Specific preparation details for each sample type
In the case where ample tissue is not available, please contact Erin and Courtney to discuss strategy.
Cell culture samples
Please submit a minimum of two vials each with ~10 million cells or more.
Cells should be washed with 1x PBS, then pelleted again.
The supernatant should be removed.
The pellet should be flash frozen in liquid nitrogen (or between dry ice) and stored at -80°C. Please ship the cell pellets on dry ice.
Vertebrate tissue samples
Soft tissue samples with a high content of nucleic acid (such as spleen, liver, heart) are preferable to those with more connective tissue (muscle, skin).
Submitting sterile or very clean samples is of greatest importance. Guts, gills, skin, other connective tissues and hair should be removed before flash freezing, if possible. Rinse newly collected sample with cold saline to remove blood and other contaminants before freezing.
Dissect fresh tissue samples on ice into pieces less than 0.5 cm in at least one dimension (or into pieces of 50 mg or less). Pack the samples into labeled cryo vials and flash freeze them in liquid nitrogen immediately. Store at -80°C and ship on dry ice. Please ensure the tissue sections are not jammed into the tubes and can be easily removed from the tubes without thawing.
Submit at least 1 g of soft tissue per sample if possible. When working with small animals (smaller than a penny) provide the entire organism in a tube and flash freeze the specimen. If you are unsure if your sample is appropriately sized for splitting, please contact the CCGP technical board to discuss how best to split small samples.
Samples should be flash-frozen immediately. Please contact the CCGP technical board to discuss storage options in the event that flash freezing in not possible.
Blood samples
If blood samples will arrive within two days after the blood draw, it is generally better to not freeze the samples. Instead keep the samples cold at all times (refrigerator; 4°C) and transport them between a generous number of cold packs.
Please contact both UCDavis (Ruta Sahasrabudhe, rmsaha@ucdavis.edu) and UCSC (Sam Sacco, ssacco@ucsc.edu) at least a week in advance to set up
an appointment if you plan to ship fresh blood samples with overnight shipping.For the archival samples, please flash freeze prior to shipping to UCLA.
Mammals: Minimum of 2 samples containing ~5 ml of mammalian blood in EDTA (1.5mg/ ml) are required each for HWM DNA isolation. For smaller animals submit samples with at least 2.5 ml of blood.
Birds and reptiles: For blood samples with nucleated RBCs such as birds and reptiles, 500μl (0.5 ml) of unfrozen whole blood in EDTA anticoagulant (1.5mg/ml) is sufficient.
Fish: Use acid citrate dextrose (ACD) as anticoagulant for unfrozen fish blood samples. 500 μl (0.5 ml) or more should suffice.
All tubes should be sealed and individually double packed in packaging that protects the tubes from physical damage and vibrations. A secondary cyro-tube box within the shipping packaging is sufficient.
EDTA-blood samples can also be flash frozen in liquid nitrogen and stored at –80°C. Frozen samples should be shipped on dry ice.
Purple top Vacutainer tubes are unsuitable for flash freezing, so please transfer EDTA-blood to cryovials before flash freezing.
Fish samples
Fresh blood is the preferred sample type (see section on blood samples).
Heart and gills (the latter only if microbial contamination can be avoided).
Fin clips and tissue biopsies that include non-scaly skin pieces are also suitable options for specimens that cannot be sacrificed.
Use acid citrate dextrose (ACD) as anticoagulant for unfrozen fish blood samples. 500 μl (0.5 ml) or more should suffice.
For fish that live in very cold water please avoid muscle tissue.
Plant samples
Submit 5 to 10g of young leaf tissue for each shipping address ( *at least >1g to UCSC).
Wash the leaves and remove the midrib and any other hard tissue.
Flash freeze the tissue distributed in several aluminum foil envelopes or cryotubes in liquid nitrogen and store at -80°C.
Transport the samples on dry ice.
Please contact the CCGP technical board if your plant does not have leaves.
Additional notes:
If sending leaves:
Please send as younger leaves as possible (better if light-starved for 3-4 days, but not essential).
In addition to washing with water (surface cleaning), before freezing, remove any older/senescing leaves/parts, any stem part, thick mid-ribs (once frozen, it is hard to differentiate and remove these tissues at the core). These tissues, especially senescing parts and thickened stem will reduce the quality of the final DNA/read length.
If sending floral tissues:
We prefer younger floral buds and not open flowers which may carry senescing tissues.
If collecting from an inflorescence, please remove any open flowers and thickened inflorescence branches, and thickened pedicels. In other words, only freeze the younger buds.
Both young leaves and floral buds are equally good and if sending both, please freeze them separately. In theory, 1-2 grams of good quality tissues is sufficient for standard extraction. In practice, plants often present surprising challenges which either require more extractions or cleanups. Hence, it is appreciated to have ~5 grams or more from an individual and more than one individual if possible as a backup.
Insects and Other Small Animals
Animals should best NOT be fed for appropriate time spans before collection, to avoid isolating food DNA and to reduce microbial content. Two days is probably sufficient.
Pupae or larvae tend to provide the best DNA samples and are preferable to mature animals.
If possible, pupae and larvae should be shipped live. In this case the shipment has to be coordinated with the receiving lab.
Please contact both UCDavis (Ruta Sahasrabudhe, rmsaha@ucdavis.edu) and UCSC (Sam Sacco, ssacco@ucsc.edu) at least a week in advance to set up
an appointment if you plan to ship fresh live animals.For the archival samples, please flash freeze prior to shipping to UCLA.
Insects, pupae and larvae can also be packed in cryo-vials and flash-frozen in liquid nitrogen,
stored at -80°C and shipped on dry ice.
If you feel a single individual does not contain enough tissue to split between at least UC Davis and UC Santa Cruz, please submit multiple individuals to each shipping destination