Welcome to UEF Chromatin Center (UEFCC)

The UEFCC is a part of Biocenter Kuopio and a node in Biocenter Finland Genome-wide Methods Network. The UEFCC can provide on a collaborative basis expertise and methodological services in the areas of chromatin and gene transcription. Our expertise covers promoter and enhancer activity assays (reporter gene assays in cultured cells), electrophoretic mobility assays (EMSAs) as well as chromatin immunoprecipitation (ChIP) and ChIP-seq library preparation from cultured cells and tissues.

 

ChIP can be performed either from cultured cells or from tissue samples and it provides information on:

  • Occupancy of transcription factors on chromatin in specific genomic loci in whole genome
  • Histone marks linked to gene activation or repression at specific genomic loci/whole genome 
  • DNA methylation at specific genomic loci/whole genome
     

We can perform DNA Library Preparation for Illumina next-generation sequencing (ChIP-seq)

Sample requirement for library generation:

  • 10 ng purified ChIPped DNA in max. 44 µl water or TE-buffer
  • Majority of fragments within size range 150 – 300 bp
  • Use 1.5 ml low binding tubes (e.g. Eppendorf)

We are using the NEBNext® ChIP-Seq Library Prep kit for Illumina with multiplexing and barcoding capabilities. After library preparation, the yield is still too low to be visible on a regular agarose gel, even though it is sufficient for cluster generation. Therefore, libraries are quality controlled (size, purity, and concentration of the sample) by Agilent Technologies 2100 Bioanalyzer.

For more information about the Illumina next-generation sequencing, please visit the Illumina web site.

The best way to start your experiments is to arrange a meeting with us. In the meeting, we will figure out your experimental design and the questions related to your sample preparation.

Contacts

Prof. Jorma Palvimo
jorma.palvimo (at) uef.fi