I have a question.
I want to see if in my slides the DNA is locked on surface (polylysina)
immediately after spotting procedure.
My Boss said me that there are some product like "Vista Green" that
allow to see immediately (with scanner) if the DNA are onto slides, and
after I can clean the same slide and perform a normal hybridization
Someone can help me to understand which product I can use and if it's
"gberna" <[Only registered users see links. ]> wrote in message
Hi gberna ,
I _guess_ from your post that you are working with DNA Microarray's and
that you are using the sort where DNA oligo's are spotted on poly-lysine
coated slides. If that is true look here for more information :
[Only registered users see links. ]
I use a special designed random 9-mer Oligo which has a 5'-Cy5 label.I do
one or two test hybridisations with this Oligo for each batch of printed
Microarray's , just following our standard protocol.This will stain all the
spotted DNA's equally , if the Microarray's are OK
I've seen your link , but I'm finding,if it's possible, a tecnique that
allow me to look immediatly after spotting if my DNA (PCR) are blocked
I need this becouse, I work in a university, but the spotter and the
scanner are located in a a differt city were I can only Spotting and
(This is the Italy!!!)
"gberna" <firstname.lastname@example.org> wrote in message
Hi gberna ,
you can see the autofluorescence of the spotted DNA just after spotting and
baking or UV croslinking with a normal scanner . Fast . After washing and
blocking , the autofluorscence of the DNA is nolonger visible. However you
can stain the array , at that point , very quicky with SbrGreen or SybrGold
.. Dip , wash with MilliQ and dry . Fast . We use the hybridisation with the
synthetic Oligo because this tests the whole process from begin to end and ,
in our hands , is the most reliable quality control .
Or you could buy Affi- or ABI chips . Faster .
They have another advantage : they are the only one accepted for publication
! You will not get a publication with home brew chips in any serious
There are a number of companies that provide a complete service. You send
them your RNA , they give you a DVD with the gene regulations and the
bioinformatics . Completely interpreted . The fastest
"Peter Ellis" <[Only registered users see links. ].uk> wrote in message
news:[Only registered users see links. ]...
This search string : Ellis P[author] AND (microarray OR Array OR "DNA
Array") in Pubmed finds 3
Two different Peters , 1 does not use array's
Maybe I am missing something
The analysis is done by someone who does know about both statistics and
bioinformatics . You may know everything about your favourite organism .
Both knowledge is needed . I saw a few examples where good biologists lost
themselves in bioinformatics.
"GysdeJongh" <[Only registered users see links. ]> wrote in message
news:443ed8a0$0$2026$[Only registered users see links. ].planet.nl. ..
It seems to me that the whole issue with microarrays is vastly over-rated
They can be as complicated as you wish. Microarrays, with 1000s of genes,
allow you to do some pretty fancy studies. But you don't need to extract ALL
possible information from a microarray experiment for it to be useful. It's
just a big dot-blot, after all...
It's not difficult to design and obtain very useful information, with
home-brew or otherwise arrays, using relatively uncomplicated tools. Just
have a stroll by the BioConductor forum, for instance.
I have one good example of dealing with a company who "thought" they
understood the experiment a colleague wanted to do, and proposed rather
ludicrous controls. Fortunately we could stop that before it became
expensive. Sure, companies may provide a useful service. We are in fact
going to use Nimblegen for a particular experiment. But there's no
substitute for doing your own analysis, at least to some extent. After all
you are the one who knows exactly what the questions are...
Home-made arrays can be just as good as any commercial ones, providing you
follow some common sense QC procedures. Why are you so dogmatic?