Services | DNA Sequencing | 96 Well Plates

Many customers have a significant number of templates to examine simultaneously and have the ability to provide these in a 96-well format. 

Please note that due to the fact that all samples in a plate undergo the same sequencing reaction, it is critical that customers submit a plate with samples that are of a similar composition:

  1. All normal templates (plasmid or PCR)
  2. Entirely GC-rich templates (requiring GC additive + optimized sequencing reaction)

MRC PPU DNA Sequencing and Services is happy to take on these reactions for you. We encourage you to review the information below prior to submission so that your reaction has the potential to yield the most robust information for your studies.


Materials Required Per Reaction

  • Plasmid: 250-300 ng plasmid in 15 ul (approximately 20ng/ul concentration)
  • Primer: 3.2 pmole (3.2 picomoles is 1µl of a 3.2 uM stock)
    • NOTE: we will NOT add primers to samples; you must add the primer yourself.

Please ensure template is diluted plasmids in water or a buffer that does not contain EDTA (such as Tris-EDTA buffer) which can inhibit the sequencing reaction. 

Please review the table below regarding the amount of PCR template to submit based on length of DNA:

PCR Product Length

PCR Product Required
(per reaction)

Primer Quantity Required*
(per reaction)

100-200 bp

2-6 ng

3.2 pmole

200-500 bp

6-20 ng

3.2 pmole

500-1000 bp

10-40 ng

3.2 pmole

1000-2000 bp

20-80 ng

3.2 pmole

>2000 bp

80-200 ng

3.2 pmole

Samples sent in 96 well plates must only contain enough material for one reaction. 

Special Considerations

96-well Plate Recommendations

You are free to send us your samples in any standard 96 well plate of your choice. However, please note that it must be a standard 96 well plate containing 12 columns of 8 wells. Please ensure it is clear which corner is the "A1" well. 

When sealing the top of the plate, there are various methods you can use such as heat sealing, adhesive film or a silicon sealing mat. We recommend only using a silicon mat as in our experience adhesive film does not stick well and can result in leakage out of wells; moreover heat sealing is difficult for us to remove in order to access the samples. For customers wishing to use silicon mats, we recommend mats from Elkay Labs. The ones we use have product code "MAT-PCR-96". We will return mats in batches to customers for re-use. If using these mats, we recommend VWR 96 well half skirted plates (732-2390). The combination of mat and plate provide a very good seal and there should be no leakage of contents.

For those customers who only require a small number of plates/mats and do not wish to buy entire boxes of both, please contact us and we will supply you with the number of plates/mats you need at £10 per plate (including postage & packing) along with a protective base plate and a silicon sealing mat to keep your samples in the wells when you return the plate together with your samples.  


Organization of Samples on Plate

You may send either 48 or 96 samples per plate. If you send less than 48 or 96 samples, you will be charged for the full 48 or 96 samples. Please organize the samples into the wells in the format given below. Failure to do this will result in the samples not being processed. Please ensure that you know where each of your samples is on the plate, since result files will be numbered as illustrated below (i.e. consecutively from 1...48 or 1...96).

Organising 48 and 96 Well Plates

Please note the cut corner on the plate (upper right) and the reference numbers/letters that will also appear on the microtitre plate. Please ensure that your samples are placed exactly as per the illustrations above or you will not receive your samples back in the correct order. Once all your samples are ready, seal the plate and send to us.

As above, please contact us if you want us to supply you with a plate/mat for the samples.  

Result File Labeling

Results files for 96 well plate sequencing are labeled according to sample number (as shown in the plate image above). Samples have the following format "Sample number_Capillary number". For example "01_008". This is sample "1" and is located in well A1 of the plate. Sample 2 would be "02_007", etc. We include the capillary number in the name of the sample result file since it helps us if there are issues with samples.

Read Length

There are many factors that can affect the read length one obtains. Our facility will endeavour to provide customers with the longest read possible depending on service requested. Our new ABI 3730 sequencer uses the latest technology and provides really excellent results.

With a template of appropriate quality, customers can expect read lengths of up to 1000 bases of sequence from a single primer when sequencing standard templates (<20kb). For other types of template (especially for large templates), read lengths can decrease to issues of template quality and quantity. If you have problems achieving good read lengths with high quality template, please take a look at our resources section. If you still need more help, please feel free to contact us.


FOR STANDARD PLASMIDS:  If all your templates are of a similar composition (<20kb and do not contain secondary structure/high GC-content) each sample on a 96-well plate can be processed at a cost of £4.50 per well


# of Samples/Plate Sample Cost/Well Total Cost/Plate
48 £4.50 £216
96 £4.50 £432


FOR PLASMIDS WITH HIGH GC-CONTENT:  If all your templates are of a similar composition (<20kb, containing secondary structure/high GC-content) each sample on a 96-well plate can be processed at a cost of £5.50 per well. This is due to the fact that an 'Augmented Protocol' will be used for plamids known to contain secondary structure/high GC-content.

# of Samples/Plate Sample Cost/Well Total Cost/Plate
48 £5.50 £264
96 £5.50 £528


Do you routinely sequence a large number of 96-well plates?

Why not contact our staff to learn about savings options?

Our pre-payment option will help you save more per reaction!

Learn more about all our pricing and turnaround.

Please note that prices are exclusive of VAT, which customers outside The University of Dundee will be charged at the appropriate rate (currently 20%) on all products and that all sales are subject to MRC PPU DNA Sequencing and Services' Terms and Conditions.

Turnaround Time

 Results are routinely supplied to customers within 36 hours upon receipt of plates and involves the following steps:

  • Cycle sequencing reactions are performed on the day the plates are supplied to us
  • Evaluation of productions on our sequencers is the final step in the process


Do you need any help? Please get in touch and we’ll be happy to lend a hand.