Project Summary
Amplicon List
Welcome to the presentation of NAME21 data

In the NAME21 project, DNA methylation patterns were analyzed for 190 gene promoter regions on chromosome 21 by using bisulfite conversion and subclone sequencing in five human cell types (leukocytes, fibroblasts, human embryo kidney cell line HEK293, hepatocellular liver carcinoma cell line HepG2 and trisomic-21 fibroblasts derived from a Down syndrome patient). A total of 28626 subclones were sequenced at high accuracy using (long-read) Sanger sequencing resulting in the measurement of the DNA methylation state of 580427 CpG-sites [Zhang et al., 2009].

All bisulfite genomic sequencing data were derived by sublconing of single molecules and analyzed using the BiQ Analyzer software [Bock et al., 2005]. Data were compiled and prepared for presentation using BDPC software [Rohde et al., 2008]. The extracted raw data are available at here.

A compilation of the overall methylation levels of each PCR product integrating the results from direct sequencing and pyrosequencing is available at the amplicon list. There, also information is provided about the corresponding gene name, the amplicon identifier, the strand targeted by PCR, the genomic position of the PCR product, the amplicon size, the number CG-sites analyzed, the GC content as well as the CpG observed/expected of the sequence analyzed, the overall methylation results for each cell type, the primers used and the DNA sequence of the region analyzed. From the amplicon table links lead to further detailed presentations of the data:

  • Visualization of the overall methylation results for each PCR product in the UCSC genome Browser (click on the link below "position" in the amplicon list). The results are displayed in different colors according to the methylation percentage of the PCR product. From each of the annotated PCR products the outside link from the UCSC genome browser leads back to the detailed methylation data.

    Methylation scale:
  • For each amplicon a corresponding overview comprises technical information and provides for each PCR product a graphical representation of the methylation average of each CG-site (click on the link below "Amp_name" in the amplicon list). There for each PCR product a link leads to the presentation of the detailed methylation data.