I'm extracting RNA from bacteria and I only get a yield ~20% of the time.
I can take one culture, split it into multiple tubes, prep them in parallel, and only one tube will give me RNA.
I resuspend in TRIzol, bead beat, and then clean up using isopropanol precipitation or column-based kits. Both only work ~20% of the time.
I've replaced my reagents with brand new stuff. (Isopropanol, water, ethanol, chloroform, tips, Glycogen, tubes)
I've remade the cultures
I've switched my tubes and made sure they're certified "Sterile, RNase-free"
I wipe my bench, pipettes, and gloves with RNase AWAY
How many cells are you trying to lyse?
The problems of RNA isolation are usually because of a) the cells are not lysed properly, so the RNA is not completely released b) the sample is too concentrated (high cell density) even though it is lysed but it is higher than the cutoff of the membrane (the column), so the RNA could be simply stuck on the membrane and what you are eluting is just 20% of what you expect.
I would suggest:
a) do a cell count and start with 5-10e6 cell per extraction
b) double-check the cutoff of the membrane if you are using a column
Good luck
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