

Can I re-order sequencing runs?

You can order new sequencing reactions from stored samples within 6 weeks no matter if you have sent the samples in tubes or plates. 

If you have sent the samples in tube format, just use the TubeSeq Service order page and type in the initials of the respective sample. The system prepopulates all stored samples with these initials.

If you want to re-order reactions from a few samples originally sent in plates, use our TubeSeq Service order form, select the stored plate and specify the new reactions for the respective samples.

Re-ordering sequencing reactions for an entire plate is possible via the PlateSeq Service order form.

Under "My samples & primers" you can check the expiration date of your samples and primers.

Can I order additional services when using prepaid barcodes?

With prepaid barcodes, you can order additional services such as primer synthesis DNA mini preparations. You will be billed separately for this.

Sample Preparation

How should I send my sequencing samples?

You will find all information about sample format, template and primer concentration as well as shipping information for each of our sequencing services in the respective "Sample Submission" tab.

How should I determine the concentration of my samples?

Please measure the OD with a spectrophotometer at 260 nm and 280 nm. The OD 260 values should be in the range of 0.05 to 0.8 to give reproducible and reliable results. The OD 260/280 ratio should be about 1.8. Values lower than 1.6 and higher than 2.0 indicate contaminants in the sample that interfere with the determination of the concentration and might inhibit the sequencing reaction.

If possible, we recommend measuring the ODs at 230 nm and 320 nm, too. A high value at OD 320 indicates a contaminant. This should be ideally 0.0. The OD 230/260 ratio should be lower than 0.6.

We also recommend ensuring the quality of your DNA by running your sample on an agarose gel.

Which purification method should I use?

For plasmids, we recommend the use of commercially available plasmid mini scale preparation kits employing spin columns. From our experience, repeating the washing step will improve the quality of the DNA and therefore improve the sequencing results. Please do not send DNA prepared with alkaline lysis methods or with the boiling method (Holmes and Quigley, 1981) without column purification. For PCR products please use commercially available PCR purification spin column kits.

Can I send my DNA samples in Tris-EDTA (TE)?

No, please don't.
EDTA binds bivalent cations such as Mg2+ that are essential for the Taq polymerase. Your DNA is stable in double distilled water or Tris-HCl at room temperature for several days or even longer if it is dried down.

Should I submit my DNA samples cooled?

This is not necessary; DNA is stable in water at room temperature for several days. Just send your samples either in Tris-HCl, distilled water or air dried. Please, do not use EDTA as this will inhibit the Taq polymerase.

Can I send unpurified PCR products or clones?

Yes, for all sequencing services we offer template preparation and PCR product purification as an additional service.

Which E.coli strain should I use?

Successful isolation of plasmid DNA is possible from most E.coli strains, though the strain which is used can have a significant influence on the quality of the purified DNA. Host strains such as DH10b, DH5 alpha, XL10 Gold and TOP10 normally result in high quality DNA in combination with many commercially available plasmid DNA isolation kits and are therefore ideal for the propagation of plasmids to be sequenced. Lower quality DNA is derived from strains producing large amounts of carbohydrates, which are released during lysis and inhibit enzyme activity. Examples are HB101 and its derivatives such as TG1 and the JM100 series. Also strains with medium or high levels of endonuclease activity like HB101, JM101 or BL21 generate DNA of lower quality, hence a proteinase K treatment should be considered.

Do I need to clean up my PCR product if there is only one band visible?

Yes, primers and dNTPs must be removed from the product. The primers would produce a mixed sequence (5% contamination with a primer results in unreadable mixed sequences!) and the dNTPs would interfere with the dNTP/ddNTP concentration in the sequencing reaction. We recommend purification by using commercially available PCR spin column kits. Alternatively we can perform the PCR product purification for you as additional service.

I see unspecific bands in my PCR reaction. Do I need to gel purify my product?

If you want to employ one of the PCR primers in the sequencing reaction you must elute the product of interest from an agarose gel. Otherwise, a mixed sequence will be produced as the primer is most likely to bind both the specific and unspecific products. If you employ a specific nested primer in the sequencing reaction, it might work. However, producing only one product in the PCR reaction is the best guarantee for a good sequence. In almost all cases, improving the PCR conditions (specific primer design, higher annealing temperature and/or lower primer concentration) helps to avoid unspecific products.

Primers & More

Which standard primers do you offer?

More than 80 different standard primers are available for your DNA sequencing order. Please click here to find the complete list of Eurofins standard primers and here for all GATC standard primers which are available free of charge.

Can I send my own primers for sequencing ?

Yes of course. Just specify your enclosed primers in your sequencing order with name and sequence. The primers should be sent in a solution and concentration specified in the respective "Sample Submission" pages.

Can you synthesise a primer for me? How do I order the synthesis?

Yes, we can synthesise your sequencing primer in our oligo production. Just specify your primer for synthesis in your sequencing order with the respective name and sequence. Please note, that we keep these primers for 6 weeks at Eurofins and 6 month for GATC service for re-order possibilities.

How should I send my primers and how much primer do you need?

Please find information about primer format, primer concentration and primer shipment information for each of our sequencing services in the respective "Sample Submission" tabs.

Can I pay for primer synthesis using barcodes?

The primer synthesis along with Eurofins sequencing services can be payed with TubeSeq Labels.

For the primer synthesis along with GATC services the primer synthesis is billed separately.

Technical Questions

What are IUPAC bases? Which results will I receive?

DNA base call identification is based on the nomenclature system issued by the International Union of Pure and Applied Chemistry (IUPAC). At positions of ambiguity, the following IUPAC codes are used:

G/T = K C/T = Y A/C/G = V
A/G = R A/C = M C/T/G/ = B
G/C = S A/G/T = D A/C/G/T = N
A/T = W A/C/T = H

What is the plate result summary?

The plate result summary is the result overview of your sequenced samples per plate.
It contains the names of each sample, the read lengths of each sample, the quality clipping positions and the overall quality value of the sequence.

What are Q20 (Q30 / Q40) bases?

Eurofins Genomics is using a quality base calling software which examines the peaks around each base call to assign a quality score (Q) to each base call. Quality scores (Q) range from 4 to about 60, with higher values corresponding to higher quality. The quality scores are logarithmically linked to error probabilities, as shown in the following table:

Quality ScoreProbability of a wrong base callAccuracy of a base call
Q 10 1 in 10 90 %
Q 20 1 in 100 99 %
Q 30 1 in 1.000 99.9 %
Q 40 1 in 10.000 99.99 %
Q 50 1 in 100.000 99.999 %

Which sequencing method do you use?

For all our Custom Sequencing Services we are using the cycle sequencing technology (dideoxy chain termination / cycle sequencing) on ABI 3730XL sequencing machines.

Could you explain the cycle sequencing technique?

Cycle sequencing is a modification of the traditional Sanger sequencing method. The components are DNA, primer, heat resistant DNA polymerase, 4 dNTPs, 4 ddNTPs (dideoxy terminator nucleotides) fluorescently labelled with four different dyes and buffer containing Mg++ and K+. The single primer binds to the complementary DNA strand and is extended in a linear mode.
This extension continues until by chance and depending on the complementary base a particular ddNTP is incorporated. Because of the latter's dideoxy-configuration the polymerase cannot add any other base to this fragment and the extension is terminated. Thus at the end of the selected number of cycles, numerous fragments with different lengths and one labelled nucleotide at the end are generated.

Stoichiometric manipulation of the reaction components ensure that the fragments of every possible length starting from n+1 say 2000 bases are generated with n being the number of bases in the primer. The key difference between the traditional Sanger method and cycle sequencing is the employment of a thermo stable DNA polymerase. The advantage of using such a polymerase, is that the sequencing reaction can be repeated over and over again in the same tube by heating the mixture to denature the DNA and then allowing it to cool down to anneal the primers and polymerise new strands. Therefore less template DNA is needed than for conventional sequencing reactions.

After a post sequencing reaction cleanup, the samples are electro kinetically injected into the array of 96-capillary sequencers. The negatively charged fragments migrate toward the anode by size, the smallest ones move fastest. Their tagged ddNTP terminators can be read as the fragment's base sequence. A laser beam excites these dye molecules as the fragments reach a detection window, producing fluorescent signals that are collected from all 96-capillaries at once, spectrally separated and focused onto a CCD (charge coupled device) camera. Sophisticated optical and electronic devices produce a colour readout that is translated with the help of sequence analysis software into a sequence.

What is the quality report?

The quality report is the trace file in *.pdf format in which the quality value of each single base is shown in colour code below each single peak. Different colours represent the four specified quality ranges.

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