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Hi I recently joined the committee. I am using Solexa to do chIP seq and mappining newly synthesized DNA. For some reason the cluster pictures for G and T nucleotides look way too intense and blurry while the A and C look great. Because of this I am getting lower number of reads. However my control genomic samples give perfectly fine reads for G and T. The two differences between the nascent DNA and genomic samples are:
1. Nascent DNA has been precipitated using glycogen and
2. Nascent DNA obtained from cells was labelled with a nucleotide analog BrdU (Bromodeoxyuridine).
Has any one done sequencing with BrdU labelled DNA and come across this problem. Otherwise also has anyone has had bad reads due to issues with lasers unable to read G and T from the clusters.
1. Nascent DNA has been precipitated using glycogen and
2. Nascent DNA obtained from cells was labelled with a nucleotide analog BrdU (Bromodeoxyuridine).
Has any one done sequencing with BrdU labelled DNA and come across this problem. Otherwise also has anyone has had bad reads due to issues with lasers unable to read G and T from the clusters.