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Dear all,
In my lab, we are using the TruSeq ChIP Sample Prep Kit A from Illumina to prepare ChIP libraries. We started with 8 to 80 ng DNA from histone modification ChIP with either DNA fragmentation or MNAse digestion (native ChIP). Instead of size selection using a gel, we use Ampure beads. Usually, we get about 40-80 ng/µl library DNA conc. and a Bioanalyzer peak at around 280 bp.
The problem is, we randomly loose the DNA for some samples, although we are pipetting all samples together using multichannel pipettes. If we repeat the same samples with the same kit and consumables, they work perfectly fine! We got this problem with 3 different types of 96 well plates (ThermoScientific -> AB-0600, BioRad ->, Eppendorf -> 0030133390) and 2 different kit lot numbers. We are two people facing this problem. We have also checked, whether DNA is lost after 15’ bead drying time for small bead amounts (25 µl) as used for size selection, but even after 40’, there was no DNA loss. We have no idea where this problem comes from. Could it be the tips (Rainin -> 17001118 or -28)? Did anyone had a similar problem and managed to solve it?
Thanks in advance,
Christin
In my lab, we are using the TruSeq ChIP Sample Prep Kit A from Illumina to prepare ChIP libraries. We started with 8 to 80 ng DNA from histone modification ChIP with either DNA fragmentation or MNAse digestion (native ChIP). Instead of size selection using a gel, we use Ampure beads. Usually, we get about 40-80 ng/µl library DNA conc. and a Bioanalyzer peak at around 280 bp.
The problem is, we randomly loose the DNA for some samples, although we are pipetting all samples together using multichannel pipettes. If we repeat the same samples with the same kit and consumables, they work perfectly fine! We got this problem with 3 different types of 96 well plates (ThermoScientific -> AB-0600, BioRad ->, Eppendorf -> 0030133390) and 2 different kit lot numbers. We are two people facing this problem. We have also checked, whether DNA is lost after 15’ bead drying time for small bead amounts (25 µl) as used for size selection, but even after 40’, there was no DNA loss. We have no idea where this problem comes from. Could it be the tips (Rainin -> 17001118 or -28)? Did anyone had a similar problem and managed to solve it?
Thanks in advance,
Christin