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Name Authors DOI Group Summary Associated Publications RRIDs used Affiliations External URL Version Publication Date Proper Citation Record Last Update
Super simple In vivo Hoechst staining of unicellular protists
 
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Maria Rubio-Brotons 10.17504/protocols.io.gg6btze Protist Research to Optimize Tools in Genetics (PROT-G), Multicellgenomelab IBE CSIC-UPF 3 2016 Maria Rubio-Brotons 2016. Super simple In vivo Hoechst staining of unicellular protists. protocols.io dx.doi.org/10.17504/protocols.io.gg6btze 2021-03-29 03:10:33
The culturing of axenic Ochromonas sp. strain CCMP1393
 
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Alle Lie 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 dx.doi.org/10.17504/protocols.io.ey8bfzw 2021-03-29 03:10:38
Algal culture harvest and RNA extraction for RNA-Seq
 
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Alle Lie 10.17504/protocols.io.ewjbfcn Protist Research to Optimize Tools in Genetics (PROT-G), Caron Lab - Protistan Ecology 1 2016 Alle Lie 2016. Algal culture harvest and RNA extraction for RNA-Seq. protocols.io dx.doi.org/10.17504/protocols.io.ewjbfcn 2021-03-29 03:10:37
Nanodrop Spectrophotometer (ND-1000) for Nucleic Acid
 
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Steven Wilhelm 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 dx.doi.org/10.17504/protocols.io.id2ca8e 2021-03-29 03:10:44
pTpPuc3_TpSil3p-eGFP
 
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Jernej Turnsek 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 dx.doi.org/10.17504/protocols.io.7ghhjt6 2021-03-29 03:10:50
Quick staining procedure of nuclei in Euplotes using DAPI
 
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Rachele Cesaroni 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 dx.doi.org/10.17504/protocols.io.2ajgacn 2021-03-29 03:10:47
Acriflavine Direct Detection Technique for Labyrinthulomycetes
 
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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. 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 dx.doi.org/10.17504/protocols.io.hfib3ke 2021-03-29 03:10:47
Euplotes crassus transformation using Lipofectamine 2000 as vehicle
 
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RACHELE CESARONI 10.17504/protocols.io.g5aby2e Protist Research to Optimize Tools in Genetics (PROT-G) University of Bern, Institute of Biology 4 2017 RACHELE CESARONI 2017. Euplotes crassus transformation using Lipofectamine 2000 as vehicle. protocols.io dx.doi.org/10.17504/protocols.io.g5aby2e 2021-03-29 03:11:02
High Efficiency Microfluidic Electrotransformation
 
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Paulo A. Garcia, Zhifei Ge, Laura Kelley, Steven Holcomb, Cullen R. Buie 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 dx.doi.org/10.17504/protocols.io.hapb2dn 2021-03-29 03:11:09
Dot blot to verify microinjection efficacy in Euplotes crassus
 
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RACHELE CESARONI, Rachele Cesaroni 10.17504/protocols.io.2aqgadw Protist Research to Optimize Tools in Genetics (PROT-G) University of Bern, Institute of Biology, Universität Bern 1 2019 RACHELE CESARONI, Rachele Cesaroni 2019. Dot blot to verify microinjection efficacy in Euplotes crassus. protocols.io dx.doi.org/10.17504/protocols.io.2aqgadw 2021-03-29 03:09:32
Small-scale silencing experiment in vegetative Euplotes crassus (provisional)
 
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Rachele Cesaroni 10.17504/protocols.io.2asgaee Protist Research to Optimize Tools in Genetics (PROT-G) Universität Bern 1 2019 Rachele Cesaroni 2019. Small-scale silencing experiment in vegetative Euplotes crassus (provisional). protocols.io dx.doi.org/10.17504/protocols.io.2asgaee 2021-03-29 03:09:28
Euplotes crassus transformation using FuGene HD Transfection Reagent as vehicle
 
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RACHELE CESARONI 10.17504/protocols.io.g43byyn Protist Research to Optimize Tools in Genetics (PROT-G) University of Bern, Institute of Biology 5 2017 RACHELE CESARONI 2017. Euplotes crassus transformation using FuGene HD Transfection Reagent as vehicle. protocols.io dx.doi.org/10.17504/protocols.io.g43byyn 2021-03-29 03:09:32
Simple DNA Extraction for Phytoplankton Using Chelex 100
 
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G Jason Smith 10.17504/protocols.io.hinb4de Protist Research to Optimize Tools in Genetics (PROT-G), Environmental Biotechnology Lab This is a modification of the origianl Chelex 100 extraction described by Walsh, Metzger and Higuchi (1991 BioTechniques 10(4):506). Adding PVPP facilitates working with environmental samples as well as pure cultures hi in phenolics or other contaminants. Moss Landing Marine Laboratories 1 2017 G Jason Smith 2017. Simple DNA Extraction for Phytoplankton Using Chelex 100. protocols.io dx.doi.org/10.17504/protocols.io.hinb4de 2021-03-29 03:09:34
Bodo saltans transfection with plasmid for tagging EF1alpha gene__IG BsTub
 
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Fatma Gomaa, Roberto Docampo, Zhuhong Li, Peter Girguis, Virginia Edgcomb 10.17504/protocols.io.7fchjiw Protist Research to Optimize Tools in Genetics (PROT-G) Stable transfection of B. saltans has been achieved using plasmid for EF 1 alpha C terminal tagging. 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 Harvard University, University of Georgia, University of Georgia, Harvard University, Woods Hole Oceanographic Institution https://doi.org/10.1038/s41592-020-0796-x 1 2019 Fatma Gomaa, Roberto Docampo, Zhuhong Li, Peter Girguis, Virginia Edgcomb 2019. Bodo saltans transfection with plasmid for tagging EF1alpha gene__IG BsTub. protocols.io dx.doi.org/10.17504/protocols.io.7fchjiw 2021-03-29 03:09:32
How to culture corallochytrean Corallochytrium limacisporum, a unicellular relative to animals
 
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Maria Rubio-Brotons 10.17504/protocols.io.gqmbvu6 Protist Research to Optimize Tools in Genetics (PROT-G), Multicellgenomelab IBE CSIC-UPF 1 2016 Maria Rubio-Brotons 2016. How to culture corallochytrean Corallochytrium limacisporum, a unicellular relative to animals. protocols.io dx.doi.org/10.17504/protocols.io.gqmbvu6 2021-03-29 03:09:36
Electroporation of natural communities in sea water
 
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Andrés Ramírez, Albane Ruaud, Fernan Federici, Peter von Dassow 10.17504/protocols.io.hpnb5me Protist Research to Optimize Tools in Genetics (PROT-G) This protocol has been optimized for electroporation of natural communities in coastal surface waters. As natural communities may vary in different places we recomend to use this protocol as a starting point and re-optimize according to the results. Guidelines are provided.  Instituto Milenio de Oceanografía, Instituto Milenio de Oceanografía, Instituto Milenio de Oceanografía, Instituto Milenio de Oceanografía 2 2017 Andrés Ramírez, Albane Ruaud, Fernan Federici, Peter von Dassow 2017. Electroporation of natural communities in sea water. protocols.io dx.doi.org/10.17504/protocols.io.hpnb5me 2021-03-29 03:09:38
RNAqueous with TURBO DNA-free and SUPERase-In
 
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Daniel Richter 10.17504/protocols.io.iqzcdx6 Ecology of Marine Plankton (ECOMAP) team - Roscoff, Protist Research to Optimize Tools in Genetics (PROT-G) Daniel Richter, Nov 29, 2011based on RNAqueous May 29, 2008 protocol revision C, TURBO DNA-free June 9, 2009 protocol 1907M revision F

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

https://elifesciences.org/articles/34226 1 2017 Daniel Richter 2017. RNAqueous with TURBO DNA-free and SUPERase-In. protocols.io dx.doi.org/10.17504/protocols.io.iqzcdx6 2021-03-29 03:09:44
Increased sensitivity of Euplotes crassus to selective agents using 0.3 M glucose-based culture conditions.
 
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Lawrence A. Klobutcher 10.17504/protocols.io.gwnbxde Protist Research to Optimize Tools in Genetics (PROT-G) Numerous unpublished studies indicate that Euplotes crassus is resistant to extremely high concentrations of commonly used selective agents when grow in artificial seawater. We have found that when E. crassus is grown in 1 part artificial seawater + 9 parts 0.3 M glucose, they are much more sensitive to a number of selective agents. For example, 1080 ug/ml paromomycin in artificial seawater only inhibited growth, as little as 120 ug/ml was effective in killing cells when grown with 0.3 M glucose. Similarly, G418 at 400 ug/ml had little effect in seawater, but as little as 100 ug/ml blocked growth in 0.3 M glucose. This may not prove true for all selective agents, as we saw no effect with paclitaxel up to 100 uM under either growth condition. University of Connecticut Health Center 1 2017 Lawrence A. Klobutcher 2017. Increased sensitivity of Euplotes crassus to selective agents using 0.3 M glucose-based culture conditions.. protocols.io dx.doi.org/10.17504/protocols.io.gwnbxde 2021-03-29 03:09:51
High-Throughput Beta-glucuronidase (GUS) assay for Phaeodactylum tricornutum
 
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Erin Garza, Vincent Bielinski 10.17504/protocols.io.bbexijfn Protist Research to Optimize Tools in Genetics (PROT-G), JCVI West Protocols A high-throughput method for measuring β-glucuronidase (GUS) activity in the diatom Phaeodactylum tricornutum. This protocol has been optimized for 250 μl volumes. For larger volumes see the following protocol dx.doi.org/10.17504/protocols.io.hefb3bn, which this protocol was based off of. J. Craig Venter Institute, J. Craig Venter Institute, Synthetic Biology & Bioenergy Group 1 2020 Erin Garza, Vincent Bielinski 2020. High-Throughput Beta-glucuronidase (GUS) assay for Phaeodactylum tricornutum. protocols.io dx.doi.org/10.17504/protocols.io.bbexijfn 2021-03-29 03:09:50
Generating Stable Transfection in Bodo saltans
 
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Fatma Gomaa, Zuhong Li, Roberto Docampo, Peter Girguis, Virginia Edgcomb 10.17504/protocols.io.sh3eb8n Protist Research to Optimize Tools in Genetics (PROT-G) B. saltans cells were electroporated using a square-wave electroporator (Nepa21, Bulldog Bio, Inc.) using one poring pulse of 200 volts with a pulse duration of 25 ms and five transfer pulses of 60 volts with a pulse duration of 99 ms, with plasmid targeting the 18S region (18S-GFP). A schematic representation of the plasmid, the target locus and the expected site of integration into the B. saltans genome is shown in Figure 1. Electroporated cells were selected with 1 µg/ml of G418, added 24 hours after electroporation. Cells were washed and subcultured into fresh selection medium every 3-4 days. G418 resistant cells started to emerge 7-9 days post-electroporation. Cells were processed for genotyping analysis to confirm plasmid integration 3 weeks post-electroporation. DNA was extracted from pools of transfected and wild cells using the Qiagen DNeasy Blood & Tissue kit. PCR analyses were used to characterize the 18S-GFP tagging using 6 sets of PCR primers, as shown in Figure 1 C. Gel electrophoresis image (Figure 2) showing the amplified PCR products at the expected sizes. Amplified PCR#1 with primer sets Ribo_tag_forward & GFP reverse (800 bp)Amplified PCR #2 with primer sets Neo_forward & Ribo_tag_reverse (1000 bp)Amplified PCR #3 with primer sets TubR & IG forward ( 3 bands)Amplified PCR #4 with primer sets Tub_forward & IG reverse (3 bands)Amplified PCR #5 with primer sets Ribo_tag_forward & Ribo_tag_reverse (Wild (C) cells band at 350 bp, transfected cells S1 and S2 two bands, 350 bp and 2800 bp)Electroporated cells were selected with 1 µg/ml of G418, added 24 hours after electroporation. Cells were washed and subcultured into fresh selection medium every 3-4 days. G418 resistant cells started to emerge 7-9 days post-electroporation. Cells were processed for genotyping analysis to confirm plasmid integration 3 weeks post-electroporation. DNA was extracted from pools of transfected and wild cells using the Qiagen DNeasy Blood & Tissue kit. PCR analyses were used to characterize the 18S-GFP tagging using 6 sets of PCR primers, as shown in Figure 1 C. Gel electrophoresis image (Figure 2) showing the amplified PCR products at the expected sizes. Amplified PCR#1 with primer sets Ribo_tag_forward & GFP reverse (800 bp)Amplified PCR #2 with primer sets Neo_forward & Ribo_tag_reverse (1000 bp)Amplified PCR #3 with primer sets TubR & IG forward ( 3 bands)Amplified PCR #4 with primer sets Tub_forward & IG reverse (3 bands)Amplified PCR #5 with primer sets Ribo_tag_forward & Ribo_tag_reverse (Wild (C) cells band at 350 bp, transfected cells S1 and S2 two bands, 350 bp and 2800 bp)Cells were processed for genotyping analysis to confirm plasmid integration 3 weeks post-electroporation. DNA was extracted from pools of transfected and wild cells using the Qiagen DNeasy Blood & Tissue kit. PCR analyses were used to characterize the 18S-GFP tagging using 6 sets of PCR primers, as shown in Figure 1 C. Gel electrophoresis image (Figure 2) showing the amplified PCR products at the expected sizes. Amplified PCR#1 with primer sets Ribo_tag_forward & GFP reverse (800 bp)Amplified PCR #2 with primer sets Neo_forward & Ribo_tag_reverse (1000 bp)Amplified PCR #3 with primer sets TubR & IG forward ( 3 bands)Amplified PCR #4 with primer sets Tub_forward & IG reverse (3 bands)Amplified PCR #5 with primer sets Ribo_tag_forward & Ribo_tag_reverse (Wild (C) cells band at 350 bp, transfected cells S1 and S2 two bands, 350 bp and 2800 bp)PCR analyses were used to characterize the 18S-GFP tagging using 6 sets of PCR primers, as shown in Figure 1 C. Gel electrophoresis image (Figure 2) showing the amplified PCR products at the expected sizes. Amplified PCR#1 with primer sets Ribo_tag_forward & GFP reverse (800 bp)Amplified PCR #2 with primer sets Neo_forward & Ribo_tag_reverse (1000 bp)Amplified PCR #3 with primer sets TubR & IG forward ( 3 bands)Amplified PCR #4 with primer sets Tub_forward & IG reverse (3 bands)Amplified PCR #5 with primer sets Ribo_tag_forward & Ribo_tag_reverse (Wild (C) cells band at 350 bp, transfected cells S1 and S2 two bands, 350 bp and 2800 bp)Gel electrophoresis image (Figure 2) showing the amplified PCR products at the expected sizes. Amplified PCR#1 with primer sets Ribo_tag_forward & GFP reverse (800 bp)Amplified PCR #2 with primer sets Neo_forward & Ribo_tag_reverse (1000 bp)Amplified PCR #3 with primer sets TubR & IG forward ( 3 bands)Amplified PCR #4 with primer sets Tub_forward & IG reverse (3 bands)Amplified PCR #5 with primer sets Ribo_tag_forward & Ribo_tag_reverse (Wild (C) cells band at 350 bp, transfected cells S1 and S2 two bands, 350 bp and 2800 bp)Amplified PCR#1 with primer sets Ribo_tag_forward & GFP reverse (800 bp)Amplified PCR #2 with primer sets Neo_forward & Ribo_tag_reverse (1000 bp)Amplified PCR #3 with primer sets TubR & IG forward ( 3 bands)Amplified PCR #4 with primer sets Tub_forward & IG reverse (3 bands)Amplified PCR #5 with primer sets Ribo_tag_forward & Ribo_tag_reverse (Wild (C) cells band at 350 bp, transfected cells S1 and S2 two bands, 350 bp and 2800 bp)Figure 1: Schematic representation of the (A); the 18S- GFP plasmid; (B) Ribosomal operon in B. saltans genome (C); and the expected site of plasmid integration in B. saltans genome through homologous regions 1 and 2 (HR1, HR2).Figure 2: Agarose gel electrophoresis image of the amplified PCR products for B. saltans cells transfected with 18S-GFP Cassette (S1 and S2) and the wild type cells (C). The primers sets and the expected product sizes are mentioned above in the text.Figure 3: B. saltans cells transfected with 18S-GFP tagging cassette. On the left: a light microscopy image showing the B. saltans cells (around 4 cells at different level). On the right: GFP fluorescent signal detected in the transfected cell. Scale bar 10 μm. Harvard University, University of Georgia, University of Georgia, Harvard University, Woods Hole Oceanographic Institution 1 2018 Fatma Gomaa, Zuhong Li, Roberto Docampo, Peter Girguis, Virginia Edgcomb 2018. Generating Stable Transfection in Bodo saltans. protocols.io dx.doi.org/10.17504/protocols.io.sh3eb8n 2021-03-29 03:09:55

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