CHIP on Chip array - (Nov/02/2005 )

Hello:

I am wondering if anybody could help me here?

Nimbgen has a genome wide CHIP array. I like to know if I could do a CHIP assay by using some methy-specific antibody (5-methyl cytosine or MeCP2?) to identify genes that were hypo- or hyper- methylated after drug treatment?

Does this sound right?

Thanks!

sounds absolutely plausible to me, if fact we are about to start experiments with the nimblegen chips as well!

Nick

Hi, Nick:

Which antibody should I use, anti 5-methylcytosine or anti CG binding protein?

I also talked to Upenn genomics core, they have the promer array sevice too. Seems cheaper.

promoter array would be cheaper and be the better option if all you are looking at is methylation of genes after drug treatment.

As for antibody to use, if you could, use a range of antibodies including Anti-5meC and MeCP2 and MBD's just to cover yourself as it may well be plausible that MBD proteins do not associate with all methylated promoter regions.....although this has yet to be tested out.

Microarray analysis will tell you where to look and you would need to confirm the results with another methylation based assay.

Good luck!

Thanks a lot!

I am going to start working on this. Looks like Agilent has the promoter array too.

Affy are about to release human genomic tiling arrays suited for ChIP.

Ain't holding my breath for them as they are known for the high cost for the arrays and the analysis platform

Nick

I just learned that too. Affy is behind though. Looks like this is a hot area. Too many projects we could do with this Chip on Chip.
Nimblegen said they could reuse the glass slide to lower the cost, I don't feel good about that.

Hi, Nick:

Do you mind to let me know why you choose Nimblegen? It is so difficult to decide which company to go since everybody said theirs better. It is so hard to know which one is better unless to compare the data side by side.
Thanks!

nimblegen

does the array hyb and data extraction in house (you send the DNA/RNA to them).

Their array design uses isothermal oligos thus reducing the variation of signal ratios that could be due to hybridisation inefficiencies with variable Tm oligos.

these were the two main reasons.

Does anyone have experience using Nimblegen's whole genome set of 38 tiling arrays? If so, I'd appreciate hearing about the pros/cons as well as the costs. Thanks in advance!