I'm a 1st year Msc student of Bioinformatics and my background is Comput Science.
I'm trying to review an article called "An Extended Transcriptional Network
for Pluripotency of Embryonic Stem Cells" by Kim et al. And I'm trying to figure out the diference between bioChIP and ChIP. Because they used it and in the begining they compared the results of them.
I think I know more or less what is chip and these are the steps that I'm going to talk on the presentation:
1- cross link POI to its bind site on the DNA strand
2- cut the dna in small fragments
3- use an antibody to grab the POI. They can have some magnetic head or they can be attached to the surface
4- wash everything and digest the protein-antibody complex
5-tag the resulting DNA strands with fluorescent compound (of course we can amplify before tagging)
6-and make them anneal to its complementary strand in a microarray with all the genome or just one portion we want to check
7-use computer to read the “green” squares
8-normalize the date and eventually localize where are the protein bounding sites
And as far as I understood, bioChIP is just an alternative to ChIP where one uses biotinylation to mark the protein of interest (POI). And so, instead just using antibody for each protein, just need to use an anti-biotin. Is that correct?
Here is the image I made to explain that:
Please tell if you agree and don't bother if the language is not correct, since I'm not a biologist I'm just trying to hit the general point of it.