Skip to main content Skip to docs navigation

Sample Collection and Storage by Sample


View on GitHub

Page last modified on: 2024, December 17

On this page

This page offers a short and concise overview on how to collect and store certain sample types.

General Protein Storage (“Protein Purification,” 2022): For short-term storage (~24h), most proteins can be kept at 4°C. For long-term storage, protein samples are typically kept at -20°C or -80°C. Protein storage at -20°C usually requires the addition of 50% glycerol to your sample to avoid freezing at this temperature. If we plan to store a protein at -20°C, we generally run the final size exclusion chromatography step in 2x storage buffer and then dilute the sample 1:1 with 100% glycerol. Alternatively, the protein sample can also be dialysed against the storage buffer already containing 50% glycerol. Proteins stored at -20ºC are often stable for several months, although the exact time frame is protein-dependent and should be determined experimentally. Protein samples stored at -80ºC will be frozen. As repeated freeze-thaw cycles usually have a negative influence on protein samples, it is best to prepare small-sized, single-use aliquots that will be used up during the course of an experiment. 5-10% glycerol or other additives that protect against the effect of freezing and thawing can be added as well. After preparing your protein sample aliquots, it is important to flash-freeze them in liquid nitrogen before importing them into the -80ºC freezer for long-term storage. Many proteins are stable for months to years when stored under appropriate conditions at -80°C, but the exact time frame varies from protein to protein and should be determined experimentally.

Sample Procedure Source or Link
Activated sludge from wastewater collected samples stored at 4°C for transport, within 6 h centrifuged at 6 500 g for 15 min at 4°C, supernatant removed and pellets stored at -20°C (Morin et al., 2020)
Antarctic ticks collected from rocks, placed in RNALater and stored at -80°C within 4-8 h of collection (Wille et al., 2020)
Atlantic salmon dissection samples placed in RNAlater and stored at -80°C (Karlsen et al., 2022)
Faeces/gut content flash freeze in liquid nitrogen and store at -80°C (dissolve in Stool DNA Stabilizer (INVITEK Molecular) while thawing; or if you have more time dissolve in Stool DNA Stabilizer right after collection and normally freeze and store at -80°C) (in-house protocol provided by Johannes Masson)
Frog swabbing rinse caught frog with 50 ml sterilised water to remove transient bacteria, swab entire skin surface with a sterile Dacron swab for 30 sec, place swab in microcentrifuge tube containing PBS and store on ice, then transfer to -80°C storage (Ellison et al., 2021)
Frog toes stored in sterile 1.5 ml tubes at -80°C (Boyle et al., 2004)
Fruit fly larvae sterilise larvae with a solution of 0.5 % Tween 80, 0.5 % sodium hypochlorite and 80 % ethanol for 30 sec, rinse them 3 times in PBS for 30 sec, use sterile pestle to crush larvae and store in BHI containing 20 % glycerol at -80°C (Majumder et al., 2020)
Hooded seal brain whole samples are placed in 4°C glucose artificial cerebrospinal fluid (aCSF) saturated with 95 % O2 - 5 % CO2. After experiment (induced normoxia and hypoxia), tissues were stored in RNAlater stabilisation fluid (Life Technologies, USA) and kept at 4°C. (in-house protocol provided by Justine Vandedorpe)
Invertebrates whole samples are stored in 80 % ethanol, in fridge for short-term storage, and in -20°C freezer for long-term storage (in-house protocol provided by Justine Vandedorpe)
Leaves surface sterilise: rinse for 5 sec 95% ethanol, 30 sec in 70% ethanol, 30 sec in 10% bleach, followed by three 2-minute washes in sterile water, air-dry for 5 min, then add to 2 ml tube containing 350 µL 10 mM MgSO4 and a sterile 5 mm steel ball and homogenise using a TissueLyser (QIAGEN) run at max speed (50 Hz) for up to 60 sec, then flash freeze in liquid nitrogen and store at -80°C (Humphrey & Whiteman, 2020)
Maternal Milk (with glycerol) Minimum of 2ml of milk was self-collected by the mothers in sterile falcon tubes with added 20% glycerol while wearing disposable gloves. Samples without were stored at -20C for cultivation experiments. Note that for colostrum and other milk samples within the first week of life the 2ml min quantity might not be possible. In that case, the mother collected whatever quantity was possible in 10 min timespan. (in-house protocol provided by Pamela Ferretti)
Maternal Milk (without glycerol) Minimum of 2ml of milk was self-collected by the mothers in sterile falcon tubes while wearing disposable gloves. No buffer was added. Samples were stored at -4C right after collection and moved to -80C within a week. Note that for colostrum and other milk samples within the first week of life the 2ml min quantity might not be possible. In that case, the mother collected whatever quantity was possible in 10 min timespan. (in-house protocol provided by Pamela Ferretti)
Mosquitos human bait adult catching method, pool 3-5 mosquitos, store at -80°C (Ali et al., 2021)
Oral swabs after collection swab is immersed in 10:1 Tris-EDTA buffer immediately and stored at −80 °C (Gao et al., 2020)
Penguin cloacal swaps placed in tubes containing viral transport medium (brain heart infusion [BHI] broth-based medium [Oxoid] with 0.3 mg/ml penicillin, 5 mg/ml streptomycin, 0.1 mg/ml gentamicin, and 2.5 μg/ml amphotericin B), kept on ice for 4 hours, then stored at -80°C (Wille et al., 2020)
Pooled tear collection centrifuged at 270 g for 3 min, supernatant stored in 1.5 ml microcentrifuge tubes at -80°C (Willis et al., 2020)
Prokaryotes in sea water water sampled without filtration, 2% final concentration glutaraldehyde added, stored at 4°C for 15 min in the dark, flash-frozen in liquid nitrogen and stored at -80°C (Baltar et al., 2018)
Saliva passive drooling procedure in sterile 50 ml screw top tubes (approximately 3 ml of saliva per sample). About 30 minutes before collection, all volunteers performed a mouth rinse with drinking water. Samples were vortexed before 2 ml of each was centrifuged at 10,000 × g for 10 minutes to collected the bacterial pellets. Total DNA was extracted using the PowerSoil DNA Isolation Kit (MoBio), according to manufacturer’s instructions. DNA was stored at −20 °C until used. (in-house protocol provided by Pamela Ferretti)
Seawater filtered through a 200 µm, then a 20 µm mesh, then vacuum filtered through a 0.8 µm filter, then a 0.2 µm filter, flash frozen in liquid nitrogen & stored at -80°C (all done with ~4h; water at 4°C during processing) (Acinas et al., 2021)
Seawater filtered through a 0.2 µm filter, filter stored in 2 ml tubes containing lysis buffer (EDTA 40 mmol l−1 pH 8.0, Tris-HCl 50 mmol l−1 pH 8.0, sucrose 0.75 mol l−1) flash frozen in liquid nitrogen, filtered & unfiltered water stored in 15 ml falcons at -20°C (Michoud et al., 2021)
Skin swab Skin samples were collected using Catch-All-Swabs (Epicentre Technologies, Wisconsin, USA) shortly after birth but before the skin-to-skin contact with the infant, by swabbing the upper area of the maternal breast (intermammary cleft). After pre-moistening with 2 ml SCF-1 buffer (50 mM Tris buffer, pH 7.6, 1mM EDTA, pH 8.0, and 0.5% Tween-20) (Human Microbiome Project Consortium, 2012) contained in a 15 ml sterile screw top collection tube (Sarstedt, Nümbrecht, Germany), the swab head was rubbed back and forth for approximately 30 seconds over the area (repeating twice) before the swab was returned to the buffered solution. The lower part of the swab was broken to ensure closure of the tube (see below). After sampling, deterge the sampled area with a clean pad of cotton and water. (in-house protocol provided by Pamela Ferretti)
Sponges washed three times with filter-sterilised natural seawater, one fragment placed in 70% ethanol, one fragment placed in RNALater, stored at -20°C (Ruocco et al., 2021)
Stool samples samples were self-collected using collection tubes specific for faecal material (Sarstedt, Nümbrecht, Germany). Toilet paper was placed at the bottom of the WC, to prevent stool samples from sinking and getting contaminated. The collection was performed at the upper part of the feces, the one not in contact with the toilet paper, WC walls or other material. Subjects were instructed, whenever possible, to urinate before evacuating the stools. Samples were collected in variable quantity, depending on availability (meconium is usually only one spoon). Once collected the tube was placed at -4C as soon as possible, and then transferred to -80C within a week. (in-house protocol provided by Pamela Ferretti)
Swedish cervical biobank stored in liquid at -25°C, using liquid-based cytology cells suspended and fixed in Thinprep (TP) containing 20 ml PreservCyt (ThinPrep Hologic, Boxborough, MA). 4 ml of liquid-based cytology sample from the bottom of the patient tube is transferred into a conical tube and allowed to sediment for 30 min. 300 µl of the sediment are transferred to a cryotube and stored at -25°C (Perskvist et al., 2013)
Tongue dorsum swabs Skin samples were collected using Catch-All-Swabs (Epicentre Technologies, Wisconsin, USA). Samples were collected by rubbing a swab on the central area of the back of the tongue for approximately 5 seconds. The swab head was then placed in a 15 ml collection tube containing 2 ml SCF-1 buffer (see photos above). Samples were collected while wearing protective disposable gloves to avoid skin contamination. (in-house protocol provided by Pamela Ferretti)
Turkey Trachea swabs placed in 1 ml PBS, then stored at -20°C (Kursa et al., 2021)
Vaginal swabs Skin samples were collected using Catch-All-Swabs (Epicentre Technologies, Wisconsin, USA). The swab was rubbed 5 times, with a circular motion, in the vaginal introitus and then the swab head was placed in a 15 ml sterile screw top collection tube containing 2 ml SCF-1 buffer (see photos above). (in-house protocol provided by Pamela Ferretti)
Yoghurt after purchase, samples were placed immediately at 4°C for transport and within 12 h stared at -80°C (Islam et al., 2021)

References

  1. Protein purification. (2022). In EMBL. https://www.embl.org/groups/protein-expression-purification/services/protein-purification
  2. Morin, L., Goubet, A., Madigou, C., Pernelle, J.-J., Palmier, K., Labadie, K., Lemainque, A., Michot, O., Astoul, L., Barbier, P., & et al. (2020). Colonization Kinetics and implantation follow-up of the sewage microbiome in an urban wastewater treatment plant. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-68496-z
  3. Wille, M., Harvey, E., Shi, M., Gonzalez-Acuña, D., Holmes, E. C., & Hurt, A. C. (2020). Sustained RNA virome diversity in Antarctic penguins and their ticks. The ISME Journal, 14(7), 1768–1782. https://doi.org/10.1038/s41396-020-0643-1
  4. Karlsen, C., Tzimorotas, D., Robertsen, E. M., Kirste, K. H., Bogevik, A. S., & Rud, I. (2022). Feed microbiome: Confounding factor affecting Fish Gut Microbiome Studies. ISME Communications, 2(1). https://doi.org/10.1038/s43705-022-00096-6
  5. Ellison, S., Knapp, R., & Vredenburg, V. (2021). Longitudinal patterns in the skin microbiome of wild, individually marked frogs from the Sierra Nevada, California. ISME Communications, 1(1). https://doi.org/10.1038/s43705-021-00047-7
  6. Boyle, D. G., Boyle, D. B., Olsen, V., Morgan, J. A. T., & Hyatt, A. D. (2004). Rapid quantitative detection of chytridiomycosis (batrachochytrium dendrobatidis) in amphibian samples using real-time Taqman PCR assay. Diseases of Aquatic Organisms, 60, 141–148. https://doi.org/10.3354/dao060141
  7. Majumder, R., Sutcliffe, B., Taylor, P. W., & Chapman, T. A. (2020). Fruit host-dependent fungal communities in the microbiome of wild Queensland fruit fly larvae. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-73649-1
  8. Humphrey, P. T., & Whiteman, N. K. (2020). Insect herbivory reshapes a native leaf microbiome. Nature Ecology &Amp; Evolution, 4(2), 221–229. https://doi.org/10.1038/s41559-019-1085-x
  9. Ali, R., Jayaraj, J., Mohammed, A., Chinnaraja, C., Carrington, C. V., Severson, D. W., & Ramsubhag, A. (2021). Characterization of the virome associated with Haemagogus Mosquitoes in Trinidad, West Indies. Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-95842-6
  10. Gao, L., Kang, M., Zhang, M. J., Reza Sailani, M., Kuraji, R., Martinez, A., Ye, C., Kamarajan, P., Le, C., Zhan, L., & et al. (2020). Polymicrobial periodontal disease triggers a wide radius of effect and unique virome. Npj Biofilms and Microbiomes, 6(1). https://doi.org/10.1038/s41522-020-0120-7
  11. Willis, K. A., Postnikoff, C. K., Freeman, A., Rezonzew, G., Nichols, K., Gaggar, A., & Lal, C. V. (2020). The closed eye harbours a unique microbiome in dry eye disease. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-68952-w
  12. Baltar, F., Gutiérrez-Rodríguez, A., Meyer, M., Skudelny, I., Sander, S., Thomson, B., Nodder, S., Middag, R., & Morales, S. E. (2018). Specific effect of trace metals on marine heterotrophic microbial activity and Diversity: Key role of iron and zinc and hydrocarbon-degrading bacteria. Frontiers in Microbiology, 9. https://doi.org/10.3389/fmicb.2018.03190
  13. Acinas, S. G., Sánchez, P., Salazar, G., Cornejo-Castillo, F. M., Sebastián, M., Logares, R., Royo-Llonch, M., Paoli, L., Sunagawa, S., Hingamp, P., & et al. (2021). Deep Ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. Communications Biology, 4(1). https://doi.org/10.1038/s42003-021-02112-2
  14. Michoud, G., Ngugi, D. K., Barozzi, A., Merlino, G., Calleja, M. L., Delgado-Huertas, A., Morán, X. A., & Daffonchio, D. (2021). Fine-scale metabolic discontinuity in a stratified prokaryote microbiome of a red sea deep halocline. The ISME Journal, 15(8), 2351–2365. https://doi.org/10.1038/s41396-021-00931-z
  15. Ruocco, N., Esposito, R., Zagami, G., Bertolino, M., De Matteo, S., Sonnessa, M., Andreani, F., Crispi, S., Zupo, V., & Costantini, M. (2021). Microbial diversity in Mediterranean sponges as revealed by metataxonomic analysis. Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-00713-9
  16. Perskvist, N., Norman, I., Eklund, C., Litton, J.-E., & Dillner, J. (2013). The Swedish cervical cytology Biobank: Sample handling and storage process. Biopreservation and Biobanking, 11(1), 19–24. https://doi.org/10.1089/bio.2012.0036
  17. Kursa, O., Tomczyk, G., Sawicka-Durkalec, A., Giza, A., & Słomiany-Szwarc, M. (2021). Bacterial communities of the upper respiratory tract of turkeys. Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-81984-0
  18. Islam, S. M., Tanzina, A. Y., Foysal, M. J., Hoque, M. N., Rumi, M. H., Siddiki, A. M., Tay, A. C.-Y., Hossain, M. J., Bakar, M. A., Mostafa, M., & et al. (2021). Insights into the nutritional properties and microbiome diversity in sweet and sour yogurt manufactured in Bangladesh. Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-01852-9