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Ecoli NightSeq – Sanger Sequencing Directly from E. coli Colonies

Ecoli NightSeq - Sanger sequencing service for plasmids
 
 
Sequence your plasmids directly from E. coli colonies without plasmid DNA preparation. Pick a colony, send it to Microsynth and receive your sequencing results the next working day.
Save time, reduce hands-on lab work and accelerate your research by one full day.

Available for drop boxes in Switzerland, France and Germany connected to our same-day courier system.

Why Choose Ecoli NightSeq?

  • No DNA Preparation Required - Send E. coli colonies directly — no plasmid isolation needed.
  • Fast Overnight Results - Receive your sequencing results the next working day before 2 pm (tubes).
  • Save Time & Costs - Reduce hands-on time and avoid unnecessary plasmid purification steps.
  • Robust & Reliable - Standardized in-house workflow ensures consistent, high-quality sequencing results.

Product Video

 
 
Don't forget to turn on the sound.

How It Works

  1. Pick a single E. coli colony
  2. Transfer it into a Microsynth tube or 96-well plate
  3. Drop your sample into a Microsynth drop box
  4. Receive your sequencing results the next day
Timetable Ecoli NightSeq

Applications

  • Plasmid sequencing directly from E. coli colonies
  • Clone screening and validation
  • High-throughput colony testing
  • Screening of low-copy plasmids

What is Ecoli NightSeq?

Ecoli NightSeq is an innovative Sanger sequencing service that allows direct sequencing of plasmids from E. coli colonies without prior DNA preparation.
This streamlined workflow enables faster decision-making by eliminating plasmid isolation and delivering results within one working day.

Output & Data

You receive standard Sanger sequencing data including:

  • Chromatogram files (.ab1)
  • Base-called sequences

Additional Features

  • Works with various E. coli strains
  • Suitable for low-copy plasmids
  • Consistent results due to standardized processing

How to Order

Procedure to order labels for our Ecoli NightSeq:

  • Enter our webshop
  • Click on Tubes or Plates under "Ecoli NightSeq" and follow the further instructions
  • You can choose between prepaid and non-prepaid labels
 
Procedure to use our Ecoli NightSeq for sequencing:
 
  • Enter our webshop
  • Click on one of the options under Ecoli NightSeq (prepaid or non-prepaid) and follow the further instructions
 
See also Microsynth's user guide on the right side for more detailed information.

Frequently Asked Questions

Technical Questions

Is it necessary to add antibiotics to the liquid in the tube?

No, an antibiotic is not necessary.

Do I really have to pick from a colony that is at least 1 mm in diameter?

The colony might be a bit smaller, but it must be clearly visible.

I want to inoculate the Ecoli NightSeq® Tube and streak out on an agar plate with the same toothpick. What should I do first: Inoculate the Ecoli NightSeq® tube or streak out my agar plate?

First the Ecoli NightSeq® tube.

Does Ecoli NightSeq® work for low copy plasmids as well?

Yes.

I do not work with agar plates, but with liquid culture. Can I also inoculate the Ecoli NightSeq® tubes with liquid culture?

Yes, please add 5 µl.

For how long does Microsynth store my Ecoli NightSeq® samples?

Isolated templates are available for 1 month.

Does the Ecoli NightSeq® also work for BACs or other organisms?

We know that the Ecoli NightSeq® works with BACs and other organisms, but in some cases not as successful as with E.coli. We recommend performing pilot tests beforehand. A good option to increase the quality is to make a raw isolation of the plasmid / BAC and add 1 µl of this isolate in the Ecoli NightSeq® tubes.

We had good results with:

- Direct picking of Pseudomonas putida, Sinorhizobium meliloti, Fusobacterium nucleatum, Bacillus megaterium, Priestia megaterium. We recommend to try and in the case of fail, isolate the plasmid and add 1 µl into our tubes.
- Yeast which were pretreated in 20mM NaOH at 95°C, 10 min. Add 5 µl to our Ecoli NightSeq® tubes and heat 95 °C, 15 min.

 

 

Stability

How long can I use Ecoli NightSeq® tubes? How shall I store them?

Storage time: 4 years, Storage conditions: 4 °C. Expiry date and storage conditions are indicated on the packaging bag.

Multiple reactions from one single clone

I would like to pick a clone and sequence it with a forward and reverse sequencing primer. Is that possible?

Yes. You have two possibilities:

  1. Pick the colony in one Ecoli NightSeq® tube, mix it and transfer the liquid into a second Ecoli NightSeq® tube, mix it again and split the liquid between the two Ecoli NightSeq® tubes. Equally the same number of cells shall be in both tubes.
  2. Pick the colony in one Ecoli NightSeq® tube and label it with a barcode. Send us the Ecoli NightSeq® tube along with a second Ecoli NightSeq® label within a transparent plastic bag.


In both cases you have to register the forward as well as the reverse reaction on our webshop.

I would like to perform a second reaction with a different primer after I received the result from the first reaction. Is that possible?

Yes, it is for tubes. Proceed as following:

  1. Because Microsynth has already isolated your plasmid, you can perform any additional sequencing reactions by using the cheaper Economy Run service. Therefore, enter the Economy Run ordering mask, define the additional reaction by using a prepaid Economy Run barcode.
  2. On the last page of the ordering mask, please add following information into the comment box: Please use my sample(s) from order number XY.

Please note:

  1. Isolated templates are kept for 4 weeks only when using the Ecoli NightSeq service.
  2. Additional reactions are performed as soon as possible, but our time promise is no longer valid.
  3. Please contact us if you do not have the possibility to use prepaid labels Economy Run in order to find a workaround, such as using the non prepaid version of Microsynth’s Economy Run service.

Logistics

I do not have a Microsynth drop box in my vicinity. May I also mail it, even if it stays over the weekend?

Yes. We have tested a correspondingly long storage at room temperature and it doesn't harm the sample.

Do I receive the results on Saturday, when I drop the samples on Friday into the drop box?

No, only on Monday before 2 pm.

How should I send / label the sequencing primer?
The same way as with our other types of services.
Concentration 10 µM, at least 20 µl volume and write the name of the primer on the tube.

Testimonials

“Thanks to the new Ecoli NightSeq service from Microsynth, we are now able to sequence in high-throughput format and save up to two days compared to the previous service. Time really is money for us since we can significantly shorten critical project timelines. The easy sample preparation, the high-quality sequences, the long read-lengths as well as the competent, fast and uncomplicated customer support were convincing us, too.”
Andreas Lehmann, Molecular Partners AG

“We’ve been using the Ecoli NightSeq service proposed by Microsynth for 6 months now and have only seen advantages to the system. It allows you to save one day in your cloning process by sending directly your colonies for sequencing. The most important aspect is that you do not need to extract the DNA saving bench time and money. This reduces in effect the general price of the read. We’ve been surprised by the quality of the reads which you cannot distinguish from extracted DNA reads. Overall, it’s a plus!”
Thomas Lunardi, EPFL SV ISREC UPLIN

“I have used the Ecoli NightSeq service primarily to test whether a site directed mutagenesis has worked, as well as to check cloned CrisprCas9 plasmids. For such applications this service is very convenient, as they need to be confirmed with sequencing anyways and hence Ecoli NightSeq allowed me to save unnecessary minipreps.”
Barbara Hauert, University of Bern

“The main benefits of Ecoli NightSeq are saving one day as well as saving time and consumable costs for the mini-prep of 3-5 picked colonies from each clone. Another benefit is that Microsynth Seqlab provides the option for standard primers, which makes life easier for many constructs. In terms of quality, whenever poor sequence reads were found, Microsynth Seqlab has repeated the sequencing with no extra cost. Taken together, I’m extremely satisfied with the new Ecoli NightSeq service, an additional high standard sequencing service from Microsynth Seqlab.”
Dr. Shubhendu Palei, TU Dortmund