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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Protocol B: Preparation of ATP for transfection Resource Report Resource Website |
David Booth | DOI:10.17504/protocols.io.h8ub9ww | King Lab, Protist Research to Optimize Tools in Genetics (PROT-G) | University of California, San Francisco | 1 | 2018 | David Booth 2018. Protocol B: Preparation of ATP for transfection. protocols.io https://dx.doi.org/10.17504/protocols.io.h8ub9ww | 2021-04-15 09:16:22 | ||||
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Parabodo caudatus post-electroporation cell viability quantification using exponential decay electroporation Resource Report Resource Website |
Fatma Gomma, Paulo A. Garcia, Jennifer Delaney, Peter R. Girguis, Cullen R. Buie, Virginia P. Edgcomb | DOI:10.17504/protocols.io.hmhb436 | Protist Research to Optimize Tools in Genetics (PROT-G) | The process of developing transient transfection protocols in P. caudatus involved initial testing and determination of proper electroporation buffers and parameters (voltage strength, pulse duration and number) to maximize cell viability. Our results suggest that the type of electroporation buffer is critical for maintaining cell viability throughout the experiment and is essential for determining the optimum electric field range. | Woods Hole Oceanographic Institute, MIT, Harvard, Woods Hole Oceanographic Institute, MIT, Harvard, Woods Hole Oceanographic Institute, MIT, Harvard, Woods Hole Oceanographic Institute, MIT, Harvard, Woods Hole Oceanographic Institute, MIT, Harvard, Woods Hole Oceanographic Institute, MIT, Harvard | 3 | 2017 | Fatma Gomma, Paulo A. Garcia, Jennifer Delaney, Peter R. Girguis, Cullen R. Buie, Virginia P. Edgcomb 2017. Parabodo caudatus post-electroporation cell viability quantification using exponential decay electroporation. protocols.io https://dx.doi.org/10.17504/protocols.io.hmhb436 | 2021-04-15 09:16:25 | |||
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Euplotes crassus transfection through microinjection into the macronucleus Resource Report Resource Website |
Rachele Cesaroni | DOI:10.17504/protocols.io.2argad6 | Protist Research to Optimize Tools in Genetics (PROT-G) | Universität Bern | 1 | 2019 | Rachele Cesaroni 2019. Euplotes crassus transfection through microinjection into the macronucleus. protocols.io https://dx.doi.org/10.17504/protocols.io.2argad6 | 2021-04-15 09:16:25 | ||||
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Nanodrop Spectrophotometer (ND-1000) for Nucleic Acid Resource Report Resource Website |
Steven Wilhelm | DOI:10.17504/protocols.io.id2ca8e | Protist Research to Optimize Tools in Genetics (PROT-G), The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs), CyanoHABs | Please contact Dr. Steven Wilhelm ([email protected]) for additional information regarding this protocol.Adapted from Nanodrop ND-1000 User Manual | The University of Tennessee, Knoxville | 1 | 2017 | Steven Wilhelm 2017. Nanodrop Spectrophotometer (ND-1000) for Nucleic Acid. protocols.io https://dx.doi.org/10.17504/protocols.io.id2ca8e | 2021-04-15 09:16:54 | |||
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The culturing of axenic Ochromonas sp. strain CCMP1393 Resource Report Resource Website |
Alle Lie | DOI:10.17504/protocols.io.ey8bfzw | Protist Research to Optimize Tools in Genetics (PROT-G), Caron Lab - Protistan Ecology | 1 | 2016 | Alle Lie 2016. The culturing of axenic Ochromonas sp. strain CCMP1393. protocols.io https://dx.doi.org/10.17504/protocols.io.ey8bfzw | 2021-04-15 09:16:51 | |||||
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pTpPuc3_TpSil3p-eGFP Resource Report Resource Website |
Jernej Turnsek | DOI:10.17504/protocols.io.7ghhjt6 | Protist Research to Optimize Tools in Genetics (PROT-G) | Map and nucleotide sequence of the conjugation episome used to generate a TpSIl3p-EGFP expressing T. pseudonana strain reported in Faktorová D. et al. | 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 | University of California, Berkeley | https://doi.org/10.1101/718239 | 1 | 2019 | Jernej Turnsek 2019. pTpPuc3_TpSil3p-eGFP. protocols.io https://dx.doi.org/10.17504/protocols.io.7ghhjt6 | 2021-04-15 09:16:55 | |
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Acriflavine Direct Detection Technique for Labyrinthulomycetes Resource Report Resource Website |
This protocol is modified from: Raghukumar S, Schaumann K. 1993. An epifluorescence microscopy method for direct detection and enumeration of the, the thraustochytrids. Limnol. Oceanogr. | DOI:10.17504/protocols.io.hfib3ke | Protist Research to Optimize Tools in Genetics (PROT-G), Collier Lab | This protocol is modified from: Raghukumar S, Schaumann K. 1993. An epifluorescence microscopy method for direct detection and enumeration of the fungilike marine protists, the thraustochytrids. Limnol. Oceanogr. 38(1): 182-187. | , , | 1 | 2017 | This protocol is modified from: Raghukumar S, Schaumann K. 1993. An epifluorescence microscopy method for direct detection and enumeration of the, the thraustochytrids. Limnol. Oceanogr. 2017. Acriflavine Direct Detection Technique for Labyrinthulomycetes. protocols.io https://dx.doi.org/10.17504/protocols.io.hfib3ke | 2021-04-15 09:16:29 | |||
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Quick staining procedure of nuclei in Euplotes using DAPI Resource Report Resource Website |
Rachele Cesaroni | DOI:10.17504/protocols.io.2ajgacn | Protist Research to Optimize Tools in Genetics (PROT-G) | Universität Bern | 1 | 2019 | Rachele Cesaroni 2019. Quick staining procedure of nuclei in Euplotes using DAPI. protocols.io https://dx.doi.org/10.17504/protocols.io.2ajgacn | 2021-04-15 09:16:29 | ||||
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Antibiotic sensitivity testing - Pyramimonas, Bigelowiella, Eutreptiella, Neovahlkampfia, Pseudonitzschia Resource Report Resource Website |
Anna Vanclová and Naoji Yubuki | DOI:10.17504/protocols.io.hh3b38n | Protist Research to Optimize Tools in Genetics (PROT-G) | Organisms used for DNA transformation experiments were tested for sensitivity to five antibiotics in two different concentrations. Cell culture growing in F2 media with 3% seawater was divided to fifteen 15ml tubes, i.e. three tubes for testing each of the antibiotics: antibiotic was added to two samples to the final concentrations noted in Table 1, the third tube in the set served as a control. The cultures were incubated under 12h light cycle and 20°C and checked by light microscophy 1, 4, 7 and 19 days after the addition of antibiotics. ABCDEF1antibiotic puromycin blasticidin geneticin hygromycin zeocin 2concentration 1 5 μg/ml 5 μg/ml 200 μg/ml 200 μg/ml 100 μg/ml 3concentration 2 10 μg/ml 10 μg/ml 400 μg/ml 400 μg/ml 200 μg/ml Table 1: Tested antibiotics and concentrations | Charles University in Prague | 1 | 2017 | Anna Vanclová and Naoji Yubuki 2017. Antibiotic sensitivity testing - Pyramimonas, Bigelowiella, Eutreptiella, Neovahlkampfia, Pseudonitzschia. protocols.io https://dx.doi.org/10.17504/protocols.io.hh3b38n | 2021-04-15 09:16:35 | |||
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High Efficiency Microfluidic Electrotransformation Resource Report Resource Website |
Paulo A. Garcia, Zhifei Ge, Laura Kelley, Steven Holcomb, Cullen R. Buie | DOI:10.17504/protocols.io.hapb2dn | Protist Research to Optimize Tools in Genetics (PROT-G) | Synthetic biology holds great potential for addressing pressing challenges for mankind and our planet. One technical challenge in tapping into the full potential of synthetic biology is the low efficiency and low throughput of genetic transformation for many types of cells. In this paper, we discuss a novel microfluidic system for improving bacterial electrotransformation efficiency and throughput. Our microfluidic system is comprised of non-uniform constrictions in microchannels to facilitate high electric fields with relatively small applied voltages to induce electroporation. Additionally, the microfluidic device has regions of low electric field to assist in electrophoretic transport of nucleic acids into the cells. The device features hydro- dynamically controlled electric fields that allow cells to experience a time dependent electric field that is otherwise difficult to achieve using standard electronics. Results suggest that transformation efficiency can be increased by ∼4×, while throughput can increase by 100–1000× compared to traditional electroporation cuvettes. This work will enable high-throughput and high efficiency genetic transformation of microbes, fa- cilitating accelerated development of genetically engineered organisms. | MIT, MIT, MIT, MIT, MIT | 1 | 2017 | Paulo A. Garcia, Zhifei Ge, Laura Kelley, Steven Holcomb, Cullen R. Buie 2017. High Efficiency Microfluidic Electrotransformation. protocols.io https://dx.doi.org/10.17504/protocols.io.hapb2dn | 2021-04-15 09:16:35 | |||
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Antibiotic sensitivity test for dinoflagellates and Chromera Resource Report Resource Website |
Yoshihisa Hirakawa, Hirokazu Sakamoto, Takashi Shiratori, Elisabeth Hehenberger, Nick Irwin, Patrick Keeling | DOI:10.17504/protocols.io.vcke2uw | Protist Research to Optimize Tools in Genetics (PROT-G) | University of Tsukuba, University of Tsukuba, University of Tsukuba, University of British Columbia, University of British Columbia, University of British Columbia | 1 | 2018 | Yoshihisa Hirakawa, Hirokazu Sakamoto, Takashi Shiratori, Elisabeth Hehenberger, Nick Irwin, Patrick Keeling 2018. Antibiotic sensitivity test for dinoflagellates and Chromera. protocols.io https://dx.doi.org/10.17504/protocols.io.vcke2uw | 2021-04-15 09:16:32 | ||||
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Nucleofector Protocol for Dinoflagellates using Lonza’s 4D-Nucleofector X Unit Resource Report Resource Website |
Senjie Lin, Huan Zhang, Brittany Sprecher | DOI:10.17504/protocols.io.7n8hmhw | Protist Research to Optimize Tools in Genetics (PROT-G) | This protocol is intended to work for many dinoflagellates but focusses on the method used to successfully transform Karlodinium veneficum. | University of Connecticut, University of Connecticut, University of Connecticut | http://biorxiv.org/lookup/doi/10.1101/718239 | 2 | 2019 | Senjie Lin, Huan Zhang, Brittany Sprecher 2019. Nucleofector Protocol for Dinoflagellates using Lonza’s 4D-Nucleofector X Unit. protocols.io https://dx.doi.org/10.17504/protocols.io.7n8hmhw | 2021-04-15 09:16:33 | ||
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Pour plating protocol for Emiliania huxleyi (single colonies) Resource Report Resource Website |
Inbal Nussbaum, Daniella Schatz | DOI:10.17504/protocols.io.p4ydqxw | Protist Research to Optimize Tools in Genetics (PROT-G) | A protocol for generating single colonies of Emiliania huxleyi embedded in soft-agarose. | Weizmann Institute of Science, Weizmann Institute of Science | 1 | 2018 | Inbal Nussbaum, Daniella Schatz 2018. Pour plating protocol for Emiliania huxleyi (single colonies). protocols.io https://dx.doi.org/10.17504/protocols.io.p4ydqxw | 2021-04-15 09:16:36 | |||
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mRNA approach for transient expression in dinoflagellates Resource Report Resource Website |
Claudio Slamovits | DOI:10.17504/protocols.io.gwgbxbw | Protist Research to Optimize Tools in Genetics (PROT-G), Slamovits Lab | !!! ~~~~~ IN DEVELOPMENT ~~~~~ !!!This approach uses in-vitro transcription to generate a dinoflagellate-type mRNA (i.e. capped with the dino-SL leader), which is introduced into cells using an RNA transformation reagent. Screening for expression of the protein encoded in the mRNA follows. | Dalhousie University | 1 | 2017 | Claudio Slamovits 2017. mRNA approach for transient expression in dinoflagellates. protocols.io https://dx.doi.org/10.17504/protocols.io.gwgbxbw | 2021-04-15 09:16:40 | |||
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In vitro synthesized mRNA transfection to Perkinsus marinus Resource Report Resource Website |
Yoshihisa Hirakawa, Hirokazu Sakamoto, Elisabeth Hehenberger, Nick Irwin, Patrick Keeling | DOI:10.17504/protocols.io.vcme2u6 | Protist Research to Optimize Tools in Genetics (PROT-G) | University of Tsukuba, University of Tsukuba, University of British Columbia, University of British Columbia, University of British Columbia | 1 | 2018 | Yoshihisa Hirakawa, Hirokazu Sakamoto, Elisabeth Hehenberger, Nick Irwin, Patrick Keeling 2018. In vitro synthesized mRNA transfection to Perkinsus marinus. protocols.io https://dx.doi.org/10.17504/protocols.io.vcme2u6 | 2021-04-15 09:16:41 | ||||
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Protocol I: Transfection of Salpingoeca rosetta with Lonza 4d nucleofector Resource Report Resource Website |
David S. Booth, Heather Middleton, and Nicole King | DOI:10.17504/protocols.io.h68b9hw | King Lab, Protist Research to Optimize Tools in Genetics (PROT-G), Alegado Lab | The protocol describes the transformation of the choanoflagellate Salpingoeca rosetta using a Nucleofector 4d Device and SF kit from Lonza. Plasmids that use S. rosetta promoters and regulatory elements to drive the expression of luciferase and fluorescent protein reporters are being deposited at Addgene. | 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 | University of California, Berkeley and Howard Hughes Medical Institute, University of California, Berkeley and Howard Hughes Medical Institute, University of California, Berkeley and Howard Hughes Medical Institute | https://doi.org/10.1038/s41592-020-0796-x | 2 | 2018 | David S. Booth, Heather Middleton, and Nicole King 2018. Protocol I: Transfection of Salpingoeca rosetta with Lonza 4d nucleofector. protocols.io https://dx.doi.org/10.17504/protocols.io.h68b9hw | 2021-04-15 09:16:45 | |
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ESAW Media for Marine Phytoplankton Resource Report Resource Website |
Ashley Humphrey | DOI:10.17504/protocols.io.gc9bsz6 | Protist Research to Optimize Tools in Genetics (PROT-G), The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs) | University of Tennessee, Microbiology. | 3 | 2016 | Ashley Humphrey 2016. ESAW Media for Marine Phytoplankton. protocols.io https://dx.doi.org/10.17504/protocols.io.gc9bsz6 | 2021-04-15 09:17:00 | ||||
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Lipid extractions from labyrinthulomycetes Resource Report Resource Website |
Laura Halligan, Jackie Collier | DOI:10.17504/protocols.io.qbddsi6 | Protist Research to Optimize Tools in Genetics (PROT-G), Collier Lab | This protocol is a two-part lipid extraction for labyrinthulomycetes. The only strain we have tried this protocol on so far is Aurantiochytrium limacinum ATCC MYA-1381.This protocol was modified from: Higgins, B.T., A. Thornton-Dunwoody, J.M. Labavitch, J.S. VanderGheynst. 2014. Microplate assay for quantitation of neutral lipids in extracts from microalgae. Anal. Biochem. 465: 81-89. | State University of New York at Stony Brook, State University of New York at Stony Brook | 1 | 2018 | Laura Halligan, Jackie Collier 2018. Lipid extractions from labyrinthulomycetes . protocols.io https://dx.doi.org/10.17504/protocols.io.qbddsi6 | 2021-04-15 09:16:50 | |||
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Media and reagents for Seminavis robusta cultivation and experiments Resource Report Resource Website |
Lev Tsypin, Aaron Turkewitz | DOI:10.17504/protocols.io.33xgqpn | Protist Research to Optimize Tools in Genetics (PROT-G) | This protocol describes the culturing conditions used to grow S. robusta in the lab for all experiments. | California Institute of Technology, University of Chicago | 1 | 2019 | Lev Tsypin, Aaron Turkewitz 2019. Media and reagents for Seminavis robusta cultivation and experiments. protocols.io https://dx.doi.org/10.17504/protocols.io.33xgqpn | 2021-04-15 09:16:48 | |||
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Euplotes crassus micronuclear enrichment by PFGE Resource Report Resource Website |
Rachele Cesaroni, Angela Piersanti | DOI:10.17504/protocols.io.zwff7bn | Protist Research to Optimize Tools in Genetics (PROT-G) | Universität Bern, University of Camerino | 2 | 2019 | Rachele Cesaroni, Angela Piersanti 2019. Euplotes crassus micronuclear enrichment by PFGE. protocols.io https://dx.doi.org/10.17504/protocols.io.zwff7bn | 2021-04-15 09:16:48 |
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