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Capillary electrophoresis

We operate two 3730 sequencers with 48 capillaries manufactured by Applied Biosystems. The standard service includes a CleanSEQ based purification of sequencing reactions and subsequent sequencing run. Furthermore, a simple separation of dye-labeled fragments without prior cleaning is available, such as for microsatellites analysis.

ABI 3730 electropherogram

 

The charges will be calculated on the basis of the expenses for the capillaries, general chemicals and maintenance (see price lists for details). The sequence service is available only for members of the University of Cologne or as research collaboration project.

Template DNA and Protocols

Note that the quality of the template is usually the most important factor for the quality of the sequencing reaction. In addition, the capillary sequencer runs best when you stick to a given concentration range. Please do not use more as this yields poor results and can block the capillaries! Successfully working protocols used by the CCG itself can be downloaded here.

We highly recommend you to get in touch with us - especially in case of any trouble or poor data quality!

If you plan to prepare DNA from tissues at a high throughput level (e.g. blood up to 10ml) you also should take a look at our biobanking service.

How to start

  • For first time users of a newly established group we need some group leader information:
    • Name, email, phone, fax and billing address
    • The information if the sequence download portal should be open for all people of the group or not.
  • New users always have to send us:
    • Two letter group code
    • Your name, email, phone
  • After that you will get a unique three (in future may be four) letter user code and a password which are required for logging into the order and download portal   where you will find many other useful information.
  • Sequence reactions must be provided in 8-strip PCR tubes or plates from given companies which can be purchased at the CCG.

How to order and download  sequences

There is a simple Browser based (latest Mozilla Firefox is recommended) interface  . Use it to:

  • Give orders
  • Attach your own sample names which later will be part of the file names
  • Watch your order, sample and invoice status
  • Download sequences
  • Watch some statistics about data quantity, data quality …

Please note that sequence data remain downloadable only about a month. Then they are archived on tape and again made available on request. For reasons of internal quality checks, all sequence data are analyzed using Phred. These results are also available for you via download and the order history page.

How to label and where to place sequence reactions?

Sequence reactions must be labeled with a serial number, respectively, such that the sample numbering is understandable. Please further attach your order id and user code outside the tubes/plates. Then bring the samples to our center.

Cologne Center for Genomics
Weyertal 115b
50931 Köln

open: 9 am -16 pm

Samples, which are delivered before 11 am, will normally sequenced on the same day. They can be deposited in a closet in the on weekdays freely accessible foyer of the building. You also can give us the samples personally. In that case conact us with the help of the wall telephone close to the foyer door or the intercom left hand to the front door. As usual, please sign in the order information into the book on top of the box as well!

Please use only the black racks which have been labeled with AG NU for the storage of samples! Your own racks are only temporarily stored and disposed of if necessary.

 

ccg_sample_delivery

Use the black racks labeled with AG NU, sign into the book
and put the samples inside the metal box. We ckeck for new samples between 8 am - 16 pm.
(until 11 am for processing on the same day)

 

Plate handling

Plates like other consumables have to be from given companies (see the download portal for further information). Plates are always considered as completely occupied but we also accept half 96er plate.

We support 96er and 384er plate formats (394er currently only for fragment analysis).

Software

Further analysis of sequencing data requires the use of software. The following table presents some programs that are used by the CCG team for their own projects. If you are interested in using commercial software on the CCG or have any questions about open source software that was developed at our center, please contact us!

 

SoftwareAvailabilityUsage
GeneMapper® Commercial; Computers in the CCG may be used for analysis microsatellite analysis
GeneMarker® Commercial; network based license managment (the software must be installed local on your PC but the license is controlled by our server) microsatellite analysis
DNASTAR® Lasergene SeqMan Commercial; Computers in the CCG may be used for analysis (old version!) sequence analysis; small and medium sized projects
Mutation Surveyor® Commercial; network based license managment (the software must be installed local on your PC but the license is controlled by our server) sequence analysis; large-scale projects; mutation screening
GeneExplorer open source webtool developed at the CCG automatic primer design for any gene that is stored inside the ENSEMBL database; supports merging of multiple transcripts and masking of SNPs

Contact

Please contact our team by using the following email adress.

 

Links

Good luck with sequencing!