Genome Chips

[Darwin420]

I found this quite interesting and suggest you guys check this out if you are interested.

http://www.plantenergy.uwa.edu.au/educa ... oarray.pdf

This is just simple overview of how it works.
So let me get this straight:

This chip can have the cDNA of the organism and who ever using this tool gets their own sample where they place it in the chip with the cDNA. The two strands of DNA hybridize and the computer picks up on which sequences do and don't bind. The sequences that don't bind signify that this particular individual is not expressing that protein, right?

When using your sample DNA how do you know if you are using the right strand (the strand complimentary to the cDNA)?

[Darwin420]

Wow, a lot of views, I am impressed.

[biohazard]

If I got this right, you don't use DNA from your samples, but mRNA instead. This is converted to cDNA, which then binds to its corresponding gene sequence on the chip. So the active genes can be seen on the chip, because they are the ones that produce mRNA.

[canalon]

Yep and the signal intensity is supposed to be proportional to the level of expression of each gene.
But the conclusion is correct.
I bet that if you look up affymetrix you will find much more details. And you will probably be able to order your own custom chip(s)

[Darwin420]

So if I wanted to get a genome sequence, I would have to give them the DNA sample, where they will convert it to mRNA for me?

That is the only part I am confused about with this chip, everything else I understand.

[canalon]

No chips work only for previously known sequences.
Basically, all the cDNA for the genes of interest (which do not need to be a complete genome) are produced and installed on the chip. Then you take your test organisms and test them in different conditions (say a stress and a control for example) and hybridize each with a chip and compare which genes are activated in the treatment vs the control.
Another use is to put plenty of known genes not necessarily from one organism (such as antibiotic resistance genes, or virulence genes) and to hybridize different wild organisms to test the prevalence of said genes in the wild populations.