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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null | null | null | dx.doi.org/10.17504/protocols.io.emfbc3n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in <a href="https://www.protocols.io/view/Generating-viral-metagenomes-from-the-coral-holobi-ejgbcjw" target="_blank">Generating viral metagenomes from the coral holobiont</a>.
[STEPS]
?.
?.
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?. | [] |
28,283 | MojoSort™ Selection Kits Column Protocol - 5 | null | dx.doi.org/10.17504/protocols.io.7u3hnyn | null | Sam Li | TITLE: MojoSort™ Selection Kits Column Protocol - 5
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>BioLegend MojoSort™ nanobeads work in commonly used separation columns, based on our internal research as well as validation by external testing by academic labs. This simple pro... | ["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... |
79,867 | Flag co-immunoprecipitation | 1 | dx.doi.org/10.17504/protocols.io.4r3l27rpjg1y/v1 | https://www.protocols.io/view/flag-co-immunoprecipitation-cr83v9yn | michela.deleidi, Pascale Baden | TITLE: Flag co-immunoprecipitation
AUTHORS: michela.deleidi, Pascale Baden
[DESCRIPTION]
Protocol used to pull down V5-FLAG-Gcase interacting proteins in HEK cells
[STEPS]
SECTION: Flag co-immunoprecipitation
1. Detach HEK cells using Accutase for 5 minutes at 37°C and collect them.
SECTION: Flag co-immunoprecipitati... | ["[Flag co-immunoprecipitation] Detach HEK cells using Accutase for 5 minutes at 37°C and collect them.", "[Flag co-immunoprecipitation] Spin cells in a centrifuge at 250g for 5 minutes at room temperature.", "[Flag co-immunoprecipitation] Remove the supernatant and wash cells in PBS.", "[Flag co-immunoprecipitation] R... |
60,231 | A real-time PCR method to genotype mutant mouse models with altered affinity for cardiotonic steroids on the Na,K-ATPase | 4 | dx.doi.org/10.17504/protocols.io.b63frgjn | https://www.protocols.io/view/a-real-time-pcr-method-to-genotype-mutant-mouse-mo-b63frgjn | Peter W W Chomczynski, Kianna M Vires, Michal Rymascewski, Judith A. Heiny | TITLE: A real-time PCR method to genotype mutant mouse models with altered affinity for cardiotonic steroids on the Na,K-ATPase
AUTHORS: Peter W W Chomczynski, Kianna M Vires, Michal Rymascewski, Judith A. Heiny
[DESCRIPTION]
The highly conserved, cardiotonic steroid binding site (also termed ouabain binding sit... | ["[Pre-experiment preparation] In the interest of time and consistency, it is recommended that certain stock solutions and buffers be prepared ahead.", "[Pre-experiment preparation] Prepare a 10X stock solution of Tail Lysis Buffer and store in freezer.", "[Pre-experiment preparation] Prepare assay mixes.\nPrimers and ... |
47,349 | One-Step RT-qPCR for SARS-CoV-2 Wastewater Surveillance: N1, PMMoV, BCoV, SOC, CrAssphage, Bacteroides rRNA, 18S rRNA | 4 | dx.doi.org/10.17504/protocols.io.bsgvnbw6 | https://www.protocols.io/view/one-step-rt-qpcr-for-sars-cov-2-wastewater-surveil-bsgvnbw6 | Hannah Greenwald, Lauren Kennedy, Vinson Fan, Rose Kantor, Kara Nelson | TITLE: One-Step RT-qPCR for SARS-CoV-2 Wastewater Surveillance: N1, PMMoV, BCoV, SOC, CrAssphage, Bacteroides rRNA, 18S rRNA
AUTHORS: Hannah Greenwald, Lauren Kennedy, Vinson Fan, Rose Kantor, Kara Nelson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The following protocol describes the reverse t... | ["[Experimental Protocol]\nClean and set up: Clean the work surface and equipment (including recently calibrated pipettes, vortex, tube spinner, and personal gloves) with 10% bleach followed by 70% ethanol followed by .\nWe worked with University of California, Berkeley EH&S to adapt our protocol for safety considerati... |
null | null | null | dx.doi.org/10.17504/protocols.io.qsgdwbw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Adapted from: Ortmann and Suttle (2009) <em>Determination of Virus Abundance by Epifluorescence microscopy</em>. Ch. 10 Methods of Molecular Biology.</p>
<div>
<div>
<div data-clipboard-target="copy-target-228943496" data-redirect-target="/items/228943496/copy">Contact Dr. St... | [] |
42,018 | Cape Vulture (Gyps coprotheres) Breeding Monitoring Protocol | 4 | dx.doi.org/10.17504/protocols.io.bmaak2ae | https://www.protocols.io/view/cape-vulture-gyps-coprotheres-breeding-monitoring-bmaak2ae | Kerri Wolter | TITLE: Cape Vulture (Gyps coprotheres) Breeding Monitoring Protocol
AUTHORS: Kerri Wolter
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The Cape Vulture (Gyps coprotheres) is southern Africa’s only endemic vulture species and is listed as Endangered by the IUCN 2015. More recently, the Cape Vultur... | ["[Background Information Collection]\nHas this colony ever been visited or monitored before, and if so, how many birds, pairs, nests and fledglings were counted on each visit?", "[Background Information Collection]\nHas anything ever been published on the colony?", "[Background Information Collection]\nHave the number... |
32,047 | The role of serum adipokine levels in preeclampsia: a systematic review | null | dx.doi.org/10.17504/protocols.io.bbipikdn | null | Ioannis Bellos | TITLE: The role of serum adipokine levels in preeclampsia: a systematic review
AUTHORS: Ioannis Bellos
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Preeclampsia represents a serious pregnancy complication with high fetal and maternal morbidity and mortality rates.Accurate prediction of the diseas... | ["Review question The present systematic review aims to investigate whether adipokine levels differ among preeclamptic and healthy pregnant women. Population: Pregnant women in any gestational trimester Exposure: Preeclampsia Comparison: Healthy pregnant women Outcome: Adipokine serum levels Study type: Observational s... |
28,244 | MojoSort™ Selection Kits Column Protocol - 1 | null | dx.doi.org/10.17504/protocols.io.7tuhnnw | null | Sam Li | TITLE: MojoSort™ Selection Kits Column Protocol - 1
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">BioLegend MojoSort™ nanobeads work in commonly used separation columns, based on our internal research as well as validation by external testing by academic labs. This simple protocol ... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes. Kits for human samples have been optimized for PBMCs, please prepare the cells using a suitable method.", "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) ... |
96,944 | GenomeTrakr WGS Protocol Collection and Workflow for MiSeq | 1 | dx.doi.org/10.17504/protocols.io.3byl4bwyjvo5/v3 | https://www.protocols.io/view/genometrakr-wgs-protocol-collection-and-workflow-f-dawq2fdw | Tina Lusk Pfefer, Julie Haendiges, Maria Balkey, Candace Hope Bias, Ruth Timme | TITLE: GenomeTrakr WGS Protocol Collection and Workflow for MiSeq
AUTHORS: Tina Lusk Pfefer, Julie Haendiges, Maria Balkey, Candace Hope Bias, Ruth Timme
[DESCRIPTION]
Here we have created a collection of all the protocols used for WGS using the MiSeq, in order, from sample extraction to NCBI submission.
This collec... | ["[WGS Wet Lab Workflow for Illumina MiSeq] DNA Extraction - Manual", "[WGS Wet Lab Workflow for Illumina MiSeq] DNA Quantification", "[WGS Wet Lab Workflow for Illumina MiSeq] Library Preparation", "[WGS Wet Lab Workflow for Illumina MiSeq] Sequencing", "[Dry Lab Workflow for Sequence QC and NCBI Submission - Direct S... |
87,004 | Immunolabeling and PI staining Drosophila melanogaster germaria | 4 | null | https://www.protocols.io/view/immunolabeling-and-pi-staining-drosophila-melanoga-cy74xzqw | shelbilrussell | TITLE: Immunolabeling and PI staining Drosophila melanogaster germaria
AUTHORS: shelbilrussell
[DESCRIPTION]
Protocol for staining (Wolbachia-infected) Drosophila ovaries for immunolabeling germarium proteins.
[STEPS]
1. Make devitellinizing (DV) solution
a. Measure and add to a 1.5 ml eppendorf tube in the fume hoo... | ["Make devitellinizing (DV) solution\na. Measure and add to a 1.5 ml eppendorf tube in the fume hood:\n 10x PBS 100 ul\n dH20 400 ul\n 32% EM-grade paraformaldehyde 500 ul **opened < 10 days ago**\n NP40 detergent 5.0 ul\n ____________________\n ~ 1 mL DV solution\nb. Vortex this until NP40 is no long... |
84,819 | Protocol for the purification of total DNA from soil samples | 1 | dx.doi.org/10.17504/protocols.io.n2bvj3x85lk5/v1 | https://www.protocols.click/view/protocol-for-the-purification-of-total-dna-from-so-cw3txgnn | Ruslan Kalendar | TITLE: Protocol for the purification of total DNA from soil samples
AUTHORS: Ruslan Kalendar
[DESCRIPTION]
The protocol can also be used for other 'complex' samples (e.g. faeces) and tissues containing high amounts of polymeric molecules, pigments that cannot be separated in any other way. The scale in this example is... | ["[Lysis] The tubes are centrifuged at +4С for 10 minutes at 10,000 rpm and any supernatant is discarded. A brown DNA precipitate containing soil components was formed at the bottom of the tube.", "[Grinding] The sample is ground at -80°C by freezing in liquid nitrogen or at -80°C and ground in a mortar or stirrer chi... |
47,892 | Push-pull microdialysis sampling protocol | 4 | dx.doi.org/10.17504/protocols.io.bszunf6w | https://www.protocols.io/view/push-pull-microdialysis-sampling-protocol-bszunf6w | Christiana.bjorkli | TITLE: Push-pull microdialysis sampling protocol
AUTHORS: Christiana.bjorkli
[DESCRIPTION]
Our modified push-pull microdialysis method was first validated ex vivo with human CSF samples, and thenin vivoin in an AD mouse model, permiting assessment of dynamic changes of CSF Aβ and tau and allowing for better translat... | ["[Setting up the system] Set a refrigerated fraction collector (CMA 470) to6 °C for the storage of collected CSF in polypropylene plastic vials.", "[Setting up the system] Place fluorinated ethylene propylene (FEP) peristaltic tubing (CMA Microdialysis AB, Kista, Sweden) inside each plastic vial for collection and con... |
94,340 | BaseScope In Situ Hybridization | 4 | dx.doi.org/10.17504/protocols.io.5qpvo364zv4o/v1 | https://www.protocols.io/view/basescope-in-situ-hybridization-c8dczs2w | madalynn.erb Erb | TITLE: BaseScope In Situ Hybridization
AUTHORS: madalynn.erb Erb
[DESCRIPTION]
BaseScope in situ hybridization on mouse brain sections
[STEPS]
SECTION: Day 1
1. Use 35μM floating brain sections
SECTION: Day 1
2. Wash sections 3 times (5 minutes) in PBS to remove cryoprotectant solution
SECTION: Day 1
3. Mount tissue ... | ["[Day 1] Use 35μM floating brain sections", "[Day 1] Wash sections 3 times (5 minutes) in PBS to remove cryoprotectant solution", "[Day 1] Mount tissue onto Superfrost plus slides", "[Day 1] Dry slides at room temp and then dip in mQ H2O to remove salt", "[Day 1] Dry slides at 60°C for 2 hours", "[Day 1] Let tissue dr... |
108,117 | DeepSlice Automated Alignment | 0 | dx.doi.org/10.17504/protocols.io.3byl4946ogo5/v1 | https://www.protocols.io/view/deepslice-automated-alignment-dmtv46n6 | Michael Henderson | TITLE: DeepSlice Automated Alignment
AUTHORS: Michael Henderson
[DESCRIPTION]
This protocol explains how to use DeepSlice in the Quint Workflow
[BEFORE_START]
DeepSlice is a deep neural network that automatically aligns mouse histology images through the Allen Brain Atlas coordinate framework. Alignments are viewable... | ["[DeepSlice Automated Alignment] Open DeepSlice in your web browser.", "[DeepSlice Automated Alignment] Select Choose Files.\na. Upload all images for registration from the QVN folder", "[DeepSlice Automated Alignment] Ensure Mouse is selected for species, and Model Ensemble is checked (uses two DeepSlice versions to ... |
78,767 | Fast-scan cyclic voltammetry to assess dopamine release in ex vivo mouse brain slices | 1 | dx.doi.org/10.17504/protocols.io.4r3l271zxg1y/v1 | https://www.protocols.click/view/fast-scan-cyclic-voltammetry-to-assess-dopamine-re-cq6pvzdn | Katherine Brimblecombe, Stephanie J Cragg | TITLE: Fast-scan cyclic voltammetry to assess dopamine release in ex vivo mouse brain slices
AUTHORS: Katherine Brimblecombe, Stephanie J Cragg
[DESCRIPTION]
This protocol is to assess whether a drug changes the dopamine concentration released following a single pulse (1p) electrical stimulation.
[BEFORE_START]
Pri... | ["[Preparation of ex vivo mouse brain slices] Prepare HEPES buffer solution, chill and oxygenate.", "[Preparation of ex vivo mouse brain slices] Prepare vibratome settings: 300 μm slices, 0.44 mm/s speed, Δ1.45 mm vibration. Chill plate and buffer tray in freezer, rinse razor blade in acetone.", "[Preparation of ex viv... |
52,794 | Light-Seq | 4 | dx.doi.org/10.17504/protocols.io.x54v9jno4g3e/v1 | https://www.protocols.io/view/light-seq-bxs2pnge | Jocelyn Y. Kishi, Ninning Liu, Emma R. West, Kuanwei Sheng, Jack J. Jordanides, Matthew Serrata, Constance L. Cepko, Sinem K. Saka, and Peng Yin | TITLE: Light-Seq
AUTHORS: Jocelyn Y. Kishi, Ninning Liu, Emma R. West, Kuanwei Sheng, Jack J. Jordanides, Matthew Serrata, Constance L. Cepko, Sinem K. Saka, and Peng Yin
[DESCRIPTION]
We present Light-Seq, an approach for multiplexed spatial indexing of intact biological samples using light-directed DNA barcoding inf... | ["[Before Starting] This protocol is for selective sequencing of cells within fixed tissue sections that have been sectioned on to a coverslip or microscope slide. \n\nClean workspace (bench, pipettes, etc.) with ethanol before starting. When the protocol calls for water, always use UltraPure water. All reagents should... |
null | null | null | dx.doi.org/10.17504/protocols.io.jrucm6w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Please see attached protocol</p>
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.fckbiuw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>One-step metabarcoding PCR. Used to amplify either mitochondrial 12S or cytochrome B regions from environmental DNA sampled from freshwater to identify fish species. PCR product contains the sequencing primers ready for sequencing on the Illumina MiSeq (custom oligos required... | [] |
68,787 | Media for culturing cells | 4 | dx.doi.org/10.17504/protocols.io.n2bvj652xlk5/v1 | https://www.protocols.io/view/media-for-culturing-cells-cfettjen | Rebecca Berrens | TITLE: Media for culturing cells
AUTHORS: Rebecca Berrens
[DESCRIPTION]
common ES cell media for mouse embryonic stem cells
[STEPS]
SECTION: ES cell media
1. ES Medium
Reagent Volume Supplier Cat.number DMEM without sodium pyruvate* 500 ml Invitrogen 41965-039 Fet... | ["[ES cell media] ES Medium\n Reagent Volume Supplier Cat.number DMEM without sodium pyruvate* 500 ml Invitrogen 41965-039 Fetal calf serum ** (13% final) 75 ml GlobePharm Non-essential amino acids, 100x 5 ml Invitrogen 1... |
97,404 | Bladder responses to thoracolumbar epidural stimulation in female urethane-anesthetized rats with graded contusion spinal cord injuries | 0 | null | https://www.protocols.io/view/bladder-responses-to-thoracolumbar-epidural-stimul-dbc42iyw | Natasha Lorraine Wilkins | TITLE: Bladder responses to thoracolumbar epidural stimulation in female urethane-anesthetized rats with graded contusion spinal cord injuries
AUTHORS: Natasha Lorraine Wilkins
[DESCRIPTION]
The current experiment utilizes epidural stimulation at T13, L3, or L6 to modulate urinary function in rats with graded spinal c... | ["[Spinal cord contusion] Under aseptic conditions, the body temperature was maintained within the range of 36–37°C via a warm water recirculator.", "[Spinal cord contusion] All animals were anesthetized with a mix of ketamine/xylazine (80/10 mg/kg, intraperitoneally).", "[Spinal cord contusion] A dorsal longitudinal i... |
null | null | null | dx.doi.org/10.17504/protocols.io.vcre2v6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol decribes how to make 1 L of Pseudomonas isolation agar for the culturing of Pseudomonas bacterial species on plates.
The use of a genus specific isolation media such as Pseudomonas isolation media reduces the risk of plate contamination with a diiferent bacterial ... | ["Add 45.03 g Pseudomonas isolation agar and 20 mL of 100% glycerol per 980 mL of water.", "Mix well by inverting bottle several times until powder dissolved.", "Sterilize by autoclaving for 20 min at 15 psi (1.05 kg/cm2) on liquid cycle.", "Following autoclave (while media still liquid) pour Pseudomonas isolation agar... |
37,378 | NCBI submission protocol for microbial pathogen surveillance | 1 | dx.doi.org/10.17504/protocols.io.bgrajv2e | https://www.protocols.io/view/ncbi-submission-protocol-for-microbial-pathogen-su-bgrajv2e | Ruth Timme, Maria Balkey, Robyn Randolph, Julie Haendiges, Sai Laxmi Gubbala Venkata, William Wolfgang, Errol Strain | TITLE: NCBI submission protocol for microbial pathogen surveillance
AUTHORS: Ruth Timme, Maria Balkey, Robyn Randolph, Julie Haendiges, Sai Laxmi Gubbala Venkata, William Wolfgang, Errol Strain
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">PURPOSE: </span><span>St... | ["[Establish submission environmnet at NCBI]\nSet up a new NCBI submission environment for your lab:1.1: Create an NCBI user account1.2: Set up an NCBI submission user group for your lab1.4: Bookmark the link to your submission portal1.5. Identify or establish new BioProjects (detailed in Step 3)Ready for data submissi... |
null | null | null | dx.doi.org/10.17504/protocols.io.mtsc6ne | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Cryofreezing cells for preservation.</p>
[STEPS]
?.
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52,523 | Library Generation using Slide-seqV2 | 1 | dx.doi.org/10.17504/protocols.io.bxijpkcn | https://www.protocols.io/view/library-generation-using-slide-seqv2-bxijpkcn | Robert Stickels, Evan Murray, Jamie Marshall, Karol Balderrama, Irving Barrera, Evan Macosko, Fei Chen | TITLE: Library Generation using Slide-seqV2
AUTHORS: Robert Stickels, Evan Murray, Jamie Marshall, Karol Balderrama, Irving Barrera, Evan Macosko, Fei Chen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a protocol detailing the steps necessary to generate libraries using previously manufa... | ["[Tissue Sectioning and RNA capture]\nEquilibrate fresh frozen tissue to -20 °C in a cryostat for ~20 minutes prior to sectioning. The tissue can be mounted onto a chuck using OCT, and the tissue should be aligned and sectioned as is standard in other protocols. Sections for Slide-seq should be 10 μm in thickness.", "... |
27,147 | DASH Protocol | null | dx.doi.org/10.17504/protocols.io.6rjhd4n | null | Amy Lyden, Emily Crawford, Jenai Quan, Saharai Caldera, David Dynerman | TITLE: DASH Protocol
AUTHORS: Amy Lyden, Emily Crawford, Jenai Quan, Saharai Caldera, David Dynerman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is for performing Depletion of Abundant Sequences by Hybridization (DASH) after preparing sequencing libraries and pooling together.</div... | ["[Prepare indexed RNA-seq library]\nFollow all steps using NEB Ultra II RNA library preparation kit. Use an input RNA volume of 25ng if available, or less if not available. Perform 12-18 cycles of indexing PCR.", "[Prepare indexed RNA-seq library]\nChoose one option:a. Pooled DASH: If there are multiple samples, you m... |
76,164 | Resource 3: SSC Collection Optics and Calibration | 5 | dx.doi.org/10.17504/protocols.io.5qpvor7r7v4o/v1 | https://www.protocols.io/view/resource-3-ssc-collection-optics-and-calibration-cnmcvc2w | Joshua A Welsh, Jennifer Jones | TITLE: Resource 3: SSC Collection Optics and Calibration
AUTHORS: Joshua A Welsh, Jennifer Jones
[DESCRIPTION]
Flow cytometry (FCM) is a common extracellular particles (EPs), including viruses and extracellular vesicles (EVs), characterization method. Frameworks such as MIFlowCyt-EV exist to provide reporting guidelin... | ["Calculate the stock traceable size calibration reference bead particle concentration using percent solids value and particle density provided by the manufacturer and the following formula, whereis the concentration (particles mL-1),, is the percent solids,is the particle density (g mL-1), andis the average diameter (... |
40,768 | Copy of ELISA for quantification of IL-7 in human serum. | 6 | dx.doi.org/10.17504/protocols.io.bj28kqhw | https://www.protocols.io/view/copy-of-elisa-for-quantification-of-il-7-in-human-bj28kqhw | Angel Justiz-Vaillant | TITLE: Copy of ELISA for quantification of IL-7 in human serum.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cel... | ["An anti-human IL-9 coating antibody is adsorbed onto microwells by incubation overnight at 4°C.", "Add 50 µl of human serum. Human IL-9 present in the serum sample binds to antibodies adsorbed to the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and later wash to remove unbound proteins.",... |
null | null | null | dx.doi.org/10.17504/protocols.io.jwrcpd6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Antibody incubation steps for quantitative immunoblotting in the Campbel Lab.</p>
[STEPS] | [] |
42,999 | Bacterial Glycerol Stocks for Long-term Storage | 1 | dx.doi.org/10.17504/protocols.io.bm8xk9xn | https://www.protocols.io/view/bacterial-glycerol-stocks-for-long-term-storage-bm8xk9xn | Jiaxin Li | TITLE: Bacterial Glycerol Stocks for Long-term Storage
AUTHORS: Jiaxin Li
[STEPS]
?. Add 750 μL of the overnight culture to 250 μL of 60% glycerol in a 2 mL cryotube and gently mix.
?. Freeze the glycerol stock tube at -80°C. | ["Add 750 μL of the overnight culture to 250 μL of 60% glycerol in a 2 mL cryotube and gently mix.", "Freeze the glycerol stock tube at -80°C."] |
null | null | null | dx.doi.org/10.17504/protocols.io.si8echw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol on how to publish your protocols on protocol.io. </p>
[BEFORE_START]
<p>Create a protocol. A tutorial on how to enter new protocols can be found <a href="https://www.youtube.com/watch?v=WVLu5hoVs7w" target="_blank" rel="noopener noreferrer">here</a>. </p>
[GUIDELIN... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.gzrbx56 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for LiAc <em>S. cerevisiae</em> competent cell preparation and transformation, from Aalto University Molecular Biotechnology group.</p>
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.dp75rm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in "Isolation of cyanophages by plaque assays"
[GUIDELINES]
For example, purified agar or agarose (1% w/v) is added to your media of choice and autoclaved. This will provide a support base for the top agar/agarose overlay as well as nutrients for the host cells. For bes... | [] |
104,334 | DNeasy® PowerSoil® Pro Kit | 0 | null | https://www.protocols.io/view/dneasy-powersoil-pro-kit-dh5n385e | Ellen Dow | TITLE: DNeasy® PowerSoil® Pro Kit
AUTHORS: Ellen Dow
[DESCRIPTION]
QIAGEN DNeasy‱ PowerSoil‱ Pro Kit Protocol adapted for microbiome research with students and during courses.
[BEFORE_START]
Ensure that the PowerBead Pro Tubes rotate freely in the centrifuge without rubbing.
If Solution CD3 has precipitated, heat a... | ["[Suspend Sample] Spin the PowerBead Pro Tube briefly to ensure that the beads have settled at the bottom.\n\nNote: After the sample has been loaded into the PowerBead Pro Tube, the next step is a homogenization and lysis procedure. The PowerBead Pro Tube contains a buffer that will (a) help disperse the soil particle... |
31,291 | Vegan Latkes with JUST Egg | null | dx.doi.org/10.17504/protocols.io.bas3iegn | null | Lenny Teytelman, Hannah Gershik, JUST | TITLE: Vegan Latkes with JUST Egg
AUTHORS: Lenny Teytelman, Hannah Gershik, JUST
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This recipe is a traditional Eastern-European Jewish latkes (potato pancakes). </div></div>
[STEPS]
?. [Grate potatoes and onion]
Peel and wash .
[russet potatoes]
?. [Mi... | ["[Grate potatoes and onion]\nPeel and wash .\n[russet potatoes]", "[Mix all ingredients]\nIn a large mixing bowl mix the grated potatoes and onions with , , and .\n[of salt]\n[flour]\n[JUST Egg]", "[Grate potatoes and onion]\nCut up and grate the potatoes and .\n[small yellow onion]\nEither with a food processor fitte... |
55,784 | Protocol for chronic implantation of patch electrodes on the gastric muscle wall of the rat | 1 | dx.doi.org/10.17504/protocols.io.b2qgqdtw | https://www.protocols.io/view/protocol-for-chronic-implantation-of-patch-electro-b2qgqdtw | Robert Phillips, Deborah Jaffey, Terry Powley | TITLE: Protocol for chronic implantation of patch electrodes on the gastric muscle wall of the rat
AUTHORS: Robert Phillips, Deborah Jaffey, Terry Powley
[DESCRIPTION]
Electrical stimulation is a potential therapy for gastric disorders. Here we describe our surgical procedure for the implantation of patch electrod... | ["[Subjects] Male and/or female rats of the appropriate age and weight for the experimental design were used. Note: we have successfully implanted rats across a range of ages (3 to 6 months) and weights (250 to 550 grams).", "[Subjects] Two days prior to surgery, start the rats on antibiotics (one 2 mg Baytril tablet p... |
36,749 | Sampling and viral concentration for SARS-CoV-2 detection in wastewater | null | dx.doi.org/10.17504/protocols.io.bf5mjq46 | https://www.protocols.io/view/sampling-and-viral-concentration-for-sars-cov-2-de-bf5mjq46 | Veronica Antelo, Gregorio Iraola | TITLE: Sampling and viral concentration for SARS-CoV-2 detection in wastewater
AUTHORS: Veronica Antelo, Gregorio Iraola
[STEPS]
?. [Sampling wastewater]
Autoclave plastic containers and expose to UV for 10 min.
?. [Sampling wastewater]
Fill bottles with wastewater at sampling points using sterile gloves.
Sampling ... | ["[Sampling wastewater]\nAutoclave plastic containers and expose to UV for 10 min.", "[Sampling wastewater]\nFill bottles with wastewater at sampling points using sterile gloves.\nSampling points may be diverse and accessibility to water sources will be sometimes difficult depending on site infrastructure. Consider the... |
63,824 | Media Prep: 500mL of 1x PBS | 4 | null | https://www.protocols.io/view/media-prep-500ml-of-1x-pbs-cajqscmw | Melanie Palma Avila, George Testo | TITLE: Media Prep: 500mL of 1x PBS
AUTHORS: Melanie Palma Avila, George Testo
[DESCRIPTION]
Phosphate-buffered saline (PBS) is an isotonic solution that is used in many biological research applications.PBS (phosphate buffered saline) is a balanced salt solution used for a variety of cell culture applications, such as... | ["Perform a 1:10 dilution of 10x PBS using a sterile media bottle of 1L volume or greater (if necessary).", "Place cap directly on top of sterile media bottle (DO NOT tighten cap).", "Autoclave sterile media with 1x PBS: Liquid cycle: media (30 min).", "Retrieve autoclaved 1x PBS & fully cap sterile media bottle for st... |
81,816 | TS Procure 812 - primary fixation Karnovsky's - transwells (TM - 013) | 4 | dx.doi.org/10.17504/protocols.io.e6nvwjwpwlmk/v2 | https://www.protocols.io/view/ts-procure-812-primary-fixation-karnovsky-39-s-tra-ct5ywq7w | sandra.crameri | TITLE: TS Procure 812 - primary fixation Karnovsky's - transwells (TM - 013)
AUTHORS: sandra.crameri
[DESCRIPTION]
The method is used to Karnovsky's EM fixed transwells to Procure 812 resin blocks. The presence of 4% paraformaldehyde is only used to satisfy microsecurity requirements.
[GUIDELINES]
Sample is not o... | ["[HEADER] SAN:\n\n\n\n\nSPEC No:\n\n\n\n\nOPERATOR & STEPS:\n\n\n\n\nOPERATOR & STEPS:", "[Conventional] Karnovsky's fixative: 2.5 % volume and 4 % volume in 0.1 Molarity (M) Sorenson's Phosphate buffer (pH 7.2, 300mosmol/kg) for at least 40 min or overnight", "[Conventional] 0.1 Molarity (M) buffer 15 min", "[Co... |
104,018 | Impact of Atrial fibrillation on the outcome of patients with Brugada syndrome: A meta-analysis | 0 | dx.doi.org/10.17504/protocols.io.36wgqnby5gk5/v1 | https://www.protocols.io/view/impact-of-atrial-fibrillation-on-the-outcome-of-pa-dhts36ne | Max Aboutorabi | TITLE: Impact of Atrial fibrillation on the outcome of patients with Brugada syndrome: A meta-analysis
AUTHORS: Max Aboutorabi
[DESCRIPTION]
Background: A systematic review and meta-analysis will be conducted to assess the effects of atrial fibrillation (AF) on patients with brugada syndrome (BrS).
Methods: Studies... | ["Identify the question\nPopulation - patients with Brugada syndrome with and without AF (No constraints were set in terms of type of atrial fibrillation or type of brugada syndrome).\nComparison - assessing whether concurrent AF has an effect on patients with brugada syndrome.\nOutcomes - Rates of major arrhythmic ev... |
88,513 | Image Processing and 3D Reconstruction | 4 | null | https://www.protocols.io/view/image-processing-and-3d-reconstruction-c2n9ydh6 | Annan SI Cook | TITLE: Image Processing and 3D Reconstruction
AUTHORS: Annan SI Cook
[DESCRIPTION]
This workflow was used to analyze a Krios dataset of the PI3KC3-C1/RAB1A Complex and generate a reconstruction of three distinct conformational states of the VPS34 lipid kinase domain.
[STEPS]
SECTION: Data Import
1. Import the raw Cry... | ["[Data Import] Import the raw Cryo-EM data sets into cryoSPARC v3.", "[Motion Correction and Fourier Cropping] Apply motion correction to the super-resolution movies.", "[Motion Correction and Fourier Cropping] Perform Fourier cropping 2x on the motion-corrected data using cryoSPARC's implementation of Patch Motion Co... |
31,013 | Food4Gut multicenter randomized placebo-controlled trial. | 1 | dx.doi.org/10.17504/protocols.io.baidica6 | https://www.protocols.io/view/food4gut-multicenter-randomized-placebo-controlled-baidica6 | Sophie Hiel, Marco A. Gianfrancesco, Julie Rodriguez, Daphnée Portheault, Quentin Leyrolle, Laure B. Bindels, Carolina Gomes da Silveira Cauduro, Maria D.G.H. Mulders, Giorgia Zamariola, Anne-Sophie Azzi, Gaetan Kalala, Barbara D. Pachikian, Camille Amadieu, Audrey M. Neyrinck, Audrey Loumaye, Patrice D. Cani, Nicolas ... | TITLE: Food4Gut multicenter randomized placebo-controlled trial.
AUTHORS: Sophie Hiel, Marco A. Gianfrancesco, Julie Rodriguez, Daphnée Portheault, Quentin Leyrolle, Laure B. Bindels, Carolina Gomes da Silveira Cauduro, Maria D.G.H. Mulders, Giorgia Zamariola, Anne-Sophie Azzi, Gaetan Kalala, Barbara D. Pachikian, Cami... | [] |
47,071 | ARTIC-NEB: SARS-CoV-2 Library Prep | 1 | null | https://www.protocols.io/view/artic-neb-sars-cov-2-library-prep-br77m9rn | Lusajo Mwakibete, Cristina Tato, Vida Ahyong, Amy Kistler, Manu Vanaerschot, Angela Detweiler, Michelle Tan | TITLE: ARTIC-NEB: SARS-CoV-2 Library Prep
AUTHORS: Lusajo Mwakibete, Cristina Tato, Vida Ahyong, Amy Kistler, Manu Vanaerschot, Angela Detweiler, Michelle Tan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This experiment was carried out to investigate the effect of fragmentation time on the genome... | ["[Dilution of Input Viral RNA]\nDiluting samples based on Ct values to prevent overloading.Caution! Carryout the following dilution steps with DNAse/RNAse free water in PCR-pre, RNAse free environment (Biosafety cabinet). RNA was extracted using the Zymo Quick DNA/RNA Viral MagBead Kit (R2141). RT-PCR CT values dictat... |
86,191 | ITS1 Amplicon Prep | 1 | dx.doi.org/10.17504/protocols.io.n92ldmzd8l5b/v2 | https://www.protocols.io/view/its1-amplicon-prep-cyepxtdn | aglazer | TITLE: ITS1 Amplicon Prep
AUTHORS: aglazer
[DESCRIPTION]
This protocol was provided by IDT in the the xGen ITS1 Amplicon Panel manual.
[STEPS]
SECTION: Prepare panel-specific Multiplex PCR Reaction Mix
1. Before mixing reagents, calculate the total volume of the Master Mix based on the number of reactions required, w... | ["[Prepare panel-specific Multiplex PCR Reaction Mix] Before mixing reagents, calculate the total volume of the Master Mix based on the number of reactions required, with 15% overage for pipetting.", "[Prepare panel-specific Multiplex PCR Reaction Mix] Make the Multiplex PCR Reaction Mix according to the table below an... |
null | null | null | dx.doi.org/10.17504/protocols.io.inecdbe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Gen-IALFirst All-tissue DNA extraction kit -This protocol provides an efficient DNA extraction and purification of fresh sample (tissue material)</p>
[BEFORE_START]
<p>Clean</p>
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.maqc2dw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Modification on the coventional protocol for insect microinjection was performed. This protocol describe a simple and unique protocol for microinjecting <em>Spodoptera frugiperda</em>. Insect eggs with thin chorions such as <em>S. frugiperda</em> or with chorions that are rem... | [] |
65,710 | Dentitox Pro: Does Dentitox Drops scam or real? | 1 | dx.doi.org/10.17504/protocols.io.6qpvr6zebvmk/v1 | https://www.protocols.io/view/dentitox-pro-does-dentitox-drops-scam-or-real-ccenstde | Litsa Pro | TITLE: Dentitox Pro: Does Dentitox Drops scam or real?
AUTHORS: Litsa Pro
[DESCRIPTION]
Dentitox Pro: Does Dentitox Drops scam or real?
[STEPS]
SECTION: Dentitox Pro: Does Dentitox Drops scam or real? Regularly brushing one's teeth won't help goo complaint or tooth decay. According to the medical communit... | ["[Dentitox Pro: Does Dentitox Drops scam or real?\t Regularly brushing one's teeth won't help goo complaint or tooth decay. According to the medical community, indeed persons who seek to maintain excellent oral health by drawing their teeth regularly might succumb to these oral issues. This is due to the abs... |
34,400 | Isolation of cancer stem cells by sphere formation assay | null | dx.doi.org/10.17504/protocols.io.bdt8i6rw | https://www.protocols.io/view/isolation-of-cancer-stem-cells-by-sphere-formation-bdt8i6rw | Kwangok P Nickel, Austin M. Maas, Randall Kimple | TITLE: Isolation of cancer stem cells by sphere formation assay
AUTHORS: Kwangok P Nickel, Austin M. Maas, Randall Kimple
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Cancer stem cells (CSCs) are a small subpopulation of tumor cells that are thought to be responsible for recurrence and metastasi... | ["Prepare Sphere Formation Media () Base media is DMEM/F12 Penicillin and Streptomycin B-27 bFGF hEGF of DMEM/F12.\n100 ml\n1 ml\n2 ml\n20 µl\n10 µl\n96.97 ml", "Dilute cells to a final concentration of 2000 cells/ml in Sphere Formation Media.Note that the final concentration of cells/ml should be optimized to you... |
20,130 | U Mass - Electrolytes | null | dx.doi.org/10.17504/protocols.io.xwafpae | null | Jason Kim | TITLE: U Mass - Electrolytes
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-Luminex technology base... | ["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... |
50,705 | Subrenal capsule (SRC) implantation of tumor tissue | 4 | dx.doi.org/10.17504/protocols.io.bvrrn556 | https://www.protocols.io/view/subrenal-capsule-src-implantation-of-tumor-tissue-bvrrn556 | Shubhangi Agarwal, donna.peehl , Renuka Sriram | TITLE: Subrenal capsule (SRC) implantation of tumor tissue
AUTHORS: Shubhangi Agarwal, donna.peehl , Renuka Sriram
[DESCRIPTION]
This protocol describes the steps required for the successful implantation of tumor tissues under the subrenal capsule. The subrenal capsule is an optimum site for the propagation of ... | ["[Preparation before surgery] Fire bent glass pipette: Prepare the bent pipette by exposing the pipette tip to fire and slightly bending it into an inverted C shape with the help of forceps. The image below shows an example of bent pipettes. \n\n \nNote: Make sure there are no sharp edges on the pipette tip as that w... |
81,375 | 10x Protocols: Chromium Nuclei Isolation Kit Sample Prep -- University of Minnesota TMCs (CG000505 Rev A) | 1 | dx.doi.org/10.17504/protocols.io.14egn2d3yg5d/v1 | https://www.protocols.click/view/10x-protocols-chromium-nuclei-isolation-kit-sample-ctp7wmrn | 10x Genomics | TITLE: 10x Protocols: Chromium Nuclei Isolation Kit Sample Prep -- University of Minnesota TMCs (CG000505 Rev A)
AUTHORS: 10x Genomics
[DESCRIPTION]
Protocol ID# (CG) and Revision letter provided here:
10x CG000505, Revision A -- Nuclei isolation kit by 10x Genomics
Note: These protocols may not be the current v... | ["Current Sample prep website: https://www.10xgenomics.com/support/single-cell-gene-expression-flex/documentation/steps/sample-prep/chromium-nuclei-isolation-kit-sample-prep-user-guide"] |
64,832 | How Does Heal n Soothe Work so Well? | 1 | dx.doi.org/10.17504/protocols.io.kxygxz41wv8j/v1 | https://www.protocols.io/view/how-does-heal-n-soothe-work-so-well-cbi8skhw | kashdjx | TITLE: How Does Heal n Soothe Work so Well?
AUTHORS: kashdjx
[DESCRIPTION]
Consistent joint or back pain is one of the most prevalent health Heal n Soothe conditions that individuals face, second only to diabetes and coronary illness. Individuals all around the world have found that pain treatment drugs are hard... | [] |
86,386 | In situ immunoglobulin G (IgG) detection in formalin-fixed, paraffin-embedded (FFPE) pig tissues | 4 | dx.doi.org/10.17504/protocols.io.e6nvwdjxzlmk/v1 | https://www.protocols.io/view/in-situ-immunoglobulin-g-igg-detection-in-formalin-cyksxuwe | Jayne E Wiarda, Crystal Loving | TITLE: In situ immunoglobulin G (IgG) detection in formalin-fixed, paraffin-embedded (FFPE) pig tissues
AUTHORS: Jayne E Wiarda, Crystal Loving
[DESCRIPTION]
An immunohistochemistry (IHC) staining protocol for in situ identification of IgG in pig tissue.
[BEFORE_START]
Starting specimens:
Starting samples = FFPE tis... | ["[Baking] Before starting the assay: \nPreheat a dry oven to 60℃ \nLoad slides for assay into vertical slide rack\n\nBaking\nBake slides 20 min 60℃\n\nWhile slides bake:\nPrepare 0.05% PBS-T (can store at RT up to 1 month)", "[Deparaffinizing & Rehydrating] Immediately before deparaffinizing:\nAdd ~200 mL xylenes ... |
null | null | null | dx.doi.org/10.17504/protocols.io.mwcc7aw | null | null | TITLE: No Title
AUTHORS:
[STEPS] | [] |
17,459 | Cremophor EL agar (EL slant) | 1 | dx.doi.org/10.17504/protocols.io.n92ld3m87g5b/v1 | https://www.protocols.click/view/cremophor-el-agar-el-slant-vate2en | Amy Gladfelter | TITLE: Cremophor EL agar (EL slant)
AUTHORS: Amy Gladfelter
[DESCRIPTION]
This media is used to determine the ability of Malassezia species to utilize Cremophor EL.
[GUIDELINES]
This media is used to determine the ability of Malassezia species to utilize Cremophor EL.
[STEPS]
1. SDA 65 g
2. Cremophor EL (Sigma) 10 ... | ["SDA 65 g", "Cremophor EL (Sigma) 10 mL", "dH2O 900 mL", "Sterilize by autoclaving."] |
90,824 | Immunohistochemistry | 1 | dx.doi.org/10.17504/protocols.io.bp2l6xmzdlqe/v1 | https://www.protocols.io/view/immunohistochemistry-c4xgyxjw | Leonardo A Parra-Rivas | TITLE: Immunohistochemistry
AUTHORS: Leonardo A Parra-Rivas
[DESCRIPTION]
Immunohistochemistry
[STEPS]
1. Mice were euthanized using isoflurane (VetOne Cat#502017) inhalation followed by
cervical dislocation. At autopsy, mouse brains were removed from the calvarium
and rapidly placed in a 4% paraformaldehyde (PFA) so... | ["Mice were euthanized using isoflurane (VetOne Cat#502017) inhalation followed by\ncervical dislocation. At autopsy, mouse brains were removed from the calvarium\nand rapidly placed in a 4% paraformaldehyde (PFA) solution (Thermo Scientific,\nCat# J19943-K2) for drop fixation.", "For immunohistochemistry, 5 mm sagitta... |
77,654 | Evans blue assay to stain dead cells. | 4 | null | https://www.protocols.io/view/evans-blue-assay-to-stain-dead-cells-cp3wvqpe | Santosh Sathe | TITLE: Evans blue assay to stain dead cells.
AUTHORS: Santosh Sathe
[DESCRIPTION]
Evans blue (Sigma, USA, catalog no: E2129) is a dye that can enter the compromised cell membranes of dead cells and stain them blue. I used this assay to differentiate dead cells in algal cultures of Chlorella and Chlamydomonas (the same... | ["[Evans blue assay to stain dead cells.] Contact: Santosh Sathe (santosh.sathe@uni-konstanz.de)", "[Introduction] Evans blue (Sigma, USA, catalog no: E2129) is a dye that can enter the compromised cell membranes of dead cells and stain them blue. I used this assay to differentiate dead cells in algal cultures of Chlor... |
43,637 | Calculating Colony-forming Units | 3 | dx.doi.org/10.17504/protocols.io.bnuvmew6 | https://www.protocols.io/view/calculating-colony-forming-units-bnuvmew6 | Jiri Hulcr, You Li | TITLE: Calculating Colony-forming Units
AUTHORS: Jiri Hulcr, You Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to estimate the number of colony-forming units.</div><div class = "text-block"><span>This protocol is part of the Bark Beetle Mycobiome (BBM) Research Coord... | [] |
66,887 | Les personnes les plus influentes dans l'industrie du Diaetoxil 600mg[Diatoxile] [Diaetoxyl 600 mg] [Diaetoxil 600 MG] [Detoxil 600 mg] [Diaetoxyl 600 mg Avis] [Detoxil 600 Mg En Pharmacie] | 1 | dx.doi.org/10.17504/protocols.io.n2bvj64y5lk5/v1 | https://www.protocols.io/view/les-personnes-les-plus-influentes-dans-l-39-indust-cdjfs4jn | jackballors | TITLE: Les personnes les plus influentes dans l'industrie du Diaetoxil 600mg[Diatoxile] [Diaetoxyl 600 mg] [Diaetoxil 600 MG] [Detoxil 600 mg] [Diaetoxyl 600 mg Avis] [Detoxil 600 Mg En Pharmacie]
AUTHORS: jackballors
[DESCRIPTION]
➢Nom du produit — DiaeToxil Erfahrungen
➢Principaux avantages - Traite efficaceme... | ["[Les personnes les plus influentes dans l'industrie du Diaetoxil 600mg[Diatoxile] [Diaetoxyl 600 mg] [Diaetoxil 600 MG] [Detoxil 600 mg] [Diaetoxyl 600 mg Avis] [Detoxil 600 Mg En Pharmacie]]"] |
84,086 | GFP pull down assay | 4 | dx.doi.org/10.17504/protocols.io.e6nvwd6x2lmk/v1 | https://www.protocols.io/view/gfp-pull-down-assay-cwcwxaxe | Elias Adriaenssens | TITLE: GFP pull down assay
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol describes GFP pull down assay.
[STEPS]
SECTION: GFP pull down assay
1. Mix GFP-tagged TBK1 with 20 µL of equilibrated GFP-Trap agarose beads (Chromotek) at a final concentration of 1 micromolar (µM). Make sure to wash beads 2x in dH2O... | ["[GFP pull down assay] Mix GFP-tagged TBK1 with 20 µL of equilibrated GFP-Trap agarose beads (Chromotek) at a final concentration of 1 micromolar (µM). Make sure to wash beads 2x in dH2O before washing with bead assay buffer to equilibrate the beads adding the protein to the beads.", "[GFP pull down assay] To this e... |
99,417 | WATER PRODUCTION FOR AWARE (Parasite) | 0 | dx.doi.org/10.17504/protocols.io.3byl49bdzgo5/v1 | https://www.protocols.io/view/water-production-for-aware-parasite-ddbz22p6 | Celia Manaia | TITLE: WATER PRODUCTION FOR AWARE (Parasite)
AUTHORS: Celia Manaia
[DESCRIPTION]
The protocol summarises the procedures used for analytical control. The protocol describes the Standard Operating Procedure (SOP) for the optimization of advanced tertiary treatment of water, based on a comprehensive quality and risk asse... | ["[Parasite] The water production for AWARE main activities includes three stages – disinfection by ultraviolet C radiation (UVC), storage for720 min-1440 min(according to water load and season) and ozonation. The water quality is monitored at these three stages, for the parameters indicated in Figure 1 below.", "[Para... |
104,967 | Processing wastewater samples for bacterial & viral targets enrichment | 0 | null | https://www.protocols.io/view/processing-wastewater-samples-for-bacterial-amp-vi-dirf4d3n | Victor Mabasa | TITLE: Processing wastewater samples for bacterial & viral targets enrichment
AUTHORS: Victor Mabasa
[DESCRIPTION]
This wastewater sample processing protocol by the Wastewater Genomics Syndicate at the National Institute of Communicable Diseases (NICD) is designed to enrich bacteria and viruses from the settled s... | ["[Sample Collection & Handling] Using correct personal protective equipment (PPE), collect a 1,000 ml grab wastewater sample from each location in a sterile bottle and transfer them to the laboratory in a cold chain (keep in a lab fridge at 4°C). it is important to proceed to the next step within the next 23 hours... |
70,040 | Immunoassay of SARS-CoV-2 in dogs and cats V.1 | 4 | dx.doi.org/10.17504/protocols.io.5qpvorn29v4o/v1 | https://www.protocols.io/view/immunoassay-of-sars-cov-2-in-dogs-and-cats-v-1-cgmytu7w | Dumar A. Jaramillo-Hernández, María C. Chacón, María A. Velásquez, Adolfo Vásquez-Trujillo, Ana P. Sánchez, Luis F. Salazar Garces, Gina L. García, Yohana M. Velasco-Santamaría, Luz N. Pedraza, Lida C. Lesmes-Rodríguez | TITLE: Immunoassay of SARS-CoV-2 in dogs and cats V.1
AUTHORS: Dumar A. Jaramillo-Hernández, María C. Chacón, María A. Velásquez, Adolfo Vásquez-Trujillo, Ana P. Sánchez, Luis F. Salazar Garces, Gina L. García, Yohana M. Velasco-Santamaría, Luz N. Pedraza, Lida C. Lesmes-Rodríguez
[DESCRIPTION]
This protocol describes... | ["[Before you start] Collect the serum, plasma or whole blood samples from dogs, cats, mink, ferrets, cattle, sheep, goats, horses and any other susceptible species.", "[Procedure] Allow the reagents to reach room temperature (21 °C ± 5 °C) before use.", "[Procedure] Homogenize all reagents and serum samples by immersi... |
96,329 | Heron Data Suite: biomedical quantitative analysis applications for Skyline results files | 0 | dx.doi.org/10.17504/protocols.io.8epv5xwj5g1b/v1 | https://www.protocols.io/view/heron-data-suite-biomedical-quantitative-analysis-dabh2aj6 | Mary Cunningham, Stephen Cunningham, Matthew Renfrow | TITLE: Heron Data Suite: biomedical quantitative analysis applications for Skyline results files
AUTHORS: Mary Cunningham, Stephen Cunningham, Matthew Renfrow
[DESCRIPTION]
This protocol describes the use of the Heron Data Suite application (https://www.herondata.app/). The Heron Data Suite simplifies the analysis of ... | ["[1. Using Heron Data: Replicate Absolute Quantification with your Skyline 'Peptide Ratio Results" .csv export] Once you have your \"Peptide Ratio Results\" .csv Excel export file from Skyline, visit the app's website: https://www.herondata.app/", "[1. Using Heron Data: Replicate Absolute Quantification with... |
46,196 | Experiment Data Depot (EDD) Data Import | 1 | dx.doi.org/10.17504/protocols.io.bp2l6bd15gqe/v1 | https://www.protocols.io/view/experiment-data-depot-edd-data-import-brcum2ww | Jennifer Gin, Christopher J Petzold | TITLE: Experiment Data Depot (EDD) Data Import
AUTHORS: Jennifer Gin, Christopher J Petzold
[DESCRIPTION]
This protocol details how to import data into an EDD Study. Data can be shared with collaborators via exported CSV files or through the REST API.
For more information about the EDD visit: Experiment Data Depot G... | ["Click the Import Data button on the top right.", "Go through the set of data import steps:\n\nIdentify what protocol was used. Click Shotgun (Discovery) Proteomics.\nSelect the layout of your data. Click Generic.\n\nClick Start Import on the bottom right.", "Example data layouts:\n\nHere, we have measured the amou... |
null | null | null | dx.doi.org/10.17504/protocols.io.n8kdhuw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Emotions are signaled by complex arrays of face and body actions. The main point of contention in contemporary treatments is whether these arrays are discrete, holistic constellations reflecting emotion categories, or whether they are compositional -- comprised of smaller com... | [] |
51,643 | smilzcbdgummies | 1 | dx.doi.org/10.17504/protocols.io.bwn3pdgn | https://www.protocols.io/view/smilzcbdgummies-bwn3pdgn | health | TITLE: smilzcbdgummies
AUTHORS: health
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><a href="http://topcbdoilmart.com/smilz-cbd-gummies" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;font-weight:bold;">Smilz CBD Gummies</span></a><span style = ":;font-weight:bol... | ["[Smilz CBD Gummies]\nSmilz CBD Gummies: It is entire of its nutrients strength to apply and make your health best. When a frame takes a small amount of Smilz CBD Gummies, it increases your frame’s metabolism and gives proper functions for making specific health with out stress and ache. Thus, try to take the best qu... |
88,660 | Flow cytometry-based measurement of trafficking of Golgi to the lysosome via autophagy V3 | 4 | dx.doi.org/10.17504/protocols.io.yxmvm3y8nl3p/v1 | https://www.protocols.io/view/flow-cytometry-based-measurement-of-trafficking-of-c2tuyenw | Harper JW, Kelsey Hickey, sharan_swarup | TITLE: Flow cytometry-based measurement of trafficking of Golgi to the lysosome via autophagy V3
AUTHORS: Harper JW, Kelsey Hickey, sharan_swarup
[DESCRIPTION]
Protocol for flow cytometry-based measurement of Golgi trafficking to lysosomes via autophagy using Keima-YIPF3/4 reporters in HEK293 cells.
[STEPS]
SECTION: ... | ["[Generation of stable Keima cell lines] pLenti vectors expressing either Keima-YIPF4, Keima-YIPF3, or GALNT2-Keima were packaged in 293T cells and the lentivirus was used to infect WT or FIP200-/- HEK293 cells (for Keima-YIPF3 and Keima-YIPF4). GALNT2-Keima was used to infect WT, FIP200-/- and DKO (YIPF3-/-, YIPF4-/-... |
67,836 | Support Protocol 1: Installing MIDAS2 | 5 | dx.doi.org/10.17504/protocols.io.yxmvmnrj5g3p/v1 | https://www.protocols.io/view/support-protocol-1-installing-midas2-ceg4tbyw | miriam.goldman , chunyu.zhao | TITLE: Support Protocol 1: Installing MIDAS2
AUTHORS: miriam.goldman , chunyu.zhao
[DESCRIPTION]
MIDAS2 is written in Python 3 and can be executed on a 64-bit Linux system. MIDAS2 and its dependencies need to be pre-installed in order to run the commands described in the basic protocols. We recommend the conda pack... | ["Installing Midas2 has 2 options Conda and Docker", "Install Miniconda", "Configure conda channel.", "Install MIDAS2", "If Docker is properly installed on the system, users can also use the pre-built Docker container.", "Verify your installation."] |
69,775 | Short HPLC gradient method for 20-Hydroxyecdysone (20E) quantification in malaria vectors | 6 | dx.doi.org/10.17504/protocols.io.5qpvoymezg4o/v2 | https://www.protocols.io/view/short-hplc-gradient-method-for-20-hydroxyecdysone-cgdpts5n | Oswald Yedjinnavenan Djihinto, Luc S. Djogbenou, Luisa Nardini, Armorel Van Eyk, Lizette L. Koekemoer | TITLE: Short HPLC gradient method for 20-Hydroxyecdysone (20E) quantification in malaria vectors
AUTHORS: Oswald Yedjinnavenan Djihinto, Luc S. Djogbenou, Luisa Nardini, Armorel Van Eyk, Lizette L. Koekemoer
[DESCRIPTION]
Ecdysteroids are arthropod steroid hormones that are primarily involved in insect moulting. In a... | ["[Instrument] Analytical HPLC separations were performed on the Flexar LC system (Perkin Elmer) with a UV/Vis Detector and a Phenomenex Kinetex RP C18–5 µm column (4.6 x 150 mm). \nThe detection wavelength was set at 245 nm. \nThe flow rate was 1 mL/minute. \nThe mobile phase included gradient elution with Methanol:Ac... |
74,702 | Protocol for vagus nerve stimulation in awake pigs (subject-3) | 1 | dx.doi.org/10.17504/protocols.io.rm7vzb692vx1/v1 | https://www.protocols.io/view/protocol-for-vagus-nerve-stimulation-in-awake-pigs-ck7nuzme | Oliver Armitage | TITLE: Protocol for vagus nerve stimulation in awake pigs (subject-3)
AUTHORS: Oliver Armitage
[DESCRIPTION]
The Vagus nerve innervates a number of thoracic and visceral organs. Exogenous nervous signal, for example, Vagus nerve stimulation (VNS) provides a route to modulating their function for therapeutic purposes. ... | ["[Surgery] Position pig prone and mark neck where the skin implant is to be placed along with the incisions on the neck.", "[Subjects] Female swine of adult age and weight between 35—55 kg for the experimental design were used.", "[Surgery] Cut out circle for skin implant to go through and make an incision where the i... |
81,527 | SARS-CoV-2 incursion scenario in the city Fantastica | 1 | null | https://www.protocols.io/view/sars-cov-2-incursion-scenario-in-the-city-fantasti-ctuxwnxn | Benjamin Schwessinger | TITLE: SARS-CoV-2 incursion scenario in the city Fantastica
AUTHORS: Benjamin Schwessinger
[DESCRIPTION]
This protocols is part of the ANU Biosecurity mini-research project #2 "An SARS-CoV-2 incursion scenario: Genomics, phylogenetics, and incursions." This mini-research project is modeled on the yearly Quality Assura... | ["Now you import all the data needed in Geneious. Track and drop the \"FantasticaSARSCoV2Sequences\" and the reference sequence \"MN908947.3\" into this in class folder.\n\n \nYou are ready for all your analysis now.", "[Section II: Generation of a multiple sequence alignment in Geneious] Now you will select all seque... |
97,990 | Hematoxylin and Eosin (H&E) Staining of Tissues following Multiplexed Imaging on Phenocycler-Fusion | 0 | dx.doi.org/10.17504/protocols.io.36wgqn55xgk5/v1 | https://www.protocols.io/view/hematoxylin-and-eosin-h-amp-e-staining-of-tissues-dbxe2pje | Emily Soja, Santhosh Sivajothi, William F Flynn, Elise T Courtois | TITLE: Hematoxylin and Eosin (H&E) Staining of Tissues following Multiplexed Imaging on Phenocycler-Fusion
AUTHORS: Emily Soja, Santhosh Sivajothi, William F Flynn, Elise T Courtois
[DESCRIPTION]
Phenocycler-Fusion assay enables multiplexed antibody based imaging of FFPE or fresh frozen tissues. Hematoxylin and Eo... | ["[Flow cell removal] The flow cell needs to be removed from the slide in order to continue with H&E staining. Retrieve tissue slides with attached flow cells either from the storage buffer or directly after Phenocycler run.", "[H & E staining] Place the slides in 100% ethanol for 2 min. Raise and dip the slides 10... |
null | null | null | dx.doi.org/10.17504/protocols.io.qp8dvrw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The protocol describes guidelines and steps for taking repeated measurements of sportive population: postural stability, body weight distribution during quiet stance, and the foot type diagnostic. The parameters calculated from repeated measurements can be used for separate a... | ["[Postural stability - centre of pressure displacement measurements (COP)] Perform measuring process by following the Guidelines:\n1) 30 s of narrow stance\n2) 60 s of one-leg stance \n3) 60 s of one-leg stance - the second leg", "Register:\n1) percentage of body weight distribution form narrow stance test.\n2) total... |
69,895 | Electroporatic transformation of Rhodobacter sphaeroides | 4 | dx.doi.org/10.17504/protocols.io.eq2ly7d6wlx9/v1 | https://www.protocols.io/view/electroporatic-transformation-of-rhodobacter-sphae-cghftt3n | Jaya K Yakha, Deborah K Hanson, Rosemarie Wilton, laible | TITLE: Electroporatic transformation of Rhodobacter sphaeroides
AUTHORS: Jaya K Yakha, Deborah K Hanson, Rosemarie Wilton, laible
[DESCRIPTION]
The expression host for R. sphaeroides DrshI wasconstructed by deleting Type II restriction enzyme RshI (locus tag RSP_3759; recognition sequence CGATCG) from strain DD11 is ... | ["In a microfuge tube on ice, mix 40 µL cells with 100 ng of plasmid DNA.", "Turn on the electroporator and select the voltage to 2500 V with other setting of 25uF and 400 ohm.", "Transfer the cells-DNA mixture to a chilled electroporation cuvette on ice.", "Return the cuvette to ice and add 1ml GYCC immediately; rec... |
16,209 | plasma preparation exRNAQC | 1 | dx.doi.org/10.17504/protocols.io.t3reqm6 | https://www.protocols.io/view/plasma-preparation-exrnaqc-t3reqm6 | Anneleen Decock | TITLE: plasma preparation exRNAQC
AUTHORS: Anneleen Decock
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to prepare different plasma fractions from venous blood draw (10 ml) according to the extracellular RNA quality control study. </div></div>
[STEPS]
?. [Centrifugati... | ["[Centrifugation step 1: 20 min at 400 g (rcf) - preparation of PRP]\nInvert tubes 5 times before centrifugation.Spin tubes for 20 min at 400 g (rcf) (without brake), at room temperature. Note time point of centrifugation start.Pipette platelet-rich plasma (PRP) carefully into a new collection tube, leave ± 0.5 cm abo... |
59,924 | Immunological detection of APP and proteins of the endolysosomal system | 4 | dx.doi.org/10.17504/protocols.io.kqdg36jeeg25/v2 | https://www.protocols.io/view/immunological-detection-of-app-and-proteins-of-the-b6rurd6w | Hankum Park, Frances V Hundley, Harper JW | TITLE: Immunological detection of APP and proteins of the endolysosomal system
AUTHORS: Hankum Park, Frances V Hundley, Harper JW
[DESCRIPTION]
Here we present a general protocol for immunological detection by Western blotting of APP and proteins of the endolysosomal system, including EEA1, RAB5, PSEN1, LAMP1, LA... | ["[Western blotting] Lyse cell pellets by homogenization in KPBS buffer, urea buffer, or RIPA buffer with protease and phosphatase inhibitors. For some experiments, we employ 293 cells or 293EL APPSw,T700N cells expressing 3xFLAG-EEA1, TMEM192-3xHA, and APP harboring Swedish and T700N mutations as described in dx.doi.o... |
27,226 | siRNA Electroporation of Hydra | null | dx.doi.org/10.17504/protocols.io.6t2heqe | null | Adrienne Cho | TITLE: siRNA Electroporation of Hydra
AUTHORS: Adrienne Cho
[STEPS]
?. Wash animals (fed one day earlier) 5 times with Milli-Q water and incubate for 45 minutes at 18°C
?. Place 20 animals into electroporation cuvetter with 0.4cm gap and remove as much liquid as possible.
?. Add 200 µL sterilized 10mM HEPES (pH7.0) co... | ["Wash animals (fed one day earlier) 5 times with Milli-Q water and incubate for 45 minutes at 18°C", "Place 20 animals into electroporation cuvetter with 0.4cm gap and remove as much liquid as possible.", "Add 200 µL sterilized 10mM HEPES (pH7.0) containing 4µM siRNA", "Tap cuvette 10 times to evenly distribute animal... |
79,829 | HotSHOT genomic DNA extraction | 4 | dx.doi.org/10.17504/protocols.io.j8nlkw945l5r/v2 | https://www.protocols.io/view/hotshot-genomic-dna-extraction-cr7vv9n6 | FishFloorUCL, FishFloorUCL | TITLE: HotSHOT genomic DNA extraction
AUTHORS: FishFloorUCL, FishFloorUCL
[DESCRIPTION]
How to extract genomic DNA from larvae or finclips using the HotSHOT method.
[STEPS]
SECTION: Materials
1. Prepare the BASE stock solution (50X):
14.03 g KOH crystals (1.25M final concentration)
4 mL of 0.5M EDTA (10 mM final conc... | ["[Materials] Prepare the BASE stock solution (50X):\n14.03 g KOH crystals (1.25M final concentration)\n4 mL of 0.5M EDTA (10 mM final concentration)\nddH2O to 200 mL total volume\nCan be stored at room temperature for up to four years", "[Materials] Prepare the NEUTRALISATION stock solution (50X)\n63.04 g Tris-HCL (2M... |
77,743 | Calcium fluorimetry with the FLIPR Calcium 6 kit on FlexStation 3 | 1 | dx.doi.org/10.17504/protocols.io.3byl4jdmjlo5/v2 | https://www.protocols.io/view/calcium-fluorimetry-with-the-flipr-calcium-6-kit-o-cp6pvrdn | Angus Li, Samuel Liu, Rennica Huang, Seungkirl Ahn, Robert J Lefkowitz | TITLE: Calcium fluorimetry with the FLIPR Calcium 6 kit on FlexStation 3
AUTHORS: Angus Li, Samuel Liu, Rennica Huang, Seungkirl Ahn, Robert J Lefkowitz
[DESCRIPTION]
This protocol details an experimental procedure used to generate results described in the manuscript Li, A., Liu, S., Huang, R., Ahn, S., & Lefkowitz, R... | ["Plate U2OS-TetOn-AT1R in microplates (Black with clear bottom, lysine- coated Corning 3842) at 15000 cells/well 2 days prior to assay", "Add doxycycline and optionally PTX to wells 14 hours before replacement with loading buffer", "Remove one vial of Calcium 6 Assay Reagent (Component A, good for 2 plates) from the f... |
40,766 | ELISA for quantification of IL-7 in human serum. | 6 | dx.doi.org/10.17504/protocols.io.bj26kqhe | https://www.protocols.io/view/elisa-for-quantification-of-il-7-in-human-serum-bj26kqhe | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-7 in human serum.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells. They... | ["An anti-human IL-7 coating antibody is adsorbed onto microwells by incubation overnight at 4°C.", "Add 50 µl of human serum. Human IL-7 present in the serum sample binds to antibodies adsorbed to the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and later wash to remove unbound proteins.",... |
88,537 | Biochemistry and Molecular Biology | 4 | dx.doi.org/10.17504/protocols.io.dm6gp3d18vzp/v1 | https://www.protocols.io/view/biochemistry-and-molecular-biology-c2pzydp6 | liweiwei, Xu-Xu Fan, Xue-Jing Cao, Zhao-Yu Zhu, Dan-Shi Pei, Yi-Zhuo Wang, Ji-Yan Zhang | TITLE: Biochemistry and Molecular Biology
AUTHORS: liweiwei, Xu-Xu Fan, Xue-Jing Cao, Zhao-Yu Zhu, Dan-Shi Pei, Yi-Zhuo Wang, Ji-Yan Zhang
[DESCRIPTION]
This protocol contains instructions on how to conduct molecular biology experiments, including transfection and reporter assays, RNA extraction and qPCR, coimmunoprec... | ["[Transfection and reporter assays] The cells were transfected by standard calcium phosphate precipitation or Lipofectamine 2000. To normalize the transfection efficiency, pRL-TK (Renillaluciferase) reporter plasmid (10 ng) was added to each transfection. To ensure that each transfection received the same amount of to... |
null | null | null | dx.doi.org/10.17504/protocols.io.k3vcyn6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The presence and structure of EFNs in <em>Opuntia robusta</em> had not been investigated. We used light, scanning-electron, and transmission-electron microscopy to examine morphology, anatomy, and ultrastructure of the secretory spines in areoles in female and hermaphrodite i... | [] |
85,793 | KAPP-Sen TMC: Dissociation of Pancreatic Islets (non-recovered) | 1 | dx.doi.org/10.17504/protocols.io.ewov1qnrkgr2/v1 | https://www.protocols.io/view/kapp-sen-tmc-dissociation-of-pancreatic-islets-non-cxz9xp96 | Juliana Alcoforado Diniz, Jessica Garofalo, Dylan Baker, Paul Robson | TITLE: KAPP-Sen TMC: Dissociation of Pancreatic Islets (non-recovered)
AUTHORS: Juliana Alcoforado Diniz, Jessica Garofalo, Dylan Baker, Paul Robson
[DESCRIPTION]
The dispersed samples were shipped cold from PRODOLABS. Prior to scRNA-seq dispersed samples from brain dead donor’s pancreatic islets were dissociated as f... | ["[Cell Dissociation with Accutase]", "[Fixation of Cells & Nuclei for Chromium Fixed RNA Profiling] Cells were fixated prior to scRNAseq according to https://dx.doi.org/10.17504/protocols.io.x54v9py5zg3e/v1", "[Cell Dissociation with Accutase] Transfer cell suspension of pure islets to a new 50ml tube. Use additio... |
82,354 | CD34+ Cell RNP Nucleofection | 4 | dx.doi.org/10.17504/protocols.io.q26g7y541gwz/v2 | https://www.protocols.io/view/cd34-cell-rnp-nucleofection-cunswvee | Daniel A Kuppers, Patrick Paddison | TITLE: CD34+ Cell RNP Nucleofection
AUTHORS: Daniel A Kuppers, Patrick Paddison
[DESCRIPTION]
Human CD34+ hematopoietic stem and progenitor cells (HSPCs) are a standard source of cells for clinical HSC transplantations as well as experimental xenotransplantation to generate “humanized mice”. To further extend the rang... | ["[Synthetic sgRNA reconstitution] Briefly centrifuge your tubes or plates containing synthetic modified single guide RNA (sgRNA) oligos to ensure that the dried RNA pellet is collected at the bottom.", "[Synthetic sgRNA reconstitution] Carefully dissolve sgRNA in the provided nuclease-free 1X TE Buffer (Tris-EDTA, pH ... |
null | null | null | dx.doi.org/10.17504/protocols.io.guwbwxe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>IRDye NHS esters react with unblocked amines in peptides. NHS ester reactions usually proceed quickly and cleanly in either organic or aqueous solvents. While NHS esters continue to be widely used tools for biomolecule modification, their application to large peptides may be ... | ["[Aqueous Solution-Phase Labeling] {\"blocks\":[{\"key\":\"6vrda\",\"text\":\"Dissolve peptides in aqueous buffers that do not contain extraneous nucleophiles such asTris, sodium azide, DTT, BME, etc.\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"a9qe1\",\"tex... |
30,836 | Anti-iNKT MicroBeads Isolation protocol | null | dx.doi.org/10.17504/protocols.io.bacuiaww | null | Ajit N Shah, Rachel Hatano | TITLE: Anti-iNKT MicroBeads Isolation protocol
AUTHORS: Ajit N Shah, Rachel Hatano
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">isolation of 6b11 positive cells </div></div>
[STEPS]
?. Determine cell number.
?. Centrifuge cell suspension at 300×g for 10 minutes. Aspirate supernatant completely.
... | ["Determine cell number.", "Centrifuge cell suspension at 300×g for 10 minutes. Aspirate supernatant completely.", "Resuspend cell pellet in 400 μL of buffer per 10⁸ total cells. Add 100 μL of Anti-iNKT MicroBeads per 10⁸ total cells.", "Mix well and incubate for 15 minutes in the refrigerator (2−8 °C).", "Wash cells b... |
21,415 | Cell Surface Mild Acid Elution of MHC-bound Immunopeptides | null | dx.doi.org/10.17504/protocols.io.y6ffzbn | null | Teesha Luehr | TITLE: Cell Surface Mild Acid Elution of MHC-bound Immunopeptides
AUTHORS: Teesha Luehr
[STEPS]
?. [Culturing Cells]
Culture cells. If culturing THP-1s, follow the protocol.
{"blocks":[{"key":"48pd2","text":"THP-1 cells are a human monocyte suspension cell line from peripheral blood of a 1 year old infant who had acut... | ["[Culturing Cells]\nCulture cells. If culturing THP-1s, follow the protocol.\n{\"blocks\":[{\"key\":\"48pd2\",\"text\":\"THP-1 cells are a human monocyte suspension cell line from peripheral blood of a 1 year old infant who had acute mnocytic leukemia. \",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"en... |
76,475 | Soil Organic Carbon Stocks and Change | 1 | null | https://www.protocols.io/view/soil-organic-carbon-stocks-and-change-cnw3vfgn | SCarolina Córdova, Curtis Dell, Mark Liebig, michel.cavigelli, Phil Robertson | TITLE: Soil Organic Carbon Stocks and Change
AUTHORS: SCarolina Córdova, Curtis Dell, Mark Liebig, michel.cavigelli, Phil Robertson
[DESCRIPTION]
The change in soil organic carbon (SOC) accumulation or decreases over time serves as an integrated indicator of carbon (C) balance in cropping systems, and as an integral m... | [] |
34,067 | Cell-mediated and serology-based tests for Mycobacterium ulcerans disease: A systematic review and meta-analysis. | null | dx.doi.org/10.17504/protocols.io.bdhti36n | null | Michael S. Avumegah, Nilakshi T. Waidyatillake, Wojtek P. Michalski, Daniel P. O’Brien, Tiffanie M. Nelson, Eugene Athan | TITLE: Cell-mediated and serology-based tests for Mycobacterium ulcerans disease: A systematic review and meta-analysis.
AUTHORS: Michael S. Avumegah, Nilakshi T. Waidyatillake, Wojtek P. Michalski, Daniel P. O’Brien, Tiffanie M. Nelson, Eugene Athan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">... | ["[Review question]\nReview questionWhat attempts have been made to develop cell-mediated and/or serology-based tests for Mycobacterium ulcerans disease within at risk population?Context and rationaleCurrent methods of diagnosis of the Buruli ulcer disease include, polymerase chain reaction, histopathology and culture ... |
77,523 | PAS Staining of Fresh Frozen or Paraffin Embedded Human Kidney Tissue | 1 | dx.doi.org/10.17504/protocols.io.x54v98nkzl3e/v3 | https://www.protocols.io/view/pas-staining-of-fresh-frozen-or-paraffin-embedded-cpxtvpnn | Elizabeth Neumann, Jamie Allen, Angela Kruse, Jennifer Harvey, Maya Brewer, Carrie Romer, Mark De Caestecker, Jeff Spraggins | TITLE: PAS Staining of Fresh Frozen or Paraffin Embedded Human Kidney Tissue
AUTHORS: Elizabeth Neumann, Jamie Allen, Angela Kruse, Jennifer Harvey, Maya Brewer, Carrie Romer, Mark De Caestecker, Jeff Spraggins
[DESCRIPTION]
Scope:
The PAS stain is used to demonstrate polysaccharides such as glycogen, and mucosubst... | ["[Start with FFPE here:] Allow PAS “kit” to come to room temperature on the bench.", "[Start with FFPE here:] For paraffin sections, deparaffinize in xylene, two changes, 3 min each.", "[Start with FFPE here:] Hydrate through graded alcohols, 1 min each:\n100%, 100%, 95%, 70%, water", "[Start with FFPE here:] Rinse ... |
101,515 | DNA / RNA isolation from whole blood with universal mini column kit for molecular analysis | 0 | dx.doi.org/10.17504/protocols.io.n2bvjn98wgk5/v1 | https://www.protocols.io/view/dna-rna-isolation-from-whole-blood-with-universal-dfdj3i4n | Sudhir Bhatia, Gudrun Baersch | TITLE: DNA / RNA isolation from whole blood with universal mini column kit for molecular analysis
AUTHORS: Sudhir Bhatia, Gudrun Baersch
[DESCRIPTION]
Whole blood is a simple source of DNA/RNA, however while there are several isolation methods in the literature, they are not capable of isolating pure enough nucleic ac... | ["Add 300µl of Tube A and 15µl of Tube K to the 50µl whole blood sample in the tube.\nUse EDTA whole blood sample and avoid heparin whole blood sample as heparin is known to inhibit PCR reaction.\n\nNote: If user has problem, the blood can be diluted with equal volume of PBS to be used as input. Sometimes, one has to u... |
77,718 | In situ Ki-67 detection in formalin-fixed, paraffin-embedded (FFPE) pig tissues | 4 | dx.doi.org/10.17504/protocols.io.36wgqjyx3vk5/v1 | https://www.protocols.io/view/in-situ-ki-67-detection-in-formalin-fixed-paraffin-cp5wvq7e | Jayne E Wiarda, Crystal Loving | TITLE: In situ Ki-67 detection in formalin-fixed, paraffin-embedded (FFPE) pig tissues
AUTHORS: Jayne E Wiarda, Crystal Loving
[DESCRIPTION]
An immunohistochemistry (IHC) staining protocol for in situ identification of porcine Ki-67
[BEFORE_START]
Starting specimens:
Starting samples = FFPE tissues cut to 4 micron th... | ["[Baking] Before starting the assay: \nPreheat a dry oven to 60℃ \nLoad slides for assay into vertical slide rack\n\nBaking\nBake slides 20 min 60℃\n\nWhile slides bake:\nPrepare 0.05% PBS-T (can store at RT up to 1 month)", "[Deparaffinizing & Rehydrating] Immediately before deparaffinizing:\nAdd ~200 mL xylenes ... |
39,292 | MARVICS: A Robust and Safe Magnetic Nanoparticle based RNA Extraction Method Compatible with Phenol-chloroform Inactivated Infectious Samples | 1 | dx.doi.org/10.17504/protocols.io.bik4kcyw | https://www.protocols.io/view/marvics-a-robust-and-safe-magnetic-nanoparticle-ba-bik4kcyw | Mo Li, Gerardo Ramos-Mandujano | TITLE: MARVICS: A Robust and Safe Magnetic Nanoparticle based RNA Extraction Method Compatible with Phenol-chloroform Inactivated Infectious Samples
AUTHORS: Mo Li, Gerardo Ramos-Mandujano
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Diagnosis and surveillance of emerging pathogens such as SARS-... | ["Silica magnetic nanoparticles (SiMNP) synthesis.SiMNP synthesis was done following the published protocols in BOMB.bio: BOMB magnetic core nanoparticles synthesis and BOMB coating ferrite MNPs with silica oxide.", "COVID-19 patient samples.Oropharyngeal or nasopharyngeal swabs are steeped in acid guanidinium thiocya... |
43,391 | Perseus: A Bioinformatics Platform for Integrative Analysis of Proteomics Data in Cancer Research | 4 | dx.doi.org/10.17504/protocols.io.bnk7mczn | https://www.protocols.io/view/perseus-a-bioinformatics-platform-for-integrative-bnk7mczn | Juergen Cox, Stefka Tyanova | TITLE: Perseus: A Bioinformatics Platform for Integrative Analysis of Proteomics Data in Cancer Research
AUTHORS: Juergen Cox, Stefka Tyanova
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Mass spectrometry-based proteomics is a continuously growing field marked by technological and methodological ... | ["The Methods section contains several modules covering the most frequently performed steps in the analysis of proteomics data. Often, a proteomics study benefits from a global overview of the data, which usually includes the total number of identified and quantified proteins, dynamic range, coverage of specific pathwa... |
47,406 | Blood Draw | 4 | dx.doi.org/10.17504/protocols.io.261ge4w5dv47/v1 | https://www.protocols.io/view/blood-draw-bsinncde | Clemens Scherzer, Bradley Hyman, Charles Jennings | TITLE: Blood Draw
AUTHORS: Clemens Scherzer, Bradley Hyman, Charles Jennings
[DESCRIPTION]
This protocol explains the Standard Operating Protocol for Blood Drawing.
[GUIDELINES]
PROTOCOLS NO LONGER IN USE
SERUM
MATERIALS: One 4 ml yellow top SST Gel and Clot Activator SERUM tube (BD Franklin Lakes, NJ., Ref# 36797... | ["[Blood Draw] Store all tubes at Room temperature (18ºC to 25ºC) before use.", "[Blood Draw] Label all tubes with the subject ID# prior to the blood draw.", "[Blood Draw] The PAXgene™ Blood RNA Tubes should be the first tubes drawn in the phlebotomy procedure. Collect all other tubes after collecting the PAXgene™ Bloo... |
41,809 | XPRIZE SHINE - In-tube Fluorescent SARS-CoV-2 Saliva Test | 1 | dx.doi.org/10.17504/protocols.io.bk3rkym6 | https://www.protocols.io/view/xprize-shine-in-tube-fluorescent-sars-cov-2-saliva-bk3rkym6 | Jon Arizti-Sanz, Catherine A. Freije, Chloe K. Boehm, Sameed M. Siddiqui, Allen M. Goodman, Tinna-Solveig F. Kosoko-Thoroddsen, A'Doriann Y. Bradley, Jeremy Johnson, Pardis C. Sabeti, Cameron Myhrvold | TITLE: XPRIZE SHINE - In-tube Fluorescent SARS-CoV-2 Saliva Test
AUTHORS: Jon Arizti-Sanz, Catherine A. Freije, Chloe K. Boehm, Sameed M. Siddiqui, Allen M. Goodman, Tinna-Solveig F. Kosoko-Thoroddsen, A'Doriann Y. Bradley, Jeremy Johnson, Pardis C. Sabeti, Cameron Myhrvold
[DESCRIPTION]
<div class = "text-blocks"><di... | ["[Sample Collection and Viral Lysis]\nExpel approximately one drop of saliva into the sample collection tube and cap the tube. Saliva collection tube contains necessary volume of FastAmp® Viral and Cell Solution.", "[Sample Collection and Viral Lysis]\nMix saliva sample and FastAmp® Viral and Cell Solution by vorte... |
50,075 | Recombinant a-synuclein pre-formed fibril generation | 1 | dx.doi.org/10.17504/protocols.io.bu53ny8n | https://www.protocols.io/view/recombinant-a-synuclein-pre-formed-fibril-generati-bu53ny8n | Alain Ndayisaba | TITLE: Recombinant a-synuclein pre-formed fibril generation
AUTHORS: Alain Ndayisaba
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details the generation of a-synuclein pre-formed fibrils.</div></div>
[STEPS]
?. [Recombinant a-synuclein pre-formed fibril generation]
Reconstitute of... | ["[Recombinant a-synuclein pre-formed fibril generation]\nReconstitute of lyophilized monomeric synuclein with cold sterile DPBS (do not pipet, close tube immediately).\n1 mg\n100 µl\non ice", "[Recombinant a-synuclein pre-formed fibril generation]\nTransfer tubes on wet ice to cold room and rotate on tube rotator ... |
48,733 | Detection of bacteria in antibiotic-treated diatom cultures and cell harvesting | 4 | dx.doi.org/10.17504/protocols.io.btt5nnq6 | https://www.protocols.io/view/detection-of-bacteria-in-antibiotic-treated-diatom-btt5nnq6 | Francesco Manfellotto, Monia Teresa Russo, Pina Marotta, Antonella Ruggiero, Mariella Ferrante | TITLE: Detection of bacteria in antibiotic-treated diatom cultures and cell harvesting
AUTHORS: Francesco Manfellotto, Monia Teresa Russo, Pina Marotta, Antonella Ruggiero, Mariella Ferrante
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We illustrate a simple and rapid method for detecting the pre... | ["For the antibiotic treatment to obtain axenic cultures, see the published protocol: Axenic Diatoms cultures protocoldx.doi.org/10.17504/protocols.io.bgudjws6Transfer 1 mL of Culture in a new 2 mL tube.", "Add 1,6% of neutralized formaldehyde to fix cells and mix gently by inversion", "Add 1uL of DAPI 1 mg/mL and mi... |
47,411 | CPT Processing | 4 | dx.doi.org/10.17504/protocols.io.n92ld9w87g5b/v1 | https://www.protocols.io/view/cpt-processing-bsitncen | Clemens Scherzer, Bradley Hyman, Charles Jennings | TITLE: CPT Processing
AUTHORS: Clemens Scherzer, Bradley Hyman, Charles Jennings
[DESCRIPTION]
This protocol explains the Standard Operating Protocol for processing CPT.
[GUIDELINES]
FREEZER STORAGE
Freezers are divided into 4 shelves, with 6 racks per shelf, and 24 boxes that can be held in each shelf. In total,... | ["[Processing Protocol] ***Prep Steps:\nLabel the appropriate number of cryopreservation vials with program and sample name, cell type, and date. Put on ice. \nPrepare before processing CPTs: \nFBS (heat shocked/heat inactivated) and put on ice to pre-cool. \nCreate solution to equal 10 % (v/v) in 90 % (v/v) (heat shoc... |
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