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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58,584 | Well-tempered Metadynamics protocol | 5 | dx.doi.org/10.17504/protocols.io.b5fyq3pw | https://www.protocols.io/view/well-tempered-metadynamics-protocol-b5fyq3pw | Vidya Niranjan, Akshay Uttarkar | TITLE: Well-tempered Metadynamics protocol
AUTHORS: Vidya Niranjan, Akshay Uttarkar
[DESCRIPTION]
Metadynamics is a technique in which the potential for one or more chosen variables ("collective variables") is modified by periodically adding a repulsive potential of Gaussian shape at the location given by particula... | ["Protein preparation.\nThe crystal structure is imported into Maestro GUI. The Protein Preparation Wizard panel44 is used to add hydrogen atoms, patch end groups, add missing side chains and missing loops, assign protonation states of histidine, aspartate and glutamate at pH 7.045 and optimize the polar hydrogen or... |
31,403 | Ligation Independent Cloning | null | dx.doi.org/10.17504/protocols.io.bawjifcn | null | Addgene the nonprofit plasmid repository | TITLE: Ligation Independent Cloning
AUTHORS: Addgene the nonprofit plasmid repository
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes Ligation Independent Cloning (LIC). To see the full abstract and additional resources, please visit the </span><a href="https://www.addg... | ["Design Your PrimersPrimer design for LIC is often as simple as using the backbone manufacturer's suggested leader sequence fused to your gene of interest, in frame with the start codon or tag sequences (where appropriate). The primer length is dependent on the T4 Pol \"chew back\" reaction, in which a single dNTP is ... |
70,094 | Fractionation of synaptosomes | 4 | dx.doi.org/10.17504/protocols.io.x54v9d85zg3e/v1 | https://www.protocols.io/view/fractionation-of-synaptosomes-cgpntvme | Chuyu Chen, Ciarra Smith, Loukia Parisiadou | TITLE: Fractionation of synaptosomes
AUTHORS: Chuyu Chen, Ciarra Smith, Loukia Parisiadou
[DESCRIPTION]
This protocol details a step by step method to prepare pure fractions of synaptosomes for biochemical analysis.
[STEPS]
1. Pre-chill the homogeniser and buffers on ice. Weigh the tissue
2. Add 4x volume of ice-col... | ["Pre-chill the homogeniser and buffers on ice. Weigh the tissue", "Add 4x volume of ice-cold homogenizing buffer to glass homogenizers", "Apply 12 strokes of even tension with the homogeniser rod", "Transfer to 1.5ml tube (original tube)", "Determine which tissue has the smallest volume and use that volume for all sam... |
null | null | null | dx.doi.org/10.17504/protocols.io.ng6dbze | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Este protocolo describe los pasos para propagar <em>in vitro</em> hongos tipo <strong>terraza</strong> (Ver <a href="https://www.protocols.io/view/cultivo-in-vitro-de-hongos-tipo-sombrero-ng4dbyw" target="_blank">este</a> protocolo para hongos tipo <strong>sombrero</strong>).... | [] |
53,941 | Food safety knowledge, attitudes, and eating behavior under the global coronavirus pandemic | 3 | dx.doi.org/10.17504/protocols.io.bywvpxe6 | https://www.protocols.io/view/food-safety-knowledge-attitudes-and-eating-behavio-bywvpxe6 | Zhe Liu | TITLE: Food safety knowledge, attitudes, and eating behavior under the global coronavirus pandemic
AUTHORS: Zhe Liu
[DESCRIPTION]
The objective of this lab protocol was to evaluate the relationships among food safety knowledge, attitude and eating behavior of consumers during lockdowns in the advent of the COVID-19 ... | [] |
45,862 | ATP_microplate_settings | 4 | null | https://www.protocols.io/view/atp-microplate-settings-bq2emybe | Elizabeth Fozo | TITLE: ATP_microplate_settings
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">ATP assay- Using microplate reader</div></div>
[STEPS]
?. [ATP assay- Using microplate reader]
Sign up for the microplate when planning the experiment and power on before ~15 minutes of use
?. [AT... | ["[ATP assay- Using microplate reader]\nSign up for the microplate when planning the experiment and power on before ~15 minutes of use", "[ATP assay- Using microplate reader]\nMix your samples and reagents in the microplate following the manufacturer’s protocol", "[ATP assay- Using microplate reader]\nStart a new proto... |
40,183 | Determination of minimum inhibitory concentration values (MICs) against Sporothrix brasiliensis and Sporothrix schenckii | 3 | dx.doi.org/10.17504/protocols.io.bjgxkjxn | https://www.protocols.io/view/determination-of-minimum-inhibitory-concentration-bjgxkjxn | luanaborba | TITLE: Determination of minimum inhibitory concentration values (MICs) against Sporothrix brasiliensis and Sporothrix schenckii
AUTHORS: luanaborba
[STEPS] | [] |
39,295 | Fitting enzyme kinetics data with Solver | 1 | null | https://www.protocols.io/view/fitting-enzyme-kinetics-data-with-solver-bik7kczn | Nithesh Chandrasekharan, Chris Berndsen | TITLE: Fitting enzyme kinetics data with Solver
AUTHORS: Nithesh Chandrasekharan, Chris Berndsen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Reaction kinetics are a fundamental component of the biochemical characterization of a biomolecule. The V</span><span style = "vertical-align:sub;">m... | ["[Calculating intial rates]\nCalculate the initial rate from the slope of the product formed vs. time plot.\nIt is important to calculate the rate when the plot of product formed vs. time is linear with time. This ensures that the enzyme is in the steady-state. Typically this is in the early part of the reaction befo... |
70,185 | Roadmap to the bioinformatic study of gene and protein phylogeny and evolution - a practical guide | 5 | dx.doi.org/10.17504/protocols.io.36wgq77e3vk5/v3 | https://www.protocols.io/view/roadmap-to-the-bioinformatic-study-of-gene-and-pro-cgshtwb6 | florian.jacques, Paulina Bolivar, Kristian Pietras, Emma Hammarlund | TITLE: Roadmap to the bioinformatic study of gene and protein phylogeny and evolution - a practical guide
AUTHORS: florian.jacques, Paulina Bolivar, Kristian Pietras, Emma Hammarlund
[DESCRIPTION]
Developments in sequencing technologies and the sequencing of an ever-increasing number of genomes have revolutionisedstu... | ["[Sequence collection and comparison] Collecting sequence data and bibliography on genes and proteins\n\nEvolutionary analyses on molecular data (genes, genomes, proteins, mRNA, transposable elements, ribosomal RNA or other parts of the genome), require retrieving sequences and other information from public databases.... |
91,495 | Transformation of Plasmid into Competent E. coli Cells (e.g., DH5α) | 4 | dx.doi.org/10.17504/protocols.io.eq2lyj2ywlx9/v1 | https://www.protocols.io/view/transformation-of-plasmid-into-competent-e-coli-ce-c5kfy4tn | Hussain Zubair | TITLE: Transformation of Plasmid into Competent E. coli Cells (e.g., DH5α)
AUTHORS: Hussain Zubair
[DESCRIPTION]
This is a detailed experimental protocol for the transformation of plasmid DNA into competent E. coli cells, specifically using the DH5α strain. The protocol encompasses the entire process, from the prepara... | ["[Preparation of LB Agar Plates with Antibiotics] Prepare LB (Luria-Bertani) agar plates.\nOnce the agar has cooled but not solidified, add ampicillin at a ratio of 1:1000 to the agar.\nPour the LB agar into 90 mm Petri dishes and allow to solidify.", "[Thawing of Competent Cells] Retrieve the competent E. coli cells ... |
73,861 | Colorimetric determination of L-lactate in supernatant of cells using LDH activity | 4 | dx.doi.org/10.17504/protocols.io.dm6gpj9j5gzp/v1 | https://www.protocols.io/view/colorimetric-determination-of-l-lactate-in-superna-ckddus26 | Francisco Venegas Solis, Kira Schmiedeknecht, Andreas Kaufmann, Stefan Bauer | TITLE: Colorimetric determination of L-lactate in supernatant of cells using LDH activity
AUTHORS: Francisco Venegas Solis, Kira Schmiedeknecht, Andreas Kaufmann, Stefan Bauer
[DESCRIPTION]
As a product of anaerobic glycolysis L-lactate has shown to be an important indicator of the cellular metabolic status and can be... | ["[Assay buffer preparation] For L-lactate determination in a 96-well plate preparation of 5 mL of Assay Buffer is necessary:\n4250 μL of Tris-Base (0,2 mol/L, pH=8.2)\n500 μL of β-NAD\n250 μL of INT\n1 μL of L-LDH \n1,1 μL of 1-Methoxy-PMS", "[Standard preparation] L-lactate standards with the concentrations of 12, 6,... |
17,991 | Protocol for selective growth of Acetobacter pomorum (Ap) and Lactobacillus plantarum (Lp) | null | dx.doi.org/10.17504/protocols.io.vtfe6jn | null | Lúcia Serra, Sílvia Henriques, Carlos Ribeiro | TITLE: Protocol for selective growth of Acetobacter pomorum (Ap) and Lactobacillus plantarum (Lp)
AUTHORS: Lúcia Serra, Sílvia Henriques, Carlos Ribeiro
[STEPS]
?. - Inoculate fresh mannitol (200 ml) and MRS (10 ml) media (less than a week old) with a single colony of Ap and Lp, respectively. Incubate Ap at 30 ºC, 180... | ["- Inoculate fresh mannitol (200 ml) and MRS (10 ml) media (less than a week old) with a single colony of Ap and Lp, respectively. Incubate Ap at 30 ºC, 180 rpm; and Lp at 37 ºC, without shaking.", "- Dilute 250 µl Lp culture in fresh 10 ml MRS media. - Ask for MRS, MRS + Kanamycin (50 µg/ml) and MRS + Ampicillin (10 ... |
64,449 | Keto Blast Gummies Side Effects | 1 | dx.doi.org/10.17504/protocols.io.j8nlkkrxdl5r/v1 | https://www.protocols.io/view/keto-blast-gummies-side-effects-ca69shh6 | ketoblastgummiessideeffectsus | TITLE: Keto Blast Gummies Side Effects
AUTHORS: ketoblastgummiessideeffectsus
[DESCRIPTION]
Keto Blast Gummies Side Effects
Keto Blast Gummies Side Effects is a ketogenic diet that is low in carbohydrates or calories and high in nutrients, multi-vitamins and proteins. It is clinically proven and especially designed ... | ["Keto Blast Gummies Side Effects : Negative Reviews, Bad Complaints & Side Effects?Pills Advanced BHB Boost Ketogenic Supplement Exogenous Ketones for Men Women 60 Capsules 2 Bottles", "Keto Blast Gummies Side Effects\nKeto Blast Gummies Side Effects is a ketogenic diet that is low in carbohydrates or calories and hig... |
68,908 | De-novo assembly of Xanthomonas genomes from Illumina NovaSeq reads | 5 | null | https://www.protocols.io/view/de-novo-assembly-of-xanthomonas-genomes-from-illum-cfiktkcw | David J Studholme, Jamie Harrison | TITLE: De-novo assembly of Xanthomonas genomes from Illumina NovaSeq reads
AUTHORS: David J Studholme, Jamie Harrison
[DESCRIPTION]
This protocol describes the de-novo assembly of Xanthomonas genome sequences from short-read genomic shotgun sequencing data. It includes quality control of the raw sequence reads, assemb... | ["Bibliography", "Perform quality-based filtering and adapter trimming using fastp.", "Perform de-novo assembly using SPAdes.", "Polishing with Pilon", "Software pre-requisites."] |
59,637 | Nissl (Cresyl Violet) staining | 1 | dx.doi.org/10.17504/protocols.io.dm6gpbzxplzp/v1 | https://www.protocols.io/view/nissl-cresyl-violet-staining-b6gvrbw6 | Christiana.bjorkli , Karoline Hovde, Bruno Monterotti | TITLE: Nissl (Cresyl Violet) staining
AUTHORS: Christiana.bjorkli , Karoline Hovde, Bruno Monterotti
[DESCRIPTION]
Nissl (Cresyl Violet) staining protocol
[STEPS]
1. Dehydrate sections – 10 dips in each: 50, 70, 80, 90, 100, 100, and 100% ethanol
2. Leave in xylene for 2min
3. Rehydrate sections – 10 dips in each... | ["Dehydrate sections – 10 dips in each: 50, 70, 80, 90, 100, 100, and 100% ethanol", "Leave in xylene for 2min", "Rehydrate sections – 10 dips in each: 100, 100, 100, 90, 80, 70, and 50% ethanol", "Quick wash in running water", "Leave sections in Cresyl Violet for 3min on shake", "Leave sections in Citric Acid for 1min... |
19,302 | HIV-Flow assay | null | dx.doi.org/10.17504/protocols.io.w4efgte | null | Marion Pardons , Nicolas Chomont | TITLE: HIV-Flow assay
AUTHORS: Marion Pardons , Nicolas Chomont
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpose of this document is to define the procedure of the HIV-Flow protocol, an assay developed to measure the size the translation-competent viral reservoir in HIV-infected individu... | ["[Day 1]\nThaw cryopreserved PBMCs (10-50 x10^6 cells depending on cell availability and CD4 counts) collected from an HIV-infected individual and an equivalent number of cells from an uninfected control. After thawing, resuspend the cells in 25mL of cRPMI.", "[Day 1]\nCount the cells with Trypan Blue.", "[Day 1]\nKee... |
75,235 | Whole Mouse Brain Delipidation, Immunolabeling, and Expansion Microscopy | 6 | dx.doi.org/10.17504/protocols.io.n92ldpwjxl5b/v1 | https://www.protocols.click/view/whole-mouse-brain-delipidation-immunolabeling-and-cmqbu5sn | Naveen Ouellette, Andrew Recknagel, Kevin Cao, Judith Baka, Molly Logsdon, Jayaram Chandrashekar | TITLE: Whole Mouse Brain Delipidation, Immunolabeling, and Expansion Microscopy
AUTHORS: Naveen Ouellette, Andrew Recknagel, Kevin Cao, Judith Baka, Molly Logsdon, Jayaram Chandrashekar
[DESCRIPTION]
The mammalian brain contains approximately 1,000 brain areas and each brain area contains multiple (up to 100) cell typ... | ["[Gelation and Digestion] Day 1 – MBS equilibration", "[Gelation and Digestion] Wash sample in MBS at Room temperature, filling vial to the top (typically 4 mL). Replace solution for each step:\nMBS for 60 min \nMBS for 60 min", "[Gelation and Digestion] Replace MBS and store on ice at 4 °C", "[Gelation and Digestion... |
null | null | null | dx.doi.org/10.17504/protocols.io.veje3cn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
How to run Prodigal version 2.6.3 (Hyatt et al. 2010) through the iMicrobe plaform.
Prodigal is a protein-coding gene prediction software tool for bacterial and archaeal genomes. Prodigal runs smoothly on finished genomes, draft genomes, and metagenomes. Please note that Prodi... | ["[Run prodigal on a single genome] {\"blocks\":[{\"key\":\"b6alv\",\"text\":\"Note : This protocol uses as an example the bacterial isolate sample available in iMicrobe. \",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[{\"offset\":0,\"length\":92,\"style\":\"italic\"}],\"entityRanges\":[{\"offset\":44,\"len... |
44,812 | Total particulate carbohydrate from microalgae | 4 | dx.doi.org/10.17504/protocols.io.yxmvmk24ng3p/v1 | https://www.protocols.io/view/total-particulate-carbohydrate-from-microalgae-bpzkmp4w | Ying-Yu Hu, Zoe V. Finkel | TITLE: Total particulate carbohydrate from microalgae
AUTHORS: Ying-Yu Hu, Zoe V. Finkel
[DESCRIPTION]
Here we describe a protocol to estimate the total particulate carbohydrate from microalgae. Carbohydrate samples are initially vortexed in 9 M H2SO4 for 15 s. The solution is diluted for a final H2SO4 molarity of 1.6... | ["[Day 1 - Samples] Considering the working hours from 9 am to 4 pm, suggested sample number is:\n# blank + # samples = 24", "[Day 1- Hydrolysis] Transfer 18 M H2SO4 into a 30 mL precombusted glassware (scint vial, beaker... etc)", "[Day 1- Hydrolysis] Add 4.5 mL MilliQ, tightly cap the centrifuge tube, and vortex for ... |
80,771 | Efficacy and safety of statins and ezetimibe in primary prevention of cardiovascular disease in the elderly: A systematic review protocol. | 1 | dx.doi.org/10.17504/protocols.io.eq2ly7y7elx9/v1 | https://www.protocols.io/view/efficacy-and-safety-of-statins-and-ezetimibe-in-pr-cs5bwg2n | Fernandez-Gonzalez J, Irigoyen-Rodriguez I, Alzueta-Isturiz N, Echeverría-Gorriti A, Lozano C, Garjon-Parra J | TITLE: Efficacy and safety of statins and ezetimibe in primary prevention of cardiovascular disease in the elderly: A systematic review protocol.
AUTHORS: Fernandez-Gonzalez J, Irigoyen-Rodriguez I, Alzueta-Isturiz N, Echeverría-Gorriti A, Lozano C, Garjon-Parra J
[DESCRIPTION]
Cardiovascular diseases (CVD) are the le... | ["[Title] Efficacy and safety of statins and ezetimibe in primary prevention of cardiovascular disease\nin the elderly: A systematic review protocol.", "[Author Contributions] JFG: conceptualization, methodology, developing the search strategy and literature search, data\nselection, extraction, statistical analysis, an... |
null | null | null | dx.doi.org/10.17504/protocols.io.hedb3a6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
20,510 | U Michigan - Nerve Conduction Velocity | null | dx.doi.org/10.17504/protocols.io.x96fr9e | null | Eva Feldman | TITLE: U Michigan - Nerve Conduction Velocity
AUTHORS: Eva Feldman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">To confirm the presence of diabetic neuropathy, nerve conduction velocity (NCV) studies are performed. ... | ["[Settings]\nMotor tests o Duration .02 ms o Range 25 mA o low frequency filter 1 Hz o High frequency filter 10 kHz o Sensitivity 1 mV o Time 2 ms/div Sensory test o Duration .02 ms o Range 25 mA o low frequency filter 1 Hz o High frequency filter 10 kHz o Sensitivity 50 μV o Time 2 ms/div", "[Procedure:]\nTo confirm ... |
96,309 | Rabies Virus Bat-Clade Sequencing | 4 | dx.doi.org/10.17504/protocols.io.8epv5x3bng1b/v2 | https://www.protocols.io/view/rabies-virus-bat-clade-sequencing-daav2ae6 | Fernanda Godinho, Aline Campos, rosana-huff, Amanda Ruivo, Milena Bauermann, Thales Bermann, Gabriel Luz Wallau, Paulo Michel Roehe, Richard Salvato | TITLE: Rabies Virus Bat-Clade Sequencing
AUTHORS: Fernanda Godinho, Aline Campos, rosana-huff, Amanda Ruivo, Milena Bauermann, Thales Bermann, Gabriel Luz Wallau, Paulo Michel Roehe, Richard Salvato
[DESCRIPTION]
Join us in advancing global genomic surveillance of the rabies virus.
We are actively engaged in pioneeri... | ["[Primer Preparation] Reconstitute each primer shown in Table 1 (See Materials section), using nuclease-free water to get a 100 µM stock solution.", "[Primer Preparation] Prepare RABV-BAT primer pools A and B as described here.", "[Primer Preparation] Separate all primers at 100 µM into two separate boxes labeled as P... |
null | null | null | dx.doi.org/10.17504/protocols.io.cqhvt5 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.e22bgge | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Note: If the percentage of CD45+ cells in your sample is less than 50%, please follow Protocol A. If it is higher than 50% then please follow protocol B.</strong></p>
<p> </p>
<p>The cells targeted by the Nanobeads are either selected or depleted by incubating your sa... | [] |
26,548 | U Michigan - Massons Trichrome staining | null | dx.doi.org/10.17504/protocols.io.56ug9ew | null | Jeff Hodgin | TITLE: U Michigan - Massons Trichrome staining
AUTHORS: Jeff Hodgin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Massons Trichrome staining is used for detection of collagen fibers for tubulointerstitial fibrosis on... | ["Wash 2x for 5 minutes in Xylene", "Wash 2x for 3 minutes in 100% EtOH", "Wash 1x for 2 minutes in 95% EtOH", "Wash 1x for 1 minutes in 70% EtOH", "Wash in running tap water for 3 minutes", "Place in Bouins for one hour in 55 -56 degree oven or overnight at room temperature if needed.", "Wash well in running water for... |
69,591 | Size exclusion chromatography of cell lysates containing Tau aggregates | 4 | dx.doi.org/10.17504/protocols.io.4r3l27mjpg1y/v1 | https://www.protocols.io/view/size-exclusion-chromatography-of-cell-lysates-cont-cf7xtrpn | Patricia Yuste Checa, Itika Saha, F. Ulrich Hartl, Mark S. Hipp | TITLE: Size exclusion chromatography of cell lysates containing Tau aggregates
AUTHORS: Patricia Yuste Checa, Itika Saha, F. Ulrich Hartl, Mark S. Hipp
[DESCRIPTION]
This protocolcan be used to fractionate Tau aggregates from cell lysates by size exclusion chromatography. The protocol was optimized using HEK293 cells ... | ["Lyse cell pellets with Triton buffer, Complete EDTA-free protease inhibitor cocktail (Roche) and benzonase for 20 min on ice. NOTE: Triton buffer: 0.05% Triton X-100/PBS or 1% Triton X-100/PBS (more efficient lysis) can be used to lyse cell pellets.", "Clarify the lysates by centrifugation at 1,000 x g for 5 min at 4... |
95,156 | Cylinder test in rats | 1 | dx.doi.org/10.17504/protocols.io.kxygx36zdg8j/v1 | https://www.protocols.io/view/cylinder-test-in-rats-c86uzzew | eduard.bentea, María Sanchiz Calvo, Veerle Baekelandt | TITLE: Cylinder test in rats
AUTHORS: eduard.bentea, María Sanchiz Calvo, Veerle Baekelandt
[DESCRIPTION]
Protocol for performing the cylinder test in rats. The cylinder test evaluates asymmetry in forelimb use, and can be used in animal models with unilateral lesions of the nigrostriatal dopaminergic pathway.
[STEPS... | ["[Test] Bring cages to the behavioral room for at least 60 min prior to the test for habituation", "[Test] Place each rat in a glass cylinder (20-cm wide), surrounded by mirrors to allow a full 360 degree view. Videotape from the front for 5 min or until the rat performs a minimum of 20 weight-bearing forepaw contacts... |
33,944 | First Strand Synthesis with Reverse Transcriptase (M0253) | 1 | dx.doi.org/10.17504/protocols.io.bddyi27w | https://www.protocols.io/view/first-strand-synthesis-with-reverse-transcriptase-bddyi27w | New England Biolabs | TITLE: First Strand Synthesis with Reverse Transcriptase (M0253)
AUTHORS: New England Biolabs
[DESCRIPTION]
This protocol is for First Strand Synthesis with M-MuLV Reverse Transcriptase (M0253).
[BEFORE_START]
Prepare the following solutions:
10X RT buffer:
Tris-HCl (pH 8.3 @ 25°C) 500 mM KCl 750 mM... | ["In a sterile microfuge tube add the following:", "Heat for 3-5 minutes at 65 °C-80 °C.", "Spin briefly and place promptly on ice.", "Add:\n2 µL \n1 µL \n1 µL \n\nFinal volume: 20 µL", "Incubate at 42 °C for 60 min.", "Inactivate enzyme at 90 °C for 10 min.", "Store products at -20 °C or proceed to next step(s)."] |
90,206 | A SARS-CoV-2 Synthetic Control Mixture Preparation Protocol | 4 | dx.doi.org/10.17504/protocols.io.261ged2jjv47/v1 | https://www.protocols.io/view/a-sars-cov-2-synthetic-control-mixture-preparation-c4b6ysre | Jannatul Ferdous, April N Harris, wtaylo, Jessica A Schlueter, Cynthia Gibas | TITLE: A SARS-CoV-2 Synthetic Control Mixture Preparation Protocol
AUTHORS: Jannatul Ferdous, April N Harris, wtaylo, Jessica A Schlueter, Cynthia Gibas
[DESCRIPTION]
Wastewater-based sequencing surveillance has been a powerful tool for monitoring SARS-CoV-2 and making public health decisions. Along with sequencing w... | ["[Selection of Synthetic Controls] Synthetic controls chosen for Ferdous et al. 2023 - Control 15 (Alpha-103909), Control 17 (Gamma-104044), Control 23 (Delta-104533), Control 48 (Omicron - BA.1 lineage-105204), Control 51 (B.1.1.529+BA.2-England-105346), Control 2 (Wuhan hu-1 from china-102024), Control 6 (Wuhan hu-... |
26,993 | 4% Paraformaldehye in .1M PB preparation | 1 | dx.doi.org/10.17504/protocols.io.ewov1yr6kvr2/v1 | https://www.protocols.io/view/4-paraformaldehye-in-1m-pb-preparation-6krhcv6 | Monique Copeland | TITLE: 4% Paraformaldehye in .1M PB preparation
AUTHORS: Monique Copeland
[DESCRIPTION]
For perfusion solution.
[STEPS]
SECTION: Paraformaldehyde prep
1. Add 400 mL of MilliQ water to a 1000 mL
SECTION: Paraformaldehyde prep
2. Add stir bar in beaker and set on hot plate at 50 °C
SECTION: Paraformaldehyde pre... | ["[Paraformaldehyde prep] Add 400 mL of MilliQ water to a 1000 mL", "[Paraformaldehyde prep] Add stir bar in beaker and set on hot plate at 50 °C", "[Paraformaldehyde prep] Add 5 drops (500ul) of 10N NaOH (from 60ml dropper)\n\n \n(this makes the solution basic to help dissolve the paraformaldehyde)", "[Paraformaldehyd... |
91,356 | Beam test | 1 | dx.doi.org/10.17504/protocols.io.kxygx322og8j/v1 | https://www.protocols.io/view/beam-test-c5f4y3qw | Marina Lorente Picón, Núria Peñuelas, Ariadna Laguna, Miquel Vila | TITLE: Beam test
AUTHORS: Marina Lorente Picón, Núria Peñuelas, Ariadna Laguna, Miquel Vila
[DESCRIPTION]
Beam test for mice
[STEPS]
1. Mice are placed at the beginning of an elevated horizontal plexiglass beam
bar covered on scotch tape to avoid limb slip (1m length – 2.5cm width- 0.5m
elevation). At the beginning o... | ["Mice are placed at the beginning of an elevated horizontal plexiglass beam\nbar covered on scotch tape to avoid limb slip (1m length – 2.5cm width- 0.5m\nelevation). At the beginning of the beam we place a little lamp and at the end\nof the beam we place a dark box to motivate the animal to go towards the dark\nside.... |
null | null | null | dx.doi.org/10.17504/protocols.io.dsd6a5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
If one wishes to have a stock of high molecular weight viral DNA that can be stored for long periods of time with minimal shearing or degradation, the viruses can be embedded in agarose before extraction. Extraction of embedded cells is the standard procedure for sizing the geno... | [] |
87,182 | Spider Monkey Genome Assembly and Annotation Script | 5 | dx.doi.org/10.17504/protocols.io.6qpvr3892vmk/v1 | https://www.protocols.io/view/spider-monkey-genome-assembly-and-annotation-scrip-czdnx25e | Gabriela Pozo, Martina Albuja Quintana, Lizbeth Larreátegui, Maria de Lourdes Torres | TITLE: Spider Monkey Genome Assembly and Annotation Script
AUTHORS: Gabriela Pozo, Martina Albuja Quintana, Lizbeth Larreátegui, Maria de Lourdes Torres
[DESCRIPTION]
Oxford Nanopore long reads obtained from sequencing the DNA of an Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps), were used to assem... | ["[ONT Raw Reads: Filtering, Trimming and Sequencing Statistics] NANOFILT \n\nNanoFilt -q 7 < raw_reads.fastq > nanofilt_trimmed.fastq", "[ONT Raw Reads: Filtering, Trimming and Sequencing Statistics] PORECHOP \n\nporechop -i nanofilt_trimmed.fastq.gz -o porechop_reads.fastq.gz", "[ONT Raw Reads: Filtering, Trimming ... |
null | null | null | dx.doi.org/10.17504/protocols.io.ncudaww | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Water-aerobics has been purposed as an attractive alternative to land-based exercise for achieving improved health and fitness in populations with orthopaedic or musculoskeletal limitations, excess adiposity or other medical recommendations. This is reflected in the growing i... | [] |
37,962 | HTAPP_Depletion of CD45+ cells from ovarian cancer ascites single cell suspensions for single-cell RNA-Seq | 1 | dx.doi.org/10.17504/protocols.io.bhbij2ke | https://www.protocols.io/view/htapp-depletion-of-cd45-cells-from-ovarian-cancer-bhbij2ke | Benjamin Izar, Parin Shah, Mei-Ju Su, Isaac Wakiro, Sara Napolitano, Jingyi Wu, Sébastien Vigneau, Asaf Rotem, Orit Rozenblatt-Rosen, Bruce Johnson, Aviv Regev | TITLE: HTAPP_Depletion of CD45+ cells from ovarian cancer ascites single cell suspensions for single-cell RNA-Seq
AUTHORS: Benjamin Izar, Parin Shah, Mei-Ju Su, Isaac Wakiro, Sara Napolitano, Jingyi Wu, Sébastien Vigneau, Asaf Rotem, Orit Rozenblatt-Rosen, Bruce Johnson, Aviv Regev
[DESCRIPTION]
<div class = "text-blo... | ["[Quality Control]\nMix 5 µL of red blood cell-free ascites single-cell suspension with 5 µL Trypan blue and load on hemocytometer. The ascites cell suspension can be obtained following the \"HTAPP_Processing human ovarian cancer ascites to a single-cell suspension for single-cell RNA-seq\" protocol.", "[Quality Contr... |
87,762 | DNA extraction v9.0 (modified BOMB) | 4 | dx.doi.org/10.17504/protocols.io.e6nvwdbb7lmk/v1 | https://www.protocols.io/view/dna-extraction-v9-0-modified-bomb-czxsx7ne | Guan Jie Phang, Tsu-Chun Hung, Yin-Tse Huang | TITLE: DNA extraction v9.0 (modified BOMB)
AUTHORS: Guan Jie Phang, Tsu-Chun Hung, Yin-Tse Huang
[DESCRIPTION]
DNA extraction using yttria-stabilized zirconia beads lysing and automated magnetic bead-based extraction.
[STEPS]
SECTION: Sample Collection
1. Add 200 µL of 0.5 mm beads to a 2mL screw tube.
SECTION: S... | ["[Sample Collection] Add 200 µL of 0.5 mm beads to a 2mL screw tube.", "[Sample Collection] Add 200 µL of 1 mm beads to a 2mL screw tube.", "[Sample Collection] Add870 µL Lysis master mix to 2mL screw tube. The final look:", "[Sample Collection] Collect 20-50 mg of sample to 2mL screw tube", "[Sample lysis] Put the 2m... |
null | null | null | dx.doi.org/10.17504/protocols.io.dkk4uv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Protocol to fix marine samples for flow cytometry analysis of phtoplankton and bacteria with SYBR-Green. <br />Fix at least 2 samples per depth sampled and at least 6 to 10 depths per vertical profile<br /><br /><strong>Reference<br /></strong><a href="https://www.researchgate.n... | [] |
82,048 | LAMP Protocol for Entomopathogenic Serratia spp. in Insect Frass | 4 | dx.doi.org/10.17504/protocols.io.bp2l69j7zlqe/v1 | https://www.protocols.io/view/lamp-protocol-for-entomopathogenic-serratia-spp-in-cuc8wszw | Nicholas P Doidge | TITLE: LAMP Protocol for Entomopathogenic Serratia spp. in Insect Frass
AUTHORS: Nicholas P Doidge
[DESCRIPTION]
A protocol for the detection of insect-associated Serratia spp. in the frass of live insects, using a LAMP assay targeting the ureD gene of urease-positive species from the Serratia marcescens complex. In o... | ["[Bacterial Separation and Concentration] Collect 300 mg fresh per DNA extraction and store at -20 °C until processing.", "[DNA Extraction] Briefly spin the PowerBead Pro tube to ensure the beads have settled at the bottom of the tube.", "[LAMP Assay] Make up stock solutions of the LAMP primers using MG H20. Add the... |
88,423 | JMN-MSMP Volumetric Muscle Loss Surgery | 1 | dx.doi.org/10.17504/protocols.io.ewov1qdm2gr2/v2 | https://www.protocols.io/view/jmn-msmp-volumetric-muscle-loss-surgery-c2kfyctn | ccherry | TITLE: JMN-MSMP Volumetric Muscle Loss Surgery
AUTHORS: ccherry
[DESCRIPTION]
VML Surgery
[STEPS]
1. Disinfect all surfaces and anesthetic equipment (induction chamber, nose cone) with Vimoba (Quip Laboratories VIMTAB).
2. Prepare sterile surgical area and a separate surgical prep area (shaving, Rimadyl injection). A... | ["Disinfect all surfaces and anesthetic equipment (induction chamber, nose cone) with Vimoba (Quip Laboratories VIMTAB).", "Prepare sterile surgical area and a separate surgical prep area (shaving, Rimadyl injection). Anesthesia should be available in both areas.", "Anesthetize the mouse. The following settings should ... |
29,925 | Lemna minor (duckweed) sterilization protocol | null | dx.doi.org/10.17504/protocols.io.9gdh3s6 | null | Jason Laurich | TITLE: Lemna minor (duckweed) sterilization protocol
AUTHORS: Jason Laurich
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is designed to sterilize fronds of the common duckweed (</span><span style = "font-style:italic;">Lemna minor</span><span>) but should also be applicable to... | ["[Duckweed Sterilization : Preparation]\nIn a tea-strainer, strain duckweed plants under running water (doesn’t have to be sterile). This step gets rid of some surface algae.", "[Duckweed Sterilization : Preparation]\nMove surface-rinsed duckweed into a water bath; remove up to 50 plants from water bath and place in 5... |
null | null | null | dx.doi.org/10.17504/protocols.io.ntkdekw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
83,932 | E7805 NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina® Protocol for use with Inputs ≤ 100 ng | 1 | dx.doi.org/10.17504/protocols.io.14egnypmv5dy/v2 | https://www.protocols.click/view/e7805-nebnext-ultra-ii-fs-dna-library-prep-kit-for-cv74w9qw | jbonnevie | TITLE: E7805 NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina® Protocol for use with Inputs ≤ 100 ng
AUTHORS: jbonnevie
[DESCRIPTION]
The NEBNext Ultra II FS DNA Module contains the enzymes and buffers required to convert a broad range of input amounts of DNA into high quality libraries for next generation sequ... | ["[Starting Material] 100 pg–500 ng purified, genomic DNA. We recommend that the DNA be in 1X TE (10 mM Tris pH 8.0, 1 mM EDTA), however, 10 mM Tris pH 7.5–8, low EDTA TE or H2O are also acceptable. If the input DNA is less than 26 µl, add TE (provided) to a final volume of 26 µl.", "[Fragmentation/End Prep] Fragmentat... |
71,840 | In Silico analysis links the NSL complex to Parkinson’s disease and the mitochondria – Protein-protein interaction data to functional enrichment analysis | 5 | dx.doi.org/10.17504/protocols.io.5qpvorb19v4o/v1 | https://www.protocols.io/view/in-silico-analysis-links-the-nsl-complex-to-parkin-cid8ua9w | Katie Kelly, c.manzoni, Patrick Lewis, Helene Plun-Favreau | TITLE: In Silico analysis links the NSL complex to Parkinson’s disease and the mitochondria – Protein-protein interaction data to functional enrichment analysis
AUTHORS: Katie Kelly, c.manzoni, Patrick Lewis, Helene Plun-Favreau
[DESCRIPTION]
Whilst the majority (~90-95%) of PD cases are sporadic, much of our understa... | ["[Downloading the Protein-Protein Interaction (PPI) Data] All code can be found here : v1.0.0_W-PPI-NA_NSL\nThe pipeline to derive the first layer interactome can be found in Figure 1.", "[Downloading the Protein-Protein Interaction (PPI) Data] Collect PPIs for NSL seeds using 3 different web-based tools;\n\n1) PINOT ... |
62,969 | 10 Ways Tamra Judge CBD Gummies Can Improve Health! Reduce Chronic Pain! | 3 | dx.doi.org/10.17504/protocols.io.ewov1n79kgr2/v1 | https://www.protocols.io/view/10-ways-tamra-judge-cbd-gummies-can-improve-health-b9qzr5x6 | Tamra Judge CBD Gummies | TITLE: 10 Ways Tamra Judge CBD Gummies Can Improve Health! Reduce Chronic Pain!
AUTHORS: Tamra Judge CBD Gummies
[DESCRIPTION]
Tamra Judge CBD Gummies is a chewable gummy supplement that offers a variety of natural health benefits for stress relief. ORDER NOW THIS IS MY OFFICIAL WEBSITE!
BUY NOW - https://www.elitegro... | [] |
40,598 | Pouring LB Agar Plates - Chem 584 | 1 | dx.doi.org/10.17504/protocols.io.bjvwkn7e | https://www.protocols.io/view/pouring-lb-agar-plates-chem-584-bjvwkn7e | Addgene The Nonprofit Plasmid Repository, Ken Christensen | TITLE: Pouring LB Agar Plates - Chem 584
AUTHORS: Addgene The Nonprofit Plasmid Repository, Ken Christensen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The following protocol is for making LB agar plates for the purpose of bacterial selection (500mL of LB agar makes about 25 LB agar plates... | ["Measure of agar powder and pre-mixed LB powder per L of molten agar you’d like to make. The precise mass you measure out will be based on the number of plates you’d like to pour.\n15 g\n20 g\nExample: Because we’d like to make 20 plates, and our plates can hold a maximum of , we’ll want of media total.Importantl... |
85,603 | ORFanID Web-based Search Engine to Identify Orphan and Taxonomically Restricted Genes | 1 | dx.doi.org/10.17504/protocols.io.14egn37jql5d/v1 | https://www.protocols.io/view/orfanid-web-based-search-engine-to-identify-orphan-cxubxnsn | Thushara Galbadage, Vinodh Gunasekera, Emanuel Tundrea, Richard S. Gunasekera | TITLE: ORFanID Web-based Search Engine to Identify Orphan and Taxonomically Restricted Genes
AUTHORS: Thushara Galbadage, Vinodh Gunasekera, Emanuel Tundrea, Richard S. Gunasekera
[DESCRIPTION]
ORFanID is a web-based software engine designed to identify ORFan genes from genomes of interest; from a given list of DNA or... | ["[Accessing ORFanID] Navigate to ORFanID's webpage at http://www.orfangenes.com/", "[Accessing ORFanID] Click \"Get Started\" on the home page to access the search system.", "[Input Methods] Choose between searching for a gene sequence or using an accession number. For instance, to search a Homo sapiens sample, use th... |
103,787 | Strategies to Minimize Variability Between Individual qPCR Reactions | 0 | dx.doi.org/10.17504/protocols.io.n2bvjnz6pgk5/v1 | https://www.protocols.io/view/strategies-to-minimize-variability-between-individ-dhkj34un | Jonathan Phillips, David Chen, Gregor Blaha | TITLE: Strategies to Minimize Variability Between Individual qPCR Reactions
AUTHORS: Jonathan Phillips, David Chen, Gregor Blaha
[DESCRIPTION]
Precise pipetting is paramount for generating precise and reliable qPCR results. Despite meticulous pipetting, significant variability can arise in qPCR, even between technical... | [] |
34,391 | Data for manuscript: Selection of forage oat genotypes through GGE Biplot and BLUP | null | dx.doi.org/10.17504/protocols.io.bdtxi6pn | null | Franklin Santos, Felix Marza | TITLE: Data for manuscript: Selection of forage oat genotypes through GGE Biplot and BLUP
AUTHORS: Franklin Santos, Felix Marza
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>In Bolivia, there is a low predominance of forage oat productivity. Therefore, it was proposed to select more product... | [] |
83,343 | Taxon Group Protists: Barcoding | 1 | dx.doi.org/10.17504/protocols.io.4r3l22m1pl1y/v1 | https://www.protocols.io/view/taxon-group-protists-barcoding-cvmpw45n | Estelle Kilias | TITLE: Taxon Group Protists: Barcoding
AUTHORS: Estelle Kilias
[DESCRIPTION]
This protocol describes the DNA barcoding process for protists in the Darwin Tree of Life project.
[STEPS]
SECTION: DNA extraction
1. Extract genomic DNA from protists cultures using e.g. the DNeasy Plant or MagAttract kit (Qiagen) or equi... | ["[DNA extraction] Extract genomic DNA from protists cultures using e.g. the DNeasy Plant or MagAttract kit (Qiagen) or equivalent and follow the manufacturer’s protocol/instructions. Depending on the taxa, DNA extraction can require an alternative pre-protocol approach, e.g. including a Plant DNAzol Reagent (Gibco BRL... |
88,193 | NEDC matrix application for metabolite imaging using MALDI-MSI | 1 | dx.doi.org/10.17504/protocols.io.ewov1q28kgr2/v1 | https://www.protocols.io/view/nedc-matrix-application-for-metabolite-imaging-usi-c2c9yaz6 | Antonia Fecke, Karl W Smith, Siva Swapna Kasarla, Philipp Bäuml, Prasad Phapale | TITLE: NEDC matrix application for metabolite imaging using MALDI-MSI
AUTHORS: Antonia Fecke, Karl W Smith, Siva Swapna Kasarla, Philipp Bäuml, Prasad Phapale
[DESCRIPTION]
Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has emerged as a analytical technique more than 30 years ago. Originally ... | ["[Matrix Application] Matrix Application for MALDI-MSI", "[Sample preparation and cryosectioning] Remove fresh frozen tissue sample stored at -80°C and place in cryostat at -20°C (kidney)/ -17°C (liver)/ -22°C (brain)", "[Sample preparation and cryosectioning] Mount the sample on chuck by pipetting small droplets of w... |
71,063 | Determining biofilm growth amount (absorbance) | 4 | dx.doi.org/10.17504/protocols.io.n2bvj8x95gk5/v1 | https://www.protocols.io/view/determining-biofilm-growth-amount-absorbance-chmxt47n | An.Huang | TITLE: Determining biofilm growth amount (absorbance)
AUTHORS: An.Huang
[DESCRIPTION]
This protocol describes a method to determine the growth amount of biofilm at the early stage of biofilm formation by measuring absorbance. Here we use our own engineered bacteria, and it requires induction of IPTG and cultured with... | ["[IPTG induction] Escherichia coli grown overnight was diluted by LB to OD600=0.4-0.6.", "[IPTG induction] IPTG was added to cell culture to 1mM IPTG finally, and incubated 3h at 171 rpm, 37℃ in orbital shaking incubator.", "[Sample preparation] Preparing several flasks by filling the flasks with MBBR carrier K1. Auto... |
null | null | null | dx.doi.org/10.17504/protocols.io.ezrbf56 | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p><strong>Reagent List:</strong></p>
<ul>
<li>Sterile PBS</li>
<li>Cell culture medium (IMDM supplemented with 10% FBS)</li>
<li>Sterile plastic petri dishes</li>
<li>RBC Lysis Buffer (Cat. No. 420301)</li>
<li>Anti-mouse CD3ε, clone 145-2C11 (LEAF™ format, Cat. No. 100314)</li>... | [] |
58,893 | Preparing Borax RapidBuffer for electrophoresis | 4 | dx.doi.org/10.17504/protocols.io.ewov1nqopgr2/v1 | https://www.protocols.io/view/preparing-borax-rapidbuffer-for-electrophoresis-b5rmq546 | Jenny Molloy, Nadine Mowoh, Stephane Fadanka, Cordellia Fulai | TITLE: Preparing Borax RapidBuffer for electrophoresis
AUTHORS: Jenny Molloy, Nadine Mowoh, Stephane Fadanka, Cordellia Fulai
[DESCRIPTION]
Molecular biologists often use tris-based conduction buffers like TBE or TAE in running DNA gels. These buffers are known to overheat at high voltages, causing problems with gel ... | ["[Preparation of 10x Borax RapidBuffer Solution] Pour the prepared solution into a clean, labelled screw-top 1000 mL glass or plastic storage bottle and store at Room temperature until use.", "[Preparation of 10x Borax RapidBuffer Solution] Add distilled or de-ionised water to a total of 1000 mL and stir again for 3 m... |
63,588 | VOC and VOI (SARS-Cov-2) identification by Sanger Sequencing | 1 | dx.doi.org/10.17504/protocols.io.ewov1nxqkgr2/v2 | https://www.protocols.io/view/voc-and-voi-sars-cov-2-identification-by-sanger-se-caccsasw | Laís Ceschini, Matheus Filgueira Bezerra, Viviane do Carmo Vasconcelos de Carvalho, Cássia Docena, Marcelo Henrique Santos Paiva, Gabriel Luz Wallau | TITLE: VOC and VOI (SARS-Cov-2) identification by Sanger Sequencing
AUTHORS: Laís Ceschini, Matheus Filgueira Bezerra, Viviane do Carmo Vasconcelos de Carvalho, Cássia Docena, Marcelo Henrique Santos Paiva, Gabriel Luz Wallau
[DESCRIPTION]
The method hereby described is an update of a rapid and accessi... | ["[cDNA Synthesis] Mix the following components in an 0.2mL 8-strip tube or 96 well PCR plate;\n\nComponent Value\n\n 10X RT B uffer 2.0 µL \n dNTP Mix (100mM) 0.8 µL \n10X RT Ra... |
97,568 | Recipe for 50x TAE buffer | 1 | null | https://www.protocols.io/view/recipe-for-50x-tae-buffer-dbh82j9w | Anna Behle, Alice Pawlowski | TITLE: Recipe for 50x TAE buffer
AUTHORS: Anna Behle, Alice Pawlowski
[DESCRIPTION]
Stock solution for 50x TAE. TAE buffer is a solution made up of Tris base, acetic acid and EDTA (Tris-acetate-EDTA). It is a common buffer for DNA separation using standard agarose gel electrophoresis.
[STEPS]
SECTION: Preparation of ... | ["[Preparation of a 0.5 M EDTA stock solution] For 500 ml:\nweigh out 93.05 grams of EDTA disodium salt (MW=372.24 g/mol)\nDissolve in 400 milliliter deionized water and adjust the pH with solid sodium hydroxide (NaOH) plates, EDTA will not go completely into solution until the pH is adjusted to about 8.0!\nTop up the ... |
65,365 | K3T0 Keto Gummies | 1 | dx.doi.org/10.17504/protocols.io.3byl4b83rvo5/v1 | https://www.protocols.io/view/k3t0-keto-gummies-cb3vsqn6 | vallakhalisi | TITLE: K3T0 Keto Gummies
AUTHORS: vallakhalisi
[DESCRIPTION]
Product name:- K3T0 Keto Gummies
Company:- Keto Blast
Key Ingredients:- BHB and ACV
Side Effects:- Not yet reported
Price:- $59.74
Ratings:- 4.5/5
Official Website: - https://www.globalfitnessmart.com/get-k3to-keto-gummies
Check Report Of Myco Mode Nootro... | [] |
94,188 | Open field test | 4 | dx.doi.org/10.17504/protocols.io.5qpvo3677v4o/v1 | https://www.protocols.io/view/open-field-test-c78kzruw | mariangela.massarocenere | TITLE: Open field test
AUTHORS: mariangela.massarocenere
[DESCRIPTION]
The open field test is a simple test to evaluate general motor and explorative behavior in rodents
[STEPS]
2. Place the animal in the center of open field cylindrical arena (100 cm diameter) with dark walls (35 cm) and floor, under dim lighting ... | ["Place the animal in the center of open field cylindrical arena (100 cm diameter) with dark walls (35 cm) and floor, under dim lighting (300 lux)", "Habituate the animal for 1 h to the testing room before the test", "Leave the animal free to explore the arena for 10min and record with a video camera suspended above t... |
73,689 | Opentrons pipeline: gDNA bead cleanup | 4 | dx.doi.org/10.17504/protocols.io.3byl4j9pzlo5/v1 | https://www.protocols.io/view/opentrons-pipeline-gdna-bead-cleanup-cj7zurp6 | Jhakelin Reyes Vasquez, P. Sánchez-Vendizú, Mrinalini Watsa, Gideon Erkenswick | TITLE: Opentrons pipeline: gDNA bead cleanup
AUTHORS: Jhakelin Reyes Vasquez, P. Sánchez-Vendizú, Mrinalini Watsa, Gideon Erkenswick
[DESCRIPTION]
This protocol is an automated pipeline to clean a plate of extracted DNA using SPRI bead cleanup. It is functional for both. It is typically used to clean up a portion of... | ["[BEFORE STARTING] Materials:\nAutoclave and UV the items you will use to ensure sterility. Some items can be autoclaved and reused as indicated below.\n \n ItemquantitycheckstatusAutoclavedUVOpentrons 20µL Filter Tips31NEWOpentrons 200µL Filter Tips21NEW1NEST 1-Well Reservoirs, 195 mL11REUSED11NEST 12-Well Reser... |
108,988 | Zymo OneStep PCR Inhibitor Removal Kit | 0 | dx.doi.org/10.17504/protocols.io.5qpvokmrbl4o/v1 | https://www.protocols.io/view/zymo-onestep-pcr-inhibitor-removal-kit-dnn45dgw | Shannon Fitz, Alex Shaw, michael Owusu, Dilip Abraham | TITLE: Zymo OneStep PCR Inhibitor Removal Kit
AUTHORS: Shannon Fitz, Alex Shaw, michael Owusu, Dilip Abraham
[DESCRIPTION]
Features:
• For high quality DNA or RNA that is free of enzymatic inhibitors including polyphenolics, humic/fulvic acids, tannins, melanin, etc.
• Fast, one-step procedure for “cleaning” impure sa... | ["[Column Preparation] Insert column into a Collection Tube. \n\n*Please note that matrix in the column may appear dehydrated, or powdery. This is normal.", "[Column Preparation] Open the cap, add 600 µl of Prep-Solution and centrifuge at 8,000 x g for 3 minutes.", "[Column Preparation] Inhibitor Removal:\n\nTransfer t... |
68,886 | Liposome tubulation | 1 | dx.doi.org/10.17504/protocols.io.e6nvwkx2dvmk/v1 | https://www.protocols.io/view/liposome-tubulation-cfhwtj7e | Xinbo Wang, Pietro De Camilli | TITLE: Liposome tubulation
AUTHORS: Xinbo Wang, Pietro De Camilli
[DESCRIPTION]
This protocol details methods for the LRRK2-induced liposome tubulation experiment and its analysis by confocal fluorescence microscopy and negative stained electron microscopy.
[STEPS]
SECTION: Confocal fluorescence microscopy analysis
1... | ["[Confocal fluorescence microscopy analysis] Prepare the samples in a PCR tube with 300 nanomolar (nM) LRKK2 proteins (WT or mutant full length LRRK2 or RCKW), 20 micromolar (µM) liposomes with or without 1 millimolar (mM) GMPPNP (or other guanylnucleotides).", "[Confocal fluorescence microscopy analysis] Immediately ... |
28,404 | MojoSort™ Mouse Neutrophil Isolation Kit Protocol | null | dx.doi.org/10.17504/protocols.io.7yuhpww | null | Sam Li | TITLE: MojoSort™ Mouse Neutrophil Isolation Kit Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Product description and procedure summary:</span></div><div class = "text-block">Target cells are depleted by incubating your sample with the bio... | ["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... |
40,883 | Astrios EQ instrument setup and sample acquisition | 1 | dx.doi.org/10.17504/protocols.io.bj6tkren | https://www.protocols.io/view/astrios-eq-instrument-setup-and-sample-acquisition-bj6tkren | Aizea Morales-Kastresana, Joshua Welsh, Jennifer Jones | TITLE: Astrios EQ instrument setup and sample acquisition
AUTHORS: Aizea Morales-Kastresana, Joshua Welsh, Jennifer Jones
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In this protocol the authors describe the general steps to follow in order to achieve optimallaser:stream:detectors alignment and... | ["Turn on the instrument at least an hour before running the samples. Let the pressure and stream to stabilize and prime the fluidics system to remove bubbles in the circuit. Turn lasers on and allow them to warm up whilst shuttered.", "Wash the sample line with FACS Rinse solution for about 20 minutes at a high differ... |
null | null | null | dx.doi.org/10.17504/protocols.io.cg6tzd | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?. | [] |
85,278 | Using MultiQuant software and Excel software to evaluate and report multi-analyte targeted LC-MS/MS data | 5 | null | https://www.protocols.click/view/using-multiquant-software-and-excel-software-to-ev-cxh6xj9e | Natalie ZM Homer | TITLE: Using MultiQuant software and Excel software to evaluate and report multi-analyte targeted LC-MS/MS data
AUTHORS: Natalie ZM Homer
[DESCRIPTION]
This protocol describes how to evaluate and report targeted LC-MS/MS data that has been collected in Analyst software on AB Sciex mass spectrometers. It describes usin... | ["[Using MultiQuant to evaluate Analyst acquired LC-MS/MS data] Create a new result file in MultiQuant 3.0.3 by opening the software, selecting a data file, selecting some or all of the samples in the batch of the file, selecting a processing method and allowing the software to evaluate the data, before defining calibr... |
26,143 | What is the Arch Enemy of Women Health – A Brief Introduction to Breast Cancer | null | dx.doi.org/10.17504/protocols.io.5r7g59n | null | Echo Han | TITLE: What is the Arch Enemy of Women Health – A Brief Introduction to Breast Cancer
AUTHORS: Echo Han
[STEPS]
?. An Introduction to Breast Cancer Breast cancer (BC) is regarded as the lethal cancer to women’s life on a worldwide scale. The majority of breast cancers are carcinomas that are generated from cells linin... | ["An Introduction to Breast Cancer Breast cancer (BC) is regarded as the lethal cancer to women’s life on a worldwide scale. The majority of breast cancers are carcinomas that are generated from cells lining the milk-forming ducts of the mammary gland. Breast cancer, as a kind of disease of which the cause can not be c... |
97,858 | Open Field | 0 | dx.doi.org/10.17504/protocols.io.6qpvr8ejplmk/v1 | https://www.protocols.io/view/open-field-dbta2nie | Sabina Marciano, Roberta Marongiu | TITLE: Open Field
AUTHORS: Sabina Marciano, Roberta Marongiu
[DESCRIPTION]
Protocol for general locomotion in rodents using open field arenas and Ethovision video tracking.
Purpose: Assess cognitive, spontaneous motor activity, and anxiety
Note that there are many variations of this test. We perform this test during t... | ["[Protocol for spontaneous activity measurement:] Days 1-2 – training\nThe purpose of the training days is to reduce to the minimum the influence of cognitive and anxiety states on motor activity by acclimating the mice to the equipment. Additional training days can be added if preferred.", "[Protocol for spontaneous ... |
null | null | null | dx.doi.org/10.17504/protocols.io.mnrc5d6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Objective </strong></p>
<p>To determine whether the topical application of platelet-rich plasma (PRP) promotes healing in experimentally-induced full-thickness skin wounds in animals, a systematic review and meta-analysis will be performed.</p>
<p><strong>Methods</str... | [] |
88,707 | UPitt TriState SenNet TMC FFPE Specimen Section | 1 | dx.doi.org/10.17504/protocols.io.q26g7pxz8gwz/v1 | https://www.protocols.io/view/upitt-tristate-sennet-tmc-ffpe-specimen-section-c2vbye2n | John Sembrat, Marta Bueno | TITLE: UPitt TriState SenNet TMC FFPE Specimen Section
AUTHORS: John Sembrat, Marta Bueno
[DESCRIPTION]
To perform imaging analysis of the FFPE blocks were submitted to hematoxylin and eosin stain. Initially FFPE blocks were prepare by the Research Histology Pitt Biospecimen Core and kept at room temperature (preserv... | ["[Section Collection] Using a Histo-Quill Pen, hand label all slides with project number and block ID (add type of stain if needed) .", "[Section Collection] Ensure paraffin block is at room temperature.", "[Section Collection] Place block into holder of microtome.", "[Section Collection] Use clean, sharp microtome kn... |
94,477 | α-Synuclein aggregation monitored by thioflavin-T (ThT) fluorescence in a plate reader | 1 | dx.doi.org/10.17504/protocols.io.8epv5x87dg1b/v1 | https://www.protocols.io/view/synuclein-aggregation-monitored-by-thioflavin-t-t-c8hmzt46 | Patricia Yuste-Checa, F Ulrich Hartl | TITLE: α-Synuclein aggregation monitored by thioflavin-T (ThT) fluorescence in a plate reader
AUTHORS: Patricia Yuste-Checa, F Ulrich Hartl
[DESCRIPTION]
This protocol details how to efficiently monitor α-Synuclein aggregation by thioflavin T fluorescence in a plate reader.
[STEPS]
SECTION: α-Synuclein aggregation mo... | ["[α-Synuclein aggregation monitored by thioflavin-T (ThT) fluorescence in a plate reader] Mix reagents to a final concentration of 200 micromolar (µM) α-Synuclein, 0.05 % NaN3,\n10 micromolar (µM) ThT in α-Synuclein fibril buffer. Prepare a mix for 4.5 reactions per condition (per condition, four technical replicates ... |
54,010 | Microfluidics 4: PDMS Chip Soft Lithography | 1 | dx.doi.org/10.17504/protocols.io.byy2pxye | https://www.protocols.io/view/microfluidics-4-pdms-chip-soft-lithography-byy2pxye | Serhat Sevli, C. Yunus Sahan | TITLE: Microfluidics 4: PDMS Chip Soft Lithography
AUTHORS: Serhat Sevli, C. Yunus Sahan
[DESCRIPTION]
Microfluidics materials are of various types and application-specific. PDMS is one of the most preferred and cost-effective solutions for research and low-volume manufacturing. After having the mold, PDMS replicas a... | ["[Mixing Components of PDMS] 1.0.1. PDMS constituents are mixed in 10:1; Sylgard184 monomer : Hardening agent", "[Mixing Components of PDMS] 1.1.1. Switch on weighing machine power. \n\n1.1.2. Place an empty 50 mL tube on the weighing machine and tare the balance.\n\n1.1.3. Pour the Sylgard184 monomer inside a 50mL tu... |
30,607 | Immunohistochemistry Protocol for Keratin Antibodies | null | dx.doi.org/10.17504/protocols.io.95ph85n | null | Sam Li | TITLE: Immunohistochemistry Protocol for Keratin Antibodies
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Clear Slides: Removes paraffin and hydrates the tissue]
Note:If using frozen sections, allow slides to come to room temperature for 15 minutes & proceed to step (F) only A. Xylene:
5... | ["[Clear Slides: Removes paraffin and hydrates the tissue]\nNote:If using frozen sections, allow slides to come to room temperature for 15 minutes & proceed to step (F) only A. Xylene:\n5 minutes in each of (3) different 250mL containersB. 100% alcohol\n5 minutes in each of (3) different 250mL containersC. 95% alcohol\... |
42,207 | ND5 sequencing of Oncorhynchus masou masou | 4 | dx.doi.org/10.17504/protocols.io.bmf7k3rn | https://www.protocols.io/view/nd5-sequencing-of-oncorhynchus-masou-masou-bmf7k3rn | Yoko Kato-Unoki | TITLE: ND5 sequencing of Oncorhynchus masou masou
AUTHORS: Yoko Kato-Unoki
[STEPS]
?. Amplify the ND5 region (1597 bp) with the following PCR mixture and program. AB1ComponentAmount25× Phusion HF buffer (New England BioLabs)2 μl3Phusion DNA Polymerase (New England BioLabs)0.1 μl410 mM dNTPs0.2 μl510 μM primer ND5-F10... | ["Amplify the ND5 region (1597 bp) with the following PCR mixture and program. AB1ComponentAmount25× Phusion HF buffer (New England BioLabs)2 μl3Phusion DNA Polymerase (New England BioLabs)0.1 μl410 mM dNTPs0.2 μl510 μM primer ND5-F10.5 μl610 μM primer ND5-R0.5 μl7Genomic DNA10–50 ng8Nuclease-free waterVariable9Total ... |
42,246 | Example PLSR for Predicting Leaf Traits from Leaf Spectra | 3 | dx.doi.org/10.17504/protocols.io.bmhek33e | https://www.protocols.io/view/example-plsr-for-predicting-leaf-traits-from-leaf-bmhek33e | Angela C Burnett, Jeremiah Anderson, Kenneth J Davidson, Kim S Ely, Julien Lamour, Qianyu Li, Bailey Morrison, Dedi Yang, Alistair Rogers, Shawn P Serbin | TITLE: Example PLSR for Predicting Leaf Traits from Leaf Spectra
AUTHORS: Angela C Burnett, Jeremiah Anderson, Kenneth J Davidson, Kim S Ely, Julien Lamour, Qianyu Li, Bailey Morrison, Dedi Yang, Alistair Rogers, Shawn P Serbin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for predicting ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.qagdsbw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p> </p>
<p>Embodied cognition research suggests that bodily experiences might ground mental representations of emotional valence in the vertical dimension of space (i.e., positive is up and negative is down). Accordingly, recent studies show that upward and downward arm movemen... | [] |
44,807 | Performance Study of Wireless Fecobionics Device in Canine | 1 | dx.doi.org/10.17504/protocols.io.bpzfmp3n | https://www.protocols.io/view/performance-study-of-wireless-fecobionics-device-i-bpzfmp3n | Yanmin Wang, Hans Gregersen | TITLE: Performance Study of Wireless Fecobionics Device in Canine
AUTHORS: Yanmin Wang, Hans Gregersen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We developed a novel wireless device (Fecobionics) for mapping colonic and anorectal neuromuscular function. The hypothesis of this protocol is that ... | ["[Cannula test]\nAfter a laparotomy, a cannula was implanted into the proximal of the colon (4-5 cm to cecum)", "[Cannula test]\nThe external end of the cannula was screwed by a cap, which is able to open for device insertion", "[Cannula test]\nAfter 10-14 days recovery, the Fecobionics was inserted through the cannul... |
57,445 | Southern transect resurvey 2022 | 1 | dx.doi.org/10.17504/protocols.io.b4cdqss6 | https://www.protocols.io/view/southern-transect-resurvey-2022-b4cdqss6 | Lauren Ponisio | TITLE: Southern transect resurvey 2022
AUTHORS: Lauren Ponisio
[DESCRIPTION]
This protocol details the Ponisio Lab's collecting protocol for the 2022 Moldenke re-survey of the southern transect. Each site consists of two 900m long transects, marked every 100m with flagging tape and a nail. Each transect has three 10m... | ["[Field station prep] Prior to collection, it is important to make sure that the following preparations are made:\n\nShared sampling box:\nGPS x2\nspare batteries \nflagging tape\npin flags \nspare sharpies, microns etc \ntransect tapes \norange cones \n\nShared collection equipment/consumables:\nFreezeproof snap caps... |
null | null | null | dx.doi.org/10.17504/protocols.io.e2jbgcn | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p>Use with Ultra Streptavidin Detection Kit (<a href="https://antibody.biolegend.com/datasheet.php?UpProd=&catalogno=SIG-32250" target="_blank">SIG-32250)</a> or (<a href="https://antibody.biolegend.com/datasheet.php?UpProd=&catalogno=SIG-32248" target="_blank">SIG-32248... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.kzmcx46 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Genotyping by sequencing (GBS) is a restriction enzyme based targeted approach developed to reduce the genome complexity and discover genetic markers when <em>a priori</em> sequence information is unavailable. Sufficient coverage at each locus is essential to distinguish hete... | [] |
73,640 | IDEXX as a Quantitative Detection Method for Antibiotic Resistant (ABR) E. coli | 1 | dx.doi.org/10.17504/protocols.io.5qpvorkz9v4o/v1 | https://www.protocols.io/view/idexx-as-a-quantitative-detection-method-for-antib-cj6gurbw | Gracie Hornsby | TITLE: IDEXX as a Quantitative Detection Method for Antibiotic Resistant (ABR) E. coli
AUTHORS: Gracie Hornsby
[DESCRIPTION]
This SOP describes the validated modification to the standard IDEXX defined substrate assay for detecting both E. coli and Cefotaxime resistant E. coli in environmental matrices. This method wa... | ["[GROWING AND ESTIMATING E. COLI CONCENTRATIONS FROM A STANDARD STOCK] Follow standard protocol for starting and preparing the laminar flow hood (BSL-2)", "[GROWING AND ESTIMATING E. COLI CONCENTRATIONS FROM A STANDARD STOCK] Sterilize bench with 10% bleach solution then 70% ethanol solution", "[GROWING AND ESTIMATING... |
null | null | null | dx.doi.org/10.17504/protocols.io.nhxdb7n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<section>
<p><a href="http://bioinformatics.psb.ugent.be/webtools/trapid/" target="_blank">TRAPID</a> is an online tool for the fast, reliable and user-friendly analysis of <em>de novo</em> transcriptomes, developed and maintained by the CNB group at VIB-UGent Center for Plant S... | [] |
100,565 | Automated Bar-Seq Library Preparation and Pooling | 0 | dx.doi.org/10.17504/protocols.io.3byl49qdjgo5/v1 | https://www.protocols.io/view/automated-bar-seq-library-preparation-and-pooling-defv3bn6 | David Ross, Nina Alperovich | TITLE: Automated Bar-Seq Library Preparation and Pooling
AUTHORS: David Ross, Nina Alperovich
[DESCRIPTION]
Protocol for automated Bar-Seq Library preparation
This protocol prepares 96 DNA samples, representing 24 samples from 4 different timepoints, for multiplexed Illumina sequencing. The process starts with two r... | ["[Transfer Plasmid DNA to PCR Plate and Dilute with DI water] Pre-heat the on deck thermocycler (ODTC) for 1st PCR step", "[Transfer Plasmid DNA to PCR Plate and Dilute with DI water] Remove lids from PCR-Plate 1, Sample-Plate, and Reagent Plate", "[Transfer Plasmid DNA to PCR Plate and Dilute with DI water] Transfer ... |
31,431 | Classic Latke's Recipe | null | dx.doi.org/10.17504/protocols.io.baxfifjn | null | Lenny Teytelman, Dmitry Lupyan | TITLE: Classic Latke's Recipe
AUTHORS: Lenny Teytelman, Dmitry Lupyan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This recipe is traditional Eastern-European Jewish latkes (potato pancakes). This latke recipe was adapted from </span><a href="https://cooking.nytimes.com/recipes/1015533-... | ["Do not peel! No need to peel! Wash 6 Russet potatoes.", "With either food processor or hand grater, use the coarse disc/side to grate the potatoes and the onion into the bowl", "Transfer potato/onion mixture into a cloth towel and squeeze all the moisture possible. (this is a critical step for the latkes to come ou... |
44,911 | Feacalis_colony_PCR | 4 | null | https://www.protocols.io/view/feacalis-colony-pcr-bp4pmqvn | Elizabeth Fozo | TITLE: Feacalis_colony_PCR
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-style:italic;">E. faecalis</span><span> colony PCR using taq polymerase</span></div></div>
[STEPS]
?. [E. faecalis colony PCR using taq polymerase]
Transfer 1 colony, depending on ... | ["[E. faecalis colony PCR using taq polymerase]\nTransfer 1 colony, depending on size to 50-100µLwater. Normal size colonies can go in ~65µLwater.", "[E. faecalis colony PCR using taq polymerase]\nTo a PCR tube add:15 µL colony water*1.25 µL primer 1 (20 µM stock)1.25 µL primer 2 (20 µM stock)2.5 µL10X thermopolbuffer0... |
45,730 | sci-RNA-seq2 Pipeline for the Human Biomolecular Atlas Program (HuBMAP) | 1 | dx.doi.org/10.17504/protocols.io.bqwamxae | https://www.protocols.io/view/sci-rna-seq2-pipeline-for-the-human-biomolecular-a-bqwamxae | Shin Lin, Cole Trapnell, Jay Shendure | TITLE: sci-RNA-seq2 Pipeline for the Human Biomolecular Atlas Program (HuBMAP)
AUTHORS: Shin Lin, Cole Trapnell, Jay Shendure
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This document provides an overview of the protocols used by the Caltech-UW TMC to perform sci-RNA-seq2. This involves sequenci... | ["Collection and processing of human tissues.Sample procurement: dx.doi.org/10.17504/protocols.io.biqpkdvnFlash freezing: dx.doi.org/10.17504/protocols.io.biqqkdvw", "sci-RNA-seq2 assaydx.doi.org/10.17504/protocols.io.binskdee"] |
62,551 | MIBI staining | 1 | dx.doi.org/10.17504/protocols.io.dm6gprk2dvzp/v4 | https://www.protocols.io/view/mibi-staining-b9bxr2pn | Marc MB Bosse, Sean Bendall, Mike Angelo | TITLE: MIBI staining
AUTHORS: Marc MB Bosse, Sean Bendall, Mike Angelo
[DESCRIPTION]
This protocol is the standard FFPE tissue staining procedure recommended for Multiplex Ion Beam Imaging Time of Flight instrument (MIBI_TOF) developed in the Sean C. Bendall and Michael R. Angelo labs. The protocol has been successf... | ["[Slide for MIBI] FFPE or frozen sections should be deposited on special conductive slides for MIBI\nIt is recommended to use freshly cut tissue sections. Otherwise tissue section slides should be stored properly using different state of the art methods (vacuum chamber, nitrogen chamber or vacuum sealed bags)", "[Sli... |
null | null | null | dx.doi.org/10.17504/protocols.io.mgjc3un | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is an epigenomic profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing. As only the t... | [] |
29,138 | Cell-free 3PGA energy solution | null | dx.doi.org/10.17504/protocols.io.8pshvne | https://www.protocols.io/view/cell-free-3pga-energy-solution-8pshvne | Nadanai Laohakunakorn | TITLE: Cell-free 3PGA energy solution
AUTHORS: Nadanai Laohakunakorn
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Energy solution for E. coli lysate based on 3PGA. Adapted from Sun 2013 and Cai 2015. Successfully implemented at the University of Edinburgh by Nadanai Laohakunakorn, LBNC-EPFL by Z... | ["[Amino acids stock solution]\nMake stock solution of amino acids, 1000 uL at 50 mM.", "[Amino acids stock solution]\nWeigh each amino acid (excluding tyrosine) on parafilm paper, record the weight, and carefully add together in one tube. Alternative: carrying out at 10x quantities makes weighing much easier. ABC1Ami... |
93,465 | Protocol for Isolation of total RNA from Wastewater | 4 | null | https://www.protocols.io/view/protocol-for-isolation-of-total-rna-from-wastewate-c7hzzj76 | andyhatch | TITLE: Protocol for Isolation of total RNA from Wastewater
AUTHORS: andyhatch
[DESCRIPTION]
This protocol describe the workflow for fractioning wastewater and performing RNA isolation from each fraction.
[GUIDELINES]
Use good lab practices at all times.
Prior to performing any procedure, ensure that proper PPE is do... | ["[Wastewater Fractioning and RNA Isolation] Sample handling\n\nThe samples must be kept at 4°C at all times after collection. Keep wastewater sample containers closed throughout the entire procedure except where noted. \n\nWastewater preparation and fractioning is to be performed in a biosafety cabinet inside a BSL-2 ... |
101,119 | Purification of mCherry-WIPI2d/WIPI3 | 0 | dx.doi.org/10.17504/protocols.io.4r3l2qqyql1y/v1 | https://www.protocols.io/view/purification-of-mcherry-wipi2d-wipi3-dey73fzn | Elias Adriaenssens, Dorotea Fracchiolla | TITLE: Purification of mCherry-WIPI2d/WIPI3
AUTHORS: Elias Adriaenssens, Dorotea Fracchiolla
[DESCRIPTION]
This protocol details the purification of mCherry- WIPI2d/WIPI3.
[STEPS]
SECTION: Purification procedure
1. To purify mCherry-WIPI2d and mCherry-WIPI3, as described previously for WIPI2d (Fracchiolla et al. 2020... | ["[Purification procedure] To purify mCherry-WIPI2d and mCherry-WIPI3, as described previously for WIPI2d (Fracchiolla et al. 2020, J Cell Biol, PMID: 32437499), fuse the coding sequence of WIPI2d or WIPI3 to a N-terminal 6xHis-TEV-mCherry-tag through cloning into a pET-DUET1 vector (available from Addgene).", "[Purifi... |
42,115 | Intestinal Organoid Dissociation and Nuclei Isolation for Single Cell ATAC-Seq | 4 | dx.doi.org/10.17504/protocols.io.bmdbk22n | https://www.protocols.io/view/intestinal-organoid-dissociation-and-nuclei-isolat-bmdbk22n | Heather Eckart, Ran Zhou, Nadia Khan | TITLE: Intestinal Organoid Dissociation and Nuclei Isolation for Single Cell ATAC-Seq
AUTHORS: Heather Eckart, Ran Zhou, Nadia Khan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol provides a procedure for human intestinal organoid dissociation into a single cell suspension and nuclei i... | ["[Organoid Dissociation]\nIncubate organoid in TrypLE for up to 20 minutes at 37°C .", "[Nuclei Isolation]\nFor freshly dissociated cells, perform 1-2 washes with PBS + 0.04% BSA (20ul BSA/1mL 1X PBS).\nConsult 10X Genomics protocol for using frozen cells.", "[Nuclei Isolation]\nDetermine the cell count after washing ... |
30,899 | SPARC - Millipore Metabolic Rat Multiplex Bead Assay for Flow Cytometry | 1 | dx.doi.org/10.17504/protocols.io.14egn82ymg5d/v1 | https://www.protocols.io/view/sparc-millipore-metabolic-rat-multiplex-bead-assay-baetiben | Doris Kemler | TITLE: SPARC - Millipore Metabolic Rat Multiplex Bead Assay for Flow Cytometry
AUTHORS: Doris Kemler
[DESCRIPTION]
This protocol describes methods of performing a Milliplex Assay in half of a 384-well plate, with each half-plate accommodating 12 rats (at 5 samples per rat) and duplicate controls (24 x 4 wells).
Assay... | ["[Preparation] Remove the kits from the cold room and allow everything to come to Room temperature (about 30 min before starting the assay).", "[Preparation] Switch on the Mini-Orbital Shaker (pictured below is: Bellco Biotechnology 7744-08096 0-1150 RPM Mini-Orbital Mixer Stirrer Shaker, but newer alternatives such a... |
106,587 | Quantification of AAV Transduced Olfactory Sensory Neuron Terminals in the Olfactory Bulb Glomerular Layer | 0 | dx.doi.org/10.17504/protocols.io.n2bvjn1rxgk5/v1 | https://www.protocols.io/view/quantification-of-aav-transduced-olfactory-sensory-dkb34sqn | Benjamin David Webster Belfort | TITLE: Quantification of AAV Transduced Olfactory Sensory Neuron Terminals in the Olfactory Bulb Glomerular Layer
AUTHORS: Benjamin David Webster Belfort
[DESCRIPTION]
Pipeline for quantifying olfactory sensory neuron axon terminal expression of AAV-derived TdTomato within olfactory bulb tissue sections. This protocol... | ["[Quantification of AAV Transduced Olfactory Sensory Neuron Terminals in the Olfactory Bulb Glomerular Layer] After 2 weeks, harvest and process olfactory bulb tissue:", "[Quantification of AAV Transduced Olfactory Sensory Neuron Terminals in the Olfactory Bulb Glomerular Layer] Image OB sections using a confocal micr... |
101,226 | Embedding of Tissues in Paraffin | 0 | null | https://www.protocols.io/view/embedding-of-tissues-in-paraffin-de4i3gue | Bertrand Payet | TITLE: Embedding of Tissues in Paraffin
AUTHORS: Bertrand Payet
[DESCRIPTION]
Protocol aim
The aim of this protocol is to provide instructions for paraffin embedding of fixed, cell laden constructs. Embedded samples can, among other applications, be stained for immunofluorescence and immunohistology analysis. Follow ... | ["[Paraffin Embedding] Preparation of paraffin\n\n- Paraffin\n- Dry oven at 58°C\n\nFill ¾ of a suitable container with paraffin and put in the 58°C dry oven to melt.\n\nNote: This may take several hours to melt. Do not increase the temperature of the oven, higher temperatures will make the paraffin hard and brittle.",... |
null | null | null | dx.doi.org/10.17504/protocols.io.jhwcj7e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p style="text-align: justify; text-indent: 1.0cm; line-height: 200%;"><span style="font-family: 'Times New Roman','serif'; color: black;">The novel c.804delG mutation, occurring in the seventh exon of the <em>ILDR1 </em>gene, abolishes a FauI restriction site. The FauI restrict... | [] |
106,313 | Methods for human brainstem tissue processing and capture for spatial transcriptomics using 10x-Genomics Visium Spatial platform. | 0 | dx.doi.org/10.17504/protocols.io.dm6gpzm3dlzp/v2 | https://www.protocols.io/view/methods-for-human-brainstem-tissue-processing-and-dj3h4qj6 | Sandy S. Pineda, Hongyun Li, Zhixiang Wu, Amy Burke, Ping Wu, YuHong Fu, Glenda Halliday | TITLE: Methods for human brainstem tissue processing and capture for spatial transcriptomics using 10x-Genomics Visium Spatial platform.
AUTHORS: Sandy S. Pineda, Hongyun Li, Zhixiang Wu, Amy Burke, Ping Wu, YuHong Fu, Glenda Halliday
[DESCRIPTION]
This protocol details the process of preparing formalin fixed human ti... | ["[Tissue preparation] Selected formalin fixed & paraffin embedded (FFPE) blocks of human post-mortem, midbrains\nand pons were cut in a rotary microtome at 6 µm thickness.\nTwo or three tissue sections were cut and placed on each poly-prep slides. Slides were dried in an oven for 180 min at 42 °C and placed in desicca... |
43,306 | Annotating genes in Diaphorina citri genome version 3 | 5 | dx.doi.org/10.17504/protocols.io.bniimcce | https://www.protocols.io/view/annotating-genes-in-diaphorina-citri-genome-versio-bniimcce | Teresa Shippy, S Miller, C Massimino, C Vosburg [Indian River State College, PS Hosmani, M Flores-Gonzalez, LA Mueller, WB Hunter, JB Benoit, SJ Brown, T D'elia, S Saha | TITLE: Annotating genes in Diaphorina citri genome version 3
AUTHORS: Teresa Shippy, S Miller, C Massimino, C Vosburg [Indian River State College, PS Hosmani, M Flores-Gonzalez, LA Mueller, WB Hunter, JB Benoit, SJ Brown, T D'elia, S Saha
[STEPS]
?. Gather background information about the gene you have chosen. Use Pub... | ["Gather background information about the gene you have chosen. Use Pubmed to find relevant publications about orthologs in other insects. Reading these papers will help you know what to expect when you begin annotating the D. citri gene (i.e. exon number, domains, isoforms, etc.). You can also use DiaphorinaCyc, Ort... |
55,849 | Connecting HTC Vive in SV location | 1 | null | https://www.protocols.io/view/connecting-htc-vive-in-sv-location-b2shqeb6 | Ryan Straight | TITLE: Connecting HTC Vive in SV location
AUTHORS: Ryan Straight
[DESCRIPTION]
Connecting the HTC Vive for VR play while mirrored on television.
[BEFORE_START]
Double check that the Titan workstation is not reserved by anyone else.
[STEPS]
SECTION: Laptop setup
1. Save all work on the laptop.
SECTION: Laptop se... | ["[Laptop setup] Save all work on the laptop.", "[Laptop setup] Restart the laptop.", "[Clean headset] While the laptop is restarting, get the corded HTC Vive from the display.", "Log into Windows.", "[Television] Turn on television.", "[Television] Right-click on the speaker icon and choose \"Sound settings.\"", "[Tel... |
null | null | null | dx.doi.org/10.17504/protocols.io.d5a82d | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This tutorial shows you how to create a pipeline on the University of Arizona HPC. Specifically, we will be creating a pipeline to run blast, using scripts you are writing or have already written from ABE 487 weeks <a href="https://github.com/kyclark/abe487/tree/master/lab/week... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.p9adr2e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Method for isolating mesophyll protoplasts from Arabidopsis as a system for monitoring RNA stability using transcriptional inhibitors (e.g. cordycepin) under stress treatments (e.g. high-light or hydrogen peroxide treatment).</p>
<p> </p>
<p>Adapted from Yoo S.-D., Cho Y.-H. ... | [] |
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