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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Flagellar transformation of Naegleria gruberi Resource Report Resource Website |
Anastasios Tsaousis | DOI:10.17504/protocols.io.hnhb5b6 | Protist Research to Optimize Tools in Genetics (PROT-G) | University of Kent | 1 | 2017 | Anastasios Tsaousis 2017. Flagellar transformation of Naegleria gruberi. protocols.io https://dx.doi.org/10.17504/protocols.io.hnhb5b6 | 2021-04-15 09:15:13 | ||||
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FlowCam Standard Operating Procedure Resource Report Resource Website |
Jacob Harris | DOI:10.17504/protocols.io.hgjb3un | Protist Research to Optimize Tools in Genetics (PROT-G), Alverson Lab | The FlowCam can be used to take quick cell density measurements of liquid samples. | 3 | 2017 | Jacob Harris 2017. FlowCam Standard Operating Procedure. protocols.io https://dx.doi.org/10.17504/protocols.io.hgjb3un | 2021-04-15 09:15:38 | ||||
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Biolistic dye loading protocol for marine phytoplankton Resource Report Resource Website |
Glen Wheeler, Colin Brownlee | DOI:10.17504/protocols.io.hpzb5p6 | Protist Research to Optimize Tools in Genetics (PROT-G) | A method to load algal cells with dextran-conjugated fluorescent dyes. This is a good way of testing and optimising conditions for biolistic DNA delivery. | Marine Biological Association, Marine Biological Association | 1 | 2017 | Glen Wheeler, Colin Brownlee 2017. Biolistic dye loading protocol for marine phytoplankton. protocols.io https://dx.doi.org/10.17504/protocols.io.hpzb5p6 | 2021-04-15 09:15:40 | |||
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Genome-wide Kozak Sequence Over-represented Motif Analysis Resource Report Resource Website |
Mariana Rius, Joshua Rest | DOI:10.17504/protocols.io.hikb4cw | Protist Research to Optimize Tools in Genetics (PROT-G), Collier Lab | Bioinformatic approach to identifying over-represented motifs in the region framing the start codon (25 bp up and downstream) for genes annotated in the three sequenced Labyrinthulomycete genomes (Aurantiochytrium limacinum, Schizochytrium aggregatum, and Aplanochytrium kergulense). | Stony Brook University, Stony Brook University | 1 | 2017 | Mariana Rius, Joshua Rest 2017. Genome-wide Kozak Sequence Over-represented Motif Analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.hikb4cw | 2021-04-15 09:15:38 | |||
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Cryopreservation of labyrinthulomycetes with DMSO and horse serum Resource Report Resource Website |
Jackie Collier | DOI:10.17504/protocols.io.pgudjww | Protist Research to Optimize Tools in Genetics (PROT-G), Collier Lab | Modified from one of the methods tested by Cox et al. 2009 | Stony Brook University | 1 | 2018 | Jackie Collier 2018. Cryopreservation of labyrinthulomycetes with DMSO and horse serum. protocols.io https://dx.doi.org/10.17504/protocols.io.pgudjww | 2021-04-15 09:15:15 | |||
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Stable transfection of unicellular relative of animals, Corallochytrium limacisporum, using Lonza Nucleofector Resource Report Resource Website |
Aleksandra Kozyczkowska, Sebastian Najle, Eduard Ocaña-Pallarès, Cristina Aresté, Iñaki Ruiz-Trillo, Elena Casacuberta | DOI:10.17504/protocols.io.bpfgmjjw | Protist Research to Optimize Tools in Genetics (PROT-G), Multicellgenomelab, Emerging Organisms for Biology | This protocol describes the transfection of Corallochytrium limacisporum, one of the unicellular relatives of animals. The transfection is performed using Lonza Nucleofector System X and reporter cassettes that contain endogenous regulatory elements of C. limacisporum. | Institut de Biologia Evolutiva (UPF-CSIC) Barcelona, Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), IIBB, Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Institute of Evolutionary Biology | 2 | 2020 | Aleksandra Kozyczkowska, Sebastian Najle, Eduard Ocaña-Pallarès, Cristina Aresté, Iñaki Ruiz-Trillo, Elena Casacuberta 2020. Stable transfection of unicellular relative of animals, Corallochytrium limacisporum, using Lonza Nucleofector. protocols.io https://dx.doi.org/10.17504/protocols.io.bpfgmjjw | 2021-04-15 09:15:17 | |||
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Bodo saltans tagging plasmid: 69 kDa paraflagellar rod protein 2C cassette for C terminal tagging_BsTub Resource Report Resource Website |
Fatma Gomaa, Roberto Docampo, Virginia Edgcomb, Peter Girguis, Zuhong Li | DOI:10.17504/protocols.io.s5peg5n | Protist Research to Optimize Tools in Genetics (PROT-G) | Harvard University, University of Georgia, Woods Hole Oceanographic Institution, Harvard University, University of Georgia | 2 | 2018 | Fatma Gomaa, Roberto Docampo, Virginia Edgcomb, Peter Girguis, Zuhong Li 2018. Bodo saltans tagging plasmid: 69 kDa paraflagellar rod protein 2C cassette for C terminal tagging_BsTub. protocols.io https://dx.doi.org/10.17504/protocols.io.s5peg5n | 2021-04-15 09:15:20 | ||||
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Staining Unfixed Labyrinthulomycetes with Nile Red Resource Report Resource Website |
This protocol modified from: Pandey A, Bhathena Z. 2014. Prevalence of PUFA Rich Thraustochytrids sps. along the Coast of Mumbai for Produ | DOI:10.17504/protocols.io.hghb3t6 | Protist Research to Optimize Tools in Genetics (PROT-G), Collier Lab | This protocol modified from: Pandey A, Bhathena Z. 2014. Prevalence of PUFA Rich Thraustochytrids sps. along the Coast of Mumbai for Production of Bio Oil. Journal of Food and Nutrition Research 2(12): 993-999. | , | 1 | 2017 | This protocol modified from: Pandey A, Bhathena Z. 2014. Prevalence of PUFA Rich Thraustochytrids sps. along the Coast of Mumbai for Produ 2017. Staining Unfixed Labyrinthulomycetes with Nile Red. protocols.io https://dx.doi.org/10.17504/protocols.io.hghb3t6 | 2021-04-15 09:15:19 | |||
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Abeoforma whisleri transient transfection protocol Resource Report Resource Website |
Elena Casacuberta, Aleksandra Kozyczkowska, Sebastian Najle | DOI:10.17504/protocols.io.zexf3fn | Protist Research to Optimize Tools in Genetics (PROT-G), Multicellgenomelab, Emerging Organisms for Biology | This is a protocol for transient transfection of the Icthyosporean Abeoforma whisleri. This protocol has an efficiency of 1-2% calculated from fluorescent positive cell from Flow Cytometry data, using the amount of cells and DNA described in the protocol. Increasing DNA from above 1 microgram/microliter does not increase transfection. | Faktorová D, Nisbet RER, Robledo JAF, Casacuberta E, Sudek L, Allen AE, Ares M, Aresté C, Balestreri C, Barbrook AC, Beardslee P, Bender S, Booth DS, Bouget F, Bowler C, Breglia SA, Brownlee C, Burger G, Cerutti H, Cesaroni R, Chiurillo MA, Clemente T, Coles DB, Collier JL, Cooney EC, Coyne K, Docampo R, Dupont CL, Edgcomb V, Einarsson E, Elustondo PA, Federici F, Freire-Beneitez V, Freyria NJ, Fukuda K, García PA, Girguis PR, Gomaa F, Gornik SG, Guo J, Hampl V, Hanawa Y, Haro-Contreras ER, Hehenberger E, Highfield A, Hirakawa Y, Hopes A, Howe CJ, Hu I, Ibañez J, Irwin NAT, Ishii Y, Janowicz NE, Jones AC, Kachale A, Fujimura-Kamada K, Kaur B, Kaye JZ, Kazana E, Keeling PJ, King N, Klobutcher LA, Lander N, Lassadi I, Li Z, Lin S, Lozano J, Luan F, Maruyama S, Matute T, Miceli C, Minagawa J, Moosburner M, Najle SR, Nanjappa D, Nimmo IC, Noble L, Vanclová AMGN, Nowacki M, Nuñez I, Pain A, Piersanti A, Pucciarelli S, Pyrih J, Rest JS, Rius M, Robertson D, Ruaud A, Ruiz-Trillo I, Sigg MA, Silver PA, Slamovits CH, Smith GJ, Sprecher BN, Stern R, Swart EC, Tsaousis AD, Tsypin L, Turkewitz A, Turnšek J, Valach M, Vergé V, Dassow Pv, Haar Tvd, Waller RF, Wang L, Wen X, Wheeler G, Woods A, Zhang H, Mock T, Worden AZ, Lukeš J, Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nature Methods 17(5). doi: 10.1038/s41592-020-0796-x | Institute of Evolutionary Biology, Institute of Evolutionary Biology, Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra) | https://doi.org/10.1038/s41592-020-0796-x | 1 | 2019 | Elena Casacuberta, Aleksandra Kozyczkowska, Sebastian Najle 2019. Abeoforma whisleri transient transfection protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.zexf3fn | 2021-04-15 09:15:21 | |
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Protocols for mRNA electroporation Resource Report Resource Website |
Natalia Wandyszewska and Anna Vanclova | DOI:10.17504/protocols.io.hh4b38w | Protist Research to Optimize Tools in Genetics (PROT-G) | This protocol we have used for the electroporation of mRNA encoding reporter gene Lucipherase into following organisms: Chromera velia, Alexandrium minutum, Euglena gracilis, Pyramimonas parkease, Pyramimonas orientalis, Eutreptiella gymnastica, Pseudonitzschia multiseries and Trichomonas vaginalis (a control). In any case we have not detected a specific lucipharease activity. | Charles University in Prague | 1 | 2017 | Natalia Wandyszewska and Anna Vanclova 2017. Protocols for mRNA electroporation. protocols.io https://dx.doi.org/10.17504/protocols.io.hh4b38w | 2021-04-15 09:15:24 | |||
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Transcriptome sequencing of 19 diverse species of choanoflagellates Resource Report Resource Website |
Daniel Richter, Parinaz Fozouni, Michael Eisen, Nicole King | DOI:10.17504/protocols.io.kwscxee | Ecology of Marine Plankton (ECOMAP) team - Roscoff, King Lab, Protist Research to Optimize Tools in Genetics (PROT-G) | The origin of animals, which occurred over 600 million years ago, left no evidence in the fossil record. To trace the earliest events in animal prehistory, we compare extant animals to their closest living relatives, the choanoflagellates, in order to reconstruct the gene content of their last common ancestor and how it evolved on the stem lineage leading to animals. In this project, we increase the accuracy of ancestral animal and choanoflagellate gene content reconstructions by sequencing the transcriptomes of 19 species of choanoflagellates selected for their phylogenetic diversity. | Richter, Daniel J and Fozouni, Parinaz and Eisen, Michael and King, Nicole. Gene family innovation, conservation and loss on the animal stem lineage. 2018;7:e34226 https://doi.org/10.7554/eLife.34226 | Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin - UMR 7144 CNRS UPMC, University of California, San Francisco, University of California, Berkeley, University of California, Berkeley | http://kinglab.berkeley.edu/ | 1 | 2017 | Daniel Richter, Parinaz Fozouni, Michael Eisen, Nicole King 2017. Transcriptome sequencing of 19 diverse species of choanoflagellates. protocols.io https://dx.doi.org/10.17504/protocols.io.kwscxee | 2021-04-15 09:15:48 | |
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Genetic transformation of Parabodo caudatus using square wave electroporation system and pUB-GFP plasmid Resource Report Resource Website |
Fatma Gomaa, Paulo A. Garcia, Jennifer Delany, Peter Girguis, Cullen R. Buie, and Virginia Edgcomb | DOI:10.17504/protocols.io.hmeb43e | Protist Research to Optimize Tools in Genetics (PROT-G) | Woods Hole Oceanographic Institute, Harvard, MIT, Woods Hole Oceanographic Institute, Harvard, MIT, Woods Hole Oceanographic Institute, Harvard, MIT, Woods Hole Oceanographic Institute, Harvard, MIT, Woods Hole Oceanographic Institute, Harvard, MIT, Woods Hole Oceanographic Institute, Harvard, MIT | 2 | 2017 | Fatma Gomaa, Paulo A. Garcia, Jennifer Delany, Peter Girguis, Cullen R. Buie, and Virginia Edgcomb 2017. Genetic transformation of Parabodo caudatus using square wave electroporation system and pUB-GFP plasmid. protocols.io https://dx.doi.org/10.17504/protocols.io.hmeb43e | 2021-04-15 09:15:49 | ||||
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Conjugation of Thalassiosira pseudonana Resource Report Resource Website |
Jernej Turnsek | DOI:10.17504/protocols.io.f55bq86 | Protist Research to Optimize Tools in Genetics (PROT-G) | This protocol was used to express a nourseothricin (nou/nat) resistance gene and a gene encoding a silaffin precursor TpSil3p-APEX2 fusion protein in Thalassiosira pseudonana (Tp) strain CCMP1335 using conjugation by largely following Karas et al. (2015). In addition to the protocol, I am listing some of my observations working with this diatom species. Please check the 'Before start' and 'Guidelines' sections for more information including a list of Tp episomes I've constructed and which are available upon request. For additional background on my overacrching experimental aim, please refer to this document. 1. E. V. Armbrust, The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution, and Metabolism. Science. 306, 79–86 (2004).2. B. J. Karas et al., Designer diatom episomes delivered by bacterial conjugation. Nat. Commun. 6, 6925 (2015).Keeping in mind that diatom episomes contain a yeast centromere, it would be very interesting to see if conjugation could be adapted to organisms beyond diatoms. | Harvard Medical School, Department of Systems Biology | UC San Diego, Scripps Institution of Oceanography | http://openwetware.org/images/c/c1/Turnsek_EMBL_16%27.pdf | 3 | 2016 | Jernej Turnsek 2016. Conjugation of Thalassiosira pseudonana. protocols.io https://dx.doi.org/10.17504/protocols.io.f55bq86 | 2021-04-15 09:15:48 | ||
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Calcium phosphate transfection of Oxyrrhis marina with an Alexa488-labelled DNA fragment Resource Report Resource Website |
Pia Elustondo | DOI:10.17504/protocols.io.ha4b2gw | Protist Research to Optimize Tools in Genetics (PROT-G), Slamovits Lab | 1 | 2017 | Pia Elustondo 2017. Calcium phosphate transfection of Oxyrrhis marina with an Alexa488-labelled DNA fragment. protocols.io https://dx.doi.org/10.17504/protocols.io.ha4b2gw | 2021-04-15 09:15:25 | |||||
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Selection of stable transformants in Ostreococcus tauri and Bathycoccus prasinos Resource Report Resource Website |
Francois-Yves bouget | DOI:10.17504/protocols.io.hddb226 | Protist Research to Optimize Tools in Genetics (PROT-G) | This protocol describes the selection and growth of stable transformants in semi solid agarose medium. Developped initially for Ostreococcus tauri, it also works for Bathycoccus. | Laboratoire d'Oceanographie Microbienne. Banyuls sur Mer | 2 | 2017 | Francois-Yves bouget 2017. Selection of stable transformants in Ostreococcus tauri and Bathycoccus prasinos. protocols.io https://dx.doi.org/10.17504/protocols.io.hddb226 | 2021-04-15 09:15:31 | |||
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Glass beads-based transformation protocol for Perkinsus marinus Resource Report Resource Website |
Imen Lassadi | DOI:10.17504/protocols.io.g36byre | Protist Research to Optimize Tools in Genetics (PROT-G) | Faktorová D, Nisbet RER, Robledo JAF, Casacuberta E, Sudek L, Allen AE, Ares M, Aresté C, Balestreri C, Barbrook AC, Beardslee P, Bender S, Booth DS, Bouget F, Bowler C, Breglia SA, Brownlee C, Burger G, Cerutti H, Cesaroni R, Chiurillo MA, Clemente T, Coles DB, Collier JL, Cooney EC, Coyne K, Docampo R, Dupont CL, Edgcomb V, Einarsson E, Elustondo PA, Federici F, Freire-Beneitez V, Freyria NJ, Fukuda K, García PA, Girguis PR, Gomaa F, Gornik SG, Guo J, Hampl V, Hanawa Y, Haro-Contreras ER, Hehenberger E, Highfield A, Hirakawa Y, Hopes A, Howe CJ, Hu I, Ibañez J, Irwin NAT, Ishii Y, Janowicz NE, Jones AC, Kachale A, Fujimura-Kamada K, Kaur B, Kaye JZ, Kazana E, Keeling PJ, King N, Klobutcher LA, Lander N, Lassadi I, Li Z, Lin S, Lozano J, Luan F, Maruyama S, Matute T, Miceli C, Minagawa J, Moosburner M, Najle SR, Nanjappa D, Nimmo IC, Noble L, Vanclová AMGN, Nowacki M, Nuñez I, Pain A, Piersanti A, Pucciarelli S, Pyrih J, Rest JS, Rius M, Robertson D, Ruaud A, Ruiz-Trillo I, Sigg MA, Silver PA, Slamovits CH, Smith GJ, Sprecher BN, Stern R, Swart EC, Tsaousis AD, Tsypin L, Turkewitz A, Turnšek J, Valach M, Vergé V, Dassow Pv, Haar Tvd, Waller RF, Wang L, Wen X, Wheeler G, Woods A, Zhang H, Mock T, Worden AZ, Lukeš J, Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nature Methods 17(5). doi: 10.1038/s41592-020-0796-x | Biochemistry department, Cambridge university, UK. | https://doi.org/10.1038/s41592-020-0796-x | 1 | 2017 | Imen Lassadi 2017. Glass beads-based transformation protocol for Perkinsus marinus. protocols.io https://dx.doi.org/10.17504/protocols.io.g36byre | 2021-04-15 09:15:30 | ||
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Euplotes crassus transfection using FuGene HD Transfection Reagent as vehicle (provisional) Resource Report Resource Website |
RACHELE CESARONI, Rachele Cesaroni | DOI:10.17504/protocols.io.2apgadn | Protist Research to Optimize Tools in Genetics (PROT-G) | University of Bern, Institute of Biology, Universität Bern | 1 | 2019 | RACHELE CESARONI, Rachele Cesaroni 2019. Euplotes crassus transfection using FuGene HD Transfection Reagent as vehicle (provisional). protocols.io https://dx.doi.org/10.17504/protocols.io.2apgadn | 2021-04-15 09:15:30 | ||||
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Dinoflagellate transformation Resource Report Resource Website |
Lu Wang, Brittany Sprecher, Huan Zhang, Senjie Lin | DOI:10.17504/protocols.io.7prhmm6 | Protist Research to Optimize Tools in Genetics (PROT-G) | Protocol of dinoflagellate cell transformation | University of Connecticut, University of Connecticut, University of Connecticut, University of Connecticut | http://biorxiv.org/lookup/doi/10.1101/718239 | 2 | 2019 | Lu Wang, Brittany Sprecher, Huan Zhang, Senjie Lin 2019. Dinoflagellate transformation. protocols.io https://dx.doi.org/10.17504/protocols.io.7prhmm6 | 2021-04-15 09:15:38 | ||
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Cultivation of Seminavis robusta Resource Report Resource Website |
Lev Tsypin, Aaron Turkewitz | DOI:10.17504/protocols.io.337gqrn | Protist Research to Optimize Tools in Genetics (PROT-G) | This protocol describes how we grew S. robusta and stored cultures at 4 C. Under these condtiions, the cells grow to a maximum density of 2-2.5 x 106 cells/mL. | California Institute of Technology, University of Chicago | 1 | 2019 | Lev Tsypin, Aaron Turkewitz 2019. Cultivation of Seminavis robusta. protocols.io https://dx.doi.org/10.17504/protocols.io.337gqrn | 2021-04-15 09:15:38 | |||
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Biolistic transformation of Isochrysis galbana Resource Report Resource Website |
Glen Wheeler, Rowena Stern | DOI:10.17504/protocols.io.2pugdnw | Protist Research to Optimize Tools in Genetics (PROT-G) | Faktorová D, Nisbet RER, Robledo JAF, Casacuberta E, Sudek L, Allen AE, Ares M, Aresté C, Balestreri C, Barbrook AC, Beardslee P, Bender S, Booth DS, Bouget F, Bowler C, Breglia SA, Brownlee C, Burger G, Cerutti H, Cesaroni R, Chiurillo MA, Clemente T, Coles DB, Collier JL, Cooney EC, Coyne K, Docampo R, Dupont CL, Edgcomb V, Einarsson E, Elustondo PA, Federici F, Freire-Beneitez V, Freyria NJ, Fukuda K, García PA, Girguis PR, Gomaa F, Gornik SG, Guo J, Hampl V, Hanawa Y, Haro-Contreras ER, Hehenberger E, Highfield A, Hirakawa Y, Hopes A, Howe CJ, Hu I, Ibañez J, Irwin NAT, Ishii Y, Janowicz NE, Jones AC, Kachale A, Fujimura-Kamada K, Kaur B, Kaye JZ, Kazana E, Keeling PJ, King N, Klobutcher LA, Lander N, Lassadi I, Li Z, Lin S, Lozano J, Luan F, Maruyama S, Matute T, Miceli C, Minagawa J, Moosburner M, Najle SR, Nanjappa D, Nimmo IC, Noble L, Vanclová AMGN, Nowacki M, Nuñez I, Pain A, Piersanti A, Pucciarelli S, Pyrih J, Rest JS, Rius M, Robertson D, Ruaud A, Ruiz-Trillo I, Sigg MA, Silver PA, Slamovits CH, Smith GJ, Sprecher BN, Stern R, Swart EC, Tsaousis AD, Tsypin L, Turkewitz A, Turnšek J, Valach M, Vergé V, Dassow Pv, Haar Tvd, Waller RF, Wang L, Wen X, Wheeler G, Woods A, Zhang H, Mock T, Worden AZ, Lukeš J, Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nature Methods 17(5). doi: 10.1038/s41592-020-0796-x | Marine Biological Association, Marine Biological Association | https://doi.org/10.1038/s41592-020-0796-x | 1 | 2019 | Glen Wheeler, Rowena Stern 2019. Biolistic transformation of Isochrysis galbana. protocols.io https://dx.doi.org/10.17504/protocols.io.2pugdnw | 2021-04-15 09:15:38 |
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