Hi, I am seeing a strange amplicon ~2Kb long in all my libraries beside expected ~250-300bp amplicon (picture attached).
I perform ChIP using DNA sheared with bioruptor which peaks ~500bp. I work with low cell number so I get ~5-10 ng after ChIP. Post IP this DNA is further sheared using Covaris and processed for library preparation as per the Solid ChIP-seq library preparation protocol. I used to get ~250-300 bp DNA as expected but in all my recent samples I could see a higher size amplicon ~2 KB beside the expected amplicon. I am not able to find any logical explanation for this!! Has anyone seen this before?
Can I still use these libraries for sequencing after size selection? I am afraid I might introduce bias in my samples. Please help.
I perform ChIP using DNA sheared with bioruptor which peaks ~500bp. I work with low cell number so I get ~5-10 ng after ChIP. Post IP this DNA is further sheared using Covaris and processed for library preparation as per the Solid ChIP-seq library preparation protocol. I used to get ~250-300 bp DNA as expected but in all my recent samples I could see a higher size amplicon ~2 KB beside the expected amplicon. I am not able to find any logical explanation for this!! Has anyone seen this before?
Can I still use these libraries for sequencing after size selection? I am afraid I might introduce bias in my samples. Please help.
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