DNA: E-cadherin Methylation:

PMID: 17272646
Manufacturer: NA
Platform: PCR amplification and sequencing of sodium bisulfite modified DNA.
Platform Description: Genomic DNA (5 micrograms) from each cell line was treated with sodium bisulfite at 50 degrees C for 17 hr. The DNA was then re-suspended in 125 microliters of 10-mM Tris with 1 mM EDTA pH 7.4. Nested PCR amplification and sequencing of the DNA were carried out using either converted or unconverted DNA as template for the PCR. Primers were based on the E-cad promoter DNA sequence (GenBank accession no. L34545). One-strand automated sequencing of the PCR products was performed. For primers and more detailed information see citation.
Molecular Target: DNA
Principal Collaborators: Gene Logic (D Dolginow), SAIC (D Munroe), Johns Hopkins Univ. (A Feinberg)
Genomics and Pharmacology Facility, DTB, CCR, NCI, NIH (W Reinhold)
Raw Data: sequence tracings
Processing Method: Multiple sequence tracings were grouped by bisulfite conversion and sequencing date, calculated as a group mean for each CpG within these groups, and then combined as a mean of these groups.

Table of DNA: E-cadherin Methylation/none: Table of gene metadata and result values processed using none

Intensity values: Methylation values

Gene symbol: Official gene names as defined by the HUGO Gene Nomenclature Committee (http://www.genenames.org/).

Entrez gene id: Gene identifiers may be found by using the search function at Gene (http://www.ncbi.nlm.nih.gov/gene).

Chromosome number, Start, End and Cytoband: Parameters are as reported by he National Center for Biotechnology Information (NCBI), based on the Entrez gene identifier (https://www.ncbi.nlm.nih.gov/gene?Db=gene&Cmd=ShowDetailView).