Please find few papers which will give you protocols for extracting secondary metabolites from algae in general and cyanobacteria in particular.
1.Solid-phase/supercritical-fluid extraction for liquid chromatography of phenolic
compounds in freshwater microalgae and selected cyanobacterial species,B. Klejdus a, J. Kopecky, L. Benesová,J. Vaceka,Journal of Chromatography A, 1216 (2009) 763–771
2.Metabolites from algae with economical impact,Karina H.M. Cardozo a
, Thais Guaratini , Marcelo P. Barros , Vanessa R. Falcão ,Angela P. Tonon ,, Norberto P. Lopes , Sara Campos , Moacir A. Torres,Anderson O. Souza , Pio Colepicolo a,⁎, Ernani Pinto.
3.Enzyme-assistant extraction (EAE) of bioactive components: A useful approach for recovery of industrially important metabolites from seaweeds: A review
W Wijesinghe, YJ Jeon - Fitoterapia, 2012 - Elsevier
4.Isolation and Biological Evaluation of 8-epi-Malyngamide C from the Floridian Marine Cyanobacterium Lyngbya majuscula,JC Kwan, M Teplitski, SP Gunasekera… - Journal of natural …, 2010 - ACS Publications