id float64 1.55k 110k ⌀ | title stringlengths 1 256 ⌀ | template_id float64 0 6 ⌀ | doi stringlengths 39 49 ⌀ | url stringlengths 40 92 ⌀ | authors stringlengths 1 933 ⌀ | protocol_text stringlengths 34 1.08M | steps_list stringlengths 2 269k |
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79,952 | Autofluorescence Microscopy Data Acquisition | 1 | dx.doi.org/10.17504/protocols.io.5jyl8jozdg2w/v1 | https://www.protocols.io/view/autofluorescence-microscopy-data-acquisition-csbqwamw | Angela Kruse, Heath Patterson, Jamie Allen, Katerina V Djambazova, Maya Brewer, Elizabeth Neumann, Mark De Caestecker, Danielle Gutierrez, Jeff Spraggins | TITLE: Autofluorescence Microscopy Data Acquisition
AUTHORS: Angela Kruse, Heath Patterson, Jamie Allen, Katerina V Djambazova, Maya Brewer, Elizabeth Neumann, Mark De Caestecker, Danielle Gutierrez, Jeff Spraggins
[DESCRIPTION]
Scope:
Obtain autofluorescence microscopy images of tissues.
Expected Outcome:
An RGB a... | ["If sectioned tissue is frozen, return to room temperature (~20oC) within a vacuum desiccator (~30 min), otherwise proceed directly to step 2.", "Place microscope slide within adapter and insert into the Zeiss AxioScan Z1 Slide Scanner. Be sure to orient the slide with the label facing downward in the adapter. \n\nFor... |
null | null | null | dx.doi.org/10.17504/protocols.io.mdgc23w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Probiotics are live microbial feed supplements that promote growth and health to the host by minimizing non-essential and pathogenic microorganisms in the host’s gastrointestinal tract (GIT). The campaign to minimize excessive use of antibiotics in poultry production has nece... | [] |
47,396 | Disease model screen protocol | 4 | dx.doi.org/10.17504/protocols.io.bsicncaw | https://www.protocols.io/view/disease-model-screen-protocol-bsicncaw | Ida Barlow | TITLE: Disease model screen protocol
AUTHORS: Ida Barlow
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Protocol for screening the disease model </span><span style = "font-style:italic;">C. elegans</span><span> strains under baseline and bluelight conditions using the Hydra (Loopbio) imaging ... | ["[Pick L4 worms for bleaching (-10 days before tracking; eg Monday)]\nPick 5 x L4s per strain onto 3 x 60mm plates (pre-seeded with OP50) for each strain", "[Pick L4 worms for bleaching (-10 days before tracking; eg Monday)]\nTake out 90mm plates from cold room to allow to dry at room temperature\n3 x 90mm plates per ... |
45,428 | Measuring [K+] from sample | 4 | null | https://www.protocols.io/view/measuring-k-from-sample-bqkumuww | Elizabeth Fozo | TITLE: Measuring [K+] from sample
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Measuring [K</span><span style = "vertical-align:super;">+</span><span>] from a sample using Dr. Fozo's K</span><span style = "vertical-align:super;">+</span><span> ISE</span></div></div>
... | ["[Standardize electrode]\nMake standards using 100 ppm solution to 100, 10, and 1 ppm. (Meter not accurate below 0.04 ppm. You can also do any M range of KCl from 1M to 10^-6M). Add 2mL ISA (NaCl) to 100mL solution (or 200uLto 10mL, etc).", "[Standardize electrode]\nOn the ppm mode screen, hit STD again and repeat ste... |
21,749 | Childhood Obesity Policy Document Analysis | null | dx.doi.org/10.17504/protocols.io.zgvf3w6 | null | NotreallyItzhak Yanovitzky, Matthew S. Weber | TITLE: Childhood Obesity Policy Document Analysis
AUTHORS: NotreallyItzhak Yanovitzky, Matthew S. Weber
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Evidence-based decision-making is critical to the formulation of effective policy and practice, but despite efforts to increase the availability of ... | [] |
21,767 | Polymerase Chain Reaction | null | dx.doi.org/10.17504/protocols.io.zhff33n | null | Lis Rocha | TITLE: Polymerase Chain Reaction
AUTHORS: Lis Rocha
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This was the PCR protocol used for each set of primers in the study Comparative genomics of </span><span style = "font-style:italic;">Staphylococcus aureus </span><span>associated with subclinic... | ["[primers cl3309sub F/R]\n35 cycles of denaturation at 95.0 °C for 45 s,", "[primers cl3309sub F/R]\nAnealing: 55 °C for 45s", "[primers cl3309sub F/R]\nExtension: 72 °C for 45 s", "[primers cl3309sub F/R]\nfinal extension at 72.0 °C for 10 min", "[primers cl3316F/R]\ninitial denaturation: 95.0 °C for 5 min;", "[prime... |
78,941 | 10 Years of Science at Tetiaroa | 4 | null | https://www.protocols.io/view/10-years-of-science-at-tetiaroa-crb5v2q6 | Erin Robinson | TITLE: 10 Years of Science at Tetiaroa
AUTHORS: Erin Robinson
[DESCRIPTION]
This is a protocol documenting the proposed approach to conducting a scientific research review at a field station.
[STEPS]
SECTION: Document Tetiaroa Projects
1. Identify the projects with Tetiaroa Ecostation leadership, staff, and research... | ["[Document Tetiaroa Projects] Identify the projects with Tetiaroa Ecostation leadership, staff, and researchers", "[Document Tetiaroa Projects] Review the RAMS applications for each project", "[Document Tetiaroa Projects] Create (or update) a landing page for the project with a DOI, a short description, and connection... |
null | null | null | dx.doi.org/10.17504/protocols.io.p4qdqvw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol gives basic instructions and advice to beginners on tipping Drosophila flies between food vials when maintaining stock lines or during an experiment. It will be helpful to read this before commencing your stock care or experiment, however the best way to get bet... | [] |
41,808 | XPRIZE SHINE - Paper-based SARS-CoV-2 NP Test | 4 | dx.doi.org/10.17504/protocols.io.bk3qkymw | https://www.protocols.io/view/xprize-shine-paper-based-sars-cov-2-np-test-bk3qkymw | Jon Arizti-Sanz, Catherine A. Freije, Chloe K. Boehm, Sameed M. Siddiqui, Allen M. Goodman, Tinna-Solveig F. Kosoko-Thoroddsen, A'Doriann Y. Bradley, Jeremy Johnson, Pardis C. Sabeti, Cameron Myhrvold | TITLE: XPRIZE SHINE - Paper-based SARS-CoV-2 NP Test
AUTHORS: Jon Arizti-Sanz, Catherine A. Freije, Chloe K. Boehm, Sameed M. Siddiqui, Allen M. Goodman, Tinna-Solveig F. Kosoko-Thoroddsen, A'Doriann Y. Bradley, Jeremy Johnson, Pardis C. Sabeti, Cameron Myhrvold
[DESCRIPTION]
<div class = "text-blocks"><div class = "... | ["[Sample Collection and Viral Lysis]\nOpen the nasopharyngeal (NP) collection tube and rotate the nasal swab (attached to the NP collection tube cap) 4 times around the inside of each nostril. Return the swab to the collection tube and cap the tube. Nasopharyngeal collection tube contains necessary volume of FastAm... |
42,745 | Zymoclean Gel DNA Recovery--CHEM 584 | 4 | dx.doi.org/10.17504/protocols.io.bmyzk7x6 | https://www.protocols.io/view/zymoclean-gel-dna-recovery-chem-584-bmyzk7x6 | Ken Christensen | TITLE: Zymoclean Gel DNA Recovery--CHEM 584
AUTHORS: Ken Christensen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Product Description</span></div><div class = "text-block">The Zymoclean™ Gel DNA Recovery Kit provides a hassle-free method for high yield recovery o... | ["[Gel purification from agarose gel]\nExcise the DNA fragment from the agarose gel using a razor blade, scalpel or other device and transfer it into a 1.5 ml microcentrifuge tube.\nThe amount of agarose excised from the gel should be as small as possible. Be sure to excise the desired band with very little or no extra... |
42,409 | 18S-V4 rRNA amplification from sorted cells (low-concentration DNA) for NGS Illumina sequencing (Metabarcoding) | 4 | dx.doi.org/10.17504/protocols.io.81wgb71k1vpk/v1 | https://www.protocols.io/view/18s-v4-rrna-amplification-from-sorted-cells-low-co-bmnhk5b6 | Estelle Bigeard, Adriana Lopes Dos Santos, Catherine Ribeiro | TITLE: 18S-V4 rRNA amplification from sorted cells (low-concentration DNA) for NGS Illumina sequencing (Metabarcoding)
AUTHORS: Estelle Bigeard, Adriana Lopes Dos Santos, Catherine Ribeiro
[DESCRIPTION]
For metabarcoding purpose, the first step involves the amplification by PCR of a given gene region (for example V... | ["[Samples : Acid nucleic extraction and quantification] Extract DNA/RNA from the samples using the method/kit appropriate to the specific samples.\n\nFiltered environmental samples usually have more DNA than sorted cells samples, so the V4 region of the 18S rRNA gene can be amplified by a single PCR reaction (without ... |
106,762 | Preparation of pharmacological agents | 0 | dx.doi.org/10.17504/protocols.io.e6nvw1nbzlmk/v1 | https://www.protocols.io/view/preparation-of-pharmacological-agents-dkhi4t4e | Alexandra Nelson, Allison Girasole, Michael Ryan | TITLE: Preparation of pharmacological agents
AUTHORS: Alexandra Nelson, Allison Girasole, Michael Ryan
[DESCRIPTION]
This is a description of how we prepare different drugs for use in live animals (in vivo) or in brain slices (ex vivo).
[STEPS]
SECTION: This protocol provides a description of the preparation, dilut... | ["[This protocol provides a description of the preparation, dilution, application and administration of pharmacological agents.] 6-OHDA (Sigma Aldrich) for MFB dopamine depletions was prepared at 5 μg/μL in\nnormal saline solution.", "Levodopa (Sigma Aldrich) was administered with benserazide (Sigma Aldrich) and prepar... |
48,198 | Chimeric Protein-LAG and Protein LA sandwich ELISA | 1 | dx.doi.org/10.17504/protocols.io.btbenije | https://www.protocols.io/view/chimeric-protein-lag-and-protein-la-sandwich-elisa-btbenije | Angel Justiz-Vaillant | TITLE: Chimeric Protein-LAG and Protein LA sandwich ELISA
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This ELISA was used to study the interactions between protein-LAG (PLAG) and protein-LA (SpLA) with different immunoglobulin preparations from mammalian and avia... | ["This ELISA was used to study the interactions between protein-LAG (PLAG) and protein-LA (SpLA) with different immunoglobulin preparations from mammalian and avian species. The 96 well microtiter plate was coated overnight at 4°C with 2 µg/µl per well of PLAG in carbonate-bicarbonate buffer pH 9.6.", "The plate was th... |
null | null | null | dx.doi.org/10.17504/protocols.io.jhvcj66 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Sanger sequencing was performed on available samples from all affected family members to determine whether the potential mutation in the causative gene co-segregated with the disease phenotype. In order to amplify exon 7 of the <em>ILDR1</em> gene, we designed the following p... | [] |
60,237 | prime-seq | 1 | dx.doi.org/10.17504/protocols.io.81wgb1pw3vpk/v2 | https://www.protocols.io/view/prime-seq-b63mrgk6 | Aleksandar Janjic, Lucas Esteban Wange, Johannes JWB Bagnoli, Johanna Geuder, Phong Nguyen, Daniel Richter, Christoph Ziegenhain, Wolfgang Enard, Beate Vieth | TITLE: prime-seq
AUTHORS: Aleksandar Janjic, Lucas Esteban Wange, Johannes JWB Bagnoli, Johanna Geuder, Phong Nguyen, Daniel Richter, Christoph Ziegenhain, Wolfgang Enard, Beate Vieth
[DESCRIPTION]
Cost-efficient library generation by early barcoding has been central in propelling single-cell RNA sequencing. H... | ["[Preparation] Clean all surfaces and pipettes with RNase Away", "[Preparation] Thaw frozen buffers and primers on ice", "[Preparation] Prepare 80% EtOH (approximately 45 mL for 96 samples)", "[Prepare Cleanup Beads (22% PEG)] Prepare PEG Solution (22%) by adding all ingredients to a 50 mL falcon tube", "[Prepare Clea... |
44,865 | Lab 7 Notebook | 3 | dx.doi.org/10.17504/protocols.io.bp29mqh6 | https://www.protocols.io/view/lab-7-notebook-bp29mqh6 | TITLE: Lab 7 Notebook
AUTHORS:
[STEPS] | [] | |
null | null | null | dx.doi.org/10.17504/protocols.io.ddj24m | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For <a href="https://www.protocols.io/view/One-step-growth-curves-for-Cellulophaga-phages-ddh235" target="_blank">One-step growth curves for Cellulophaga phages protocol</a>.
[STEPS]
?.
?.
?.
?. | [] |
67,219 | Multiplex PCR Assay for Clade-typing Salmonella Enteritidis | 1 | dx.doi.org/10.17504/protocols.io.4r3l2ok1jv1y/v1 | https://www.protocols.io/view/multiplex-pcr-assay-for-clade-typing-salmonella-en-cdvts66n | Sarah Gallichan, Blanca M. Perez-Sepulveda, Nicholas A. Feasey, Jay C. D. Hinton, Anthony M. Smith | TITLE: Multiplex PCR Assay for Clade-typing Salmonella Enteritidis
AUTHORS: Sarah Gallichan, Blanca M. Perez-Sepulveda, Nicholas A. Feasey, Jay C. D. Hinton, Anthony M. Smith
[DESCRIPTION]
Salmonella Enteritidis is one of the most commonly reported serovars of non-typhoidal Salmonella causing human disease and is re... | ["[Preparation of control panel isolates] Select twelve Salmonella Enteritidis isolates that represent the Global Epidemic, Outlier, East African and West African clades (three biological replicates per clade) predicted by the hierBAPS (hierarchical Bayesian Analysis of Population Structure) algorithm.", "[Preparation ... |
21,948 | Protein Estimation by BCA | null | dx.doi.org/10.17504/protocols.io.zn4f5gw | null | Vidur Sabharwal | TITLE: Protein Estimation by BCA
AUTHORS: Vidur Sabharwal
[STEPS]
?. Make the following dilutions of autoclaved dd. H20 in triplicatesBSA conc(µg/ml) 0 5 10 15 20 25Water(µl) 25 22.5 20 17.5 15 ... | ["Make the following dilutions of autoclaved dd. H20 in triplicatesBSA conc(µg/ml) 0 5 10 15 20 25Water(µl) 25 22.5 20 17.5 15 12.5BSA(2mg/ml)(µl) 0 2.5 5 ... |
43,009 | Simoa Extracellular Vesicle assays | 4 | dx.doi.org/10.17504/protocols.io.bm89k9z6 | https://www.protocols.io/view/simoa-extracellular-vesicle-assays-bm89k9z6 | Maia Norman, Dima Ter-Ovanesyan, Roey Lazarovits, Wendy Trieu , Ju Hyun Lee, David Walt | TITLE: Simoa Extracellular Vesicle assays
AUTHORS: Maia Norman, Dima Ter-Ovanesyan, Roey Lazarovits, Wendy Trieu , Ju Hyun Lee, David Walt
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Extracellular Vesicles (EV) are reservoirs of biomarkers such as mRNA and post-translationally modified protein... | ["[Bead Coupling Protocol]\nThis beads coupling protocol is based on the coupling protocols developed by Quanterix. The manual for these can be found at Quanterix.com. Each bead coupling procedure below has been optimized for the given antibody and assay. Where differences arrise between the procedures they are noted."... |
35,437 | Optical Image Collection | null | dx.doi.org/10.17504/protocols.io.beumjeu6 | null | Guanshi Zhang, Dusan Velickovic, Annapurna Pamreddy, Jessica Lukowski, Theodore Alexandrov, Chris Anderton, Kumar Sharma | TITLE: Optical Image Collection
AUTHORS: Guanshi Zhang, Dusan Velickovic, Annapurna Pamreddy, Jessica Lukowski, Theodore Alexandrov, Chris Anderton, Kumar Sharma
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Mass spectrometry imaging is an exciting technology, which enables simultaneous analysis o... | ["[Autofluorescence (AF) and Bright Field Imaging]\nBefore the matrix application, right after defrosting in desiccator, the AF image (pre-AF) is captured on a confocal microscope.\nUTHSA: 10× objective on a Leica TSC SP8PNNL: 20x objective on a Zeiss 710 LSM; 10x objective PALM MicroBeam (Zeiss inverse microscope Axio... |
66,888 | Où acheter Detoxil Avis ,Detoxil Pharmacie Et Detoxil en Pharmacie prix En France Sur Le Site Officiel Achetez Maintenant ! | 1 | dx.doi.org/10.17504/protocols.io.5qpvobzyxl4o/v1 | https://www.protocols.io/view/o-acheter-detoxil-avis-detoxil-pharmacie-et-detoxi-cdjgs4jw | jpscarter | TITLE: Où acheter Detoxil Avis ,Detoxil Pharmacie Et Detoxil en Pharmacie prix En France Sur Le Site Officiel Achetez Maintenant !
AUTHORS: jpscarter
[DESCRIPTION]
➢ Nom du produit - Detoxil Avis
➢Bénéfices clés - Améliorer la santé
➢ Structure - Composé Organique Naturel
➢ Effets secondaires - NA
➢ Note - ★★★★★... | ["[Où acheter Detoxil Avis ,Detoxil Pharmacie Et Detoxil en Pharmacie prix En France Sur Le Site Officiel Achetez Maintenant !]"] |
87,380 | Sanger Tree of Life HMW DNA Extraction: Automated MagAttract v.2 | 4 | dx.doi.org/10.17504/protocols.io.kxygx3y4dg8j/v1 | https://www.protocols.io/view/sanger-tree-of-life-hmw-dna-extraction-automated-m-czjux4nw | graeme oatley, Amy Denton, Caroline Howard | TITLE: Sanger Tree of Life HMW DNA Extraction: Automated MagAttract v.2
AUTHORS: graeme oatley, Amy Denton, Caroline Howard
[DESCRIPTION]
This protocol describes the automated extraction and SPRI of HMW DNA from multiple different tissue samples from a variety of species intended for long-read sequencing using the Qia... | ["[Sample lysis] Prepare a lysis buffer master mix:\n ReagentVolume per samplePhosphate buffered solution (PBS)200 µLProteinase K20 µLRNase A4 µLBuffer AL150 µL", "[Sample lysis] Set a heat block to 25 °C.", "[Sample lysis] For samples which have been cryogenically homogenised:\nTransfer 25 mg of the sample into a 2 m... |
80,333 | Isolation of Schistosoma mansoni eggs, miracidia, and sporocysts for in vitro cultivation | 4 | dx.doi.org/10.17504/protocols.io.81wgbye5yvpk/v1 | https://www.protocols.io/view/isolation-of-schistosoma-mansoni-eggs-miracidia-an-cspmwdk6 | Sarah K Buddenborg | TITLE: Isolation of Schistosoma mansoni eggs, miracidia, and sporocysts for in vitro cultivation
AUTHORS: Sarah K Buddenborg
[DESCRIPTION]
The purpose of this procedure is to isolate eggs from livers collected from mice infected with Schistosoma mansoni. This protocol ensures a sterile prep of eggs to be used for cult... | ["[Liver washing] In tissue culture hood, prepare three petri dishes with 1x DPBS+2% anti-anti, one with 70% ethanol, and one clean petri dish arranged in the following order:", "[Liver washing] Decant the livers into the first petri dish using ethanol-cleaned tweezers to submerge and continuously move them for 1 minut... |
67,395 | Culture and transfection of HEK293T cells | 4 | dx.doi.org/10.17504/protocols.io.eq2lynkzpvx9/v1 | https://www.protocols.io/view/culture-and-transfection-of-hek293t-cells-cd3bs8in | Hanqin Li, Dirk Hockemeyer | TITLE: Culture and transfection of HEK293T cells
AUTHORS: Hanqin Li, Dirk Hockemeyer
[DESCRIPTION]
This protocol describes a standard procedure culturing and transfecting HEK293T cells
Protocol overview:
A. Culturing HEK293T cells
B. Transfection of HEK293T cells with Lipofectamine 2000
[STEPS]
SECTION: A. Culturin... | ["[A.\tCulturing HEK293T cells] HEK293T cells are cultured in HEK293T medium in 10 cm dishes.", "[A.\tCulturing HEK293T cells] Passage cells when the culture reaches 80% confluency.", "[A.\tCulturing HEK293T cells] Remove medium", "[A.\tCulturing HEK293T cells] Wash once with 5 ml DPBS", "[A.\tCulturing HEK293T cells] ... |
87,219 | Borrelia burgdorferi ospC Genotyping Using Luminex Technology | 4 | dx.doi.org/10.17504/protocols.io.5jyl899k8v2w/v2 | https://www.protocols.io/view/borrelia-burgdorferi-ospc-genotyping-using-luminex-czetx3en | Patrick Pearson, Olivia Skaltsis, Chu-Yuan Luo, Guang Xu, Zachary Oppler, Dustin Brisson, Stephen M Rich | TITLE: Borrelia burgdorferi ospC Genotyping Using Luminex Technology
AUTHORS: Patrick Pearson, Olivia Skaltsis, Chu-Yuan Luo, Guang Xu, Zachary Oppler, Dustin Brisson, Stephen M Rich
[DESCRIPTION]
Borrelia burgdorferi is an important tickborne human pathogen and can be grouped into separate strains based on the outer ... | ["[PREPARING SOLUTIONS] 1X xTAG buffer\n\nAdd 1 mL of 10X xTAG buffer to 9 mL of molecular grade water. Scale volume up or down as necessary.\nStore at 4°C until use", "[PREPARING SOLUTIONS] Bead mix solution (75 beads/μL)\n\nThe specific Luminex microspheres (beads) are sold in concentrations of 2.5X10^6 beads/mL. The... |
86,600 | Geographic Information Systems (GIS)-based spatial analysis of cell distribution | 1 | dx.doi.org/10.17504/protocols.io.ewov1o697lr2/v2 | https://www.protocols.io/view/geographic-information-systems-gis-based-spatial-a-cytgxwjw | Adalberto Merighi, Laura Lossi | TITLE: Geographic Information Systems (GIS)-based spatial analysis of cell distribution
AUTHORS: Adalberto Merighi, Laura Lossi
[DESCRIPTION]
This protocol describes how to perform a Geographic Information System (GIS)-based spatial analysis of cerebellar images focused on the distribution of the Purkinje neurons. It ... | ["[Calculation of cells' X-Y coordinates]", "[Calculation of cells X-Y coordinates] Open the image to be analyzed using Fiji: File → Open", "[Calculation of cells X-Y coordinates] Set the appropriate scale for the image using Analyze → Set Scale. In the pop-up window report the distance in pixels related to the kn... |
79,823 | Rotarod test | 4 | dx.doi.org/10.17504/protocols.io.eq2ly7b1mlx9/v1 | https://www.protocols.click/view/rotarod-test-cr7pv9mn | michela.deleidi, Bianca Marchetti, Federico Bertoli, Carmela Giachino, carmela.giachino | TITLE: Rotarod test
AUTHORS: michela.deleidi, Bianca Marchetti, Federico Bertoli, Carmela Giachino, carmela.giachino
[DESCRIPTION]
Rotarod test was used to evaluate the effect of LPS treatment on motor performance during aging process between genotypes.
[STEPS]
SECTION: ROTAROD
1. To test motor performance, we used t... | ["[ROTAROD] To test motor performance, we used the accelerated Rotarod (five-lane accelerating rotarod; Ugo Basile, Comerio, Italy), a motor behavioral test widely used to assess motor deficit in neurodegenerative disease models in rodents. Mice have to keep their balance on a horizontal rotating rod (diameter, 3 cm) a... |
29,258 | Fluorescent caspase-3 staining to assess induction of apoptosis in A6 cells (Plos One) | null | dx.doi.org/10.17504/protocols.io.8tihwke | null | Elin Verbrugghe | TITLE: Fluorescent caspase-3 staining to assess induction of apoptosis in A6 cells (Plos One)
AUTHORS: Elin Verbrugghe
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The largest current disease-induced loss of vertebrate biodiversity is due to chytridiomycosis and despite the increasing under... | ["Prepare Cell Medium A: L15 medium: 70%Distilled water: 20%Fetal bovine serum 10%", "Prepare Cell Medium B: L15 medium: 40%Distilled water: 55%Fetal bovine serum: 5%", "Coat coverslips with Rat tail collagen: Add glass coverslips in a 24-well tissue culture plate. Coat the glass coverslips at 37°C for 2 hours. Therefo... |
15,152 | Recommendations to grow algal culture - Roscoff Culture Collection | null | dx.doi.org/10.17504/protocols.io.s2qegdw | null | Roscoff Culture Collection | TITLE: Recommendations to grow algal culture - Roscoff Culture Collection
AUTHORS: Roscoff Culture Collection
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Recommendations for algal cultures from the Roscoff Culture Collection</div></div>
[STEPS]
?. [Before ordering strains from the RCC]
Every cu... | ["[Before ordering strains from the RCC]\nEvery culture in the RCC catalogue has a detailed form on our website (http://roscoff-culture-collection.org/), where you will find a range of information concerning culture conditions for the strain in question (temperature, medium, light intensity, etc.).", "Prepare media (no... |
21,417 | SPARC_Duke_PelotGrill_OT2-OD025340_RatVagusNerve_Morphology | 1 | dx.doi.org/10.17504/protocols.io.y6hfzb6 | https://www.protocols.io/view/sparc-duke-pelotgrill-ot2-od025340-ratvagusnerve-m-y6hfzb6 | Nicole A. Pelot, Gabriel B. Goldhagen, Jake E. Cariello, Warren M. Grill | TITLE: SPARC_Duke_PelotGrill_OT2-OD025340_RatVagusNerve_Morphology
AUTHORS: Nicole A. Pelot, Gabriel B. Goldhagen, Jake E. Cariello, Warren M. Grill
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The protocol describes image segmentation and image analysis methods to quantify rat vagus nerve morpho... | ["[Image Segmentation]\nWe used Nikon's NIS Elements software (v5.02.01, Build 1270) to segment rat vagus nerve micrographs stained with Masson's trichrome using the General Analysis RGB tool.", "[Image Segmentation]\nWe converted the binary segmented image into “Graticule Masks”, binary images saved as TIFs.", "[Image... |
60,514 | CODEX® Multiplexed Imaging | Microscope Setup and Tissue Imaging | 1 | dx.doi.org/10.17504/protocols.io.e6nvwke6zvmk/v1 | https://www.protocols.io/view/codex-multiplexed-imaging-microscope-setup-and-tis-b7carise | Diane Saunders, Conrad Reihsmann, Marcela Brissova, Alvin C. Powers | TITLE: CODEX® Multiplexed Imaging | Microscope Setup and Tissue Imaging
AUTHORS: Diane Saunders, Conrad Reihsmann, Marcela Brissova, Alvin C. Powers
[DESCRIPTION]
This protocol describes the imaging workflow currently in use by the Vanderbilt Diabetes Research Center Islet & Pancreas Analysis (IPA) Core and Powers/Br... | ["[Experiment Preparation] Check and power up equipment: CODEX® Instrument and Keyence BZ-X810 microscope.", "[Experiment Preparation] Prepare 1 L of 1X CODEX Buffer (100 mL 10X CODEX Buffer in 900 mL MilliQ/ddH2O).", "[Experiment Preparation] Fill bottles for the CODEX Instrument accordingly:\n\nBottle 1 - 1X CODEX Bu... |
103,703 | Determining the horizontal transfer of antibiotic resistance genes: using high-throughput fluorescence-based sorting approaches | 0 | dx.doi.org/10.17504/protocols.io.14egn6ebpl5d/v1 | https://www.protocols.io/view/determining-the-horizontal-transfer-of-antibiotic-dhhx337n | Qiu E Yang, Yanshuang Yu | TITLE: Determining the horizontal transfer of antibiotic resistance genes: using high-throughput fluorescence-based sorting approaches
AUTHORS: Qiu E Yang, Yanshuang Yu
[DESCRIPTION]
Despite the significant role of plasmids play in the global spread of antimicrobial resistance (AMR), current methods to study the trans... | ["[Molecular cloning of plasmid vector pSL1521::gfp (4-5 days)] Plasmid extraction: extract plasmid DNA from up to 5 mL of overnight culture of E. coli DH5α strain containing the pSL1521 plasmid (Addgene, 160729) via a TIANprep Mini Plasmid Kit (TIANGEN, DP103-02). Measure plasmid DNA concentration using the Qubit Flex... |
96,916 | Cell culture, transfection, immunocytochemistry, and imaging | 0 | dx.doi.org/10.17504/protocols.io.5qpvokx3bl4o/v1 | https://www.protocols.io/view/cell-culture-transfection-immunocytochemistry-and-davu2e6w | Nisha Mohd Rafiq, Pietro De Camilli | TITLE: Cell culture, transfection, immunocytochemistry, and imaging
AUTHORS: Nisha Mohd Rafiq, Pietro De Camilli
[DESCRIPTION]
This protocol describes the maintenance, transfection, immunocytochemistry, and imaging of RPE1 and also transfection, immunocytochemistry, and imaging of iPSCs, i3 Neurons and DA neurons.
[S... | ["[General cell culture for RPE1] Grow hTERT-RPE1 cells in DMEM/F12 (Thermo Fisher Scientific) supplemented with 10% FBS (Thermo Fisher Scientific), 1% glutaMAX, 1% penicillin-streptomycin. Keep cells at 37 °C with 5% CO2 in an enclosed incubator.", "[Cell transfection for RPE1] For live-cell imaging experiments, seed ... |
63,361 | Expression and Purification of recombinant Bst DNA polymerase (Bst) | 4 | dx.doi.org/10.17504/protocols.io.dm6gpb2e8lzp/v1 | https://www.protocols.io/view/expression-and-purification-of-recombinant-bst-dna-b949r8z6 | Diana A Tapia-Sidas, Brenda Vargas-Hernández, José Abrahán Ramírez-Pool, Leandro A Nuñez-Muñoz, Berenice Calderón-Pérez, Rogelio González-González, Luis Gabriel Brieba, Rosalía Lira-Carmona, Eduardo Ferat-Osorio, Constantino López-Macías, Roberto Ruiz-Medrano, Beatriz Xoconostle-Cázares | TITLE: Expression and Purification of recombinant Bst DNA polymerase (Bst)
AUTHORS: Diana A Tapia-Sidas, Brenda Vargas-Hernández, José Abrahán Ramírez-Pool, Leandro A Nuñez-Muñoz, Berenice Calderón-Pérez, Rogelio González-González, Luis Gabriel Brieba, Rosalía Lira-Carmona, Eduardo Ferat-Osorio, Constantino López-M... | ["[Preparation of Bst expression cells] Preparation of chemically competent BL21 (DE3) cells harboring pKJE7 plasmid.", "[Preparation of Bst expression cells] Take BL21(DE3) cells harboring pKJE7 plasmid from a frozen glycerol stock using a bacterial inoculating loop and inoculate 3 mL with30 µg/mL. Incubate at", ... |
93,464 | Single-limb fast FR4 operant task (Mendonça et al 2024) | 1 | dx.doi.org/10.17504/protocols.io.5qpvo3439v4o/v1 | https://www.protocols.io/view/single-limb-fast-fr4-operant-task-mendon-a-et-al-2-c7hyzj7w | Marcelo D Mendonça | TITLE: Single-limb fast FR4 operant task (Mendonça et al 2024)
AUTHORS: Marcelo D Mendonça
[DESCRIPTION]
Single-limb fast FR4 operant task methods from Mendonça et al 2024.
[BEFORE_START]
Mice were placed on food restriction throughout training, and fed daily after the training sessions with approximately 1.5 -2.5g o... | ["[Single-limb fast FR4 operant task behavior] At the beginning of each session there was the onset of a light, and the animals were required to perform a sequence of presses at a minimum frequency in order to obtain a sucrose reward.", "[Single-limb fast FR4 operant task behavior] Session 1: To facilitate learning, an... |
93,782 | LIFEPLAN Cyclone Sampling protocol | 1 | dx.doi.org/10.17504/protocols.io.6qpvr3zn2vmk/v1 | https://www.protocols.io/view/lifeplan-cyclone-sampling-protocol-c7twznpe | Gaia Giedre Banelyte, Arielle M Farrell, Hanna M.K. Rogers, Bess Hardwick, Deirdre Kerdraon, Nerea Abrego | TITLE: LIFEPLAN Cyclone Sampling protocol
AUTHORS: Gaia Giedre Banelyte, Arielle M Farrell, Hanna M.K. Rogers, Bess Hardwick, Deirdre Kerdraon, Nerea Abrego
[DESCRIPTION]
Lifeplan is a global biodiversity monitoring project with the aim of assessing the current state of biodiversity worldwide, and using this knowledge... | ["[Site selection and installation of the cyclone sampler] Site selection\n\nSelect a site that:\n\nIs roughly in the center of the selected one-hectare plot.\n\nIs easy to access, since you might need to carry heavy batteries. To avoid dust from traffic in the samples, it is recommended that the sampler is at least 15... |
67,404 | Alpha Extracts Pure Hemp Oil Reviews Canada: Free Trial and Price of Alpha Extracts CBD Oil | 3 | dx.doi.org/10.17504/protocols.io.5jyl89yr6v2w/v1 | https://www.protocols.io/view/alpha-extracts-pure-hemp-oil-reviews-canada-free-t-cd3ks8kw | aidanbutter | TITLE: Alpha Extracts Pure Hemp Oil Reviews Canada: Free Trial and Price of Alpha Extracts CBD Oil
AUTHORS: aidanbutter
[DESCRIPTION]
Alpha Extracts Pure Hemp Oil
[STEPS] | [] |
89,827 | Quick guide to use EPU for Cryo-em data collection | 1 | dx.doi.org/10.17504/protocols.io.14egn3m5ql5d/v1 | https://www.protocols.io/view/quick-guide-to-use-epu-for-cryo-em-data-collection-c3ybypsn | Marta Sanz Murillo, Amalia Villagran Suarez | TITLE: Quick guide to use EPU for Cryo-em data collection
AUTHORS: Marta Sanz Murillo, Amalia Villagran Suarez
[DESCRIPTION]
This quick guide provides key minimal steps for preparing the Microscope/EPU for single-particle data collection
Please note that this guide might be slightly different for each microscope and f... | ["[Preparation before alignments] Load samples into the microscope. Slot 1 is reversed for the carbon cross-grid which is used for alignments. \nTo load, add grids into the cassette at LN2 temperatures and transfer into the NanoCab filled with LN2.\n Transfer NanoCab into the microscope, load grids and remove the NanoC... |
95,873 | Care and Cleaning of pH Probes | 0 | null | https://www.protocols.io/view/care-and-cleaning-of-ph-probes-c9u9z6z6 | francesca.galdi | TITLE: Care and Cleaning of pH Probes
AUTHORS: francesca.galdi
[DESCRIPTION]
This is the protocol we use to clean the probes used with the OGI Bio pH Module.
[BEFORE_START]
Ensure sterile conditions are maintained all through the protocol.
[GUIDELINES]
The probes should be cleaned immediately after an experiment t... | ["[Prior to Running an Experiment] Prior to removing the storage sleeve, visually inspect the probe for trapped air bubbles within the electrolyte solution. If bubbles are present, shake probe in a downward motion to remove them.", "[Prior to Running an Experiment] Unwrap the parafilm and remove the storage sleeve fro... |
28,288 | MojoSort™ Streptavidin Nanobeads Protocol - Negative Selection | null | dx.doi.org/10.17504/protocols.io.7u8hnzw | null | Sam Li | TITLE: MojoSort™ Streptavidin Nanobeads Protocol - Negative Selection
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Product description and procedure summary:</span><span style = "font-weight:bold;">
</span></div><div class = "text-block"><span sty... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes.", "In the final wash of your sample preparation, resuspend the cells in MojoSort™ Buffer by adding up to 4 mL in a 5 mL (12 x 75 mm) polypropylene tube.Note: Keep MojoSort™ Buffer on ice throughout the procedure.", "Filter the cells with... |
93,468 | GCaMP6f imaging using a mini-epifluorescence microscope (Mendonça et al 2024) | 1 | dx.doi.org/10.17504/protocols.io.kqdg3xdx7g25/v1 | https://www.protocols.io/view/gcamp6f-imaging-using-a-mini-epifluorescence-micro-c7h4zj8w | Marcelo D Mendonça | TITLE: GCaMP6f imaging using a mini-epifluorescence microscope (Mendonça et al 2024)
AUTHORS: Marcelo D Mendonça
[DESCRIPTION]
GCaMP6f imaging using a mini-epifluorescence microscope methods from Mendonça et al 2024.
[BEFORE_START]
Mice are briefly anesthetized using a mixture of isoflurane and oxygen (1% isoflurane... | ["[GCaMP6f imaging] Once the baseplate (that is attached to the mouse) is attached to the mini-epifluorescence microscope, mice are recovered in their home cage for 15-20 minutes prior to starting imaging.", "[GCaMP6f imaging] With the baseplate attached to the microscope, mice are them imaged during the FR4/1s task in... |
72,821 | Sample collection and eDNA extraction from Sterivex filter units | 4 | dx.doi.org/10.17504/protocols.io.rm7vz39w5gx1/v2 | https://www.protocols.io/view/sample-collection-and-edna-extraction-from-sterive-cjcvuiw6 | Oscar E Chiang, Pedro Inostroza | TITLE: Sample collection and eDNA extraction from Sterivex filter units
AUTHORS: Oscar E Chiang, Pedro Inostroza
[DESCRIPTION]
The following workflow covers several steps in the DNA analysis of environmental samples, from the water collection to the analysis back in the lab. The samples can be taken from several water... | ["[Sample collection] A portable peristaltic pump (Vampire sampler; Buerkle) is used for sampling at an approximate 30-50 mL/min flow rate. The tubing inserted in the unit's head has a suction hose (Marprene; 4.8 mm inner diameter), connected to a flexible silicone hose. A suitable adapter connects both hoses.", "[Samp... |
23,977 | Prepare 2L of 2X freezer buffer to freeze down C. elegans | null | dx.doi.org/10.17504/protocols.io.3nhgmb6 | null | Cancer Research UK / Wellcome Gurdon Institute media kitchen | TITLE: Prepare 2L of 2X freezer buffer to freeze down C. elegans
AUTHORS: Cancer Research UK / Wellcome Gurdon Institute media kitchen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol accompanies you in the preparation of 2 litres of 2X freezer buffer, which is the buffer used to ... | ["ABC1IngredientsQuantity2NaCl 1M200ml31M KH2PO4 pH 6100ml4Glycerol 600ml5Double\n distilled H2Oup to 2L6 Autoclave7 80.1M\n MgSO4 300 microlitres9 per 100ml bottle\nABC1IngredientsQuantity2NaCl 1M200ml31M KH2PO4 pH 6100ml4Glycerol 600ml5Double\n distilled H2Oup to 2L6 Autoclave7 80... |
34,272 | One-pot native barcoding of amplicons v2 | null | dx.doi.org/10.17504/protocols.io.bdp8i5rw | null | Josh Quick | TITLE: One-pot native barcoding of amplicons v2
AUTHORS: Josh Quick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This one-pot native barcoding protocol was developed in conjunction with Oxford Nanopore Technologies, New England Biolabs and BCCDC.</div></div>
[STEPS]
?. Set up the following react... | ["Set up the following reaction for each sample:Component VolumePCR dilution from previous step Nuclease-free water Ultra II End Prep Reaction Buffer Ultra II End Prep Enzyme Mix Total\n5 µl\n7.5 µl\n1.75 µl\n0.75 µl\n15 µl", "Incuba... |
93,407 | Marble Burying | 4 | dx.doi.org/10.17504/protocols.io.q26g7pj8qgwz/v1 | https://www.protocols.io/view/marble-burying-c7f7zjrn | Tim Sampson | TITLE: Marble Burying
AUTHORS: Tim Sampson
[DESCRIPTION]
Description: Marble burying is a typical behavior in mice that has
been shown to be sensitive to differences based on strain, hippocampal lesions,
and biological/chemical treatments1,2,3,4. The marble burying assay
is quick and requires no specialized equipment... | ["[Set-up] The night before assessment gather and autoclave enough standard mouse cages for each mouse to be assessed.", "[Set-up] Day of assessment fill each cage with 1.5\" of sterile unscented mouse bedding.", "[Set-up] Autoclave enough marbles to have 20 per cage (marbles should be flat on one side and rounded on t... |
68,419 | Double stranded RNA extraction by cellulose | 4 | dx.doi.org/10.17504/protocols.io.4r3l2odrjv1y/v1 | https://www.protocols.io/view/double-stranded-rna-extraction-by-cellulose-ce3btgin | Vahid Jalali Javaran | TITLE: Double stranded RNA extraction by cellulose
AUTHORS: Vahid Jalali Javaran
[DESCRIPTION]
In this protocol, the viral dsRNA extraction from infected-grapevine plants is explained.
[STEPS]
SECTION: Total nucleic acid extraction
1. Weigh ~ 1.5 g of fresh or frozen leaves. Put the leaves in a 50 ml capped centrif... | ["[Total nucleic acid extraction] Weigh ~ 1.5 g of fresh or frozen leaves. Put the leaves in a 50 ml capped centrifuge tube containing 8X 8-mm stainless balls (sterilized). Immerse the tube in the liquid nitrogen for 5 mins. Rapidly mount the tubes in a foam holder and move to the MiniG chamber.\nFix the tubes correctl... |
68,368 | SDS-PAGE | 4 | null | https://www.protocols.io/view/sds-page-cezqtf5w | Ana Belem García González, Georgina Diego, Irán Alessandra Chaparro Rodríguez, Jair Alexis Gardea Sáenz | TITLE: SDS-PAGE
AUTHORS: Ana Belem García González, Georgina Diego, Irán Alessandra Chaparro Rodríguez, Jair Alexis Gardea Sáenz
[DESCRIPTION]
This protocol shows the steps carried out by team Tec-Chihuahua to perform SDS-PAGE
[STEPS]
SECTION: Protocol
1. Clean the components of the electrophoresis camera with 70% et... | ["[Protocol] Clean the components of the electrophoresis camera with 70% ethanol and gauze 's.", "[Protocol] Assemble the chamber and check that there are no leaks by pouring distilled water between the glasses.", "[Protocol] Prepare polyacrylamide gels:", "[Protocol] Pour the solution between the glasses with a 1 mL m... |
23,741 | TPGY BROTH (TRYPTONE PEPTONE GLUCOSE YEAST EXTRACT BROTH) | 1 | null | https://www.protocols.io/view/tpgy-broth-tryptone-peptone-glucose-yeast-extract-3e5gjg6 | Roey Angel, Ana Lara-Rodriguez, Eva Petrova | TITLE: TPGY BROTH (TRYPTONE PEPTONE GLUCOSE YEAST EXTRACT BROTH)
AUTHORS: Roey Angel, Ana Lara-Rodriguez, Eva Petrova
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">For the enrichment of Clostridium sp. from soil samples, sufficient for 100 cultivation tubes.</div></div>
[STEPS]
?. [Medium prepara... | ["[Medium preparation]\nFinal pH ( at 25°C) 7.0±0.2\n[Casein Hydrolysate]\n[Peptic Digest from Animal Tissue (Peptone A)]\n[Yeast Extract]\n[Dextrose]\n[Sodium Thioglycolate ]\nHeat if necessary, to dissolve the medium completely.", "[Medium preparation]\nSterilize by autoclaving at 15 lbs pressure for .\n121 °C", "[... |
40,234 | Bias in Bias Recognition - Research Materials | 1 | dx.doi.org/10.17504/protocols.io.bjiikkce | https://www.protocols.io/view/bias-in-bias-recognition-research-materials-bjiikkce | Qi Wang, Hee Jin Jeon | TITLE: Bias in Bias Recognition - Research Materials
AUTHORS: Qi Wang, Hee Jin Jeon
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Biases perpetuate when people think that they are innocent whereas others are guilty of biases. We examined whether people would detect biased thinking and behavior in ... | ["[Bias in bias recognition]"] |
63,399 | ACV Keto Gummies Canada : Shark Tank Reviews Official Store (Website)! | 3 | dx.doi.org/10.17504/protocols.io.14egn7jxyv5d/v1 | https://www.protocols.io/view/acv-keto-gummies-canada-shark-tank-reviews-officia-b96fr9bn | ACVKetoorder | TITLE: ACV Keto Gummies Canada : Shark Tank Reviews Official Store (Website)!
AUTHORS: ACVKetoorder
[DESCRIPTION]
Apple juice vinegar has been used for a seriously prolonged stretch of time by people due to its recovering qualities, as shown by Health Harvard.
[STEPS] | [] |
69,945 | Gene expression analysis by quantitative Real-Time PCR (qPCR) | 4 | dx.doi.org/10.17504/protocols.io.ewov1oyz2lr2/v1 | https://www.protocols.io/view/gene-expression-analysis-by-quantitative-real-time-cgiztuf6 | miquel.vila | TITLE: Gene expression analysis by quantitative Real-Time PCR (qPCR)
AUTHORS: miquel.vila
[DESCRIPTION]
Quantitative Real-Time PCR (qPCR)
[STEPS]
SECTION: Thermocycling
3. Perform PCR using the following cycling conditions in a LightCycler® 480 System (Roche):
50˚C for 2min
95˚C for 2min
95˚C for 15s + 60˚C for 1min... | ["[Thermocycling] Perform PCR using the following cycling conditions in a LightCycler® 480 System (Roche):\t\n50˚C for 2min\n95˚C for 2min\n95˚C for 15s + 60˚C for 1min (x40cycles)", "[Data an] Using the LightCycler Software obtain the threshold cycles (CT) signals from each samples.", "[Data an] Perform ΔΔCT-method to... |
76,183 | DNA extraction protocol for the Bungarus multicinctus by using AxyPrepTM Multisource Genomic DNA Miniprep Kit | 4 | dx.doi.org/10.17504/protocols.io.n92ldp2m8l5b/v1 | https://www.protocols.io/view/dna-extraction-protocol-for-the-bungarus-multicinc-cnmxvc7n | Boyang Liu, Liangyu Cui, Yue Ma, Diancheng Yang, Yanan Gong, Yanchun Xu, Shuhui Yang, Song Huang | TITLE: DNA extraction protocol for the Bungarus multicinctus by using AxyPrepTM Multisource Genomic DNA Miniprep Kit
AUTHORS: Boyang Liu, Liangyu Cui, Yue Ma, Diancheng Yang, Yanan Gong, Yanchun Xu, Shuhui Yang, Song Huang
[DESCRIPTION]
Genomic DNA was extracted from the muscle of a Bungarus multicinctus using the Axy... | ["The following protocol is a modification of the protocol by using the AxyPrepTM Multisource Genomic DNA Miniprep Kit. \n\nApproximately 10mg tissue was minced with sterilized scissors on ice.\non ice", "Add 350 µl Buffer PBS and 15 µl SDS Lysis Buffer and shake for 30s.\n30 s", "Add 150 µl Buffer C-L and 20 µl Protei... |
33,654 | Aquatic eDNA sampling and plant community metabarcoding with portable Nanopore Flongle sequencing (v0.0.3) | null | dx.doi.org/10.17504/protocols.io.bc4wiyxe | https://www.protocols.io/view/aquatic-edna-sampling-and-plant-community-metabarc-bc4wiyxe | Jordan Callahan, Robert Harbert | TITLE: Aquatic eDNA sampling and plant community metabarcoding with portable Nanopore Flongle sequencing (v0.0.3)
AUTHORS: Jordan Callahan, Robert Harbert
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Aquatic eDNA sampling, extraction, and plant metabarcoding on Oxford Nanopore's Flongle platform.... | ["[Aquatic eDNA sampling]\nAssemble hose ends and drill pump and attach to wooden bracket with zip ties. Lock drill driver to pump spindle.", "[Aquatic eDNA sampling]\nAttach fresh, sterile 0.045 μm filter funnel assembly (Fisher Sci catalog #09 740 30K) to hose on the “In” side of the pump and tighten hose clamp. Be s... |
46,170 | Embedding and Cutting of Eye Tissue at UAB | 1 | dx.doi.org/10.17504/protocols.io.brb2m2qe | https://www.protocols.io/view/embedding-and-cutting-of-eye-tissue-at-uab-brb2m2qe | David Anderson, Jeffrey Messinger, Jamie Allen, Angela Kruse, Elizabeth Neumann, Nathan Heath Patterson, Richard Caprioli, Kevin Schey, Jeff Spraggins, Christine Curcio | TITLE: Embedding and Cutting of Eye Tissue at UAB
AUTHORS: David Anderson, Jeffrey Messinger, Jamie Allen, Angela Kruse, Elizabeth Neumann, Nathan Heath Patterson, Richard Caprioli, Kevin Schey, Jeff Spraggins, Christine Curcio
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">T... | ["Prior to embedding, the posterior pole is trimmed to a 14-mm-wide belt of retina, choroid, and sclera containing major landmarks to help orientation. This includes the optic nerve head, fovea, and horizontal meridian of the visuotopic map and extending anteriorly to pigmented tissue (ora serrata) at the edge of the ... |
94,800 | Long-read sequencing and data processing | 4 | dx.doi.org/10.17504/protocols.io.bp2l6x5pklqe/v1 | https://www.protocols.io/view/long-read-sequencing-and-data-processing-c8tqzwmw | Peter Kilfeather | TITLE: Long-read sequencing and data processing
AUTHORS: Peter Kilfeather
[DESCRIPTION]
Long-read sequencing and data processing methods from Kilfeather, Khoo et al., 2024
[STEPS]
SECTION: Protocol
1. Twelve TRAP samples and three TOTAL samples were sequenced using the Oxford Nanopore Technologies MinION platform. TR... | ["[Protocol] Twelve TRAP samples and three TOTAL samples were sequenced using the Oxford Nanopore Technologies MinION platform. TRAP samples were equally divided by age and genotype (N = 3 per age:genotype). Library preparation was performed using the cDNA-PCR kit (SQK-PCS109). Raw fast5 data was basecalled and demulti... |
68,277 | Post-Surgical Dissection of Uterine Body | 4 | dx.doi.org/10.17504/protocols.io.8epv59yb4g1b/v1 | https://www.protocols.io/view/post-surgical-dissection-of-uterine-body-cewvtfe6 | Stephen Fisher, Marielena Grijalva, Rong Guo, sarahjoh, Hieu Nguyen, John Renz, Jean G Rosario, Steven Rudich, Brian Gregory, Junhyong Kim, Kate O'Neill | TITLE: Post-Surgical Dissection of Uterine Body
AUTHORS: Stephen Fisher, Marielena Grijalva, Rong Guo, sarahjoh, Hieu Nguyen, John Renz, Jean G Rosario, Steven Rudich, Brian Gregory, Junhyong Kim, Kate O'Neill
[DESCRIPTION]
This protocol describes dissection of the uterine body in preparation for 10X Visium, 10X Multi... | ["Ensure you have a clean cutting surface and fresh, disposable surgical blades.", "Remove uterus from ice and dry it.", "Divide the cervix and uterus into halves in coronal or frontal place.", "Identify internal cervical os.", "Working on the anterior side of the uterine body, slice it into three horizontal sections f... |
91,909 | Janelia Atalanta series plasmid cloning | 4 | dx.doi.org/10.17504/protocols.io.bp2l6bjokgqe/v3 | https://www.protocols.io/view/janelia-atalanta-series-plasmid-cloning-c5zdy726 | David Stern | TITLE: Janelia Atalanta series plasmid cloning
AUTHORS: David Stern
[DESCRIPTION]
The Janelia Atalanta plasmids allows simple cloning of a gRNA and homology arms for CRISPR/Cas9 mediated homology directed repair in Drosophila. Gateway-compatible arms are synthesized with appropriate attL recognition sequences and homo... | ["[Make plasmid DNA] Transform the pJAT into ccdB Survival cells following the standard protocol. Plate cells on LB _ Ampicillin (100ug/mL) and grow at 37°C at least 15 hours.", "[Make plasmid DNA] Pick one colony and grow in 3mL LB + antibiotics. I normally grow in Ampicillin, but the plasmid encodes three antibiotic ... |
49,453 | Preparing Data for vContact from Proteins (Cyverse) | 1 | dx.doi.org/10.17504/protocols.io.buimnuc6 | https://www.protocols.io/view/preparing-data-for-vcontact-from-proteins-cyverse-buimnuc6 | Benjamin Bolduc | TITLE: Preparing Data for vContact from Proteins (Cyverse)
AUTHORS: Benjamin Bolduc
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Preparing data for use in vContact by using VirSorted </span><a href="https://github.com/MicroB3-IS/osd-analysis" style = "text-decoration:underline;color:blue;cu... | ["[Generating Gene-to-Genome Mapping]\nOpen vContact2-Gene2GenomeAfter we have the prodigal proteins file renamed, we can open \"vContact2-Gene2Genome\" from the \"Apps\" menu.", "[Generating Gene-to-Genome Mapping]\nSelect InputsUnder the 'Inputs' tab, select that renamed fileFor Proteins file:", "[Generating Gene-to-... |
null | null | null | dx.doi.org/10.17504/protocols.io.nsgdebw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This method is best used on colonies grown on solid media and subcultures in 7H9 liquid media. This method is high yeilding and is very efficient for short read NGS. It is not appropriate for direct tissue or fecal extraction. It is also not appropriate for liquid media conta... | [] |
82,330 | Immunohistochemistry on mouse brain sections | 3 | dx.doi.org/10.17504/protocols.io.261ge3yywl47/v1 | https://www.protocols.io/view/immunohistochemistry-on-mouse-brain-sections-cum2wu8e | Shiyi Wang | TITLE: Immunohistochemistry on mouse brain sections
AUTHORS: Shiyi Wang
[DESCRIPTION]
Immunohistochemistry on mouse brain sections
[STEPS] | [] |
39,668 | SOLUTION- 03 - Dextran solution 5% | 3 | dx.doi.org/10.17504/protocols.io.biyukfww | https://www.protocols.io/view/solution-03-dextran-solution-5-biyukfww | Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino | TITLE: SOLUTION- 03 - Dextran solution 5%
AUTHORS: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
[STEPS] | [] |
70,548 | Preparation of 1L of Foraging Medium | 4 | dx.doi.org/10.17504/protocols.io.bp2l69n3rlqe/v1 | https://www.protocols.io/view/preparation-of-1l-of-foraging-medium-cg5uty6w | Alfonso Pérez Escudero, Alid Al-Asmar, gabrielmadirolas | TITLE: Preparation of 1L of Foraging Medium
AUTHORS: Alfonso Pérez Escudero, Alid Al-Asmar, gabrielmadirolas
[DESCRIPTION]
Protocol is mainly inspired from: WormBook Methods http://www.wormbook.org/chapters/www_strainmaintain/strainmaintain.html.
This protocol is for making medium for foraging experiments with the wo... | ["In order to perform this protocol, you will need the following solutions:\n5 mg/mL cholesterol in absolute ethanol (stored in freezer)\npH=6 phosphate buffer (as prepared in: https://www.protocols.io/view/preparation-of-0-5l-of-phosphate-buffer-ph-6-0-n2bvj8r7bgk5/v1)\n1 M magnesium sulfate (as prepared in: https://w... |
75,106 | LEGACY01: REGULATORY ISSUES | 1 | null | https://www.protocols.io/view/legacy01-regulatory-issues-cmkau4se | Katrina M Pollock, Calliope Dendrou | TITLE: LEGACY01: REGULATORY ISSUES
AUTHORS: Katrina M Pollock, Calliope Dendrou
[DESCRIPTION]
This protocol details regulatory issues in an experimental medicine study of seasonal influenza vaccination responses in Lymph nodE single-cell Genomics in AnCestrY (LEGACY01).
[GUIDELINES]
ETHICS APPROVAL
The Study Coordin... | [] |
97,151 | Bulk RNAseq - University of Minnesota TMCs | 0 | dx.doi.org/10.17504/protocols.io.14egn6bypl5d/v1 | https://www.protocols.io/view/bulk-rnaseq-university-of-minnesota-tmcs-da472gzn | Laura J Niedernhofer, David A Bernlohr | TITLE: Bulk RNAseq - University of Minnesota TMCs
AUTHORS: Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
Bulk RNA sequencing is the method of choice for transcriptomic analysis of pooled cell populations, tissue sections, or biopsies. It measures the average expression level of individual genes across hundreds... | ["[Library Preparation] Sample Quality Assessment: Total eukaryotic RNA isolates are quantified using a fluorimetric RiboGreen assay. Total RNA integrity is assessed using capillary electrophoresis (e.g. Agilent BioAnalyzer 2100), generating an RNA Integrity Number (RIN). For samples to pass the initial QC step, they... |
null | null | null | dx.doi.org/10.17504/protocols.io.cunwvd | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?. | [] |
102,208 | Creating Simulated Synapse Images | 0 | dx.doi.org/10.17504/protocols.io.kxygxy7n4l8j/v1 | https://www.protocols.io/view/creating-simulated-synapse-images-df283qhw | Justin T Savage | TITLE: Creating Simulated Synapse Images
AUTHORS: Justin T Savage
[DESCRIPTION]
How to create simulated synapse images using FIJI.
[STEPS]
SECTION: Prepare images
1. Copy some synapse images into a folder to serve as a source of synaptic puncta. Example images are available on Zenodo at DOI: 10.5281/zenodo.1219180... | ["[Prepare images] Copy some synapse images into a folder to serve as a source of synaptic puncta. Example images are available on Zenodo at DOI: 10.5281/zenodo.12191805", "[Run ImageJ Macro] Open 20240312_sim_synapse_data_sparse.ijm from the SynBot GitHub by dragging it into FIJI", "[Prepare images] Set up a larger fo... |
22,887 | SPARC Adenosine 2A Receptor Immunohistochemistry Protocol in Rat Tissues Labeled with Cholera Toxin B-fragment | null | dx.doi.org/10.17504/protocols.io.2kfgctn | null | Elisa Gonzalez-Rothi, Yasin Seven, Latoya Allen, Marissa Ciesla, Gordon Mitchell | TITLE: SPARC Adenosine 2A Receptor Immunohistochemistry Protocol in Rat Tissues Labeled with Cholera Toxin B-fragment
AUTHORS: Elisa Gonzalez-Rothi, Yasin Seven, Latoya Allen, Marissa Ciesla, Gordon Mitchell
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the immunofluorescen... | ["Day 1: primary antibodies required:Adenosine 2A Receptor: Mouse anti-A2A (Millipore #05-717)Cholera toxin B-fragment: Goat anti-CT-B (Millipore #227040)", "Place 40um transverse spinal cord sections into 1xPBS-Triton (0.1%) in 12 well cell culture plates", "3x washes in 1xPBS-Triton (0.1%) for 5 minutes each at room... |
28,911 | Mycoplasma | 1 | dx.doi.org/10.17504/protocols.io.8gphtvn | https://www.protocols.io/view/mycoplasma-8gphtvn | Andrea Argouarch | TITLE: Mycoplasma
AUTHORS: Andrea Argouarch
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Detection of mycoplasma utilizing the bulldog-bio kit. Steps include, gDNA isolation from cells, nanodrop, PCR, and running an agarose gel to detect mycoplasma within a cell culture line. </div><div class = "... | ["[Nanodrop]\nItems to bring to nanodrop machine a. p2 pipette, p2 tips, pen, kimwipes, ice bucket b. Keep samples on ice\non ice", "[Nanodrop]\nOpen the NanoDrop 1000 software and select nucleic acid from the main menu", "[Nanodrop]\nClean the nanodrop pedestal with a kimwipe", "[Nanodrop]\nAdd 2 µl o... |
79,758 | NGS grade DNA isolation from plant | 4 | null | https://www.protocols.io/view/ngs-grade-dna-isolation-from-plant-cr5nv85e | Anurag Daware | TITLE: NGS grade DNA isolation from plant
AUTHORS: Anurag Daware
[DESCRIPTION]
NGS grade DNA isolation from plant (maize) leaf tissue
[STEPS]
SECTION: Steps
1. Pre-heat water baths (65°C and 37°C) before beginning the extraction
SECTION: Steps
2. Prepare the extraction buffer as follows:
5 mL 1 M Tris, pH 8 (final... | ["[Steps] Pre-heat water baths (65°C and 37°C) before beginning the extraction", "[Steps] Prepare the extraction buffer as follows: \n\n5 mL 1 M Tris, pH 8 (final conc. 100 mM) \n2.5 mL 0.5 M EDTA (final conc. 25 mM) \n2.5 mL 5 M NaCl (final conc. 250 mM) \n0.5 g PVP-40 (final conc. 1% w/v)\n40 mL Water", "[Steps] Grin... |
34,086 | DAB Staining of FFPE Slides | null | dx.doi.org/10.17504/protocols.io.bdiei4be | null | Jerelyn Nick, Franchesca Farris, Marda Jorgensen | TITLE: DAB Staining of FFPE Slides
AUTHORS: Jerelyn Nick, Franchesca Farris, Marda Jorgensen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Standard IHC staining, such as this DAB protocol, is included in the validation of new antibodies at the University of Florida Tissue Mapping Center, TMC-Flori... | ["[Day 1 Prepare Slides for staining]\nDe-paraffinize and rehydrate slides.Place slides in a xylene-compatible rack.", "[Day 1 Prepare Slides for staining]\nImmerse slide holder in first xylene station for 5 minutes.", "[Day 1 Prepare Slides for staining]\nImmerse slide holder in second xylene station for 5 minutes.",... |
99,259 | Performance of five dynamic models in predicting tuberculosis incidence in three prisons in Thailand | 0 | dx.doi.org/10.17504/protocols.io.n92ld8z8xv5b/v1 | https://www.protocols.io/view/performance-of-five-dynamic-models-in-predicting-t-dc632zgn | Nithinan Mahawan, Wiroj Jiamjarasrangsi, Thanapoom Rattananupong, Puchong Sri-Uam | TITLE: Performance of five dynamic models in predicting tuberculosis incidence in three prisons in Thailand
AUTHORS: Nithinan Mahawan, Wiroj Jiamjarasrangsi, Thanapoom Rattananupong, Puchong Sri-Uam
[DESCRIPTION]
This study examined the ability of the following five dynamic models for predicting pulmonary tuberculosis... | ["[Exposure assessment] Baseline risk assessment of TB transmission was conducted for each cell based on each of the five dynamic models: the classic Wells–Riley equation, Rudnick & Milton’s, and Issarow et al.’s modified Wells–Riley equations, and the applied SEIR model. The detailed procedure has been described previ... |
64,141 | BTI mobile plant phenotyping system: PhenoRig and PhenoCage construction | 1 | dx.doi.org/10.17504/protocols.io.3byl4b1wrvo5/v1 | https://www.protocols.io/view/bti-mobile-plant-phenotyping-system-phenorig-and-p-cavmse46 | Li'ang Yu, Magdalena M Julkowska | TITLE: BTI mobile plant phenotyping system: PhenoRig and PhenoCage construction
AUTHORS: Li'ang Yu, Magdalena M Julkowska
[DESCRIPTION]
Phenotyping Infrastructures are the basis to enable productive data collection and management. Here - we describe how we constructed the PhenoRig and PhenoCage, the two cost-effecti... | ["[Overview] This protocol is a part of BTI mobile plant phenotyping system (https://github.com/Leon-Yu0320/BTI-Plant-phenotyping). In this part, we'll introduce constructing a set of lightweight phenotyping facilities paired with the phenotying computational pipelines we developed.", "[Materials] Construction of pheno... |
49,724 | Titan Illumina PE SARS-CoV-2 Strain Characterization Workflow for the Terra Platform | 5 | null | https://www.protocols.io/view/titan-illumina-pe-sars-cov-2-strain-characterizati-bus4nwgw | Jill V Hagey, Kevin Libuit, Frank J Ambrosio, Technical Outreach and Assistance for States Team | TITLE: Titan Illumina PE SARS-CoV-2 Strain Characterization Workflow for the Terra Platform
AUTHORS: Jill V Hagey, Kevin Libuit, Frank J Ambrosio, Technical Outreach and Assistance for States Team
[DESCRIPTION]
The Titan_Illumina_PE workflow is a part of the Public Health Viral Genomics Titan series for SARS-CoV-2 g... | ["[Setup Terra and Google Cloud Accounts]", "[Import Titan Illumina PE workflow from Dockstore] Importing the Titan Workflow from Dockstore to the User Workspace\n\nWe will first walk through step by step how to import the Titan workflow and at the end there is a video showing the full process.\n\nFirst create a new wo... |
58,763 | Protocol for counting pathogen spores on hemocytometer | 3 | null | https://www.protocols.io/view/protocol-for-counting-pathogen-spores-on-hemocytom-b5mjq44n | Meghan Duffy | TITLE: Protocol for counting pathogen spores on hemocytometer
AUTHORS: Meghan Duffy
[DESCRIPTION]
This is a protocol to quantify the number of pathogen spores you have in a sample using a hemocytometer.
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.dyb7sm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
An alternate version to the protocol "<a href="https://www.protocols.io/private/2096bf1717edac7e2f89155c2fb3779a" target="_blank">Simultaneous measurement of grazing and viral lysis of phytoplankton v1</a>"
[GUIDELINES]
<em><strong>Sampling and physicochemical variables<br /><b... | [] |
34,861 | UF H&E Staining | null | dx.doi.org/10.17504/protocols.io.beamjac6 | null | Marda Jorgensen, Franchesca Farris | TITLE: UF H&E Staining
AUTHORS: Marda Jorgensen, Franchesca Farris
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Hematoxylin and Eosin stains are the prefered method for histopathologic assessment of tissue sections.</div><div class = "text-block">Hematoxylin is used to illustrate nuclear detail i... | ["Prepare staining line with reagents in order of use, based on steps three through 25.", "Place slides into a xylene compatible slide rack.", "Immerse slide holder in the first xylene staining station for 5 minutes.", "Immerse slide holder in the second xylene staining station for 5 minutes.", "Remove slide holder fro... |
29,588 | Transmission electron microscopy protocol for anaerobic ciliates | null | dx.doi.org/10.17504/protocols.io.85uhy6w | null | Johana Rotterova, Ivan Čepička | TITLE: Transmission electron microscopy protocol for anaerobic ciliates
AUTHORS: Johana Rotterova, Ivan Čepička
[STEPS]
?. [Fixation]
Isolate 1 ml of thriving culture of ciliate cells, fix with 2.5% (v/v) glutaraldehyde (Polysciences) and subsequently centrifuge at 800×g for 5 min at 4 °C.
?. [Fixation]
Carefully repl... | ["[Fixation]\nIsolate 1 ml of thriving culture of ciliate cells, fix with 2.5% (v/v) glutaraldehyde (Polysciences) and subsequently centrifuge at 800×g for 5 min at 4 °C.", "[Fixation]\nCarefully replace supernatant with 1 ml of 2.5% (v/v) glutaraldehyde in 0.2M SCB (Sodium Cacodylate buffer, pH 7.2) and incubate 1 hou... |
25,008 | NEBNext Ultra II Ligation Module (NEB # E7595) for NEBNext Ultra II End Repair/dA Tailing Module (NEB #E7546) | null | dx.doi.org/10.17504/protocols.io.4nqgvdw | null | New England Biolabs, Menna Teffera | TITLE: NEBNext Ultra II Ligation Module (NEB # E7595) for NEBNext Ultra II End Repair/dA Tailing Module (NEB #E7546)
AUTHORS: New England Biolabs, Menna Teffera
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This module is part of the Ultra™ II workflow, and is optimized for use with the NEB... | ["[Ligation/End Prep]\nAdd the following products directly to the End Prep Reaction Mixture: AB1ComponentVolume2End Prep Reaction Mixture60 µl3(red) NEBNext Ultra II Ligation Master Mix*30 µl4(red) NEBNext Ligation Enhancer1 µl5(red) NEBNext Adaptor for Illumina**2.5 µl6Total Volume93.5 µl* Mix the Ultra II Ligation M... |
105,260 | SARS-CoV-2 nsp3 macrodomain Time-Resolved FRET peptide displacement assay | 1 | dx.doi.org/10.17504/protocols.io.eq2ly7r2mlx9/v4 | https://www.protocols.io/view/sars-cov-2-nsp3-macrodomain-time-resolved-fret-pep-di2k4gcw | Haim Barr, Noa Lahav | TITLE: SARS-CoV-2 nsp3 macrodomain Time-Resolved FRET peptide displacement assay
AUTHORS: Haim Barr, Noa Lahav
[DESCRIPTION]
This protocol details the Time-Resolved FRET (TR-FRET) assay for SARS-CoV-2 nsp3 macrodomain (Mac1) binding of adenosine diphosphate (ADP)–ribosylated (ADPr) peptide. This method measures the af... | ["[Prepare Reagents] PREPARE all of the reagents/buffers required for this experiment.\n\n Assay Buffer\n \n Reagents (dilute reagents in assay buffer for required volume)\n \nDetection Solution (dilute reagents in assay buffer for required volume)", "[Prepare 384-well Plate] PRIME Multi-Drop Combi Tube Dispensing Cass... |
92,429 | GGAssmbler Library Construction | 1 | dx.doi.org/10.17504/protocols.io.81wgbxqkolpk/v3 | https://www.protocols.io/view/ggassmbler-library-construction-c6hmzb46 | Shlomo Yakir Hoch, Ravit Netzer, Lucas Krauss, Karen Hakeny, Sarel J Fleishman | TITLE: GGAssmbler Library Construction
AUTHORS: Shlomo Yakir Hoch, Ravit Netzer, Lucas Krauss, Karen Hakeny, Sarel J Fleishman
[DESCRIPTION]
This protocol describes methods for GGAssembler.
[BEFORE_START]
Please note that protocols with Q5® High-Fidelity DNA Polymerase may differ from protocols with other polymerases... | ["[Amplify constant fragments] Set up the following reaction on ice:", "[Amplify constant fragments] Gently mix the reaction.", "[Amplify constant fragments] Collect all liquid to the bottom of the tube by a quick spin if necessary.", "[Amplify constant fragments] Quickly transfer PCR tubes to a PCR machine preheated t... |
null | null | null | dx.doi.org/10.17504/protocols.io.p4ydqxw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A protocol for generating single colonies of Emiliania huxleyi embedded in soft-agarose. </p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
18,665 | Cleaning up a biohazardous spill in a biosafety cabinet | null | dx.doi.org/10.17504/protocols.io.wghfbt6 | null | Steven Wilhelm, Gary LeCleir, Ashley Humphrey | TITLE: Cleaning up a biohazardous spill in a biosafety cabinet
AUTHORS: Steven Wilhelm, Gary LeCleir, Ashley Humphrey
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">BIOLOGICAL SPILL RESPONSE </span><span>method to be used in the event of a biosafety incident. </spa... | ["Let the BSC run. Do not turn off.", "Remove broken glass with forceps, tweezers or other tools and place glass in a sharps container. Do not wipe up broken glass.", "Cover spill with paper towels.", "Pour (don’t spray) disinfectant to contaminated surface by pouring it around the periphery of the covered spill movin... |
75,752 | RootBot Image Scoring Instructions | 5 | null | https://www.protocols.io/view/rootbot-image-scoring-instructions-cm8gu9tw | Mia Ruppel, Sven K. Nelson, Grace Sidberry, Madison Mitchell, Daniel Kick, Shawn K. Thomas, Katherine E. Guill, Melvin J. Oliver, Jacob D. Washburn | TITLE: RootBot Image Scoring Instructions
AUTHORS: Mia Ruppel, Sven K. Nelson, Grace Sidberry, Madison Mitchell, Daniel Kick, Shawn K. Thomas, Katherine E. Guill, Melvin J. Oliver, Jacob D. Washburn
[DESCRIPTION]
Instruction for scoring RootBot images.
[STEPS]
SECTION: Installation and setup
1. Download and install I... | ["[Installation and setup] Download and install Image J (https://imagej.net/software/fiji/downloads)", "[Installation and setup] Download the Smart Root Explorer plugin by following the website instructions\na) Website - https://smartroot.github.io/SmartRoot-Installation/\nb) Instructions - on the SR Explorer website c... |
36,439 | The future of feedback: Motivating performance improvement through future-focused feedback --Study 3 | null | dx.doi.org/10.17504/protocols.io.bftxjnpn | https://www.protocols.io/view/the-future-of-feedback-motivating-performance-impr-bftxjnpn | Jackie Gnepp, Joshua Klayman, Ian O. Williamson, Sema Barlas | TITLE: The future of feedback: Motivating performance improvement through future-focused feedback --Study 3
AUTHORS: Jackie Gnepp, Joshua Klayman, Ian O. Williamson, Sema Barlas
[STEPS]
?. The procedure is essentially the same as in Study 2, post-only group. The differences are that (a) there is an additional page of... | ["The procedure is essentially the same as in Study 2, post-only group. The differences are that (a) there is an additional page of instructions (two versions, for which the results did not differ significantly), which is intended to focus the participants on the goal of promoting improved performance, and (b) the pos... |
23,631 | In Vitro Transcription for dgRNA | null | dx.doi.org/10.17504/protocols.io.3bpgimn | null | Amy Lyden, Emily Crawford, Jenai Quan, Saharai Caldera, Lara Pesce-Ares | TITLE: In Vitro Transcription for dgRNA
AUTHORS: Amy Lyden, Emily Crawford, Jenai Quan, Saharai Caldera, Lara Pesce-Ares
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">For FLASH, DASH, and other CRISPR-cas9 protocols, we use T7 to transcribe our crRNA and tracrRNA to make dgRNA for cas9. It is more... | ["[Annealing T7 to crRNA and tracrRNA template]\nPool your crRNA in equimolar amounts. Usually, we order 96-well plates of 96 crRNA templates from IDT, with the oligos diluted in water at a concentration of 10µM", "[Annealing T7 to crRNA and tracrRNA template]\nAdd an equimolar amount of T7 primer to your crRNA pool. F... |
21,838 | Hepatotoxicity during 6-thioguanine treatment: protocol for a systematic review | null | dx.doi.org/10.17504/protocols.io.zjnf4me | null | Linea Natalie Toksvang, Rikke Hebo Larsen, Thomas Leth Frandsen, Kjeld Schmiegelow, Cecilie Utke Rank | TITLE: Hepatotoxicity during 6-thioguanine treatment: protocol for a systematic review
AUTHORS: Linea Natalie Toksvang, Rikke Hebo Larsen, Thomas Leth Frandsen, Kjeld Schmiegelow, Cecilie Utke Rank
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify">He... | [] |
28,885 | Transformation and Preparation of Chemically Competent Bacillus subtilis cells | null | dx.doi.org/10.17504/protocols.io.8fvhtn6 | null | iGEM Dusseldorf | TITLE: Transformation and Preparation of Chemically Competent Bacillus subtilis cells
AUTHORS: iGEM Dusseldorf
[STEPS]
?. [Preparation of Chemically Competent Bacillus subtilis cells]
For 20 ml or 50 ml PARIS-Medium mix: ABCD1final concentrationStockfor 50 mlfor 20 ml2100 mM potassium phosphate buffer pH 7.0360 mM K2... | ["[Preparation of Chemically Competent Bacillus subtilis cells]\nFor 20 ml or 50 ml PARIS-Medium mix: ABCD1final concentrationStockfor 50 mlfor 20 ml2100 mM potassium phosphate buffer pH 7.0360 mM K2HPO41 M (3.48 g in 20 ml for stock)3 ml1.2 ml440 mM KH2PO40.5 M (1.36 g in 20 ml for stock)4 ml1.6 ml53 mM trisodium cit... |
37,333 | Stereotaxic Surgery for Delivery of Tracers by Iontophoresis | null | dx.doi.org/10.17504/protocols.io.bgpvjvn6 | https://www.protocols.io/view/stereotaxic-surgery-for-delivery-of-tracers-by-ion-bgpvjvn6 | Allen Institute for Brain Science | TITLE: Stereotaxic Surgery for Delivery of Tracers by Iontophoresis
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the delivery of a neuronal tracer using the iontophoretic method. The surgery uses a stereotaxic system to target spe... | [] |
45,587 | Eurotransplant Kidney Allocation Simulations | 5 | dx.doi.org/10.17504/protocols.io.bqrtmv6n | https://www.protocols.io/view/eurotransplant-kidney-allocation-simulations-bqrtmv6n | Matthias Niemann, Nils Lachmann, Kirsten Geneugelijk, Eric Spierings | TITLE: Eurotransplant Kidney Allocation Simulations
AUTHORS: Matthias Niemann, Nils Lachmann, Kirsten Geneugelijk, Eric Spierings
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify">Background:</div><style>
.justify:after {
content:... | ["[Data aquisition]\nCollect demographic data from Eurotransplant Annual Report pageage distribution per countrydonor blood group distribution per countryrecipient blood group distribution per country on the initial waiting listnumber of DBD donors per country number of DCD donors per countryDBD/DCD acceptance matrix, ... |
86,988 | Protocol to isolate and cryopreserve fresh mouse PBMCs | 4 | null | https://www.protocols.io/view/protocol-to-isolate-and-cryopreserve-fresh-mouse-p-cy7kxzkw | Elisabeth Rebboah | TITLE: Protocol to isolate and cryopreserve fresh mouse PBMCs
AUTHORS: Elisabeth Rebboah
[DESCRIPTION]
This protocol describes isolation of cells from adult mouse PBMCs, preparation of a single cell suspension, and cryopreservation. This protocol takes about 3 hours from start to finish.
The results are approximately... | ["[Setup] Set centrifuge to 19C.", "[Setup] Prepare 1 ice bucket.", "[Setup] Thaw and filter FBS with a cell culture filter unit and aliquot into 50 mL conical tubes.", "[Setup] Prepare PBS-EDTA by adding EDTA powder to PBS and filter with a cell culture filter unit. 500 mL of PBS-EDTA should be enough for around 16 sa... |
50,242 | Determination of the lipid composition of the GPI anchor | 4 | dx.doi.org/10.17504/protocols.io.bvban2ie | https://www.protocols.io/view/determination-of-the-lipid-composition-of-the-gpi-bvban2ie | Auxiliadora Aguilera-Romero †, Susana Sabido-Bozo †, Sergio Lopez, Alejandro Cortes-Garcia, Sofia Rodriguez-Gallardo, Ana Maria Perez-Linero, Isabelle Riezman, Howard Riezman, Manuel Muñiz | TITLE: Determination of the lipid composition of the GPI anchor
AUTHORS: Auxiliadora Aguilera-Romero †, Susana Sabido-Bozo †, Sergio Lopez, Alejandro Cortes-Garcia, Sofia Rodriguez-Gallardo, Ana Maria Perez-Linero, Isabelle Riezman, Howard Riezman, Manuel Muñiz
[DESCRIPTION]
<div class = "text-blocks"><div class = "te... | ["[Yeast growth and culture]\nTransform the yeast strain with a centromeric plasmid expressing GFP-tagged Gas1p under control of its own promoter (pRS416-GAS1-GFP).", "[Yeast growth and culture]\nPick up a colony and streak it on a SD agar plate with appropriate nutritional supplements (SC-URA) and incubate them at 24 ... |
45,720 | PCR-RFLP protocols for genotyping VEGF-A rs28357093 | 1 | dx.doi.org/10.17504/protocols.io.bqvymw7w | https://www.protocols.io/view/pcr-rflp-protocols-for-genotyping-vegf-a-rs2835709-bqvymw7w | Caroline Christine Pincela da Costa , Nayane Soares de Lima, Rodrigo da Silva Santos, Angela Adamski da Silva Reis | TITLE: PCR-RFLP protocols for genotyping VEGF-A rs28357093
AUTHORS: Caroline Christine Pincela da Costa , Nayane Soares de Lima, Rodrigo da Silva Santos, Angela Adamski da Silva Reis
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left"><span> T... | ["[PCR amplification of the VEGF-A rs28357093 locus]\nAmplication by conventional PCR using the primer sequences (Please, check note box in the end of this section for primer paper reference):Forward: 5′ - CCC CTG CCC CCT TCA ATA -3'Reverse: 5’- AGC CTC AGC CCC TCC ACA -3’ Master mix for reactions are sufficient for ... |
74,131 | Measurement of biogenic silica from plankton | 6 | dx.doi.org/10.17504/protocols.io.8epv5jjzjl1b/v2 | https://www.protocols.io/view/measurement-of-biogenic-silica-from-plankton-ckmtuu6n | Ying-Yu Hu, Nuwanthi Samarasinghe, Zoe V. Finkel | TITLE: Measurement of biogenic silica from plankton
AUTHORS: Ying-Yu Hu, Nuwanthi Samarasinghe, Zoe V. Finkel
[DESCRIPTION]
Here, we present a method for measuring biogenic silica from plankton. Biogenic silica is digested using a wet-alkaline method, in which 2 M sodium carbonate is used to hydrate and depolymerize a... | ["[Sample collection] Estimation:\nThe low limit of detection is approximately 0.6 uM silicate in the molybdate method. For siliceous plankton, sample requires no less than 4 ug PON (particulate organic nitrogen) per filter when using a 50 mL volumetric flask, or 2 ug PON per filter when using a 25 mL volumetric flask.... |
54,350 | Consistency in Identity Related Sequential Decisions | 2 | null | https://www.protocols.io/view/consistency-in-identity-related-sequential-decisio-bzbnp2me | Dikla Perez, Yael Steinhart, Amir Grinstein, Meike Morren | TITLE: Consistency in Identity Related Sequential Decisions
AUTHORS: Dikla Perez, Yael Steinhart, Amir Grinstein, Meike Morren
[DESCRIPTION]
We conducted four lab and online experiments, and a field experiment to test our hypotheses and to rule out an alternative explanation. The design of each of the five experimen... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.n97dh9n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes how to prepare a 100x BG-11 +N stock.</p>
<p>1x BG-11 media could be created from the stock and supplemental stocks and trace metals could be added afterwards.</p>
<p>This protocol is based on Anne Behle M.Sc. <a href="https://www.protocols.io/view/rec... | [] |
55,411 | Total DNA extraction from microalgae strain samples using NucleoSpin Plant modified kit (Macherey Nagel) | 4 | dx.doi.org/10.17504/protocols.io.b2ctqawn | https://www.protocols.io/view/total-dna-extraction-from-microalgae-strain-sample-b2ctqawn | Sarah Romac | TITLE: Total DNA extraction from microalgae strain samples using NucleoSpin Plant modified kit (Macherey Nagel)
AUTHORS: Sarah Romac
[DESCRIPTION]
This DNA extraction protocol allows to get both eukaryotic and prokaryotic DNA from microalgae strains, so the microbiome diversity can be studied in cultures by using thi... | ["[Cell Lysis] Transfer 2mL from the strain in a sterile 2mL microtube.\nCentrifuge 5 min at 5000g to pellet the strain.\nDiscard the supernatant.\nPellet are ready for extraction or can stored at -20°C until extraction.", "[Cell Lysis] Add 400µL PL1 + 25µL proteinase K 20 mg/mL.\nVortex.\n\nIf you don't need to extrac... |
92,334 | Patient PBMC differentiation to macrophages | 4 | dx.doi.org/10.17504/protocols.io.6qpvr3w83vmk/v1 | https://www.protocols.io/view/patient-pbmc-differentiation-to-macrophages-c6enzbde | Rebecca Wallings | TITLE: Patient PBMC differentiation to macrophages
AUTHORS: Rebecca Wallings
[DESCRIPTION]
Patient PBMC differentiation to macrophages
[STEPS]
1. After cryorecovery, plate PBMCs at a final concentration of 3 x 106/mL in a poly-D-lysine coated, 96-well plate, resulting in 3x105 cells per well.
Incubate PBMCs at 37°... | ["After cryorecovery, plate PBMCs at a final concentration of 3 x 106/mL in a poly-D-lysine coated, 96-well plate, resulting in 3x105 cells per well. \n\nIncubate PBMCs at 37°C for 2-hours to allow adherent cells to adhere. \n\nWash cells washed 2 x sterile PBS to wash off non-adherent cells, and incubate in growth me... |
20,947 | UC Davis - IN-VIVO Glucose-stimulates Insulin Secretion Test | null | dx.doi.org/10.17504/protocols.io.yptfvnn | null | Fawaz G. Haj | TITLE: UC Davis - IN-VIVO Glucose-stimulates Insulin Secretion Test
AUTHORS: Fawaz G. Haj
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">
An in-vivo glucose-stimulates insulin secretion test is designated to determine ... | ["Fast mice for 16 hours by taking away food the day before (3:00pm)", "The following day, Calibrate the glucose meter according to the manufacturer’s instructions.", "Deprive mice from water then measure blood glucose level using a glucometer and remove immediately approximately 50 μl of blood from the tail via a tail... |
49,895 | Artisanal Production of Prefusion-Stabilized SARS-CoV-2 Spikes | 4 | dx.doi.org/10.17504/protocols.io.buyfnxtn | https://www.protocols.io/view/artisanal-production-of-prefusion-stabilized-sars-buyfnxtn | Jean-Francois Rivest, Claudia Goupil, Yannick Doyon | TITLE: Artisanal Production of Prefusion-Stabilized SARS-CoV-2 Spikes
AUTHORS: Jean-Francois Rivest, Claudia Goupil, Yannick Doyon
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">The two-part protocol presented here describes the establishment of a stable pool of 29... | ["[Thawing and general handling of 293-F cells before transfection (Timing: 11 days)]\nBefore thawing the cells, prewarm 30 ml of FreeStyle 293 Expression Medium in a 250 ml tissue culture shaker flask at 37°C, preferably in a humidified atmosphere with 8% CO2. Also, prewarm a 9 ml aliquot of culture medium at 37°C in ... |
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