Hey,
I am a newbie who has been trying to build ChIP libraries using the TruSeq ChIP Sample preparation kit.
After doing protocol optimization we decided to use MinElute columns for pre-PCR purification instead of using Ampure beads XP. After the PCR, we did a Ampure XP clean-up to remove adapter dimers with the recommended ratio of 1:1.
For the Gel size selection, we are using the E-Gel Size-Select Gels to select fragments between 250-300bp of size.
However, now we are having another type of problems, which is the reason of this post. The libraries that we prepared using this method show a shoulder before the peak and the peak is of a much higher weight than the expected one.
Does anyone know the reason for these shoulders?
Do they affect sequencing quality?
Is it possible to eliminate them?
I used the search function and couldn't find a satisfactory answer.
I am a newbie who has been trying to build ChIP libraries using the TruSeq ChIP Sample preparation kit.
After doing protocol optimization we decided to use MinElute columns for pre-PCR purification instead of using Ampure beads XP. After the PCR, we did a Ampure XP clean-up to remove adapter dimers with the recommended ratio of 1:1.
For the Gel size selection, we are using the E-Gel Size-Select Gels to select fragments between 250-300bp of size.
However, now we are having another type of problems, which is the reason of this post. The libraries that we prepared using this method show a shoulder before the peak and the peak is of a much higher weight than the expected one.
Does anyone know the reason for these shoulders?
Do they affect sequencing quality?
Is it possible to eliminate them?
I used the search function and couldn't find a satisfactory answer.
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