Hello,
I am getting ready to prepare some libraries using the Truseq DNA sample prep kit using a Bioruptor for fragmentation. Before starting the actual samples (150,000 bp), I am running a test sonication on some Ecoli gDNA.
I ran my test samples at 15" on 90" off for 9 cycles. According to Diagenode this should approximately give a fragment size of 350 bp. I ran the samples on a Bioanalyzer DNA 1000 chip afterwards to size the fragments. It wasn't even close to 350 bp! Here is what I got:
Sample 1: 100 ul in EB at 20 ng/ul. Average size: 870 bp!
Samples 2: 52.5 ul in EB at 20 ng/ul (as the protocol asks for). DNA 1000 didn't pick up anything. Hmmm...
Therefore I am wondering what fellow sequencers run there Truseq DNA sample prep samples at on the Bioruptor?
I would be thankful for any input!
I am getting ready to prepare some libraries using the Truseq DNA sample prep kit using a Bioruptor for fragmentation. Before starting the actual samples (150,000 bp), I am running a test sonication on some Ecoli gDNA.
I ran my test samples at 15" on 90" off for 9 cycles. According to Diagenode this should approximately give a fragment size of 350 bp. I ran the samples on a Bioanalyzer DNA 1000 chip afterwards to size the fragments. It wasn't even close to 350 bp! Here is what I got:
Sample 1: 100 ul in EB at 20 ng/ul. Average size: 870 bp!
Samples 2: 52.5 ul in EB at 20 ng/ul (as the protocol asks for). DNA 1000 didn't pick up anything. Hmmm...
Therefore I am wondering what fellow sequencers run there Truseq DNA sample prep samples at on the Bioruptor?
I would be thankful for any input!
Comment