I am trying to RNA extraction from dinoflagellate algae.

And according to other papers, 

Its extraction was easily done by method of frozen - thawing and using bead beater.

I tried several experiments and the procedures & results were as below.

1. I started with 10^5 cells and added 1ml Trizol 5min roomtemperature incubation.

2. 0.2ml Chloroform added to 1. and 3min RT incubation.

3. Centrifugation at 12000g 10min 4 celcius degrees

4. transfer sup to new tube and 0.5ml Chloroform adding

5. Centrifugation and transfer sup to new tube and 0.5ml isopropanol adding

6. -80 celcius degrees 1hr incubation

7. Centrifugation and 70% DEPC Ethol 1ml washing

8. 30ul elution of pellet and Qubit  quantification.

about 100ng/ul was detected, but after gel electrophoresis, 

the degradation of RNA was observed and there was no two band.

In second experiments, I added step of homogenization using auto tissue homogenizer and started with the sample resuspended in Trizol and stored at -80 degrees.

What 's the problem?

Is there a difference between using homogenizer and bead beater??

Please give me some advise.