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Old 11-30-2008, 06:53 AM   #1
kaixinsjtu
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Exclamation question on DNA fragment size after shear the DNA (in Chip-seq)

Hi, everyone,
Is there any manual that tells you what is the distribution of the DNA fragment size (length) after you use ultrasound (or whatever) to break (shear) the DNA (then you will use immunoprecipitation to take out the DNA fragments with binding proteins, I just want to get length information on those fragment size). This issue is very important for my current research, and I could not find the information!
Hope someone can give me any clue, greatly appreciate!!
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Old 01-02-2009, 02:18 PM   #2
dolaimi
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I think you can check the attached manual of Bioruptor System.
Attached Files
File Type: pdf manual_Bioruptor_0408V2.pdf (849.2 KB, 128 views)
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Old 01-02-2009, 05:56 PM   #3
ECO
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Moving this to library construction, as I don't think it qualifies as Bioinfx!

Also, Covaris has some pretty good information about the capabilities of their system here:

http://www.covarisinc.com/controlled_dna_shearing.htm
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Old 04-05-2012, 03:25 AM   #4
DomiP
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Hi Kaixinsjtu!
Actually there is a pretty good consensus in most papers about ChIP-seq regarding the "optimal DNA size range".
It corresponds to 100 to 600 base pairs. This size range can easily be obtained using sonication but you will have to optimize your fixation, lysis and shearing conditions anyway (whatever the sonication system you might use).

DomiP
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Old 04-05-2012, 03:36 AM   #5
kaixinsjtu
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Quote:
Originally Posted by DomiP View Post
Hi Kaixinsjtu!
Actually there is a pretty good consensus in most papers about ChIP-seq regarding the "optimal DNA size range".
It corresponds to 100 to 600 base pairs. This size range can easily be obtained using sonication but you will have to optimize your fixation, lysis and shearing conditions anyway (whatever the sonication system you might use).

DomiP
Whoa! I wish I could remember what I did for that ancient project
But still appreciate that!
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