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Sanger DNA sequencing and fragment analysis

 

A white and blue lab machine with a glass window in front.
Photo from ThermoFisher Scientific.

The instrument

Since March 2018 the lab is equipped with an ABI 3500 Genetic Analyzer (8 capillaries). The ABI 3500 is a capillary electrophoresis instrument with the ability to carry out both Sanger sequencing and fragment analysis. The instrument is able to run 8 samples in parallel, and one injection of 8 samples set to long sequences (> 600bp) takes approx. 125 minutes to run. The capillary length is 50 cm and the polymer used is POP7.

Services available

  • Sanger sequencing 
  • Fragment analysis

We also provide BigDye v 1.1 for discounted price for users.

Opening hours

The Sanger lab is open for sample submission Monday to Thursday at lunchtime. 
If you plan to hand in samples after Thursday lunch time contact the facility to check whether there will be time to run them before the weekend. Also, contact the facility before you hand in a larger number of samples (more than one full plate).

Samples submission

Samples should be submitted in 8-tube 0.2ml strips or 96-well plates (not in individual tubes).
Place samples for Sanger sequencing and fragment analysis in dedicated place in the freezer, in room B240 in the Ecology building (Floor 2). When depositing samples into the freezer, also send an e-mail to anna [dot] sterngren [at] biol [dot] lu [dot] se.

Labeling and sample sheet

Preferably label the samples sequentially, 1, 2, 3…and so on, or use the plate well numbers (A1, B1, C1…). If you want to label your samples with more complicated names, use the sample sheet and replace “empty” with your labeling. Save the sample sheet as an .txt file and send it electronically to the facility when submitting the samples. Download sample sheet here (.txt; 2 kB).

Results

Result files are shared via LU Box. The sample turnaround time is normally 1-2 days depending on the sample load.

Sanger sequencing

Sample Requirements

Sequencing reagents used should be the BigDye® Terminator v1.1 Cycle sequencing Kit. Most users deliver sequencing ready pellets of purified DNA ready to run on the ABI 3500. 

Information requirements

  1. Name
  2. E-mail address
  3. Date
  4. The expected length of the fragments 
  5. Where to send the bill (name and kostnadsställe)

This information can be included in an e-mail or on a note attached to the samples. 

Cost

ABI3500 Sequencing: 25 SEK/sample (the number of samples will be rounded up to the nearest multiple of 8)

Fragment analysis

Our instrument is set up to run fragment analysis on samples labeled with Dye set D (FAM, HEX, NED, ROX) with the Genescan ROX500 size standard.

Sample Requirements

PCR products labeled with the dyes FAM, HEX and/or NED .

Information requirements

  1. Name
  2. E-mail address
  3. Date
  4. Dyes used to label samples
  5. Where to send the bill (name and kostnadsställe)

Cost

ABI3500 Fragment analysis: 31 SEK/sample (the number of samples will be rounded up to the nearest multiple of 8).

Page Manager:

Contact information

The sequencing Facility is situated at Department of Biology, in the Ecology Building, Sölvegatan 37 on Floor 2 (staircase A).

For inquiries about Illumina MiSeq sequencing, analyses on Agilent BioAnalyzer and/or fragmentation of DNA/RNA on Covaris, contact:

Tomas Johansson
Researcher
MEMEG

Telephone: +46 46-222 45 49
Mobile: +46 709-57 18 04
E-mail: Tomas [dot] Johansson [at] biol [dot] lu [dot] se

For inquiries about ABI Sanger Sequencing and Fragment Analysis contact:

Anna Sterngren
Research Engineer
MEMEG

Telephone: +46 46-222 08 70
Mobile: +46 72-203 33 56
E-mail: Anna [dot] Sterngren [at] biol [dot] lu [dot] se

Funding

The facility acknowledges generous financial support during the years from the Knut and Alice Wallenberg Foundation (SWEGENE programme), the Crafoord Foundation and the Faculty of Science, Lund University.