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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59,931 | Volume Electron Microscopy Protocol for the ASP-1000 | 1 | dx.doi.org/10.17504/protocols.io.q26g74mr8gwz/v1 | https://www.protocols.io/view/volume-electron-microscopy-protocol-for-the-asp-10-b6r3rd8n | Erin S Stempinski, Jessica Riesterer, Steven Adamou, Claudia S Lopez | TITLE: Volume Electron Microscopy Protocol for the ASP-1000
AUTHORS: Erin S Stempinski, Jessica Riesterer, Steven Adamou, Claudia S Lopez
[DESCRIPTION]
Volume electron microscopy (vEM) requires a multitude of heavy metal stains to ensure adequate sample contrast and conductivity under the electron beam. Bench proto... | ["[Prepare reagents and accessories] Prepare the reagents in the concentrations outlined in the materials section.\n\nFreshly prepare day-of:\nOsmium tetroxide (OsO4) solutions if from aqueous vials\n1% w/v thiocarbohydrazide (TCH), aqueous - requires 1 hour to dissolve at 60°C, swirling every 10 minutes.\nEMBed812 re... |
55,942 | Test protocol II | 1 | null | https://www.protocols.io/view/test-protocol-ii-b2veqe3e | Abby Moore | TITLE: Test protocol II
AUTHORS: Abby Moore
[DESCRIPTION]
This is a test protocol
Here's an protocol reference:
Here's a citation:
[BEFORE_START]
This is what you should know before you start
[GUIDELINES]
Responsibilities....
[STEPS]
1. Use 80:20 MeOH:H2O for this step. This is not easy to access... | ["Use 80:20 MeOH:H2O for this step. This is not easy to access by machine.", "If you haven't already, make a solution with the following components:\n\n80 % volume \n20 % volume", "If you haven't already, make a solution with the following components:\n\n80 % volume \n20 % volume", "Use this piece of equipment:", "... |
18,995 | Protocol of data recording for the recognition of familiar speech in the presence of competitive noise | null | dx.doi.org/10.17504/protocols.io.wstfeen | null | Kelly Andrade, Thamyres Ataíde Bezerra Verçosa, Aline Tenório Lins Carnaúba, Pedro Menezes | TITLE: Protocol of data recording for the recognition of familiar speech in the presence of competitive noise
AUTHORS: Kelly Andrade, Thamyres Ataíde Bezerra Verçosa, Aline Tenório Lins Carnaúba, Pedro Menezes
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for data collection of speech rec... | [] |
78,988 | Fecobionics Test in Normal Subjects | 1 | dx.doi.org/10.17504/protocols.io.5qpvor1ybv4o/v1 | https://www.protocols.io/view/fecobionics-test-in-normal-subjects-crdkv24w | Yanmin Wang, Hans Gregersen | TITLE: Fecobionics Test in Normal Subjects
AUTHORS: Yanmin Wang, Hans Gregersen
[DESCRIPTION]
It is the protocol of Fecobionics test in normal subjects. Briefly, the device will be inserted into participants' rectum and several motions (cough, squeeze, straining, push) will be done. After the motions, the bag will be... | ["Make sure the participant is eligible to do the study, and make sure he/she understands the study and has signed the informed consent form.", "Ask the subject to empty bladder and rectum before the test.", "Participant changes clothes and lies on left side.", "Calibrate the Fecobionics device and make sure the transm... |
93,238 | DAT-TRAP Protocol | 4 | dx.doi.org/10.17504/protocols.io.6qpvr4eo2gmk/v2 | https://www.protocols.io/view/dat-trap-protocol-c7awzife | Peter Kilfeather | TITLE: DAT-TRAP Protocol
AUTHORS: Peter Kilfeather
[DESCRIPTION]
This protocol describes the capture of eGFP-L10a-tagged ribosomes and mRNA from DAT-expressing cells in mouse ventral midbrain.
[GUIDELINES]
Prepare all reagents under RNAse-free conditions, preferably with the use of a PCR hood.
[STEPS]
SECTION: Tissu... | ["[Tissue Collection] Prepare all dissection instruments and collection tubes on ice. Set a refrigerated centrifuge to 4 °C. Be prepared to work swiftly, to minimise changes in translation occurring after death. Collection materials should be prepared in an RNase-free manner, to minimise the risk of sample degradation.... |
94,220 | selSeq: A method for the enrichment of non-polyadenylated RNAs including enhancer and long non-coding RNAs for sequencing | 4 | dx.doi.org/10.17504/protocols.io.j8nlkwpk6l5r/v2 | https://www.protocols.io/view/selseq-a-method-for-the-enrichment-of-non-polyaden-c79kzr4w | Jason D Limberis, Joel Ernst, John Metcalfe, Alina Nalyvayko | TITLE: selSeq: A method for the enrichment of non-polyadenylated RNAs including enhancer and long non-coding RNAs for sequencing
AUTHORS: Jason D Limberis, Joel Ernst, John Metcalfe, Alina Nalyvayko
[DESCRIPTION]
Non-polyadenylated RNA includes a large subset of crucial regulators of RNA expression and constitutes a s... | ["[poly-A tailed cDNA synthesis] Mix the following in a 0.2ml tube\n COMPONENT Volume Total RNA 1 Oligo dTs 1.5 10 mM dNTP 1.5 Nuclease-free H2O 10", "[poly-A tailed cDNA synthesis] Spin tube briefly and add the following and mix by pipetting\n COMPON... |
98,098 | Primer design using NIH's Primer-BLAST tool. | 0 | dx.doi.org/10.17504/protocols.io.rm7vzj8j5lx1/v1 | https://www.protocols.io/view/primer-design-using-nih-39-s-primer-blast-tool-db2s2qee | Pedro C. Díaz, Francisco Franco García Calderon | TITLE: Primer design using NIH's Primer-BLAST tool.
AUTHORS: Pedro C. Díaz, Francisco Franco García Calderon
[DESCRIPTION]
This protocol demonstrates the basic usage of the Primer-BLAST tool in order to design PCR primers from a given FASTA sequence.
The results should show the sequence of at least one pair of pri... | ["[Go to NIH's Primer-BLAST tool] Open your internet browser (Google Chrome recommended).", "[Go to NIH's Primer-BLAST tool] Go to https://www.ncbi.nlm.nih.gov/tools/primer-blast/", "[Enter FASTA sequence] Copy and paste your FASTA sequence in the text box or upload a FASTA file using the ¨Choose File¨ button... |
100,855 | NCBI submission protocol for HPAI milk surveillance | 1 | dx.doi.org/10.17504/protocols.io.q26g711b1gwz/v1 | https://www.protocols.io/view/ncbi-submission-protocol-for-hpai-milk-surveillanc-deqx3dxn | Ruth Timme | TITLE: NCBI submission protocol for HPAI milk surveillance
AUTHORS: Ruth Timme
[DESCRIPTION]
PURPOSE: This DRAFT protocol provides detailed instructions on how to submit raw targeted amplicon sequence data and associated contextual data of H5N1 to NCBI. The protocol includes essential steps to create a new NCBI submi... | ["[Establish submission environment at NCBI] Set up a new NCBI submission environment for your lab:\n\n1.1: Create an NCBI user account\n1.2: Set up an NCBI submission user group for your lab\n1.4: Bookmark the link to your submission portal\n1.5. Identify or establish new BioProjects (detailed in Step 3)\n\n\nReady fo... |
28,233 | Tail Flick | null | dx.doi.org/10.17504/protocols.io.7thhnj6 | null | Eva Feldman | TITLE: Tail Flick
AUTHORS: Eva Feldman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">The Tail Flick assay is a pain receptive assay in which a mouse is placed within a restraining tube with its tail protruding. The t... | ["Setup:− Must clean equipment with sporeklenz before entering the animal room − All restrainers need to be exclusively used in same room. If restrainer has been in another animal room, it CANNOT be used!− Never remove cable from test head or back of tail flick machine when it is on. Failure to pay attention may damage... |
62,998 | Gemini Keto Gummies Where To Buy | 1 | dx.doi.org/10.17504/protocols.io.rm7vzy1k4lx1/v1 | https://www.protocols.io/view/gemini-keto-gummies-where-to-buy-b9rwr57e | finnbalorsz | TITLE: Gemini Keto Gummies Where To Buy
AUTHORS: finnbalorsz
[DESCRIPTION]
Gemini Keto Gummies
is a highly remarkable weight loss supplement that works with a simple formula to remove all the stubborn fat from your body. This product works quite differently from any other supplement. As it lets a person lose weight ... | ["[Gemini Keto Gummies Where To Buy]"] |
20,117 | U Mass - Cytokines Panel II - multiplex | null | dx.doi.org/10.17504/protocols.io.xvvfn66 | null | Jason Kim | TITLE: U Mass - Cytokines Panel II - multiplex
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">
This experiment provides the quantification of multiple cytokines and chemokines using multiplexed-Lumin... | ["Add 200 μL of Wash Buffer into each well of the plate. Seal and mix on a plate shaker for 10 minutes at room temperature (20-25°C).", "Decant Wash Buffer and remove the residual amount from all wells by inverting the plate and tapping it smartly onto absorbent towels several times.", "Add 25 μL of each Standard or Co... |
28,606 | DNA Clean & Concentrator | null | dx.doi.org/10.17504/protocols.io.766hrhe | null | iGEM Dusseldorf | TITLE: DNA Clean & Concentrator
AUTHORS: iGEM Dusseldorf
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><ul style = "list-style-type:disc;"><li style = "counter-reset:ol0;list-style-type:disc;">Plasmid DNA</li><li style = "counter-reset:ol0;list-style-type:disc;">Binding Buffer </li><li style = "c... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.dh438v | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Add an equal volume of Solution B to Solution A in the hood.<br />Cover bottle with aluminum foil to reduce light exposure.<br />Remake every month.
[STEPS] | [] |
40,291 | Competitive ELISA to study the inhibition of the SpA- binding to Ab-3 by Ab-2. | 6 | dx.doi.org/10.17504/protocols.io.bjkbkksn | https://www.protocols.io/view/competitive-elisa-to-study-the-inhibition-of-the-s-bjkbkksn | Angel Justiz-Vaillant | TITLE: Competitive ELISA to study the inhibition of the SpA- binding to Ab-3 by Ab-2.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This immunoassay tested the ability of anti-anti-SpA (Ab-2) to inhibit or interfere with the binding of anti-anti-anti-SpA (Ab-3) to t... | ["Prepare materials and ELISA buffer solutions and reagents.", "Pipette 53 μl of purified Ab-3 (100 μg/ml) mixed with 2.8 ml of coating buffer into each well.", "Incubate the microplate at 37°C for 4 hrs.", "Aspirate the contents of the wells.", "Fill each well with an appropriately diluted washing solution and aspira... |
90,826 | Proteomics :On-bead/in-solution digestion and phosphopeptide enrichment | 1 | dx.doi.org/10.17504/protocols.io.rm7vzx195gx1/v1 | https://www.protocols.io/view/proteomics-on-bead-in-solution-digestion-and-phosp-c4xiyxke | Leonardo A Parra-Rivas | TITLE: Proteomics :On-bead/in-solution digestion and phosphopeptide enrichment
AUTHORS: Leonardo A Parra-Rivas
[DESCRIPTION]
Proteomics :On-bead/in-solution digestion and phosphopeptide enrichment
[STEPS]
1. Protein digestion of GST samples was performed following published protocols
2.
Digestion buffer (50... | ["Protein digestion of GST samples was performed following published protocols", "Digestion buffer (50 mM NH4HCO3) was added to\nthe sample, followed by treatment with 1 mM dithiothreitol (DTT, Thermo\nScientific Cat#R0861) at room temperature for 30 min. Subsequently, 5 mM\niodoacetamide (IAA, Sigma Cat#I1149) was add... |
75,362 | DNA Barcoding Standard Operating Protocol, Plants and Lichens at RBGE, Sample Data | 1 | null | https://www.protocols.io/view/dna-barcoding-standard-operating-protocol-plants-a-cmuau6se | Laura L Forrest, David Bell, Michelle Hart | TITLE: DNA Barcoding Standard Operating Protocol, Plants and Lichens at RBGE, Sample Data
AUTHORS: Laura L Forrest, David Bell, Michelle Hart
[DESCRIPTION]
This is part of the collection DToL Taxon-specific Standard Operating Procedures for the Plant Working Group (protocols.io). The SOP collection contains guidance o... | [] |
71,515 | Native Barcoding | 1 | null | https://www.protocols.io/view/native-barcoding-ch33t8qn | Carlos Goller, Carly Sjogren | TITLE: Native Barcoding
AUTHORS: Carlos Goller, Carly Sjogren
[DESCRIPTION]
This protocol describes how to carry out native barcoding of genomic DNA using the Native Barcoding Kit 24 (SQK-NBD112.24). There are 24 unique barcodes available, allowing the user to pool up to 24 different samples in one sequencing experim... | ["[Preparation Before Starting] Prepare for your experiment", "[Preparation Before Starting] Extract your DNA, and check its length, quantity and purity. The quality checks performed during the protocol are essential in ensuring experimental success.", "[Preparation Before Starting] Ensure you have your sequencing kit,... |
58,308 | Neurospora culture and basic imaging | 4 | null | https://www.protocols.io/view/neurospora-culture-and-basic-imaging-b47cqziw | gamclaug | TITLE: Neurospora culture and basic imaging
AUTHORS: gamclaug
[DESCRIPTION]
Details about culturing Neurospora, imaging, making freezer stocks, and media recipe
[GUIDELINES]
Neurospora spores can travel through the air, so work with the spores/cells in a fume hood to avoid contamination. Only open slants and plates... | ["[Intro] Neurospora spores can travel through the air, so work with the spores/cells in a fume hood to avoid contamination. Only open slants and plates in the fume hood. \n\nhttp://www.fgsc.net/Neurospora/neurospora.htmlis a good neurospora resource", "[Cell Culture] Neurospora spores are generally mailed between labs... |
null | null | null | dx.doi.org/10.17504/protocols.io.ejtbcnn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
The identity of a nucleotide or the presence of a bulky modification or strand break in an RNA can be determined by several approaches. When the 3′ region of the analyzed RNA is known, extending a (radio)labeled primer by reverse transcription and analyzing the reaction products... | [] |
86,062 | Grid patterning protocol for Cryo-FIB/ET workflow | 1 | null | https://www.protocols.io/view/grid-patterning-protocol-for-cryo-fib-et-workflow-cyanxsde | Farhaz Shaikh, Josh Hutchings, Tamar Basiashvili, Elizabeth Villa | TITLE: Grid patterning protocol for Cryo-FIB/ET workflow
AUTHORS: Farhaz Shaikh, Josh Hutchings, Tamar Basiashvili, Elizabeth Villa
[DESCRIPTION]
Cryo-Electron Tomography combined with Cryo-Focused Ion Beam milling provides a novel way to study the structure of proteins and the architecture of organelles in situ. Elec... | ["[1. Passivation] Place a PDMS stencil (14 mm with 2x2 4 mm wells)into a 35 mm confocal dish (MatTek P35G-1.5-20-C).", "[2. Preparing Microscope] Switch on a light source, microscope, microscope light, Primo (button on the back and key to the right), PC, then PCO camera – in that order.", "[2. Preparing Microscope] Op... |
101,491 | Fabrication of laser inscribed graphene (LIG) 3-electrode plug-and-play chip | 0 | dx.doi.org/10.17504/protocols.io.dm6gpze1dlzp/v3 | https://www.protocols.io/view/fabrication-of-laser-inscribed-graphene-lig-3-elec-dfct3iwn | Lisseth Casso-Hartmann, Geisianny AM Moreira, Yifan Tang, Diana Vanegas, Eric S McLamore | TITLE: Fabrication of laser inscribed graphene (LIG) 3-electrode plug-and-play chip
AUTHORS: Lisseth Casso-Hartmann, Geisianny AM Moreira, Yifan Tang, Diana Vanegas, Eric S McLamore
[DESCRIPTION]
Laser inscribed graphene (LIG) is a versatile material that is commonly used to prepare electrochemical sensors (Moreira et... | ["Step 1) Fabrication of USB-A Adapter \nHeat the soldering iron, and prepare a wet sponge and solder wick. \nSee the following for an introduction to soldering techniques (link)\nSolder one 28AWG jumper wire to each of the two outer contacts in the USB-A adapter. \nCreate an electrical connection (i.e., “jump”) the tw... |
39,258 | Target Guide Sequence Cloning Protocol | 4 | dx.doi.org/10.17504/protocols.io.bij2kcqe | https://www.protocols.io/view/target-guide-sequence-cloning-protocol-bij2kcqe | Skye Waterland, Yang Li | TITLE: Target Guide Sequence Cloning Protocol
AUTHORS: Skye Waterland, Yang Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Create single gRNA vectors for targeted cloning utilizing CRISPR or CRISPR-based systems. </div></div>
[STEPS]
?. [Lentiviral vector digestion]
Digest and dephosphorylate ... | ["[Lentiviral vector digestion]\nDigest and dephosphorylate of the with for at .\n[(equivalent to 1µg)]\n37 °C\n*Note: we used BsmBI Cat #R0580, NEB, but this one has been discontinued. #R0739L is considered as an effective replacement.*", "[Lentiviral vector digestion]\nAdd to a .\n40 µl\n1.5 mL", "[Lentiviral vect... |
32,294 | Frozen Tissue Nuclei Extraction | null | dx.doi.org/10.17504/protocols.io.bbseinbe | null | Carly Martin, Abdul Abdul, Charles Vanderburg, Naeem Nadaf, Ashley Feirrera, Evan Macosko | TITLE: Frozen Tissue Nuclei Extraction
AUTHORS: Carly Martin, Abdul Abdul, Charles Vanderburg, Naeem Nadaf, Ashley Feirrera, Evan Macosko
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for extraction of nuclei from frozen tissue in preparation for single-nuclei sequencing (droplet-based/10... | ["Make dissociation buffer, 50 mLs per sample:", "Make extraction buffer, 3 mLs per sample: Dissociation Buffer + 1% Kollidon VA64 + 1% Triton X100 + 1:40 RNase-inhibitor", "Chill all buffers to 4C, and keep all buffers on ice when in use.", "Prepare equipment: Set out and chill the following equipment/supplies. The... |
25,118 | Over-Agar Antibiotic Plating | null | dx.doi.org/10.17504/protocols.io.4r6gv9e | null | Addgene The Nonprofit Plasmid Repository | TITLE: Over-Agar Antibiotic Plating
AUTHORS: Addgene The Nonprofit Plasmid Repository
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is for over-agar antibiotic plating. To see the full abstract and additional resources, visit </span><a href="https://www.addgene.org/protocols/ov... | ["[Day 1]\nPrepare carbenicillin to a concentration of 1 mg/mL – 4 mg/mL in LB medium.\nThe concentration of antibiotic required for effective over-agar selection has been empirically determined. See selection curve below.\nCarbenicillin is used here in place of ampicillin because carbenicillin is more stable, so it is... |
null | null | null | dx.doi.org/10.17504/protocols.io.f5jbq4n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 19">
<div class="section">
<div class="layoutArea">
<div class="column">
<p>The ISOLATE II Biofluids RNA Kit isolates total RNA with minimal amounts of genomic DNA contamination using the supplied Genomic DNA Removal Column. However, additional DNas... | [] |
28,953 | Streptavidin immovilization stressed test | null | dx.doi.org/10.17504/protocols.io.8hzht76 | null | Jorge Fernández | TITLE: Streptavidin immovilization stressed test
AUTHORS: Jorge Fernández
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The following protocol was performed to test the affinity of the protein streptavidin for the nitrocellulose when applied a continuous flow of solvent.</div></div>
[STEPS]
?. Cu... | ["Cut the FF80HP nitrocellulose membranes in 2 rectangles of 0.8cm x 4 cm dimensions. Repeat this procedure with the FF170HP nitrocellulose to obtain a total of 4 nitrocellulose pieces.", "Stamp the microfluidic design, following the protocol microfluidic channels wax priming on:One piece of the FF170Hp nitrocellulos... |
39,167 | Algae strain maintenance (Chlamydomonas reinhardtii) | 4 | null | https://www.protocols.io/view/algae-strain-maintenance-chlamydomonas-reinhardtii-big7kbzn | Joao Vitor Molino | TITLE: Algae strain maintenance (Chlamydomonas reinhardtii)
AUTHORS: Joao Vitor Molino
[STEPS]
?. [Plate preparation]
Always follow aseptic techniquesAutoclavate freshly prepared TAP media with with a magnetic bar insideMix the flask using a magnetic stirrer to evenly dissolve the agar in the solutionFor antibiotic ... | ["[Plate preparation]\nAlways follow aseptic techniquesAutoclavate freshly prepared TAP media with with a magnetic bar insideMix the flask using a magnetic stirrer to evenly dissolve the agar in the solutionFor antibiotic containing plates, cool down the flask temperarute until - or until it is possible to hold... |
48,188 | Peptostreptococcal Protein L and Protein LG sandwich ELISA | 1 | dx.doi.org/10.17504/protocols.io.bta4nigw | https://www.protocols.io/view/peptostreptococcal-protein-l-and-protein-lg-sandwi-bta4nigw | Angel Justiz-Vaillant | TITLE: Peptostreptococcal Protein L and Protein LG sandwich ELISA
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This ELISA was used to study the interactions between Staphylococcal protein-L (SpL) and protein-LG with different immunoglobulin preparations from mammal... | ["This ELISA was used to study the interactions between Staphylococcal protein-L (SpL) and protein-LG 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 SpL in carbonate-bicarbonate buffer pH 9.6.", "The plate wa... |
21,218 | Vandy - Hyperinsulinemic-euglycemic Clamp | null | dx.doi.org/10.17504/protocols.io.yyafxse | null | Li Kang | TITLE: Vandy - Hyperinsulinemic-euglycemic Clamp
AUTHORS: Li Kang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">Mice with catheters implanted in the jugular vein (infusions) and carotid artery (sampling) are used for ... | ["Surgical catheterization of the carotid artery and jugular vein in mice at least 5 days prior to the day of the study (refer to protocol for Surgical Catheterization of the Carotid Artery and Jugular Vein).", "Weigh mouse and start fast (suggested starting time between 7:00 and 8:00 AM) by placing mouse in a plastic ... |
51,125 | Bacterial abundance from soil or shrub leaf litter - Flow cytometry | 4 | dx.doi.org/10.17504/protocols.io.bv6vn9e6 | https://www.protocols.io/view/bacterial-abundance-from-soil-or-shrub-leaf-litter-bv6vn9e6 | Banafshe Khalili, Claudia Weihe, Jennifer B H Martiny | TITLE: Bacterial abundance from soil or shrub leaf litter - Flow cytometry
AUTHORS: Banafshe Khalili, Claudia Weihe, Jennifer B H Martiny
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Bacterial abundance is a fundamental metric for understanding the population dynamics of soil bacteria and t... | ["Add 1%Pi buffered GTA buffer to 0.1-0.2 g of soil or ground shrub leaf litter in a 50 ml tube. Store at in the dark up to 30 days.\n5 mL\n4 °C", "When you are ready to extract bacteria from your samples add TSP solution and Tween 80 to a final concentration of\n1.2 mL\n31 µl", "Vortex each sample and transfer th... |
101,431 | Análise filogenômica | 0 | dx.doi.org/10.17504/protocols.io.q26g71mb1gwz/v1 | https://www.protocols.io/view/an-lise-filogen-mica-dfax3ifn | Thiago Mafra Batista | TITLE: Análise filogenômica
AUTHORS: Thiago Mafra Batista
[DESCRIPTION]
This tutorial will guide students and researchers in constructing phylogenetic trees from genomic data. The step-by-step process includes data acquisition, assessment of genome completeness, identification of complete and single-copy orthologs pre... | ["[Aquisição dos genomas no formato fasta] A primeira etapa da construção da árvore filogenômica consiste em baixar os genomas que serão analisados. Para isso, é necessário visitar a pagina Genome do NCBI no link https://www.ncbi.nlm.nih.gov/datasets/genome/. Digite o nome das espécies de interesse e anote, em uma tabe... |
55,889 | One-step RT-PCR Ins214EPE assay for Omicron (B.1.1.529) variant detection | 4 | dx.doi.org/10.17504/protocols.io.b2trqem6 | https://www.protocols.io/view/one-step-rt-pcr-ins214epe-assay-for-omicron-b-1-1-b2trqem6 | Nikita Yolshin , Kirill Varchenko, Kseniya Komissarova, Daria Danilenko, Andrey Komissarov, Dmitry Lioznov | TITLE: One-step RT-PCR Ins214EPE assay for Omicron (B.1.1.529) variant detection
AUTHORS: Nikita Yolshin , Kirill Varchenko, Kseniya Komissarova, Daria Danilenko, Andrey Komissarov, Dmitry Lioznov
[DESCRIPTION]
On 26 November 2021 WHO designated a new variant of concern B.1.1.529 named Omicron. This variant ha... | ["Order oligonucleotides with following sequences 5'->3':\n \n Ins214EPE F ATATTCTAAGCACACGCCTATT Ins214EPE P1 ROX-AGCCAGAAGATCTCCCTCAGGGTT-BHQ Ins214EPE P2 ROX-TGCGTGAGCCAGAAGATCTCCCT-BHQ Ins214EPE R GGCAAATCTACCAATGGTTCTA", "Briefly vortex and centrifuge reagents before us... |
null | null | null | dx.doi.org/10.17504/protocols.io.taneide | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Total genomic DNA was extracted from leaf tissue to amplify and sequence <span style="display: inline !important; float: none; background-color: transparent; color: #000000; font-family: 'Open Sans',sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-w... | ["Total genomic DNA was extracted from leaf tissue using the NucleoSpin®Plant-Kit (Macherey-Nagel, Düren, Germany) following the manufacturer’s instructions.", "Amplification of the target loci were was conducted in a Mastercycler (Eppendorf, Hamburg, Germany). Each 20 μl volume contains 2.00 μl 10× PCR buffer (without... |
14,794 | Human and Mouse Islet Single-cell Dispersion for Patch-clamp and Imaging | 1 | dx.doi.org/10.17504/protocols.io.spiedke | https://www.protocols.io/view/human-and-mouse-islet-single-cell-dispersion-for-p-spiedke | Aliya Spigelman, Austin B, Xiaoqing Dai, Amanda Gomes, Patrick Macdonald | TITLE: Human and Mouse Islet Single-cell Dispersion for Patch-clamp and Imaging
AUTHORS: Aliya Spigelman, Austin B, Xiaoqing Dai, Amanda Gomes, Patrick Macdonald
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Detailed protocol for dispersing human and mouse islets into single cells for patch clamp ... | ["Pick islets into 15 mL falcon tube with as little media as possible.", "Add 1ml of Gibco cell dissociation buffer (cat # 13150-016).\n[Cell dissociation buffer]", "Incubate in 37°C water bath for 10 minutes.\n37 °C", "Pipette islets up and down with 1 ml pipette to produce single cells", "Add 9 ml of human islet cult... |
null | null | null | dx.doi.org/10.17504/protocols.io.qakdscw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Even though, progesterone is a hormone naturally produced by ovary, but whether the external progesterone is as beneficial as the natural for female? What alteration occurs due to their prolonged use in different organs of female reproductive tract? We aimed to observe the hi... | [] |
95,330 | Generation of stable LysoTag expressing cell lines and LysoTag immunoprecipitation of lysosomes | 1 | dx.doi.org/10.17504/protocols.io.261gedz2ov47/v1 | https://www.protocols.io/view/generation-of-stable-lysotag-expressing-cell-lines-c9caz2se | Daniel Saarela, Dario Alessi | TITLE: Generation of stable LysoTag expressing cell lines and LysoTag immunoprecipitation of lysosomes
AUTHORS: Daniel Saarela, Dario Alessi
[DESCRIPTION]
Molecular homeostasis in cells is regulated in part by protein degradation, which is facilitated by the proteasome and lysosomal proteolysis. Lysosomes are membrane... | ["[Packaging LysoTag and HA-Empty (Mock) construct] Prepare a transfection mix to generate LysoTag expressing lentivirus in 1.5ml Eppendorf tube containing:\na. 3.8 µg pGag/Pol plasmid\nb. 2.2 µg pVSVG plasmid\nc. 6 µg pLJC5 TMEM192 3XHA plasmid\nd. 300 µL OptiMem", "[Packaging LysoTag and HA-Empty (Mock) construct] Pr... |
42,258 | Why does yahoo mail keep stopping -How to fix it? | 3 | dx.doi.org/10.17504/protocols.io.bmhsk36e | https://www.protocols.io/view/why-does-yahoo-mail-keep-stopping-how-to-fix-it-bmhsk36e | George more | TITLE: Why does yahoo mail keep stopping -How to fix it?
AUTHORS: George more
[STEPS] | [] |
63,128 | Stranded Transcript Count Table Generation from Long Reads | 1 | dx.doi.org/10.17504/protocols.io.5qpvonn2bl4o/v16 | https://www.protocols.io/view/stranded-transcript-count-table-generation-from-lo-b9vyr67w | David A Eccles | TITLE: Stranded Transcript Count Table Generation from Long Reads
AUTHORS: David A Eccles
[DESCRIPTION]
This protocol is for generating count tables for different samples at the transcript level, using long reads that are mapped to transcripts.
Input(s): demultiplexed and oriented fastq files (see protocol Preparing... | ["[Demultiplex Reads] Demultiplex and orient reads as per the protocol Preparing Reads for Stranded Mapping. It is expected that these demultiplexed reads will be split up in the current directory, and coupled with a 'barcode_counts.txt' file. If that's the case, the following should work:\n \nExample expected output:\... |
30,097 | Post Processing: Abundance and Distribution of Species in Open Vegetation Plots | null | dx.doi.org/10.17504/protocols.io.9mrh456 | null | Sabine St-Jean | TITLE: Post Processing: Abundance and Distribution of Species in Open Vegetation Plots
AUTHORS: Sabine St-Jean
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Here we describe the standardised protocol used by the </span><a href="http://www.caboscience.org/" style = "text-decoration:underline;... | ["[Photo Annotations]\nIf the different species are difficult to tell apart visually, annotate the drone pictures.", "[Photo Annotations]\nFrom Fulcrum, download on your computer the small drone pictures from the 9 subplots of a given plot by following Vegetation Surveys: Herbs and Shrubs → Cover Estimates: Subplots → ... |
18,789 | Protocol for use with NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (E6310) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760, E7765) | null | dx.doi.org/10.17504/protocols.io.wkdfcs6 | null | New England Biolabs | TITLE: Protocol for use with NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (E6310) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760, E7765)
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The NEBNext rRNA Depletion Kit (Human/Mouse/Rat) depletes ... | ["[Probe Hybridization to RNA]\nAdd of the above mix to total RNA (from Step 1), resulting in a total volume of .\n3 µl\n12 µl\n15 µl", "[Probe Hybridization to RNA]\nMix by pipetting up and down at least 10 times.", "[Probe Hybridization to RNA]\nSpin down briefly in a microcentrifuge.", "[Probe Hybridization to RNA... |
98,624 | KAPP-Sen TMC: Term Placental Tissue Collection | 0 | dx.doi.org/10.17504/protocols.io.bp2l62b9dgqe/v1 | https://www.protocols.io/view/kapp-sen-tmc-term-placental-tissue-collection-dci82uhw | Sonja Suvakov, Elizabeth Ann L. Enninga, Bridget A. Schley, Janelle Santos, Vesna D. Garovic | TITLE: KAPP-Sen TMC: Term Placental Tissue Collection
AUTHORS: Sonja Suvakov, Elizabeth Ann L. Enninga, Bridget A. Schley, Janelle Santos, Vesna D. Garovic
[DESCRIPTION]
The placenta samples are obtained within 15 minutes after delivery. As soon as the placenta is delivered it is placed in the box at room temperature ... | ["Maternal side samples were collected within 3-5 cm range from the place where UC would be projected, cut into ~1 cm cubes and placed either in the cold MACS or cassettes with 10% buffered formalin.", "Dissection of the fetal side of the placenta were made within 3-5 cm range from the UC and cut into ~1 cm cubes and p... |
61,870 | Titan XL Male Enhancement (WORKS & HOAX) For That Body Requires During Bed Performance. | 3 | dx.doi.org/10.17504/protocols.io.x54v9y37qg3e/v1 | https://www.protocols.io/view/titan-xl-male-enhancement-works-amp-hoax-for-that-b8nnrvde | haiannise | TITLE: Titan XL Male Enhancement (WORKS & HOAX) For That Body Requires During Bed Performance.
AUTHORS: haiannise
[DESCRIPTION]
Titan XL
[STEPS] | [] |
49,456 | In vivo tissue-specific chromatin profiling in Drosophila | 4 | dx.doi.org/10.17504/protocols.io.buiqnudw | https://www.protocols.io/view/in-vivo-tissue-specific-chromatin-profiling-in-dro-buiqnudw | Vikki M. Weake, Juan P Jauregui-Lozano | TITLE: In vivo tissue-specific chromatin profiling in Drosophila
AUTHORS: Vikki M. Weake, Juan P Jauregui-Lozano
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Chromatin regulation plays an essential role in many nuclear processes, and genome-wide chromatin profiling approaches contribute to unders... | ["[Recipes]\nHomogenization/wash [WB] buffer40 mM HEPES, pH 7.5120 mM KCl0.4% NP40 (IGEPAL)Dilution buffer [cold]40 mM HEPES, pH 7.5120 mM KClBead washing buffer [cold]1X Phosphate Buffer Saline (PBS) buffer, pH 7.42.5 mM MgCl2## Omni-ATAC Omni-ATAC tagmentation mix25 µL 2X buffer2.5 µL Tn516.5 µL PBS0.5 µL 1% digitoni... |
21,157 | UC Davis - Superoxide Dismutase | null | dx.doi.org/10.17504/protocols.io.ywdfxa6 | null | Peter Havel | TITLE: UC Davis - Superoxide Dismutase
AUTHORS: Peter Havel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Significant amounts of superoxide dismutase (SOD) in cellular and extracellular environments are crucial for t... | ["Calculation1. Calculate the average absorbance of each standard and sample. If assayed, subtract sample background absorbance from the sample.2. Divide standard A's absorbance by itself and divide standard A's absorbance by all the other standards and samples absorbances to yield the linearized rate (LR) (i.e., LR fo... |
75,197 | Human axillary lymph node fine-needle aspirate sample processing and cyropreservation | 4 | null | https://www.protocols.io/view/human-axillary-lymph-node-fine-needle-aspirate-sam-cmn5u5g6 | Jacqueline HY Siu, cdendrou | TITLE: Human axillary lymph node fine-needle aspirate sample processing and cyropreservation
AUTHORS: Jacqueline HY Siu, cdendrou
[DESCRIPTION]
This protocol was used to generate a single-cell suspension from fine-needle aspirate samples of the adult human axillary lymph nodes and cyropreserved in CS10 for < 6 months.... | ["[Sample processing] Upon sample arrival, top up tubes with cold RPMI + 5% human AB serum (serum has been previously heat inactivated and sterile filtered) as required to ensure even volumes.", "[Sample processing] Centrifuge at 400xg at 4ºC for 10 min. 400 x g, 10 min, 4 °C", "[Sample processing] Remove the supernata... |
34,049 | Low-cost tissue collection and genomic DNA extraction for plants | 1 | dx.doi.org/10.17504/protocols.io.bdg9i3z6 | https://www.protocols.io/view/low-cost-tissue-collection-and-genomic-dna-extract-bdg9i3z6 | Rachel Howard-Till, Claudia Osorio, Bradley Till | TITLE: Low-cost tissue collection and genomic DNA extraction for plants
AUTHORS: Rachel Howard-Till, Claudia Osorio, Bradley Till
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes low-cost methods for the collection and desiccation of plant tissues and subsequent extracti... | ["Collection and dessication of plant tissues", "[Collection and desiccation of plant tissues]\nCollect plant tissue and place in a sealed container with silica gel orange, or equivalent. For larger samples, collect tissue in 50 ml falcon tubes. For Berberis darwinii leaves, which are tough and spiny, approximately 30 ... |
null | null | null | dx.doi.org/10.17504/protocols.io.d2s8ed | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
OptiPrep gradients, as described for purifying viral isolates, may also be used for purifying marine viral assemblages. There are as yet, however, few descriptions of this application in the literature. CsCl gradients, on the other hand, have been used extensively for purificati... | [] |
39,560 | Quantitative Estimation of IgM and IgG Antibodies Against SARS-CoV-2 | 4 | dx.doi.org/10.17504/protocols.io.bivgke3w | https://www.protocols.io/view/quantitative-estimation-of-igm-and-igg-antibodies-bivgke3w | Abhinay Gontu, Sreenidhi Srinivasan, Meera Surendran Nair, Scott E Lindner, Allen M Minns, Randall Rossi, Suresh Kuchipudi, Vivek Kapur | TITLE: Quantitative Estimation of IgM and IgG Antibodies Against SARS-CoV-2
AUTHORS: Abhinay Gontu, Sreenidhi Srinivasan, Meera Surendran Nair, Scott E Lindner, Allen M Minns, Randall Rossi, Suresh Kuchipudi, Vivek Kapur
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [ELISA procedure]
Coating of ELISA pla... | ["[ELISA procedure]\nCoating of ELISA platesCoat the ELISA plates with 50 μL (per well) of the receptor-binding domain (RBD) of SARS-CoV-2 spike antigen at a concentration of 2 μg/mL diluted in phosphate-buffered saline (PBS, pH 7.3±0.1). A summary of recombinant RBD antigen production protocol is included in the Mater... |
79,828 | FPCount protocol - in-lysate (purification free) protocol | 4 | dx.doi.org/10.17504/protocols.io.dm6gpw43plzp/v2 | https://www.protocols.io/view/fpcount-protocol-in-lysate-purification-free-proto-cr7uv9nw | Eszter Csibra, Guy-Bart Stan | TITLE: FPCount protocol - in-lysate (purification free) protocol
AUTHORS: Eszter Csibra, Guy-Bart Stan
[DESCRIPTION]
FPCount is a complete protocol for fluorescent protein calibration, consisting of:
FP expression and production of cell lysates.
FP concentration determination in a microplate reader.
FP fluorescenc... | ["[Expression] Set up a 50ml culture for the overnight expression of the calibrant fluorescent protein.\n\nMix the following in a 200ml flask:\n•\t50ml culture medium (such as LB Miller)\n•\t50µl chloramphenicol\n•\t50µl 20% arabinose (for a final concentration of 0.02%)\n•\tscraping of an expression vector for the cal... |
97,470 | Hybrid protocol for Nuclei Isolation and 10X Genomics Single Cell 5' Gene Expression for Human Ovary Explants | 0 | dx.doi.org/10.17504/protocols.io.x54v928dpl3e/v1 | https://www.protocols.io/view/hybrid-protocol-for-nuclei-isolation-and-10x-genom-dbe62jhe | Nicolas Martin | TITLE: Hybrid protocol for Nuclei Isolation and 10X Genomics Single Cell 5' Gene Expression for Human Ovary Explants
AUTHORS: Nicolas Martin
[DESCRIPTION]
This is the 10X Genomics Single Cell 5' Gene Expression hybrid protocol using nuclei suspension isolated from fresh, frozen human ovary explants. The Chromium X... | ["[Nuclei Isolation Protocol for Human Ovary Explants] Chapter 1—Single Cell Gene Expression & Chromium Fixed RNA Profiling of the protocol CG000505 REV A was used to isolate nuclei from frozen human ovary explants with the following modifications: 1) a cordless motor pestle (VWR, Catalog number 47747-370) was used for... |
null | null | null | dx.doi.org/10.17504/protocols.io.rq3d5yn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?. | ["Studies followed https://www.protocols.io/private/90C4D66F3DAF2BEDBF93273D5ED75E1F, but the diet was permuted over the 26 generations of the study.", "Generations 1-4 were fed 1:2 P:C laboratory diet, 5-20 the 1:16 P:C diet and 21-26 the 1:2 P:C diet.", "Two addition population cage studies were then completed.", "In... |
null | null | null | dx.doi.org/10.17504/protocols.io.kqhcvt6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Fluorescent labeling of reovirus virions with succinimidyl ester-conjugated fluorescent probes</p>
[BEFORE_START]
<p>You will need purified reovirus and dimethylformamide.</p>
<p>Sodium bicarbonate must be made on the day of labeling.</p>
<p>SE-conjugated dyes are not limite... | [] |
28,910 | Splitting p1 (1xT75) to p2 (2xT150) | 1 | dx.doi.org/10.17504/protocols.io.8gnhtve | https://www.protocols.io/view/splitting-p1-1xt75-to-p2-2xt150-8gnhtve | Andrea Argouarch | TITLE: Splitting p1 (1xT75) to p2 (2xT150)
AUTHORS: Andrea Argouarch
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol includes splitting growing cell line from a T75 flask into two T150 flasks for expansion. </div></div>
[STEPS]
?. [Observations]
At 90-100% confluency, split T75 flask in... | ["[Observations]\nAt 90-100% confluency, split T75 flask into 2xT150 flasks", "[Preparation]\nTurn off UV lights and clean hood with 70% ethanol", "[Preparation]\nClean items with 70% ethanol and bring into hood a. DPBS -/- b. Sterile Filtered Media c. Label 2xT150 flasks with ID, date, and p2, add 28 mls ... |
65,540 | Intravenous injections | 4 | dx.doi.org/10.17504/protocols.io.5qpvob14zl4o/v1 | https://www.protocols.io/view/intravenous-injections-cb9csr2w | Goran Tomic | TITLE: Intravenous injections
AUTHORS: Goran Tomic
[DESCRIPTION]
Protocol for mouse tail-vein injections of cell lines.
[BEFORE_START]
I block randomise* the injections when multiple groups/treatments are present (e.g. Ctrl and KO or isotype control/depleting antibody). The goal is for each cage to have all of the ... | ["Grow the cells 48-72 h before injection (around 70-80% confluent).", "Wash the cells with PBS and detach with 1 mL trypsin. Stop the reaction with 3-4 mL complete medium (+10% FBS). Aspirate up and down, and filter through a 40 um filter into sterile FACS tubes.", "Count the cells. Calculate the total required number... |
97,132 | Study Protocol for the AIRCARD Study: A Prospective Cohort Study Utilizing DANCAVAS and VIVA Screening Trials | 0 | dx.doi.org/10.17504/protocols.io.kxygxykqzl8j/v1 | https://www.protocols.io/view/study-protocol-for-the-aircard-study-a-prospective-da4k2guw | Stephan Peronard Mayntz, Roda Abdulkadir Mohamed, Anna Mejldal, Jens-Jakob Kjer Møller, Jes Lindholt, Axel Diederichsen, Lise Marie Frohn, Jørgen Brandt, Matthias Ketzel, Jibran Khan, Jess Lambrechtsen | TITLE: Study Protocol for the AIRCARD Study: A Prospective Cohort Study Utilizing DANCAVAS and VIVA Screening Trials
AUTHORS: Stephan Peronard Mayntz, Roda Abdulkadir Mohamed, Anna Mejldal, Jens-Jakob Kjer Møller, Jes Lindholt, Axel Diederichsen, Lise Marie Frohn, Jørgen Brandt, Matthias Ketzel, Jibran Khan, Jess Lambr... | ["[Project design] This study will be designed as a prospective registry-based observational cohort study using modelled air and noise pollution data. The population is males from two Danish clinical trials (DANCAVAS and VIVA trials).", "[Study population] DANCAVAS (39-41) was a population-based randomized, multicenter... |
40,662 | Direct ELISA for investigating the binding of recombinant or chemically-made Protein-AG to immunoglobulins. | 6 | dx.doi.org/10.17504/protocols.io.bjxwkppe | https://www.protocols.io/view/direct-elisa-for-investigating-the-binding-of-rec-bjxwkppe | Angel Justiz-Vaillant | TITLE: Direct ELISA for investigating the binding of recombinant or chemically-made Protein-AG to immunoglobulins.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protein AG (SpAG) is an immunoglobulin-binding protein that interacts with the Fc regions of many ma... | ["This ELISA is used to study the interaction of protein-AG (SpAG) with diverse immunoglobulins.", "The 96 well microtitre plate is coated overnight at 4°C with 1 µg/µl per well of purified immunoglobulins or 50 µl of any animal sera in carbonate-bicarbonate buffer pH 9.6.", "Then plate is treated with bovine serum alb... |
94,618 | Laptop setup and piranhaGUI install | 5 | dx.doi.org/10.17504/protocols.io.ewov1q642gr2/v2 | https://www.protocols.io/view/laptop-setup-and-piranhagui-install-c8m2zu8e | Aine.OToole, rachel.colquhoun, c.ansley, Zoe Vance, Daniel Maloney, Joyce Akello, Catherine Troman, Erika Bujaki, Javier Martin, Alex Shaw, Nick Grassly, Andrew Rambaut | TITLE: Laptop setup and piranhaGUI install
AUTHORS: Aine.OToole, rachel.colquhoun, c.ansley, Zoe Vance, Daniel Maloney, Joyce Akello, Catherine Troman, Erika Bujaki, Javier Martin, Alex Shaw, Nick Grassly, Andrew Rambaut
[DESCRIPTION]
This protocol provides step-by-step guidance on installing MiKNOW, piranhaGUI and it... | ["[Install piranha through piranhaGUI] PiranhaGUI can be installed on a Windows, MacOSX or Linux machine. \nTo install piranhaGUI, navigate to piranhaGUI GitHub on a web browser. You should see a page similar to the one below, which shows the latest releases of piranha GUI, along with some installation instructions.", ... |
47,769 | Neuro-muscular Impairments in Prolapsed Lumbar Intervertebral Disc (PLID) according to Structural Diagnosis and Management (SDM) | 1 | dx.doi.org/10.17504/protocols.io.bsvzne76 | https://www.protocols.io/view/neuro-muscular-impairments-in-prolapsed-lumbar-int-bsvzne76 | Md. Shahadat Hossain , K M Amran Hossain, Sapia Akter, Foisal Mohammad Mosiul Alom | TITLE: Neuro-muscular Impairments in Prolapsed Lumbar Intervertebral Disc (PLID) according to Structural Diagnosis and Management (SDM)
AUTHORS: Md. Shahadat Hossain , K M Amran Hossain, Sapia Akter, Foisal Mohammad Mosiul Alom
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The study aims to determ... | ["[Observation and Validation]\nFinalizing Protocol", "[Observation and Validation]\nApplication for Ethical Approval", "[Observation and Validation]\nPlanning and Preparation for Data Collection", "[Observation and Validation]\nAssessment and Documentation of PLID patients according to SDM", "[Observation and Validati... |
55,431 | Inducing apoptosis using chemical treatment and acidic pH, and detecting it using the Annexin V flow cytometric assay | 4 | dx.doi.org/10.17504/protocols.io.b2dfqa3n | https://www.protocols.io/view/inducing-apoptosis-using-chemical-treatment-and-ac-b2dfqa3n | Catherine M. Worsley, Rob B. Veale, Elizabeth S. Mayne | TITLE: Inducing apoptosis using chemical treatment and acidic pH, and detecting it using the Annexin V flow cytometric assay
AUTHORS: Catherine M. Worsley, Rob B. Veale, Elizabeth S. Mayne
[DESCRIPTION]
Cell death is a key component of mammalian physiology, and can happen as a result of structural damage, or active... | ["[Cell culture of mammalian solid tumour cells lines] Bring all reagents to 37°C in a waterbath.\n Note: ensure that all surfaces and equipment are cleaned with 70% ethanol. Perform all work in a laminar airflow cabinet.", "[Cell culture of mammalian solid tumour cells lines] In a 10cm culture dish, add 10m... |
null | null | null | dx.doi.org/10.17504/protocols.io.nkwdcxe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is the correct protocol if you are using the C3019H cells. If you are using the C3019I cells, please refer to <a href="High-Efficiency-Transformation-Protocol-using-NEB-imstq5" target="_blank">this protocol</a>.
[GUIDELINES]
<strong>Transformation Protocol Variables</stron... | [] |
35,171 | Nucleic acids extraction from single cell using MasterPure Complete DNA purification (Epicenter) | null | dx.doi.org/10.17504/protocols.io.bekbjcsn | null | Sarah Romac | TITLE: Nucleic acids extraction from single cell using MasterPure Complete DNA purification (Epicenter)
AUTHORS: Sarah Romac
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Radiolaria are protists which can't be cultivated. These microoganisms have to be isolated by single-cell for genetic identific... | ["[1. Cell Isolation]\nIsolate individually protist cells (at least 50µm in length) using a glass bent micropipette under a binocular microscope.", "[1. Cell Isolation]\nWash each cell in three successive baths of 0.22µm-filtered and sterile seawater.", "[1. Cell Isolation]\nTransfer subsequently cells in a 1.... |
87,309 | Sanger Tree of Life HMW DNA Fragmentation: Diagenode Megaruptor®3 for LI PacBio | 4 | dx.doi.org/10.17504/protocols.io.81wgbxzq3lpk/v1 | https://www.protocols.io/view/sanger-tree-of-life-hmw-dna-fragmentation-diagenod-czhmx346 | Adam AB Bates, Iszy Clayton-Lucey, Caroline Howard | TITLE: Sanger Tree of Life HMW DNA Fragmentation: Diagenode Megaruptor®3 for LI PacBio
AUTHORS: Adam AB Bates, Iszy Clayton-Lucey, Caroline Howard
[DESCRIPTION]
This protocol describes the fragmentation of HMW DNA from one of the MagAttract v.2, Plant MagAttract v.3, or Plant MagAttract v.4 Sanger Tree of Life HMW DNA... | ["[Laboratory protocol] Label the required number of Diagenode Hydro Tube for each DNA sample that will be sheared; ensure to label the tubes both on the lid and on the side.", "[Laboratory protocol] Prior to transferring the DNA sample from its original tube, first mix the DNA sample by pipetting carefully with wide-b... |
53,222 | Open Science and COVID-19 RCTs | 1 | dx.doi.org/10.17504/protocols.io.x54v9jx7zg3e/v1 | https://www.protocols.io/view/open-science-and-covid-19-rcts-bx8eprte | John Borghi | TITLE: Open Science and COVID-19 RCTs
AUTHORS: John Borghi
[DESCRIPTION]
Open science is an umbrella term that covers a wide variety of efforts focused on making scientific research more transparent and accessible. Practices related to open science exist along a continuum of openness and an individual research eff... | ["[Literature Searching] Search Strategies \n\nThe following are the copy and paste-able versions of our literature searches.\n\nPUBMED\n\n((\"randomized controlled trial\" [pt] OR \"controlled clinical trial\" [pt] OR randomized [tiab] OR randomly [tiab] OR randomised [tiab] OR randomization [tiab] OR randomisation... |
51,557 | DNA clean-up and size selection for long-read sequencing | 1 | dx.doi.org/10.17504/protocols.io.bwkdpcs6 | https://www.protocols.io/view/dna-clean-up-and-size-selection-for-long-read-sequ-bwkdpcs6 | Ashley Jones, Neeraj Purushotham, Jamila Nasim, Benjamin Schwessinger | TITLE: DNA clean-up and size selection for long-read sequencing
AUTHORS: Ashley Jones, Neeraj Purushotham, Jamila Nasim, Benjamin Schwessinger
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>DNA extractions often contain impurities which limit the output of long-read sequencing technologies. H... | ["[RNA AND PROTEIN REMOVAL]\nAliquot 10-30 μg of DNA into a 1.5 mL eppendorf tube. Increase volume to 200 μL with 10 mM Tris-HCl pH 8.\nDNA quantification must be based on Qubit Fluorometer (Thermo Fisher Scientific), or similar device. A high quantity of RNA may be present. Volume can exceed 200 μL, maximum of 600 μL ... |
92,595 | Automation Protocol for High-Efficiency and High-Quality Genomic DNA Extraction from Saccharomyces Cerevisiae | 4 | dx.doi.org/10.17504/protocols.io.8epv592p5g1b/v4 | https://www.protocols.io/view/automation-protocol-for-high-efficiency-and-high-q-c6ntzden | Nina Alperovich, David Ross, Benjamin M Scott | TITLE: Automation Protocol for High-Efficiency and High-Quality Genomic DNA Extraction from Saccharomyces Cerevisiae
AUTHORS: Nina Alperovich, David Ross, Benjamin M Scott
[DESCRIPTION]
Here, we describe a protocol for automated extraction of genomic DNA (gDNA) from yeast liquid culture and colonies. The protocol uses... | ["[Preparation of Zymolyase Stock] Prepare stock of Zymolyase 20T by dissolving to a concentration of 1 U/µL in 1x PBS.", "[Preparation of Zymolyase Stock] Divide Zymolyase solution into 800 µL aliquots and store at -20 °C until use.", "[Preparation of 2-Mercaptoethanol Stock] Prepare 0.001 % stock of 2-Mercaptoethanol... |
66,041 | HiFi-Slide spatial RNA-Sequencing | 4 | dx.doi.org/10.17504/protocols.io.3byl4by18vo5/v1 | https://www.protocols.io/view/hifi-slide-spatial-rna-sequencing-ccqzsvx6 | Tian-Yang Xu, Pei Lin, Diming Zhu, Sheng Zhong | TITLE: HiFi-Slide spatial RNA-Sequencing
AUTHORS: Tian-Yang Xu, Pei Lin, Diming Zhu, Sheng Zhong
[DESCRIPTION]
HiFi-Slide sequencing is a super-resolution spatial transcriptomics sequencing technology. This technique captures and spatially resolves genome-wide RNA expression in a submicron resolution for fresh-fr... | ["Flow Cell Generation and Collection\n\nRecycled illumina flow cell was used to provide spatial coordinate for RNA molecules. \nFor MiniSeq flow cells, a pre-run modification is necessary to replace the NaOCl solution with the Tween-20 solution in the reagent cartridge. We replaced the NaOCl solution inside the MiniSe... |
86,171 | Stereotactic Injections with Headframe Implant | 4 | dx.doi.org/10.17504/protocols.io.eq2lyj72elx9/v1 | https://www.protocols.io/view/stereotactic-injections-with-headframe-implant-cyd3xs8n | Avalon Amaya, Katrina Nguyen | TITLE: Stereotactic Injections with Headframe Implant
AUTHORS: Avalon Amaya, Katrina Nguyen
[DESCRIPTION]
This protocol describes the surgical procedure, instrumentation, and reagents necessary for performing stereotactic injections and securing a headframe to an adult mouse brain for in-vivo recording procedures.
[B... | ["[Perform Stereotactic Injections] Fill burr holes with bone wax or Kwick-Cast.", "[Headframe Placement] Attach Dovetail Clamp to stereotaxic arm and attach stylus. Center stylus over headframe fiducial point and then raise stylus slightly.", "[Headframe Placement] Replace the stylus with the headframe and lower until... |
87,890 | Oral Fat Tolerance Test (OFTT) in Human | 1 | dx.doi.org/10.17504/protocols.io.36wgq3dy5lk5/v1 | https://www.protocols.io/view/oral-fat-tolerance-test-oftt-in-human-cz3sx8ne | Francine dos Santos-Macedo, Dilliane da Paixão Rodrigues Almeida, Bianca Martins Gregório, Fernanda Amorim de Morais Nascimento Braga, Caroline Fernandes-Santos | TITLE: Oral Fat Tolerance Test (OFTT) in Human
AUTHORS: Francine dos Santos-Macedo, Dilliane da Paixão Rodrigues Almeida, Bianca Martins Gregório, Fernanda Amorim de Morais Nascimento Braga, Caroline Fernandes-Santos
[DESCRIPTION]
Following the consumption of a standardized high-fat meal, the oral fat tolerance test (... | ["[OFTT meal preparation (milkshake)] Weight the ingredients", "[OFTT meal preparation (milkshake)] Identify the cup with the participant's name.", "[OFTT meal preparation (milkshake)] Weigh the empty cup and record it (W1).", "[OFTT meal preparation (milkshake)] Add the ingredients to the blender and mix.", "[OFTT mea... |
18,055 | How to Produce an Epitope-specific Antibody by Using Recombinant Repetitive Oligonucleotides | null | dx.doi.org/10.17504/protocols.io.vvfe63n | null | bello smitu | TITLE: How to Produce an Epitope-specific Antibody by Using Recombinant Repetitive Oligonucleotides
AUTHORS: bello smitu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left"><span>Epitope, known as antigenic determinant, is a part of antigen and can be rec... | [] |
38,931 | Thawing adherent cancer cell lines | 1 | null | https://www.protocols.io/view/thawing-adherent-cancer-cell-lines-bh9tj96n | Emily Souster, Verity Goodwin, Charlotte Beaver, Adam Jackson, Fiona Behan, Rizwan Ansari, Mathew Garnett | TITLE: Thawing adherent cancer cell lines
AUTHORS: Emily Souster, Verity Goodwin, Charlotte Beaver, Adam Jackson, Fiona Behan, Rizwan Ansari, Mathew Garnett
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This SOP is for thawing an adherent cancer cell line from a frozen cryovial.</div><div class = ... | ["Remove the cryovial from liquid nitrogen storage and place on dry-ice for transfer to cell culture lab.", "Take the cryovial from the dry-ice and hold in a waterbath until thawed. Dry the cryovial thoroughly, spray with 70% ethanol and transfer to cell culture hood.\n37 °C\nBe careful here to avoid submerging the l... |
95,289 | Rotarod (40 RPM and 20 RPM with docking) | 4 | null | https://www.protocols.io/view/rotarod-40-rpm-and-20-rpm-with-docking-c9azz2f6 | daniel.dautan, Per Svenningsson | TITLE: Rotarod (40 RPM and 20 RPM with docking)
AUTHORS: daniel.dautan, Per Svenningsson
[DESCRIPTION]
This protocol describes motor function testing in mice using the rotarod by the Svenningsson lab.
Two options for the protocol are included: 1) 40 RPM constant speed after habituation and 2) 20 RPM with docking.
... | ["Naive mice were placed in groups of 5 on the rotatord (Ugo Basile 47650) for 2-3 minutes for habituation.", "Following habituation, the rotarod program was initiated and lasted for a maximum of 2 minutes.", "The time to fall as defined with the moment the mice fall in the receptacle or the moment the mice turn around... |
13,824 | Sephadex/sephacryl purification of AFLP products | 1 | dx.doi.org/10.17504/protocols.io.rq8d5zw | https://www.protocols.io/view/sephadex-sephacryl-purification-of-aflp-products-rq8d5zw | Michal Ronikier, Tomasz Suchan | TITLE: Sephadex/sephacryl purification of AFLP products
AUTHORS: Michal Ronikier, Tomasz Suchan
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Preparation of 96x plates]
Put the Sephacryl bottle on the shaker for 5-10 minutes, adjust speed to 4-5 to make it liquid. For the last minute add also the Sephad... | ["[Preparation of 96x plates]\nPut the Sephacryl bottle on the shaker for 5-10 minutes, adjust speed to 4-5 to make it liquid. For the last minute add also the Sephadex mixture bottle and decrease the speed to 3-4.", "[Preparation of 96x plates]\nPrepare a 1:1 (v/v) solution of pre-prepared 5% Sephadex G50 and Sephacry... |
40,860 | Enzyme-linked immunosorbent assay (ELISA) for studying the presence of anti-Salmonella antibody in layer hen's egg yolks. | 6 | dx.doi.org/10.17504/protocols.io.bj54kq8w | https://www.protocols.io/view/enzyme-linked-immunosorbent-assay-elisa-for-studyi-bj54kq8w | Angel Justiz-Vaillant | TITLE: Enzyme-linked immunosorbent assay (ELISA) for studying the presence of anti-Salmonella antibody in layer hen's egg yolks.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Enzyme-linked immunosorbent assay (ELISA) for studying... | ["U-shaped bottom's ninety-six well polystyrene microplate purchased at Sigma-Aldrich, St. Louis USA was incubated with (2 µg/well) of the LPS (Sigma –Aldrich) from Salmonella Typhimurium in coating buffer (overnight at 4 ºC.)", "The microtiter plates was washed four times, with 10 % PBS-Tween-20.", "The microplate was... |
68,365 | Ligation | 4 | dx.doi.org/10.17504/protocols.io.5jyl89417v2w/v3 | https://www.protocols.io/view/ligation-cezmtf46 | Brian Teague | TITLE: Ligation
AUTHORS: Brian Teague
[DESCRIPTION]
A DNA ligase is an enzyme that forms phosphodiester bonds -- it can "glue" together two pieces of DNA. The ligase we're using comes from the T4 bacteriophage virus.
Why do we need to do a ligation anyway? Remember, we're going to use a Cas9 protein to "cut" your ... | ["[Ligation] Dilute the annealed oligonucleotides in to make 100 µL of working stock at a final concentration of 200 nanomolar (nM)", "[Ligation] In the PCR tube, mix in order:\n4 µL \n2 µL of the L2-01 DNA plasmid backbone\n 2 µL of the diluted annealed oligos\n1 µL \n1 µL", "[Ligation] Flick the tube several t... |
37,281 | PCR Prep from cDNA for IVT Reactions | null | dx.doi.org/10.17504/protocols.io.bgm9ju96 | https://www.protocols.io/view/pcr-prep-from-cdna-for-ivt-reactions-bgm9ju96 | Allen Institute for Brain Science | TITLE: PCR Prep from cDNA for IVT Reactions
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes PCR1 and PCR2 reactions beginning with cDNA to generate transcript templates ready for IVT reaction. This protocol is written for 192 (2x96)... | [] |
28,521 | Om-mCherry-hsp90 | null | dx.doi.org/10.17504/protocols.io.74hhqt6 | null | Claudio Slamovits, Pia Elustondo, Ronie Haro, Susana sbreglia@dal.ca | TITLE: Om-mCherry-hsp90
AUTHORS: Claudio Slamovits, Pia Elustondo, Ronie Haro, Susana sbreglia@dal.ca
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Map and sequence of the construct used to transform Oxyrrhis marina using electroporation. </div></div>
[STEPS]
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.nszdef6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Basic protocol to split Human Embryonic Kidney 293 (HEK293) cells to maintain them throughout the week and move on to cell culture plating with leftover cells for future experiments.</p>
[BEFORE_START]
<p style="text-align: left;">Make complete DMEM:</p>
<p style="text-align... | [] |
94,364 | Gallyas Silver Staining | 4 | dx.doi.org/10.17504/protocols.io.5qpvo366zv4o/v1 | https://www.protocols.io/view/gallyas-silver-staining-c8d4zs8w | madalynn.erb Erb | TITLE: Gallyas Silver Staining
AUTHORS: madalynn.erb Erb
[DESCRIPTION]
Gallyas Silver staining in mouse brain sections stains degenerating neurites black.
[STEPS]
SECTION: Day 1
1. For silver staining use the FD NeuroSilverTM Kit II (FD NeuroTechnologies INC Cat# PK301)
SECTION: Day 1
2. Staining of free-floating br... | ["[Day 1] For silver staining use the FD NeuroSilverTM Kit II (FD NeuroTechnologies INC Cat# PK301)", "[Day 1] Staining of free-floating brain sections is performed in glass staining dishes (Pyrex 36754-60) using 8-section staining nets (Ted Pella 36154-64)", "[Day 1] The sections can be transferred between wells using... |
35,778 | The calculation of gut metabolic modules form gene profile | null | dx.doi.org/10.17504/protocols.io.be7ajhie | https://www.protocols.io/view/the-calculation-of-gut-metabolic-modules-form-gene-be7ajhie | Qi Wang | TITLE: The calculation of gut metabolic modules form gene profile
AUTHORS: Qi Wang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The calculation of gut metabolic modules form gene profile</div></div>
[STEPS]
?. Step 1: the putative amino acid sequences were translated from the gene catalogues and... | ["Step 1: the putative amino acid sequences were translated from the gene catalogues and aligned against the proteins/domains in the KEGG databases (release 79.0, with animal and plant genes removed) using BLASTP (v2.2.26, default parameter except that -e 0.01 -b 100 -K 1 -F T -m 8). Each protein was assigned to the KO... |
null | null | null | dx.doi.org/10.17504/protocols.io.edrba56 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol provides methods for quality control of metagenomic data. Included is adapter trimming, quality trimming, decontamination, negative control removal, and pre-processing results. Based on the methods found in the following publication:<br /><br />Hannigan, Geoffrey D... | [] |
86,297 | Immunohistochemistry of Human Brain Striatum: ciliation of cholinergic neurons and astrocytes | 4 | dx.doi.org/10.17504/protocols.io.j8nlkowj1v5r/v1 | https://www.protocols.io/view/immunohistochemistry-of-human-brain-striatum-cilia-cyhzxt76 | Shahzad S. Khan, Ebsy Jaimon, Yu-En Lin, Suzanne R Pfeffer | TITLE: Immunohistochemistry of Human Brain Striatum: ciliation of cholinergic neurons and astrocytes
AUTHORS: Shahzad S. Khan, Ebsy Jaimon, Yu-En Lin, Suzanne R Pfeffer
[DESCRIPTION]
We study cholinergic neurons and astrocytes of the dorsal striatum that are important components of the nigrostriatal circuit. We have... | ["[Identification of the Striatum] Use paintbrushes to retrieve a tissue section from a 15 mL falcon tube containing brain tissue sections.", "[Identification of the Striatum] Add 1mL of 10 mM Sodium Citrate Buffer pH 6.0 into a clean 1.5mL Eppendorf tube for each dissected tissue piece and preheat these tubes on a 95°... |
null | null | null | dx.doi.org/10.17504/protocols.io.vjme4k6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocols is for RNA extraction from Whatman filter paper.
[STEPS]
SECTION: Lyse RBC
?.
SECTION: Precipitate the DNA and separate phases
?.
SECTION: Determine the DNA yield
?.
SECTION: Precipitate the DNA and separate phases
?.
SECTION: Precipitate the DNA and separate... | ["[Lyse RBC] Filter paper disc containing blood cut and placed into 1.5 mL EP tubes.", "[Precipitate the DNA and separate phases] {\"blocks\":[{\"key\":\"amdgo\",\"text\":\"Centrifuge at 20,000 \\u00d7 g for , discard the supernatant with a micropipettor.\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"... |
68,653 | Knockout PCR | 4 | null | https://www.protocols.io/view/knockout-pcr-cfamtic6 | Brian Teague | TITLE: Knockout PCR
AUTHORS: Brian Teague
[DESCRIPTION]
The polymerase chaine reaction (PCR) amplifies linear DNA using a DNA polymerase enzyme and a pair of short single-stranded DNA "primers." This protocol amplifies a region that spans the Cas9 cut site so you can verify whether or not the URA3 "patch" inserted ... | ["Check that the thermocycler is programmed with the following program and holding at 98 °C", "Grab an ice bucket and fill it with ice. If you don't have an ice bucket, a beaker will work in a pinch.", "If necessary, dilute the primers to a concentration of 10 micromolar (µM) in . (Make 100 µL of each dilution.)", "Mi... |
103,299 | Simple and fast technique for separating human mononuclear cells from small amounts of blood and buffy coat with high cell yield | 0 | dx.doi.org/10.17504/protocols.io.14egn6m9zl5d/v1 | https://www.protocols.io/view/simple-and-fast-technique-for-separating-human-mon-dg5b3y2n | Sudhir Bhatia, Gudrun Baersch | TITLE: Simple and fast technique for separating human mononuclear cells from small amounts of blood and buffy coat with high cell yield
AUTHORS: Sudhir Bhatia, Gudrun Baersch
[DESCRIPTION]
We are again describing a rare and very simple protocol here:
The applications for human mononuclear cells (MNCs) are increasin... | ["[A. Isolation of MNC from human peripheral blood or buffy coat:] Add 900µl Genekam Quick MNC Isolator to each tube containing up to 100µl whole blood or buffy coat in a sterile tube (1:10). Otherwise, the ratio of solution to sample should be (1:5). For example, if you want to isolate MNC from 2 ml of buffy coat, add... |
78,068 | Home made direct RNA detection | 4 | null | https://www.protocols.click/view/home-made-direct-rna-detection-cqguvtww | Hower Lee, Marco Grillo, Mats Nilsson | TITLE: Home made direct RNA detection
AUTHORS: Hower Lee, Marco Grillo, Mats Nilsson
[DESCRIPTION]
Highly multiplexed spatial profiling of mRNAs has recently gained traction as a tool to explore cellular diversity, allowing to visualize the cell composition of tissues directly in-situ.
We propose a sensitive, open-so... | ["[Tissue preparation and fixation] Embed fresh-frozen tissues in OCT (optimal cutting temperature) compound and store them at -80°C until cryosectioning. \n\nSection the tissues at 5-20 μm thickness and collect on SuperFrost Plus adhesion slides and store at -80°C until used for experiment.\n \nWhen working with Droso... |
91,915 | Glucosyl extraction from glycogen, by acid hydrolysis (v1) | 1 | dx.doi.org/10.17504/protocols.io.n2bvj3bqwlk5/v1 | https://www.protocols.io/view/glucosyl-extraction-from-glycogen-by-acid-hydrolys-c5zjy74n | Daniel T Hass, James B. Hurley | TITLE: Glucosyl extraction from glycogen, by acid hydrolysis (v1)
AUTHORS: Daniel T Hass, James B. Hurley
[DESCRIPTION]
This protocol is designed to extract glycogen from samples and hydrolyze glycogen to glucose monomers that can be detected using an enzymatic system or using liquid chromatography-linked mass spectro... | ["[Make buffers and prepare heating element] The extraction buffer is 80% methanol, 20% ethanol.\n\nThe hydrolysis buffer is 2N HCl (hydrochloric acid) in H2O.\n\nThe neutralization buffer is 2N NH4OCOOH (ammonium bicarbonate) in H2O.\n\nNotes:\nPlan to make at least 1.5 mL of extraction buffer per sample.\nIf the extr... |
32,895 | Project YES! Youth Engaging for Success: Arthur Davison Children's Hospital Pathology Laboratory's Standard Operating Procedures for HIV viral load and resistance testing | null | dx.doi.org/10.17504/protocols.io.bcc7iszn | null | Julie Denison, Jonathan Mwansa, Sam Miti | TITLE: Project YES! Youth Engaging for Success: Arthur Davison Children's Hospital Pathology Laboratory's Standard Operating Procedures for HIV viral load and resistance testing
AUTHORS: Julie Denison, Jonathan Mwansa, Sam Miti
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Arthur Davison Children'... | [] |
43,873 | AMPure Purification Protocol | 4 | dx.doi.org/10.17504/protocols.io.bn39mgr6 | https://www.protocols.io/view/ampure-purification-protocol-bn39mgr6 | Vasso Makrantoni, Daniel Robertson, Adele L. Marston | TITLE: AMPure Purification Protocol
AUTHORS: Vasso Makrantoni, Daniel Robertson, Adele L. Marston
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A plethora of biological processes like gene transcription, DNA replication, DNA recombination, and chromosome segregation are mediated through protein–DN... | ["[AMPure Purification Protocol]\nAMPure purification relies on the principle of solid-phase reversible immobilization (SPRI) as previously described [16]. SPRI beads are paramagnetic and coated with carboxyl molecules, which reversibly bind DNA in the presence of polyethylene glycol (PEG) and salt (20% PEG, 2.5 M NaCl... |
51,828 | Flow Cytometry ICS Nuclear Antigens | 4 | dx.doi.org/10.17504/protocols.io.bwuupeww | https://www.protocols.io/view/flow-cytometry-ics-nuclear-antigens-bwuupeww | Michael Betts, Gregory Golden | TITLE: Flow Cytometry ICS Nuclear Antigens
AUTHORS: Michael Betts, Gregory Golden
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">High-parameter flow cytometry enables identification and characterization of a wide range of cell populations within a biological sample. A combined analysis of extracell... | ["[Procedure]\nThawing and Restinga. Pre-warm R10 media in a water bath. b. Thaw samples in-vial using a water bath.c. Add thawed cells to of R10, then spin cells at 500 xg for 5 min.d. Resuspend cell pellet in of R10 and count cells. e. Rest cells at least 3 hours (up to overnight) at 2x106 cells/mL in R10 medium +... |
68,811 | Growth Curve Stress Test | 4 | null | https://www.protocols.io/view/growth-curve-stress-test-cffjtjkn | Brian Teague | TITLE: Growth Curve Stress Test
AUTHORS: Brian Teague
[DESCRIPTION]
This is one (fairly quantitative and reproducible) way to run a yeast growth study to analyze the effect of a stressor on yeast. It is not the only way! It is also less of a "protocol" and more of a "template" -- it measures the growth of a single ... | ["[Assay setup] Vortex the yeast culture briefly to resuspend the yeast cells.", "[Assay setup] Set up four wells according to the following table:\n \nWell 1Well 2Yeast culture50 µl50 µlChemical X, 100 mM10 µl--Water40 µl50 µl", "[Assay setup] Set up the plate reader as follows:\nTemperature: 30°C\nMode: Kinetic\nWave... |
57,770 | Resuspension and concentration of iron chloride precipitated viruses from seawater for HMW DNA extraction | 1 | dx.doi.org/10.17504/protocols.io.b4niqvce | https://www.protocols.io/view/resuspension-and-concentration-of-iron-chloride-pr-b4niqvce | Natalie Solonenko | TITLE: Resuspension and concentration of iron chloride precipitated viruses from seawater for HMW DNA extraction
AUTHORS: Natalie Solonenko
[DESCRIPTION]
This protocol describes an alternative resuspension protocol for iron chloride flocculated viruses from natural water. This method produces much higher molecular we... | ["[Resuspension] Prepare 0.2M citrate 0.2M MgCl2 buffer, pH 6-6.5.", "[Resuspension] Make sure the precipitate is accessible to the buffer - if filters were folded precipitate side in, this will necessitate unfolding and re-folding the filter. If you do not want to resuspend the whole filter (i.e., the filer has 20L pr... |
95,610 | W-2 WATER PROCESSING | 4 | dx.doi.org/10.17504/protocols.io.ewov1opwplr2/v2 | https://www.protocols.io/view/w-2-water-processing-c9k2z4ye | REDI-NET Consortium | TITLE: W-2 WATER PROCESSING
AUTHORS: REDI-NET Consortium
[DESCRIPTION]
OBJECTIVE
To outline procedures for total nucleic acid extraction from water samples.
SUMMARY/SCOPE
The overarching aim of the REDI-NET is to develop a collaborative laboratory network between domestic and international partnering institutions... | ["[VACUUM PUMP SET UP] Wipe the surfaces with 70% ethanol to remove contaminants.", "[VACUUM PUMP SET UP] Use tubing to connect a 3-liter Medi-Vac Canister with vacuum pump through the vacuum outlet on the lid. (If possible, the canister should be set up inside a biosafety cabinet).", "[VACUUM PUMP SET UP] Connect tubi... |
null | null | null | dx.doi.org/10.17504/protocols.io.kurcwv6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>In vitro blood recirculation model through Cytosorb device, including specific blood tubing and peristaltic pump components to analyze removal of key inflammatory mediators and toxins.</p>
[STEPS]
?. | [] |
18,045 | i-mJOA Methodology | null | dx.doi.org/10.17504/protocols.io.vu5e6y6 | null | Bryn Hilton, Jennifer Tempest-Mitchell, Benjamin Davies, Mark Kotter | TITLE: i-mJOA Methodology
AUTHORS: Bryn Hilton, Jennifer Tempest-Mitchell, Benjamin Davies, Mark Kotter
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol was used to retrospectively infer modified Japanese Orthopaedic Association (mJOA) scores in a study conducted in 2016-2017 investigat... | ["[Methodology]\nIntroduction\n\t\t\t\t\t\t\t .justify:after {\n\t\t\t\t\t\t\t content: \"\";\n\t\t\t\t\t\t\t display:inline-block;\n\t\t\t\t\t\t\t width: 100%;\n\t\t\t\t\t\t\t }\n\t\t\t\t\t\t\tThe modified Japanese Orthopaedic Association (mJOA) scoring system is well-validated tool used for grading the sev... |
62,370 | Measuring dissolved black carbon in water via aqueous, inorganic, high performance liquid chromatography of benzenepolycarboxylic acid (BPCA) molecular markers | 6 | dx.doi.org/10.17504/protocols.io.5qpvoy2b9g4o/v2 | https://www.protocols.io/view/measuring-dissolved-black-carbon-in-water-via-aque-b86arzae | Riley Barton, Sasha Wagner | TITLE: Measuring dissolved black carbon in water via aqueous, inorganic, high performance liquid chromatography of benzenepolycarboxylic acid (BPCA) molecular markers
AUTHORS: Riley Barton, Sasha Wagner
[DESCRIPTION]
Dissolved black carbon (DBC) is the condensed aromatic portion of dissolved organic matter produced ... | ["[Solid Phase Extraction: Prepare and condition cartridges] The solid phase extraction (SPE) cartridges used in this protocol (Agilent Bond Elut PPL cartridge, 1g, 6 mL) is packed with a styrene-divinylbenzene polymer resin that recovers high proportions of dissolved organic matter (DOM) on a per-carbon basis. The res... |
91,669 | Flow cytometry | 1 | dx.doi.org/10.17504/protocols.io.ewov1qm47gr2/v1 | https://www.protocols.io/view/flow-cytometry-c5rvy566 | Pranay Srivastava | TITLE: Flow cytometry
AUTHORS: Pranay Srivastava
[DESCRIPTION]
This protocol is to assess immune cell profile inn spleen (Chauhan et al. 2018).
[STEPS]
1. Spleen was removed in a 35 mm petri plate with 5 ml RPMI 1640 and digested mechanically and passed through 70 μm filter screen.
2. The cell suspension was centri... | ["Spleen was removed in a 35 mm petri plate with 5 ml RPMI 1640 and digested mechanically and passed through 70 μm filter screen.", "The cell suspension was centrifuged, and the pellet was incubated in RBC lysis buffer. The resulting cell suspension was washed in 1xPBS and blocked with Fc Block (Biolegend, Cat# 101302,... |
61,456 | Measurement of bacterial dry weight | 4 | dx.doi.org/10.17504/protocols.io.kxygxzn44v8j/v1 | https://www.protocols.io/view/measurement-of-bacterial-dry-weight-b79qrr5w | Alfonso Pérez Escudero, Gabriel Madirolas | TITLE: Measurement of bacterial dry weight
AUTHORS: Alfonso Pérez Escudero, Gabriel Madirolas
[DESCRIPTION]
Protocol to measure the biomass content of bacterial cultures, by measuring their dry weight after evaporation of water.
[STEPS]
1. Inoculate one or two colonies of bacteria into 5 mL LB in a closed 50-mL Fal... | ["Inoculate one or two colonies of bacteria into 5 mL LB in a closed 50-mL Falcon tube. Incubate with orbital shaking", "Inoculate 20 microliters of the culture prepared in step #1 into 200 mL of LB, in a 1 L flask. Cover flask with aluminium foil, and incubate for 24 hours with orbital shaking", "Wash culture resultin... |
20,335 | U Mass - Surgery – carotid artery cannulation | null | dx.doi.org/10.17504/protocols.io.x4pfqvn | null | Jason Kim | TITLE: U Mass - Surgery – carotid artery cannulation
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Chronic indwelling catheter is placed in the carotid artery for blood sampling during experiments.... | ["Anesthetize mice with an intraperitoneal injection of ketamine (100 mg/kg body weight) and xylazine (10 mg/kg body weight).", "Check the level of general anesthesia using a pinch stimulus of animal's tail and/or foot.", "Make a transverse incision (~0.5 cm) over the trachea, and isolate the carotid artery.", "Careful... |
69,486 | DISCOVER-Seq: MRE11 ChIP Seq | 1 | dx.doi.org/10.17504/protocols.io.kqdg349ypl25/v2 | https://www.protocols.io/view/discover-seq-mre11-chip-seq-cf4ntqve | Lilly van de Venn, Zacharias Kontarakis, Beeke Wienert | TITLE: DISCOVER-Seq: MRE11 ChIP Seq
AUTHORS: Lilly van de Venn, Zacharias Kontarakis, Beeke Wienert
[DESCRIPTION]
Genome editing using nucleases such as CRISPR-Cas induces programmable DNA damage at a target genomic site, but can also affect off-target sites. We develop a powerful assay for the unbiased identification... | ["[RNP editing of cells] Culture your cell line of interest so that you can edit 1x10^7 cells on the day of nucleofection.", "[RNP editing of cells] Harvest cells and spin down in falcon tube.", "[RNP editing of cells] Wash cells with 1ml PBS and transfer to eppendorf tube. Spin to pellet, discard S/N", "[RNP editing o... |
null | null | null | dx.doi.org/10.17504/protocols.io.p9gdr3w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p> </p>
<p> </p>
<p>We are still developing and optimizing these protocols!</p>
<p> </p>
<p>The aquatic vertebrate eDNA protocols are designed for persons familiar with basic molecular biology techniques and access to essential molecular biology laboratory equipment. To facili... | [] |
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