I have performed a ChIP (on 15cm plates) by making a fresh PFA solution, adding it to a 1% final concentration to my cells for 10 minutes and neutralizing the PFA with 2.0M glycine added to a 0.125M final concentration for 5 minutes. I then washed 3 times with cold PBS and I scraped the cells to collect them in 5 mL of PBS with inhibitors. I then spun them for 5 minutes at 4 degrees at 1000 rpm. I decanted off the supernatant, and I resuspended them in SDS lysis buffer with inhibitors. There were 39 million cells on the plate, and I always add 1 mL of SDS lysis buffer per 10 million cells. However, I ended up with a solution that was gel-like and very viscous. I normally take aliquots and sonicate them separately. However, when I tried to pipet the aliquots, I noticed that the solution had become very viscous. When I went to pull the pipet tip out of the solution, there was a string of material hanging on. Almost like it was genomic DNA causing this issue, although I have not had this happen before.

Things I changed in this ChIP:

Made fresh PFA (I had been using premade solutions of PFA purchased from a company - without methanol though)

Used 5 mL of PBS to collect cells instead of 2 mL