Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Golden Gate Primer Design Resource Report Resource Website |
Philip D. Weyman | DOI:10.17504/protocols.io.heyb3fw | Protist Research to Optimize Tools in Genetics (PROT-G) | An easy to follow template for adding Golden Gate adapters to PCR primers. | J. Craig Venter Institute | 1 | 2017 | Philip D. Weyman 2017. Golden Gate Primer Design. protocols.io https://dx.doi.org/10.17504/protocols.io.heyb3fw | 2021-04-15 09:15:07 | |||
|
Euplotes crassus transfection through microinjection into the macronucleus Resource Report Resource Website |
Rachele Cesaroni | DOI:10.17504/protocols.io.hi7b4hn | Protist Research to Optimize Tools in Genetics (PROT-G) | 5 | 2017 | Rachele Cesaroni 2017. Euplotes crassus transfection through microinjection into the macronucleus. protocols.io https://dx.doi.org/10.17504/protocols.io.hi7b4hn | 2021-04-15 09:15:13 | |||||
|
Diatom Transformation via Bacterial Conjugation Resource Report Resource Website |
Jeric Harper | DOI:10.17504/protocols.io.fp7bmrn | Protist Research to Optimize Tools in Genetics (PROT-G), Alverson Lab | http://www.nature.com/articles/ncomms7925 | 1 | 2016 | Jeric Harper 2016. Diatom Transformation via Bacterial Conjugation. protocols.io https://dx.doi.org/10.17504/protocols.io.fp7bmrn | 2021-04-15 09:15:38 | ||||
|
Skeletonema DNA extraction by Plant DNAzol Resource Report Resource Website |
Adrian Clarke | DOI:10.17504/protocols.io.g6bbzan | Protist Research to Optimize Tools in Genetics (PROT-G) | 1 | 2017 | Adrian Clarke 2017. Skeletonema DNA extraction by Plant DNAzol. protocols.io https://dx.doi.org/10.17504/protocols.io.g6bbzan | 2021-04-15 09:15:37 | |||||
|
G418 Kill curve protocol Resource Report Resource Website |
Fatma Gomaa, Zhuhong Li, Roberto Docampo, Peter Girguis, Virginia Edgcomb | DOI:10.17504/protocols.io.sh4eb8w | Protist Research to Optimize Tools in Genetics (PROT-G) | Bodo saltans kill curve protocol using G418 (Gentamicin)Gentamycin exhibits toxicity toward both eukaryotic and prokaryotic cells by disrupting ribosome function, thereby blocking the elongation step in protein synthesis.G418 is most commonly used as a selection agent for eukaryotic cells genetically engineered to express a neomycin resistance gene (NeoR), which is encoded by either transposon Tn601 (903) or Tn5.The resistant cells grow in medium containing G418, and may be used to establish stably transfected cell lines as all the non-resistant cells die due to G418 toxicity, typically within 6 – 14 days.To establish kill curve assay for saltans various concentrations of G418 were tested. The concentration range from 1 to 50 μg/mL for selection of eukaryotic, and then higher concentrations can be used for maintaining stable transfected cell line.Kill Curve Assay Harvest the B. saltans cells from a culture that is at peak density (1 – 3.0 x 105) by centrifugation at 800 x g for 5 min., discard the supernatant (medium). Replace the growth medium with fresh medium containing 0 – 50 μg/mL. For each concentration, test in triplicate. Using 6 wells plates, replace the medium in the wells every 3 – 4 days using fresh medium with the appropriate G418 concentration. Perform a daily visual inspection for evidence of toxicity, also cell count using hemocytometer. Note that the optimal dose of G418 for selection is the lowest one for which all cells have died after one week. A low dose is the concentration which has minimal effects on cells after 2 weeks of antibiotic selection. Conversely, a high dose is a concentration which is highly toxic to cells within 2-3 days of starting antibiotic selection. 5- The results indicate that a G418 concentration of 2 μg/mL kill the entire B. saltans population in 12 days which is considered enough time for selecting the resistant cells after transfection. G418 Sensitivity for B. saltans Cell Selection In all of our plasmids constructs we included the NeoR gene (Neomycine resistant gene) to select our transfected cells.Twenty-four hours after electroporation, the growth medium of transfected cells were supplemented with G418 antibiotic Solution (2 μg/mL) based on the kill curve results (above). 3. Replace the G418-containing medium every 3 – 5 days and examine cells for visual toxicity. Most non-transfected (non-resistant) cells will die within 10- 12 days, leaving the transfected cells to expand.Once cells grow to high confluence, they may be maintained, or frozen as a polyclonal line or plated by limited dilution to select for single clones.Replace the growth medium with fresh medium containing 0 – 50 μg/mL. For each concentration, test in triplicate. Using 6 wells plates, replace the medium in the wells every 3 – 4 days using fresh medium with the appropriate G418 concentration. Perform a daily visual inspection for evidence of toxicity, also cell count using hemocytometer. Note that the optimal dose of G418 for selection is the lowest one for which all cells have died after one week. A low dose is the concentration which has minimal effects on cells after 2 weeks of antibiotic selection. Conversely, a high dose is a concentration which is highly toxic to cells within 2-3 days of starting antibiotic selection. 5- The results indicate that a G418 concentration of 2 μg/mL kill the entire B. saltans population in 12 days which is considered enough time for selecting the resistant cells after transfection. G418 Sensitivity for B. saltans Cell Selection In all of our plasmids constructs we included the NeoR gene (Neomycine resistant gene) to select our transfected cells.Twenty-four hours after electroporation, the growth medium of transfected cells were supplemented with G418 antibiotic Solution (2 μg/mL) based on the kill curve results (above). 3. Replace the G418-containing medium every 3 – 5 days and examine cells for visual toxicity. Most non-transfected (non-resistant) cells will die within 10- 12 days, leaving the transfected cells to expand.Once cells grow to high confluence, they may be maintained, or frozen as a polyclonal line or plated by limited dilution to select for single clones.Using 6 wells plates, replace the medium in the wells every 3 – 4 days using fresh medium with the appropriate G418 concentration. Perform a daily visual inspection for evidence of toxicity, also cell count using hemocytometer. Note that the optimal dose of G418 for selection is the lowest one for which all cells have died after one week. A low dose is the concentration which has minimal effects on cells after 2 weeks of antibiotic selection. Conversely, a high dose is a concentration which is highly toxic to cells within 2-3 days of starting antibiotic selection. 5- The results indicate that a G418 concentration of 2 μg/mL kill the entire B. saltans population in 12 days which is considered enough time for selecting the resistant cells after transfection. G418 Sensitivity for B. saltans Cell Selection In all of our plasmids constructs we included the NeoR gene (Neomycine resistant gene) to select our transfected cells.Twenty-four hours after electroporation, the growth medium of transfected cells were supplemented with G418 antibiotic Solution (2 μg/mL) based on the kill curve results (above). 3. Replace the G418-containing medium every 3 – 5 days and examine cells for visual toxicity. Most non-transfected (non-resistant) cells will die within 10- 12 days, leaving the transfected cells to expand.Once cells grow to high confluence, they may be maintained, or frozen as a polyclonal line or plated by limited dilution to select for single clones.Note that the optimal dose of G418 for selection is the lowest one for which all cells have died after one week. A low dose is the concentration which has minimal effects on cells after 2 weeks of antibiotic selection. Conversely, a high dose is a concentration which is highly toxic to cells within 2-3 days of starting antibiotic selection. 5- The results indicate that a G418 concentration of 2 μg/mL kill the entire B. saltans population in 12 days which is considered enough time for selecting the resistant cells after transfection. G418 Sensitivity for B. saltans Cell Selection In all of our plasmids constructs we included the NeoR gene (Neomycine resistant gene) to select our transfected cells.Twenty-four hours after electroporation, the growth medium of transfected cells were supplemented with G418 antibiotic Solution (2 μg/mL) based on the kill curve results (above). 3. Replace the G418-containing medium every 3 – 5 days and examine cells for visual toxicity. Most non-transfected (non-resistant) cells will die within 10- 12 days, leaving the transfected cells to expand.Once cells grow to high confluence, they may be maintained, or frozen as a polyclonal line or plated by limited dilution to select for single clones.5- The results indicate that a G418 concentration of 2 μg/mL kill the entire B. saltans population in 12 days which is considered enough time for selecting the resistant cells after transfection.G418 Sensitivity for B. saltans AB1G418 (μg/ml) Cells survival (days) 250 2 320 2 415 3 510 4 65 6 73 8 82 12 91 >16 100 >16 A1G418 (μg/ml) A1Cell survival (days) Cell Selection In all of our plasmids constructs we included the NeoR gene (Neomycine resistant gene) to select our transfected cells.Twenty-four hours after electroporation, the growth medium of transfected cells were supplemented with G418 antibiotic Solution (2 μg/mL) based on the kill curve results (above). 3. Replace the G418-containing medium every 3 – 5 days and examine cells for visual toxicity. Most non-transfected (non-resistant) cells will die within 10- 12 days, leaving the transfected cells to expand.Once cells grow to high confluence, they may be maintained, or frozen as a polyclonal line or plated by limited dilution to select for single clones.3. Replace the G418-containing medium every 3 – 5 days and examine cells for visual toxicity. Most non-transfected (non-resistant) cells will die within 10- 12 days, leaving the transfected cells to expand.Once cells grow to high confluence, they may be maintained, or frozen as a polyclonal line or plated by limited dilution to select for single clones. | Harvard University, University of Georgia, University of Georgia, Harvard University, Woods Hole Oceanographic Institution | 1 | 2018 | Fatma Gomaa, Zhuhong Li, Roberto Docampo, Peter Girguis, Virginia Edgcomb 2018. G418 Kill curve protocol . protocols.io https://dx.doi.org/10.17504/protocols.io.sh4eb8w | 2021-04-15 09:15:37 | |||
|
Transfection of O. marina using particle bombardment Resource Report Resource Website |
Pia Elustondo, Claudio Slamovits | DOI:10.17504/protocols.io.ui7euhn | Protist Research to Optimize Tools in Genetics (PROT-G) | Dalhousie University, Dalhousie University | 1 | 2018 | Pia Elustondo, Claudio Slamovits 2018. Transfection of O. marina using particle bombardment. protocols.io https://dx.doi.org/10.17504/protocols.io.ui7euhn | 2021-04-15 09:15:38 | ||||
|
RNAi by feeding in Euplotes focardii (povisional) Resource Report Resource Website |
Francesca Papi, Angela Piersanti | DOI:10.17504/protocols.io.zk8f4zw | Protist Research to Optimize Tools in Genetics (PROT-G) | University of Camerino, University of Camerino | 1 | 2019 | Francesca Papi, Angela Piersanti 2019. RNAi by feeding in Euplotes focardii (povisional). protocols.io https://dx.doi.org/10.17504/protocols.io.zk8f4zw | 2021-04-15 09:15:39 | ||||
|
Transfectionof constructs in diplonemids to block NHEJ pathway using the inhibitors of KU70/80 proteins. Resource Report Resource Website |
Binnypreet Kaur1, 2, Drahomíra Faktorová1, 2 and Julius Lukeš1, 2, 3 | DOI:10.17504/protocols.io.x35fqq6 | Protist Research to Optimize Tools in Genetics (PROT-G), Julius Lukes | The process of NHEJ is completed when the DNA ligase complex ligates the broken ends of the DNA. Ku70-Ku80 are the DNA-dependent protein kinase heterodimeric regulatory factor that forms a link between two broken DNA ends and structurally support, align and protect them from further degradation. W7 inhibitor (W7(N-(6-aminohexyl)-5-chloro1-naphthalenesulfonamide) inhibits the cofactor of inositol hexakisphophate which effects the regulatory factor of Ku heterodimers. | Institute of Parasitology, Czech Academy of Sciences, Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic, Institute of Parasitology, Czech Academy of Sciences, Institute of Parasitology, Czech Academy of Sciences3, Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic, Canadian Institute for Advanced Research, Toronto, Canada | 2 | 2019 | Binnypreet Kaur1, 2, Drahomíra Faktorová1, 2 and Julius Lukeš1, 2, 3 2019. Transfectionof constructs in diplonemids to block NHEJ pathway using the inhibitors of KU70/80 proteins.. protocols.io https://dx.doi.org/10.17504/protocols.io.x35fqq6 | 2021-04-15 09:15:15 | |||
|
Staining Labyrinthulomycetes with Propidium Iodide Resource Report Resource Website |
This protocol was modified by Sabrina Geraci-Yee and is from: Pozarowski P, Darzynkiewicz Z. 2004. Analysis of cell cycle by flow cytometry. Methods Mol Bio. 281:301-311. | DOI:10.17504/protocols.io.hfjb3kn | Protist Research to Optimize Tools in Genetics (PROT-G), Collier Lab | Sabrina Geraci-Yee modified this protocol from: Pozarowski P., Darzynkiewicz Z. 2004. Analysis of cell cycle by flow cytometry. Methods Mol. Bio. 281:301-311. | , | 1 | 2017 | This protocol was modified by Sabrina Geraci-Yee and is from: Pozarowski P, Darzynkiewicz Z. 2004. Analysis of cell cycle by flow cytometry. Methods Mol Bio. 281:301-311. 2017. Staining Labyrinthulomycetes with Propidium Iodide. protocols.io https://dx.doi.org/10.17504/protocols.io.hfjb3kn | 2021-04-15 09:15:46 | |||
|
Nested Gibson Assembly Resource Report Resource Website |
Erin Garza, Vincent Bielinski | DOI:10.17504/protocols.io.bbikikcw | Protist Research to Optimize Tools in Genetics (PROT-G), JCVI West Protocols | This method can be used to increase the efficiency of Gibson Assemblies containing many pieces and/or difficult to assemble DNA fragments. | J. Craig Venter Institute, J. Craig Venter Institute, Synthetic Biology & Bioenergy Group | 1 | 2020 | Erin Garza, Vincent Bielinski 2020. Nested Gibson Assembly. protocols.io https://dx.doi.org/10.17504/protocols.io.bbikikcw | 2021-04-15 09:15:20 | |||
|
Plasmid DNAs designed for expression in Micromonas CCMP1545 Resource Report Resource Website |
Jian Guo, Alexandra Worden, Grant Hartzog, and Manuel Ares | DOI:10.17504/protocols.io.i9wch7e | Protist Research to Optimize Tools in Genetics (PROT-G) | We have available several plasmids designed for expression of Cas9, guide RNA, chloramphenicol acetyl-transferase, GFP, and beta-lactamase in Micromonas CCMP1545. For protein expression we used the promotor and 3' end elements from the endogenous RPS9 gene, and codon optimized the coding region. For expression of guide RNAs we used the Micromonas U6 snRNA promoter. DNA is available by contacting M. Ares .We have constructed and sequence verified 9 plasmids which we would like to make available to others attempting to detect transformation of DNA into Micromonas. Using the CCMP1545 genome as a source for the U6 promoter sequence, and for the promoter and 3' UTR sequences of ribosomal protein RPS9, we built the following plasmids:CRISPR/Cas9 plasmids for Micromonas1. Mp U6 promoter driving Bae cassette for guide RNA expression in pUC132. Mp RPS9-Cas9SV40-RPS9 in pUC133. Both Mp U6 promoter driving Bae cassette for guide RNA expression and Mp RPS9-Cas9SV40-RPS9 in pUC13These first three plasmids were anticipated to enable stable incorporation of transgenes at specific genomic locations. BaeI is a type IIS restriction enzyme that leaves noncompatible sticky ends. In the context of the gRNA cassette, a pair of 24 nt oligos designed to have the sticky ends compatible with BaeI cleaved plasmid are annealed and cloned into the plasmid, replacing the BaeI cassette while adding the 20 nt target complementary sequence of the desired guide RNA.Selectable/Detectable Marker genes4. Mp RPS9-codon optimized GFPsv40-RPS9 in pUC135. Mp RPS9-codon optimized chloramphenicol acetyltransferase-RPS9 in pUC13 6. Mp RPS9-codon optimized beta-lactamase-RPS9 in pUC13 These three plasmids have the indicated coding regions codon optimized for Micromonas flanked by RPS9 promoter and 3' end sequences. In the case of GFP, a nuclear localization signal from SV40 has been added to the C-terminus. Plasmids for Agrobacterium-mediated gene transfer 7. Mp RPS9-codon optimized GFPsv40-RPS9 in pOSCAR 8. Mp RPS9-codon optimized chloramphenicol acetyltransferase-RPS9 in pOSCAR 9. Mp RPS9-codon optimized beta-lactamase-RPS9 in pOSCAR | University of California, Santa Cruz, Monterey Bay Aquarium Research Institute, University of California, Santa Cruz, University of California, Santa Cruz | 1 | 2018 | Jian Guo, Alexandra Worden, Grant Hartzog, and Manuel Ares 2018. Plasmid DNAs designed for expression in Micromonas CCMP1545. protocols.io https://dx.doi.org/10.17504/protocols.io.i9wch7e | 2021-04-15 09:15:46 | |||
|
Tangential flow filtration (TFF) concentration of phytoplankton Resource Report Resource Website |
Daniel Vaulot | DOI:10.17504/protocols.io.gpybvpw | Ecology of Marine Plankton (ECOMAP) team - Roscoff, Protist Research to Optimize Tools in Genetics (PROT-G) | Concentrate phytoplankton samples about 100-fold typically from 5L down to 20 mL. Takes about 1 hour per sample. Samples can be used for flow cytometry sorting or for cultures. Enrichment by TFF usually keep growing for a longer time than unconcentrate samples.ReferenceMarie, D., Shi, X.L., Rigaut-Jalabert, F. & Vaulot, D. (2010). Use of flow cytometric sorting to better assess the diversity of small photosynthetic eukaryotes in the English Channel. FEMS Microbiology Ecology. 72. p.pp. 165–178. | Station Biologique, Roscoff, France | 2 | 2016 | Daniel Vaulot 2016. Tangential flow filtration (TFF) concentration of phytoplankton. protocols.io https://dx.doi.org/10.17504/protocols.io.gpybvpw | 2021-04-15 09:15:18 | |||
|
Sample collection from the field for downstream molecular analysis - microbial eukaryote-focused Resource Report Resource Website |
Sarah Hu | DOI:10.17504/protocols.io.hisb4ee | Protist Research to Optimize Tools in Genetics (PROT-G), Caron Lab - Protistan Ecology, SCOPE | This protocol describes steps and considerations for working in the field to collect samples to be used for molecular work targetting marine (or freshwater) microbial eukaryotes. See downstream protocols for DNA/RNA extraction and library prep (pending) for 18S rRNA gene tag sequencing.Many steps in this protocol can be modified to fit a users' specific needs or environment type. Here, we strive to make recommendations that consider the delicate nature of single-celled eukaryotes and collect samples in the field as cleanly as possible. We use this approach for RNA and DNA-based sequencing - both for tag sequencing and metatranscriptomics.This protocol is based off of the field work we conduct at the San Pedro Ocean Time-series (SPOT) station. We go out to the SPOT station once a month. Once we arrive at the SPOT station, we try to sample at the same time of day each month. Timelapse video for sampling SPOT: https://youtu.be/1US3h_qD00wMaterials required:(1) 20 L carboys (volume amount flexible)(2) Covers for carboys (we use pizza bags, black trash bags, or coolers)(3) Ice packs(4) Tubing for Niskin (5) Vacuum pump filtration system (see time-lapse video) - trap flask - pump - extra tubing & rubber/silicon stopper (to fit filter towers)(6) Filter towers that fit in vacuum pump filtration system(7) In-line filters, 47 mm(8) Nitex mesh, cut for 47 mm - 200 um & 80 um(9) RNase-spray(10) Absorbent pads (for reducing water spillage & covering countertops)(11) Liquid nitrogen - make sure to check regulations on transporting liquid nitrogen and storing it on-site/shipboard(12) 15 mL falcon tubes - RNase/DNase-free(13) RNA later or Lysis buffer (e.g. RLT buffer from this protocol)(14) Filters for collecting material, we use 0.7um GF/F filters**Our reasoning to use this filter size is that the 0.7um nominal pore size will collect the protistan fraction of the community, but it is a woven filter style, so more water can be filtered through without clogging. | University of Southern California | 1 | 2017 | Sarah Hu 2017. Sample collection from the field for downstream molecular analysis - microbial eukaryote-focused. protocols.io https://dx.doi.org/10.17504/protocols.io.hisb4ee | 2021-04-15 09:15:19 | |||
|
Transient transformation of Ostreococcus species (OTTH595, RCC809 and RCC802) and Bathycoccus Resource Report Resource Website |
Francois Yves Bouget, Francois-Yves Bouget | DOI:10.17504/protocols.io.83uhynw | Protist Research to Optimize Tools in Genetics (PROT-G) | This protocol describes the preparation of cells and introduction of DNA into the cells by electroporation. For selection of stable transformants or measure of transient gene expression see related protocols. | Laboratoire d'Oceanographie Microbienne, Laboratoire d'Oceanographie Microbienne | 3 | 2019 | Francois Yves Bouget, Francois-Yves Bouget 2019. Transient transformation of Ostreococcus species (OTTH595, RCC809 and RCC802) and Bathycoccus. protocols.io https://dx.doi.org/10.17504/protocols.io.83uhynw | 2021-04-15 09:15:22 | |||
|
Bodo saltans Cassette for tagging EF1alpha gene__IG BsTub Resource Report Resource Website |
Fatma Gomaa, Zhou Zhuha, Roberto Docampo, Virginia Edgcomb, Peter Girguis | DOI:10.17504/protocols.io.s5jeg4n | 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 | Harvard University, University of Georgia, University of Georgia, Woods Hole Oceanographic Institution, Harvard University | https://doi.org/10.1038/s41592-020-0796-x | 1 | 2018 | Fatma Gomaa, Zhou Zhuha, Roberto Docampo, Virginia Edgcomb, Peter Girguis 2018. Bodo saltans Cassette for tagging EF1alpha gene__IG BsTub. protocols.io https://dx.doi.org/10.17504/protocols.io.s5jeg4n | 2021-04-15 09:15:23 | ||
|
Selection of stable transformants in Ostreococcus tauri, Ostreococcus lucimarinus and Bathycoccus prasinos Resource Report Resource Website |
Francois-Yves bouget | DOI:10.17504/protocols.io.zj2f4qe | 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 Ostreococcus lucimarinus and Bathycoccus. | 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 | Laboratoire d'Oceanographie Microbienne. Banyuls sur Mer | https://doi.org/10.1038/s41592-020-0796-x | 3 | 2019 | Francois-Yves bouget 2019. Selection of stable transformants in Ostreococcus tauri, Ostreococcus lucimarinus and Bathycoccus prasinos. protocols.io https://dx.doi.org/10.17504/protocols.io.zj2f4qe | 2021-04-15 09:15:24 | |
|
Protocol for drug sensitivity assay with S. robusta Resource Report Resource Website |
Dan Needleman | DOI:10.17504/protocols.io.g9ebz3e | Protist Research to Optimize Tools in Genetics (PROT-G) | 1 | 2017 | Dan Needleman 2017. Protocol for drug sensitivity assay with S. robusta. protocols.io https://dx.doi.org/10.17504/protocols.io.g9ebz3e | 2021-04-15 09:15:27 | |||||
|
Reporter titrations for transfection of Micromonas commoda CCMP2709 Resource Report Resource Website |
Lisa Sudek, Alexandra Worden, Manny Ares | DOI:10.17504/protocols.io.57rg9m6 | Protist Research to Optimize Tools in Genetics (PROT-G), Worden Lab | This protocol describes the method used to test various amounts (0, 0.3, 3, 10, 20 and 30 µg) of reporter (H3proMpo-LUC) DNA. The plasmid H3proMpo-LUC carries a codon optimized Nanoluc coding region, whose expression is driven by the histone H3 promoter and 3' mRNA end formation and termination sequences. Lumen per total number of cells (including transfected and non-transfected cells within a culture) is used as a proxy for relative transfection efficiencies. It is determined in each culture based on luminescence measurements performed 72 hrs after transfection using the Nano-Glo® Luciferase Assay System. | Monterey Bay Aquarium Research Institute, Moss Landing, USA, Monterey Bay Aquarium Research Institute, Moss Landing, USA; Ocean EcoSystems Biology Unit, Marine Ecology Division, Helmholtz Centre for Ocean Research, Kiel, Germany, University of California, Santa Cruz | 1 | 2019 | Lisa Sudek, Alexandra Worden, Manny Ares 2019. Reporter titrations for transfection of Micromonas commoda CCMP2709. protocols.io https://dx.doi.org/10.17504/protocols.io.57rg9m6 | 2021-04-15 09:15:26 | |||
|
Culturing Euplotes crassus to high densities using a combination of algae and bacteria as the food source. Resource Report Resource Website |
Lawrence A. Klobutcher, Larry Klobutcher | DOI:10.17504/protocols.io.2amgac6 | Protist Research to Optimize Tools in Genetics (PROT-G) | This procedure was developed to investigate the possible use of RNAi through bacterial feeding as a means of knocking down expression of particular genes.While the utility of RNAi is still being investigated, the method is effective in growing Euplotes crassus to higher densities than is possible using algae alone. Using moderately dense cultures of algae, we typically achieve cell densities of 500-1,000 cells/ml, while with the E. coli supplemented cultures we describe here, Euplotes cell densities exceed 3,000 cells/ml. In fact, preliminary studies mixing a volume of a Euplotes culture with an equal volume of resuspended E. coli have produced a density of ~8,000 cells/ml.While the described procedure involves small cultures, it can likely be scaled up as required.For some species of Euplotes, long-term culture using bacteria as a food source has not been successful (C. Miceli, personal communication), suggesting that some essential nutrient is not being provided in sufficient quantitities | University of Connecticut Health Center, University of Connecticut, School of medicine | 1 | 2019 | Lawrence A. Klobutcher, Larry Klobutcher 2019. Culturing Euplotes crassus to high densities using a combination of algae and bacteria as the food source.. protocols.io https://dx.doi.org/10.17504/protocols.io.2amgac6 | 2021-04-15 09:15:30 | |||
|
Modified Bacterial Conjugation Protocol For Pseudo-nitzschia multiseries Resource Report Resource Website |
G Jason Smith, April Woods | DOI:10.17504/protocols.io.7vhhn36 | Protist Research to Optimize Tools in Genetics (PROT-G), Environmental Biotechnology Lab | This is a modified version of 'Conjugation of Thalassiosira pseudonana', publishedby J. Turnsek dx.doi.org/10.17504/protocols.io.f55bq86 .The protocol was modified to enhance viability in the diatom Pseudo-nitzschia multiseries. This version was used to transform Pseudo-nitzschia multiseries isolate 15091C3 with an episomal plasmid derived from pPtPUC3 to express a egfp gene under control of the P. multiseries actin promoter and termination domains. PLASMID INFOpPmAGFPC10 EPI : A P. multiseries derived expression cassette under control of P. multiseries ca 1000 bp of actin promoter and termination domains. Pm actPs::eGFP::actTs | Moss Landing Marine Laboratories, Moss Landing Marine Labs | 2 | 2019 | G Jason Smith, April Woods 2019. Modified Bacterial Conjugation Protocol For Pseudo-nitzschia multiseries. protocols.io https://dx.doi.org/10.17504/protocols.io.7vhhn36 | 2021-04-15 09:15:34 |
Can't find your Protocol?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. If you want to find a specific protocol and you know the DOI of the protocol already, it's easier to enter a DOI to search. You can refine the search results using Facets on the left side of the search results page. If you are on the table view, you can also search in a specific column by clicking the column title and enter the keywords.
If you still could not find your protocol in the search results, please help us by adding it into the system — it's easy. Create and publish your protocols at Protocols.io.
Welcome to the dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on dkNET then you can log in from here to get additional features in dkNET such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into dkNET you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
Email: info_at_ dknet.org
