Chip Seq Pair End Data

Question

[Frenkiboy]

Can somebody please point me to a publication where they used pair-end sequencing for a chip-seq experiment?

I know about Wang et al. (doi:10.1186/1471-2105-11-81) paper in BMC bioinformatics, but was searching for something done on an animal system.

Best regards.

[Sander Timmer]

I think that currently most off the time people don't use paired-end information in Chip-seq even if they do have paired-end information. Also most pipelines are not ready/usable for paired-end data.

Though I'm interested to see people proving me wrong by giving you loads of references...

Answer 1

[seidel]

Not an animal system, but Zhou and O'Shea, Molecular Cell (2011) use paired-end sequencing for ChIP Seq determination of nucleosome occupancy in yeast, while studying Pho4 and other transcription factors involved in the phospate response. The idea is to study the relationship between chromatin accessibility and transcription factor binding. They used micrococcal nuclease digestion followed by paired-end - probably to get maximum resolution and accuracy of binding location for the nucleosomes. In contrast, for Pho4 and the other txn factors in the study they used single end reads, sufficient for enrichment determination over consensus binding sites.

You might mention the reason why you want to find a publication for paired-end ChIP Seq in an animal system. What is the issue you are trying to resolve?

[Frenkiboy]

Thank you so much! I just want a pair of data with which I can get the size distribution of the fragments, and was hoping for the mouse/human because the mapping biases should stay the same in comparison to my data, but the yeast is going to do just fine. Tnx!