Difference Between Chip-Seq And Biochip-Seq

Question

[ancient_learner]

Hi all is there any difference between biochip-seq and chip-seq in terms of experimental and computational analysis part? if yes can anybody brief the differences?

Answer 1

[Jelena Aleksic]

Given that you're adding a tag, even though it's a small one, I would be concerned that it would disrupt the specificity of the TF binding. I'd therefore be somewhat distrustful of the data unless there was an alternative set of binding data to cross-validate it with (e.g. either standard ChIP-seq, or DamID if that works in your species of interest). Mind you, I'm similarly distrustful of ChIP data - I try and validate it with multiple, ideally independent, datasets whenever I can, because some of the signal tends to be non-specific, even with the best of efforts. No idea which one is messier (antibody specificity vs tag), but I'd worry that the tag would disrupt some TFs more than others, and that you wouldn't be able to tell that's what was happening from looking at the data, unless you cross-validate with an independent experimental technique.

Answer 2

[Sukhi Singh]

From this paper, Genome-wide location analysis by pull down of in vivo biotinylated transcription factors., they say

This unit provides a detailed protocol for genome-wide location analysis of in vivo biotinylated transcription factors by streptavidin pull-down followed by high-throughput sequencing (bioChIP-seq).

Which they started calling as bioChIP-Seq. I would say there won't be any difference in the analysis part and with experimental, it just a matter or labelling and cross-linking, so it shouldn't matter again though the protocols will be slightly different.