2. Sample Preparation

Tissues should be split before flash freezing. Never allow samples to thaw.

We strongly recommend using liquid nitrogen for flash freezing. If you don’t have access to liquid nitrogen, a slurry of dry ice and isopropanol will work.

Specimen Requirements for HMW-DNA IsolaTIon for Reference Genome Sequencing

General Notes

• The very highest quality DNA samples can be isolated from fresh blood and fresh or frozen cell culture samples. Suitable fresh frozen issue samples can also yield excellent data.

• Frozen samples: In general samples should be flash-frozen in liquid nitrogen, stored at -80°C and shipped on dry ice. Freeze samples after removing excess liquid.

• If there is no chance to arrange immediate flash-freezing please reach out to the CCGP technical board to discuss storage options.

• Do not pool samples of different individuals.

• Submit higher sample amounts and volumes than requested below if possible. Additional samples are also very useful for specimen-specific DNA isolation tests.

• Please use the heterogametic sex, when applicable.

  • If submitting multiple small individuals, please try to submit multiple of the same sex.

• The CCGP labs CANNOT accept samples potentially infectious to humans.

Preferred Sample Types

Based on feedback from both the UC Davis and UC Santa Cruz labs, the following is a non-exhaustive list of preferred sample types. We realize these might not be possible for some species.

See section below for specific sample preparation details for each sample type.

Shipping to UC Davis (PacBio HiFi)

• Vertebrates: blood (treated with anti-coagulants and shipped immediately or flash frozen).

Shipping to UC Santa Cruz (Dovetail Omni-C)

• Birds, Fish, Reptiles, and Amphibians: red blood cells, flash frozen; or whole blood treated with EDTA (1.5mg/ml of blood) and flash frozen or shipped fresh.

• Mammals: Blood, treated with EDTA (1.5mg/ml), flash frozen or shipped fresh.

• Plants: As much tissue as possible (ideally 5g, but at least 1g). Flash frozen.

• Invertebrates (marine or terrestrial): Whole flash frozen individuals, ideally starved.

  
  

Click here for specific sample preparation details for the following:

Specimen Requirements for RNA Isolation for Gene Annotations

General Notes

• Samples for RNA-sequencing should be freshly dissected and flash frozen in liquid nitrogen. They should be stored at -80°C and shipped on dry ice. Any thawing of the samples must be avoided.

• The objective of the RNA-sequencing is to generate data for as many different transcripts as possible. Since gene expression varies between tissues, between different life stages, and between genders it is advantageous to collect a diverse set of samples. These should comprise several tissue types and samples from different life stages if possible.

• In contrast to the samples for the DNA isolations, the samples for the RNA isolations can be derived from several individuals, and they need not be the DNA-sample individual.

• Submit a minimum of two samples per species from the same tissue type (for multiple tissue types).

• Samples should be very clean. Rinse tissues in RNAse-free water before dissecting them.

• Samples are best frozen, stored and shipped in 1.5 ml or 2 ml cryo-vials with screw caps.

• Samples for RNA isolation will be shipped to UCLA.

Plant samples

• Tissues should be best include young leaves, root tips, flowers, buds, seeds.

• Remove any woody or hard parts. Quickly cut tissues into smaller pieces (~100 mg) and deposit into pre-chilled cryo-vials and then flash-freeze them in liquid nitrogen. Please provide two samples, each of at least 100 mg, for each tissue in separate tubes.

Insects and Other Small Animals:

• Flash-freeze entire animals

• Submit different life stages if possible (pupae, larvae, mature animals).


Larger Animal Samples

• Dissect animals on ice.

• Quickly cut tissues into smaller pieces (~50 - 100 mg) on ice and flash freeze in liquid nitrogen.

• Collect multiple tissues: e.g. brain, liver, skin, testis, ovaries, spleen, lung. Brain and testes tend to express the highest number of genes and therefore are very useful tissues.