We do ChIP from frozen samples all the time. The tissue is allowed to thaw slightly on ice, minced on ice with sharp dissecting scissors, resuspended in DMEM (no FBS) then passed (scraped) through a nylon cell strainer into a 50 mL tube with ~10 mL cold DMEM, everything is kept on ice. Once the single cell suspension in DMEM is prepared formaldehyde is added to 1% final concentration and the protocol proceeds as normal.
The Excel spreadsheet from BioRad that I linked to will let you input ct values and will normalize to your housekeeping gene and output fold change values.
I think you're using too much starting material in your qPCR reaction which is why the Gapdh amplification curve looks strange. You generally don't need to degrade the RNA after making cDNA. I would do a 10-fold dilution series (10, 100, 1000, 10000 fold dilutions) and see what your amplification curves look like.
I don't do this in a hood but I'm usually only doing a few plates at a time and my the PFA is only open to the air for a few seconds. After I wash with PBS I quickly unscrew the lid of my PFA tube, add some to my plates of cells, put the lids back on the plates and recap the tube of PFA. When they're done fixing I remove the lid from the plates and immediately asperate the PFA then continue PBS washing.
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