SEQanswers

Go Back   SEQanswers > Applications Forums > Sample Prep / Library Generation



Similar Threads
Thread Thread Starter Forum Replies Last Post
ChIP- Different DNA size for Input DNA and ChIP DNA on Agilent Bioanalyzer rahulr1485 Epigenetics 19 05-17-2013 09:14 PM
Amplification of ChIP'd DNA before library prep OptimusBrien Sample Prep / Library Generation 1 07-12-2012 01:26 PM
Can Truseq DNA library get >1ug DNA library at last? rnal Illumina/Solexa 2 04-12-2012 08:36 AM
DNA/RNA hybrid ChIP-seq library preparation jazz Illumina/Solexa 1 11-02-2011 04:54 AM

Reply
 
Thread Tools
Old 03-02-2010, 07:38 PM   #1
amesapple
Junior Member
 
Location: USA

Join Date: Mar 2010
Posts: 2
Unhappy Is that possible to get library ~200 from Chip DNA ~500



Hello,

We only have a probe sonicator so my chip fragments are peaked around 500bp, ranging from 200~1000bp. The facility guy told me that he would first align the adaptors, then do the PCR (18 cycles), then do the size selection (about 200bp) from gel. My question is that if my DNA fragment centered ~500bp, there must be only a tiny fraction sizing ~100bp which can be later select from the gel. Am I right? The majority of my chip DNA would be discarded. Will this introduce bias?

Thanks a lot! Really do not want to waste my boss' money

Last edited by amesapple; 03-03-2010 at 08:42 AM.
amesapple is offline   Reply With Quote
Old 03-15-2010, 12:28 PM   #2
hon
Junior Member
 
Location: san fran

Join Date: Sep 2009
Posts: 9
Default

I wonder if it is possible to just sonicate the ChIP DNA to bring it down to around 300bp and then make the library. Recently I have this issue too, majority is on 600pb, which I don't think is good for sequencing after making library and cut the gel at 200bp. I am just trying to figure out a condition see if I can just sonicate the ChIP DNA few more cycles to bring down the size.
hon is offline   Reply With Quote
Old 03-15-2010, 07:16 PM   #3
amesapple
Junior Member
 
Location: USA

Join Date: Mar 2010
Posts: 2
Default

Hi Hon,

Thank you so much for your reply. I actually figured out the problem. I found a bioruptor recently in another building. I was so happy to say that my sonication fragments are now centered around 250bp. I would make the library from 200-350bp after adaptor ligation.
So, find a bioruptor!
amesapple is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 10:17 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO