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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27,393 | Tissue Procurement: Normal Colon | 1 | dx.doi.org/10.17504/protocols.io.6y9hfz6 | https://www.protocols.io/view/tissue-procurement-normal-colon-6y9hfz6 | Kerry Wiles | TITLE: Tissue Procurement: Normal Colon
AUTHORS: Kerry Wiles
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Tissues are procured from a variety of different anatomic sites, each with their own unique qualities to be considered during collection. Anatomic site-specific standard operating procedures... | ["[Tissue Procurement: Normal Colon]\nIdentify the tissue to be collected in the surgical pathology laboratory. Note that this protocol for collection of normal (NL) colon applies for normal adjacent tissue (NAT) in cancerous colons and also for histologically normal diverticulitis colon tissue.", "[Tissue Procurement:... |
52,487 | The efficacy of radical antegrade modular pancreatosplenectomy: a systematic review and meta-analysis protocol | 1 | dx.doi.org/10.17504/protocols.io.bxhfpj3n | https://www.protocols.io/view/the-efficacy-of-radical-antegrade-modular-pancreat-bxhfpj3n | Jun Watanabe, Kazuma Rifu, Hideki Sasanuma, Kazuhiko Kotani, Naohiro Sata | TITLE: The efficacy of radical antegrade modular pancreatosplenectomy: a systematic review and meta-analysis protocol
AUTHORS: Jun Watanabe, Kazuma Rifu, Hideki Sasanuma, Kazuhiko Kotani, Naohiro Sata
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Background:</span... | [] |
52,461 | Keto Smooth Reviews | 1 | dx.doi.org/10.17504/protocols.io.bxgmpju6 | https://www.protocols.io/view/keto-smooth-reviews-bxgmpju6 | health | TITLE: Keto Smooth Reviews
AUTHORS: health
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Nutra Empire Cbd Gummies >>>> HURRY UP LImite Stockl Left {Big Sale Only For Today} As Low As Before + Free Shipping only For US </div></div>
[STEPS]
?. Nutra Empire Keto Smooth: For millions of Americans, ... | ["Nutra Empire Keto Smooth: For millions of Americans, weight loss is a daily struggle that consumes virtually every aspect of their life. The desire to get slimmer and get healthier is constantly an uphill battle that sometimes feels impossible. This is why many Americans turn to extreme weight loss programs or d... |
43,752 | Gene knockout | 1 | dx.doi.org/10.17504/protocols.io.bnygmftw | https://www.protocols.io/view/gene-knockout-bnygmftw | Zhujun Wei | TITLE: Gene knockout
AUTHORS: Zhujun Wei
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>We use this protocol to knock out </span><span style = "font-style:italic;">yhaK</span><span> in </span><span style = "font-style:italic;">E.coli</span><span> BW25113</span></div></div>
[STEPS]
?. Transfe... | ["Transfer the pCas9 plasmid into the recipient E. coli BW25113 (Kana resistance, temperature sensitive).", "Preparation of pCas9 competent cells:", "Add 50 μL of bacterial solution to 5 mL of LB medium, incubate at 30℃, 200 rpm for about 12 h, Add 2% to 100 mL LB medium, add 0.5% of arabinose at a final concentration ... |
null | null | null | dx.doi.org/10.17504/protocols.io.naddaa6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>ABSTRACT</p>
<p>INTRODUCTION</p>
<p>The trend of survival rate of cardiac arrest patients is improving following investment in pre-hospital and hospital settings (1-4). The issue of unlimited resuscitation efforts without evaluation of the appropriateness results in financial... | [] |
92,761 | SiMOA total Rab10 Homebrew Assay | 1 | dx.doi.org/10.17504/protocols.io.dm6gp3188vzp/v1 | https://www.protocols.io/view/simoa-total-rab10-homebrew-assay-c6tzzep6 | yuan.yuan, andrew.west | TITLE: SiMOA total Rab10 Homebrew Assay
AUTHORS: yuan.yuan, andrew.west
[DESCRIPTION]
Assay for the detection of total Rab10 protein (rodent or human) in biofluids or lysates.
[STEPS]
2. Prepare the Beads
3. Conjugate
SECTION: Prepare Capture Beads Concentrate (5-6 hours)
1. Prepare capture beads using a two-step EDC... | ["Prepare the Beads", "Conjugate", "[Prepare Capture Beads Concentrate (5-6 hours)] Prepare capture beads using a two-step EDC coupling protocol. Reaction occurs between the antibody primary amino groups (-NH2) and the carboxyl groups (-COOH) on the beads. 80ug of antibody is required for 0.2 mg/ml buffer exchanged ant... |
null | null | null | dx.doi.org/10.17504/protocols.io.u6zezf6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol describes the data collection and analysis performed in "Invasion genetics of the silver carp (Hypophthalmichthys molitrix) across North America: Differentiation of fronts, introgression, and eDNA detection". Published in PLOS One, 2018.
The invasive silver carp H... | ["[Tissue sample collection & DNA extraction] Tissue samples are collected under University of Toledo IACUC protocol #205400, “Genetic studies for fishery management” to CAS. Samples are individually labeled, stored in 95% EtOH, and archived at the NOAA Pacific Marine Environmental Laboratory.\n\nGenomic DNA is extract... |
53,257 | Workflow for proteomic analysis of purified lysosomes with or without damage | 1 | dx.doi.org/10.17504/protocols.io.bx9hpr36 | https://www.protocols.io/view/workflow-for-proteomic-analysis-of-purified-lysoso-bx9hpr36 | Sharan Swarup, J. Wade Harper | TITLE: Workflow for proteomic analysis of purified lysosomes with or without damage
AUTHORS: Sharan Swarup, J. Wade Harper
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Lysosomes are a major degradative organelle within eukaryotic cells. Previous work has developed a method wherein the TMEM192 pro... | ["[Cell culture]\nGrow the appropriate cells (e.g. HEK293T) expressing TMEM192-3xHA in DMEM containing 5% FBS\nOne 15 cm plate of cells (80% confluence) is used per replicate.", "[Cell culture]\nTo damage lysosomes, add GPN ) or LLoMe (-) to cells for to .\n0.2\nThe length of time employed depends on the desired level... |
39,580 | Snap freezing brains | 1 | null | https://www.protocols.io/view/snap-freezing-brains-biv4ke8w | Molly Brennan, Olivier George | TITLE: Snap freezing brains
AUTHORS: Molly Brennan, Olivier George
[STEPS]
?. Snap freezing brains euthanize animal in either a bell jar of Isoflorane or in C02 chamber.once animal is dead you then can use scissors and or a gullitoine to remove head at nape of neck
?. Brain Removal-Use a pair of scissors to cut connec... | ["Snap freezing brains euthanize animal in either a bell jar of Isoflorane or in C02 chamber.once animal is dead you then can use scissors and or a gullitoine to remove head at nape of neck", "Brain Removal-Use a pair of scissors to cut connective tissue under the skin, reaching in between the eyes-Cut skin open, expos... |
85,757 | Medium fractionation and EV preparation | 4 | dx.doi.org/10.17504/protocols.io.81wgbx63ylpk/v1 | https://www.protocols.io/view/medium-fractionation-and-ev-preparation-cxy5xpy6 | wusj, Nancy C. Hernandez Villegas, schekman | TITLE: Medium fractionation and EV preparation
AUTHORS: wusj, Nancy C. Hernandez Villegas, schekman
[DESCRIPTION]
This protocol describes the characterization of the extracellular alpha-synuclein and DNAJC5
[STEPS]
SECTION: Extracellular vesicle (EV) preparation
8. Centrifuge the conditioned medium at 1,500 x g for 2... | ["[Extracellular vesicle (EV) preparation] Centrifuge the conditioned medium at 1,500 x g for 20 min at 4 °C in a Sorvall RC 6+ centrifuge with fixed angle rotor F14S-6X250y FiberLite", "[Extracellular vesicle (EV) preparation] Pour the supernatant into a new container without disturbing the pellet.", "[Extracellular v... |
null | null | null | dx.doi.org/10.17504/protocols.io.tkwekxe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Hypertension is a long-term medical condition in which the pressure of blood travelling through the arteries is too high. This puts increased strain on the heart which, if left untreated, can lead to increased risk of heart attack or stroke. It is extremely common and is a major... | [] |
70,190 | DNA extraction | 1 | null | https://www.protocols.io/view/dna-extraction-cgsntwde | Emma Wang | TITLE: DNA extraction
AUTHORS: Emma Wang
[DESCRIPTION]
A protocol for DNA extraction
[STEPS]
1. Grind samples
2. add solution
3. spin for 5 min | ["Grind samples", "add solution", "spin for 5 min"] |
68,807 | Diagnostic Restriction Digest (Instructor Protocol) | 4 | null | https://www.protocols.io/view/diagnostic-restriction-digest-instructor-protocol-cffftjjn | Brian Teague | TITLE: Diagnostic Restriction Digest (Instructor Protocol)
AUTHORS: Brian Teague
[DESCRIPTION]
This is the instructor protocol for
[STEPS]
SECTION: Setup
1. Aliquot the : 20 µL ul aliquots, 1 per 4 students
SECTION: Setup
2. Aliquot the enzyme: 4 µL of enzyme in 16 µL of , 1 per 4 students.
SECTION: Instr... | ["[Setup] Aliquot the : 20 µL ul aliquots, 1 per 4 students", "[Setup] Aliquot the enzyme: 4 µL of enzyme in 16 µL of , 1 per 4 students.", "[Instructor Tips & Common Student Errors] Instructor Tips\nIn a more advanced course, I would let students select which enzyme to use (chosen from the ones in the freezer.... |
26,475 | Molecular biology test for rapid detection cagAgen EPIYA motif in H.pylori isolates | null | dx.doi.org/10.17504/protocols.io.54jg8un | null | Eliana Rocio Rodríguez Gómez, William Otero Regino, Pedro A. Monterrey, Alba Alicia Trespalacios Rangel | TITLE: Molecular biology test for rapid detection cagAgen EPIYA motif in H.pylori isolates
AUTHORS: Eliana Rocio Rodríguez Gómez, William Otero Regino, Pedro A. Monterrey, Alba Alicia Trespalacios Rangel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>In this study , we aimed to determine the... | ["The entire 3´ repeat regions of the cagA gene was amplified by polymerase chain reaction (PCR) using the cagA primers, sense primer (CAGTF 5’-ACCCTAGTCGGTAATGGG-3’) and antisense primer (CAGTR 5’ GCTTTAGCTTCTGAYACYGC 3’)", "PCR amplification was carried out a volume of containing 0.3 µM concentrations of primers (In... |
69,075 | To test fork notification v.4 20220823 | 1 | dx.doi.org/10.17504/protocols.io.n92ldzjxxv5b/v4 | https://www.protocols.io/view/to-test-fork-notification-v-4-20220823-cfpttmnn | Gabriel Gasque | TITLE: To test fork notification v.4 20220823
AUTHORS: Gabriel Gasque
[DESCRIPTION]
Test for Fork notifications
[STEPS]
1. Step 1
2. Step 2
3. Step 3
4. Step 4 | ["Step 1", "Step 2", "Step 3", "Step 4"] |
null | null | null | dx.doi.org/10.17504/protocols.io.kwtcxen | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.pyqdpvw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is used for performing Type IIS assembly by either <em>BsaI</em> or <em>SapI</em>-mediated restriction/ligation using Loop assembly.</p>
<p> </p>
<p>Loop assembly comprises 8 receiver plasmids in odd and even levels (4 per level), which contain directional overh... | [] |
36,607 | Long reads nanopore sequencing to recover SARS-CoV-2 whole genome | null | dx.doi.org/10.17504/protocols.io.bfy7jpzn | https://www.protocols.io/view/long-reads-nanopore-sequencing-to-recover-sars-cov-bfy7jpzn | Paola Resende | TITLE: Long reads nanopore sequencing to recover SARS-CoV-2 whole genome
AUTHORS: Paola Resende
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">This protocol describes step-by-step instructions for building long (~2kb) amplicon libraries to recover S... | ["[Primers dilution]\nInstructions for Primer Scheme dilution:If lyophilised each primer should be resuspended to (Stock dilution 1)The primers from Primer Scheme 2kb_v1 Pool 1 and Primer Scheme 2kb_v1 Pool 2 are:Primer Scheme 2kb_v1 Pool 1: F1, R1, F3, R3, F5, R5, F7, R7, F9, R9, F11, R11, F13, R13, F15, R15, F17, R... |
46,680 | DEMoNS protocol for measurement and analysis of eye movements | 1 | null | https://www.protocols.io/view/demons-protocol-for-measurement-and-analysis-of-ey-brtym6pw | Jenny Nij Bijvank | TITLE: DEMoNS protocol for measurement and analysis of eye movements
AUTHORS: Jenny Nij Bijvank
[DESCRIPTION]
For questions, send an email to info.demonsprotocol@gmail.com or vanrijn@amsterdamumc.nl
The complete protocol and instructions on measurement and analysis of eye movements with the DEMoNS protocol.
Quantita... | ["[Protocols and instructions] Measurement and analysis protocol, and instructions on analysis and import files in Matlab.\n\nThe Eyelink measurement is created in the Experiment software of SR research and can therfore only be used with an Eyelink (SR Research) eyetracker. These zipped files contain the folders of the... |
null | null | null | dx.doi.org/10.17504/protocols.io.ejbbcin | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol outlines the analysis used to plot MetaPhlAn taxonomic assignments. Based on methods from the following publication:<br /><br />Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and D... | [] |
105,031 | Modelling human neuronal catecholaminergic pigmentation in rodents recapitulates age-related multisystem neurodegenerative deficits | 0 | dx.doi.org/10.17504/protocols.io.4r3l2qq1ql1y/v3 | https://www.protocols.io/view/modelling-human-neuronal-catecholaminergic-pigment-ditf4ejn | Ariadna Laguna, Núria Peñuelas, Miquel Vila | TITLE: Modelling human neuronal catecholaminergic pigmentation in rodents recapitulates age-related multisystem neurodegenerative deficits
AUTHORS: Ariadna Laguna, Núria Peñuelas, Miquel Vila
[DESCRIPTION]
Methods used in the manuscript entitled "Modelling
human neuronal catecholaminergic pigmentation in rodents recap... | [] |
47,345 | Quantitative Immunoblotting Analysis of LRRK2 Signalling Pathway | 4 | dx.doi.org/10.17504/protocols.io.bsgrnbv6 | https://www.protocols.io/view/quantitative-immunoblotting-analysis-of-lrrk2-sign-bsgrnbv6 | Francesca Tonelli, Dario Alessi | TITLE: Quantitative Immunoblotting Analysis of LRRK2 Signalling Pathway
AUTHORS: Francesca Tonelli, Dario Alessi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Accurate, quantitative analysis of protein expression and modifications (such as phosphorylation) is critical when studying cell signalling... | ["[Preparation of lysates]\nPlease choose the relevant method for preparation of lysate: Preparation of lysates from cultured cellsPreparation of lysates from mouse tissues", "[Preparation of lysates]\nQuickly wash cells in the tissue culture dish by carefully pouring that the cells are currently growing in into the d... |
28,269 | Cell-ELONA | null | dx.doi.org/10.17504/protocols.io.7umhnu6 | null | Guillermo Fernández Rodríguez | TITLE: Cell-ELONA
AUTHORS: Guillermo Fernández Rodríguez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">ELONA (Enzyme-Linked Oligonucleotide Assay), is a biochemical method based on enzyme linked immunosorbent assay (ELISA) that allows to demonstrate... | ["[Pre-Coating]\nInoculate a single colony of E.Coli DH5α from LB agar plate in of LB. Use a sterile pipette tip, selecting a single colony from LB agar plate. The liquid culture is incubated overnight\n10 ml\n37 °C", "[Pre-Coating]\nSpin at 4000 rpm for . Discard the supernatant, collect pellet and re-suspend in ... |
47,275 | Low Cost LAMP and RT-LAMP | 2 | dx.doi.org/10.17504/protocols.io.bsejnbcn | https://www.protocols.io/view/low-cost-lamp-and-rt-lamp-bsejnbcn | Tamara Matute, Isaac Núñez, Fernan Federici | TITLE: Low Cost LAMP and RT-LAMP
AUTHORS: Tamara Matute, Isaac Núñez, Fernan Federici
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol collection specifies how to carry out LAMP or RT-LAMP (reverse transcription - Loop-mediated isothermal amplification) reactions with homemade reagents ... | [] |
66,343 | Condor CBD Gummies Website Condor CBD Gummies Website Reviews Ingredients Price Scam Alert: Reviews From The Manufacturers | 3 | dx.doi.org/10.17504/protocols.io.4r3l2ojoqv1y/v1 | https://www.protocols.io/view/condor-cbd-gummies-website-condor-cbd-gummies-webs-cc2fsybn | Condor CBD Gummies Website | TITLE: Condor CBD Gummies Website Condor CBD Gummies Website Reviews Ingredients Price Scam Alert: Reviews From The Manufacturers
AUTHORS: Condor CBD Gummies Website
[DESCRIPTION]
https://www.outlookindia.com/outlook-spotlight/-scam-alert-condor-cbd-gummies-reviews-website-is-it-endorsed-by-shark-tank-who-own-it--news... | [] |
40,771 | ELISA for quantification of IL-12 in human serum. | 6 | dx.doi.org/10.17504/protocols.io.bj3bkqin | https://www.protocols.io/view/elisa-for-quantification-of-il-12-in-human-serum-bj3bkqin | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-12 in human serum.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells. T... | ["An anti-human IL-12 coating antibody is adsorbed onto microwells by incubation overnight at 4°C.", "Add 50 µl of human serum. Human IL-12 present in the serum sample binds to antibodies adsorbed to the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and later wash to remove unbound proteins."... |
20,024 | Addition of the adaptor to RNA substrates for 3′ RACE (mapping P ends) | null | dx.doi.org/10.17504/protocols.io.xsyfnfw | null | Matus Valach | TITLE: Addition of the adaptor to RNA substrates for 3′ RACE (mapping P ends)
AUTHORS: Matus Valach
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Simple protocol for mapping 3′-P RNA termini by RT-PCR after the addition of a 3′ adaptor using </span><span style = "font-style:italic;">E. coli<... | ["Mix the following components (9 μL): ABC1ComponentAmount [μL]Final concentration2RNA [1 µg]4100 ng/µL35′-hydroxylated 3′ RACE RNA oligo [100 µM]0.44RNase-free water (ddH2O)4.6\nABC1ComponentAmount [μL]Final concentration2RNA [1 µg]4100 ng/µL35′-hydroxylated 3′ RACE RNA oligo [100 µM]0.44RNase-free water (ddH2O)4.6",... |
null | null | null | dx.doi.org/10.17504/protocols.io.js4cngw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.h4vb8w6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.vere3d6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Human primary T cells are invaluable and feasible model systems to study the characteristics of the human immune cells in various contexts, including but not limited to cancer immunotherapy. Following isolation of T cells from fresh human blood samples, it is possible to culture... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.nz4df8w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is an excellent rhinovirus screening assay which I have used on thousands of sample extracts mostly originating from acutely ill paediatric patients, spanning well over a decade's worth of collection dates.</p>
<p> </p>
<p>I have not confirmed that it can detect every si... | [] |
28,224 | Evaluation of Mitochondrial Function | null | dx.doi.org/10.17504/protocols.io.7s8hnhw | null | E. Dale Abel | TITLE: Evaluation of Mitochondrial Function
AUTHORS: E. Dale Abel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This protocol describes the procedures used by the DiaComp for evaluating mitochondrial function.</div><... | ["[Protocols for Mitochondrial Analyses]\nSaponin-permeabilized fibers. Left ventricular cardiac fibers are prepared using previously described protocols (1,2). Briefly, small pieces (2-5 mg) of cardiac muscle are taken from the left ventricle and permeabilized with 50 µg/ml saponin at 4°C in buffer A containing (in mM... |
24,043 | Biochemical Measures of Neuropathy - Glutathione Assay (GSH) | null | dx.doi.org/10.17504/protocols.io.3qjgmun | null | Eva Feldman | TITLE: Biochemical Measures of Neuropathy - Glutathione Assay (GSH)
AUTHORS: Eva Feldman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">Oxidative stress is highly correlated with the metabolic changes caused by hypergl... | ["[Sample Preparation:]\nDo not let samples set at 0º for long periods of time.Prior to dissection, perfuse tissue with PBS pH7.4 with 0.16 mg/ml heparin1. Label 6 sets of micro centrifuge tubes. (If only doing GSH only need 3 sets)2. Prepare 3 M HClO4 and freeze.3. Cut tissue into segments and weigh. (~10 mg)4. Keepin... |
36,703 | EC isolation from human mesenteric artery for scRNA-seq | 1 | null | https://www.protocols.io/view/ec-isolation-from-human-mesenteric-artery-for-scrn-bf37jqrn | Xiaofang Tang, Kiran Sriram, Yingjun Luo, Zhen Chen | TITLE: EC isolation from human mesenteric artery for scRNA-seq
AUTHORS: Xiaofang Tang, Kiran Sriram, Yingjun Luo, Zhen Chen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines a method to efficiently isolate the human mesenteric arterial endothelial cells. Following the physical ... | ["[EC isolation from human mesenteric artery for scRNA-seq]\nWash freshly isolated human mesenteric artery (~5 cm in length) with DPBS in a 10-cm petri-dish. Use sterile surgical tools to clean the vessel (Removing the fat and outer connective tissues).", "[EC isolation from human mesenteric artery for scRNA-seq]\nCut ... |
18,781 | BG11 medium (working group Wilde) | null | dx.doi.org/10.17504/protocols.io.wj5fcq6 | null | Christin Köbler, Annegret Wilde | TITLE: BG11 medium (working group Wilde)
AUTHORS: Christin Köbler, Annegret Wilde
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">100x BG11 (500 ml)</span></div><div class = "text-block"><span>74.79 g NaNO</span><span style = "vertical-align:sub;">3</span></div><div... | [] |
105,842 | Culturing 3T3 Cells for Validating GEARBOCS Constructs | 0 | dx.doi.org/10.17504/protocols.io.e6nvw18pzlmk/v2 | https://www.protocols.io/view/culturing-3t3-cells-for-validating-gearbocs-constr-djks4kwe | Justin T Savage | TITLE: Culturing 3T3 Cells for Validating GEARBOCS Constructs
AUTHORS: Justin T Savage
[DESCRIPTION]
This protocol is for culturing Cas9 NIH/3T3 cells for the validation of GEARBOCS 2.0 and similar constructs for use in in vivo assays.
[STEPS]
1. Validation by indel sequencing in immortalized murine cell lines:
4. Se... | ["Validation by indel sequencing in immortalized murine cell lines:", "Seed Cas9 NIH/3T3 cells at 250k per well of a 6-well plate (if starting from frozen cells, you. will need to passage at least once prior to transfection. So thaw to 10cm dish, then passage to 6-well)", "24 hours after seeding, transfect Cas9 NIH/3T3... |
null | null | null | dx.doi.org/10.17504/protocols.io.u25eyg6 | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
Make sure all the necessary programs and dependencies are installed on your PC or server and work correctly.
[GUIDELINES]
Test data is available on the European Nucleotide Archive (ENA) website
https://www.ebi.ac.uk/ena/data/view/PRJEB21005
[STEPS]
SECTION: Basecalling of r... | ["[Basecalling of raw nanopore data with Albacore software.] {\"blocks\":[{\"key\":\"14f0i\",\"text\":\"\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"aeupm\",\"text\":\" \",\"type\":\"atomic\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[{\"offset\":... |
null | null | null | dx.doi.org/10.17504/protocols.io.nwydffw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a method for VSMC isolation from mouse aorta by an explant method adapted from Metz et al (2012).</p>
[STEPS]
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108,805 | Absolute quantification of AAV genomes from total DNA with digital droplet PCR (ddPCR) | 0 | dx.doi.org/10.17504/protocols.io.8epv5r84dg1b/v1 | https://www.protocols.io/view/absolute-quantification-of-aav-genomes-from-total-dnhd5b26 | Gerard Michael Coughlin | TITLE: Absolute quantification of AAV genomes from total DNA with digital droplet PCR (ddPCR)
AUTHORS: Gerard Michael Coughlin
[DESCRIPTION]
Accurate and absolute determination of AAV transduction from total DNA is important for understanding gene transfer efficiency across multiple experimental manipulations. As comp... | ["[Reagent set-up] Before beginning, ensure that you are able to specifically detect your AAV genome and design PCR reactions. We recommend using probe-based assays and designing 2 separate assays against distinct sequences in your target genome, with 2 separate fluorophores to detect each target sequence separately. D... |
72,198 | S1: Step-by-step-guide using image J in the work flow. | 5 | dx.doi.org/10.17504/protocols.io.81wgb61xolpk/v2 | https://www.protocols.io/view/s1-step-by-step-guide-using-image-j-in-the-work-fl-cireud3e | Paul Kalke, Conrad Helm | TITLE: S1: Step-by-step-guide using image J in the work flow.
AUTHORS: Paul Kalke, Conrad Helm
[DESCRIPTION]
How to use ImageJ in our 3D-workflow from data manipulation, import, alignment, segmentation and export as OBJ-file.
[STEPS]
1.
•Open Image J and import your Image Sequence
•It is possible in Image J to tra... | ["•Open Image J and import your Image Sequence\n•It is possible in Image J to transform stacks into Images Sequences and vice versa", "•Make sure your Image Sequence starts with 1 and choose Use virtual stack to save RAM\n•You can scale your data set down too", "•Make sure your data set is processablefor your computer\... |
null | null | null | dx.doi.org/10.17504/protocols.io.mdjc24n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Aim: To evaluate the efficacy and tolerability of replacing tetracycline with high dose of amoxicillin in bismuth-based quadruple therapy for H.pylori eradication.</p>
<p> </p>
<p>Methods: This randomized, open label clinical trial study was performed on 228 patients with H.p... | [] |
36,626 | PBS with 0.1% Sodium Azide | null | dx.doi.org/10.17504/protocols.io.bfzsjp6e | https://www.protocols.io/view/pbs-with-0-1-sodium-azide-bfzsjp6e | Allen Institute for Brain Science | TITLE: PBS with 0.1% Sodium Azide
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the method for preparing PBS with 0.1% Sodium Azide for storage and/or processing of fixed tissue.</div><div class = "text-block"><span style = "font-w... | [] |
99,436 | Embedding Four Brains For Serial Section Imaging | 0 | null | https://www.protocols.io/view/embedding-four-brains-for-serial-section-imaging-ddck22uw | Rob Campbell | TITLE: Embedding Four Brains For Serial Section Imaging
AUTHORS: Rob Campbell
[DESCRIPTION]
Describes how to embed four perfused mouse brains for serial section microscopy using the SWC's embedding molds.
[BEFORE_START]
A major advantage of serial sectioning is that it generates a seamless 3D data set that can be re... | ["[Preparing for agar embedding] Brains are to be suspended in a metal enclosure through which thin wires are inserted. We will mount the lower brains first. Insert 5 steel wires into mold as shown (colors on the tape are not meaningful).", "[Pouring the initial agar] Briefly shake the agar suspension then pour about 2... |
null | null | null | dx.doi.org/10.17504/protocols.io.mztc76n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>To MD analysis for one of our previous results of docking, for example to analyze the drug/target, almost 40 steps are required to finalize the MD results.</p>
<p> </p>
<p>The following protocol is according to our own experience in this project and was improved so that the e... | [] |
91,466 | Open Field Test | 1 | dx.doi.org/10.17504/protocols.io.36wgq3yz5lk5/v1 | https://www.protocols.io/view/open-field-test-c5jiy4ke | jillian.seiler | TITLE: Open Field Test
AUTHORS: jillian.seiler
[DESCRIPTION]
The Open Field Test is a measure of rodent anxiety-like behavior. The rodent’s natural “anxious” tendency is to spend time in the outer borders of the chamber, close to the walls; this is called thigmotaxis. A rodent exhibiting decreased anxiety will spend m... | ["[Procedure] Open Ethovision and apply necessary settings.", "[Procedure] If not done already, swab Open Field with 70% Ethanol and let dry.", "[Procedure] Grasp mouse lightly by the middle of the tail and place in center of the Open Field.", "[Procedure] Press “Start” in Acquisition window of Ethovision.", "[Procedur... |
63,894 | Is CarboFix the Ultimate Weight Loss Solution? | 1 | dx.doi.org/10.17504/protocols.io.x54v9yzqpg3e/v1 | https://www.protocols.io/view/is-carbofix-the-ultimate-weight-loss-solution-camwsc7e | kayelao | TITLE: Is CarboFix the Ultimate Weight Loss Solution?
AUTHORS: kayelao
[DESCRIPTION]
➢ Product Name — CarboFix
➢ Category — Weight Loss
➢ Side-Effects — NA
➢ Benefits— Weight Loss and Fat Burner
➢ Availability — Online
➢ Rating — ⭐⭐⭐⭐⭐
➢ Official Website (Sale Is Live) — Click Here to Buy CarboFix
CarboFix is a ... | [] |
95,638 | Senescence induction by DNA-damage in PCLS | 0 | dx.doi.org/10.17504/protocols.io.e6nvwdwpwlmk/v1 | https://www.protocols.io/view/senescence-induction-by-dna-damage-in-pcls-c9mwz47e | Delphine Beaulieu, Nayra Cardenes, Melanie Königshoff | TITLE: Senescence induction by DNA-damage in PCLS
AUTHORS: Delphine Beaulieu, Nayra Cardenes, Melanie Königshoff
[DESCRIPTION]
Precision-Cut Lung Slices (PCLS) are uniform, in size and thickness, tissue slices generated from human lungs that can be used for disease modeling, drug discovery and preclinical validation, ... | ["[Day -1: PCLS acclimation to growth conditions] Add 1 mL of media per well in 24-well plates DMEM F-12 media ( ) + 1% FBS + 1% Penicillin-Streptomycin + 0.3 µg/mL Amphotericin B .", "[Day -1: PCLS acclimation to growth conditions] Place one PCLS (1 cm diameter / 300 µm thick) per well with a brush.", "[Day -1: P... |
103,052 | Kinase activity assays Src and CK2 | 0 | dx.doi.org/10.17504/protocols.io.5jyl82by7l2w/v1 | https://www.protocols.io/view/kinase-activity-assays-src-and-ck2-dgvk3w4w | Elias Adriaenssens | TITLE: Kinase activity assays Src and CK2
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol details about the Kinase activity assays of Src and CK2.
[STEPS]
1. To verify the activity of kinases SRC and CK2, add 45 µL of mixes containing either only kinase
assay buffer (25 millimolar (mM) Tris-HCl pH 7.4, 150 mi... | ["To verify the activity of kinases SRC and CK2, add 45 µL of mixes containing either only kinase\nassay buffer (25 millimolar (mM) Tris-HCl pH 7.4, 150 millimolar (mM) NaCl, 1 millimolar (mM) DTT, and 2 millimolar (mM) MgCl2), kinase buffer and substrate \n(0.5 mg/mL) or kinase buffer, substrate (0.5 mg/mL) and kinase... |
76,687 | Co-extraction of RNA and DNA from plant tissue | 4 | dx.doi.org/10.17504/protocols.io.n2bvj8qxngk5/v1 | https://www.protocols.io/view/co-extraction-of-rna-and-dna-from-plant-tissue-cn5pvg5n | Dominik Buchner | TITLE: Co-extraction of RNA and DNA from plant tissue
AUTHORS: Dominik Buchner
[DESCRIPTION]
This protocol describes how to co-extract RNA and DNA from plant tissue samples. Samples are homogenized and simultaneously lyzed by bead-beating. Cell debris is then caught with a pre-filter column, the DNA is then subsequent... | ["[Sample preparation and lysis] For each sample prepare one 2 mL screwcap tube pre-filled with approximately 400 mg of 2 mm zirconia beads and 0.1 mm glass beads.", "[Sample preparation and lysis] Add up to 200 mg of plant tissue to the prepared tube.", "[Sample preparation and lysis] Add 800 µL to the sample tube.", ... |
39,591 | Direct wastewater RNA extraction via the "Milk of Silica (MoS)" method - A companion method to "Sewage, Salt, Silica and SARS-CoV-2 (4S)" | 4 | dx.doi.org/10.17504/protocols.io.biwfkfbn | https://www.protocols.io/view/direct-wastewater-rna-extraction-via-the-34-milk-o-biwfkfbn | Oscar Whitney, Basem Al-Shayeb, Alex Crits-Cristoph, Mira Chaplin, Vinson Fan, Hannah Greenwald, Adrian Hinkle, Rose Kantor, Lauren Kennedy, Anna Maurer, Robert Tjian, Kara L. Nelson, UC Berkeley Wastewater-based epidemiology consortium | TITLE: Direct wastewater RNA extraction via the "Milk of Silica (MoS)" method - A companion method to "Sewage, Salt, Silica and SARS-CoV-2 (4S)"
AUTHORS: Oscar Whitney, Basem Al-Shayeb, Alex Crits-Cristoph, Mira Chaplin, Vinson Fan, Hannah Greenwald, Adrian Hinkle, Rose Kantor, Lauren Kennedy, Anna Maurer, Robert Tjian... | ["[Preparing RNA wash buffers]\nPrepareeach of two wash buffers - Wash buffer #1 (4S-WB1) and #2 (4S-WB2), for later use during cleanup of RNA bound to silica particles.Prepare a \"Milk of Silica\" suspension of dry silica.\n1 L", "[Preparing RNA wash buffers]\n4S-WB1 composition: ABCD1ReagentOriginal molarity/%Final... |
69,560 | High content imaging of lysosomal phenotypes in iPSC-derived neurons using the Opera PhenixTM High-content Screening System | 1 | dx.doi.org/10.17504/protocols.io.yxmvm2oj9g3p/v1 | https://www.protocols.io/view/high-content-imaging-of-lysosomal-phenotypes-in-ip-cf6ytrfw | Jessica Chedid, Adahir Labrador-Garrido, Nicolas Dzamko | TITLE: High content imaging of lysosomal phenotypes in iPSC-derived neurons using the Opera PhenixTM High-content Screening System
AUTHORS: Jessica Chedid, Adahir Labrador-Garrido, Nicolas Dzamko
[DESCRIPTION]
This protocol describes the use of the Opera Phenix high-content screening system and its advanced software H... | ["[Lysosomal degradation capacity using DQ-red-BSA:] Using the “find nuclei” analysis block, with the channel in which the nuclei are stained (we used Hoechst) the user can choose the most accurate method out of 4 available and adjust parameters like threshold and splitting sensitivity for optimal Nuclei detection. The... |
41,408 | Agarose pads for microscopy | 4 | null | https://www.protocols.io/view/agarose-pads-for-microscopy-bkn8kvhw | Joao Vitor Molino | TITLE: Agarose pads for microscopy
AUTHORS: Joao Vitor Molino
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocols describe the steps required for the preparation of agarose pads for live cell fluorescent microscopy. </div></div>
[STEPS]
?. [Before start]
Check all the necessary material:... | ["[Before start]\nCheck all the necessary material:Glass slideCover slip Agarose (Agar should work as well, but probably with less imaging quality)Media or bufferChamber or well forming stick (ex: Frame-Seal™ in situ PCR and Hybridization Slide Chambers, 15 x 15 mm, 65 µl)Tube or flask for melting agarose1 mL plastic t... |
null | null | null | dx.doi.org/10.17504/protocols.io.kmncu5e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>We report a phylogeographic study of Chaetophractus villosus populations in Argentina. Control Region (CR) sequences (484 bp) were obtained for 76 C. villosus from 20 locations across the species whole distribution range. Seventeen new haplotypes were identified. The highest ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.fjnbkme | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
98,820 | In Vivo Metabolomics | 0 | dx.doi.org/10.17504/protocols.io.kqdg326b7v25/v1 | https://www.protocols.io/view/in-vivo-metabolomics-dcrc2v2w | Yoshitaka J Sei, Szu-Chi Liao, Johanna ten Hoeve-Scott, Ken Nakamura | TITLE: In Vivo Metabolomics
AUTHORS: Yoshitaka J Sei, Szu-Chi Liao, Johanna ten Hoeve-Scott, Ken Nakamura
[DESCRIPTION]
This protocol describes steps for targeting metabolites with [U-13C]glucose in mice for metabolomics analysis.
[STEPS]
SECTION: Tail vein infusion and tissue harvest
1. Materials
Surgical tools – sc... | ["[Tail vein infusion and tissue harvest] Materials\nSurgical tools – scissors, tweezers, forceps, spatula, razor\nHeating pad (K&H Thermo-Peep Heated Pad)\nTail illuminator (Braintree Scientific: MTI STD)\nGlue (Loctite 1699233)\n30g needles (BD: 305106)\nPE tubing (BD: PE#10)\nSyringe pump (WPI: SP220I)\n1mL syringes... |
77,644 | C-14 Fluroxypyr Acid Metabolite Extraction | 4 | dx.doi.org/10.17504/protocols.io.kqdg39yopg25/v1 | https://www.protocols.io/view/c-14-fluroxypyr-acid-metabolite-extraction-cp3kvqkw | olivia.todd, Scott Nissen | TITLE: C-14 Fluroxypyr Acid Metabolite Extraction
AUTHORS: olivia.todd, Scott Nissen
[DESCRIPTION]
This protocol details C-14 fluroxypyr acid metabolite extraction.
[STEPS]
SECTION: Treated Leaf Tissue
1. Remove the radioactive-herbicide treated leaf from the plant and wash in 10 mL of 10% MEOH or ACN plus 0.25% NIS ... | ["[Treated Leaf Tissue] Remove the radioactive-herbicide treated leaf from the plant and wash in 10 mL of 10% MEOH or ACN plus 0.25% NIS using the vortex mixer in a 20 ml scintillation vial.", "[Treated Leaf Tissue] Remove treated leaf from the scintillation vial and combine with the remaining shoot tissue. Add 10 mL o... |
28,954 | Lateral flow buildup | null | dx.doi.org/10.17504/protocols.io.8h2ht8e | null | Jorge Fernández | TITLE: Lateral flow buildup
AUTHORS: Jorge Fernández
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The following protocol describes how to build a half-strip simplified lateral flow sensor. Preparation of test strips, detection reagents immobilization and test development.</div><div class = "text-... | ["[Strips preparation]\nCut 4 pieces of 5mm wide x 40 mm long strips from the nitrocellulose FF80HP membrane. Label in the plastic backing of the membranes T or C where the Control or Test dots will be deposited. The dots will be positioned at 15 mm and 25 mm from the bottom of the strip. Alternating their order in t... |
41,881 | CRISPR-Enhance Lateral Flow Assay | 4 | dx.doi.org/10.17504/protocols.io.bk5zky76 | https://www.protocols.io/view/crispr-enhance-lateral-flow-assay-bk5zky76 | Piyush Jain, Long T Nguyen, Santosh Rananaware | TITLE: CRISPR-Enhance Lateral Flow Assay
AUTHORS: Piyush Jain, Long T Nguyen, Santosh Rananaware
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The CRISPR-Enhance SARS-CoV-2 detection kit has been designed to detect fragments of the Nucleocapsid (“N”) gene and Envelope gene (E) of SARS-CoV-2. An i... | ["[Nucleic Acid Extraction]\nAdd of patient sample to of pre-aliquoted QuickExtract solution. Heat the above mixture at for followed by for .\n10 µl\n10 µl\n65 °C\n98 °C", "[RT-LAMP Master Mix Preparation]\nLabel a new microcentrifuge tube for each target ( N, E and RP) and prepare a RT-LAMP Master Mix consisti... |
44,318 | 3' RNA Adapter Ligation to Input RNA | 4 | dx.doi.org/10.17504/protocols.io.bph6mj9e | https://www.protocols.io/view/3-39-rna-adapter-ligation-to-input-rna-bph6mj9e | Eric L. Van Nostrand, Thai B. Nguyen, Chelsea Gelboin-Burkhart, Ruth Wang, Steven M. Blue, Gabriel A. Pratt, Ashley L. Louie, Gene W. Yeo | TITLE: 3' RNA Adapter Ligation to Input RNA
AUTHORS: Eric L. Van Nostrand, Thai B. Nguyen, Chelsea Gelboin-Burkhart, Ruth Wang, Steven M. Blue, Gabriel A. Pratt, Ashley L. Louie, Gene W. Yeo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Profiling of RNA binding protein targets in vivo provides... | ["[Anneal Adapter]\nTake (from Dephosphorylation of Input RNA).\n[RNA]", "[Anneal Adapter]\nAdd and (see Note 3).\n[100% DMSO]\n[InvRiL19 adapter]", "[Anneal Adapter]\nIncubate at for . Place >.\n65 °C\non ice", "[Prepare Ligation Master Mix; 13.5 μL Per Sample]\nAB110× Ligase Buffer (with DTT)2.0 μL20.1 M ATP0.2 ... |
68,679 | RT-qPCR for detection of SARS-CoV-2 in wastewater | 4 | dx.doi.org/10.17504/protocols.io.x54v9j971g3e/v2 | https://www.protocols.io/view/rt-qpcr-for-detection-of-sars-cov-2-in-wastewater-cfbftijn | David Findlay, Julie Bolland, Brindusa Cerghizan, Kirsty Campbell, David Thomson, Alexander Corbishley, David Gally, Stephen Fitzgerald, Alison Tidswell, Sean McAteer, Livia C T Scorza | TITLE: RT-qPCR for detection of SARS-CoV-2 in wastewater
AUTHORS: David Findlay, Julie Bolland, Brindusa Cerghizan, Kirsty Campbell, David Thomson, Alexander Corbishley, David Gally, Stephen Fitzgerald, Alison Tidswell, Sean McAteer, Livia C T Scorza
[DESCRIPTION]
As part of the global response to the 2019 novel Coro... | ["[Sample and equipment setup] At start of day, clean all surfaces with RNase away or 10% v/v bleach solution.", "[Sample and equipment setup] Turn on UV lamps in the Master Mix preparation cabinet and Template addition cabinet for 20 minutes.", "[Sample and equipment setup] Prior to analysis; ensure there are sufficie... |
28,969 | Fluorescent in vitro model to assess adhesion and invasion of Bd in PAK | null | dx.doi.org/10.17504/protocols.io.8ihhub6 | null | Elin Verbrugghe | TITLE: Fluorescent in vitro model to assess adhesion and invasion of Bd in PAK
AUTHORS: Elin Verbrugghe
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The largest current disease-induced loss of vertebrate biodiversity is due to chytridiomycosis and despite the increasing understanding of th... | ["Prepare Cell Medium A: L15 medium: 70%Distilled water: 20%Fetal bovine serum 10%", "Prepare Cell Medium B: L15 medium: 40%Distilled water: 55%Fetal bovine serum: 5%", "Coat coverslips with Rat tail collagen: Add glass coverslips in a 24-well tissue culture plate. Coat the glass coverslips at 37°C for 2 hours. Therefo... |
109,127 | AAV-Zombie on cultured cells | 0 | dx.doi.org/10.17504/protocols.io.36wgqnz53gk5/v3 | https://www.protocols.io/view/aav-zombie-on-cultured-cells-dntf5ejn | Gerard Michael Coughlin | TITLE: AAV-Zombie on cultured cells
AUTHORS: Gerard Michael Coughlin
[DESCRIPTION]
Detection of AAV genomes in situ can facilitate understanding of AAV transduction and processing. This protocol enables detection of AAV genomes and concatemers in cultured cells and is based on the Zombie method published in Askary et ... | ["[Reagent set up] General note on reagents and consumables", "[Sample preparation] At time of collection, aspirate media and wash cells one time with 1 mL DPBS. Aspirate DPBS and add 1 mL ice-cold MAA fixation buffer. Transfer to -20 °C for 15 min .", "[Sample preparation] Transduce cells with AAVs carrying Zombie ba... |
null | null | null | dx.doi.org/10.17504/protocols.io.giubuew | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 1">
<div class="layoutArea">
<div class="column">The <strong>DNA Clean & Concentrator™-5 (DCC™-5)</strong> provides a hassle-free method for the rapid purification and concentration of high-quality DNA from PCR, endonuclease digestions, cell lys... | [] |
81,823 | NCEM Drop - Tissue Dounce Homogenisation (TM-014) | 4 | dx.doi.org/10.17504/protocols.io.eq2ly7odwlx9/v1 | https://www.protocols.io/view/ncem-drop-tissue-dounce-homogenisation-tm-014-ct57wq9n | sandra.crameri | TITLE: NCEM Drop - Tissue Dounce Homogenisation (TM-014)
AUTHORS: sandra.crameri
[DESCRIPTION]
tissue dounce homogenisation
[STEPS]
SECTION: HEADER
1. SAN:
SPEC No:
OPERATOR:
SECTION: Conventional
7. Adsorb 10 µL sample to grid 10 min , inspect to ensure sample does not dry out.
SECTION: Conventional
8. D... | ["[HEADER] SAN:\n\n\n\n\nSPEC No:\n\n\n\n\nOPERATOR:", "[Conventional] Adsorb 10 µL sample to grid 10 min , inspect to ensure sample does not dry out.", "[Conventional] Drain excess sample from grid using filter paper, leave wet.", "[Conventional] Stain 1 min", "Drain & dry using filter paper", "[Dounce Homogenisation... |
null | null | null | dx.doi.org/10.17504/protocols.io.jdhci36 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A guide to reading and extracting key points from research articles. This protocol will suit the purposes of the assignments to summarize the readings for the class. Aim for roughly one page of typed text.</p>
<p> </p>
<p>Imagine presenting the contents of your summary (exclu... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.mixc4fn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>PreC-C Primers encompass described PreC-C mutations: mutation G1896A in the PreC region and mutations A1762T and G1764A in C-gene promotor. Primers were modified according to literature-based alignment, in order to optimize the amplification of all HBV genotypes. Sequence ana... | [] |
97,019 | Quality assessment for images obtained using 3D printed stereotaxic frame | 0 | dx.doi.org/10.17504/protocols.io.4r3l2qmn3l1y/v1 | https://www.protocols.io/view/quality-assessment-for-images-obtained-using-3d-pr-day32fyn | Lucy Liang, David J Schaeffer, Tales Santini, Isabela Zimmermann Rollin, Elvira Pirondini | TITLE: Quality assessment for images obtained using 3D printed stereotaxic frame
AUTHORS: Lucy Liang, David J Schaeffer, Tales Santini, Isabela Zimmermann Rollin, Elvira Pirondini
[DESCRIPTION]
This protocol describes the steps taken to assess whether MR signal noise and distortion is introduced by utilization of a 3D... | ["[Image Acquisitions] Acquire MRI using gradient-echo sequences in the 7T MRI scanner (Magnetom, Siemens Healthcare, Erlangen, Germany) with the following parameters:\nTE/TR=8.16/40 ms\nresolution 400 μm isotropic (same as what you will acquire for your target structure)\nmatrix size=176×384×384\nflip angle=15°\naccel... |
53,112 | eDNA extraction: phenol-chloroform-isoamyl alcohol DNA purification from filters stored in Longmire buffer | 1 | dx.doi.org/10.17504/protocols.io.bx4ypqxw | https://www.protocols.io/view/edna-extraction-phenol-chloroform-isoamyl-alcohol-bx4ypqxw | Abigail Wells, Linda Park | TITLE: eDNA extraction: phenol-chloroform-isoamyl alcohol DNA purification from filters stored in Longmire buffer
AUTHORS: Abigail Wells, Linda Park
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is an organic DNA extraction method for filters preserved in 2 ml of Longmire buffer that uses a p... | ["[DNA extraction]\nheat-shock\tFilters in of at for and then allow samples to cool to room temperature\n2 mL\n95 °C\n[min]\n{\"blocks\":[{\"key\":\"5iktf\",\"text\":\"Lysis buffer recipe (Longmire et al 1997): \",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"6l... |
101,065 | MAD4HatTeR | 4 | dx.doi.org/10.17504/protocols.io.14egn779mv5d/v4 | https://www.protocols.io/view/mad4hatter-dexh3fj6 | Andres Aranda-Diaz, eric.neubauervickers | TITLE: MAD4HatTeR
AUTHORS: Andres Aranda-Diaz, eric.neubauervickers
[DESCRIPTION]
This protocol has been adapted from Paragon Genomics CleanPlex® NGS Panel
Information about the primer pools can be found here
[BEFORE_START]
A version of this protocol made an SOP in pdf format, including a didactic version, can be... | ["[mPCR] Add DNA", "[mPCR] Run PCR reaction on a thermocycler (in a separate room)\nInitial denaturation: 95 °C 10 min \nDenaturation: 98 °C 15 s with ramping 3 °C \nAnnealing/Extension: 60 °C 5 min with ramping 2 °C \nRepeat Denaturation and Annealing/Extension for X total cycles (see below). \n \nHold at 10 °C", "[Re... |
102,391 | IF Labeling Protocol | 0 | dx.doi.org/10.17504/protocols.io.4r3l2q6rql1y/v1 | https://www.protocols.io/view/if-labeling-protocol-df8x3rxn | Scott Vermilyea | TITLE: IF Labeling Protocol
AUTHORS: Scott Vermilyea
[DESCRIPTION]
This protocol details the Labelling of Immunofluorescent Protein.
[STEPS]
SECTION: Immunofluorescent Protein Labeling Protocol
1. Alex Fluor 488 Microscale Protein Labelling Kit (Invitrogen, A30006).
SECTION: Immunofluorescent Protein Labeling Protoco... | ["[Immunofluorescent Protein Labeling Protocol] Alex Fluor 488 Microscale Protein Labelling Kit (Invitrogen, A30006).", "[Immunofluorescent Protein Labeling Protocol] According to manufacturer protocol, AF 488 reactive dye has Tetrafluorophenyl (TFP) ester moiety that is more stable in solution than the commonly used s... |
59,930 | Preparation of BSA complexed free fatty acids for in vitro studies | 4 | dx.doi.org/10.17504/protocols.io.b6r2rd8e | https://www.protocols.io/view/preparation-of-bsa-complexed-free-fatty-acids-for-b6r2rd8e | Caroline CT Tremblay, Julien Ghislain, Vincent Poitout | TITLE: Preparation of BSA complexed free fatty acids for in vitro studies
AUTHORS: Caroline CT Tremblay, Julien Ghislain, Vincent Poitout
[DESCRIPTION]
This protocol describes the steps to prepare a fatty acid:BSA complex in cell culture media. It is suitable for the treatment of primary tissue (eg. isolated islets... | ["[Preparation of BSA:FA complex] Preparation of Palmitate (PA) and Oleate (OA) stock solutions\nAs PA and OA are in powder form and very hydrostatic, handle with care as the powder will stick to everything and move about readily.\n\nCarefully weigh out a sufficient amount of each to make 150 millimolar (mM) stock so... |
54,820 | Identifying ZooMS Spectra (mammals) using mMass | 5 | dx.doi.org/10.17504/protocols.io.bzscp6aw | https://www.protocols.io/view/identifying-zooms-spectra-mammals-using-mmass-bzscp6aw | Samantha Brown | TITLE: Identifying ZooMS Spectra (mammals) using mMass
AUTHORS: Samantha Brown
[DESCRIPTION]
This is a guide to identifying ZooMS spectra for mammals using the open-source program mMass (Niedermeyer and Strohalm 2012). This guide is intended as a learning tool for students and researchers at the University of Tubinge... | ["[Before you start] In this guide, you will learn the basics of identifying ZooMS spectra. This guide is based on using the nine ZooMS peptide markers (hereafter referred to as \"markers\") listed in Welker et al., 2016. There are several new markers that have since been published for certain taxa, however, we recomme... |
46,262 | Environmental Grab Sampling and Membrane Filtration | 4 | null | https://www.protocols.io/view/environmental-grab-sampling-and-membrane-filtratio-brewm3fe | Dilip Abraham, Nicola Elviss, Nicholas Feasey, Nick Grassly, Jacob John, Gagandeep Kang, John Scott Meschke, Venkata Raghava Mohan, Satheesh Nair, Jonathan Rigby, Rajan Srinivasan, Catherine Troman, Christopher Uzzell, Nicolette Zhou | TITLE: Environmental Grab Sampling and Membrane Filtration
AUTHORS: Dilip Abraham, Nicola Elviss, Nicholas Feasey, Nick Grassly, Jacob John, Gagandeep Kang, John Scott Meschke, Venkata Raghava Mohan, Satheesh Nair, Jonathan Rigby, Rajan Srinivasan, Catherine Troman, Christopher Uzzell, Nicolette Zhou
[DESCRIPT... | ["[Sample Collection] Using a bucket or another method, fill a 1L collection container with sewage or wastewater and securely close the container.", "[Sample Processing] Upon receipt in the lab the sample should be stored at 4-8ºC until filtration", "[Sample Processing] Assemble the membrane filtration apparatus accord... |
49,057 | Brain Slicing for Immunohistochemistry | 4 | null | https://www.protocols.io/view/brain-slicing-for-immunohistochemistry-bt59nq96 | Angelica Martinez, McKenzie Pavlich, Caitlin Crook, Kokila Shankar, Giordano De Guglielmo, Olivier George | TITLE: Brain Slicing for Immunohistochemistry
AUTHORS: Angelica Martinez, McKenzie Pavlich, Caitlin Crook, Kokila Shankar, Giordano De Guglielmo, Olivier George
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol is used for sectioning brains in order to use in downstream IHC experiments.</d... | ["Wash brain with 1x", "Dispose of the current solution that brain is in into the proper waste stream", "Transfer brain into with of 1x PBS. Invert the tube to wash and pour out PBS.\n20 mL", "Repeat 2x for a total of 3 washes", "Place cleaned brain flat onto petri dish. Using straight razor blade, cut of back half of... |
85,662 | Pythium Zoospore Production Soaking Solution | 4 | null | https://www.protocols.io/view/pythium-zoospore-production-soaking-solution-cxv6xn9e | Nimalka M Weerasuriya | TITLE: Pythium Zoospore Production Soaking Solution
AUTHORS: Nimalka M Weerasuriya
[DESCRIPTION]
Creation of soaking solutions for Pythium myriotylum to be used for large-scale zoospore production.
[STEPS]
SECTION: Soaking Solutions
2. Make soaking solutions 1, 2 and 3:
SECTION: Preparation
1. Have mature colonie... | ["[Soaking Solutions] Make soaking solutions 1, 2 and 3:", "[Preparation] Have mature colonies of verified Pythium myriotylum growing on CMA or 1.5-2% WA. Colony maturity ~7 days, with visible oospores.", "[Soaking Solutions] Soaking Solution #1, 0.01 Molarity (m) (1 L):\n1 L RO water at pH 7 in 1 L beaker\nAdd 1 g CaC... |
74,733 | P8 COMPROMISO DOCUMENTAL | 1 | dx.doi.org/10.17504/protocols.io.81wgbyno3vpk/v1 | https://www.protocols.io/view/p8-compromiso-documental-ck8muzu6 | cgarcia | TITLE: P8 COMPROMISO DOCUMENTAL
AUTHORS: cgarcia
[DESCRIPTION]
La Universidad Católica establecerá las funciones de supervisión de los doctorandos mediante un compromiso documental firmado por: la universidad, el doctorando, su tutor y su director. Este compromiso será rubricado a la mayor brevedad posible después de ... | ["[P8 COMPROMISO DOCUMENTAL] El tutor, en la primera reunión mantenida con el doctorando tras su matriculación en el programa de doctorado, explicará al alumno como generar el documento descargando el modelo a través del Portal del Doctorando. En dicho documento se detallará la dedicación del doctorando al programa y e... |
69,319 | Effects of the ketogenic diet on muscle hypertrophy in re-sistance-trained men and women: a systematic review & me-ta-analysis | 1 | dx.doi.org/10.17504/protocols.io.4r3l27m9qg1y/v1 | https://www.protocols.io/view/effects-of-the-ketogenic-diet-on-muscle-hypertroph-cfxftpjn | Salvador Vargas Molina, José Luis Gomez Urquiza, Jerónimo García Romero, Javier Benítez Porres | TITLE: Effects of the ketogenic diet on muscle hypertrophy in re-sistance-trained men and women: a systematic review & me-ta-analysis
AUTHORS: Salvador Vargas Molina, José Luis Gomez Urquiza, Jerónimo García Romero, Javier Benítez Porres
[DESCRIPTION]
Reviews focused on the ketogenic diet (KD) based on the increas... | ["Effect of the ketogenic diets on muscle hypertrophy in resistance-trainined men and women: a systematic review & meta-analysis\n\nCitation\n\nSalvador Vargas-Molina, José Luis Gómez-Urquiza, Jernónimo García-Romero, Javier Benítez-Porres. Effects of the ketogenic diets on muscle hypertrophy in resistance-trained men ... |
56,007 | Whole mount immunohistochemistry (WM-IHC) | 1 | dx.doi.org/10.17504/protocols.io.b2xfqfjn | https://www.protocols.io/view/whole-mount-immunohistochemistry-wm-ihc-b2xfqfjn | Marta Wawrzyniak, Nathalie Weber, Simon Blanchoud | TITLE: Whole mount immunohistochemistry (WM-IHC)
AUTHORS: Marta Wawrzyniak, Nathalie Weber, Simon Blanchoud
[DESCRIPTION]
This protocol has been successfully used with colonial tunicates has been adapted to these animals based on the following publication:
The onset of whole-body regeneration in Botryllus schloss... | ["[Fixation] Anesthetize the animals following this protocol. See Whole colony fixation V.1.", "[Fixation] Fix the animals in 4% PFA at Room temperature . See Whole colony fixation V.1.", "[Day 1] Wash in 3.3x PBS for 30 min and then in 1x PBS 60 min . Store at 4 °C .", "[Day 1]", "[Fixation] Clean the slide with the... |
97,447 | How to request an assisted sorting session for the first time | 0 | null | https://www.protocols.io/view/how-to-request-an-assisted-sorting-session-for-the-dbef2jbn | Daniel Gimenes | TITLE: How to request an assisted sorting session for the first time
AUTHORS: Daniel Gimenes
[DESCRIPTION]
Step by step protocol to create a PPMS account and to find the "Preliminary Sorting Discussion" form.
[STEPS]
SECTION: Creating a PPMS account
1. If you already have a PPMS account, please proceed to the step 6.... | ["[Creating a PPMS account] If you already have a PPMS account, please proceed to the step 6. If not, access the following link: https://ppms.embl.de/start/", "[Creating a PPMS account] Click on Flow Cytometry Core Facility", "[Creating a PPMS account] Click on \"user account creation request\".", "[Creating a PPMS acc... |
19,485 | Nsil1-Msp1 RAD-digest Detailed Protocol | null | dx.doi.org/10.17504/protocols.io.w95fh86 | null | Ben Sutherland, Claire Rycroft, Kristina Miller | TITLE: Nsil1-Msp1 RAD-digest Detailed Protocol
AUTHORS: Ben Sutherland, Claire Rycroft, Kristina Miller
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol comes with no guarantees, and is primarily used for the authors’ purposes. This protocol is an adaptation from the work in the followi... | ["[Adapter Suspension, Dilution, Annealing and Working Stock]\nSuspend lyophilized single stranded adapters to final stock concentration of 100µM in 1XEB.\n-Adapter 1 top and bottom will be combined in plate format. Each well corresponding to an individual adapter.-Adapter 2 top and bottom will be combined in strip tub... |
73,898 | High-molecular-weight DNA extraction from cheese rind microbial communities | 4 | dx.doi.org/10.17504/protocols.io.rm7vzbkj8vx1/v1 | https://www.protocols.io/view/high-molecular-weight-dna-extraction-from-cheese-r-ckeiutce | Emily C.P. Weiss | TITLE: High-molecular-weight DNA extraction from cheese rind microbial communities
AUTHORS: Emily C.P. Weiss
[DESCRIPTION]
This protocol describes extracting high-molecular-weight DNA from cheese rind microbial community samples. This DNA is suitable for Oxford Nanopore long-read sequencing.
[STEPS]
SECTION: Prepare ... | ["[Prepare TLB] Prepare a minimum of 4 mL of Tris Lysis Buffer (TLB) per extraction sample.\nFinal concentrations:\n10 mM Tris-Cl, pH 8\n100 mM EDTA, pH 8\n1% SDS\n10 mg/mL lysozyme", "[Prepare TLB] Cool to room temperature and then add RNase A to a final concentration of 20 μg/mL.", "[Prepare TLB] Heat the prepared bu... |
80,059 | Deposition of matrix using an M5 TM sprayer for high resolution MALDI analysis | 1 | dx.doi.org/10.17504/protocols.io.yxmvmnzmbg3p/v3 | https://www.protocols.io/view/deposition-of-matrix-using-an-m5-tm-sprayer-for-hi-cse3wbgn | Martin Dufresne, Angela Kruse, Jamie Allen, Danielle Gutierrez, Jeff Spraggins | TITLE: Deposition of matrix using an M5 TM sprayer for high resolution MALDI analysis
AUTHORS: Martin Dufresne, Angela Kruse, Jamie Allen, Danielle Gutierrez, Jeff Spraggins
[DESCRIPTION]
This protocol describes the use of an HTX M5 TM sprayer to deposit small molecule matrices onto tissue sections for high resolutio... | ["[Autofluorescence Scan] Remove slides from freezer and place in desiccator for 30 min", "[Autofluorescence Scan] Collect autofluorescence scan using a Zeiss AxioScan Z1: Pre-IMS Autofluorescence Microscopy", "[TM Sprayer Setup] Set nitrogen flow to 8 psi. turn on TM sprayer.", "[TM Sprayer Setup] Open HTX software", ... |
48,098 | Auto-Block Plus Digester Protocol | 1 | null | https://www.protocols.io/view/auto-block-plus-digester-protocol-bs8anhse | William Brigman, Paul Shumaker | TITLE: Auto-Block Plus Digester Protocol
AUTHORS: William Brigman, Paul Shumaker
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Previous Auto-Block Digester protocols developed by Aprel Ellison and Paul Shumaker</div></div>
[STEPS]
?. [DAY 1]
Pipette 5mL (liquids) or weigh 0.15g (solids) into dige... | ["[DAY 1]\nPipette 5mL (liquids) or weigh 0.15g (solids) into digestion tubes (always include at the end of the samples 2 blanks and 2 standards– see “standard section” for more detail)(Up to 50 samples + 2 standards + 2 blanks = 54 total)", "[DAY 1]\nNumber the digestion tubes accordingly.", "[DAY 1]\nPlace disposable... |
108,018 | Multiplex Nested PCR for Vibrio Cholera | 0 | dx.doi.org/10.17504/protocols.io.36wgqnzbkgk5/v1 | https://www.protocols.io/view/multiplex-nested-pcr-for-vibrio-cholera-dmqs45we | Shannon Fitz, Alex Shaw, Dilip Abraham, michael Owusu | TITLE: Multiplex Nested PCR for Vibrio Cholera
AUTHORS: Shannon Fitz, Alex Shaw, Dilip Abraham, michael Owusu
[DESCRIPTION]
Primers targeting various regions of the V. Cholera genome were obtained from the literature or designed, and optimized for a multiplex nested PCR assay.
The following primers were extracted fr... | ["[Multiplex nested PCR for V.Cholera] Assemble primer pool: \n \n \nBands for the V. cholera reactions: \n \n Reconstitute primers to 100 µM using nuclease-free water (or if primer manufacturer recommends otherwise, follow their recommendations for reconstituting primers).\n\n Create working stocks of 10 µM using nucl... |
24,004 | Over Expression and Rescue Constructs | null | dx.doi.org/10.17504/protocols.io.3pcgmiw | null | Yaowu Yuan | TITLE: Over Expression and Rescue Constructs
AUTHORS: Yaowu Yuan
[STEPS]
?. [PCR Insert and Purify]
Use a high-fidelity enzyme (Phusion) to amplify your insert. AB1PCR1x2dH2O12.0 µL35x Phusion Buffer4.0 µL4dNTPs (10mM)0.4 µL5DMSO (100%)0.6 µL6F Primer (5µM)*1.0 µL7R Primer (5µM)1.0 µL8Template1.0 µL9Phusion Enzyme**0... | ["[PCR Insert and Purify]\nUse a high-fidelity enzyme (Phusion) to amplify your insert. AB1PCR1x2dH2O12.0 µL35x Phusion Buffer4.0 µL4dNTPs (10mM)0.4 µL5DMSO (100%)0.6 µL6F Primer (5µM)*1.0 µL7R Primer (5µM)1.0 µL8Template1.0 µL9Phusion Enzyme**0.2 µL10Total20 µL\nAB1PCR1x2dH2O12.0 µL35x Phusion Buffer4.0 µL4dNTPs (10m... |
42,800 | Lipids annotation of Nano-DESI MSI datasets | 1 | dx.doi.org/10.17504/protocols.io.bm2qk8dw | https://www.protocols.io/view/lipids-annotation-of-nano-desi-msi-datasets-bm2qk8dw | yang1832 , Julia Laskin | TITLE: Lipids annotation of Nano-DESI MSI datasets
AUTHORS: yang1832 , Julia Laskin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Scope: </div><div class = "text-block">Annotate lipid species detected by Nano-DESI IMS analysis.</div><div class = "text-block">Expected Outcome:</div><div class = "te... | ["Create mass list from the averaged spectrum.", "Use LIPIDMAPS database to annotate each m/z value with the following search criteria:https://www.lipidmaps.org/resources/tools/bulk_structure_searches.php?database=COMP_DB1a. Positive Mode Adducts: [M+H]+, [M+Na]+, [M+K]+1b. Negative Mode Adducts: [M-H]-2. Specify Mas... |
56,521 | Protocol for CODEX Fixation Steps and Primary Antibody Staining for Induced Pluripotent Stem Cell-Derived Neurons | 1 | dx.doi.org/10.17504/protocols.io.b3fhqjj6 | https://www.protocols.io/view/protocol-for-codex-fixation-steps-and-primary-anti-b3fhqjj6 | Faria Zafar, Alejandra Torres, Laurin Heinrich, Jasmine Singh, Cassandra Hempel, Oliver Braubach, Birgitt Schuele | TITLE: Protocol for CODEX Fixation Steps and Primary Antibody Staining for Induced Pluripotent Stem Cell-Derived Neurons
AUTHORS: Faria Zafar, Alejandra Torres, Laurin Heinrich, Jasmine Singh, Cassandra Hempel, Oliver Braubach, Birgitt Schuele
[DESCRIPTION]
CO-Detection by indEXing (CODEX) is a powerful technique ... | ["[A. Pre-staining first fixation (under the chemical hood)] Add an equal volume (1.5 mL) of 4% paraformaldehyde (PFA; prepare fresh 4% PFA with PBS from 32% PFA stock) for 5 min at room temperature (RT). The final PFA concentration is 2%.", "[A. Pre-staining first fixation (under the chemical hood)] Add 3 mL 4% PFA to... |
31,336 | Latkes done properly | null | dx.doi.org/10.17504/protocols.io.baugietw | null | Lenny Teytelman | TITLE: Latkes done properly
AUTHORS: Lenny Teytelman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This recipe is a traditional Eastern-European Jewish latkes (potato pancakes). This fork is my mom's recipe . It's not vegan. We eat them with spicy cranberry sauce, apples sauce and/or sour cream. ... | ["Do not peel! No need to peel! Wash 6 Russet potatoes.", "Cut up the potatoes to large chunks. Put them in a food processor bowl. Using chopping blade in bowl process JUST until the pototoes are chopped in pieces 2 mm long (like very big rice perhaps). Some larger chunks will remain. Do not over process. Should not... |
29,236 | METHOD FOR THE METABOLIC PROFILE OF PLANT TISSUES BY GAS CHROMATOGRAPHY COUPLED TO MASS SPECTROMETRY (GC/MS) | null | dx.doi.org/10.17504/protocols.io.8suhwew | null | Nívea M. Vieira, Camilo E. Vital, Claudia S.L. Pontes, Pedro M. Vidigal, Jenny D. Gómez, Edvaldo Barros, Humberto Ramos | TITLE: METHOD FOR THE METABOLIC PROFILE OF PLANT TISSUES BY GAS CHROMATOGRAPHY COUPLED TO MASS SPECTROMETRY (GC/MS)
AUTHORS: Nívea M. Vieira, Camilo E. Vital, Claudia S.L. Pontes, Pedro M. Vidigal, Jenny D. Gómez, Edvaldo Barros, Humberto Ramos
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div cl... | ["[METABOLITE EXTRACTION]\n1) Collect samples of plant tissues, immediately freeze in liquid nitrogen and store them in freezer -80°C until use.2) Macerate the samples in liquid nitrogen using mortar and pestle. Do not allow to thaw. Weigh approximately 100mg of each sample into microtubes (2ml) and annotate the weight... |
38,733 | Virtual Screening for insilico drug designing | 4 | dx.doi.org/10.17504/protocols.io.bh3mj8k6 | https://www.protocols.io/view/virtual-screening-for-insilico-drug-designing-bh3mj8k6 | Maria . | TITLE: Virtual Screening for insilico drug designing
AUTHORS: Maria .
[STEPS]
?. 1Retrieval and Refinement of Crystal Structure
?. 2Combinatorial Library Designing
?. 3Docking and Virtual Screening
?. 4Docking Protocol applied by MOE
?. 5Docking Analysis | ["1Retrieval and Refinement of Crystal Structure", "2Combinatorial Library Designing", "3Docking and Virtual Screening", "4Docking Protocol applied by MOE", "5Docking Analysis"] |
84,159 | Rapalog-induced chemical dimerization experiments | 4 | dx.doi.org/10.17504/protocols.io.n92ldmyynl5b/v1 | https://www.protocols.io/view/rapalog-induced-chemical-dimerization-experiments-cwe7xbhn | Elias Adriaenssens | TITLE: Rapalog-induced chemical dimerization experiments
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol describes Rapalog-induced chemical dimerization experiments.
[STEPS]
SECTION: Rapalog-induced chemical dimerization experiments
1. To perform chemical-induced dimerization (CID) experiments we will first e... | ["[Rapalog-induced chemical dimerization experiments] To perform chemical-induced dimerization (CID) experiments we will first establish cell lines expressing the FRB-Fis1 and FKBP-GFP-GOI (FKBP-GFP fused to our gene of interest).", "[Rapalog-induced chemical dimerization experiments] HeLa cells are consecutively trans... |
63,819 | Wastewater QC workflow in GalaxyTrakr (SSQuAWK4) | 1 | null | https://www.protocols.io/view/wastewater-qc-workflow-in-galaxytrakr-ssquawk4-cajjsckn | Jasmine Amirzadegan, Tunc Kayikcioglu, hugh.rand , Ruth Timme, Maria Balkey | TITLE: Wastewater QC workflow in GalaxyTrakr (SSQuAWK4)
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 SSQuAWK3: SARS - CoV - 2 Sequence Quality Assuranc... | ["[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... |
31,085 | Image analysis of immediate early gene expression in spinal cord sections | null | dx.doi.org/10.17504/protocols.io.bakmicu6 | https://www.protocols.io/view/image-analysis-of-immediate-early-gene-expression-bakmicu6 | Janet Keast, Peregrine Osborne, Nicole Wiedmann | TITLE: Image analysis of immediate early gene expression in spinal cord sections
AUTHORS: Janet Keast, Peregrine Osborne, Nicole Wiedmann
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used for analysing expression pattens of immediate early gene products (e.g., c-Fos) in immunosta... | ["[Creating an image mask]\nUsing Adobe Photoshop (or similar program) open the image of the spinal cord section to create an image mask. Create a new “layer”.", "[Using the image mask]\nPaste the mask onto the image for counting. This will add a new layer. Using the 'free transform' tool, scale and rotate the mask to ... |
57,756 | Protocol - A systematic review and meta-analysis on impact of suboptimal use of antidepressants, bisphosphonates, and statins on healthcare resource utilisation and healthcare cost | 3 | dx.doi.org/10.17504/protocols.io.b4m4qu8w | https://www.protocols.io/view/protocol-a-systematic-review-and-meta-analysis-on-b4m4qu8w | Kyu Hyung Park | TITLE: Protocol - A systematic review and meta-analysis on impact of suboptimal use of antidepressants, bisphosphonates, and statins on healthcare resource utilisation and healthcare cost
AUTHORS: Kyu Hyung Park
[DESCRIPTION]
We conduct a systematic literature review and meta-analysis for the impact of adherence to a... | [] |
44,308 | Generation of hESC/iPSC Derived Midbrain Dopamine Neurons | 4 | dx.doi.org/10.17504/protocols.io.kxygxpzjzl8j/v1 | https://www.protocols.io/view/generation-of-hesc-ipsc-derived-midbrain-dopamine-bphumj6w | Su-Chun Zhang | TITLE: Generation of hESC/iPSC Derived Midbrain Dopamine Neurons
AUTHORS: Su-Chun Zhang
[DESCRIPTION]
This protocol details methods for generating Midbrain Dopamine Neuronds from hESC or iPSC sources.
[BEFORE_START]
Induction of the midbrain dopaminergic progenitors was carried out based on protocol described previo... | ["[Pre-differentiation and Differentiation (Day 1-6)] Briefly, culture hESCs (1 day after passaging) on MEF feeder layer in the neural induction medium (NIM) (DMEM/F-12, 1X NEAA, 1X N2 supplement) supplemented with 10 micromolar (µM) and 2 micromolar (µM). \n\nTo pattern the differentiating cells to the midbrain FP pro... |
4,549 | CagA phosphorylation assay and its semiquantitative analysis | 1 | dx.doi.org/10.17504/protocols.io.j8nlk8x6l5r7/v1 | https://www.protocols.io/view/caga-phosphorylation-assay-and-its-semiquantitativ-gpdbvi6 | Anna F. Zeitler, Luisa F Jimenez-Soto | TITLE: CagA phosphorylation assay and its semiquantitative analysis
AUTHORS: Anna F. Zeitler, Luisa F Jimenez-Soto
[DESCRIPTION]
CagA is the oncogenic toxic of Helicobacter pylori. The toxin is injected into host cells and tyrosine phosphorylated in the C-terminal EPIYA motifs by host kinases. Positive translocation o... | ["[Seed AGS cells 48 hours before infection will be performed.] The objective is to have a cellular confluency in the 6-well of 80-90% at the moment of infection. For you to achieve this, you have to know your cells and their multiplication speed. For AGS cells the usual splitting for 48 hours with synchronization (see... |
null | null | null | dx.doi.org/10.17504/protocols.io.jfxcjpn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Discovery of PF-06928215 as a high affinity inhibitor of cGAS enabled by a novel fluorescence polarization assay </strong></p>
<p> </p>
<p>Cyclic GMP-AMP synthase (cGAS) initiates the innate immune system in response to cytosolic dsDNA. After binding and activation fr... | [] |
34,188 | 2% Agarose Gel Electrophoresis | null | dx.doi.org/10.17504/protocols.io.bdmki44w | null | Alicia Grealy | TITLE: 2% Agarose Gel Electrophoresis
AUTHORS: Alicia Grealy
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the procedure for electropohresing DNA through an agarose gel to examine fragment size. </div></div>
[STEPS]
?. [Cast a 2%, medium sized agarose gel]
Using an electro... | ["[Cast a 2%, medium sized agarose gel]\nUsing an electronic balance, weigh out 2.2 g of agarose powder on to a weigh boat using a spatula.\nNote that gel concentration can be adjusted. The more concentrated the gel, the greater the resolution of small fragment sizes.", "[Cast a 2%, medium sized agarose gel]\nTransfer ... |
24,362 | Epithelial/Immune Dissociation for Human Colon Biopsies | null | dx.doi.org/10.17504/protocols.io.32igqce | null | Grace Burgin, Moshe Biton | TITLE: Epithelial/Immune Dissociation for Human Colon Biopsies
AUTHORS: Grace Burgin, Moshe Biton
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">To isolate immune and epithelial cells from human colon biopsies </div></div>
[STEPS] | [] |
69,913 | Establishing processes to capture standardized contextual data | 1 | null | https://www.protocols.io/view/establishing-processes-to-capture-standardized-con-cghztt76 | Paul Lorenzo A Gaite, Dr Ritchie Mae T Gamot, Prof Lyre Anni E Murao | TITLE: Establishing processes to capture standardized contextual data
AUTHORS: Paul Lorenzo A Gaite, Dr Ritchie Mae T Gamot, Prof Lyre Anni E Murao
[DESCRIPTION]
One of the obstacles of biosurveillance is the non-standard recording and storage of contextual data. This is a problem especially when establishing a nation... | ["PGC Mindanao workflow\n\nPGC Mindanao did not have a defined workflow for handling contextual data. The subsections below outline the activities done in connection to the collection, storage, and stewardship of contextual data, as well as preparation of contextual data for submission to GISAID.", "Collection of Conte... |
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