Hello,
since we have switched to paired-end sequencing for ChIP-Seq, we observe strange peaks covering some of the expressed genes. See: https://ibb.co/mEf53x. These peaks differ, when performing ChIP-Seq against the same TF in different tissues, depending on gene expression, I guess. Published (single-end) data for the TF don't show these broad peaks at genes. Known enhancer peaks for this TF match the published data. So we gain this weared peaks additionally.
They appear consistently in ChIP-Seq Experiments with different Abs (same tissue) and also in KO samples, but not in the paired-end input (same tissue and sequencer) or single-end ChIP-Seq ; although performed in a different lab (different libary prep and different sequencer).
Is this an artefact of paired-end sequencing? Anyone observed similar peaks? Any suggestion is appreciated. Thanks Franzi
The PE ChIP samples look similar to the SE samples, just smoothed out a bit, which makes sense if you're extending the coverage to account for fragments. My presumption is that your TF is interacting with the gene bodies or with the whole open chromatin region.