Sample Collection and Shipping

We provide guidelines for collection, preservation and shipping of high-quality samples for genome sequencing. Collection of cetacean tissues and international shipping may require special permits. General guidelines for collection of tissues appropriate for long-read genome sequencing can be found in the open-access publication:

Dahn, H.A. et al., 2022. Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing. GigaScience 11, 1-13. https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giac068/6659719 

Sample Collection, Shipping Protocols, and Guidelines

These protocols are the current best practices for collection of tissue and blood for the Vertebrate Genomes Laboratory at The Rockefeller University, New York.

Tissue samples

Blood samples

Frozen cells

Flash-freezing tissue with ethanol and dry ice (when liquid nitrogen is not available)

Cetacean Tissue Biopsy for Cell Culture Protocol

This protocol was developed by the San Diego Zoo and adapted for conditions required for biopsy sampling of stranded cetaceans by Phil Morin (SWFSC). 

Cetacean Tissue Biopsy for Cell Culture Protocol

Preservation of RNA

RNA is important for genome annotation, and RNA from multiple tissues can increase the diversity of expressed genes that can be identified. In addition to flash-frozen tissues for DNA sequencing, samples of various tissues can be stored in RNAlater and then frozen at -80°C. It is important to note that samples stored in RNAlater can only be use for RNA extraction, not ultra-high-quality DNA for genomic sequencing. However, RNA samples do not have to be from the same animal as the tissue used for genomic sequencing. If multiple tissues can be obtained, the order of priority is as follows: (1) brain, (2.) gonads, (3) lungs, (4) liver, (5) muscle, (6) blood, and (7) cells (cultured fibroblasts).

Permits 

International transport, and the collection, use, and storage of cetacean samples are regulated under CITES (Convention on International Trade of Endangered Species of Wild Fauna and Flora) and the U.S. Marine Mammal Protection Act (MMPA) in the United States. Information on permit requirements and shipping procedures for the Vertebrate Genomes Laboratory are included in the step-by-step guidelines. To arrange shipping, please contact us prior to arranging a shipping date to ensure appropriate permits and procedures are in place.

For shipping to:

• Southwest Fisheries Science Center, contact Kelly Robertson 
• Vertebrate Genomes Laboratory, The Rockefeller University, contact Jacqueline Mountcastle