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slide assay with vista green. It's possible?

slide assay with vista green. It's possible? - Protocols and Methods Forum

slide assay with vista green. It's possible? - Post Any Protocol, Method, Technique, Procedure or Tips / Troubleshooting for any Molecular Biology Technique.


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  #1  
Old 04-11-2006, 09:44 AM
gberna
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Default slide assay with vista green. It's possible?



Dear,
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
possible?

tanks,
gberna

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  #2  
Old 04-11-2006, 01:20 PM
GysdeJongh
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Default slide assay with vista green. It's possible?

"gberna" <[Only registered users see links. ]> wrote in message
news:1144742168.582362.54550@v46g2000cwv.googlegro ups.com...

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

hth
Gys


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  #3  
Old 04-12-2006, 02:21 PM
gberna
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Default slide assay with vista green. It's possible?

Thanks Gys,
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
onto slide.
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
scannig
(This is the Italy!!!)

Thanks,
gb

GysdeJongh ha scritto:


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  #4  
Old 04-13-2006, 11:03 AM
GysdeJongh
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Default slide assay with vista green. It's possible?


"gberna" <gberna@gmail.com> wrote in message
news:1144851682.438536.197630@z34g2000cwc.googlegr oups.com...

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
journal.

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

Take care
Gys


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  #5  
Old 04-13-2006, 06:55 PM
Peter Ellis
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Default slide assay with vista green. It's possible?

GysdeJongh wrote:

Rubbish


If you want your analysis done by someone who knows nothing about your
biological system, sure.

Peter


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  #6  
Old 04-13-2006, 10:40 PM
Christian Praetorius
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Default slide assay with vista green. It's possible?

"GysdeJongh" <[Only registered users see links. ]> wrote:


Thats definitely not true. How many references shall I pick out from
my database?
From the commercial companies you also forgot Nimblegen.

Christian

--
[X] <-- nail here for new monitor
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  #7  
Old 04-13-2006, 10:55 PM
GysdeJongh
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Default slide assay with vista green. It's possible?


"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.

Gys


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  #8  
Old 04-13-2006, 11:02 PM
GysdeJongh
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Default slide assay with vista green. It's possible?


"Christian Praetorius" <[Only registered users see links. ]> wrote in message
news:[Only registered users see links. ]...

Lets say 100

But .....

None from a large arraying facility demonstrating that _they_ can do it
None from a large arraying facility on some technical isue

I have those myself , thx

Only from a biological group solving a biological problem , please

Gys



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  #9  
Old 04-14-2006, 01:14 AM
Jose de las Heras
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Default slide assay with vista green. It's possible?


"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
(or misunderstood).

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?

Jose


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  #10  
Old 04-14-2006, 01:23 AM
Jose de las Heras
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Default slide assay with vista green. It's possible?


"GysdeJongh" <[Only registered users see links. ]> wrote in message
news:443ed6d4$0$2022$[Only registered users see links. ].planet.nl. ..


I think you are.
And if this is the Peter I think he is, then even more so.

Jose


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