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Direct Colony Sequencing
Sanger Sequencing

Submit your E. coli colonies as a liquid culture, cell pellet, or directly in a colony that needs to be grown up in our lab. 

 

 

About Direct Colony Sequencing with Sanger

Direct Colony Sanger Sequencing (DCS) enables fast, reliable plasmid DNA sequencing directly from bacterial samples without requiring plasmid preparation in your lab. This approach simplifies the Sanger sequencing workflow, reduces hands-on sample preparation, and helps you get results faster. Eurofins Genomics accepts the following sample types for Direct Colony Sequencing.

 

Eurofins Genomics offers multiple DNA preparation options for bacterial samples, allowing you to select the preparation method that best matches your Sanger sequencing needs. Choose RCA Prep, Mini Prep, or Genomic DNA Extraction, and we take care of the preparation before sequencing.

 

No DNA extraction or plasmid purification is required in your lab, although submitting prepared DNA remains an option. We can handle the preparation and Sanger sequencing for you.

  

Order in tubes


Order in plates

 

 

I. Sample Types

Start by choosing the type of biologic material you plan to submit.

  
Starting material What to send Est. Time
Liquid Culture
(recommended)		 200 µL of cloudy culture in LB media. OD600 > 0.3 recommended. Same day
Pellet Submit a cell pellet from 1–5 mL of bacterial culture. Remove as much supernatant as possible before submission.
Colony, Resuspended Pick a colony and resuspend it in a small volume of liquid. We will grow up the colony before sequencing.
+1 day 
Colony, Agar Plate Submit a clearly labeled ~1 cm² patch, or circle and label an individual >2 mm colony.

 

Note: Sample acceptance and preparation requirements may vary by prep method. Please review the Sample Submission Guidelines before submitting samples. Only bacterial samples of biosafety level 1 are supported. Fungal colonies and other sample types are not accepted.

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Choosing a Prep Option for Sanger Sequencing?

RCA Prep, Mini Prep, and Genomic DNA Extraction offer different ways to prepare your bacterial sample for Sanger sequencing. Not sure which option fits your sample and sequencing needs? See the comparison below before you order.

 

Explore the difference below link-arrow

II. Which Prep Should I Choose?

Start with where your sequencing target is located.

Is your sequencing target on a plasmid?

YES Do you primarily want to screen colonies quickly?

✓ Yes, I want rapid colony screening
Choose RCA Prep — amplify circular plasmid DNA without a traditional Mini Prep.
✓ No, I want purified plasmid DNA
Choose Mini Prep — isolate and purify the plasmid DNA before sequencing.

Is your sequencing target in the bacterial chromosome?

✓ Yes, my target is genomic
Choose Genomic DNA Extraction — isolate bacterial genomic DNA for chromosomal sequencing targets.

Quick Guide: Plasmid Screening → RCA Prep   |   Purified Plasmid → Mini Prep   |   Genomic Target → Genomic DNA Extraction

 

 

III. Pick the Prep You Want

III. Pick the Prep You Want

 

 

RCA Prep

Mini Prep

Genomic DNA Extraction

Best for

Fast plasmid screening

Purified plasmid sequencing

Chromosomal/genomic targets

Primary DNA target

Circular plasmid DNA

Plasmid DNA

Genomic DNA

Typical starting material

Colony or culture

Bacterial cells/pellet

Bacterial cells/pellet

DNA purification

No traditional plasmid purification

Yes

Yes

Ideal use

Quickly screen clones

Confirm plasmid constructs with purified template

Sequence genes located in the bacterial genome

Choose it when..

Speed and efficient plasmid screening are the priority

You want purified plasmid DNA before sequencing

Your target is genomic rather than plasmid DNA

RCA Prep

Amplify plasmid DNA directly from bacterial samples for Sanger sequencing.

Fast Plasmid Screening Without a Traditional Mini Prep

Rolling Circle Amplification (RCA) amplifies circular DNA directly from bacterial material using Phi29 DNA polymerase and random primers. Because plasmid purification is not required before amplification, RCA provides a convenient way to move from bacterial colonies or cultures directly into plasmid sequencing.

When Should I Use RCA?

Choose RCA when your target is a circular plasmid and your primary goal is to quickly screen bacterial clones.

RCA is particularly useful for:

✓ Screening colonies after cloning or transformation

✓ Confirming the presence of an expected insert

✓ Comparing multiple bacterial clones

✓ High-throughput clone screening

✓ Identifying which clone should move forward for additional work

Best suited for:
Rapid plasmid screening when you want to avoid performing a traditional Mini Prep before sequencing.

Considerations

Designed primarily for circular DNA: RCA is not the appropriate preparation method when the sequencing target is bacterial genomic DNA.

Amplification-based: The DNA template is amplified rather than simply purified from the bacterial sample.

Best suited for screening applications: Projects requiring purified plasmid DNA may be better suited for Mini Prep.

Advantages & Benefits

Advantages

✓ Fast
Eliminates the traditional plasmid Mini Prep step.
✓ Low Hands-On Effort
Send bacterial material rather than preparing purified plasmid DNA yourself.
✓ Great for Screening
Efficiently evaluate multiple colonies to identify candidates for further work.
✓ Amplifies Small Amounts of Starting DNA
RCA can generate substantial quantities of amplified circular DNA from limited starting material.

Benefits at a Glance

✓ Available for E. coli colonies or other gram-negative bacteria

✓ Up to 4 reactions per sample, per plate

✓ High-quality read lengths of up to 1,100 bases

✓ Results available the same day samples are received

✓ Free one-time repetition in case of technical failure*

✓ Multiple sequencing result file options

✓ Large selection of standard primers available free of charge

✓ Sequencing primers can be ordered or enclosed

✓ Easy re-ordering from stored DNA samples

Applications of Direct Colony Sequencing

Direct Colony Sanger Sequencing enables rapid characterization of plasmid-borne genetic elements from cultured bacterial samples. It is particularly useful for verifying plasmid constructs and screening cloning experiments before final confirmation.

Typical applications include:

✓ Plasmid construct verification

✓ Clone screening after transformation

✓ Insert confirmation

✓ Comparison of multiple bacterial clones

✓ Confirmation of known plasmid-borne genes

✓ Monitoring plasmid stability

✓ Selection of candidate clones for final confirmation

Value of Direct Colony Sequencing

Direct Colony Sequencing saves time by sequencing plasmid DNA from bacterial colonies or cultures without requiring traditional plasmid preparation. This approach helps researchers quickly screen cloning experiments and select candidates for final confirmation.

Time and Cost Efficiency
By reducing DNA extraction and purification steps, Direct Colony Sequencing can shorten the plasmid screening workflow and reduce hands-on sample preparation.
How Rolling Circle Amplification Works

The basis of the Direct Colony Sequencing workflow is Rolling Circle Amplification (RCA), which generates multiple copies of circular DNA. RCA uses random hexamer primers and Phi29 DNA polymerase to amplify the circular DNA template.

01  Start with Bacterial Material

Starting material may include bacterial cells containing a plasmid, isolated plasmids, intact M13 phage, or other circular DNA templates.

02  Random Primers Bind

Random hexamer primers anneal to the circular DNA template at multiple sites.

03  Phi29 Extends the DNA

Phi29 DNA polymerase extends each primer. When the polymerase reaches a downstream extended primer, strand-displacement synthesis occurs.

04  Circular DNA is Amplified

Displaced DNA strands become available for additional primer binding, resulting in exponential amplification and high-molecular-weight double-stranded concatemers containing multiple copies of the circular template.

RCA Process
RCA is performed at 30°C without thermal cycling. Depending on the source of starting material, amplification is typically completed in 6–18 hours. The amplified DNA can be used directly for sequencing without additional purification.
Rolling circle amplification principle
Technical Details & References

About RCA

RCA is an isothermal amplification method that can generate microgram quantities of DNA from very small amounts of circular template DNA. Phi29 DNA polymerase provides strong strand-displacement activity and proofreading capability, supporting high-fidelity DNA replication.

Starting Material

Starting material for RCA can come from a variety of sources, including a small number of bacterial cells containing a plasmid, isolated plasmids, intact M13 phage, and other circular DNA templates.

Bacterial colonies can be picked from agar plates and added directly to the submission plate. Small quantities of saturated bacterial culture or glycerol stock may also serve as starting material.

Validation Note

The Direct Colony Sequencing service has been validated primarily for plasmids in E. coli colonies. In principle, the method may also work with large constructs such as BACs and other organisms. Contact us for pilot testing and optimization of non-standard applications.

References

Dean, F. et al., Genome Research 11, 1095–1099 (2001).
Lizardi, P. et al., Nature Genetics 19, 225–232 (1998).
Esteban, J.A. et al., Journal of Biological Chemistry 268, 2719–2726 (1993).

 

 

Mini Prep

Prepare purified plasmid DNA for Sanger sequencing.

Purified Plasmid DNA Prepared for Sequencing

Mini Prep isolates and purifies plasmid DNA from bacterial cells before sequencing. Instead of performing the plasmid purification in your own laboratory, submit the appropriate bacterial starting material and Eurofins performs the preparation before Sanger sequencing.

When Should I Use Mini Prep?

Choose Mini Prep when your target is a plasmid, but you prefer to sequence a purified plasmid template rather than an RCA-amplified template.

Mini Prep is particularly useful for:

✓ Plasmid construct confirmation

✓ Insert verification

✓ Mutation confirmation

✓ Sequencing multiple regions of a plasmid

✓ Projects where purified plasmid DNA is preferred

✓ Following up on clones identified during initial screening

Best suited for:
Plasmid sequencing projects where a purified plasmid template is preferred before Sanger sequencing.
Advantages
✓ Purified Plasmid Template
Plasmid DNA is isolated from the bacterial cells before sequencing.
✓ Familiar Workflow
Uses the conventional plasmid preparation approach commonly used before Sanger sequencing.
✓ Excellent for Plasmid Confirmation
A strong choice when your clone has already been selected and you want sequence confirmation.
✓ Saves Laboratory Time
Eurofins performs the preparation rather than requiring your team to Mini Prep samples before shipment.
Considerations
Additional Preparation Step

DNA must be isolated and purified from the bacterial sample before sequencing.

Not Intended for Genomic Targets

If the sequence of interest is located on the bacterial chromosome, choose Genomic DNA Extraction instead.

May Be More Preparation Than Necessary for Initial Clone Screening

For rapid screening of many plasmid-containing colonies, RCA may provide a more streamlined workflow.

Mini Prep vs. RCA

Both Mini Prep and RCA can be used when your sequencing target is a plasmid, but they prepare the plasmid template differently.

Choose Mini Prep

When you want plasmid DNA to be isolated and purified from the bacterial cells before Sanger sequencing.

Choose RCA

When your goal is rapid plasmid screening and you want to avoid the traditional Mini Prep step by amplifying circular DNA directly from bacterial material.

 

 

Genomic DNA Extraction

Prepare high-quality genomic DNA for bacterial genome sequencing.

DNA Preparation for Bacterial Genomic Targets

Genomic DNA Extraction isolates bacterial genomic DNA for sequencing targets located within the chromosome rather than on a plasmid.

This option expands Direct Colony Sequencing beyond plasmid verification by allowing researchers to submit bacterial material when the sequence of interest is part of the bacterial genome.

When Should I Use Genomic DNA Extraction?

Choose Genomic DNA Extraction when your target is located in the bacterial chromosome rather than on a plasmid.

Potential applications include:

✓ Confirmation of genomic mutations

✓ Verification of genome edits

✓ Sequencing chromosomal gene regions

✓ Genotyping bacterial strains

✓ Confirmation of genomic insertions or deletions

✓ Analysis of specific bacterial genomic loci

Best suited for:
Sanger sequencing projects where the target sequence is located within the bacterial chromosome and genomic DNA must be isolated before sequencing.
Advantages
✓ Access Genomic Targets
Allows Sanger sequencing of regions that cannot be prepared using plasmid-focused RCA or Mini Prep workflows.
✓ No Extraction Required in Your Lab
Send the appropriate bacterial material and Eurofins performs the DNA extraction.
✓ Useful for Engineered Strains
A convenient option for confirming genomic edits or other chromosomal changes.
✓ Broader Sample Applications
Extends the service beyond plasmid-containing bacterial clones to targets located within the bacterial genome.
Considerations
More Extensive Preparation

Genomic DNA must be extracted from the bacterial cells before downstream sequencing.

Not Necessary for Plasmid-Only Targets

When the sequence of interest is located on a plasmid, RCA or Mini Prep will generally be the more appropriate preparation method.

Target-Specific Sequencing May Require Additional Workflow Considerations

Primer design and amplification requirements depend on the genomic region being investigated.

Genomic DNA Extraction vs. Plasmid Prep

The appropriate preparation method depends primarily on whether your sequencing target is located in the bacterial chromosome or on a plasmid.

Choose Genomic DNA Extraction

When your sequence of interest is located within the bacterial chromosome and genomic DNA must be extracted before sequencing.

Choose Mini Prep

When your target is located on a plasmid and you want purified plasmid DNA prepared before Sanger sequencing.

Choose RCA

When your target is a circular plasmid and your primary goal is rapid clone screening without a traditional Mini Prep.

 

 

How Direct Colony Sanger Sequencing Works? →

Same Powerful Sanger Sequencing. Less Work Before You Submit.


Why Choose Direct Colony Sequencing?

Direct Colony Sequencing reduces the amount of sample preparation researchers need to perform before submitting samples for Sanger sequencing.

Instead of maintaining separate workflows for colony screening, plasmid purification, and bacterial DNA extraction, select the preparation option that fits your project and let Eurofins handle the preparation.

✓ Less hands-on prep
Send bacterial starting material instead of preparing every DNA template yourself.		  
✓ Flexible preparation options
Choose RCA, Mini Prep, or Genomic DNA Extraction.		  
✓ Plasmid and genomic applications
Sequence targets carried on plasmids or within the bacterial genome.		  
✓ Easy transition from screening to confirmation
Use RCA for rapid plasmid screening and Mini Prep when purified plasmid confirmation is preferred.		  

 

 

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1. Submit sample

Culture, pellet, colony
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2. No Prep Req.

We handle the prep step
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3. Sequencing

Long-read sequencing

Ready to sequence your colony?

Liquid culture, cell pellet, resuspended colony, or a colony straight from the plate — choose your sample format and send it to us. We’ll handle the DNA preparation and Sanger sequencing, so you can spend less time on prep and get to your results faster.

 

Order Now !

Many Options

One Workflow

We make it easy for customers by accepting all major colony sample types, and we figure out what prep is needed.

 

 

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Liquid Culture

After growing up the bacteria, the user takes some bacterial material usually from a colony and inoculates into a growth medium such as LB. Then it is incubated so the bacteria multiple. The cloudiness in the liquid comes from the bacterial biomass suspended throughout the liquid. 

Colony → inoculate LB → incubate → bacteria multiply → cloudy culture
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Cell Pellet

A cell pellet generally starts as a liquid culture, although not always. After growing up the bacteria, the user centrifuges the culture which forces the bacterial cells to the bottom of the tube.

Liquid culture → centrifuge → cells collect at bottom → remove supernatant → cell pellet is left
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Colony, Agar Plate

This is the least processed format. We require +1 day to grow the material up in our lab if submitted as a solid colony off an agar plate. The customer grows bacteria on an agar plate, where individual bacterial cells multiply into visible colonies. Then they circle the colony they want us to use. 

Agar colony > Submit on agar plate
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Colony Resuspension

The customer picks a colony and transfers it into a small volume of liquid in a tube. This is different from a liquid culture because the bacteria generally aren't being grown to high density in that tube. The customer is primarily transferring the biomass that was already present in the colony. 

Agar colony → pick colony → resuspend cells in liquid → submit tube

Sample Submission Guide

Transform your plasmid into E. coli or streak your glycerol stock onto an agar plate. Allow individual colonies to grow to at least 2 mm in diameter, with sufficient spacing between colonies to make picking easy. For low-copy plasmids, larger colonies are preferred to provide adequate starting material.

Standard EndA− E. coli cloning strains, such as DH5α, DH10B, and TOP10, generally provide the most reliable results.

EndA+ strains, including BL21 and some JM strains, may also be submitted; however, performance can vary depending on the strain and culture conditions. Residual nuclease activity may contribute to plasmid degradation and increase the likelihood of an unsuccessful sequencing result.

Important: This workflow is intended for E. coli. Other bacterial species are not supported.

 

 

 

1. Option 1: Liquid Culture

Liquid cultures are a convenient submission option for Direct Colony Sequencing when your E. coli clone is already growing in culture.

  • Inoculate a single colony into 1–5 mL of LB medium containing the appropriate selection antibiotic.
  • Grow the culture at 37°C with shaking at approximately 200–300 rpm.
  • Allow the culture to reach sufficient cell density before submission. The culture should be visibly turbid.
  • Transfer 200 µL of well-mixed, cloudy culture in LB medium into the specified sample tube for submission.

Cultures with very low cell density may provide insufficient bacterial material for DNA preparation and can increase the likelihood of an unsuccessful sequencing result.

Important: This workflow is intended for E. coli. Other bacterial species are not supported unless otherwise specified.

Submitted sample material is not returned. Retain the remaining culture for storage, additional growth, or downstream experiments.
   
2. Option 2: Cell Pellet

Grow your E. coli culture under the appropriate conditions for your strain and construct.

 

Transfer 1–5 mL of bacterial culture to a suitable centrifuge tube and centrifuge until a compact cell pellet forms. Carefully remove the supernatant without disturbing the pellet, removing as much residual liquid as possible.

 

Do not resuspend the pellet. Securely close and label the tube, then submit the cell pellet for Direct Colony Sequencing – Sanger. Eurofins will perform the appropriate DNA preparation based on the prep option selected for your sequencing target.

 

What to submit:
A compact cell pellet prepared from 1–5 mL of bacterial culture, with the supernatant completely removed.

 

Important: This workflow is intended for E. coli. Other bacterial species are not supported unless otherwise specified.
3. Option 3: Colony

Select this option if you have not grown up your colony and need us to grow it OR if you are submitting a resuspended colony.

Colony

Submit your E. coli colonies directly on an agar plate as individual colonies or clearly labeled colony patches.

 

For colony patches:

Create approximately 1 cm² patches, with each patch originating from a single colony. Clearly number each patch so that it matches the corresponding sample number in your Sanger sequencing order.

Incubate the plate until sufficient visible bacterial growth has developed before submission.

 

For individual colonies:

Clearly circle and number each colony you would like sequenced. Each colony should be:

  • At least 2 mm in diameter
  • Well isolated from neighboring colonies
  • Clearly marked and numbered to match the corresponding sample in your sequencing order

For low-copy plasmids, larger colonies are preferred to provide sufficient starting material.

 

Before shipping:

Secure the plate lid with Parafilm and place the sealed plate inside a protective resealable bag. Use only enough Parafilm to securely seal the plate, as excessive wrapping can make the plate difficult to open.

 

Important: This workflow is intended for E. coli. Other bacterial species are not supported.
   

Colony - Resuspended

Colony resuspension provides a convenient way to submit E. coli colonies for Direct Colony Sequencing without preparing an overnight culture or performing DNA extraction yourself.

  • Select a well-isolated colony at least 2 mm in diameter.
  • Transfer as much of the colony as possible into the specified volume of LB medium in an approved PCR strip tube or compatible plate.
  • Mix thoroughly until the cells are evenly suspended.
  • The suspension should appear visibly cloudy, indicating sufficient bacterial material.
  • Securely close or seal the tube or plate and clearly label the sample to match your Sanger sequencing order.
  • Submit the prepared colony suspension according to the Direct Colony Sequencing submission requirements.

For low-copy plasmids, use a larger colony when possible to provide sufficient starting material.

Important: This workflow is intended for E. coli. Other bacterial species are not supported.

 

 

 

Tubes (<48 samples)

200 μL PCR 8-strip tubes 
  • Write the 3-character barcode on the side of the tube in clear handwriting using a thin sharpie marker. The order page automatically generates this barcode for you to make it easy.
  • Do not write the sample name on the tube. The barcode (previous point) is enough. Adding the name typically slows down processing instead of speeding it up.
  • The barcode is your initials followed by a number, e.g. John Doe would get the barcode JD1…JD2…JD3…etc.
  • If using our free barcodes, press down firmly across the entire label to make sure it is secure.
  • Always start on 1. If there are samples already sitting in your cart that start at 1, the order page will display the next available number, which is fine to use. 
  

Plates (>48 samples)

200 μL 96 well plate

  • Write the order number along the side of the plate using a thin sharpie marker.
  • After the order number, write ONT for Oxford Nanopore Samples (whole plasmid) or an S for Sanger samples.

  • Make sure all handwriting is legible. 
  • Do not submit less than 48 samples per plate. 
  • Do not skip wells. 
  • Arrange samples by column (preferred.
  

Tubes (<48 samples)

200 μL PCR 8-strip tubes 
  • Put the 8-strip inside a 50mL conical tube to protect during transit. It is a good idea to add some cushioning inside such as bubble wrap or cotton balls.
  • Print your order confirmation page, fold it so that the order barcode and sample information is on top, and place the tube(s) and confirmation page in a ziplock bag.
  • Do not cut up the 8-strip into separate tubes.
  • Make sure the caps are firmly closed. Do not use the 8-strip tubes with caps that come off easily. An easy way to distinguish between them is to look if the tubes have individual caps or a strip of caps. Strip caps come off easily and should be avoided. Individual caps typically fit more snuggly.
  • Do not use excessive parafilm to seal the tubes. This makes it difficult to open the tubes and can lead to contamination when opening the tubes. The conical tube should be enough to protect them in transit.

 

Separate Sample Types into Separate Bags 

  • It is important to separate Whole Plasmid and Sanger samples into different ziplock bags so the processing team can quickly sort packages and send the samples to the right sequencing group.
  • Include the order confirmation page in each bag, with the order barcode and sample information visible through the bag.

 

  

 

Plates (>48 samples)
200 μL 96 well plate
  • Heat seal is preferred. If using a roller on an adhesive seal, press down firmly and evenly across the entire plate to make sure it is securely sealed across all wells.
  • It is critical that plates are sealed well to avoid leakage and cross contamination between wells.
    • Inspect the seal for bubbles. Bubbles can cause cross contamination if liquid can pass between wells.
    • Wrap plates individually with bubble wrap to protect them.
  • Do not use cap strips on plates. These can cause cross contamination between wells when pulling them off.
  • Avoid stacking multiple plates on top of each other. The wells from the top plate can piece the seal of the plate underneath.

Agar Plate

  • Wrap the agar plate in parafilm to prevent leakage and place inside a ziplock bag.

  

 

 

 

 

For more details, go to the How to Submit Samples webpage.

Dropbox

  • Drop samples in the box the same day the online order is placed. The courier pickups samples on-demand, not every day. If it is past the cutoff time, the courier will pickup the following business day.
  • Package your samples in padded mailer, padded envelope or cardboard shipping box. If you are reusing material, completely remove or cover any existing labels or warnings. Multiple orders may be shipped together in the same package, provided that each order is placed in its own sealed bag and includes the corresponding order confirmation.
  • Ship samples at ambient (room) temperature. Do not include ice packs, dry ice, or other temperature-control materials.
  • Visit the dropboxes webpage for more information on dropbox options and details.
  • Search for dropboxes near to your location.
  

Digital Shipping Label

  • Select the digital shipping label option during checkout. It is found under the "sample submission method" option. Digital shipping labels are free as long as the order amount meets the threshold for free shipping, which usually around $30-35. 
  • A digital shipping label will be automatically generated on the order confirmation page. Print it. 
  • Cut out the shipping label Select the print option to print the label.
  • Package your samples in padded mailer, padded envelope or cardboard shipping box. If you are reusing material, completely remove or cover any existing labels or warnings. Multiple orders may be shipped together in the same package, provided that each order is placed in its own sealed bag and includes the corresponding order confirmation.
  • Ship samples at ambient (room) temperature. Do not include ice packs, dry ice, or other temperature-control materials.
  • For more information, visit the Digital Shipping Label webpage.
  

Ship Normally


  • Package your samples in padded mailer, padded envelope or cardboard shipping box. If you are reusing material, completely remove or cover any existing labels or warnings. Multiple orders may be shipped together in the same package, provided that each order is placed in its own sealed bag and includes the corresponding order confirmation.
  • Ship samples at ambient (room) temperature. Do not include ice packs, dry ice, or other temperature-control materials.
  • Ship using your company's standard shipping carrier (UPS, Fedex, DHL, etc). We strongly recommend shipping via the express option, e.g. overnight, next-day, express, first-class.
  • For more information, visit the Ship Normally webpage.
  

 

 

FAQ / Common Questions

Go to the FAQ page for all questions and answers regarding Whole Plasmid / Nanopore Sequencing.

 

I. Why Use Direct Colony Sequencing?

Reduce hands-on sample preparation and move efficiently from bacterial starting material to Sanger sequencing with preparation options matched to your target.

Key Benefits

✓ Less hands-on preparation    ✓ Flexible DNA preparation    ✓ Plasmid and genomic applications    ✓ Easy screening-to-confirmation workflow


II. How Does It Work?

From bacterial sample to sequencing results in four straightforward steps.

01

Submit Sample

Send your colony, culture, or pellet according to the selected service requirements.
02

DNA Preparation

Choose RCA Prep, Mini Prep, or Genomic DNA Extraction.
03

Sanger Sequencing

Your prepared DNA is sequenced using the selected or available standard primer.
04

Access Results

Download your sequencing results through your Eurofins Genomics account.


III.Sequencing Primers

Choose the primer option that best fits your sequencing project.

✓ Standard Primers — Select from more than 80 validated primers in stock.

✓ Specific Primers — Order primers with your sequencing order; stored for 4 weeks.

✓ Your Own Primers — Submit primers with your samples using Primer Barcodes.*

Optimum Primer Conditions

✓ Length: 16–25 bases
✓ Tm: 50–62°C
✓ GC content: 35–60%
✓ Ideally one G or C at the 3′ end
✓ No phosphorylation or fluorescent dyes
✓ Avoid more than three identical bases in a row where possible

Primer Concentration & Volume

✓ Concentration: 10 pmol/µl
✓ Initial volume: 15 µl
✓ Add 5 µl for each additional sequencing reaction

Wobble bases: Calculate concentration using nX × ConcPrimer, where n is the number of bases represented by the wobble code and X is the number of wobbles.


IV. Common Applications

Support routine screening, verification, and bacterial sequencing projects.

✓ Colony and clone screening
✓ Plasmid construct verification
✓ Insert confirmation
✓ Mutation verification
✓ Recombinant clone screening
✓ Genome-edit confirmation
✓ Bacterial genotyping
✓ Chromosomal target sequencing
✓ Engineered strain verification


V. Frequently Asked Questions

How is a technical failure defined?

A technical failure is a confirmed chemical, instrument, or IT-related defect occurring in the laboratory. Internal quality controls and sequencing quality parameters are used to identify potential failures. Confirmed technical failures are re-sequenced.

What is the storage time?

✓ Template DNA: 4 weeks
✓ Synthesized primers: 4 weeks free of charge
✓ Optional primer storage: up to one year at additional cost
✓ Selected sequence data: secure online archive for 6 months


Ready to Submit Your Samples?

Review the preparation and submission requirements before sending your Direct Colony Sequencing samples.

View Sample Submission Guide →

 

Testimonials

“Always a pleasure doing business with you! Excellent service and turnaround times! I have worked with Eurofins for 10 years, ever since I was a graduate student. My current lab used to order oligos and sequencing from other suppliers but I convinced them to switch to Eurofins. I advocate for you regularly to all of my lab colleagues.”

Bina N.

Bina N.

Customer

“We have been struggling with oligo quality from other providers. The ones we received from you are far and away the highest quality we have observed and at much higher yields and uniformity than we have seen elsewhere. We are incredibly impressed with the quality and have already started recommending Eurofins to collaborators and other colleagues.”

Andrew A.

Andrew A.

Customer

“Easy to navigate and order oligos. I order multiple oligos at once, each with similar specifications—purification, scale, and more—but with different sequences. The ability to set the default values after entering the first oligo made the process much faster and easier. I especially liked that feature.”

Dara L.

Dara L.

Customer

“Excellent quality oligo synthesis services”

Mona a.

Mona a.

Customer

“Best Oligo ordering system I've ever used, and I've been ordering oligos since 1992!”

Bobb PhD

Bobb PhD

Customer

“I have been using Eurofins since the past 20 years as a Lab Manager of an academic research lab in Toronto. I have found Eurofins Oligo service to be excellent in all respects. Great job Team Eurofins :)”

Talat A.

Talat A.

Customer

“You make the best primers. I love that you're able to get them to me in 24 hours with next-day shipping on oligos <= 40 bp. Free shipping, too. I've used your service for 4 of our lab's upcoming papers, and the quality is outstanding.”

Ben C.

Ben C.

Customer

“Great oligonucleotides, especially at longer lengths. Eurofins is able to process primers longer than 60 mers without requiring much longer involvement in terms of price and time.”

D. Levashova

D. Levashova

Customer

“Easy to navigate and order oligos. I order multiple oligos at once, each with similar specifications—purification, scale, and more—but with different sequences. The ability to set the default values after entering the first oligo made the process much faster and easier. I especially liked that feature.”

K. Shearer

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Customer

“I've been using Operon (now Eurofins) since 1999. I've tried other vendors, but neither the quality nor the service ever matched that of Eurofins.”

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