Methylation analysis/bisulphite sequencing

[Jeffrey H. Boatright]

We are trying to determine the methylation status of cytosine residues on
individual chromosomes by PCR amplifying genomic DNA that has been
bisulphite-treated, thus converting unmethylated cytosine residues into
uracil by deamination (Nuc. Acids Res. 22:695).

Our problem is that the bisulphite/hydroquinone treatment somehow causes
almost complete loss of starting DNA.  Is anyone attempting this and have
you met with success?

Thank you in advance for your advice/thoughts.

Jeff Boatright
Mach Bhati