Protocols and Databases


Systems Biology of Symbiosis, SymBioSys is available here. However, we no longer maintain this database so we recommend you use it at your own risk.

Also, we recommend you use the Penn State guideline to access the Lion-X Clusters User Guide.


DNA/RNA work:

RT-qPCR protocol (with aRNA)

Genomic DNA Preparation from RNAlater™ Preserved Tissues Protocol

Coral sperm collection for genome sequencing protocol

DNA extraction from frozen coral sperm protocol

RNAlater protocol

Coral RNA isolation protocol (for small prep’s in 1.5mL or 2mL tubes)

Coral RNA isolation (for large prep’s in 15mL Falcon tubes)

RNA extraction for coral larvae

Coral tissue blasting protocol

Coral grinding protocol

Coral spawning:

Coral spawning for dummies

Protein work:

Protein extraction protocol

Environmental samples: 

Sterivex water filtration protocol

Lipid in water, lipid in sediment, and filtration for nucleic acid recovery protocol by ICoMM

Water sampling and filtration

Other lab work protocols:

Probe construction for in-situ hybridizations protocol

Symbiodinium spp. genotyping protocol

Montastraea faveolata host genotyping

Medina Lab, Laboratory notebook procedures (Very important for all lab members!)

And, finally we are in the process of compiling a list of frequently asked questions on general lab procedures. This will be posted soon!

*Note Montastraea faveolata is currently known as Orbicella faveolata. For more details refer to Budd et al. (2012) Taxonomic classification of the reef coral family Mussidae (Cnidaria: Anthozoa: Scleractinia).