Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa

Similar Threads
Thread Thread Starter Forum Replies Last Post
Genomic DNA sample preparation Smriti Sample Prep / Library Generation 2 05-25-2012 02:09 PM
Sample/library prep of DNA and RNA in a metagenomic sample chrisaw01 Metagenomics 1 05-05-2011 02:59 PM
Bacterial genomic DNA sample mazinga Sample Prep / Library Generation 9 01-31-2011 10:47 AM
AIRô DNA Sample Prep Kits Now Available for Illumina-Compatible Sequencing Libraries Bioo Scientific Vendor Forum 0 10-05-2010 11:12 AM
small DNA sample library prep vlee2 454 Pyrosequencing 3 05-22-2009 12:55 PM

Thread Tools
Old 02-10-2009, 12:07 PM   #1
Location: Wahington, DC

Join Date: Jul 2008
Posts: 21
Default Illumina Genomic DNA Sample Prep

I have run 2 GA II flowcells and on each cell only about 50% of my reads align to the reference genome. The remaining 50% of the sequences are made up of high amounts of primer sequence and trash reads. As such, we going to redo our library prep and I would like to get some information from others doing the same.

I am using the Illumina protocol "Preparing Samples for Sequencing Genomic DNA". Briefly, our protocol involves sonicating 5000ng of DNA for 30 seconds in 50ul of TE. After the Qiagen PCR purification kit clean-up we are left with only about 20% of our sample as measured by Nanodrop spec.

My questions are:
How do you fragment your DNA?
If you sonicate, how much DNA do you start with and in how much and in what buffer to you sonicate?
How much of your starting material do you recover after the Qiagen clean-up?
Per sample, how much primer/trash sequence do you get back?

Thanks in advance!
kwebb is offline   Reply With Quote

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 09:44 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO