About us
The former core facility KISeq, established at CMB 1992, and the core facility for DNA sequencing and genotyping at CMM L8:00, merged year 2008 into the new core facility KIGene- genetic analysis at CMM.  

Our vision is to provide a high quality, reliable, high effeiciency and flexible core facility, aiming at providing the right solution and study set-up for the right project

The facility houses several different instruments that can be used by those who have sufficient knowledge and experience. KIGene provides start-up theoretical and technical assistance. For some applications we also offer full-service.

Services

• DNA sequencing with short turn-around time
• Genotyping
• Expression analysis
• DNA methylation analysis
• Quantity and quality determination of RNA, DNA, protein and dye incorporation
• customer support
  

Resources at KIGene

• ABI 3730 and 3130XL PRISM® DNA Analyzers
• ABI 7900HT instrument
• TaqMan® OpenArray® Genotyping and Expression Analysis Platform
• PSQ96MA instrument for Pyrosequencing Assay
• NanoDrop 1000 spectrophotometer
• Agilent 2100 Bioanalyzer
  

Our service levels
We provide three service levels for DNA sequencing;
"Hands-on" service
The user receives a short introduction by experienced personnel regarding sample preparation and operation of the instruments. Each user reserves date and time for occupying an instrument by a booking system.
"Hands-off" service
The user provides us with pre-made sequence or fragment analysis reactions and we are performing the analysis. The resulting files are transferred to each user by a FTP account or e-mail.
Full-service
The user provides us with staring materials- as blood, saliva, biopsies, DNA, oligonucleotides- and we are performing the analysis. The resulting files are transferred to each user by a FTP account or e-mail.

New FTP account
Please contact us and we will set up an account free of charge for your group. If someone in your group already has an account you should use that.

How to use a FTP account
Open your web browser and go to http://www.cmm.ki.se/ftpservice.

FTP server        : 130.229.30.18 (port 21)
username         :__________
password          :__________
initial directory  : /username
"Login."
You are connected to your account where your files are placed. To get hold of all your files simultaneously, select the folder containing your files to be copied and click "Download".

All files older than 30 days in the FTP accounts will be deleted regularly from the server. Make sure to save your own copies!

Customer support.
Please contact us!

About DNA sequence analysis at KIGene

Dye-nucleotide sequencing kits
We have the appropriate matrices set up on the sequencers for all versions of the BigDye terminators (Applied Biosystems) and DYEnamic ET terminator (Amersham Bioscience).

We recommend to use version 1.1 or 3.1 BigDye Terminators if the goal is to analyse allelic DNA sequence heterogeneity and when sequencing difficult templates (e.g. G/C-rich, G-rich, C-rich, secondary structures). Note that the version 1.1 BigDye Terminators is specifically for shorter sequencing products where a read close to the primer is important. Version 3.1 may be used for all other applications.

How do we want your DNA sequence samples?
After completion of the sequence reaction, each sample is precipitated and dried before delivery to us.

We ask you to only mark the side of the tubes with sample numbers and your initials. It is sufficient to write the complete sample names in the order form. This procedure actually prevents the risk of sample mix-ups, since it is often difficult to interpret the text written on the tubes. In addition, we need some space on the lids for our internal labelling of the tubes.

If you want us to sequence your templates, follow instructions at Full-service sequence samples .

Sample delivery.
Put your samples in an envelope together with the appropriate order form. Preferably use padded envelope if you are sending them by post.

Internal: Put the envelope in any of our two mailboxes. One is located at the entrance of CMB, Berzelius väg 35, the other at CMM outside the Neurogenetics Unit, L8:00.
NOTE; we will empty the mailboxes at 13:00 every working day. If you have full-service samples and need the data the day after, you will have to leave your template DNA and primers before 10:00 AM at the CMM mailbox!

External: KIGene, MMK, Neurogenetics unit, CMM L8:00, Karolinska University Hospital at Solna, 171 76 Stockholm.

Timescale.
Premade reactions; If we get the sequence reactions before 13:00, you will get the sequence files later the same afternoon or very occasionally before noon the following working day.

Full-service samples; If we get the templates and primers before 10:00, you will get the sequence files later the same afternoon or very occasionally before noon the following working day.

Occasional delays may occur if we experience unusually heavy loads or equipment failure.

Data storage.
We store all data. Therefore, if you lose raw data files we can retrieve these for you if you give us the relevant information (date and sample names).

Sample storage.
We save primers and templates a month in our freezers.

Updated by Annika Eriksson May, 2012