I am trying to isolate RNA from stress granules, these were obtained using immunoprecipitation, but the amount of RNA and sometimes the quality is not good enough.
this depends a lot on the conditions and method of RNA extraction, and on your downstream application. usually lower yield but higher quality RNA is more desirable. if you are using phase separation then leave a larger "buffer area" when removing the supernatant - do not try to get every single drop and disrupt the lower phase. if you are using isopropanol precipitation then incubating at -20C overnight can increase yield, and a carrier moleulce like linear acrylamide or glycogen can be helpful. if you are using a column-based method then reloading the eluate and spinning the final step a second time can slightly improve yield.
i would recommend being VERY careful during phase separation that you do not disturb the trizol layer. even if you pipet it up then back down it can cross-contaminate. Err on the side of caution and do not get near that layer, also when you do the phase separation step after that. just add a TINY amount of glyocogen and precipitate at -20C overnight. also, when washing the pellet with ethanol I like to do 2 washes with 100%. When you remove the ethanol, spin down the tube again and use a 10ul tip to remove as much as possible then air dry, but not for too long. resuspend in TE or water and heat at 60C for 5-10 minutes to fully resuspend the RNA. gently flick the tube to mix, avoid vortexing.
I would recommend trying Zymo's Directzol RNA mini prep kit - it is column-based and fast to use. and you can DNase treat on-column. They are a great company and have a "Get free sample" button and they will send you a mini kit for 5-10 reactions.