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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46,391 | Stanford and Purigen Biosystems Microfluidics Team protocol XPRIZE_Hudson Alpha | 4 | dx.doi.org/10.17504/protocols.io.brixm4fn | https://www.protocols.io/view/stanford-and-purigen-biosystems-microfluidics-team-brixm4fn | jnesvet | TITLE: Stanford and Purigen Biosystems Microfluidics Team protocol XPRIZE_Hudson Alpha
AUTHORS: jnesvet
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The Stanford University and Purigen Biosystems team's SARS-CoV-2 assay leverages on-chip microfluidics to eliminate laborious and time consuming st... | ["[Preparation for Purigen Ionic Instrument ]\nPrepare your laboratory for the receipt of the Purigen Ionic Instrument.\nNOTE: When handling nucleic acids and amplicon, it is critical to reduce contamination. Therefore, 3 separate preparation areas are required for this protocol: 1) a \"patient sample preparation area\... |
95,780 | αS PFF Assembly Protocol | 0 | dx.doi.org/10.17504/protocols.io.kxygx3j3dg8j/v1 | https://www.protocols.io/view/s-pff-assembly-protocol-c9scz6aw | Scott Vermilyea | TITLE: αS PFF Assembly Protocol
AUTHORS: Scott Vermilyea
[DESCRIPTION]
This protocol details the αS PFF assembly.
[STEPS]
SECTION: Aggregation
1. Remove monomer stock from -80 °C and thaw on ice.
SECTION: Aggregation
2. Dilute stock to desired concentration (typically 5 3189) to a final volume of 300 µL in autoclaved... | ["[Aggregation] Remove monomer stock from -80 °C and thaw on ice.", "[Aggregation] Dilute stock to desired concentration (typically 5 3189) to a final volume of 300 µL in autoclaved2 mLcentrifuge tubes.", "[Aggregation] Set thermocycler for continuous shaking (1000 rpm, 37 °C ).", "[Aggregation] Install 2 mL plate.", "... |
95,737 | Cloning protocols for Kroon et al., 2024 | 0 | dx.doi.org/10.17504/protocols.io.dm6gp37j8vzp/v1 | https://www.protocols.io/view/cloning-protocols-for-kroon-et-al-2024-c9qzz5x6 | cristina.kroon | TITLE: Cloning protocols for Kroon et al., 2024
AUTHORS: cristina.kroon
[DESCRIPTION]
Here you find the detailed protocols that describe the cloning procedures for the making of plasmids in the publication Kroon et al., 2024. All generated plasmids are in pCAX backbone (CAG promoter) and have a C-terminal tag (Flag ta... | ["[General cloning protocol] PCR was performed using KOD Hot Start DNA polymerase kit (#71086-3, Merck Millipore)\n denaturation at 95°C for 2.5 minutes\n33 cycles at 95°C for 30 seconds\nannealing at 63°C for 20 seconds\nelongation at 70°C for 50 seconds\nA final elongation for 3 minutes at 70°C\n\nNB! To amplify GC-r... |
49,796 | Comprehensive analysis of mitochondrial functions and inflammatory state of synovial membrane samples from patients suffering from arthritis | 4 | dx.doi.org/10.17504/protocols.io.buvcnw2w | https://www.protocols.io/view/comprehensive-analysis-of-mitochondrial-functions-buvcnw2w | Péter Jávor, Attila Mácsai, Edina Butt [Department of Traumatology, Bálint Baráth, Dávid Kurszán Jász, Tamara Horváth, Bence Baráth, Ákos Csonka, László Török, Endre Varga, Petra Hartmann | TITLE: Comprehensive analysis of mitochondrial functions and inflammatory state of synovial membrane samples from patients suffering from arthritis
AUTHORS: Péter Jávor, Attila Mácsai, Edina Butt [Department of Traumatology, Bálint Baráth, Dávid Kurszán Jász, Tamara Horváth, Bence Baráth, Ákos Csonka, László Török, End... | ["[Sampling]\nSynovial fluid and tissue samples from the knee joint synovium are taken with the permission and signed consent of the patients. Synovial fluid is aspirated prior to incision, with an 18 G needle. Synovium tissue samples of 1x1 cm in size are obtained from the suprapatellar pouch, sparing the Hoffa’s fat ... |
65,878 | DNA extraction (BOMB) | 4 | dx.doi.org/10.17504/protocols.io.261gen7ryg47/v1 | https://www.protocols.io/view/dna-extraction-bomb-ccjwsupe | Tsu-Chun Hung, Yin-Tse Huang | TITLE: DNA extraction (BOMB)
AUTHORS: Tsu-Chun Hung, Yin-Tse Huang
[DESCRIPTION]
DNA extraction (BOMB)
[STEPS]
SECTION: Sample Collection
1. Add 200 µL of 1mm beads to 1.5ml enppendorf tube
SECTION: Sample Collection
2. Add200 µL of 0.5mm beads to 1.5ml enppendorf tube
SECTION: Sample Collection
3. Add 225 µL o... | ["[Sample Collection] Add 200 µL of 1mm beads to 1.5ml enppendorf tube", "[Sample Collection] Add200 µL of 0.5mm beads to 1.5ml enppendorf tube", "[Sample Collection] Add 225 µL of TE buffer to 2ml enppendorf tube", "[Sample Collection] Add 375 µL of lysis buffer to 2ml enppendorf tube", "[Sample Collection] Collect 10... |
85,899 | Co-immunoprecipitation | 4 | dx.doi.org/10.17504/protocols.io.14egn32zzl5d/v1 | https://www.protocols.io/view/co-immunoprecipitation-cx5jxq4n | wusj, schekman | TITLE: Co-immunoprecipitation
AUTHORS: wusj, schekman
[DESCRIPTION]
This protocol describes a common procedure to perform co-immunoprecipitation
[STEPS]
SECTION: Co-immunoprecipitation
1. Media fractions were collected and centrifuged at 1000×g for 10 min
SECTION: Co-immunoprecipitation
2. The supernatant fractions ... | ["[Co-immunoprecipitation] Media fractions were collected and centrifuged at 1000×g for 10 min", "[Co-immunoprecipitation] The supernatant fractions were collected and concentrated (20-fold) using a 10 kDa Amicon filter.", "[Co-immunoprecipitation] Concentrated media fractions (1 ml) were incubated with 20 μl of anti-F... |
29,685 | Methangen H-cell set up | null | dx.doi.org/10.17504/protocols.io.88vhzw6 | null | Annette Rowe | TITLE: Methangen H-cell set up
AUTHORS: Annette Rowe
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines set up and use of H-cells in a three electrode set up. This protocol was developed for the work performed in Rowe et al. 2019. It was adapted from technques learned in P. Girg... | ["Assembly of Reactors: Each side of the h-cell reactor resembles a ~100 mL corning glass bottle. On one side of each component is an open circle flatten port for supporting a proton exchange membrane between the two sides. One side has two sample-ports; the side I generally use for the working electrode. You will also... |
null | null | null | dx.doi.org/10.17504/protocols.io.egnbbve | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol describes how to attach biotin to Bovine Serum Mucin (BSM). The procedure uses a botin-NHS molecule to attach biotin to amines in the mucin proteins.
[STEPS]
?.
?.
?.
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33,920 | Microplate Assay for Quantification of Soluble Protein in Ground Coral Samples | null | dx.doi.org/10.17504/protocols.io.bdc8i2zw | null | Rowan Mclachlan, James Price, Kerri Dobson, Noah Weisleder, Andrea Grottoli | TITLE: Microplate Assay for Quantification of Soluble Protein in Ground Coral Samples
AUTHORS: Rowan Mclachlan, James Price, Kerri Dobson, Noah Weisleder, Andrea Grottoli
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">This method for extracting prote... | ["[Preparation of ground coral samples]\nWeigh and partition ground coral paste. Place a pre-baked aluminum weighing pan on the balance and tare (i.e. zero). Remove the pan, and using a rubber spatula, transfer all the ground coral material from the mortar into the pan. Place the pan on the balance and record the total... |
48,508 | MarineSediment-BlueC-eDNA | 4 | dx.doi.org/10.17504/protocols.io.btk4nkyw | https://www.protocols.io/view/marinesediment-bluec-edna-btk4nkyw | Marc Angles d'Auriac, Kasper Hancke, Hege Gundersen, Helene Frigstad, Gunhild Borgersen | TITLE: MarineSediment-BlueC-eDNA
AUTHORS: Marc Angles d'Auriac, Kasper Hancke, Hege Gundersen, Helene Frigstad, Gunhild Borgersen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol was established for the Nordic Blue Carbon Project (2017–2020) for tracking the presence of kelp DNA in mari... | ["[Core sampling]\nEquipment required on vessel for core sampling", "[Core sampling]\nEquipment assembly (Gravity corer)Manual for (kc-denmark.dk): Add the necessary number of lead weights at the main rack. Mount the supporting frame and secure it by fastening the bolt. Mount the unit with the top lid. Open the fasteni... |
107,593 | Protocol: Evaluation of the quality of reporting and risk of bias of predictive models widely used in UK perioperative practice | 0 | dx.doi.org/10.17504/protocols.io.ewov19bwylr2/v1 | https://www.protocols.io/view/protocol-evaluation-of-the-quality-of-reporting-an-dmbh42j6 | Joseph Alderman | TITLE: Protocol: Evaluation of the quality of reporting and risk of bias of predictive models widely used in UK perioperative practice
AUTHORS: Joseph Alderman
[DESCRIPTION]
The aim of this targeted literature review is to critically appraise the reporting and methodological robustness of studies describing the develo... | [] |
65,140 | RNA extraction and quantitative PCR to assay inflammatory gene expression | 1 | dx.doi.org/10.17504/protocols.io.5qpvob15bl4o/v1 | https://www.protocols.io/view/rna-extraction-and-quantitative-pcr-to-assay-infla-cbuusnww | OLIVIA HARDING, Erika L.F. Holzbaur | TITLE: RNA extraction and quantitative PCR to assay inflammatory gene expression
AUTHORS: OLIVIA HARDING, Erika L.F. Holzbaur
[DESCRIPTION]
Real-time quantitative PCR (RT-qPCR) is a sensitive assay to determine the production of selected mRNA transcripts in various conditions. We required such an assay to demonstrate ... | ["[Initial RNA extraction] Aspirate media from each dish.", "[Initial RNA extraction] Add 300 µL cold TRIzol per million cells directly onto the cells and pipet up and down to homogenize.", "[Initial RNA extraction] Transfer to 1.5 mL tube.", "[Initial RNA extraction] Incubate 5 min, Room temperature.", "[Initial RNA e... |
92,960 | ECIS Data Analysis for Stimulation of Human Pulmonary Microvascular Endothelial Cells (HPMECs) with Human Serum | 4 | null | https://www.protocols.io/view/ecis-data-analysis-for-stimulation-of-human-pulmon-c6z8zf9w | Michael Bokoch | TITLE: ECIS Data Analysis for Stimulation of Human Pulmonary Microvascular Endothelial Cells (HPMECs) with Human Serum
AUTHORS: Michael Bokoch
[DESCRIPTION]
Sera from patients in our UCSF Liver Transplant Biobank are used to stimulate human pulmonary microvascular endothelial cells (HPMECs) grown to confluency on ECIS... | ["[ECIS Data Analysis for HPMEC stimulation by Liver Biobank Sera] Determine Difference in Area-under-the-Curve (Normalized Resistance at 4000 Hz)\nTo be calculated after recording full ECIS curve after stimulation with human serum from liver transplant (LT) patients.\n\nGoal: To calculate the difference in AUC between... |
39,055 | Getting started with VirSorter2 | 5 | dx.doi.org/10.17504/protocols.io.bidpka5n | https://www.protocols.io/view/getting-started-with-virsorter2-bidpka5n | Jiarong Guo | TITLE: Getting started with VirSorter2
AUTHORS: Jiarong Guo
[STEPS]
?. [Installation]
Skip this step if you already have VirSorter2 installed. You can find out by type in the following command in terminal:virsorter -hIf you see message like below, then you have VirSorter2 installed already.Usage: virsorter [OPTIONS] ... | ["[Installation]\nSkip this step if you already have VirSorter2 installed. You can find out by type in the following command in terminal:virsorter -hIf you see message like below, then you have VirSorter2 installed already.Usage: virsorter [OPTIONS] COMMAND [ARGS]... virsorter - workflow for identifying viral sequence... |
null | null | null | dx.doi.org/10.17504/protocols.io.dbn2md | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<table>
<tbody>
<tr>
<td>Tryptone</td>
<td>5 g</td>
</tr>
<tr>
<td>Yeast Extract</td>
<td>1 g</td>
</tr>
<tr>
<td>Seawater</td>
<td>1 L</td>
</tr>
<tr>
<td>Dry Ice</td>
<td>10-12 g</td>
</tr>
</tbody>
</table>
For bottom agar plates, add 15 g agar.<br />For top agar, add 4 g agar... | [] |
52,497 | Mary Berry CBD Gummies Reviews - Does (Mary Berry CBD Gummies UK) Is Really Works Or Scam? | 1 | dx.doi.org/10.17504/protocols.io.bxhrpj56 | https://www.protocols.io/view/mary-berry-cbd-gummies-reviews-does-mary-berry-cbd-bxhrpj56 | health | TITLE: Mary Berry CBD Gummies Reviews - Does (Mary Berry CBD Gummies UK) Is Really Works Or Scam?
AUTHORS: health
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><a href="http://www.healthpills24x7.com/order-bioketo-advantage" style = "text-decoration:underline;color:blue;cursor:pointer;"><span s... | ["(OFFICIAL DEAL) Click Here to Order *Mary Berry CBD Gummies UK* From From Its Official Online Store We all have a beautiful and healthy life, but it is up to us how we lead it. There are many people who are struggling with different chronic conditions, including anxiety, stress, depression and chronic joint pain.... |
60,291 | 2022 GenomeTrakr Proficiency Testing exercise (PulseNet Harmonized) | 1 | dx.doi.org/10.17504/protocols.io.e6nvw5m9dvmk/v5 | https://www.protocols.io/view/2022-genometrakr-proficiency-testing-exercise-puls-b65brg2n | Maria Balkey, Ruth Timme, Julie Haendiges | TITLE: 2022 GenomeTrakr Proficiency Testing exercise (PulseNet Harmonized)
AUTHORS: Maria Balkey, Ruth Timme, Julie Haendiges
[DESCRIPTION]
This SOP outlines guidelines on how to process the isolates for the 2022 GenomeTrakr (GT) Proficiency Testing exercise.
This SOP is applicable to all GenomeTrakr labs partici... | ["[Culture Preparation] Salmonella and Escherichia/Shigella Lyophilized cultures:\n\nDay 1\n\nDocument the isolate number(s) and the lyophilized date(s) for your records. Wipe the aluminum cover and outside of the vial with isopropyl alcohol. Using sturdy forceps, aseptically remove the aluminum cover and rubber stoppe... |
24,077 | Tache_Mulugeta_OT2OD024899_Colon tissue electrical stimulation and colonic motility measurements | 1 | dx.doi.org/10.17504/protocols.io.3rmgm46 | https://www.protocols.io/view/tache-mulugeta-ot2od024899-colon-tissue-electrical-3rmgm46 | Muriel Larauche, Yushan Wang, Po-Min Wang, James Dunn, Wentai Liu, Mulugeta Million | TITLE: Tache_Mulugeta_OT2OD024899_Colon tissue electrical stimulation and colonic motility measurements
AUTHORS: Muriel Larauche, Yushan Wang, Po-Min Wang, James Dunn, Wentai Liu, Mulugeta Million
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes a process for the measurement o... | ["[Animals]\nSix-to-seven months old (25-36 kg) male Yucatan minipigs (S&S farms, Ramona, CA), castrated at 7 days of age, were group housed in pens (either bedding or grate floor depending on housing availabilities - 2 pigs/pen, 42ft2) in an environmentally controlled room (lights on/off 6AM/6PM, 61-81ºF) under SPF co... |
49,464 | Preparation of Nuclei Suspension from Human Musculoskeletal Tissues | 4 | dx.doi.org/10.17504/protocols.io.5qpvoy8mxg4o/v1 | https://www.protocols.io/view/preparation-of-nuclei-suspension-from-human-muscul-buiynufw | Ching-Yan Chloé Yeung, Anja Jokipii-Utzon, Anders Karlsen | TITLE: Preparation of Nuclei Suspension from Human Musculoskeletal Tissues
AUTHORS: Ching-Yan Chloé Yeung, Anja Jokipii-Utzon, Anders Karlsen
[DESCRIPTION]
An adapted version of the 'Frankenstein' protocol (Luciano G Martelotto 2020. ‘Frankenstein’ protocol for nuclei isolation from fresh and frozen tissue for snRNAse... | ["[Tissue Preparation] Collect fresh tissue in a 50-ml tube containing 25 mL ice-cold 1X phosphate-buffered saline containing 50 U/ml penicillin and 50 µg/ml streptomycin and keep on ice for transport.", "[Tissue Preparation] Using a scalpel, dissect the tissue as desired on ice.", "[Tissue Preparation] Cut up tissue i... |
25,064 | Electroporation of Heterosigma akashiwo | null | dx.doi.org/10.17504/protocols.io.4qggvtw | null | Deepak Nanjappa and Kathryn Coyne | TITLE: Electroporation of Heterosigma akashiwo
AUTHORS: Deepak Nanjappa and Kathryn Coyne
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol was developed for transformation of </span><span style = "font-style:italic;">Heterosigma akashiwo </span><span>by electroporation. This speci... | ["Harvest exponential growth Heterosigma akashiwo culture (1-2 x 106 cells mL-1) by centrifugation at 1500 rpm for 90 s in a 50 mL sterile screw-cap tube. Remove the supernatant by pipetting.", "Resuspend the cell pellet in a small volume of MAX Efficiency® Transformation Reagent for Algae (Invitrogen, Thermo Fischer S... |
101,725 | Immunossuppression in Neuromyelitis Optica Spectrum Disorder: A Trial Sequential Analysis and Updated Meta-Analysis | 0 | dx.doi.org/10.17504/protocols.io.j8nlk8926l5r/v1 | https://www.protocols.io/view/immunossuppression-in-neuromyelitis-optica-spectru-dfj53kq6 | Artur Menegaz de Almeida, Maria Eduarda Cavalcanti, Francisco Cezar Aquino de Moraes, Fernando Westphal Filho, Ítalo Barros Andrade, Paulo Robeto Moss Lopes, Clara Rocha Dantas, Mariana Rachas Reis, Lilianne Fernandes, Francinny Alves Kelly | TITLE: Immunossuppression in Neuromyelitis Optica Spectrum Disorder: A Trial Sequential Analysis and Updated Meta-Analysis
AUTHORS: Artur Menegaz de Almeida, Maria Eduarda Cavalcanti, Francisco Cezar Aquino de Moraes, Fernando Westphal Filho, Ítalo Barros Andrade, Paulo Robeto Moss Lopes, Clara Rocha Dantas, Mariana Ra... | ["[Abstract] Review title:\nImmunossuppression in Neuromyelitis Optica Spectrum Disorder: A Trial Sequential Analysis and Updated Meta-Analysis", "[Abstract] PICO: \nPopulation - patients diagnosed with Neuromyelitis Optica Spectrum Disorder;\nI - Rituximab;\nC - No control or Azathioprine and/or Mycophenolato mofetil;... |
29,941 | Protocol for predicting specialist herbivore distribution from host distribution data | null | dx.doi.org/10.17504/protocols.io.9gvh3w6 | https://www.protocols.io/view/protocol-for-predicting-specialist-herbivore-distr-9gvh3w6 | Joshua Fuller | TITLE: Protocol for predicting specialist herbivore distribution from host distribution data
AUTHORS: Joshua Fuller
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A necessary, but difficult, part of ecology and conservations is to try to create order and meaning from chaos. An example of such a tas... | ["[Setting UP Software]\nFor this exercise, specific software will need to downloaded. The first and most important software available is the statistical package called MaxEnt. You can find MaxEnt in the SDM Protocol folder in a Folder titled MaxEnt. This program should be ready to use and require no installation steps... |
null | null | null | dx.doi.org/10.17504/protocols.io.mqqc5vw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.jwzcpf6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Background: </strong>DNA metabarcoding provides great potential for species identification in complex samples such as food supplements and traditional medicines. Such a method would aid CITES (the Convention on International Trade in Endangered Species of Wild Fauna a... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.dbe2jd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Method to create a long-term stable store of organisms. Especially useful if you want to store already transformed versions of organisms to aid in future experiments.
[BEFORE_START]
Have a fresh inoculated liquid culture containing the organism you would like to store.
[STEPS]... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.cinudd | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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38,587 | Protocol of a systematic review with meta-analysis: Acute effects of physical exercise on blood pressure responsiveness to non-cardiopulmonary stress tests | 1 | dx.doi.org/10.17504/protocols.io.bhw3j7gn | https://www.protocols.io/view/protocol-of-a-systematic-review-with-meta-analysis-bhw3j7gn | Igor Mariano, Ana Luiza Amaral, Guilherme Morais Puga | TITLE: Protocol of a systematic review with meta-analysis: Acute effects of physical exercise on blood pressure responsiveness to non-cardiopulmonary stress tests
AUTHORS: Igor Mariano, Ana Luiza Amaral, Guilherme Morais Puga
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Laboratory stress tests ca... | ["[Background]\nBackground Laboratory stress tests can help compose the clinical profile of individuals and predict, among others, the development of future cardiovascular events and depression [1]. These tests work by disturbing the individual's homeostasis in a controlled way to assess the body's responses to i... |
70,215 | Preparation of 0.5L of phosphate buffer (pH=6.0) | 4 | dx.doi.org/10.17504/protocols.io.n2bvj8r7bgk5/v1 | https://www.protocols.io/view/preparation-of-0-5l-of-phosphate-buffer-ph-6-0-cgtftwjn | Alfonso Pérez Escudero, Alid Al-Asmar, gabrielmadirolas | TITLE: Preparation of 0.5L of phosphate buffer (pH=6.0)
AUTHORS: Alfonso Pérez Escudero, Alid Al-Asmar, gabrielmadirolas
[DESCRIPTION]
Original source of the protocol: WormBook Methods http://www.wormbook.org/chapters/www_strainmaintain/strainmaintain.html
This protocol is for making pH=6.0 phosphate buffer, which is... | ["Add 54.2 g of monopotassium phosphate1 (KH2PO4) to a clean 0.5L bottle.\n\n1Also referred to as potassium phosphate monobasic", "Add 17.8 g of dipotassium phosphate2 (K2HPO4) to the bottle.\n\n2Also referred to as potassium phosphate dibasic", "Measure 500 mL of milliQ water in a measuring cylinder, and add it to the... |
null | null | null | dx.doi.org/10.17504/protocols.io.ikhcct6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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64,958 | House Fly (Musca domestica) laboratory rearing protocol - Gerry lab (UC Riverside) | 1 | dx.doi.org/10.17504/protocols.io.6qpvr6wz2vmk/v1 | https://www.protocols.io/view/house-fly-musca-domestica-laboratory-rearing-proto-cbn6smhe | Levi Zahn, Alec Gerry | TITLE: House Fly (Musca domestica) laboratory rearing protocol - Gerry lab (UC Riverside)
AUTHORS: Levi Zahn, Alec Gerry
[DESCRIPTION]
This protocol is designed for large scale laboratory rearing of house flies at very low cost.
[BEFORE_START]
If you are collecting flies from a field site to begin your house fly co... | [] |
79,065 | AMR Detection by dPCR | 1 | dx.doi.org/10.17504/protocols.io.3byl4j8qzlo5/v1 | https://www.protocols.io/view/amr-detection-by-dpcr-crfzv3p6 | Carlos Goller | TITLE: AMR Detection by dPCR
AUTHORS: Carlos Goller
[DESCRIPTION]
Overview
Microbes resistant to antimicrobial agents are a major worldwide health challenge. Rapid detection of antimicrobial resistant pathogens and surveillance efforts are critical. Information about antimicrobial resistance (AMR) genes is available ... | ["[Metagenomic DNA Extraction] Obtain soil and compost samples from different environments. We have access to soil and compost samples from Christopher Hopkins from efforts to learn about the composting process of “swine lagoon” sludge and have dried and “tar-like” samples. Your instructors (Horton and Phillips) also p... |
31,919 | Ann Marie's Sugar Cookies | null | dx.doi.org/10.17504/protocols.io.bbepijdn | null | Hannah Gunderman | TITLE: Ann Marie's Sugar Cookies
AUTHORS: Hannah Gunderman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Check out this recipe from Ann Marie Mesco, our Digitization Projects Manager and Data Curator for KiltHub!</div><div class = "text-block">Photo by Cayla1 on Unsplash. </div></div>
[STEPS]... | ["[Overview]\nThis is a holiday favorite to cut into shapes for Christmas, Easter, Halloween and other special occasions. Adorn them with colored sugar sprinkles, dried fruit bits or tinted frosting. Why not try some pink frosting for Valentine's Day?Makes: about 4 dozen", "[Overview]\nIngredients1/2 cup butter, room t... |
51,881 | Extraction of bacterial DNA using MagMAX™ CORE Nucleic Acid Purification Kit on KingFisher™ Flex Instrument | 1 | dx.doi.org/10.17504/protocols.io.bwwhpfb6 | https://www.protocols.io/view/extraction-of-bacterial-dna-using-magmax-core-nucl-bwwhpfb6 | Leyi Wang, Carol Maddox, Melanie Prarat, Yan Zhang, Lifang Yan, Akhilesh Ramachandran, Sai Sankara Narayanan, Girish Patil, Sarah Nemser, Mothomang Oyinloye, Olgica Ceric | TITLE: Extraction of bacterial DNA using MagMAX™ CORE Nucleic Acid Purification Kit on KingFisher™ Flex Instrument
AUTHORS: Leyi Wang, Carol Maddox, Melanie Prarat, Yan Zhang, Lifang Yan, Akhilesh Ramachandran, Sai Sankara Narayanan, Girish Patil, Sarah Nemser, Mothomang Oyinloye, Olgica Ceric
[DESCRIPTION]
Thi... | ["Click Start Button, and the machine will process and complete in around 20 mins", "Laboratory specific variations from protocol\n\nOhio ADDL: use molecular grade water to resuspend the colonies.\n\nIllinois VDL, Mississippi VRDL, and Oklahoma ADDL: use PBS to resuspend the colonies.\n\nOklahoma ADDL: uses Dry Garnet ... |
97,591 | ICGRC Portal Tripal Data Generation and Setup | 5 | dx.doi.org/10.17504/protocols.io.n2bvj3nz5lk5/v3 | https://www.protocols.io/view/icgrc-portal-tripal-data-generation-and-setup-dbix2kfn | Locedie Mansueto, ramil.mauleon, Tobias Kretzschmar, Graham King | TITLE: ICGRC Portal Tripal Data Generation and Setup
AUTHORS: Locedie Mansueto, ramil.mauleon, Tobias Kretzschmar, Graham King
[DESCRIPTION]
The data provided by the International Cannabis Genomics Research Consortium (ICGRC, https://icgrc.info) web portal consists of published results from past analyses, and resu... | ["[Prepare RNA-Seq Sequences] Next Generation Sequencing (NGS) RNA-Seq sequences are downloaded from NCBI SRA, and trimmed to remove adapters. Three sets of RNA-Seqs are prepared for: 1) Purple Kush gene prediction, 2) Finola gene prediction, 3) transcript assembly, expression level, and variant discovery for trichomes... |
13,108 | Magnetic bead cleaning of PCR products | 1 | dx.doi.org/10.17504/protocols.io.q2udyew | https://www.protocols.io/view/magnetic-bead-cleaning-of-pcr-products-q2udyew | Alexander Eiler | TITLE: Magnetic bead cleaning of PCR products
AUTHORS: Alexander Eiler
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Calculate the volume needed for the beads:0.8 * sample volume =
?. Shake the magnetic bead buffer bottle to fully resuspend magnetic particles.
?. Add Sample.
?. Add beads.
?. Pipette mix ... | ["Calculate the volume needed for the beads:0.8 * sample volume =", "Shake the magnetic bead buffer bottle to fully resuspend magnetic particles.", "Add Sample.", "Add beads.", "Pipette mix 10 times and Incubate at room temperature for 5 minutes.", "Place the reaction plate onto a Magnet Plate for 2 minutes to separate... |
35,360 | Slide Preparation for Mounting Samples for TissueCyte 1000 Sectioning and Imaging | null | dx.doi.org/10.17504/protocols.io.ber8jd9w | null | Allen Institute for Brain Science | TITLE: Slide Preparation for Mounting Samples for TissueCyte 1000 Sectioning and Imaging
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the preparation of 1x3 glass slides for mounting embedded mouse brain samples for subsequent ima... | [] |
66,987 | Skin Biopsy Protocol (Mammals): Non-lethal Sampling | 1 | null | https://www.protocols.io/view/skin-biopsy-protocol-mammals-non-lethal-sampling-cdnjs5cn | sanaz.arenivas, comizzolip, mhouck, racheljohnston, Jacquelyn Mountcastle, Budhan Pukazhenthi, phil.purdy | TITLE: Skin Biopsy Protocol (Mammals): Non-lethal Sampling
AUTHORS: sanaz.arenivas, comizzolip, mhouck, racheljohnston, Jacquelyn Mountcastle, Budhan Pukazhenthi, phil.purdy
[DESCRIPTION]
Version date: 10 November 2022
The following protocol illustrates how to collect and ship living tissue from a mammalian species u... | ["[Preparation] For general sedation, anesthetize according to standard practices. Instructions for local anesthesia are in the proceeding steps (Refer to Handbook of Wildlife Chemical Immobilization by Terry Kreeger).", "[Preparation] Shave sampling area with hair trimmer, removing as much hair as possible. Ear punche... |
null | null | null | dx.doi.org/10.17504/protocols.io.phndj5e | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.kfvctn6 | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
<span style="text-decoration: underline;"><strong>Input Files</strong></span><br /><br />You must have the appropriate input files in the displayed directory structure:<br /><br /><em>Multi-parametric mapping (MPM) input files:</em><br />
<ul>
<li><strong>R1.nii.gz</strong> -- ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.n3adgie | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The NA inhibition test using large molecular fetuin substrate is believed to be the most specific method to detect antibodies against influenza virus neuraminidase. To avoid cross-reacting with hemagglutination-inhibition antibodies we have prepared several reassortant A/H7N1... | [] |
21,344 | Yale - Non-Esterified Fatty Acids | null | dx.doi.org/10.17504/protocols.io.y38fyrw | null | John Stack, Gary Cline | TITLE: Yale - Non-Esterified Fatty Acids
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 determine the concentration of NEFA in blood, serum, and plasma. NEFA; Free fat... | ["Calibrate Cobas for NEFA analysis by running a NEFA standard.", "Sample handling as performed by the Cobas Mira Plus a) Pipette 6µL of sample into cuvette. b) Add 225 µL of NEFA Reagent A Mixture. c) Add 75 µL of NEFA Reagent B Mixture. d) Mixture is incubated at 37ºC for 10 minutes e) Absorbance is me... |
null | null | null | dx.doi.org/10.17504/protocols.io.hfxb3pn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.jg3cjyn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>We conducted fluorimetric assays for each of three hydrolytic enzymes: b-glucosidase and cellobiohydrolase, and<em> N</em>-acetyl-glucosaminidase in black microplates. We measured fluorescence at 365 nm excitation and 450 nm emission. From each sample, we recorded fluorescenc... | [] |
52,383 | Hybridization Chain Reaction on paraffin sections | 4 | null | https://www.protocols.io/view/hybridization-chain-reaction-on-paraffin-sections-bxd7pi9n | Astrid Deryckere, Ruth Styfhals, Ali Elagoz, Eve Seuntjens | TITLE: Hybridization Chain Reaction on paraffin sections
AUTHORS: Astrid Deryckere, Ruth Styfhals, Ali Elagoz, Eve Seuntjens
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left"><span>This protocol has been optimized for HCR-IHC on paraffin sections of </... | ["[Tissue preparation]\nFix tissue overnight in 4 % paraformaldehyde (PFA) in phosphate buffered saline (PBS-DEPC) at 4°C.", "[Tissue preparation]\nWash and store in PBS-DEPC at 4°C.", "[Tissue preparation]\nTransfer tissues to embedding cassettes (Tissue-Tek Biopsy - Chamber Cassette, Sakura). Immerse the cassettes in... |
81,464 | 10x Protocols: Visium v2 CytAssist FFPE Library Construction -- University of Minnesota TMCs (CG000495 Rev A) | 1 | dx.doi.org/10.17504/protocols.io.5qpvormp9v4o/v1 | https://www.protocols.io/view/10x-protocols-visium-v2-cytassist-ffpe-library-con-ctsywnfw | IOx Genomics, Laura J Niedernhofer, David A Bernlohr | TITLE: 10x Protocols: Visium v2 CytAssist FFPE Library Construction -- University of Minnesota TMCs (CG000495 Rev A)
AUTHORS: IOx Genomics, Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
Protocols from 10x Genomics for Visium Spatial Gene Expression v2 chemistry on FPPE samples with the CytAssist component.
Pro... | ["10x protocol CG000 495, Revision A (Library construction with CytAssist)", "Additional Protocols/Resources\nhttps://www.10xgenomics.com/support/spatial-gene-expression-ffpe"] |
20,611 | Case - Citric Acid Cycle and Related Intermediates | null | dx.doi.org/10.17504/protocols.io.ydbfs2n | null | Henri Brunengraber | TITLE: Case - Citric Acid Cycle and Related Intermediates
AUTHORS: Henri Brunengraber
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block"><span>Analysis of the citric acid cycle (CAC) and related intermediates (such as glu... | ["5% acetic acid in methanol/water (1:1) tissue extraction procedure 1. Weigh about 0.1-0.5 g of powdered frozen (-80 °C) tissue; eg. use a pre-weighed/tarred 15 mL conical tube chilled over dry ice; record the tissue weight (note: when using smaller sample sizes, may use less amounts of solvents and internal standards... |
56,612 | Wastewater QC workflow in GalaxyTrakr (SSQuAWK) | 1 | dx.doi.org/10.17504/protocols.io.b3icqkaw | https://www.protocols.io/view/wastewater-qc-workflow-in-galaxytrakr-ssquawk-b3icqkaw | Jasmine Amirzadegan, Tunc Kayikcioglu, hugh.rand , Ruth Timme, Maria Balkey | TITLE: Wastewater QC workflow in GalaxyTrakr (SSQuAWK)
AUTHORS: Jasmine Amirzadegan, Tunc Kayikcioglu, hugh.rand , Ruth Timme, Maria Balkey
[DESCRIPTION]
PURPOSE:
Step-by-step instructions for checking sequence quality for SARS-CoV-2 wastewater samples using SSQuAWK: SARS - CoV - 2 Sequence Quality Assurance ... | ["[Account set up] Create a GalaxyTrakr account here: https://account.galaxytrakr.org/Account/Register", "[Account set up] Log into your GalaxyTrakr account: https://galaxytrakr.org", "[Create a new history] Create a new history. \n\nWe recommend creating a new history for each new MiSeq sequence set with details and d... |
55,905 | Sample Protocol | 4 | null | https://www.protocols.io/view/sample-protocol-b2t9qer6 | Josh | TITLE: Sample Protocol
AUTHORS: Josh
[DESCRIPTION]
abstract
[STEPS]
SECTION: This is a section
1. This is a step
SECTION: This is a section
2. Second step
SECTION: Another Section
3. Eh
6. _ | ["[This is a section] This is a step", "[This is a section] Second step", "[Another Section] Eh", "_"] |
26,588 | HTMCs 3D culture method using Corning Matrigel Matrix | null | dx.doi.org/10.17504/protocols.io.574g9qw | null | Stefania Vernazza | TITLE: HTMCs 3D culture method using Corning Matrigel Matrix
AUTHORS: Stefania Vernazza
[STEPS]
?. [Cell Cultures]
Human trabecular meshwork cells (HTMC) and their Growth Medium with FBS, theTrabecular Meshwork Growth Medium (TMGM), from Cell APPLICATION INC. Maintain the HTMCs at 37◦C in a humidified atmosphere cont... | ["[Cell Cultures]\nHuman trabecular meshwork cells (HTMC) and their Growth Medium with FBS, theTrabecular Meshwork Growth Medium (TMGM), from Cell APPLICATION INC. Maintain the HTMCs at 37◦C in a humidified atmosphere containing 5% CO2, according to the manufacturer’s indications. Sub-cultured HTMCs by TripLETM Expres... |
88,825 | UPitt TriState SenNet TMC Total RNA isolation & quality analysis for bulk RNA-seq | 1 | dx.doi.org/10.17504/protocols.io.j8nlko3w5v5r/v1 | https://www.protocols.io/view/upitt-tristate-sennet-tmc-total-rna-isolation-amp-c2yzyfx6 | Jianmin Xue, Marta Bueno, Oliver Eickelberg | TITLE: UPitt TriState SenNet TMC Total RNA isolation & quality analysis for bulk RNA-seq
AUTHORS: Jianmin Xue, Marta Bueno, Oliver Eickelberg
[DESCRIPTION]
Bulk RNA sequencing (RNA-seq) is a quantitative method used to interrogate the transcriptome of a biological sample at a given point in time. This protocol des... | ["[Total RNA extraction and purification] Use 5 mg of pulverized tissue, and add 350 μl of the RLT Plus buffer prepared initially. Pipet the lysate directly into a QIAshredder spin column placed in a 2 ml collection tube, and centrifuge for 2 min at maximum speed.", "[Total RNA extraction and purification] Add 700 μl B... |
75,884 | A simple illustrated protocol to prepare over 1,000 multiplexed single cell proteomics samples per day | 1 | dx.doi.org/10.17504/protocols.io.yxmvm2w16g3p/v1 | https://www.protocols.io/view/a-simple-illustrated-protocol-to-prepare-over-1-00-cnckvauw | Benjamin Orsburn | TITLE: A simple illustrated protocol to prepare over 1,000 multiplexed single cell proteomics samples per day
AUTHORS: Benjamin Orsburn
[DESCRIPTION]
This is a simple illustrated sample preparation method for multiplexed single human cells, as described in Orsburn et al., Bumpus 2022 that better encompasses the lab S... | ["[Prepare 96-well plates for sorting with acetonitrile lysis solution] Add 2uL of LCMS grade acetonitrile to each well of a 96 well plate", "[Prepare 96-well plates for sorting with acetonitrile lysis solution] Centrifuge if necessary to ensure acetonitrile is in the bottom of the plate. 1 minute pulsing is more than ... |
99,507 | dSTORM of actin in fixed HeLa cells | 0 | dx.doi.org/10.17504/protocols.io.q26g714j8gwz/v1 | https://www.protocols.io/view/dstorm-of-actin-in-fixed-hela-cells-ddet23en | Ezra Bruggeman, ruby peters | TITLE: dSTORM of actin in fixed HeLa cells
AUTHORS: Ezra Bruggeman, ruby peters
[DESCRIPTION]
This is a protocol for the preparation of a HeLa DTS cells for dSTORM imaging of the actin network. This protocol was used to generate the data shown in Figure 4 of the following publication:
Bruggeman et al., POLCAM: Instan... | ["[Cell culture] HeLa TDS cells were cultured in DMEM (Gibco, Invitrogen) supplemented with 10 % Fetal Bovine Serum (FBS, Life Technologies), 1 % penicillin/streptomycin (Life Technologies), and 1 % glutamine (Life Technologies) at 37 °C+ 5 % CO2.", "[Cell culture] Cells were periodically tested for mycoplasma contamin... |
null | null | null | dx.doi.org/10.17504/protocols.io.ez3bf8n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is part of BioLegend's, "<a href="http://www.biolegend.com/media_assets/support_protocol/Intracellular_Staining_Protocol_082615.pdf" target="_blank">Intracellular Flow Cytometry Staining Protocol: For the Detection of Intracellular Cytokines and Other Intracellular Targe... | [] |
80,776 | Stickleback Crossing Protocol | 1 | dx.doi.org/10.17504/protocols.io.5jyl8j7j8g2w/v1 | https://www.protocols.click/view/stickleback-crossing-protocol-cs5gwg3w | Holly Valentine | TITLE: Stickleback Crossing Protocol
AUTHORS: Holly Valentine
[DESCRIPTION]
Included are the steps to remove eggs, dissect testes, and create crosses of stickleback.
[STEPS]
SECTION: Squeezing eggs from Female
1. Squeeze Female: Wearing gloves, gently squeeze gravid female. Gravid females have extended abdomens and ... | ["[Squeezing eggs from Female] Squeeze Female: Wearing gloves, gently squeeze gravid female. Gravid females have extended abdomens and their eggs have “dropped”. If eggs do not emerge with very slight pressure the female is not ready. Squeeze eggs with motion from pectoral girdle posterior to the cloaca into a 25 mm s... |
82,329 | Adeno-associated virus (AAV) production and administration | 3 | dx.doi.org/10.17504/protocols.io.8epv5jyynl1b/v1 | https://www.protocols.io/view/adeno-associated-virus-aav-production-and-administ-cumzwu76 | Shiyi Wang | TITLE: Adeno-associated virus (AAV) production and administration
AUTHORS: Shiyi Wang
[DESCRIPTION]
Adeno-associated virus (AAV) production and administration
[STEPS] | [] |
40,837 | NEXT Gel - CHEM 584 | 4 | dx.doi.org/10.17504/protocols.io.bj5dkq26 | https://www.protocols.io/view/next-gel-chem-584-bj5dkq26 | Ken Christensen | TITLE: NEXT Gel - CHEM 584
AUTHORS: Ken Christensen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">General Information:</span><span> VWR Life Science AMRESCO’s NEXT GEL® products for denaturing gel electrophoresis are proprietary, ready-to-pour solutions comprised... | ["Add of TEMED and of freshly made 10% w/v ammonium persulfate (APS) to ofNEXT Gel solution in a conical tube. Tighten cap and mix immediately by gently inverting. Pour between prepared glass plates, filling to the top.\n3 µl\n30 µl\n5 mL", "Insert an appropriate comb and allow gel to polymerize for up to minutes.... |
63,594 | 2-step PCR mixture and conditions (Barcoded-head primers for seqs pooling) | 4 | null | https://www.protocols.io/view/2-step-pcr-mixture-and-conditions-barcoded-head-pr-cacisaue | Yin-Tse Huang | TITLE: 2-step PCR mixture and conditions (Barcoded-head primers for seqs pooling)
AUTHORS: Yin-Tse Huang
[DESCRIPTION]
PCR mixture and condition (2X SUPERGREEN PCR MASTER MIX)
[STEPS]
1. Wear glove, clean up the working bench w. 1% bleach
SECTION: For 1' PCR head-primers
2. Prepare 1' PCR master mixutre for hea... | ["Wear glove, clean up the working bench w. 1% bleach", "[For 1' PCR head-primers] Prepare 1' PCR master mixutre for head-primers (prepare 1.2X of solutions for pipetting error if needed)\n \nPCR mixture for head-primers for each reaction", "[For 1' PCR head-primers] Mix the 1' PCR master mixture gently by pi... |
null | null | null | dx.doi.org/10.17504/protocols.io.dqb5sm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is the PCR protocol for Phusion Polymerase, adapeted from NEB to match the protocol followed by Northeastern_Boston.
[BEFORE_START]
Annealing temperatures should be determined. We used Benchling for all Tm calculations.
[STEPS]
?.
?.
?.
?. | [] |
9,192 | Protoplast Isolation from Zymoseptoria tritici | 1 | dx.doi.org/10.17504/protocols.io.k8gcztw | https://www.protocols.io/view/protoplast-isolation-from-zymoseptoria-tritici-k8gcztw | Haseena Khan, Megan Mcdonald, Peter Solomon | TITLE: Protoplast Isolation from Zymoseptoria tritici
AUTHORS: Haseena Khan, Megan Mcdonald, Peter Solomon
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is a basic protocol for protoplasting the fungal pathogen </span><span style = "font-style:italic;">Zymoseptoria tritici</span></div>... | ["[Inoculum]\nPrepare a culture of Zymoseptoria tritici by inoculation of 100ul dense spore suspension into 500 ml Potato Dextrose Broth (PDB), incubate culture at 22°C with 130 rpm shaking.You can also take 50ul from a dense spore suspension and inoculate 100ml PDB.", "[Spore Collection]\nCollect the spores on fourth ... |
105,019 | Striatal oxidative stress quantification (OxiSelect™ In Vitro ROS/RNS Assay Kit (Green Fluorescence)) | 0 | dx.doi.org/10.17504/protocols.io.4r3l2qbqjl1y/v1 | https://www.protocols.io/view/striatal-oxidative-stress-quantification-oxiselect-dis34egn | Livia Hecke Morais | TITLE: Striatal oxidative stress quantification (OxiSelect™ In Vitro ROS/RNS Assay Kit (Green Fluorescence))
AUTHORS: Livia Hecke Morais
[DESCRIPTION]
Striatal oxidative stress quantification (OxiSelect‱ In Vitro ROS/RNS Assay Kit (Green Fluorescence))
[STEPS]
SECTION: Sample preparation
3. Samples are diluted (1:25)... | ["[Sample preparation] Samples are diluted (1:25) in PBS. Different dilutions should be tested for different tissues and experimental conditions. Prepare enough for 110 microliters of diluted samples (50 ul x duplicates +spare volume).", "[Oxidative stress quantification(OxiSelect™ In Vitro ROS/RNS Assay Kit (Green Flu... |
null | null | null | dx.doi.org/10.17504/protocols.io.cv8w9v | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
72,604 | Methodology for Frontier Model of the Environmental Inefficiency effects on Livestock Bioeconomy | 1 | dx.doi.org/10.17504/protocols.io.5jyl8jpn9g2w/v1 | https://www.protocols.io/view/methodology-for-frontier-model-of-the-environmenta-ci54ug8w | Carlos Alberto Zuniga Gonzalez | TITLE: Methodology for Frontier Model of the Environmental Inefficiency effects on Livestock Bioeconomy
AUTHORS: Carlos Alberto Zuniga Gonzalez
[DESCRIPTION]
This protocol considers the methodology used for Stochastic Frontier Analysis on the Livestocks Bioeconomic model. The applied methodology measured the eco-effic... | ["[Stochatics Frontier Analysis] Collecting Data. The study was carried out in 102 cattle farms for milk production in six municipalities of the state of Tlaxcala Mexico, in 2020. The production units were randomly selected, and dividing them among the four regions of importance in dairy production in the state of Tlax... |
45,832 | GATK Nuclear variant discovery and consensus assembly | 5 | dx.doi.org/10.17504/protocols.io.bqzgmx3w | https://www.protocols.io/view/gatk-nuclear-variant-discovery-and-consensus-assem-bqzgmx3w | Graham Etherington | TITLE: GATK Nuclear variant discovery and consensus assembly
AUTHORS: Graham Etherington
[DESCRIPTION]
The European polecat (Mustela putorius) is a mammalian predator which breeds across much of Europe east to central Asia. In Great Britain, following years of persecution the European polecat has recently undergone a ... | ["[BWA mapping] Here we map our reads to the domestic ferret genome, run the GATK pipeline to identify variants.", "[BWA mapping] Map the reads to the reference and sort the output", "GATK Pipeline", "[GATK pipeline] Mark Duplicates, add read groups, call variants, calculate GATK parameters, filter variants, create bas... |
95,913 | Adverse Outcomes of Combined Cochlear Implant and Hearing Aid Use: A Scoping Review | 0 | dx.doi.org/10.17504/protocols.io.dm6gp37xdvzp/v1 | https://www.protocols.io/view/adverse-outcomes-of-combined-cochlear-implant-and-c9whz7b6 | Priyanka_Jaisinghani, augustina.noel | TITLE: Adverse Outcomes of Combined Cochlear Implant and Hearing Aid Use: A Scoping Review
AUTHORS: Priyanka_Jaisinghani, augustina.noel
[DESCRIPTION]
Relevant articles highlighting adverse outcomes with the combination of hearing aid and cochlear implant published between 2000 and 2023 will be searched using manual s... | ["[Review Demographic details] Title: Adverse Outcomes of Combined Cochlear Implant and Hearing Aid Use: A Scoping Review.", "[Review Demographic details] Original language title: English", "[Review Demographic details] Start Date: 25/02/2024", "[Review Demographic details] End Date: 25/02/25", "[Review Demographic det... |
41,676 | u-Smell-it olfactory test | 4 | dx.doi.org/10.17504/protocols.io.bkxkkxkw | https://www.protocols.io/view/u-smell-it-olfactory-test-bkxkkxkw | dkt | TITLE: u-Smell-it olfactory test
AUTHORS: dkt
[STEPS]
?. Receive Olfactory/Chemosensory test CARD
?. Scan QR code on the Olfactory Card (using any smart phone) and the camera function (they automatically recognize QR codes)(Note: For people without access to a smart-phone there will be an automated call-in center t... | ["Receive Olfactory/Chemosensory test CARD", "Scan QR code on the Olfactory Card (using any smart phone) and the camera function (they automatically recognize QR codes)(Note: For people without access to a smart-phone there will be an automated call-in center that will provide voice prompts for choices of scent options... |
34,481 | Populating NCBI template for submissions using BioNumerics v7.6 | 1 | dx.doi.org/10.17504/protocols.io.bdwri7d6 | https://www.protocols.io/view/populating-ncbi-template-for-submissions-using-bio-bdwri7d6 | Ruth Timme, Maria Balkey, Julie Haendiges | TITLE: Populating NCBI template for submissions using BioNumerics v7.6
AUTHORS: Ruth Timme, Maria Balkey, Julie Haendiges
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">PURPOSE: </span><span>to define the standard operating procedure for collecting isolate metadat... | ["NCBI submission settings – Submission TemplateSave submission template according to PulseNet Instructions as -GenomeTrakr-Template-.", "Import data", "Import the GenomeTrakr Metadata form for BioNumerics (GT_BioNumerics_spreadsheet_v2.csv) according to PulseNet Instructions.", "When importing rules, the field source ... |
37,436 | Targeted ExSeq -- In Situ Sequencing (Illumina Chemistry) | 1 | dx.doi.org/10.17504/protocols.io.bgs4jwgw | https://www.protocols.io/view/targeted-exseq-in-situ-sequencing-illumina-chemist-bgs4jwgw | Yi Cui, Anubhav Sinha, Ed Boyden | TITLE: Targeted ExSeq -- In Situ Sequencing (Illumina Chemistry)
AUTHORS: Yi Cui, Anubhav Sinha, Ed Boyden
[DESCRIPTION]
This protocol accompanies Expansion Sequencing (ExSeq), and describes the process of performing in situ sequencing with the Illumina chemistry.
The steps here are an extension of the prot... | ["[Illumina Sequencing: Cleavage] Iteration\n\nIf more bases need to be sequenced, .", "[Preparation] Preparation of Sample\n\nThis protocol assumes that samples have been prepared following the Targeted ExSeq Tissue Preparation protocol, and that a sequencing library has been prepared following the Targeted ExSeq Lib... |
106,907 | Assembly and sample collection in the MetaFlowTrain | 0 | dx.doi.org/10.17504/protocols.io.q26g71763gwz/v1 | https://www.protocols.io/view/assembly-and-sample-collection-in-the-metaflowtrai-dkm34u8n | Guillaume Chesneau, Johannes Herpell, Sarah Wolf, Silvina Perin, Stéphane Hacquard | TITLE: Assembly and sample collection in the MetaFlowTrain
AUTHORS: Guillaume Chesneau, Johannes Herpell, Sarah Wolf, Silvina Perin, Stéphane Hacquard
[DESCRIPTION]
The following protocol is for the preparation of a MetaFlowTrain experiment. It provides the required materials, and the procedure. We also have a video p... | ["[Procedure] DAY 1 : PREPARE MATERIAL AND BUILD MICROCHAMBER TRAINS", "[Procedure] 1.2. BUILDING MICROCHAMBER TRAINS (Video: 00:21:12) Video Protocol:\n\n1.2.1 Surface sterilize all equipment with Bacillol and expose it to UV light for 15-30 minutes. Items to be surface sterilized include boxes with autoclaved microch... |
39,554 | Invitrogen PureLink® Genomic DNA Mini Kit | 4 | null | https://www.protocols.io/view/invitrogen-purelink-genomic-dna-mini-kit-bivake2e | Shlomi Abuchatzera Green | TITLE: Invitrogen PureLink® Genomic DNA Mini Kit
AUTHORS: Shlomi Abuchatzera Green
[STEPS]
?. [Preparing lysates: Mammalian cells, tissues]
Set a water bath or heat block at
55 °C
?. [Preparing lysates: Mammalian cells, tissues]
For adherent cells (≤5 × 106 cells): remove the growth medium from the culture plate and h... | ["[Preparing lysates: Mammalian cells, tissues]\nSet a water bath or heat block at\n55 °C", "[Preparing lysates: Mammalian cells, tissues]\nFor adherent cells (≤5 × 106 cells): remove the growth medium from the culture plate and harvest cells by trypisinization or a method of choice.For suspension cells (≤5 × 106 cells... |
96,607 | Blackwater medium | 0 | null | https://www.protocols.io/view/blackwater-medium-daj72crn | Callen Hyland, Rob Steele | TITLE: Blackwater medium
AUTHORS: Callen Hyland, Rob Steele
[DESCRIPTION]
Blackwater medium is a laboratory growth medium for Hydra that replicates the chemical composition of blackwater swamps. This medium has lower low ionic strength than traditional Hydra medium and contains humic acid. Blackwater medium is ideal f... | ["[Stock solutions] Make stock solutions in 50 mL conical tubes with DI water.", "[Stock solutions] Not all of the humic acid sodium salt will go into solution. Filter the humic acid solution with a syringe filter or vacuum filter to remove undissolved particles.", "[Working solution] Prepare blackwater medium by dilut... |
96,119 | An end-to-end workflow to study newly synthesized mRNA following rapid protein depletion in Saccharomyces cerevisiae | 4 | dx.doi.org/10.17504/protocols.io.n2bvj3dj5lk5/v3 | https://www.protocols.io/view/an-end-to-end-workflow-to-study-newly-synthesized-c94xz8xn | John B. Ridenour, Rafal Donczew | TITLE: An end-to-end workflow to study newly synthesized mRNA following rapid protein depletion in Saccharomyces cerevisiae
AUTHORS: John B. Ridenour, Rafal Donczew
[DESCRIPTION]
In this protocol, we describe an end-to-end workflow for rapidly degrading a target protein using the AID system and quantifying newly synth... | ["[Saccharomyces cerevisiae growth, IAA treatment, 4tU labeling, and rapid fixation] Add 5 ml of 100% methanol to a 50 ml conical tube for each sample to be collected. Keep tubes on dry ice. Three tubes are needed for each 40 ml culture.", "[Saccharomyces cerevisiae growth, IAA treatment, 4tU labeling, and rapid fixati... |
72,117 | Staining the Human Vagus Nerve with Osmium Tetroxide and Micro CT imaging | 1 | dx.doi.org/10.17504/protocols.io.bp2l61715vqe/v2 | https://www.protocols.io/view/staining-the-human-vagus-nerve-with-osmium-tetroxi-cinvude6 | Aniruddha R. Upadhye, Nicole A Pelot, Kip A. Ludwig, Kenneth J. Gustafson, Andrew Shoffstall | TITLE: Staining the Human Vagus Nerve with Osmium Tetroxide and Micro CT imaging
AUTHORS: Aniruddha R. Upadhye, Nicole A Pelot, Kip A. Ludwig, Kenneth J. Gustafson, Andrew Shoffstall
[DESCRIPTION]
In this protocol, we describe our steps to stain nerve fibers with Osmium Tetroxide for further visualization wtih microC... | ["[Section 2: Staining] Perform 3 washes of the nerve sample with 1X Phosphate-buffered saline letting the sample shake on an orbital shaker for 5 minutes at a time.", "[Section 2: Staining] PREPERATION OF 1% OSMIUM TETROXIDE SOLUTION. \nAll the steps mentioned below must be performed INSIDE OF THE FUME HOOD\n** waste ... |
63,853 | Condor CBD Gummies Amazon Reviews - 2022 {Updated} Risky or Scam Does It Really Work ? | 1 | dx.doi.org/10.17504/protocols.io.8epv59m8dg1b/v1 | https://www.protocols.io/view/condor-cbd-gummies-amazon-reviews-2022-updated-ris-cakmscu6 | Condor CBD Gummies | TITLE: Condor CBD Gummies Amazon Reviews - 2022 {Updated} Risky or Scam Does It Really Work ?
AUTHORS: Condor CBD Gummies
[STEPS]
1. Condor CBD Gummies Amazon
Product Review: —Condor CBD Gummies AmazonUsed For: — 🔶Pain Relief🔶Health Benefits
🔶Burn excess fat
🔶Better gut health & promote digestion
🔶Improves hear... | ["Condor CBD Gummies Amazon\nProduct Review: —Condor CBD Gummies AmazonUsed For: — 🔶Pain Relief🔶Health Benefits\n🔶Burn excess fat\n🔶Better gut health & promote digestion\n🔶Improves heart health\n🔶Control your appetite\n➢ Where to Buy - 🔶Click Here to Rush Your Order from the Official Website\n➤ Price (for Sale)... |
45,826 | Standard Operating Procedure for Real-Time PCR Reaction (qPCR) | 1 | null | https://www.protocols.io/view/standard-operating-procedure-for-real-time-pcr-rea-bqzamx2e | Leonardo Ribeiro, María Cristina Vidal Pessolani | TITLE: Standard Operating Procedure for Real-Time PCR Reaction (qPCR)
AUTHORS: Leonardo Ribeiro, María Cristina Vidal Pessolani
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = ":UNDERLINE;">Goal:</span></div><div class = "text-block">This SOP aims to guide users and establish a standar... | [] |
63,418 | Derma PGX Cream Review (Clinically Tested) Natural Skin | 3 | dx.doi.org/10.17504/protocols.io.36wgq7y5ovk5/v1 | https://www.protocols.io/view/derma-pgx-cream-review-clinically-tested-natural-s-b962r9ge | Derma PGX Cream | TITLE: Derma PGX Cream Review (Clinically Tested) Natural Skin
AUTHORS: Derma PGX Cream
[DESCRIPTION]
Derma PGX Anti Aging Cream (Clinically Tested) Natural Skin Look Younger! Review, Benefits, Result, and Cost!
Revitalize Your Skin Today With Derma PGX Cream
Derma PGX Review[Organic Skin Care]More Useful Than Other P... | [] |
32,651 | ATR FTIR spectoscopy of aqueous cell culture | null | dx.doi.org/10.17504/protocols.io.bb5jiq4n | null | Emrulla Spahiu, Senol Dogan, Jörg Schnauß, Mayda Gursel, Feride Severcan | TITLE: ATR FTIR spectoscopy of aqueous cell culture
AUTHORS: Emrulla Spahiu, Senol Dogan, Jörg Schnauß, Mayda Gursel, Feride Severcan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">ATR-FTIR Spectroscopy of aqueous cell culture samples is explained step-by-step. Infrared spectra acquisition, process... | ["[Spectra acquisition]\nClean the ATR crystal using a cellulose wipe and water-ethanol-water sequence. Scratching the crystal surface must be avoided.", "[Spectra acquisition]\nLeave the crystal to air-dry", "[Spectra acquisition]\nArrange the temperature of the working environment to\n25 °C", "[Spectra acquisition]\n... |
40,507 | Detection of anti- Keyhole limpet hemocynin (anti-KLH) in rats by double immunodiffusion (Ouchterlony) technique. | 4 | dx.doi.org/10.17504/protocols.io.bjs3kngn | https://www.protocols.io/view/detection-of-anti-keyhole-limpet-hemocynin-anti-kl-bjs3kngn | Angel Justiz-Vaillant, Norma McFarlane-Anderson | TITLE: Detection of anti- Keyhole limpet hemocynin (anti-KLH) in rats by double immunodiffusion (Ouchterlony) technique.
AUTHORS: Angel Justiz-Vaillant, Norma McFarlane-Anderson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Keyhole limpet hemocyanin (KLH) is a cooper-containing protein comprising... | ["Detection of anti-keyhole limpet hemocynin antibodies in rats by double immunodiffusion is carried out.", "Briefly, 1% agarose gels are prepared and wells cut into the gel using a template.", "Initially, aliquots of 25 µl each of KLH in concentration of 1 mg/ml are applied to the centre well.", "The peripheral wells ... |
null | null | null | dx.doi.org/10.17504/protocols.io.gszbwf6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for separating total RNA under denaturing conditions using Urea-PAGE using the 10 mL Hoefer SE260 <em>Mighty Small</em> system.</p>
[BEFORE_START]
<p>Thoroughly clean all components with ethanol and RNase away.</p>
<p>Heat block to 95˚C.</p>
[STEPS]
?.
?.
?.
?. ... | [] |
28,279 | General Immunohistochemical Protocol for formalin-fixed, paraffin-embedded tissue sections | null | dx.doi.org/10.17504/protocols.io.7uxhnxn | null | Tereza Blassova | TITLE: General Immunohistochemical Protocol for formalin-fixed, paraffin-embedded tissue sections
AUTHORS: Tereza Blassova
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [General Immunohistochemical Protocol for formalin-fixed, paraffin-embedded tissue sections]
Deparaffinize slides in 3 changes of xylene... | ["[General Immunohistochemical Protocol for formalin-fixed, paraffin-embedded tissue sections]\nDeparaffinize slides in 3 changes of xylene, 5 min each.", "[General Immunohistochemical Protocol for formalin-fixed, paraffin-embedded tissue sections]\nDrain off the blocking buffer from the slides.", "[General Immunohisto... |
105,851 | GEARBOCS protocols | 0 | dx.doi.org/10.17504/protocols.io.36wgqnq15gk5/v2 | https://www.protocols.io/view/gearbocs-protocols-djk34kyn | Justin T Savage, Luke Bradley, Nicholas Brose | TITLE: GEARBOCS protocols
AUTHORS: Justin T Savage, Luke Bradley, Nicholas Brose
[DESCRIPTION]
Protocols for AAV production and use of the GEARBOCS system.
[STEPS] | [] |
62,985 | PROTOCOL – Availability of Open Access Metadata from Open Journals – A case study in DOAJ and Crossref | 1 | dx.doi.org/10.17504/protocols.io.kxygxz7ywv8j/v4 | https://www.protocols.io/view/protocol-availability-of-open-access-metadata-from-b9rhr536 | Davide Brembilla, Chiara Catizone, Giulia Venditti | TITLE: PROTOCOL – Availability of Open Access Metadata from Open Journals – A case study in DOAJ and Crossref
AUTHORS: Davide Brembilla, Chiara Catizone, Giulia Venditti
[DESCRIPTION]
This protocol is for the research about the availability of Metadata from Open Journals in the DOAJ in Crossref.
The goal is to find... | ["[‱ Data Gathering] Download DOAJ articles metadata\n\nFor starting our research we first focused on retrieving and cleaning DOAJ articles' data as we identified it as the starting point from which we could look for an answer to our research questions.", "[‱ Data Gathering] Collecting Crossref data\n\nIn order to bett... |
74,856 | Gus staining | 4 | null | https://www.protocols.io/view/gus-staining-cmcgu2tw | lilyli | TITLE: Gus staining
AUTHORS: lilyli
[DESCRIPTION]
This is a protocol for gus staining.
[STEPS]
1. 1: Fix with 90% acetone for 20 min;
2. 2: Add 1 mL GUS lotion to wash off acetone, and wash twice:
3. 3: Add GUS dye solution and vacuum on ice for 15-20 min;
4. 4: Place at 37C and observe after a while -- next, after ... | ["1: Fix with 90% acetone for 20 min;", "2: Add 1 mL GUS lotion to wash off acetone, and wash twice:", "3: Add GUS dye solution and vacuum on ice for 15-20 min;", "4: Place at 37C and observe after a while -- next, after dyeing, proceed to the following steps:", "5: Suck out the dye solution, add 1mL 70% ethanol, and s... |
95,539 | Quantifying Checking Genomic DNA | 1 | null | https://www.protocols.io/view/quantifying-checking-genomic-dna-c9itz4en | Carlos Goller | TITLE: Quantifying Checking Genomic DNA
AUTHORS: Carlos Goller
[DESCRIPTION]
Overview and Goals
Your bacterial isolate has been grown on agar plates, lysed open and genomic DNA has been isolated for sequencing. Next, we need to quantify our DNA yield and assess its integrity. For this, we will use the IMPLEN nano spec... | ["[Activity 1: Quantification of DNA with the IMPLEN Nano Spectrophotometer] Based on the Implen nanospectrophotometer protocol.\n\n \n\n\nBefore starting, watch this 3-minute video: The NanoPhotometer Introduction Video (3:43 min video).", "[Activity 1: Quantification of DNA with the IMPLEN Nano Spectrophotometer] Tur... |
27,410 | Simulation of 6300 year intergalactic journey | null | dx.doi.org/10.17504/protocols.io.6zshf6e | null | Thorsten Sommer | TITLE: Simulation of 6300 year intergalactic journey
AUTHORS: Thorsten Sommer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes a possible implementation of a simulation of a 6300 year journey from Earth to Proxima Centauri b. It is based on the description of Frédéric Marin an... | ["[Setup]\nReset: Reset i.e. clear the entire simulation.", "[Setup]\nPens: Initialize all pens of both diagrams. This is necessary so that the user can choose between a simulation on a daily or monthly basis.", "[Setup]\nCapacity: Define the capacity of the spaceship so that a maximum of 500 people can live on it.", "... |
34,269 | Adapter ligation with AMX | null | dx.doi.org/10.17504/protocols.io.bdp5i5q6 | null | Josh Quick | TITLE: Adapter ligation with AMX
AUTHORS: Josh Quick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a subprotocol for generating a library from a single amplicon pool</div></div>
[STEPS]
?. Set up the following AMX adapter ligation reaction:Component ... | ["Set up the following AMX adapter ligation reaction:Component VolumeEnd-repaired amplicon pools Ligation Buffer (LNB) Adapter Mix (AMX) ... |
99,222 | DNA Extraction from Sterivex Filters - Phenol-Chloroform | 1 | null | https://www.protocols.io/view/dna-extraction-from-sterivex-filters-phenol-chloro-dc5w2y7e | Colleen Kellogg | TITLE: DNA Extraction from Sterivex Filters - Phenol-Chloroform
AUTHORS: Colleen Kellogg
[DESCRIPTION]
This protocol is used to extract genomic DNA from 0.22μl sterivex filters using Phenol-Chlorophorm. The protocol is part of the Hakai Institute's pipeline to analyze microbial and environmental DNA from seawater samp... | ["[Lysis and Incubation] Thaw filters on ice, if applicable. \nReplace Parafilm on each sample if needed. \nPrepare extraction negative - add 1800 µL of SLB or Longmire’s buffer (filter-sterilized and UVed) into a new Sterivex. \nSeal bottom with parafilm and top with cap or parafilm, treat same as rest of samples.", "... |
15,591 | In vitro α-amylase and α-glucosidase inhibitory assay | null | dx.doi.org/10.17504/protocols.io.tgfejtn | null | Maira Rubí Segura-Campos | TITLE: In vitro α-amylase and α-glucosidase inhibitory assay
AUTHORS: Maira Rubí Segura-Campos
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Diabetes mellitus is an endocrine disease characterized by hyperglycemia that affects the metabolism of carbohydrates, proteins, and fats. The unique approa... | ["[In vitro α-amylase inhibitory assay: Preparation of the substrate solution]\nStarch suspended in 0.2 mL of 0.5 M Tris-HCl pH 6.9 (0.01M CaCl2)\n[Starch]", "[In vitro α-amylase inhibitory assay: Pre-incubation]\nBoil (5 min) and pre-incubate the substrate solution", "[In vitro α-amylase inhibitory assay ]\nAqueous ex... |
54,664 | Human_Tissue_Nuclei_Isolation_Protocol_2021_10_18 | 1 | dx.doi.org/10.17504/protocols.io.bzmgp43w | https://www.protocols.io/view/human-tissue-nuclei-isolation-protocol-2021-10-18-bzmgp43w | Jose.Bras , lee.marshall , Kimberly Paquette | TITLE: Human_Tissue_Nuclei_Isolation_Protocol_2021_10_18
AUTHORS: Jose.Bras , lee.marshall , Kimberly Paquette
[DESCRIPTION]
Homebrew protocol to isolate nuclei from human frozen brain tissue
[STEPS]
1. Homogenize
a. Transfer tissue to facs tube
b. Add 2mL of PBSTA to the facs tube containing the tissue
c. Homog... | ["Homogenize \na.\tTransfer tissue to facs tube \nb.\tAdd 2mL of PBSTA to the facs tube containing the tissue \nc.\tHomogenize on ice with hand-held mixer at lowest setting, 5 sec on, 5 sec off, repeat for a total of 4 times, (do not create bubbles, check no debris after homogenizing), store on ice \nd.\tAdd 40uL of 10... |
52,584 | Copd CBD Gummies (Hoax and Legitimate) Truth! | 3 | dx.doi.org/10.17504/protocols.io.bxkgpktw | https://www.protocols.io/view/copd-cbd-gummies-hoax-and-legitimate-truth-bxkgpktw | gayleworten | TITLE: Copd CBD Gummies (Hoax and Legitimate) Truth!
AUTHORS: gayleworten
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Copd CBD Gummies is a pain reliever formula formulated with natural ingredients which help to provide natural relief from pain.</div></div>
[STEPS] | [] |
33,943 | Library Construction Protocol | 1 | dx.doi.org/10.17504/protocols.io.4r3l28ndql1y/v1 | https://www.protocols.io/view/library-construction-protocol-bddxi27n | Dakota Betz | TITLE: Library Construction Protocol
AUTHORS: Dakota Betz
[DESCRIPTION]
Library construction workflows must be tailored and optimized to accommodate specific experimental
designs, sample characteristics, sequencing applications and equipment. The protocol provided in this document
is generic, and reaction parameters m... | ["[Enzymatic Fragmentation] Dilute the amount of dsDNA to be used for library construction as follows:\nIf the DNA preparation does not contain EDTA, dilute in 10 millimolar (mM) Tris-HCl (pH 8.0 – 8.5) in a total of 35 µL \nIf the DNA preparation does contain EDTA, dilute in the EDTA-containing buffer in which samples... |
90,726 | Rapid Staining Technique for Visualizing Arbuscular Mycorrhizal Fungi (AMF) Colonization in Legume Roots | 4 | dx.doi.org/10.17504/protocols.io.rm7vzx1oxgx1/v1 | https://www.protocols.io/view/rapid-staining-technique-for-visualizing-arbuscula-c4ueywte | Manoj-Kumar Arthikala, Kalpana Nanjareddy | TITLE: Rapid Staining Technique for Visualizing Arbuscular Mycorrhizal Fungi (AMF) Colonization in Legume Roots
AUTHORS: Manoj-Kumar Arthikala, Kalpana Nanjareddy
[DESCRIPTION]
This protocol outlines a rapid staining technique for visualizing Arbuscular Mycorrhizal Fungi (AMF) colonization in legume roots. Careful sam... | ["[Preserving root samples] If you're not proceeding with staining immediately, the FAA fixative is used for preserving root samples prior to mycorrhizal staining. Here's a brief protocol for using FAA fixative before mycorrhizal staining:", "[Preserving root samples] Prepare FAA Fixative:\n\nMix formaldehyde, acetic a... |
92,220 | NanoString GeoMx DSP TMA-TNP Phase 4 WTA assay | 1 | dx.doi.org/10.17504/protocols.io.kqdg3x157g25/v1 | https://www.protocols.io/view/nanostring-geomx-dsp-tma-tnp-phase-4-wta-assay-c6a4zagw | Jinho Lee, Gabriel Zangirolani, Koei Chin, Heidi S Feiler, Christopher Corless | TITLE: NanoString GeoMx DSP TMA-TNP Phase 4 WTA assay
AUTHORS: Jinho Lee, Gabriel Zangirolani, Koei Chin, Heidi S Feiler, Christopher Corless
[DESCRIPTION]
This protocol outlines the NanoString GeoMx Digital Spatial Profiler Whole Transcriptome Atlas (DSP WTA) assay that was applied in the Human Tumor Atlas Network (... | ["[FFPE slide sample preparation] FFPE slide preparation", "[FFPE slide sample preparation] Bake FFPE slides at 60 °C for 60 min .", "[FFPE slide sample preparation] Deparaffinize by sequential incubation with Xylene (3 min twice), 100% EtOH (1 min twice) and 95% EtOH (1 min ).", "[FFPE slide sample preparation] Brief... |
78,835 | Viral PEG purification | 4 | dx.doi.org/10.17504/protocols.io.n92ldp6dxl5b/v1 | https://www.protocols.io/view/viral-peg-purification-cq8tvzwn | sarah.schulz | TITLE: Viral PEG purification
AUTHORS: sarah.schulz
[DESCRIPTION]
Protocol for viral particle purification via PEG percipitation
[STEPS]
1. Add 30 ml of ice cold PBS to 3 g of faecal sample and mix by vortexing at high speed for 5 min, then keep on ice
2. Centrifuge sample at 5000 rpm for 10 min at 4°C and transfer t... | ["Add 30 ml of ice cold PBS to 3 g of faecal sample and mix by vortexing at high speed for 5 min, then keep on ice", "Centrifuge sample at 5000 rpm for 10 min at 4°C and transfer the supernatant to a clean 50 ml centrifuge tube", "Filter the supernatant through a 0.45 μm syringe filter", "Add 10 % 10% w/v PEG-8000 in s... |
72,202 | S3: Step-by-step-guide using Blender in the work flow. | 5 | dx.doi.org/10.17504/protocols.io.rm7vzynk5lx1/v2 | https://www.protocols.io/view/s3-step-by-step-guide-using-blender-in-the-work-fl-ciriud4e | Paul Kalke, Conrad Helm | TITLE: S3: Step-by-step-guide using Blender in the work flow.
AUTHORS: Paul Kalke, Conrad Helm
[DESCRIPTION]
Step-by-step-guide how to use Blender to analyse and visualize your segmented structures, for example exporting it as a video as mp4-file.
[STEPS]
1.
•Open Blender
•Choose under New File – General
•Delete ... | ["•Open Blender \n•Choose under New File – General\n•Delete the cube\n•Now go to File – Import-Stanford (.ply)", "Moving in Blender and Hotkeys --> https://www.youtube.com/watch?v=TPrnSACiTJ4", "•Your object/mesh is very large in Blender, change under Object Properties the Scale of X, Y and Z from 1 to 0.01", "•now imp... |
null | null | null | dx.doi.org/10.17504/protocols.io.kw5cxg6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Complementation of<em> a S. cerevisiae </em>Δ<em>pho84</em> strain with putative phosphate transporter(s)</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?. | [] |
59,486 | Staining of cells with GolgiTracker for Golgi flow cytometry analysis | 4 | dx.doi.org/10.17504/protocols.io.e6nvwk1d2vmk/v1 | https://www.protocols.io/view/staining-of-cells-with-golgitracker-for-golgi-flow-b6b6rare | Enrico Bagnoli, Rotimi Fasimoye, Dario R Alessi | TITLE: Staining of cells with GolgiTracker for Golgi flow cytometry analysis
AUTHORS: Enrico Bagnoli, Rotimi Fasimoye, Dario R Alessi
[DESCRIPTION]
We describe a method that allows the staining of intact Golgi using GolgiTracker for subsequent flow cytometry analysis. The analysis can provide a quantitative indicati... | ["[Flow cytometry] Flow cytometry analysis", "[Staining on cells + Immunoprecipitation] Staining of cultured cells with GolgiTracker", "[Staining on cells + Immunoprecipitation] Isolation of intact Golgi using GolgiTag immunoprecipitation method", "[Materials and reagents] Cell culture", "[Analysis] Data analysis using... |
41,879 | Colony PCR -- CHEM 584 | 4 | dx.doi.org/10.17504/protocols.io.bk5xky7n | https://www.protocols.io/view/colony-pcr-chem-584-bk5xky7n | Ken Christensen | TITLE: Colony PCR -- CHEM 584
AUTHORS: Ken Christensen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A quick way to screen transformants for an insert. This is faster and less expensive than doing a restriction digest.</div></div>
[STEPS]
?. [After you have colonies from a transformation]
Draw gr... | ["[After you have colonies from a transformation]\nDraw grid on clean agar plate (use the appropriate antibiotic). You will use this to inoculate an overnight culture for a positive clone.", "[After you have colonies from a transformation]\nSelect colonies to pick. Streak portion of colony to numbered sector and place ... |
40,244 | Tissue Cyclic Immunofluorescence (t-CyCIF) | 1 | dx.doi.org/10.17504/protocols.io.bjiukkew | https://www.protocols.io/view/tissue-cyclic-immunofluorescence-t-cycif-bjiukkew | Jia Ren Lin, Benjamin Izar, Zoltan Maliga, Yu-An Chen, Giorgio Gaglia, Ziming Du, Clarence Yapp, Shaolin Mei, Sandro Santagata, Peter Sorger | TITLE: Tissue Cyclic Immunofluorescence (t-CyCIF)
AUTHORS: Jia Ren Lin, Benjamin Izar, Zoltan Maliga, Yu-An Chen, Giorgio Gaglia, Ziming Du, Clarence Yapp, Shaolin Mei, Sandro Santagata, Peter Sorger
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The architecture of normal and diseased tissues stro... | ["[Pre-Staining and Background Determination]\nPre-staining and Background Determination takes approximately 16-24 hours.Make fluorophore bleaching solution. Combine 1X PBS, 30% (wt/vol) H2O2, and NaOH in a 50-ml centrifuge tube. The final working concentration is 4.5% (wt/vol) H2O2 and NaOH in PBS. fluorophore bl... |
80,171 | QST: Pressure Pain Threshold Assessment | 1 | null | https://www.protocols.io/view/qst-pressure-pain-threshold-assessment-csijwccn | Shad Smith | TITLE: QST: Pressure Pain Threshold Assessment
AUTHORS: Shad Smith
[DESCRIPTION]
This protocol describes the use of an algometer device to collect pressure pain threshold measurements at the trapezius and the lateral epicondyle.
[STEPS]
SECTION: QST: Pressure Pain Threshold Assessment
1. I. PURPOSE: To provide feedba... | ["[QST: Pressure Pain Threshold Assessment] I. PURPOSE: To provide feedback to the clinical examiner by using a pressure-measurement device, the algometer as a dynamic measuring tool to have a more uniform level of measuring pain intensity on all subjects as standard of care.\n\nII. SCOPE: Applies to trained designee i... |
94,389 | Juxtacellular Recordings in Ventral tegmental area and Locus coeruleus | 1 | dx.doi.org/10.17504/protocols.io.3byl4q4novo5/v1 | https://www.protocols.io/view/juxtacellular-recordings-in-ventral-tegmental-area-c8evzte6 | Cristian González-Cabrera, Kaushik S. More, Matthias Prigge | TITLE: Juxtacellular Recordings in Ventral tegmental area and Locus coeruleus
AUTHORS: Cristian González-Cabrera, Kaushik S. More, Matthias Prigge
[DESCRIPTION]
This protocol describes juxtacellular recordings in the VTA and LC of adult mice, involving anesthesia, precise brain targeting, and neuron labeling. Using sp... | ["[Preparation of Adult Mice for juxtacellular recordings] Use adult mice weighing 25-30 g.\nAnesthetize the animal with urethane at a dosage of 1.25 g/kg.\nPlace the mouse in the stereotaxic frame and align the head angle according to Bregma and Lambda, with a tolerance of a maximum of 50 microns between them.\nExpose... |
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