about the subarray - (Nov/22/2009 )

hi, everyone, I am a novice in the field of microarray and I have some questions.

My research object is a bacteria with about 2000 ORFs in total. And I found that many microarray manufacturers have different formats of dna chip. And some of these chips have many subarrays. Agilent for example, has chips in a 8 x 15K format.

I don't know much why we need to print as many as 8 identical subarrays on one carrier. Is this simply a technical duplication?

And I am going to study the expression profile of my bacteria under 2 different temperatures. And if I am going to use this 8 x 15K chip, I will have 8 duplications, right? Is it a great waste?

I am really puzzled at this. And thanks in advance!

Hi fzhang,

The Aglient's 8X15k means 8 identical arrays on 1 slide as you said...but doesn't mean you have to do technical replicates for the same sample on all the 8. You can actually hybridize 8 different samples which you can decide based on your interests..
Agilent offers 4 array formats..which are 1 array/slide, 2 arrays/slide, 4 arrays/slide, 8 arrays/slide..The number of probes printed varies from 244k, 105k, 44k and 15k respectively. The newer high density arrays are a million spots for the single array, 400k for 2 array/slide and so on.

You can process 8 samples on a single slide with 1 control and 7 time references (for eg.!) with 1 color expt or 16 samples (ideally control vs treated) which can be different controls for different treated samples allowing you to compare 8 different experiments in 1 slide with a dual color expt! Also since the ararys are on same slide, the variations in the washing can be greatly reduced too.

Hope this helps

gogreen