Confused about my ChIP-seq data

Could be a ton of things that could have gone wrong unfortunately. Would you mind telling me the protocol you used? As well as the number of reads?

Additionally, you could run try running plotFingerprint from the deeptools package and putting the output of --qualityMetrics here so that I can better assess what could have gone wrong.

In most cases, the protocol is the culprit, regardless of enrichment over IgG. To help you: here is a ChIP-seq protocol that our lab has optimized to be super fast (one day if you do a 1hr IP, two days if you do a overnight IP), low input (down to 1000 cells), and offers extremely high data quality (dx.doi.org/10.17504/protocols.io.vrbe52n). We've used it in both RAW and mouse brain (as well as dozens of cell lines, sorted cells, and primary tissues incase anyone else is interested!) so should work fine for your purposes. Looks like p53 has a dna binding domain so formaldehyde fixing cells for 10 minutes should suffice. You don't need any fancy smancy reagents or equipment to do this unlike other protocols.

All buffers and solutions used in our ChIP-seq protocol can be found on google (can't seem to link it here, send me a PM). If you have any questions regarding kits or whatever, let me know. I haven't included that in the protocol yet unfortunately. However, we use the NEB Library Prep kit

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