Selection of Antibodies for CHip - (Jan/04/2007 )
I have made the TESS analysis of the promotor I want to evaluete. There are a lot of transcription factors that I would like to evaluate. Does anyone knows how to select the antibodies for the CHip assay? Thank you! 
hi micegirl,
many antibodies are now certified for use with ChIP one way is to goto the antibody supplier and check the specs.
Abcam have started to do this as well as other companies.
Another method is to check the antibody's specificity by western and immunofluorescence, however this does not guarantee that the antibody will work but only suggest you that it's specific and may work.
good luck! 
Thank you MethylNick for the infromation.
I have another question
How you identify the trasncription factors to test in ChIP?
Thank you!
that's a really subjective question micegirl,
just pick one and see what it does with your pet genes of interest.
Actually, as there are so many factors around I would choose ones in a familiy that is known to regulate other related genes to your pet gene. Or if you know the developmental expression profile of the transcription factors of interest, I would start there.
but in all honesty it would be to pick one and see what it does really.
Nick
Thank you.
Which program do your recomend for predicting transcription factor binding sites in DNA?
Have a great day
tfscan is a free program with an outdated database of binding sites.
you can get it commerically.
Otherwise have a look at UCSC and there are FirstEF and TFBS conserved tracks that show first exon and TF binding sites respectivly on the genome of interest.
Nick
Thank you for all your help.
Have a great day!
Have a great day!
Hi micegirl,
We use MatInspector program (www.genomatix.de). There is a free version . You only have to register.
In this program you can search for tf binding sites with different core similarities (the most stringent search is to set core similarity to 1 but you can lower it as well).
Grooya