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Cologne Center for Genomics (CCG)

News

Regular Sanger sequencing service only until June 30, 2024 - Due to the sharp drop in demand over the past years, we are forced to discontinue the regular Sanger sequencing/ capillary electrophoresis service on June 30, 2024. Samples can still be sequenced by us starting on July 01, 2024, but the sample number should at least come close to batches of 48 or 96 samples, or a multiple thereof, respectively. Please let us know beforehand if you plan Sanger sequencing or fragment analysis of samples and send an email to ccg-seqserviceSpamProtectionuni-koeln.de.

 

 

Capillary electrophoresis

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

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!

 

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 the CCG.

Cologne Center for Genomics
Weyertal 115b
50931 Köln

We offer the sequencing service from Monday to Friday again starting May 22, 2023. Samples should be brought before 11 am on these days. Please deposite your samples in the metal closet on the left in the foyer of the CCG building that is on weekdays freely accessible. You may also hand the samples in personally. In that case please call us from the telephone hanging on the left side next to the glass door. As usual, please sign in the order information into the book on top of the metal closet 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.

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!

 

Software Availability Usage
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: ccg-seqservice@uni-koeln.de

  

Links

Good luck with sequencing!