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DNA and RNA kits by sample


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Page last modified on: 2024, December 17

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Nucleic Acid extraction kits

DNA extraction

RNA extraction

  • Mosquitos - TRIzol LS (Invitrogen) – purified with RNeasy MinElute Cleanup Kit (Qiagen)(Ali et al., 2021)
  • Sea Water - RNeasy mini kit (Qiagen)(Martínez-Pérez et al., 2022)
  • Antarctic ticks - MagMax mirVana™ Total RNA isolation Kit (ThermoFisher Scientific)(Willis et al., 2020)
  • Soil - PowerMax soil DNA isolation kit (Mo Bio)(Xu et al., 2021)
  • Cervical samples - Smarter stranded total RNA-seq kit v2—pico input mammalian (Takara Bio)(Arroyo Mühr et al., 2021)
  • Viral DNA & RNA - AllPrep DNA/RNA Mini kit (Qiagen)(Liang et al., 2020)
  • Viral RNA - QIAmp Viral RNA kit (Qiagen)(Goolam Mahomed et al., 2021)
  • Cerebellum, hippocampus and visual cortex - Uneasy Plus Universal Mini Kit (Qiagen) - in house protocol provided by Justine Vandendorpe
  • Bile samples - ZymoBIOMICS DNA/RNA Miniprep Kit - in house protocol provided by Nicole Treichel
  • mouse small intestine content - ZymoBIOMICS DNA/RNA Miniprep Kit - in house protocol provided by Nicole Treichel

References

  1. 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
  2. Cebriá-Mendoza, M., Arbona, C., Larrea, L., Díaz, W., Arnau, V., Peña, C., Bou, J. V., Sanjuán, R., & Cuevas, J. M. (2021). Deep viral blood metagenomics reveals extensive anellovirus diversity in healthy humans. Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-86427-4
  3. Martínez-Pérez, C., Greening, C., Bay, S. K., Lappan, R. J., Zhao, Z., De Corte, D., Hulbe, C., Ohneiser, C., Stevens, C., Thomson, B., & et al. (2022). Phylogenetically and functionally diverse microorganisms reside under the Ross Ice Shelf. Nature Communications, 13(1). https://doi.org/10.1038/s41467-021-27769-5
  4. 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
  5. 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
  6. 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
  7. Kim, H.-J., Oh, H. N., Park, T., Kim, H., Lee, H. G., An, S., & Sul, W. J. (2022). Aged related human skin microbiome and mycobiome in Korean women. Scientific Reports, 12(1). https://doi.org/10.1038/s41598-022-06189-5
  8. Ogai, K., Nana, B. C., Lloyd, Y. M., Arios, J. P., Jiyarom, B., Awanakam, H., Esemu, L. F., Hori, A., Matsuoka, A., Nainu, F., & et al. (2022). Skin microbiome profile of Healthy Cameroonians and Japanese. Scientific Reports, 12(1). https://doi.org/10.1038/s41598-022-05244-5
  9. Chaudhari, D. S., Dhotre, D. P., Agarwal, D. M., Gaike, A. H., Bhalerao, D., Jadhav, P., Mongad, D., Lubree, H., Sinkar, V. P., Patil, U. K., & et al. (2020). Gut, oral and skin microbiome of Indian patrilineal families reveal perceptible association with age. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-62195-5
  10. Scanes, E., Parker, L. M., Seymour, J. R., Siboni, N., Dove, M. C., O’Connor, W. A., & Ross, P. M. (2021). Microbiomes of an oyster are shaped by metabolism and environment. Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-00590-2
  11. Sousa, R., Vasconcelos, J., Vera-Escalona, I., Delgado, J., Freitas, M., González, J. A., & Riera, R. (2021). Major ocean currents may shape the microbiome of the Topshell Phorcus sauciatus in the NE Atlantic Ocean. Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-91448-0
  12. Mulec, J., Oarga-Mulec, A., Holko, L., Pašić, L., Kopitar, A. N., Eleršek, T., & Mihevc, A. (2021). Microbiota entrapped in recently-formed ice: Paradana ice cave, Slovenia. Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-81528-6
  13. Goolam Mahomed, T., Peters, R. P., Allam, M., Ismail, A., Mtshali, S., Goolam Mahomed, A., Ueckermann, V., Kock, M. M., & Ehlers, M. M. (2021). Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa. Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-99127-w
  14. Custodio, M., Espinoza, C., Peñaloza, R., Peralta-Ortiz, T., Sánchez-Suárez, H., Ordinola-Zapata, A., & Vieyra-Peña, E. (2022). Microbial diversity in intensively farmed lake sediment contaminated by heavy metals and identification of microbial taxa bioindicators of environmental quality. Scientific Reports, 12(1). https://doi.org/10.1038/s41598-021-03949-7
  15. 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
  16. Satjarak, A., Golinski, G. K., Trest, M. T., & Graham, L. E. (2022). Microbiome and related structural features of Earth’s most archaic plant indicate early plant symbiosis attributes. Scientific Reports, 12(1). https://doi.org/10.1038/s41598-022-10186-z
  17. Park, J. Y., Seo, H., Kang, C.-S., Shin, T.-S., Kim, J. W., Park, J.-M., Kim, J. G., & Kim, Y.-K. (2022). Dysbiotic change in gastric microbiome and its functional implication in gastric carcinogenesis. Scientific Reports, 12(1). https://doi.org/10.1038/s41598-022-08288-9
  18. Eun, Y.-G., Lee, J.-W., Kim, S. W., Hyun, D.-W., Bae, J.-W., & Lee, Y. C. (2021). Oral microbiome associated with lymph node metastasis in oral squamous cell carcinoma. Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-02638-9
  19. Shetty, S. A., Kuipers, B., Atashgahi, S., Aalvink, S., Smidt, H., & de Vos, W. M. (2022). Inter-species metabolic interactions in an in-vitro minimal human gut microbiome of core bacteria. Npj Biofilms and Microbiomes, 8(1). https://doi.org/10.1038/s41522-022-00275-2
  20. Hannula, S. E., Heinen, R., Huberty, M., Steinauer, K., De Long, J. R., Jongen, R., & Bezemer, T. M. (2021). Persistence of plant-mediated microbial soil legacy effects in soil and inside roots. Nature Communications, 12(1). https://doi.org/10.1038/s41467-021-25971-z
  21. Zheng, X., Jahn, M. T., Sun, M., Friman, V.-P., Balcazar, J. L., Wang, J., Shi, Y., Gong, X., Hu, F., & Zhu, Y.-G. (2022). Organochlorine contamination enriches virus-encoded metabolism and pesticide degradation associated auxiliary genes in soil microbiomes. The ISME Journal, 16(5), 1397–1408. https://doi.org/10.1038/s41396-022-01188-w
  22. 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
  23. Yahara, K., Suzuki, M., Hirabayashi, A., Suda, W., Hattori, M., Suzuki, Y., & Okazaki, Y. (2021). Long-read metagenomics using Promethion uncovers oral bacteriophages and their interaction with host bacteria. Nature Communications, 12(1). https://doi.org/10.1038/s41467-020-20199-9
  24. Lee, C. Z., Zoqratt, M. Z., Phipps, M. E., Barr, J. J., Lal, S. K., Ayub, Q., & Rahman, S. (2022). The Gut Virome in two indigenous populations from Malaysia. Scientific Reports, 12(1). https://doi.org/10.1038/s41598-022-05656-3
  25. Liang, G., Zhao, C., Zhang, H., Mattei, L., Sherrill-Mix, S., Bittinger, K., Kessler, L. R., Wu, G. D., Baldassano, R. N., DeRusso, P., & et al. (2020). The stepwise assembly of the neonatal virome is modulated by breastfeeding. Nature, 581(7809), 470–474. https://doi.org/10.1038/s41586-020-2192-1
  26. Chehoud, C., Dryga, A., Hwang, Y., Nagy-Szakal, D., Hollister, E. B., Luna, R. A., Versalovic, J., Kellermayer, R., & Bushman, F. D. (2016). Transfer of viral communities between human individuals during fecal microbiota transplantation. MBio, 7(2). https://doi.org/10.1128/mbio.00322-16
  27. Zhang, F., Zuo, T., Yeoh, Y. K., Cheng, F. W., Liu, Q., Tang, W., Cheung, K. C., Yang, K., Cheung, C. P., Mo, C. C., & et al. (2021). Longitudinal dynamics of gut bacteriome, mycobiome and Virome after fecal microbiota transplantation in graft-versus-host disease. Nature Communications, 12(1). https://doi.org/10.1038/s41467-020-20240-x
  28. 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
  29. 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
  30. 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
  31. Xu, L., Dong, Z., Chiniquy, D., Pierroz, G., Deng, S., Gao, C., Diamond, S., Simmons, T., Wipf, H. M.-L., Caddell, D., & et al. (2021). Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics. Nature Communications, 12(1). https://doi.org/10.1038/s41467-021-23553-7
  32. Arroyo Mühr, L. S., Dillner, J., Ure, A. E., Sundström, K., & Hultin, E. (2021). Comparison of DNA and RNA sequencing of total nucleic acids from human cervix for metagenomics. Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-98452-4