I'm having trouble recovering RNA and maintaining purity with use of RiboPURE blood kit (phenol/chloroform and column based extraction method). The samples are from elasmobranchs and fresh water turtles.
have you tried with trizol, trizma or other equivalent kit? It's based on phenol but more effective, I have used it for seabream and zebrafish cells, primary cultures and tissue with good results. Another option is using non-phenolic lysis buffers, there are several commercial kits available for that such as he RNeasy mini kit (Qiagen) or miRCUR RNA Isolation Kits (Exiqon) that works very well with several tissues, included frog samples from embryos and adults.
Perhaps you should ckeck on the integrity of your WBCs by seeing if they are still alive with a trypan blue stain uptake. If they take up the trypan blue they are most likely dead and the RNA content may be compromised. If they are ok, then you should try another extraction methodology that is not phenol based such as the Zymo research micro or mini RNA isolation kit. Also consider adding a DNAse step to digest genomic DNA that may be present in the specimen.
If the WBC survival is low, there are many factors which can cause this issue. If they are from stored specimens, the WBC's should be stored at -80C perhaps with a glycerol stabilizing solution.
How are you determining your RNA quantity, purity and integrity?
Are you removing the RNAlater prior to using the Ribopure kit? If not, that will interfere (very high salt content.) If this is the case you can either pellet the cells at high speed or dilute the WBC/RNAlater solution considerably in Trizol or something similar.
Read this for more information. http://www.inen.sld.pe/bttportal/archivos/RNA.pdf
I have the same problem few years ago to extract RNA from the placenta tissue stabilised in RNALater. I used TissueRuptor from GIAGEN to homogenise 50 mg tissue in 600 µl of Buffer RLT (RNeasy Mini kit, GIAGEN) for 30 seconds, then follow the instruction of RNA extraction kit. I got 15-25 µg of good quality of RNA from 50 mg of tissue. From my experiences, well homogenised tissue is essential, especially for the tissue stabilised in RNALater.
I have had a lot of luck using the RNeasy Plus kit from Qiagen to extract RNA from bone marrow aspirated that were stabilized by RNAlater. Just spin spin spin as it becomes difficult to pellet cells out of the RNA later solution.