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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82,004 | Characterization of the VKORC1 and CYP2C9 genotypes | 1 | dx.doi.org/10.17504/protocols.io.kxygx9edzg8j/v5 | https://www.protocols.io/view/characterization-of-the-vkorc1-and-cyp2c9-genotype-cubuwsnw | Mirsada Causevic, Edin Begic | TITLE: Characterization of the VKORC1 and CYP2C9 genotypes
AUTHORS: Mirsada Causevic, Edin Begic
[DESCRIPTION]
Vitamin K antagonists (e.g. warfarin) are anticoagulants which represent widely prescribed drugs for prevention and treatment of thromboembolic disorders.
Warfarin's molecular target is vitamin K epoxide re... | ["[Genomic DNA extraction] Patients' whole blood was collected in ethylenediaminetetraacetic acid (EDTA)-containing tubes and stored at -20°C until use. Genomic DNA extraction from the human whole blood, that is, leukocytes, was carried out according to the protocol described by Subbarayan PR and colleagues (doi: 10.21... |
null | null | null | dx.doi.org/10.17504/protocols.io.tb5eiq6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The GF-1 Soil Sample DNA Extraction Kit is designed for the rapid and efficient purification of bacteria DNA from soil samples without the need for precipitation or organic extraction. The kit uses a high pure specially-treated silica-based material fixed into a column to eff... | [] |
30,043 | Aquatic Monitoring Protocol for measuring and collecting ecological data | null | dx.doi.org/10.17504/protocols.io.9j3h4qn | null | Rebecca Hufft, Margo Paces, Meghan McGill, Richard A. Levy | TITLE: Aquatic Monitoring Protocol for measuring and collecting ecological data
AUTHORS: Rebecca Hufft, Margo Paces, Meghan McGill, Richard A. Levy
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the basic methods for measuring water quality and aquatic macroinvertebrate diver... | ["[Describing the Survey Location]\nBefore collecting ecological data, record information describing the survey location in a standardized way. Describe the location with the following physical location descriptors:• Country• 1st political division (state)• 2nd political division (county)• Nearest population center, to... |
null | null | null | dx.doi.org/10.17504/protocols.io.dqm5u5 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?. | [] |
67,442 | [Exposed] Stimula Blood Sugar Support Reviews - ( Scam Alert ) Ingredients, Side Effects Do The Pills Work? Don't Miss This Report! | 3 | dx.doi.org/10.17504/protocols.io.36wgq7w55vk5/v1 | https://www.protocols.io/view/exposed-stimula-blood-sugar-support-reviews-scam-cd4ss8we | trina solan | TITLE: [Exposed] Stimula Blood Sugar Support Reviews - ( Scam Alert ) Ingredients, Side Effects Do The Pills Work? Don't Miss This Report!
AUTHORS: trina solan
[DESCRIPTION]
If you've been feeling tired and lethargic for the past few months, yet nothing seems to help or change your symptoms, your blood sugar lev... | [] |
20,461 | Suppement data in APSGI-00061-2018R2 | null | dx.doi.org/10.17504/protocols.io.x8mfru6 | null | Jian Tu, Ting Xiong | TITLE: Suppement data in APSGI-00061-2018R2
AUTHORS: Jian Tu, Ting Xiong
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Methods and results of supplement figure 1</div></div>
[STEPS]
?. resultsmethods | ["resultsmethods"] |
59,598 | Stranded Mapping from Oriented Long Reads | 1 | dx.doi.org/10.17504/protocols.io.yxmvm45nv3pe/v9 | https://www.protocols.io/view/stranded-mapping-from-oriented-long-reads-b6fnrbme | David A Eccles | TITLE: Stranded Mapping from Oriented Long Reads
AUTHORS: David A Eccles
[DESCRIPTION]
This protocol demonstrates how to map strand-oriented long reads to a genome, and visualise them in a genome browser.
The general idea is to use minimap2 to create stranded BAM files, which are split for forward/reverse orientatio... | ["[Orient Reads] Orient reads as per protocol Preparing Reads for Stranded Mapping.\n\nIf this has been done, then the following command should produce output without errors:\n \nExample output:", "[Index Preparation] Prepare genome index for spliced alignment:\n \n\n \n\nPrepare a chromosome size index file:", "[Read ... |
null | null | null | dx.doi.org/10.17504/protocols.io.e2ybgfw | 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... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.rrud56w | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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?. | ["Isolation buffer: 154 mM KCl, 1 mM EDTA, pH 7.4", "Mitochondrial Assay Solution (MAS): 115 mM KCl (Sigma P9333), 10 mM KH2PO4 (Sigma P9791), 2 mM MgCl2 (Sigma M1028), 3 mM HEPES (Sigma H0887), 1mM EGTA (Sigma E4378), FA-free BSA 0.2% (A7511), adjust solution to pH 7.2 using 5N KOH.CAUTIONS: The presence of BSA in the... |
45,157 | Plasma Exosome Isolation | 4 | dx.doi.org/10.17504/protocols.io.81wgb7xnqvpk/v1 | https://www.protocols.io/view/plasma-exosome-isolation-bqcdmss6 | Silvia Cerri | TITLE: Plasma Exosome Isolation
AUTHORS: Silvia Cerri
[DESCRIPTION]
This protocol details methods for the isolation of small extracellular vesicles from plasma.
[BEFORE_START]
Keep samples on ice during the entire procedure!
[STEPS]
SECTION: Plasma Exosome Isolation
1. Incubate plasma samples (starting volume: 1-1... | ["[Plasma Exosome Isolation] Incubate plasma samples (starting volume: 1-1.5ml) on ice for complete thaw.", "[Plasma Exosome Isolation] Filter samples through a 13mm sterile syringe filters with a 0.8 µm Supor (PES) membrane.", "[Plasma Exosome Isolation] Centrifuge at 20000 x g, 60 min, 4 °C to remove large extracellu... |
86,285 | T-2 TICK PROCESSING | 4 | dx.doi.org/10.17504/protocols.io.36wgqjx75vk5/v1 | https://www.protocols.io/view/t-2-tick-processing-cyhmxt46 | REDI-NET Consortium | TITLE: T-2 TICK PROCESSING
AUTHORS: REDI-NET Consortium
[DESCRIPTION]
This protocol details tick processing.
[BEFORE_START]
BEFORE START
Pre-cool the Bullet Blender by adding dry ice into the cooling compartment and running the cooling program.
Clean the work surfaces with RNaseZap, then wipe the surfaces with 70% ... | ["[1. SORT TICK SAMPLES] Sort larvae (pooled and stored by the same genus), nymph (individual), and adults (individual) into separate vials in the lab.", "[2. PREPARING TICK e-ID (IDX): Device setup using Bluetooth] Plug in the device. On a phone or computer which has both Google Chrome and Bluetooth capabilities, visi... |
null | null | null | dx.doi.org/10.17504/protocols.io.m9tc96n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This method describes the comparison of paracetamol quantification of a whole tablet vs a tablet that has been crushed in a proprietary tablet crusher. In this case we have used paracetamol as the model drug, but this basic approach can be applied to any solid dose form with ... | [] |
79,779 | Snail husbandry for maintaining the Schistosoma mansoni life cycle | 4 | null | https://www.protocols.io/view/snail-husbandry-for-maintaining-the-schistosoma-ma-cr6bv9an | Sarah K Buddenborg | TITLE: Snail husbandry for maintaining the Schistosoma mansoni life cycle
AUTHORS: Sarah K Buddenborg
[DESCRIPTION]
Maintenance and general husbandry of schistosome-susceptible snails, including but not limited to Biomphalaria glabrata fresh water snails. The purpose of this SOP is to outline the weekly protocols requ... | ["[Preparing a new aquarium tank] Label clean aquarium with appropriate information in permanent marker (i.e. date, owner, age, numbers of individuals, exposure date, expected patent date, experiment number, etc). Example labels are attached", "[Preparing a new aquarium tank] Rinse a generous handful of autoclaved oyst... |
38,031 | Sentinel Flask Preparation for Cold Shipping Protocol of Human Islets | 1 | dx.doi.org/10.17504/protocols.io.bhdpj25n | https://www.protocols.io/view/sentinel-flask-preparation-for-cold-shipping-proto-bhdpj25n | Integrated Islet Distribution Program | TITLE: Sentinel Flask Preparation for Cold Shipping Protocol of Human Islets
AUTHORS: Integrated Islet Distribution Program
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">To establish a standardized method for the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) sponsored re... | ["[SUPPLEMENTAL MATERIALS]\nThe following supplies are necessary for the preparation of Sentinel Test Flasks for human islet distribution.Islet preparation for distributionWide mouth pipettes and pipettor30 mL shipping bottles - 1 per islet purity batch broadcasted. Shipping media that is to be used for distribution as... |
85,254 | CTAB/Chloroform-Isoamyl Alcohol DNA Extraction Protocol | 4 | dx.doi.org/10.17504/protocols.io.261gednpdv47/v1 | https://www.protocols.click/view/ctab-chloroform-isoamyl-alcohol-dna-extraction-pro-cxhexj3e | Elena L. Peredo | TITLE: CTAB/Chloroform-Isoamyl Alcohol DNA Extraction Protocol
AUTHORS: Elena L. Peredo
[DESCRIPTION]
Protocol for extracting high quality DNA.
[STEPS]
SECTION: Clean the working area.
1. Routinely, we use ethanol and bleach to clean working areas and surfaces. Wipe, wipe, wipe.
Micro pestles need to be properly tr... | ["[Clean the working area.] Routinely, we use ethanol and bleach to clean working areas and surfaces. Wipe, wipe, wipe.\n\nMicro pestles need to be properly treated beforehand. DNA is thermostable, so it might not be completely degraded by autoclaving alone. The treatment involves using bleach (DNA is more unstable at... |
null | null | null | dx.doi.org/10.17504/protocols.io.merc3d6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The preparation and staining of samples for MERFISH follows closely the typical protocols used for smFISH (Raj et al., 2008). However, there are a few places in which we have modified these protocols to optimize MERFISH staining. Again, RNase contamination can destroy samples... | [] |
71,206 | Flow cytometry-based measurement of mitophagic flux | 4 | dx.doi.org/10.17504/protocols.io.261ge34jyl47/v1 | https://www.protocols.io/view/flow-cytometry-based-measurement-of-mitophagic-flu-chset6be | Felix Kraus | TITLE: Flow cytometry-based measurement of mitophagic flux
AUTHORS: Felix Kraus
[DESCRIPTION]
Protocol for flow cytometry-based measurement of mitophagic flux
[STEPS]
SECTION: Generation of stable mtKeima cell lines
1. Generate stable cell lines expressing mitochondrial targeted mKeima. See dx.doi.org/10.17504/protoc... | ["[Generation of stable mtKeima cell lines] Generate stable cell lines expressing mitochondrial targeted mKeima. See dx.doi.org/10.17504/protocols.io.br87m9zn and dx.doi.org/10.17504/protocols.io.6qpvr4xn3gmk/v1", "[Seeding of HeLa cells] Wash HeLa cells expressing doxycycline-inducible Parkin with 1x PBS", "[Seeding o... |
58,167 | Amplification of P. vivax/P. malariae/P. falciparum cox3 gene in humans and non human primates | 2 | dx.doi.org/10.17504/protocols.io.4r3l2ooxpv1y/v1 | https://www.protocols.io/view/amplification-of-p-vivax-p-malariae-p-falciparum-c-b42xqyfn | Gabriela Ulloa Urizar | TITLE: Amplification of P. vivax/P. malariae/P. falciparum cox3 gene in humans and non human primates
AUTHORS: Gabriela Ulloa Urizar
[DESCRIPTION]
Amplification of Plasmodium mitochondrial cytochrome c oxidase III (cox3) gene to detection Plasmodium spp. by conventional PCR. Also, detection of Plasmodium falciparum, P... | [] |
27,040 | Nuclei Isolation Prep and Protocol | null | dx.doi.org/10.17504/protocols.io.6m8hc9w | null | Emmy Li, Rene Sit | TITLE: Nuclei Isolation Prep and Protocol
AUTHORS: Emmy Li, Rene Sit
[STEPS]
?. | [] |
56,178 | RNA extraction from diatom P. multistriata | 4 | dx.doi.org/10.17504/protocols.io.261gen627g47/v1 | https://www.protocols.io/view/rna-extraction-from-diatom-p-multistriata-b24sqgwe | Francesco Manfellotto, Antonella Ruggiero, Pina Marotta, Monia Teresa Russo, Anna Santin, Mariella Ferrante | TITLE: RNA extraction from diatom P. multistriata
AUTHORS: Francesco Manfellotto, Antonella Ruggiero, Pina Marotta, Monia Teresa Russo, Anna Santin, Mariella Ferrante
[DESCRIPTION]
RNA extraction protocol from diatom P. multistriata
[STEPS]
1. Collect 20/40 million cells
2. Harvest cells by filtration onto 1.... | ["Collect 20/40 million cells", "Harvest cells by filtration onto 1.2 µm pore size filter", "Cut the filter into two halves and store each half in separate 2 mL eppendorf tube.", "Add 1 mL of TRIzol® Reagent (for 5-10 × 10^6 cells) to eppendorf with half filter and vortex briefly.", "Flash freeze the eppendorf immediat... |
95,614 | Lysosome analysis with confocal microscopy | 4 | dx.doi.org/10.17504/protocols.io.e6nvwd3xwlmk/v1 | https://www.protocols.io/view/lysosome-analysis-with-confocal-microscopy-c9k6z4ze | Sjors Maassen | TITLE: Lysosome analysis with confocal microscopy
AUTHORS: Sjors Maassen
[DESCRIPTION]
This protocol provides an overview of lysosomal analysis using confocal microscopy and Fiji
[STEPS]
SECTION: Sterilize glass cover slips
1. Put the glass coverslips in a 24-well plate, submerge the coverslips in 70% ethanol, and th... | ["[Sterilize glass cover slips] Put the glass coverslips in a 24-well plate, submerge the coverslips in 70% ethanol, and then expose them to UV light in a tissue culture hood for between 20 and 30 minutes.", "[Sterilize glass cover slips] Remove the ethanol, wash the wells containing coverslips three times with sterile... |
49,725 | Titan ONT SARS-CoV-2 Strain Characterization Workflow for the Terra Platform | 5 | null | https://www.protocols.io/view/titan-ont-sars-cov-2-strain-characterization-workf-bus5nwg6 | Jill V Hagey, Frank J Ambrosio, Kevin Libuit, Technical Outreach and Assistance for States Team | TITLE: Titan ONT SARS-CoV-2 Strain Characterization Workflow for the Terra Platform
AUTHORS: Jill V Hagey, Frank J Ambrosio, Kevin Libuit, Technical Outreach and Assistance for States Team
[DESCRIPTION]
The Titan_ONT workflow is a part of the Public Health Viral Genomics Titan series for SARS-CoV-2 genomic character... | ["[Setup Terra and Google Cloud Accounts]", "[Import Titan ONT workflow from Dockstore] Importing the Titan Workflow from Dockstore to the User Workspace\n\nThe Titan_ONT workflow is hosted in the Theiagen Dockstore (https://dockstore.org/) repository and has to be imported into the user's Terra Workspace. Begin by cli... |
95,920 | PERTURB SEQ PROTOCOL FOR EARLY POST-MITOTIC DOPAMINERGIC NEURONS | 0 | null | https://www.protocols.io/view/perturb-seq-protocol-for-early-post-mitotic-dopami-c9wqz7dw | Renuka Ravi Gupta, Nona Farbehi, hendersa, Vikram Khurana, Gist Croft, Lorenz Studer, Joseph Powell | TITLE: PERTURB SEQ PROTOCOL FOR EARLY POST-MITOTIC DOPAMINERGIC NEURONS
AUTHORS: Renuka Ravi Gupta, Nona Farbehi, hendersa, Vikram Khurana, Gist Croft, Lorenz Studer, Joseph Powell
[DESCRIPTION]
We have developed a protocol where genetic perturbations via CRISPRi machinery are introduced into early post mitotic dopami... | ["[Day -1: Coating wells with Poly - L ornithine(PO)] Coat 500 ul per well in a 48-well plate with 15 ug/ml PO in DPBS.", "[Day -1: Coating wells with Poly - L ornithine(PO)] Incubate the plate overnight at 37ºC with 5% CO2 and 20.9% O2.", "[Day 0: Coating wells with Laminin and Fibronectin] Thaw Fibronectin and Lamini... |
78,272 | Green Lab Nanoparticle For 6 Well Cardiomyocyte Transfection v2 | 4 | dx.doi.org/10.17504/protocols.io.ewov1ojd2lr2/v2 | https://www.protocols.io/view/green-lab-nanoparticle-for-6-well-cardiomyocyte-tr-cqn8vvhw | Edwin Yoo | TITLE: Green Lab Nanoparticle For 6 Well Cardiomyocyte Transfection v2
AUTHORS: Edwin Yoo
[DESCRIPTION]
nanoparticle transfection
[STEPS]
SECTION: Nanoparticle Synthesis
2. DNA Dilution
For 3 technical replicate wells of one condition in 6-well plate format, mix the following in microcentrifuge tube.
60 ul DNA at... | ["[Nanoparticle Synthesis] DNA Dilution\nFor 3 technical replicate wells of one condition in 6-well plate format, mix the following in microcentrifuge tube.\n60 ul DNA at 1ug/ul\n440 ul sodium acetate\nTotal volume = 500 ul for 3 technical replicate wells per one condition", "[Nanoparticle Synthesis] Polymer Dilution (... |
null | null | null | dx.doi.org/10.17504/protocols.io.iajcacn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This single-tube library construction protocol is for degraded DNA using adapters for the Illumina platform.</p>
[BEFORE_START]
<p>Calculate the DNA input and prepare the library adapters.</p>
[STEPS]
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44,791 | Cell DIVE™ Platform | Antibody Characterization for Multiplexing | 4 | dx.doi.org/10.17504/protocols.io.bpyxmpxn | https://www.protocols.io/view/cell-dive-platform-antibody-characterization-for-m-bpyxmpxn | Liz McDonough, Chrystal Chadwick, Fiona Ginty, Christine Surrette, Anup Sood | TITLE: Cell DIVE™ Platform | Antibody Characterization for Multiplexing
AUTHORS: Liz McDonough, Chrystal Chadwick, Fiona Ginty, Christine Surrette, Anup Sood
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the process of validating antibodies (primary/secondary, direct conjug... | ["[Decoverslipping]\nFill the plastic slide box with .\n[PBS]", "[Decoverslipping]\nRest the coverslipped slides on the interior raised edges of slide box such that they are inverted (ie. coverslip down and barcode up).", "[Decoverslipping]\nIf your next round is a staining round, prepare your dilutions while you are ... |
92,103 | Immunohistochemistry (IHC) Whole-Mount Antibody Staining | 4 | null | https://www.protocols.io/view/immunohistochemistry-ihc-whole-mount-antibody-stai-c57fy9jn | Talia Pittman | TITLE: Immunohistochemistry (IHC) Whole-Mount Antibody Staining
AUTHORS: Talia Pittman
[DESCRIPTION]
Immunohistochemistry (IHC) Whole-Mount Antibody Staining protocol @FishFloorUCL
[STEPS]
SECTION: Introduction
1. Protocol based on Tom Hawkins' modified version of Jenny Regan's GFP protocol (forked)
SECTION: Fix and... | ["[Introduction] Protocol based on Tom Hawkins' modified version of Jenny Regan's GFP protocol (forked)", "[Fix and dehydrate] Depending on the antigen, you should either fix in PFA or TCA. Always start with PFA (option 1). TCA (option2) can be better for older embryos >36hrs\n\nEither:\n\n(Option 1) Fix in PFA\n\nFix ... |
21,558 | UC Davis - Laser Capture Microscopy | null | dx.doi.org/10.17504/protocols.io.zawf2fe | null | Saivageethi Nuthikattu, Jennifer Rutkowsky | TITLE: UC Davis - Laser Capture Microscopy
AUTHORS: Saivageethi Nuthikattu, Jennifer Rutkowsky
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span><span style = "font-weight:bold;"> </span></div><div class = "text-block">To quantify regions or cell type s... | ["Perform an RNA necropsy (under RNase-free conditions) on tissue (e.g. mouse brain) of interest; mold tissue immediately and place cryomold on dry ice; OR flash freeze tissue and put in -80ºC for cryomolding later. NOTE: Tissue should not be fixed for sectioning.", "Before cryosectioning, make sure you have prepared R... |
58,762 | Pasteuria farm protocol | 3 | null | https://www.protocols.io/view/pasteuria-farm-protocol-b5miq44e | Meghan Duffy, Katherine Hunsberger, Rebecca Bilich | TITLE: Pasteuria farm protocol
AUTHORS: Meghan Duffy, Katherine Hunsberger, Rebecca Bilich
[DESCRIPTION]
This is a protocol to infect and maintain Daphnia with Pasteuria ramosa for use in laboratory experiments.
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.cp5vq5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Ligation protocol for the PCR Cloning Kit (E1202)
[BEFORE_START]
For purified PCR amplicon products, the amount of insert to be added can be calculated by relative length or molar calculations. See the Guidelines for the formulas.
[GUIDELINES]
<br /><table border='0' widt... | [] |
104,831 | Immunofluorescence for detection of ALFA-tag in S. rosetta | 1 | dx.doi.org/10.17504/protocols.io.5jyl85k38l2w/v1 | https://www.protocols.io/view/immunofluorescence-for-detection-of-alfa-tag-in-s-dik74czn | Fredrick leon, David Booth | TITLE: Immunofluorescence for detection of ALFA-tag in S. rosetta
AUTHORS: Fredrick leon, David Booth
[DESCRIPTION]
Immunofluorescence (IF) allows for the visualization of protein localization in fixed-cell samples. This protocol builds upon commonly used IF methods, with a focus on retaining and minimally damaging S... | ["[Adsorb cells to Glass-Bottom Dish] Pipette 50 µL of 10 mg/mL onto the glass bottom of a glass-bottomed 96 well plate and incubate for 15 min at Room temperature.", "[Adsorb cells to Glass-Bottom Dish] Remove the excess liquid and add 50 µL. Repeat twice more for a total of 3 washes.", "[Adsorb cells to Glass-Bottom ... |
71,042 | Immunofluorescence of GM2 | 1 | dx.doi.org/10.17504/protocols.io.36wgqj4d5vk5/v1 | https://www.protocols.io/view/immunofluorescence-of-gm2-chmat42e | Hankum Park, Frances V Hundley, Harper JW | TITLE: Immunofluorescence of GM2
AUTHORS: Hankum Park, Frances V Hundley, Harper JW
[DESCRIPTION]
Selective purification of early endosomes can be achieved through affinity capture of the early endosome-associated protein EEA1 (termed Endo-IP) (Park et al. 2022). These purified endosomes can be used for proteomic and... | ["[Preparation of coverslips] Coat No.1.5 coverslips in 0.01% poly-L-lysine solution. Incubate at 37 °C for 15 min", "[Preparation of coverslips] Aspirate poly-L-lysine solution and wash coverslips three times with sterile DPBS.", "[Preparation of coverslips] Dry coverslips at 37 °C for 15 min .", "[Seed cells] Spli... |
null | null | null | dx.doi.org/10.17504/protocols.io.smeec3e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is widely used in serum biochemical indexes detection, it provides an rapid and reliable technique for obtaining relative concentrations of multiple blood biochemical indices simultaneously.</p>
[BEFORE_START]
<p>All the standard samples of every index are kept... | [] |
85,890 | Human ovarian tissue explant cultures (static or fluidic conditions) | 1 | dx.doi.org/10.17504/protocols.io.3byl4qbdjvo5/v2 | https://www.protocols.io/view/human-ovarian-tissue-explant-cultures-static-or-fl-cx5axq2e | hannah.anvari, pooja.devrukhkar, francesca.e.duncan francesca.duncan | TITLE: Human ovarian tissue explant cultures (static or fluidic conditions)
AUTHORS: hannah.anvari, pooja.devrukhkar, francesca.e.duncan francesca.duncan
[DESCRIPTION]
The Cellular Senescence Network (SenNet) was recently established to map senescent cells in the human body. As part of this initiative, our goal is to ... | ["[Processing human ovarian tissue for ovarian explant culture]", "[Processing human ovarian tissue for ovarian explant culture] Ovarian tissue samples are collected from the Northwestern Pathology department and placed immediately on ice following collection. The research coordinator will bring research specimens to t... |
null | null | null | dx.doi.org/10.17504/protocols.io.cwaxad | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is the protocol for DNA Assembly using the NEBuilder® HiFi DNA Assembly Master Mix (E2621).
[GUIDELINES]
<strong>Optimal Quantities</strong><br /><br />NEB recommends a total of 0.03–0.2 pmols of DNA fragments when 1 or 2 fragments are being assembled into a... | [] |
100,775 | Experimental procedures for TF Perturb-Seq (UT Southwestern) | 0 | null | https://www.protocols.io/view/experimental-procedures-for-tf-perturb-seq-ut-sout-denf3dbn | Lei Wang | TITLE: Experimental procedures for TF Perturb-Seq (UT Southwestern)
AUTHORS: Lei Wang
[DESCRIPTION]
Optimized procedures and best practices for Perturb-Seq data production, developed at the UT Southwestern Characterization Center
[STEPS]
SECTION: Part 1: sgRNA plasmid library construction
1.
SECTION: Part 2: Bulk se... | ["[Part 1: sgRNA plasmid library construction]", "[Part 2: Bulk sequencing of sgRNAs] Goal: This section describes procedures to construct next-generation sequencing libraries of sgRNAs, either from the plasmid library described in Part 1 or from genomic DNA where sgRNAs have been integrated into cells. Typically, we s... |
101,298 | Decreased Memory-related Regional Cerebral Perfusion in Severe Obstructive Sleep Apnoea With a Mild Cognitive Impairment | 0 | dx.doi.org/10.17504/protocols.io.rm7vzjjprlx1/v1 | https://www.protocols.io/view/decreased-memory-related-regional-cerebral-perfusi-de6s3hee | Yan Xiangbo | TITLE: Decreased Memory-related Regional Cerebral Perfusion in Severe Obstructive Sleep Apnoea With a Mild Cognitive Impairment
AUTHORS: Yan Xiangbo
[DESCRIPTION]
We will use arterial spin labeling (ASL) technology to quantify and evaluate abnormal changes in resting state cerebral blood perfusion in patients with obs... | ["[Research objectives] We will use arterial spin labeling (ASL) technology to quantify and evaluate abnormal changes in resting state cerebral blood perfusion in patients with obstructive sleep apnea (OSA) with cognitive impairment (CI) and to explore the underlying neuropathological mechanisms in patients with OSA an... |
57,918 | Roadmap to the bioinformatic study of gene and protein evolution | 5 | dx.doi.org/10.17504/protocols.io.b4s6qwhe | https://www.protocols.io/view/roadmap-to-the-bioinformatic-study-of-gene-and-pro-b4s6qwhe | florian.jacques , Paulina Bolivar, Kristian Pietras, Emma Hammarlund | TITLE: Roadmap to the bioinformatic study of gene and protein evolution
AUTHORS: florian.jacques , Paulina Bolivar, Kristian Pietras, Emma Hammarlund
[DESCRIPTION]
We present a compilation of nucleic acid and protein databases and bioinformatic tools for phylogenetic reconstructions and a wide range of studies on mol... | ["[Sequence selection and comparisons] Identification of homologues\n\nStudying the evolution of a family of genes or proteins requires the identification of homologues, i.e., genes or protein with shared ancestry. Homologues include orthologues, that are present in different species, and paralogues, that are present i... |
28,385 | MojoSort™ Human CD14+ Monocytes Isolation Kit Protocol | null | dx.doi.org/10.17504/protocols.io.7x9hpr6 | null | Sam Li | TITLE: MojoSort™ Human CD14+ Monocytes 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><span> This kit is designed for the isolation of untouched CD14</span><span style = "vertic... | ["[Platelet Removal Protocol]\nDilute blood with 2-4 times (volume/volume) 1X PBS.", "[Platelet Removal Protocol]\nCarefully layer diluted blood over 12.5mL of isolation medium in a 50mL tube.", "[Platelet Removal Protocol]\nCentrifuge at 400xg for 25 minutes at room temperature in a swinging-bucket rotor without the b... |
32,413 | Aquatic eDNA sampling and plant metabarcoding (v0.0.1) | null | dx.doi.org/10.17504/protocols.io.bbv5in86 | null | Jordan Callahan, Robert Harbert | TITLE: Aquatic eDNA sampling and plant metabarcoding (v0.0.1)
AUTHORS: Jordan Callahan, Robert Harbert
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Aquatic eDNA sampling, extraction, and plant metabarcoding on Oxford Nanopore's Flongle platform.</div><div class = "text-block">Sampling method adap... | ["[Aquatic eDNA sampling]\nAssemble hose ends and drill pump and attach to wooden bracket with zip ties. Lock drill driver to pump spindle.", "[Aquatic eDNA sampling]\nAttach fresh, sterile 0.045 μm filter funnel assembly (Fisher Sci catalog #09 740 30K) to hose on the “In” side of the pump and tighten hose clamp. Be s... |
29,361 | Planetary Dominoes - How microbes drive biogeochemical cycles | null | dx.doi.org/10.17504/protocols.io.8wrhxd6 | null | Nadia Szeinbaum, Abbigail Johnson, Thomas Swofford | TITLE: Planetary Dominoes - How microbes drive biogeochemical cycles
AUTHORS: Nadia Szeinbaum, Abbigail Johnson, Thomas Swofford
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the step to assemble your own Planetary Domino. </div><div class = "text-block"><span>We designed t... | ["Print this file into a poster, cut each piece and add an adhesive magnet. These will be the domino pieces, and they are now able to stick to any magnetic surface. The pieces here are enough for at least three different sets, as they repeat. The design was created by Image Alleviation, in collaboration with us, specif... |
92,976 | Conseils sur l'utilisation de contrôles d'analyse pour la détection directe des poliovirus par séquençage des nanopores | 3 | dx.doi.org/10.17504/protocols.io.5jyl8pxbrg2w/v1 | https://www.protocols.io/view/conseils-sur-l-39-utilisation-de-contr-les-d-39-an-c62qzgdw | Joyce Akello, Manasi Majumdar, Alex Shaw, Catherine Troman, Erika Bujaki, Javier Martin, Nick Grassly | TITLE: Conseils sur l'utilisation de contrôles d'analyse pour la détection directe des poliovirus par séquençage des nanopores
AUTHORS: Joyce Akello, Manasi Majumdar, Alex Shaw, Catherine Troman, Erika Bujaki, Javier Martin, Nick Grassly
[DESCRIPTION]
Ce document décrit le processus de laboratoire pour l'utili... | [] |
46,536 | Intracardiac perfusion and brain fixation for immunohistochemistry | 4 | dx.doi.org/10.17504/protocols.io.yxmvmk94og3p/v1 | https://www.protocols.io/view/intracardiac-perfusion-and-brain-fixation-for-immu-brpgm5jw | Daniel Manrique-Castano | TITLE: Intracardiac perfusion and brain fixation for immunohistochemistry
AUTHORS: Daniel Manrique-Castano
[DESCRIPTION]
This protocol aims to preserve brain tissue for immunohistochemistry studies. It is not valid for protein or RNA extraction studies.
[BEFORE_START]
Prepare o filtered fresh PFA and saline solution ... | ["[Animal Sacrifice] Before starting, fill a syringe with 20 mL of ice-cooled PBS and a separate syringe with 20 mL 4% Paraformaldehyde (PFA). Connect the PBS syringe to a Winged infusion set.", "[Animal Sacrifice] When perfusion is finished, harvest the brain from the cranium, carefully removing the meninges to avoid... |
54,165 | Cyanobacterial Encapsulation In Biocompatible Silica Gels | 6 | dx.doi.org/10.17504/protocols.io.by5vpy66 | https://www.protocols.io/view/cyanobacterial-encapsulation-in-biocompatible-sili-by5vpy66 | celiamm | TITLE: Cyanobacterial Encapsulation In Biocompatible Silica Gels
AUTHORS: celiamm
[DESCRIPTION]
Silica gels are a biohybrid material for the encapsulation of cyanobacteria.
Their internal structure is based on a highly porous three-dimensional SiO2 network with a mesoporous distribution of porosity, with a high num... | ["[Silica precursor] Starting from 37 % (v/v) commercial sodium silicate, a dilution solution of 5 % (v/v) sodium silicate is prepared.\n\nVolume of Na2SiO3 commercial x Percentage of Na2SiO3 commercial = Volume of Na2SiO3 solution x 5%", "[Silica precursor] Cool the solution to about 4°C for at least one day in the re... |
82,378 | iPSC differentiation into Microglia | 4 | dx.doi.org/10.17504/protocols.io.261ge3qpwl47/v1 | https://www.protocols.io/view/ipsc-differentiation-into-microglia-cupiwvke | Narayana Yadavalli, Shawn M. Ferguson | TITLE: iPSC differentiation into Microglia
AUTHORS: Narayana Yadavalli, Shawn M. Ferguson
[DESCRIPTION]
This protocol describes iPSC differentiation into microglia.
[GUIDELINES]
This protocol is adapted from the below article.
McQuade A, Coburn M, Tu CH, Hasselmann J, Davtyan H, Blurton-Jones M. Development and valid... | ["[Steps for Microglia differentiation from hematopoietic progenitors] Day 12:\nPlate 100,000 hematopoietic progenitor on Matrigel coated 6 well plate in 3 cytokine media.", "[Steps for Microglia differentiation from hematopoietic progenitors] On days 14,16,18,20 and 22 supplement with 1 mL of 3 cytokine media.", "[Ste... |
90,207 | DNA extraction - Zooplankton - 96 wells | 4 | dx.doi.org/10.17504/protocols.io.j8nlk4x7wg5r/v2 | https://www.protocols.io/view/dna-extraction-zooplankton-96-wells-c4b7ysrn | coline.royaux, Nicolas Rabet, Céline Bonillo | TITLE: DNA extraction - Zooplankton - 96 wells
AUTHORS: coline.royaux, Nicolas Rabet, Céline Bonillo
[DESCRIPTION]
This protocol was used to extract DNA from whole or parts of zooplanktonic freshwater crustaceans (Copepoda, Branchiopoda, ...) from New Caledonia.
[STEPS]
1. Prepare your 96-well extraction plate with o... | ["Prepare your 96-well extraction plate with one individual per well. Alternate genus in the wells to detect eventual contamination between wells.", "Collect one individual from a sample", "Note its genus and determine its sex with a binocular microscope", "For big individuals (more than 5 mm), dissect a few legs and p... |
67,454 | Nucentix Keto X3 Review - Shark Tank Alert of Keto X3, Read Pros & Cons! | 4 | dx.doi.org/10.17504/protocols.io.261genzojg47/v1 | https://www.protocols.io/view/nucentix-keto-x3-review-shark-tank-alert-of-keto-x-cd46s8ze | Vitality Hq Keto Gummies | TITLE: Nucentix Keto X3 Review - Shark Tank Alert of Keto X3, Read Pros & Cons!
AUTHORS: Vitality Hq Keto Gummies
[DESCRIPTION]
Nucentix Keto X3
[STEPS]
1. Nucentix Keto X3 is a ketogenic dietary supplement created to assist obese people. According to the legitimate website, it makes use of top class herbal ingr... | ["Nucentix Keto X3 is a ketogenic dietary supplement created to assist obese people. According to the legitimate website, it makes use of top class herbal ingredients to provoke ketosis, a metabolic kingdom that burns calories in no time. As a end result, the frame starts losing weight from all components, inclusive of... |
62,341 | Preparation of PBS Solution | 1 | null | https://www.protocols.io/view/preparation-of-pbs-solution-b85dry26 | Stephane Fadanka, Shalo Minette, Nadine Mowoh | TITLE: Preparation of PBS Solution
AUTHORS: Stephane Fadanka, Shalo Minette, Nadine Mowoh
[DESCRIPTION]
Phosphate buffered saline ( PBS) is a buffer solution commonly used in biological research. It is a salty solution containing sodium chloride, sodium phosphate, and (in some formulations) potassium chloride and... | ["[Preparing reagents and workspace] Before beginning the procedure put on Personal Protective Equipment (Lab Gown, Gloves, shoes, masks and goggles).\n\nClean up work surfaces and environment using disinfection solution (Bleach and after 70% alcohol).\n\nCheck to be sure all reagents and equipment needed for the proce... |
35,947 | LAM-HGTGTS (Linear Amplification-mediated high-throughput genome-wide translocation sequencing) Our Working Protocol. | null | dx.doi.org/10.17504/protocols.io.bfcjjiun | https://www.protocols.io/view/lam-hgtgts-linear-amplification-mediated-high-thro-bfcjjiun | Eric Danner | TITLE: LAM-HGTGTS (Linear Amplification-mediated high-throughput genome-wide translocation sequencing) Our Working Protocol.
AUTHORS: Eric Danner
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">LAM-HTGTS = linear amplification mediated high-throughput genomic translocations sequencing</div><div cl... | ["[Prepare Reagents]\nLysis Buffer Preparation5M NaCl Dissolve 292.5 g of NaCl in H2O and bring to 1 liter. Autoclave, store at room temperature (RT; 20–25 °C) for up to 1 year.0.5 M EDTA (pH 8.0) Dissolve 186.12 g of EDTA–Na2·2H2O in H2O, adjust the pH to 8.0 using 2.5 N NaOH and then adjust the total volume to 1 lite... |
22,592 | Euplotes - Miceli Lab | null | dx.doi.org/10.17504/protocols.io.2a8gahw | null | Angela Piersanti, Rachele Cesaroni, Larry Klobutcher, cristina miceli, Sandra Pucciarelli | TITLE: Euplotes - Miceli Lab
AUTHORS: Angela Piersanti, Rachele Cesaroni, Larry Klobutcher, cristina miceli, Sandra Pucciarelli
[STEPS] | [] |
64,510 | Mesostats --- A multiplexed, low-cost, do-it-yourself continuous culturing system for experimental evolution of mesocosms | 4 | dx.doi.org/10.17504/protocols.io.ca86shze | https://www.protocols.io/view/mesostats-a-multiplexed-low-cost-do-it-yourself-co-ca86shze | Erika M M Hansson, Dylan Z. Childs, Andrew P. Beckerman | TITLE: Mesostats --- A multiplexed, low-cost, do-it-yourself continuous culturing system for experimental evolution of mesocosms
AUTHORS: Erika M M Hansson, Dylan Z. Childs, Andrew P. Beckerman
[DESCRIPTION]
Microbial experimental evolution allows studying evolutionary dynamics in action and testing theory predictions... | ["[Assembling the mesostats for the first time] Place all vessels and machinery in their intended location before cutting the tubing to ensure sufficient lengths and to minimise mistakes. See Fig 3--5 in the Guidelines for visual representation of how the parts connect, given here is a more detailed description with po... |
46,066 | Gel DNA Extraction | 1 | dx.doi.org/10.17504/protocols.io.bq8smzwe | https://www.protocols.io/view/gel-dna-extraction-bq8smzwe | Kenneth Schackart | TITLE: Gel DNA Extraction
AUTHORS: Kenneth Schackart
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol details how to extract DNA from agarose gel using </span><a href="https://www.thermofisher.com/order/catalog/product/K0691#/K0691" style = "text-decoration:underline;color:blue;c... | ["[Gel Electrophoresis]\nPerform Gel Electrophoresis on your DNA sample to separate the DNA bands.\nThe protocol recommends for TBE/agarose gel and for TAE/agarose gel.Recommended well depth is 1 mm / 1 μL sample.Other recommendations can be found in the original protocol, such as recommended voltage.", "[Gel Ele... |
88,791 | Primer stock preparation | 4 | null | https://www.protocols.io/view/primer-stock-preparation-c2xxyfpn | Brian Lovett, Kristen Pierce | TITLE: Primer stock preparation
AUTHORS: Brian Lovett, Kristen Pierce
[DESCRIPTION]
General protocol for preparation of lyophilized primer stocks from IDT.
[GUIDELINES]
Recommended: When you receive your lyophilized primers, check the name of the primer, primer sequence and the concentration listed on the tube. IDT p... | ["[Preparation of stock solution] Reconstitute lyophilized primers in required volume of molecular grade water (i.e., RNase/DNase free) to 100 micromolar (µM).", "[Preparation of working solution] Allow stock solution to thaw completely at Room temperature.", "[Use of primers] For a typical 25 µL PCR reaction, 1 µL of ... |
93,101 | Concentration and nucleic acid extraction of viruses from wastewater influent | 4 | dx.doi.org/10.17504/protocols.io.3byl4qezjvo5/v2 | https://www.protocols.io/view/concentration-and-nucleic-acid-extraction-of-virus-c66mzhc6 | Ari N Machtinger, Olivia S Hershey, William J Bradshaw, Michael R McLaren | TITLE: Concentration and nucleic acid extraction of viruses from wastewater influent
AUTHORS: Ari N Machtinger, Olivia S Hershey, William J Bradshaw, Michael R McLaren
[DESCRIPTION]
This protocol details our workflow for performing concentration and total nucleic acid extraction from wastewater influent for the purpo... | ["[Part 1: Influent Handling, Dissociation, Centrifugation, Filtration] Add 400 µL of 10 % (v/v) Tween 20 stock solution to each centrifuge tube for a final concentration of 1 % (v/v) Tween 20.", "[Part 1: Influent Handling, Dissociation, Centrifugation, Filtration] Prepare the negative control.\nUsing a fresh 50 mL se... |
84,318 | Sequencing of Canine Parvovirus (CPV) from Rectal Swab Samples V.1 | 4 | dx.doi.org/10.17504/protocols.io.36wgq3563lk5/v1 | https://www.protocols.click/view/sequencing-of-canine-parvovirus-cpv-from-rectal-sw-cwj6xcre | Sara França de Araújo dos Santos, Ueric José Borges de Souza, Martha Trindade Oliveira, Jairo Jaime, Fernando Rosado Spilki, Ana Cláudia Franco, Paulo Michel Roehe, Fabrício Souza Campos | TITLE: Sequencing of Canine Parvovirus (CPV) from Rectal Swab Samples V.1
AUTHORS: Sara França de Araújo dos Santos, Ueric José Borges de Souza, Martha Trindade Oliveira, Jairo Jaime, Fernando Rosado Spilki, Ana Cláudia Franco, Paulo Michel Roehe, Fabrício Souza Campos
[DESCRIPTION]
Canine parvovirus (CPV) is a highly... | ["[Nucleic Acid Extraction using Quick-DNA/RNA Viral MagBead (Zymo Research)] Elute each dry into 400 µL of 1X viral DNA/RNA buffer.", "[Nucleic Acid Extraction using Quick-DNA/RNA Viral MagBead (Zymo Research)] For each sample, add 10 µL of beads and 4 µL of proteinase K.\n\nObs: when working with many samples, on... |
41,858 | Find SARS-CoV-2 testing protocol | 4 | dx.doi.org/10.17504/protocols.io.bk5aky2e | https://www.protocols.io/view/find-sars-cov-2-testing-protocol-bk5aky2e | jose.nuno | TITLE: Find SARS-CoV-2 testing protocol
AUTHORS: jose.nuno
[STEPS]
?. Collect a sample of of saliva (up to the filling line) in a 0.45 um syringeless filter vial (provided with the kit). The sample should be collected at least 60 minutes after the last food ingestion and after a mouth rinse with plain water to clea... | ["Collect a sample of of saliva (up to the filling line) in a 0.45 um syringeless filter vial (provided with the kit). The sample should be collected at least 60 minutes after the last food ingestion and after a mouth rinse with plain water to clean the mouth\n400 µl\nBe careful of cleaning the surface of the vial if... |
27,984 | Removal of kanamycinR gene from Keio collection strain | null | dx.doi.org/10.17504/protocols.io.7jqhkmw | null | Ben Kuipers | TITLE: Removal of kanamycinR gene from Keio collection strain
AUTHORS: Ben Kuipers
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to remove the kanamycinR gene from the JW3367 strain from the Keio Collection.</div><div class = "text-block">References Datsenko, K.A., and Wanner... | ["Chemical competent cells of E. coli JW0336 were prepared with the mix and go protocol.", "Day 1: Transformation of the recombinase plasmid pCP20The competent cells were transformed with plasmid pCP20. (This plasmid has a temperature-sensitive origin of replication, resistant to ampicillin and chloramphenicol. With th... |
18,967 | Plant leaf tooth feature extraction | null | dx.doi.org/10.17504/protocols.io.wrxfd7n | null | Wang Hu, Li Chu, Tian Yan, Zhou Haoyu, Tian Di | TITLE: Plant leaf tooth feature extraction
AUTHORS: Wang Hu, Li Chu, Tian Yan, Zhou Haoyu, Tian Di
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Previous studies extract features that are not strictly defined in botany; therefore, a uniform standard to compare the accuracies of various feature ext... | ["[Experiment]\nTo verify whether the proposed leaf structure feature description algorithm is scientific and effective, we implemented the algorithm using MATLAB 2017 (MathWorks, Natick, MA, USA) on a standard desktop PC (4.2 GHz CPU, 24 GB RAM). Processing of a single leaf took approximately 1.4 s. This could undoubt... |
null | null | null | dx.doi.org/10.17504/protocols.io.duv6w5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This recipe is from: <br /> <span class="cit-auth cit-auth-type-author">Alexander WG</span> <span class="cit-sep cit-sep-separator">, </span> <span class="cit-auth cit-auth-type-author">Doering DT</span> <span class="cit-sep cit-sep-separator">,</span> <span class="cit-sep cit-s... | [] |
93,623 | Sedimentation Assay | 1 | dx.doi.org/10.17504/protocols.io.eq2lyjb9mlx9/v1 | https://www.protocols.io/view/sedimentation-assay-c7nxzmfn | Michael X. Henderon | TITLE: Sedimentation Assay
AUTHORS: Michael X. Henderon
[DESCRIPTION]
This protocol details sedimentation assay for alpha-synuclein fibrils.
[STEPS]
SECTION: With Sucrose Cushion
1.
Dilute 4 µL of 5 mg/mL α-synuclein PFFs to 40 µL in PBS in ultracentrifuge tubes.
SECTION: With Sucrose Cushion
2. Add 40 µL 20% su... | ["[With Sucrose Cushion] Dilute 4 µL of 5 mg/mL α-synuclein PFFs to 40 µL in PBS in ultracentrifuge tubes.", "[With Sucrose Cushion] Add 40 µL 20% sucrose beneath PFFs.", "[With Sucrose Cushion] Ultracentrifuge at 100000 x g (45000 rpm) for 30 min at 22 °C.", "[With Sucrose Cushion] Remove 70 µL supernatant and add to ... |
46,348 | VALAP protocol | 4 | null | https://www.protocols.io/view/valap-protocol-brhkm34w | Elizabeth Fozo | TITLE: VALAP protocol
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">VALAP is a biologically inert method for sealing coverslips, making it usefulfor live cell imaging.</div></div>
[STEPS]
?. [Use: Method 1 - "Painting" it on]
Put the jar or bottle on a hotplate on the lowe... | ["[Use: Method 1 - \"Painting\" it on]\nPut the jar or bottle on a hotplate on the lowest temperature setting. Do not leave unattended!!!", "[Use: Method 1 - \"Painting\" it on]\nWait for the Valap to melt fully.", "[Use: Method 1 - \"Painting\" it on]\nUsing a cotton-tipped applicator, make sure it is well loaded wit... |
43,804 | SPRI bead mix | 4 | dx.doi.org/10.17504/protocols.io.bnz4mf8w | https://www.protocols.io/view/spri-bead-mix-bnz4mf8w | Philippe Jolivet, Joseph W. Foley | TITLE: SPRI bead mix
AUTHORS: Philippe Jolivet, Joseph W. Foley
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the preparation of stocks and buffers for inexpensive, convenient, and scalable DNA and RNA purification from aqueous solutions by solid-phase reversible immobiliza... | ["[Preparing stock solutions]\nIn 50 mL volumetric flasks, prepare a separate 50 mL stock solution for each of the following components with the specified weights of solids.Some gentle heating may be necessary. Ensure the solution comes back to room temperature before completing the volume to the mark on the flask. Sto... |
34,865 | Pathogen-Oriented Low-cost Assembly & Re-sequencing (POLAR): A highly sensitive and high-throughput SARS-CoV-2 diagnostic based on whole genome sequencing | null | dx.doi.org/10.17504/protocols.io.bearjad6 | https://www.protocols.io/view/pathogen-oriented-low-cost-assembly-amp-re-sequenc-bearjad6 | Brian Glenn St Hilaire, Neva C. Durand, Namita Mitra, Saul Godinez, Ragini Mahajan, Alyssa Blackburn, Zane Colaric, Joshua W. M. Theisen, David Weisz, Olga Dudchenko, Andreas Gnirke, Suhas S.P. Rao, Parwinder Kaur, Aviva Presser Aiden, Erez Lieberman Aiden | TITLE: Pathogen-Oriented Low-cost Assembly & Re-sequencing (POLAR): A highly sensitive and high-throughput SARS-CoV-2 diagnostic based on whole genome sequencing
AUTHORS: Brian Glenn St Hilaire, Neva C. Durand, Namita Mitra, Saul Godinez, Ragini Mahajan, Alyssa Blackburn, Zane Colaric, Joshua W. M. Theisen, David Weisz... | ["[cDNA preparation]\nMake a mastermix of the dNTPs and Random Hexamers for 96 samples (account for pipette error), pipette to mix and add from mastermix to each well in a 96-well plate. To each well, add of RNA extract eluted in Step 7.\n1 µl\n5.5 µl", "[cDNA preparation]\nSet-up and run the following program on a t... |
49,284 | Human Islet Isolation Enzyme Preparation Version 1.0 | 1 | dx.doi.org/10.17504/protocols.io.budcns2w | https://www.protocols.io/view/human-islet-isolation-enzyme-preparation-version-1-budcns2w | James Lyon, Aliya Spigelman, Jocelyn E Manning Fox, Patrick Macdonald | TITLE: Human Islet Isolation Enzyme Preparation Version 1.0
AUTHORS: James Lyon, Aliya Spigelman, Jocelyn E Manning Fox, Patrick Macdonald
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the preparation of enzymes used in the isolation of human research islets by the Alberta ... | ["[Preparation of HBSS Perfusion Solution - 10L]\nHank's Balanced Salt Solution - HBSS (perfusion, rinse, priming solutions) (10L)\nReagentFinal ConcentrationWeight/VolumeSupplierCatalgue NumberHBSS Powder9.51 g/L1 bottleMediatech/Corning55-022-PBCaCl2 (anhydrous)3.60 mM4.0gMP Biochemicals LLC15350290\nMgSO4 (anhydrous... |
42,240 | Mm Control Media (Green Cap) | 4 | dx.doi.org/10.17504/protocols.io.bmg8k3zw | https://www.protocols.io/view/mm-control-media-green-cap-bmg8k3zw | Ada de la Cruz | TITLE: Mm Control Media (Green Cap)
AUTHORS: Ada de la Cruz
[STEPS]
?. [Equipment for making media]
For making media you will need: 2 --> 500 mL graduated cylinders1 --> 100 mL graduated cylinder1 --> 10 mL graduated cylinder2 --> small funnels2 --> weigh boats1 --> lab spatula 1 --> pipette + tip1 --> 1000 mL or 2000... | ["[Equipment for making media]\nFor making media you will need: 2 --> 500 mL graduated cylinders1 --> 100 mL graduated cylinder1 --> 10 mL graduated cylinder2 --> small funnels2 --> weigh boats1 --> lab spatula 1 --> pipette + tip1 --> 1000 mL or 2000 mL flask (depending on if you're making 1 L or 2 L of media)", "[Mak... |
21,328 | Yale - Blood Urea Nitrogen | null | dx.doi.org/10.17504/protocols.io.y3qfymw | null | John Stack, Gary Cline | TITLE: Yale - Blood Urea Nitrogen
AUTHORS: John Stack, Gary Cline
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Procedure used to measure the concentration of Blood Urea Nitrogen(BUN) in blood, plasma, and serum. Ure... | ["Calibrate Cobas for BUN analysis by running a multi analyte standard and two assayed control serums.", "Sample handling as performed by the Cobas Mira Plus. a) Cobas pipettes 2 µL of sample into a cuvette slot. b) Absorbance is measured at 340 nm. c) Add 200 µL of BUN liquid reagent. d) Mixture is incubat... |
null | null | null | dx.doi.org/10.17504/protocols.io.hg7b3zn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div>
<div>
<div>
<p>This protocol is from 'Flower Ca<sup>2+</sup> channel in CME and ADBE' of Yao CK et al.</p>
<div>
<div>
<p> </p>
<p>Please see the manuscript for the full method details.</p>
</div>
</div>
</div>
</div>
</div>
[BEFORE_START]
<p>You'll need: </p>
<p> </p>
<p... | [] |
67,134 | Reduction and alkylation of protein lysates for LC-MS (proteomics) using dithiothreitol (DTT) and iodoacetamide (IAM) | 1 | dx.doi.org/10.17504/protocols.io.6qpvr6573vmk/v1 | https://www.protocols.io/view/reduction-and-alkylation-of-protein-lysates-for-lc-cds6s6he | ronan.ocualain | TITLE: Reduction and alkylation of protein lysates for LC-MS (proteomics) using dithiothreitol (DTT) and iodoacetamide (IAM)
AUTHORS: ronan.ocualain
[DESCRIPTION]
This protocol details the procedure of the reduction and alkylation using dithiothreitol (DTT) and iodoacetamide (IAM).
[BEFORE_START]
Initial preparation... | ["[Before you begin] Remove the DTT and IAM aliquots from fridge 2.", "[Before you begin] Take one of each for your preparation. Place the boxes back in the fridge.", "[Before you begin] To make a 100 millimolar (mM) solution of DTT and IAM, add the volume of water indicated on the box from which you took the pre-weigh... |
44,061 | Library construction of metabarcoding at DNBSEQ-G400 with MGIEasy universal DNA library prep Kit | 4 | dx.doi.org/10.17504/protocols.io.bn95mh86 | https://www.protocols.io/view/library-construction-of-metabarcoding-at-dnbseq-g4-bn95mh86 | Xiaohuan Sun, Yuehua Hu, Zewei Song | TITLE: Library construction of metabarcoding at DNBSEQ-G400 with MGIEasy universal DNA library prep Kit
AUTHORS: Xiaohuan Sun, Yuehua Hu, Zewei Song
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Library construcion steps following MGIEasy universal DNA library prep set user manual started from e... | ["End-repair and A-tailingsteps are performed with ERAT Enzyme Mix in MGIEasy Universal DNA Library Prep Set (Cat. No: 1000006985).", "Adaptor ligation step following the instruction bellow by using MGIEasy DNA Adaptors.\n5 mL", "Cleanup of Adapter-ligated DNA by using DNA clean beads and freshly prepared 80% ethanol,... |
62,352 | Preparing LB Broth or Agar +/- Antibiotic | 1 | null | https://www.protocols.io/view/preparing-lb-broth-or-agar-antibiotic-b85qry5w | Stephane Fadanka, Shalo Minette, Nadine Mowoh | TITLE: Preparing LB Broth or Agar +/- Antibiotic
AUTHORS: Stephane Fadanka, Shalo Minette, Nadine Mowoh
[DESCRIPTION]
In order for bacteria to be successfully cultured, they must be grown in the appropriate media. LB, also known as Lysogeny broth (also known as Luria broth, Lennox broth, or Luria-Bertani medium.)... | ["Dispense the resulting 120ml mixture into the following flasks; \n2x 50ml LB broth in 250ml conical flasks\n1x 5 ml and 1 x 10 ml in 50 ml conical flask", "[Weighing components for LB Broth] Weight all powders Yeast Extract CAS 8013-01-2, NaCl CAS 7647-14-5 and Tryptone CAS 91079-40-2 as indicated in the table below ... |
103,563 | Ceres Nanoparticles Concentration and Extraction using MagMAX Wastewater kit | 0 | dx.doi.org/10.17504/protocols.io.n2bvjnpwxgk5/v1 | https://www.protocols.io/view/ceres-nanoparticles-concentration-and-extraction-u-dhdj324n | Shannon Fitz, Alex Shaw, Dilip Abraham, michael Owusu | TITLE: Ceres Nanoparticles Concentration and Extraction using MagMAX Wastewater kit
AUTHORS: Shannon Fitz, Alex Shaw, Dilip Abraham, michael Owusu
[DESCRIPTION]
Ceres Nanotrap Microbiome A Particles are used to capture and concentrate important pathogens from samples. https://www.ceresnano.com/protocols Protocol APP-0... | ["[Concentration and extraction] Manual Ceres Nanotrap concentration using Nanotrap Microbiome A Particles for a 35 mL environmental sample", "[Concentration and extraction] Invert the environmental water sample 5 times to mix. Then, let it sit for 45 seconds at room temperature. (No need to wait for samples to reach r... |
27,408 | Isolation of Nuclei from Frozen Human Peripheral Nerve | null | dx.doi.org/10.17504/protocols.io.6zqhf5w | null | Alexander Chamessian | TITLE: Isolation of Nuclei from Frozen Human Peripheral Nerve
AUTHORS: Alexander Chamessian
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details the efficient isolation of intact nuclei from frozen peripheral nerve from human (e.g. sciatic, tibial, etc.)</div></div>
[STEPS]
?. [Tis... | ["[Tissue Procurement]\nNerve samples should be collected as quickly as possible from the donor.Place the nerve in a clean, labeled container.Snap-freeze in liquid nitrogenStore at -80C until usage", "[Cryo-Pulverization]\nRemove the sample from -80C storage and maintain on dry ice. Do not let it thaw."] |
87,835 | sgRNA library re-amplification in liquid culture | 1 | dx.doi.org/10.17504/protocols.io.n92ldmr7xl5b/v1 | https://www.protocols.io/view/sgrna-library-re-amplification-in-liquid-culture-czz3x78n | Erik.Haussner, micboe | TITLE: sgRNA library re-amplification in liquid culture
AUTHORS: Erik.Haussner, micboe
[DESCRIPTION]
In this protocol, we describe a stepwise procedure for the re-amplification of sgRNA libraries in liquid culture. In our hands, this protocol works reliably to amplify pre-cloned sgRNA libraries (e.g. order from Addgen... | ["[Library transformation] Prepare and for electroporation.", "[Library transformation] Add 100 ng into 25 µL , carefully mix by pipetting up and down.", "[Library transformation] Add 25 µL of the plasmid/cell mix into a cuvette, electroporate at 1.2 kV, 25 uF and 200 ohm or alternative setting (see note... |
46,358 | Preparation of oxalate reagent | 6 | null | https://www.protocols.io/view/preparation-of-oxalate-reagent-brhwm37e | Yingyu Hu, Zoe V Finkel | TITLE: Preparation of oxalate reagent
AUTHORS: Yingyu Hu, Zoe V Finkel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to prepare oxalate reagent, which is used to remove surface adsorbed phosphorus, so that the intracellular phosphorus quotas in microalgae can be measure... | ["[10 M NaOH solution]\nAdd MilliQ water in a 250 mL beaker.\n50 mL", "[10 M NaOH solution]\nWeigh NaOH and slowly pour into the beaker.\n40 g", "[10 M NaOH solution]\nUse squeeze bottle to rinse the weighing boat and transfer rinse water into the same beaker.", "[10 M NaOH solution]\nUse glass rod to gently stir and... |
24,625 | Helicase-like transcription factor (Hltf) gene-deletion promotes oxidative phosphorylation (OXPHOS) in colorectal tumors of AOM/DSS-treated mice | null | dx.doi.org/10.17504/protocols.io.4argsd6 | null | Rebecca Ann Helmer, Gurvinder Kaur, Lisa Ann Smith, Beverly S. Chilton | TITLE: Helicase-like transcription factor (Hltf) gene-deletion promotes oxidative phosphorylation (OXPHOS) in colorectal tumors of AOM/DSS-treated mice
AUTHORS: Rebecca Ann Helmer, Gurvinder Kaur, Lisa Ann Smith, Beverly S. Chilton
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The </span><sp... | [".justify:after {\n\t\t\t\t\t\t\t content: \"\";\n\t\t\t\t\t\t\t display:inline-block;\n\t\t\t\t\t\t\t width: 100%;\n\t\t\t\t\t\t\t }\n\t\t\t\t\t\t\tMaterials and methods\n\t\t\t\t\t\t\t .justify:after {\n\t\t\t\t\t\t\t content: \"\";\n\t\t\t\t\t\t\t display:inline-block;\n\t\t\t\t\t\t\t width: 100... |
50,741 | Western blotting for LRRK2 signalling in macrophages | 4 | dx.doi.org/10.17504/protocols.io.3byl4k67jvo5/v1 | https://www.protocols.io/view/western-blotting-for-lrrk2-signalling-in-macrophag-bvsvn6e6 | sherbst | TITLE: Western blotting for LRRK2 signalling in macrophages
AUTHORS: sherbst
[DESCRIPTION]
This protocol describes the immunoblotting for components of the LRRK2 signalling pathway (LRRK2, LRRK2 pS935 and phospho-Rabs) using Invitrogen NuPage SDS-PAGE reagents and the BioRad Turbo Blot transfer system.
[STEPS]
SEC... | ["[Preparation of protein lysates] Culture cells as usual in a 12-well or 6-well plate.", "[Preparation of protein lysates] Wash cells once in PBS", "[SDS-PAGE] Prepare protein lysates by adding sample loading buffer and reducing agent (eg NuPAGE LDS sample buffer and reducing agent).", "[Transfer] Transfer SDS gel int... |
39,577 | Perfusion | 1 | null | https://www.protocols.io/view/perfusion-bivzke76 | Molly Brennan, Olivier George | TITLE: Perfusion
AUTHORS: Molly Brennan, Olivier George
[STEPS]
?. WHOLE ANIMAL FIXATION VIA TRANSCARDIAL PERFUSIONList of Stuff Needed for Perfusion-4% Formaldehyde-0.9% Hep-saline-Bottles & pump-Surgical tool (scissors, clamps, bone rongeurs, spatula)-Vials-timer
?. Preparation-Switch waste flow to deposit into chem... | ["WHOLE ANIMAL FIXATION VIA TRANSCARDIAL PERFUSIONList of Stuff Needed for Perfusion-4% Formaldehyde-0.9% Hep-saline-Bottles & pump-Surgical tool (scissors, clamps, bone rongeurs, spatula)-Vials-timer", "Preparation-Switch waste flow to deposit into chemical waste bucket-Prepare perfusion pumps with 0.9% saline and 4% ... |
24,517 | Chromatographic separation of strontium isotopes in human dental enamel for Thermal Ionisation Mass Spectrometry (TIMS) analysis | null | dx.doi.org/10.17504/protocols.io.37dgri6 | null | Esther Plomp, Richard Smeets, Gareth Davies | TITLE: Chromatographic separation of strontium isotopes in human dental enamel for Thermal Ionisation Mass Spectrometry (TIMS) analysis
AUTHORS: Esther Plomp, Richard Smeets, Gareth Davies
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for sample collection, dissolution and chromatographic... | ["[Tooth collection]\nCollect the teeth in cleaned 50 mL plastic centrifuge tubes (rinsed >3 times with Milli-Q (purified H2O) and 1 time with ethanol (Purity Grade: absolut, CHROMASOLV®, for high-performance liquid Chromatography)). Dry the teeth on a hotplate at (mind that plastic melts at higher temperatures).\n50 ... |
104,916 | URMC TriState SenNet Mouse Lung Digestion | 1 | dx.doi.org/10.17504/protocols.io.5qpvok9z9l4o/v2 | https://www.protocols.io/view/urmc-tristate-sennet-mouse-lung-digestion-dipu4dnw | Gagandeep Kaur, Irfan Rahman | TITLE: URMC TriState SenNet Mouse Lung Digestion
AUTHORS: Gagandeep Kaur, Irfan Rahman
[DESCRIPTION]
The objective of this document is to share the material and kits used and steps involved in digesting the mouse lungs to perform scRNA analyses. This study was performed for the TriState SenNet TMC Bioanalyses Core at ... | ["[Lung Tissue Dissociation] Immediately transfer the tubes to MACS Tissue Dissociator and run user-defined program named m_lung_01_02 for mouse lungs.", "[Lung Tissue Dissociation] Mince tissue finely, place into 50ml GentleMACS C-tube with liberase enzymatic cocktail .", "[Lung Tissue Dissociation] Thereafter, place ... |
102,180 | Protocols for Recinto et al. "A rewiring of the earliest immune events leading to T-cell mediated disease following intestinal microbial infection in a PINK1 KO mouse model of Parkinson’s disease" | 0 | dx.doi.org/10.17504/protocols.io.kxygxy77ol8j/v1 | https://www.protocols.io/view/protocols-for-recinto-et-al-34-a-rewiring-of-the-e-df2c3qaw | Sherilyn Junelle Recinto, adam.macdonald, Moein Yaqubi, Alexandra Kazanova | TITLE: Protocols for Recinto et al. "A rewiring of the earliest immune events leading to T-cell mediated disease following intestinal microbial infection in a PINK1 KO mouse model of Parkinson’s disease"
AUTHORS: Sherilyn Junelle Recinto, adam.macdonald, Moein Yaqubi, Alexandra Kazanova
[DESCRIPTION]
Our grou... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ns6dehe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The protocol describes guidelines and steps for taking repeated stabilometry measurements. The parameters calculated from repeated measurements can be user for reliability analysis of certain center of pressure parameters used to describe postural control and balancing capabi... | [] |
99,663 | Bacterial eDNA Collection, Purification, and amplification with fresh water | 0 | null | https://www.protocols.io/view/bacterial-edna-collection-purification-and-amplifi-ddjp24mn | Madeline Weeks, Brian Alfaro | TITLE: Bacterial eDNA Collection, Purification, and amplification with fresh water
AUTHORS: Madeline Weeks, Brian Alfaro
[DESCRIPTION]
A protocol to extract and purify bacterial eDNA from fresh-water lakes was determined using lysis by alkali and ethanol precipitation. This was confirmed through the use of 16S forwar... | ["[Solutions for Alkaline Lysis Protocol] [Note, we can make a 1L solution of the buffer minus lysozyme. Then, when we’re ready to extract a batch, we aliquot smaller volumes and then add the lysozyme. E.g. for 50 ml of buffer solution, we can add 200 mg of lysozyme.]\n\nTo make 1L of lysis buffer without lysozyme: \n2... |
40,348 | Dot Blots Analysis in the Separation of Anti-HIV Antibodies. | 4 | dx.doi.org/10.17504/protocols.io.bjm4kk8w | https://www.protocols.io/view/dot-blots-analysis-in-the-separation-of-anti-hiv-a-bjm4kk8w | Angel Justiz-Vaillant | TITLE: Dot Blots Analysis in the Separation of Anti-HIV Antibodies.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Dot blot frequently is underutilized or is not frequently used because it cannot assess the molecular weight of macromolecules, but it is simple to perf... | ["Two (2) µl of 1:2 dilutions of chicken IgY or 2 µl of serum from rats and cats is dotted onto nitrocellulose paper. This animal specimens tested positive for the presence of anti-HIV antibodies by ELISA, after being immunized with HIV proteins.", "Place the nitrocellulose membrane in a BioDot SF apparatus (Bio-Rad La... |
61,872 | RUN 001 | 1 | dx.doi.org/10.17504/protocols.io.bp2l6137kvqe/v1 | https://www.protocols.io/view/run-001-b8nqrvdw | maria | TITLE: RUN 001
AUTHORS: maria
[DESCRIPTION]
test
[STEPS]
1. test 001
Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Quis autem vel eum iure reprehenderit qui in ea voluptate velit esse quam nihil molestiae consequatur, vel illum qui dolorem eum fugiat quo voluptas nulla pariatur? Etiam sapien elit, con... | ["test 001\n\nLorem ipsum dolor sit amet, consectetuer adipiscing elit. Quis autem vel eum iure reprehenderit qui in ea voluptate velit esse quam nihil molestiae consequatur, vel illum qui dolorem eum fugiat quo voluptas nulla pariatur? Etiam sapien elit, consequat eget, tristique non, venenatis quis, ante. Pellentesqu... |
null | null | null | dx.doi.org/10.17504/protocols.io.gribv4e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>SpinSmart Plasmid Miniprep kits</strong> are designed to rapidly purify plasmid DNA from bacterial cultures.</p>
<p> </p>
<p>The protocol below is appropriate for both <a href="https://www.denvillescientific.com/products/spinsmart%E2%84%A2-plasmid-miniprep-dna-purific... | [] |
63,883 | POLE TEST PROTOCOL | 4 | dx.doi.org/10.17504/protocols.io.n92ldzjkxv5b/v1 | https://www.protocols.io/view/pole-test-protocol-camjsc4n | Michael Lee | TITLE: POLE TEST PROTOCOL
AUTHORS: Michael Lee
[DESCRIPTION]
This protocol details pole test.
[GUIDELINES]
Detailed records should be kept on every experiment, noting date, timing, subject test order, procedural details followed and any relevant observations pertaining to the assay (e.g. specific behavior or procedur... | ["[Test] Place animal on horizontal pole facing the top.", "[Test] Place pole upright with mouse facing upward.", "[Test] Record the time to turn (orient facing down), and time to reach the bottom of the pole.", "[Test] Maximum duration 2 min.", "[Test] All animals tested for 3 trials with a minimum of 20 min between t... |
34,790 | Informed consent | null | dx.doi.org/10.17504/protocols.io.bd8ei9te | https://www.protocols.io/view/informed-consent-bd8ei9te | Juan Jesús Torres-Gordillo, Fernando Guzmán-Simón, Beatriz García-Ortiz | TITLE: Informed consent
AUTHORS: Juan Jesús Torres-Gordillo, Fernando Guzmán-Simón, Beatriz García-Ortiz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">INFORMED CONSENT AND COMMITMENT to participate in a research</div></div>
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ksrcwd6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Uses a custom Centrifuge pipeline to assign taxonomy to gene calls. </p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.imrcc56 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>We simulate paired-end reads for testing the accuracy and sensitivity of our computer program for detection of transportable element (TE) insertions (also called Mobile Element Insertions, MEIs). we named the software "Specific Insertions Detector (SID)".</p>
[BEFORE_START]
... | [] |
78,460 | Calculating multiplicity of infection (MOI) | 4 | dx.doi.org/10.17504/protocols.io.yxmvm2b2ng3p/v1 | https://www.protocols.io/view/calculating-multiplicity-of-infection-moi-cqu4vwyw | Januka Athukoralage, Adair Borges | TITLE: Calculating multiplicity of infection (MOI)
AUTHORS: Januka Athukoralage, Adair Borges
[DESCRIPTION]
This is a simple protocol for the calculations that we routinely do to determine phage multiplicity of infection (MOI) in our experiments.
It's really important to know what MOI you are using. Ideally, you wo... | ["[Calculating colony-forming units per mL (CFU/mL)] Grow your bacteria to your target OD600 using the same culture conditions that you will use in your experiments.", "[Calculating colony-forming units per mL (CFU/mL)] Create a 10-fold dilution series of your bacterial culture. Use glass beads to seed an LB agar plate... |
98,631 | Parkinson’s Progression Markers Initiative Online Study (PPMI Online) | 0 | dx.doi.org/10.17504/protocols.io.q26g718y9gwz/v1 | https://www.protocols.io/view/parkinson-s-progression-markers-initiative-online-dcjf2ujn | Caroline M Tanner, Ken Marek | TITLE: Parkinson’s Progression Markers Initiative Online Study (PPMI Online)
AUTHORS: Caroline M Tanner, Ken Marek
[DESCRIPTION]
This protocol details the Parkinson’s Progression Markers Initiative Online Study (PPMI Online).
[STEPS]
SECTION: PURPOSE OF STUDY
1. The Parkinson Progression Marker Initiative (PPMI) stud... | ["[PURPOSE OF STUDY] The Parkinson Progression Marker Initiative (PPMI) study is a longitudinal, observational, multi-center natural history study to assess progression of clinical features, digital outcomes, imaging, biologic, and genetic markers of Parkinson’s disease (PD) progression in study participants with manif... |
41,636 | SensingSelf S4 Multiplex Covid-19 /MERS-CoV/ Influenza A/B Rapid Antigens Test Kit (Saliva/Sputum/Stool) | 4 | dx.doi.org/10.17504/protocols.io.bkwckxaw | https://www.protocols.io/view/sensingself-s4-multiplex-covid-19-mers-cov-influen-bkwckxaw | Shripal Gandhi, Santo Purnama, Keyur Patel, Praveen Sukumara, Dr Rinu R Ravi | TITLE: SensingSelf S4 Multiplex Covid-19 /MERS-CoV/ Influenza A/B Rapid Antigens Test Kit (Saliva/Sputum/Stool)
AUTHORS: Shripal Gandhi, Santo Purnama, Keyur Patel, Praveen Sukumara, Dr Rinu R Ravi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div... | ["[SALIVA SAMPLE COLLECTION]\nSaliva should be collected with the assistance of a healthcare worker or technician.", "[SALIVA SAMPLE COLLECTION]\nBefore collection, clean hands using alcohol-based sanitizer or soap and water (no fragrances) and wear appropriate PPE (at minimum, gloves and a mask).", "[SALIVA SAMPLE COL... |
84,093 | In vitro phosphatase assay | 4 | dx.doi.org/10.17504/protocols.io.ewov1qyepgr2/v1 | https://www.protocols.io/view/in-vitro-phosphatase-assay-cwc5xay6 | Elias Adriaenssens | TITLE: In vitro phosphatase assay
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol describes in vitro phosphatase assay.
[STEPS]
SECTION: In vitro phosphatase assay
1. Seed HAP1 wild-type or FIP200 knockout cells in 6 well plates and grow until confluency.
SECTION: In vitro phosphatase assay
2. Collect cells b... | ["[In vitro phosphatase assay] Seed HAP1 wild-type or FIP200 knockout cells in 6 well plates and grow until confluency.", "[In vitro phosphatase assay] Collect cells by trypsinization and pellet by centrifugation at 300 x g, 5 min, 4 °C.", "[In vitro phosphatase assay] After a PBS wash to remove the remaining cell medi... |
84,532 | Preparation of Artificial Urine | 1 | dx.doi.org/10.17504/protocols.io.kxygx3exzg8j/v1 | https://www.protocols.click/view/preparation-of-artificial-urine-cwsuxeew | alow | TITLE: Preparation of Artificial Urine
AUTHORS: alow
[DESCRIPTION]
A method for producing artificial urine as a media for bacterial experiments
[STEPS]
1. Take twelve 50 mL tubes and label with sufficient information. There are 12 reagents (Table 1 in Materials) which require plastic tube storage so you can label the... | ["Take twelve 50 mL tubes and label with sufficient information. There are 12 reagents (Table 1 in Materials) which require plastic tube storage so you can label these 1 to 12 but missing out number 4 for Urea. You will need two tubes for reagent 9, Potassium oxalate.", "Weight out the chemical powders to the labelled ... |
35,762 | Plaque Assay | null | dx.doi.org/10.17504/protocols.io.be6sjhee | https://www.protocols.io/view/plaque-assay-be6sjhee | Alice Lee | TITLE: Plaque Assay
AUTHORS: Alice Lee
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Bacteriophages (phage) are viruses that infect bacteria and can be found anywhere that bacteria is found. Performing plaque assays is a technique to purify a population of viruses and can also be used to determine... | ["[Inoculating a liquid bacterial culture overnight]\nThe day before performing the plaque assay experiment, grow the bacteria associated with the phage of interest.", "[Inoculating a liquid bacterial culture overnight]\nTake out an already streaked bacteria plate from the room.\n4 °C", "[Inoculating a liquid bacteri... |
50,422 | VPS13D DNA plasmid generation | 1 | dx.doi.org/10.17504/protocols.io.bvgwn3xe | https://www.protocols.io/view/vps13d-dna-plasmid-generation-bvgwn3xe | Andrés Guillén-Samander, Marianna Leonzino, Pietro De Camilli | TITLE: VPS13D DNA plasmid generation
AUTHORS: Andrés Guillén-Samander, Marianna Leonzino, Pietro De Camilli
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span> This protocol describes the basic molecular cloning technique utilized for the generation of VPS13D constructs in </span><a href="... | ["[VPS13D DNA plasmid generation]\nLinearize the backbone with restriction enzymes or by PCR amplification.", "[VPS13D DNA plasmid generation]\nAmplify the insert by PCR with primers including 15nt of overlapping sequence with the target backbone.\nSuggestion: Takara has an online tool to help with primer design at: ht... |
42,972 | Preparation of electrocompetent Escherichia coli | 4 | null | https://www.protocols.io/view/preparation-of-electrocompetent-escherichia-coli-bm74k9qw | lewis.bingle | TITLE: Preparation of electrocompetent Escherichia coli
AUTHORS: lewis.bingle
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Preparation of competent </span><span style = "font-style:italic;">Escherichia coli</span><span> cells for electroporation.</span></div></div>
[STEPS]
?. Inoculate st... | ["Inoculate starter culture of the desired strain from single colony (e.g. LB broth in universal bottle). Incubate (37°C with shaking at 200-220 rpm) .\n5 mL", "Dilute overnight culture 1 / 100 into fresh LB broth (supplemented with appropriate antibiotic if required) and incubate (37°C with shaking at 200-220 rpm) to... |
97,787 | The design and manufacture of massively scalable inertial focusing prototype microfluidic devices | 0 | dx.doi.org/10.17504/protocols.io.n2bvjnrmpgk5/v1 | https://www.protocols.io/view/the-design-and-manufacture-of-massively-scalable-i-dbq32myn | Thomas Carvell | TITLE: The design and manufacture of massively scalable inertial focusing prototype microfluidic devices
AUTHORS: Thomas Carvell
[DESCRIPTION]
Microfluidics is a rapidly expanding field and microfluidic devices have been used in a variety of biomedical applications such as cell sorting, disease diagnostics and various... | ["[Design of exemplar parts] Open computer-aided design software and ensure 3D-modelling format is\nselected and units are set to millimetres.", "[Design of exemplar parts] Select the rectangle tool and enter x-y coordinates for origin (0, 0). The width is 35 and the height is 70. This generates the ‘device rectangle’.... |
68,257 | Ligation (Instructor Protocol) | 4 | null | https://www.protocols.io/view/ligation-instructor-protocol-cev9te96 | Brian Teague | TITLE: Ligation (Instructor Protocol)
AUTHORS: Brian Teague
[DESCRIPTION]
This is the instructor protocol for the student Ligation protocol.
The abstract for the student protocol explains the basics. I pre-digest the L2-01 backbone for my students, but I generally do not gel-purify it. I find that the ligation is... | ["[Grow & miniprep L2-01] At least 48 hours before the lab, strike out the L2-01 E. coli strain from a frozen stock on an LB+Kan plate.", "[Grow & miniprep L2-01] At least 24 hours before the lab: pick a colony of L2-01 into 5 mL LB+Kan liquid media. Grow in a round-bottomed test-tube overnight on a shaker,", "... |
73,380 | pH Testing of Coffee Samples | 1 | null | https://www.protocols.io/view/ph-testing-of-coffee-samples-cjwcupaw | Shannon.logan | TITLE: pH Testing of Coffee Samples
AUTHORS: Shannon.logan
[DESCRIPTION]
Measure the pH levels of coffee samples across a range of roasts.
[STEPS]
2. Boil kettle with 250ml of deionised water.
1. Grind coffee to desired consistency and weigh 20g to put in cafetiere.
3. Pour boiling water into beaker and allow to co... | ["Boil kettle with 250ml of deionised water.", "Grind coffee to desired consistency and weigh 20g to put in cafetiere.", "Pour boiling water into beaker and allow to cool to 93°C, using a digital thermometer to ensure accuracy of temperature.", "Once the water has cooled to the desired temperature, pour into the cafeti... |
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