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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95,973 | HMW gDNA purification proto | 0 | null | https://www.protocols.io/view/hmw-gdna-purification-proto-c9ydz7s6 | Ivette Cornejo Corona, Devon Boland, tpd | TITLE: HMW gDNA purification proto
AUTHORS: Ivette Cornejo Corona, Devon Boland, tpd
[DESCRIPTION]
Optimized protocol for efficient extraction of HMW gDNA from the polysaccharide-rich microalga Botryococcus, enabling long-read sequencing on the Oxford Nanopore Technologies platform.
[BEFORE_START]
Ensure Bench Clean... | ["[Biomass harvesting and HMW gDNA isolation] Biomass preparation \n• Harvest the biomass by filtration using a 10 μm nylon net.", "[Biomass pre-wash] • Add 1 ml sorbitol wash buffer to 1.5 ml eppendorf tube containing ~100 mg ground biomass. \n• Allow sample to thaw while vortexing for 10 seconds \n• Keep samples on i... |
101,308 | Enhancing precision flood mapping: Pahang's vulnerability unveiled | 0 | dx.doi.org/10.17504/protocols.io.kxygxyy6zl8j/v1 | https://www.protocols.io/view/enhancing-precision-flood-mapping-pahang-39-s-vuln-de643hgw | Dr. Tahmina Afrose Keya, Siventhiran S B, Maheswaran S, Sreeramanan S, Low J An, Leela A, Prahankumar R, Lokeshmaran A, Boratne AV, Abdullah, M. T | TITLE: Enhancing precision flood mapping: Pahang's vulnerability unveiled
AUTHORS: Dr. Tahmina Afrose Keya, Siventhiran S B, Maheswaran S, Sreeramanan S, Low J An, Leela A, Prahankumar R, Lokeshmaran A, Boratne AV, Abdullah, M. T
[DESCRIPTION]
Flooding in Malaysia is considered one of the most impactful natural di... | ["[Conceptual framework] Develop an Integrated GIS-Based Framework. \nThe objective is to establish a robust GIS-based framework for flood susceptibility mapping in the Pahang\nState. This involves compiling and integrating geospatial datasets related to topography, hydrology, land use, and climate variables to create ... |
31,682 | Eudiometry (18th century analysis of the percentage of O2 in the atmosphere) | null | dx.doi.org/10.17504/protocols.io.ba7aihie | null | Josep Grau, Josep Bonet, Jordi Ferre | TITLE: Eudiometry (18th century analysis of the percentage of O2 in the atmosphere)
AUTHORS: Josep Grau, Josep Bonet, Jordi Ferre
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Reproduction of a XVIII century procedure for the analysis of the volumetric percentage of Oxygen in the atmosphere. The p... | ["[Preparation of the reactants]\nIn order to prepare 500 ml of polysulfide solution (sufficient for 4-5 measures), mix 391.5 g of distilled water with 74.5 g of S and 34 g of CaO. If larger volumes are required, take care to maintain the same percentages by weight (78.3 of water, 14.9 of S, and 6.8 of CaO)", "[Prepara... |
79,725 | A recipe for extremely reproducible enrichment analysis | 5 | dx.doi.org/10.17504/protocols.io.j8nlkwpdxl5r/v1 | https://www.protocols.io/view/a-recipe-for-extremely-reproducible-enrichment-ana-cr4mv8u6 | Mark Ziemann, Anusuiya Bora | TITLE: A recipe for extremely reproducible enrichment analysis
AUTHORS: Mark Ziemann, Anusuiya Bora
[DESCRIPTION]
Enrichment analysis is a popular computational biology technique for interpreting omics data, but typically these are conducted irreproducibly with web-based and graphical interface tools, which risks omit... | ["[Install Docker] Open a terminal. Docker is a tool for working with containers, including building and running them. It is essential for ensuring reprducibility. We will install it using the command line interface, also known as the \"terminal\". We're assuming this is the first time using Ubuntu, so you'll need know... |
98,197 | Biofilm DNA metabarcoding protocol | 0 | dx.doi.org/10.17504/protocols.io.j8nlk8em6l5r/v1 | https://www.protocols.io/view/biofilm-dna-metabarcoding-protocol-db5v2q66 | Amy Thorpe, Tim Goodall, Lindsay Kate Newbold, Joe Taylor, Jonathan Warren, kerry.walsh, Daniel S Read | TITLE: Biofilm DNA metabarcoding protocol
AUTHORS: Amy Thorpe, Tim Goodall, Lindsay Kate Newbold, Joe Taylor, Jonathan Warren, kerry.walsh, Daniel S Read
[DESCRIPTION]
Full protocol for the extraction of DNA from river biofilm samples, 2-step PCR amplification of 16S rRNA, 18S rRNA, ITS2 and rbcL gene regions and ampl... | ["[1. DNA extraction] Defrost and gently vortex samples to resuspend sample material.", "[1. DNA extraction] Transfer 100 µL of sample material to each tube of the 96-tube lysis rack. Make a note of sample positions and leave at least one tube free of sample material as a negative extraction control.", "[1. DNA extract... |
34,533 | The ARF-AID system: Methods that preserve endogenous protein levels and facilitate rapidly inducible protein degradation | null | dx.doi.org/10.17504/protocols.io.bdydi7s6 | null | Kizhakke Mattada Sathyan, Thomas G. Scott, Michael J. Guertin | TITLE: The ARF-AID system: Methods that preserve endogenous protein levels and facilitate rapidly inducible protein degradation
AUTHORS: Kizhakke Mattada Sathyan, Thomas G. Scott, Michael J. Guertin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The ARF-AID (Auxin Response Factor-Auxin Inducible De... | [] |
41,759 | FireLAMP Protocol | 4 | dx.doi.org/10.17504/protocols.io.bkz7kx9n | https://www.protocols.io/view/firelamp-protocol-bkz7kx9n | Daniel Benner, Ozlem Yaren | TITLE: FireLAMP Protocol
AUTHORS: Daniel Benner, Ozlem Yaren
[STEPS]
?. SETTING UP THE GENIE II
?. Take a swab
?. Preparing a sample batch (up to 8 samples different testees)
?. Plug In
?. Set the block temperature to. Make sure temperatures are reached to set temperature before placing the assay tubes into heat-block... | ["SETTING UP THE GENIE II", "Take a swab", "Preparing a sample batch (up to 8 samples different testees)", "Plug In", "Set the block temperature to. Make sure temperatures are reached to set temperature before placing the assay tubes into heat-block for amplification.\n65 °C", "Open sample swab with caution and transfe... |
44,110 | Investigaciones de impacto que estudian los factores contextuales que afectan a la Eficacia Escolar en el periodo 2014-2019 | 1 | dx.doi.org/10.17504/protocols.io.bpbnmime | https://www.protocols.io/view/investigaciones-de-impacto-que-estudian-los-factor-bpbnmime | Pablo Delgado-Galindo, Javier Rodríguez-Santero, Juan Jesus Torres-Gordillo | TITLE: Investigaciones de impacto que estudian los factores contextuales que afectan a la Eficacia Escolar en el periodo 2014-2019
AUTHORS: Pablo Delgado-Galindo, Javier Rodríguez-Santero, Juan Jesus Torres-Gordillo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.s9meh46 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The assay was carried out following the protocol reported by Dineshkumar et al. [8]. Starch (2 mg) was suspended in a tube containing 0.2 mL of 0.5 M Tris-HCl (Sigma-Aldrich, USA) buffer (pH 6.9) with 0.01 M calcium chloride as substrate. The tube was boiled for 5 min and the... | [] |
68,884 | Liposome binding | 1 | dx.doi.org/10.17504/protocols.io.yxmvmndqng3p/v1 | https://www.protocols.io/view/liposome-binding-cfhutj6w | Xinbo Wang, Pietro De Camilli | TITLE: Liposome binding
AUTHORS: Xinbo Wang, Pietro De Camilli
[DESCRIPTION]
This protocol details methods for LRRK2-liposome binding experiments analyzed by co-sedimentation or confocal fluorescence microscopy, respectively.
[STEPS]
SECTION: Co-sedimentation analysis
1. Prepare samples in Beckman microfuge tubes wit... | ["[Co-sedimentation analysis] Prepare samples in Beckman microfuge tubes with 300 nanomolar (nM) LRRK2 or RCKW, 20 micromolar (µM) PS liposomes in the absence or presence of 1 millimolar (mM) GMPPNP.", "[Co-sedimentation analysis] Incubate samples at 37 °C for 30 min.", "[Co-sedimentation analysis] Centrifuge samples a... |
106,286 | Protocol for use with NEBNext ULTRAEXPRESS® RNA Library Prep Kit (NEB#E3330) and NEBNext rRNA Depletion Kits (NEB #E7400, #E7405) and non indexed adaptor | 1 | dx.doi.org/10.17504/protocols.io.e6nvw14o2lmk/v1 | https://www.protocols.io/view/protocol-for-use-with-nebnext-ultraexpress-rna-lib-dj2n4qde | Juliet Bonnevie | TITLE: Protocol for use with NEBNext ULTRAEXPRESS® RNA Library Prep Kit (NEB#E3330) and NEBNext rRNA Depletion Kits (NEB #E7400, #E7405) and non indexed adaptor
AUTHORS: Juliet Bonnevie
[DESCRIPTION]
The NEBNext UltraExpress RNA Library Prep Kit contains the enzymes and buffers required to to rapidly convert 25–250 ng... | ["[Preparation of 1X Fragmentation Mix for RNA elution] Thaw the Fragmentation Master Mix (2X) and prepare 1X composition as follows:", "[Probe Hybridization to RNA] Dilute 25 ng–250 ng of total RNA with Nuclease-free Water to a final volume of 11 µL in a PCR tube. Keep the RNA on ice.", "[Probe Hybridization to RNA] A... |
44,766 | AxyPrep magnetic Bead normalization and PCR clean up For dual index | 4 | dx.doi.org/10.17504/protocols.io.36wgq4j13vk5/v1 | https://www.protocols.io/view/axyprep-magnetic-bead-normalization-and-pcr-clean-bpx6mpre | Alexander J Bradshaw | TITLE: AxyPrep magnetic Bead normalization and PCR clean up For dual index
AUTHORS: Alexander J Bradshaw
[DESCRIPTION]
In-house protocol used to prepare PCR amplicons with AxyPrep beads for Illumina sequencing.
[STEPS]
1. Place Elution buffer, Magnetic Beads, and binding buffer on the bench and allow each to reach r... | ["Place Elution buffer, Magnetic Beads, and binding buffer on the bench and allow each to reach room temperature before using.\n\nRoom temperature", "Mix magnetic beads until homogenous (no seriously, vortex the shit out of them)", "Add 10ul of magnetic beads to each well. Pipette Up and down 5 times to mix completely\... |
28,599 | Bradford protein assay in 96-Well plate | null | dx.doi.org/10.17504/protocols.io.76xhrfn | null | iGEM Dusseldorf | TITLE: Bradford protein assay in 96-Well plate
AUTHORS: iGEM Dusseldorf
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Assay for quantification of protein by comparing measured Absorbance at 595 nm to bovine serum albumine standard</div><div class = "text-block"><ul style = "list-style-type:disc;">... | [] |
75,077 | Enteric neuron activity during spontaneous motor complexes in mouse colon | 4 | dx.doi.org/10.17504/protocols.io.6qpvr4oz3gmk/v2 | https://www.protocols.io/view/enteric-neuron-activity-during-spontaneous-motor-c-cmjdu4i6 | Kristen Smith-Edwards | TITLE: Enteric neuron activity during spontaneous motor complexes in mouse colon
AUTHORS: Kristen Smith-Edwards
[DESCRIPTION]
This protocol describes the steps to prepare mouse colon and image GCaMP calcium activity in myenteric neurons during spontaneous colonic motor complexes.
[STEPS]
1. Euthanize EIIa-GCaMP mice... | ["Euthanize EIIa-GCaMP mice (offspring from the pairing of B6.FVB-Tg(EIIa-cre)C5379Lmgd/J [RRID:IMSR_JAX:003724;cat. 003724; Jax Labs] and B6J.Cg-Gt(ROSA)26Sortm96(CAG-GCaMP6s)Hze/MwarJ [RRID:IMSR_JAX:028866;cat. 028865; Jax Labs]), by inhalation of isoflurane and thoracotomy. Remove the entire colon from mouse and pla... |
20,518 | PMMA Spin-coating | null | dx.doi.org/10.17504/protocols.io.yaefsbe | null | Kenneth Schackart, Kattika Kaarj | TITLE: PMMA Spin-coating
AUTHORS: Kenneth Schackart, Kattika Kaarj
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details how to spin coat a thin layer of PMMA on a glass cover slip.</div></div>
[STEPS]
?. [Prepare surface]
Wipe cover slip with 70% ethanol using a delicate task wipe.... | ["[Prepare surface]\nWipe cover slip with 70% ethanol using a delicate task wipe.", "[Spin-coat]\nPlace cove slip into spin coater, centering with the square in the spin coater.", "[Spin-coat]\nDispense PMMA solution onto the center of the cover slip.\n30 µl", "[Spin-coat]\nSpin for at 2000 rpm.\nThis step can be varie... |
103,429 | Intra-cardiac mouse perfusion | 0 | dx.doi.org/10.17504/protocols.io.8epv5r3ddg1b/v1 | https://www.protocols.io/view/intra-cardiac-mouse-perfusion-dg9d3z26 | Lauren C. Faget, Thomas Hnasko | TITLE: Intra-cardiac mouse perfusion
AUTHORS: Lauren C. Faget, Thomas Hnasko
[DESCRIPTION]
Hnasko lab intra-cardiac mouse perfusion protocol
[STEPS]
SECTION: Prepare subject
1. Anesthetize with a lethal dose of pentobarbital (200 mg/kg i.p. or 0.1-0.2 ml at 10 mL/kg in 0.9% NaCl).
SECTION: Prepare subject
2. After 2-... | ["[Prepare subject] Anesthetize with a lethal dose of pentobarbital (200 mg/kg i.p. or 0.1-0.2 ml at 10 mL/kg in 0.9% NaCl).", "[Prepare subject] After 2-3min, verify that the animal is completely anesthetized by checking for absence of response to hind paws / tip of tail pinch using nails or small tweezers.", "[Prepar... |
null | null | null | dx.doi.org/10.17504/protocols.io.c3myk5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol describes the preparation of and treatment with DNase I to degrade DNA in solutions containing iron chloride, EDTA–Mg ascorbate buffer, and cesium chloride. DNase I treatment, CsCl purification, and sucrose purification methods were compared using replicated ... | [] |
62,955 | DNA extraction from fecal samples | 4 | dx.doi.org/10.17504/protocols.io.3byl4k912vo5/v3 | https://www.protocols.io/view/dna-extraction-from-fecal-samples-b9qjr5un | Yoshiyuki Matsuo | TITLE: DNA extraction from fecal samples
AUTHORS: Yoshiyuki Matsuo
[DESCRIPTION]
DNA extraction method for metagenomic sequencing of the gut microbiota
[STEPS]
SECTION: Preparation of fecal samples
1. Place 50-100 mg of fecal sample into tube.
SECTION: Preparation of fecal samples
2. Add 1 mL of PBS per 100 mg of fec... | ["[Preparation of fecal samples] Place 50-100 mg of fecal sample into tube.", "[Preparation of fecal samples] Add 1 mL of PBS per 100 mg of feces.", "[Preparation of fecal samples] Mix thoroughly by vortexing.", "[Preparation of fecal samples] Allow the sample to stand for 2 min to sediment large debris.", "[Preparatio... |
106,387 | Coil construction | 0 | dx.doi.org/10.17504/protocols.io.n2bvjneewgk5/v1 | https://www.protocols.io/view/coil-construction-dj5t4q6n | Clarice D. Aiello | TITLE: Coil construction
AUTHORS: Clarice D. Aiello
[DESCRIPTION]
To systematically quantify magnetic field effects in cell biology, it is crucial to produce fields that can be automatically adjusted and that are stable throughout an experiment's duration, usually operating inside an incubator. Here, we report on the ... | ["[Materials] Here are the materials required and the assembly instructions for the coils.\n\n* Copper wire (0.71 mm diameter);\n* 3D-printed coil holder in thermoplastic material (CAD files found here);\n* Machined coil enclosure made out of Delrin or aluminum (CAD files also found here); \n* Thermally conductive glue... |
32,864 | Swedish Traditional Gingersnaps | null | dx.doi.org/10.17504/protocols.io.bcb8isrw | null | Angelina Spotts | TITLE: Swedish Traditional Gingersnaps
AUTHORS: Angelina Spotts
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><h2><span style = "font-weight:bold;">Ingredients</span></h2></div><div class = "text-block"><h2></h2></div><div class = "text-block"><ul style = "list-style-type:disc;"><li style = "count... | [] |
84,627 | Sexing | 5 | null | https://www.protocols.click/view/sexing-cwvtxe6n | Diego Peralta, Juan I. Túnez, Ulises E. Rodríguez Cruz, Santiago G. Ceballos | TITLE: Sexing
AUTHORS: Diego Peralta, Juan I. Túnez, Ulises E. Rodríguez Cruz, Santiago G. Ceballos
[DESCRIPTION]
Assigning sex to individuals without previous information is a common objective of molecular ecology. Here, we developed a framework for sexing animals by using two indexes based on the different propertie... | ["“When sex scarce: A rapid approach to sexing individuals by RAD-seq using a reference genome”\n\nDiego M. Peralta, Juan I. Túnez, Ulises E. Rodríguez Cruz, Santiago G. Ceballos", "Objective\n\nDetermining the sex of different individuals using GBS and a reference genome, based on the distinct properties of mammalian ... |
null | null | null | dx.doi.org/10.17504/protocols.io.mt2c6qe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol builds on Suchan <em>et al. </em>(2016). It has been modified to work on fresh and museum samples of birds, specifically tested on Regent Honeyeater (<em>Anthochaera phrygia</em>).</p>
<p>The detailed protocol contains three main sections: (A) preparing ddRAD li... | [] |
91,033 | Bulk FLASH-seq | 4 | dx.doi.org/10.17504/protocols.io.3byl4jynolo5/v2 | https://www.protocols.io/view/bulk-flash-seq-c45zyy76 | Rebecca A Siwicki, Vincent Hahaut, Simone Picelli | TITLE: Bulk FLASH-seq
AUTHORS: Rebecca A Siwicki, Vincent Hahaut, Simone Picelli
[DESCRIPTION]
Bulk RNA sequencing has revolutionized the study of transcriptomes, enabling the analysis of gene expression in complex tissues and heterogenous cell populations. While single cell RNA sequencing (scRNA-seq) has gained popul... | ["[Prepare Lysis Mix] Prepare the following Lysis Mix:\n \nABC Reagent Final Concentration Volume 96 rxn Triton-X100 (10% v/v) 0.02 2.208 dNTP mix (25 mM each) 0.24 26.496 SMART dT30VN (100uM) 0.018 1.9872 RNase Inhibitor (40 U/ul) 0.03 3.312 DTT (100 mM) 0.012 1.3248... |
null | null | null | dx.doi.org/10.17504/protocols.io.rdyd27w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>CAR-T (Chimeric Antigen Receptor T-Cell Immunotherapy), a <a href="https://www.creative-biolabs.com/car-t/cellrapeutics-chimeric-antigen-receptor-car-technology.htm" target="_blank" rel="noopener noreferrer">chimeric antigen receptor T cell</a> immunotherapy, has been in use ... | [] |
58,125 | Gentamicin Protection assay (Intracellular Survival Assay) for Salmonella Typhimurium/Typhi | 4 | dx.doi.org/10.17504/protocols.io.b4zmqx46 | https://www.protocols.io/view/gentamicin-protection-assay-intracellular-survival-b4zmqx46 | Kasturi Chandra | TITLE: Gentamicin Protection assay (Intracellular Survival Assay) for Salmonella Typhimurium/Typhi
AUTHORS: Kasturi Chandra
[DESCRIPTION]
Salmonella invades the epithelial cells by inducing bacterial uptake, whereas phagocytes readily take up the bacteria by phagocytosis. Intracellular Salmonella is resistant to gent... | ["Epithelial cells were infected with mid-log phase culture of bacteria grown in LB (OD600 0.3)\n\nOR\n\nphagocytes were infected with overnight culture (OD600 0.3). The multiplicity of infection (MOI) of 10 was used in each case.", "Bacterial attachment to host cells was enhanced by centrifuging at 600 rpm for 10 min.... |
90,520 | Protocol to isolate, cryopreserve, and fix mouse PBMCs for IGVF | 4 | null | https://www.protocols.io/view/protocol-to-isolate-cryopreserve-and-fix-mouse-pbm-c4myyu7w | Elisabeth Rebboah | TITLE: Protocol to isolate, cryopreserve, and fix mouse PBMCs for IGVF
AUTHORS: Elisabeth Rebboah
[DESCRIPTION]
This protocol describes isolation of peripheral blood mononuclear cells (PBMCs, tissue ID: 20) from whole blood of 10 week old mice, cryopreservation, thawing, and fixation for single-cell RNA-seq using the... | ["[Setup] Set centrifuge to 19C.", "[Setup] Prepare 1 ice bucket.", "[Setup] Thaw and filter FBS with a cell culture filter unit and aliquot into 15 mL conical tubes.", "[Setup] Prepare PBS-EDTA by adding EDTA powder to PBS and filter with a cell culture filter unit. 500 mL of PBS-EDTA should be enough for around 16 sa... |
27,086 | Cell line block and microarray preparation | null | dx.doi.org/10.17504/protocols.io.6pnhdme | https://www.protocols.io/view/cell-line-block-and-microarray-preparation-6pnhdme | Rona Ortenberg, Erez Nissim Baruch | TITLE: Cell line block and microarray preparation
AUTHORS: Rona Ortenberg, Erez Nissim Baruch
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol allows to prepare paraffin block of any cell line or co-cultured cells and subsequently these blocks could be used for cell microarray construc... | ["Maintain cell lines in proper medium at 37°C in a humidified atmosphere of 5% CO2 in air.Assess cell confluence. If confluence is 70-80%, proceed.", "Harvest adherent cells with trypsin solution or cell dissociation solution.Note:Harvesting cell with a cell scraper is not recommended, since it will lead to morphologi... |
71,948 | Isolation, activation, and retroviral transduction of primary T cells from murine splenocytes | 4 | dx.doi.org/10.17504/protocols.io.bp2l691q5lqe/v1 | https://www.protocols.io/view/isolation-activation-and-retroviral-transduction-cihkub4w | Diana Rose E Ranoa, Preeti Sharma, Claire P. Schane, Amber N Lewis, Amber N Lewis, Edward Valdez, Edward J. Roy, David M. Kranz | TITLE: Isolation, activation, and retroviral transduction of primary T cells from murine splenocytes
AUTHORS: Diana Rose E Ranoa, Preeti Sharma, Claire P. Schane, Amber N Lewis, Amber N Lewis, Edward Valdez, Edward J. Roy, David M. Kranz
[DESCRIPTION]
This protocol outlines the steps for retroviral transduction of ac... | ["Day 1: Plating Platinum-E (Plat-E) retroviral packaging cell lines", "Coat wells of 6 well plates with 1 mL of poly-L-lysine. Let sit at RT for 10 mins.", "Aspirate supernatant from early passage # Plat-E cells (Cell Biolabs RV-101)", "Add 5 mL 0.05% Trypsin-EDTA to detach cells. Incubate at 37’C for 2-3 mins", "Quen... |
null | null | null | dx.doi.org/10.17504/protocols.io.fcbbisn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Purpose:</strong> To quantify infectious viruses and evaluate the infectivity of a viral sample.</p>
<p><strong>Summary:</strong> 50 µL of serially-diluted (10<sup>-3</sup> to 10<sup>-10</sup>) virus sample is added to 150 µL of exponentially growing host cells in tri... | [] |
29,591 | construct a taro linkage map using onemap | 1 | dx.doi.org/10.17504/protocols.io.85xhy7n | https://www.protocols.io/view/construct-a-taro-linkage-map-using-onemap-85xhy7n | Michael Kantar, M Renee Bellinger, Roshan Paudel | TITLE: construct a taro linkage map using onemap
AUTHORS: Michael Kantar, M Renee Bellinger, Roshan Paudel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">R script for taro linkage mapping using program onemap. </div><div class = "text-block">This script was applied to create a linkage map for a ta... | ["[Set up your R working environment]\n### There are two ways to install onemap###-------------------###### Option 1. ####Download and install Rtools in your computer before running this script###https://cran.r-project.org/bin/windows/Rtoolsfind_rtools(debug = TRUE)###Install required packagesinstall.packages(\"devtool... |
99,542 | Detection of Bordetella holmesii and Bordetella bronchiseptica Using the ABI 7500 Real-time PCR System | 0 | dx.doi.org/10.17504/protocols.io.36wgqn7zygk5/v1 | https://www.protocols.io/view/detection-of-bordetella-holmesii-and-bordetella-br-ddfw23pe | Martin Cheung, Tracy Lee, Robert B Azana, Loretta Janz, Natalie Prystajecky, Linda Hoang | TITLE: Detection of Bordetella holmesii and Bordetella bronchiseptica Using the ABI 7500 Real-time PCR System
AUTHORS: Martin Cheung, Tracy Lee, Robert B Azana, Loretta Janz, Natalie Prystajecky, Linda Hoang
[DESCRIPTION]
This procedure provides instructions for how to perform qualitative PCR (qPCR) for the detection ... | ["[Procedure A: Preparing 20X PCR Master Mix] All primer and probe sequences are listed in the materials section of this protocol. \n\nOrder all necessary primers and probes; if received lyophilized reconstitute as per the manufacturers instructions before making the desired stock dilutions.", "[Procedure A: Preparing ... |
13,470 | SIngle-strand library protocol adapter barcodes | 3 | null | https://www.protocols.io/view/single-strand-library-protocol-adapter-barcodes-rd6d29e | Tomasz Suchan | TITLE: SIngle-strand library protocol adapter barcodes
AUTHORS: Tomasz Suchan
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS] | [] |
79,775 | Gcase co-immunoprecipitation | 1 | dx.doi.org/10.17504/protocols.io.14egn2ompg5d/v1 | https://www.protocols.io/view/gcase-co-immunoprecipitation-cr57v89n | michela.deleidi, Federico Bertoli, María José Pérez J., Hariam Raji | TITLE: Gcase co-immunoprecipitation
AUTHORS: michela.deleidi, Federico Bertoli, María José Pérez J., Hariam Raji
[DESCRIPTION]
We developed this protocol to identify protein-protein interactions between the enzyme glucocerebrosidase (GCase) and other proteins in human iPSC-derived Neural Precursor Cells.
[STEPS]
SE... | ["[Gcase co-immunoprecipitation] Wash cells 1X with phosphate-buffered saline (PBS, Sigma‒Aldrich) and detach using Accutase.", "[Gcase co-immunoprecipitation] Pellet the cell suspension at 280 rcf, 5 min, 23 °C.", "[Gcase co-immunoprecipitation] Lyse the pellets in IP/lysis buffer (Thermo Fisher, #87787) supplemented ... |
38,757 | SPARC_Duke_PelotGrill_OT2-OD025340_HumanVagusNerve_Claudin1IHC_Morphology | 1 | dx.doi.org/10.17504/protocols.io.bh4dj8s6 | https://www.protocols.io/view/sparc-duke-pelotgrill-ot2-od025340-humanvagusnerve-bh4dj8s6 | Nicole A. Pelot, J. Ashley Ezzell, Gabriel B. Goldhagen, Jake E. Cariello, Kara A. Clissold, Warren M. Grill | TITLE: SPARC_Duke_PelotGrill_OT2-OD025340_HumanVagusNerve_Claudin1IHC_Morphology
AUTHORS: Nicole A. Pelot, J. Ashley Ezzell, Gabriel B. Goldhagen, Jake E. Cariello, Kara A. Clissold, Warren M. Grill
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The protocol describes immunohistochemistry with anti... | ["[Immunohistochemistry]\nBake slides with sections of paraffin-embedded vagus nerve overnight at 50oC and then cool overnight.", "[Immunohistochemistry]\nDeparaffinize the slides and hydrate them to distilled water: xylene (2x 6 min), 100% ethanol (5 min), 95% ethanol (4 min), 70% ethanol (3 min), deionized water (2x ... |
74,627 | The 7th Life Environment and Workplace Stress Survey | 1 | dx.doi.org/10.17504/protocols.io.14egn24nmg5d/v1 | https://www.protocols.io/view/the-7th-life-environment-and-workplace-stress-surv-ck5buy2n | Kei Muroi, Mami Ishitsuka, Tomohiko Ikeda, Tsukasa Takahashi, Daisuke Hori, Shotaro Doki, Shinichiro Sasahara, Tamaki Saito, Ichiyo Matsuzaki | TITLE: The 7th Life Environment and Workplace Stress Survey
AUTHORS: Kei Muroi, Mami Ishitsuka, Tomohiko Ikeda, Tsukasa Takahashi, Daisuke Hori, Shotaro Doki, Shinichiro Sasahara, Tamaki Saito, Ichiyo Matsuzaki
[DESCRIPTION]
This is a summary of The 7th Life Environment and Workplace Stress Survey conducted by Tsukuba... | ["[Tsukuba Science City Network] The Tsukuba Science City Network is an organization of the city’s research and academic institutes that aims to promote cooperation among its member institutes.\nThe Tsukuba Science City Network conducts a mental health survey every 5 years of the researchers and engineers from the memb... |
24,002 | Agro Transformation for Mimulus in Planta Transformation | null | dx.doi.org/10.17504/protocols.io.3pagmie | null | Yaowu Yuan | TITLE: Agro Transformation for Mimulus in Planta Transformation
AUTHORS: Yaowu Yuan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is part of a </span><a style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">collection for </span><span style = ":;font... | ["[Agro Transformation]\nPlease select from the following two options: 1. Agro Transformation - Using Electroporator2. Agro Transformation - Using Freeze -Thaw Method", "[Agro Transformation]\nChill 2-mm electroporation cuvette on ice.", "[Agro Transformation]\nAliquot into eppie tube.\n[LB]", "[Agro Transformation]... |
47,914 | Development of a multiplexed RT-qPCR for the surveillance of SARS-CoV-2 variants of world-wide concern | 4 | dx.doi.org/10.17504/protocols.io.bs2ingce | https://www.protocols.io/view/development-of-a-multiplexed-rt-qpcr-for-the-surve-bs2ingce | Ellinor Marving, Alonzo Alfaro-Núñez, Sofie Holdflod Nielsen, Michelle Jørgensen, Anna S. Fomsgaard, Shila Mortensen, Morten Rasmussen, Ria Lassaunière, Charlotte Polacek Strandh, Claus Nielsen, Maiken Worsøe Rosenstierne, Arieh Cohen, Anders Fomsgaard, Katja Spiess | TITLE: Development of a multiplexed RT-qPCR for the surveillance of SARS-CoV-2 variants of world-wide concern
AUTHORS: Ellinor Marving, Alonzo Alfaro-Núñez, Sofie Holdflod Nielsen, Michelle Jørgensen, Anna S. Fomsgaard, Shila Mortensen, Morten Rasmussen, Ria Lassaunière, Charlotte Polacek Strandh, Claus Nielsen, Maiken... | ["ProtocolWork on ice Vortex and centrifuge reagents before use, except the Luna WarmStart® RT Enzyme Mix here only mix carefully by pipetting or short vortexingDilute the primer and probe stock (100µM) 1:5 with nuclease free water to a working concentration of 20µMPrepare mastermix on ice containing the following: ... |
null | null | null | dx.doi.org/10.17504/protocols.io.rh4d38w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes briefly how to perform colonization of aposymbiotic Aiptasia with <em>Symbiodinium</em> cultures.</p>
<p> </p>
<p>The method is based on the one described in Xiang et al., 2013.</p>
[BEFORE_START]
<p>The colonizationworks most efficiently with <em>Sym... | [] |
20,155 | U Mass - Glucagon | null | dx.doi.org/10.17504/protocols.io.xw3fpgn | null | Jason Kim | TITLE: U Mass - Glucagon
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This experiment provides the quantification of multiple hormones using multiplexed-Luminex technology based on beads containin... | ["Add 200 µL of Assay Buffer into each well of the plate. Seal and mix on a plate shaker for 10 minutes at room temperature (20-25°C).", "Decant Assay Buffer and remove the residual amount from all wells by inverting the plate and tapping it smartly onto absorbent towels several times.", "Add 10 µL of appropriate matr... |
48,283 | DNA Cleanup and Concentration Using the Monarch® PCR & DNA Cleanup Kit (5 μg) (NEB #T1030) | 1 | dx.doi.org/10.17504/protocols.io.btd3ni8n | https://www.protocols.io/view/dna-cleanup-and-concentration-using-the-monarch-pc-btd3ni8n | New England Biolabs | TITLE: DNA Cleanup and Concentration Using the Monarch® PCR & DNA Cleanup Kit (5 μg) (NEB #T1030)
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Protocol for DNA Cleanup and Concentration Using the Monarch® PCR & DNA Cleanup Kit (5 μg) (</span><a href="https://ww... | ["[Buffer Preparation]\nAdd ethanol to Monarch DNA Wash Buffer prior to use (4 volumes of ≥ 95% ethanol per volume of Monarch DNA Wash Buffer).For 50-prep kit add 20 ml of ethanol to 5 ml of Monarch DNA Wash BufferFor 250-prep kit add 100 ml of ethanol to 25 ml of Monarch DNA Wash BufferAlways keep all buffer bottles t... |
22,177 | FLASH | null | dx.doi.org/10.17504/protocols.io.zv9f696 | null | Ibrahim Ilik, Tugce Aktas, Daniel Maticzka, Rolf Backofen, Asifa Akhtar | TITLE: FLASH
AUTHORS: Ibrahim Ilik, Tugce Aktas, Daniel Maticzka, Rolf Backofen, Asifa Akhtar
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Determination of the </span><span style = "font-style:italic;">in vivo</span><span> binding sites of RNA-binding proteins (RBPs) is paramount to underst... | ["[Lysate preparation]\nCrosslink cells with with UV-C (0.15 - 0.2 mJ/cm2) irradiation.Type, amount, state of the cells varies depending on the intended application. As a rule of thumb, crosslink cells in 15cm-plates on water/ice and as close to the lamp as possible (3-6 cm distance). Wash the cells with ~6mL of ice-co... |
null | null | null | dx.doi.org/10.17504/protocols.io.kekctcw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Cerebral aneurysms are a major risk factor for intracranial bleeding with devastating consequences for the patient. One recently established treatment is the implantation of flow diverters (FD). Methods to predict their treatment success before or directly after implantation ... | [] |
52,457 | Immunofluorescence of autophagic cargo receptors and p-TBK1 at LAMP1 lysosomes during lysophagy | 1 | dx.doi.org/10.17504/protocols.io.bxghpjt6 | https://www.protocols.io/view/immunofluorescence-of-autophagic-cargo-receptors-a-bxghpjt6 | Vinay V. Eapen, Sharan Swarup, Melissa Hoyer, Harper JW | TITLE: Immunofluorescence of autophagic cargo receptors and p-TBK1 at LAMP1 lysosomes during lysophagy
AUTHORS: Vinay V. Eapen, Sharan Swarup, Melissa Hoyer, Harper JW
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Lysophagy-the selective elimination of damaged lysosomes by the autophagy pathway... | ["[Immunofluorescence of autophagic cargo receptors and p-TBK1 at LAMP1 lysosomes during lysophagy]\nPlate the cells (to be selected by the investigator) into 12 well glass bottom dishes (No. 1.5, 14 mm glass diameter, MatTek) are grown to 50-70% confluency in media.\nFor HeLa cells, we use Dulbecco’s MEM (DMEM), high ... |
61,922 | https://ipsnews.net/business/2022/02/28/holly-willoughby-keto-diet-pills-uk-united-kingdom-how-does-work-keto-burn-dx-holly-willoughby-uk/ | 1 | dx.doi.org/10.17504/protocols.io.x54v9y3kmg3e/v1 | https://www.protocols.io/view/https-ipsnews-net-business-2022-02-28-holly-willou-b8qarvse | thomwillo | TITLE: https://ipsnews.net/business/2022/02/28/holly-willoughby-keto-diet-pills-uk-united-kingdom-how-does-work-keto-burn-dx-holly-willoughby-uk/
AUTHORS: thomwillo
[DESCRIPTION]
Name Of Product@>>>Holly Willoughby Diet Pills UK
Instinctive fat is for the most part connected with weight and brings about the gamble ... | ["[Holly Willoughby Diet Pills UK]"] |
86,242 | KAPP-Sen TMC: Pancreas Tissue Blocks Paraffin Embedding | 1 | dx.doi.org/10.17504/protocols.io.36wgq3j1olk5/v1 | https://www.protocols.io/view/kapp-sen-tmc-pancreas-tissue-blocks-paraffin-embed-cygaxtse | Cristina Aguayo-Mazzucato, Kanako Iwasaki | TITLE: KAPP-Sen TMC: Pancreas Tissue Blocks Paraffin Embedding
AUTHORS: Cristina Aguayo-Mazzucato, Kanako Iwasaki
[DESCRIPTION]
The paraffin cassettes were fixed in 4% paraformaldehyde for 24 hours and processed for paraffin embedding at Joslin Histology Core as described here.
[STEPS]
SECTION: Tissue processing usi... | ["[Tissue processing using the Citadel 2000 Table Top Processor] Tissue is processed overnight.", "[Tissue processing using the Citadel 2000 Table Top Processor] Tissue blocks are transferred to a vacuum paraffin bath.", "[Tissue processing using the Citadel 2000 Table Top Processor] Cassettes are submersed in 50% EtOH... |
85,808 | Qubit dsDNA HS Assay | 1 | null | https://www.protocols.io/view/qubit-dsdna-hs-assay-cx2qxqdw | Lakme Caceres | TITLE: Qubit dsDNA HS Assay
AUTHORS: Lakme Caceres
[DESCRIPTION]
How to use the Qubit 2.0 fluorometer to quantify dsDNA samples. It is most accurate for sample concentrations from 5 pg/uL to 120 ng/uL.
[GUIDELINES]
All reagents are stored at 4C. Allow them to equilibriate to room temperature before use:
HS Reagent (k... | ["To prepare the Qubit working solution, a mixture of HS Reagent and HS Buffer, take the number of samples you will be running and multiply that by 199 uL. Then add 380 for the HS Standards. Round this number up to the nearest tenth (for excess). This is the amount of HS Buffer you will need. Divide this number by 200 ... |
null | null | null | dx.doi.org/10.17504/protocols.io.j2dcqa6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Background </strong>Autochthonous cutaneous and visceral leishmaniasis caused by <em>Leishmania martiniquensis</em> and <em>Leishmania siamensis</em> have been considered an emerging infectious disease in Thailand. The disease burden is significantly underestimated, e... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ehdbb26 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol provides a method for identifing CRIPR repeats using the program PilerCR on assembled contigs. Based on the methods from the following publication: <br /><br />Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Dive... | [] |
28,451 | Toehold switch assembly | null | dx.doi.org/10.17504/protocols.io.72bhqan | null | Junyan Qian | TITLE: Toehold switch assembly
AUTHORS: Junyan Qian
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">General toehold assemble method using NEB Q5 High-Fidelity 2x Master Mix. Here we took Boir Noir toeholds as an example, it has four candidates we wanted to test. In order to have a higher yield, run ... | ["[PCR preparation]\nPrepare 4 effendorfs label them, each one will contain the master mix of a certain toehold primer.Attention: Keep the polymerase on ice avoiding denaturation.(Order of pipetting: H2O -> Q5 MasterMix -> primers) ABCDEF1Number of reactions per Master mix:52Reaction Volume:2534Reference (25 uL)Master... |
40,025 | 6-plex IF Protocol on the BOND RX (Leica Biosystems) | 1 | dx.doi.org/10.17504/protocols.io.bjbzkip6 | https://www.protocols.io/view/6-plex-if-protocol-on-the-bond-rx-leica-biosystems-bjbzkip6 | Maura A Sticco-Ivins, Abdallah Flaifel, Miriam Ficial | TITLE: 6-plex IF Protocol on the BOND RX (Leica Biosystems)
AUTHORS: Maura A Sticco-Ivins, Abdallah Flaifel, Miriam Ficial
[DESCRIPTION]
A 6-plex immunofluorescence protocol was optimized on Leica Bond RX Autostainer.
[STEPS]
SECTION: Preparation
1.
Multiplex IF assay on the Bond RX Autostainer (Leica Biosystem... | ["[Preparation] Multiplex IF assay on the Bond RX Autostainer (Leica Biosystems) using the Opal multiplex IHC system (PerkinElmer/Akoya Biosciences Cat# NEL871001KT) and the BOND Polymer Refine Detection Kit (Leica Biosystems Cat# DS9800). \n\n- Prepare the antibody and the fluorophore dilutions in 6mL Leica BOND tubes... |
62,995 | VitalCare Nutrition Keto Gummies | 3 | dx.doi.org/10.17504/protocols.io.eq2lyn16rvx9/v1 | https://www.protocols.io/view/vitalcare-nutrition-keto-gummies-b9rtr56n | G A | TITLE: VitalCare Nutrition Keto Gummies
AUTHORS: G A
[DESCRIPTION]
gives me the power to make changes for the good. I can feel better immediately with just a few tweaks.
[STEPS] | [] |
77,377 | Multiplex real-time PCR assay for the detection of SARS-CoV-2 variants | 1 | dx.doi.org/10.17504/protocols.io.8epv5jm26l1b/v1 | https://www.protocols.io/view/multiplex-real-time-pcr-assay-for-the-detection-of-cps9vnh6 | Jianfa Bai, Cori Ondrashek | TITLE: Multiplex real-time PCR assay for the detection of SARS-CoV-2 variants
AUTHORS: Jianfa Bai, Cori Ondrashek
[DESCRIPTION]
This document describes a real-time 4-plex, TaqMan based RT-PCR assay used for the detection of the majority of SARS-CoV-2 strains, and differentiation of both Delta and Omicron variants. 18S... | ["[Probe preparation] Prepare 100 µM individual probe stock solution with 1 × TE buffer.", "[Probe preparation] Centrifuge the lyophilized probe tube at 6000 × g (8,000 rpm) for 5 min .", "[Probe preparation] Dissolve lyophilized probe based on its molarity, and not molecular weight. \ni.e., add 455 µL of 1× TE buffer ... |
88,419 | Cell lysis and immunoblotting | 1 | dx.doi.org/10.17504/protocols.io.4r3l226e4l1y/v1 | https://www.protocols.io/view/cell-lysis-and-immunoblotting-c2kbycsn | Kelsey Hickey, Sharan Sharan Swarup, Harper JW | TITLE: Cell lysis and immunoblotting
AUTHORS: Kelsey Hickey, Sharan Sharan Swarup, Harper JW
[DESCRIPTION]
This is cell lysis and immunoblotting protocol.
[STEPS]
SECTION: Harvest and Lyse cells
1. Cells were cultured in the presence of the corresponding stress to 60-80% confluency in 6-well plates, 10 cm or 15 cm d... | ["[Harvest and Lyse cells] Cells were cultured in the presence of the corresponding stress to 60-80% confluency in 6-well plates, 10 cm or 15 cm dishes. After removing the media, the cells were washed with DPBS three times.", "[Harvest and Lyse cells] To lyse cell urea buffer (8M urea, 50 mM TRIS 7.5, 150 mM NaCl, cont... |
31,735 | Safety Training - Rice/Correa Lab | null | dx.doi.org/10.17504/protocols.io.ba8xihxn | null | Samantha Coy | TITLE: Safety Training - Rice/Correa Lab
AUTHORS: Samantha Coy
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In order to work in the Correa Lab, new members must complete both the General Laboratory Safety Training and Blood Bourne Pathogen Safety Training offered by Rice University. They must als... | ["Navigate to Rice University's Environmental Health Safety Training Schedule and Registration Page", "If this is your first time receiving this training, you must attend sessions in person for 1) General Laboratory Safety Training, and 2) Biosafety and Bloodborne Pathogens Safety Training before you can work in the Co... |
null | null | null | dx.doi.org/10.17504/protocols.io.fa7bihn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Demo for identifying marker genes using <a href="https://ribodb.univ-lyon1.fr/ribodb/ribodb-in.cgi" target="_blank">RiboDB</a>. </p>
[GUIDELINES]
<p>Why important?</p>
<ol>
<li>Identify novel taxonomic lineages</li>
<li>Understanding evolutionary processes (Speciation, Geogr... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.qq7dvzn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is used to clarity the process of RNA extration for our Betta splendens genome.</p>
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.dm649d | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
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?.
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?.
?.
?. | [] |
22,532 | Producing rooted cassava plantlets for use in pot experiments | null | dx.doi.org/10.17504/protocols.io.z9cf92w | null | Matema Imakumbili | TITLE: Producing rooted cassava plantlets for use in pot experiments
AUTHORS: Matema Imakumbili
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Cassava is normally propagated using stem cuttings of various sizes. Rooted plantlets are however best for pot experiments, due to the short timeframes of t... | ["[Collecting cassava stem cuttings]\nCassava stem cuttings of about 1 m to 1.5 m long must be collected from mature healthy looking cassava plants of the respective test cassava variety. A machete will be needed to collect the cuttings. Not so many of these long stem cuttings will be needed as you will cut them into m... |
43,134 | Protocol 1: PCR | 5 | null | https://www.protocols.io/view/protocol-1-pcr-bnc6maze | TITLE: Protocol 1: PCR
AUTHORS:
[STEPS]
?. Find a Sequence You will need to look up the gene for the sequence you are trying to amplify and download your file (any type described above)
?. Go to PrimerQuest ToolYou will need to go to the PrimerQuest Tool webpage, https://www.idtdna.com/Primerquest/Home/Index, in ord... | ["Find a Sequence You will need to look up the gene for the sequence you are trying to amplify and download your file (any type described above)", "Go to PrimerQuest ToolYou will need to go to the PrimerQuest Tool webpage, https://www.idtdna.com/Primerquest/Home/Index, in order to insert file type of choice", "Select a... | |
63,889 | https://www.facebook.com/DietToxilAustria/ | 1 | dx.doi.org/10.17504/protocols.io.3byl4bdp2vo5/v1 | https://www.protocols.io/view/https-www-facebook-com-diettoxilaustria-camrsc56 | roxyhima | TITLE: https://www.facebook.com/DietToxilAustria/
AUTHORS: roxyhima
[DESCRIPTION]
Diaetoxil ist ein Nahrungsergänzungsmittel, das Ihrem Körper hilft, jede Diät zu bewältigen. Da die kombinierte Zufuhr von Wirkstoffen in den Bio-Kapseln extrem stark ist, fördert sie den Gewichtsverlust den ganzen Tag über.
Dies ist... | ["[DietToxil Erfahrungen] Diaetoxil ist ein Nahrungsergänzungsmittel, das Ihrem Körper hilft, jede Diät zu bewältigen. Da die kombinierte Zufuhr von Wirkstoffen in den Bio-Kapseln extrem stark ist, fördert sie den Gewichtsverlust den ganzen Tag über. \nDies ist auf die Tatsache zurückzuführen, dass es eine synergetisch... |
96,579 | Visium Direct Mount FFPE v3 -- University of Minnesota TMCs | 1 | dx.doi.org/10.17504/protocols.io.kxygx3qpkg8j/v3 | https://www.protocols.io/view/visium-direct-mount-ffpe-v3-university-of-minnesot-dajb2cin | Laura J Niedernhofer, David A Bernlohr | TITLE: Visium Direct Mount FFPE v3 -- University of Minnesota TMCs
AUTHORS: Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
The Visium Spatial Gene Expression for FFPE is designed to measure mRNA in tissue sections derived
from formalin fixed & paraffin embedded (FFPE) tissue samples and requires a Visium Spatial... | ["[Deparaffinization, H&E Staining, Imaging & Decrosslinking]", "[Library Preparation & Sequencing]", "[FASTQ Generation] BCL data from Illumina sequencer is demultiplexed and converted into FASTQ format using bcl2fastq software version 2.20.0"] |
48,745 | PCLS Viability Assay Protocol | 4 | null | https://www.protocols.io/view/pcls-viability-assay-protocol-btuhnnt6 | Morrisey Lab | TITLE: PCLS Viability Assay Protocol
AUTHORS: Morrisey Lab
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">PCLS Viability Assay Protocol- Calcein AM/ethidium homodimer-1 (“LIVE⁄DEAD®) staining and quantitative image analysis</span><span style = "font-weight:bold;fon... | [] |
87,096 | General genotyping of Myzus persicae using PCR with microsatellite markers and gel electrophoresis | 4 | dx.doi.org/10.17504/protocols.io.bp2l6x29klqe/v1 | https://www.protocols.io/view/general-genotyping-of-myzus-persicae-using-pcr-wit-czayx2fw | Mariska M. Beekman, Marcel Dicke, Bas J. Zwaan, Eveline Verhulst, bart.pannebakker | TITLE: General genotyping of Myzus persicae using PCR with microsatellite markers and gel electrophoresis
AUTHORS: Mariska M. Beekman, Marcel Dicke, Bas J. Zwaan, Eveline Verhulst, bart.pannebakker
[DESCRIPTION]
This protocol can be used to 'roughly' genotype green peach aphids, Myzus persicae (Sulzer), based on micr... | ["[Materials] Chelex and proteinase K based DNA extraction\nPipettes and pipette tips\nEppendorf tubes \nCentrifuge \nHeat block or water bath \nUltrapure water \nChelex 100 resin (Bio-Rad, Hercules, CA, USA)\nProteinase K (20 mg/mL; Promega, Southampton, UK)\n\nPCR\nPipettes and pipette tips \nPCR machine \nPCR tubes ... |
null | null | null | dx.doi.org/10.17504/protocols.io.tzzep76 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Protocol for resuspending viruses from soils and sediments. See attached file for considerations, adaptations, and references. This version does not include CsCl purification, see version 2 for CsCl information.
[BEFORE_START]
Preparations
AKC Buffer (Make before and s... | ["[Day 1- Resuspension of Viral-Like Particles] {\"blocks\":[{\"key\":\"9849q\",\"text\":\"In 4\\u00b0C cold room, add 25 ml of AKC' buffer.\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"5q9e9\",\"text\":\" \",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRang... |
92,530 | Glucosylceramide and glucosylsphingosine analysis | 4 | null | https://www.protocols.io/view/glucosylceramide-and-glucosylsphingosine-analysis-c6kszcwe | Tae-Un Han, Carley Corado | TITLE: Glucosylceramide and glucosylsphingosine analysis
AUTHORS: Tae-Un Han, Carley Corado
[DESCRIPTION]
This protocol was used to analysis glucosylceramide and glucosylsphingosine levels in mouse brain and liver.
It was also described in previous publication (Mol Cell Neurosci. 2020 Jan:102:103451, doi: 10.1016)
[S... | ["[Tissue preparation] The mouse brain and liver tissues (100 - 300 mg) were homogenized in 2% CHAPS solution (4 mL/g wet tissue) in 2 mL Omni homogenization tubes containing 8 mm ceramic beads", "[Tissue preparation] The homogenates were processed on the Bead Ruptor 24 (Omni International, Kennesaw, GA) for two 30 sec... |
100,730 | Sampling leaf tissue for analysis of NPQ Relaxation using Technologica Chlorophyll Fluorescence Imager Data. | 4 | null | https://www.protocols.io/view/sampling-leaf-tissue-for-analysis-of-npq-relaxatio-dek23cye | Lynn Doran | TITLE: Sampling leaf tissue for analysis of NPQ Relaxation using Technologica Chlorophyll Fluorescence Imager Data.
AUTHORS: Lynn Doran
[DESCRIPTION]
Sampling leaf tissue for analysis of NPQ Relaxation using Technologica Chlorophyll Fluorescence Imager Data.
[STEPS]
SECTION: Leaf Tissue Sampling
1. Cut #1 Whatman f... | ["[Leaf Tissue Sampling] Cut #1 Whatman filter paper into small squares that are just bigger than the well on a 24-well culture plate.", "[Leaf Tissue Sampling] Using a #2 Humboldt cork borer, take leaf tissue samples from each plot for each technical replicate. Hold the leaf flat against the rubber stopper, press the... |
98,939 | Intracranial injections of viral vectors in mouse striatum | 0 | dx.doi.org/10.17504/protocols.io.n2bvjnxmpgk5/v1 | https://www.protocols.io/view/intracranial-injections-of-viral-vectors-in-mouse-dcu32wyn | Shinil Raina, Simon Bossi, Stephanie J Cragg | TITLE: Intracranial injections of viral vectors in mouse striatum
AUTHORS: Shinil Raina, Simon Bossi, Stephanie J Cragg
[DESCRIPTION]
The following protocol outlines the steps necessary for intracranial injections of viral vectors in dorsal or ventral striatum in mice. These steps are generalisable for different virus... | ["[Pre-Surgery Preparation] Collect virus from frozen storage (-80°C freezer) and keep on ice.", "[Pre-Surgery Preparation] Check health of mice to undergo stereotaxic surgery: mice should look well-groomed and exhibit normal exploratory behaviour, have pink colouration to show good blood perfusion and oxygenation. \n\... |
27,723 | MojoSort™ Mouse Neutrophil Isolation Kit Column Protocol | null | dx.doi.org/10.17504/protocols.io.7bjhikn | null | Sam Li | TITLE: MojoSort™ Mouse Neutrophil Isolation Kit Column Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>BioLegend MojoSort™ nanobeads work in commonly used separation columns, based on our internal research as well as validation by external testing by academic labs. Thi... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes.", "In the final wash of your sample preparation, resuspend the cells in MojoSort™ Buffer by adding up to 4 mL in a 5 mL (12 x 75 mm) polypropylene tube.Note: Keep MojoSort™ Buffer on ice throughout the procedure.", "Filter the cells with... |
52,516 | Manual Proibido da Seducao PDF DOWNLOAD GRATIS (BAIXAR) | 3 | dx.doi.org/10.17504/protocols.io.bxicpkaw | https://www.protocols.io/view/manual-proibido-da-seducao-pdf-download-gratis-bai-bxicpkaw | manualproibidodaseducaopdf | TITLE: Manual Proibido da Seducao PDF DOWNLOAD GRATIS (BAIXAR)
AUTHORS: manualproibidodaseducaopdf
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Manual Proibido da Seducao PDF DOWNLOAD GRATIS (BAIXAR)</div></div>
[STEPS] | [] |
47,335 | Egg Prep for Bleach Synchronization (Cabreiro Lab) | 1 | null | https://www.protocols.io/view/egg-prep-for-bleach-synchronization-cabreiro-lab-bsgfnbtn | Saul Moore | TITLE: Egg Prep for Bleach Synchronization (Cabreiro Lab)
AUTHORS: Saul Moore
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Egg prep protocol for bleach synchronisation of </span><span style = "font-style:italic;">C. elegans. </span></div></div>
[STEPS]
?. [Prepare worms]
Leave the Falcon... | ["[Prepare worms]\nLeave the Falcon tube to stand for a while until the worm settle to the bottom in a loose pellet.", "[Egg Prep - Bleaching]\nAdd 350μL bleach mix to the 2mL solution of worms in M9", "[Prepare worms]\nWash worms off the plates with a few mL of M9 buffer into a 15mL Falcon tube.", "[Prepare Bleach Mix... |
28,190 | Thermolabile Proteinase K Typical Reaction Protocol | null | dx.doi.org/10.17504/protocols.io.7r6hm9e | https://www.protocols.io/view/thermolabile-proteinase-k-typical-reaction-protoco-7r6hm9e | New England Biolabs | TITLE: Thermolabile Proteinase K Typical Reaction Protocol
AUTHORS: New England Biolabs
[STEPS]
?. Reactions may be scaled-up linearly to accommodate larger amounts of substrate and larger reaction volumes. Optimal buffering reagents, enzyme quantity, incubation temperatures and times may vary for particular substrat... | ["Reactions may be scaled-up linearly to accommodate larger amounts of substrate and larger reaction volumes. Optimal buffering reagents, enzyme quantity, incubation temperatures and times may vary for particular substrates. Typical restriction enzyme cleanup conditions are as follows:To a restriction enzyme digest co... |
52,125 | CODEX Sample Preparation and Staining Experiment Protocol | 4 | dx.doi.org/10.17504/protocols.io.j8nlk4pmxg5r/v1 | https://www.protocols.io/view/codex-sample-preparation-and-staining-experiment-p-bw55pg86 | Kavya.Anjani , Miguel.Rivera , Zoltanlaszik | TITLE: CODEX Sample Preparation and Staining Experiment Protocol
AUTHORS: Kavya.Anjani , Miguel.Rivera , Zoltanlaszik
[DESCRIPTION]
CODEX system is the combination of an (1) oligo-nucleotide based antibody labeling-detection technique, (2) a microfluidics instrument coupled with an inverted microscope capable of w... | ["[Tissue Sample Preparation Prior to CODEX Staining] Gather necessary materials", "[Tissue Sample Preparation Prior to CODEX Staining] Coat coverslips with poly-lysine.", "[Tissue Sample Preparation Prior to CODEX Staining] Gently place 20 coverslips on the bottom of the glass beaker and slowly swirl the beaker to fan... |
53,062 | Growth of mixed E. coli colonies | 4 | dx.doi.org/10.17504/protocols.io.bx3epqje | https://www.protocols.io/view/growth-of-mixed-e-coli-colonies-bx3epqje | Wolfram Moebius | TITLE: Growth of mixed E. coli colonies
AUTHORS: Wolfram Moebius
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Growth of mixed </span><span style = "font-style:italic;">E. coli</span><span> colonies on agar plates and between an agar plate and an agar pad</span></div></div>
[STEPS]
?. [Mak... | ["[Make plates]\nAutoclave Lennox LB (10 g/l tryptone / casein digest peptone, 5 g/l NaCl, 5 g/l yeast extract) with 1.5 % agar (w/v).", "[Make plates]\nOptional: Add antibiotics at desired concentration after medium has cooled down sufficiently.", "[Make plates]\nPipette of LB and agar in Petri dishes with diameter o... |
32,655 | Novel coronavirus (2019-nCoV) real-time RT-PCR N gene 2020 (Wuhan-N; 2019-nCoV-related test) -NOT RECOMMENDED | null | dx.doi.org/10.17504/protocols.io.bb5piq5n | null | Judy A. Northill, Ian Mackay | TITLE: Novel coronavirus (2019-nCoV) real-time RT-PCR N gene 2020 (Wuhan-N; 2019-nCoV-related test) -NOT RECOMMENDED
AUTHORS: Judy A. Northill, Ian Mackay
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><ul style = "list-style-type:disc;"><li style = "counter-reset:ol0;list-style-type:disc;"><span s... | ["[Mix]\nOligonucleotides ABC1Oligo NameSequence 5'-3'Location based on NC_045512*2Wuhan-TM2020ForTCGTGCTACAACTTCCTCAAG28648-286683Wuhan-TM2020Probe6FAM-CCGCCTCTGCTCCCTTCTGC-BHQ128714-286954Wuhan-TM2020RevCTGCCWGGAGTTGAATTTCTTG28780-28759\nABC1Oligo NameSequence 5'-3'Location based on NC_045512*2Wuhan-TM2020ForTCGTGCT... |
63,163 | Quantification of SARS-CoV-2 variant mutations (HV69-70, E484K/N501Y, del156-157/R158G, del143-145, LPPA24S, S:477-505, and ORF1a Del 141-143) in settled solids using digital RT-PCR | 1 | dx.doi.org/10.17504/protocols.io.14egnzrrzg5d/v7 | https://www.protocols.io/view/quantification-of-sars-cov-2-variant-mutations-hv6-b9w3r7gn | Bridgette Hughes, Bradley J. White, Marlene K. Wolfe, Alexandria B B Boehm | TITLE: Quantification of SARS-CoV-2 variant mutations (HV69-70, E484K/N501Y, del156-157/R158G, del143-145, LPPA24S, S:477-505, and ORF1a Del 141-143) in settled solids using digital RT-PCR
AUTHORS: Bridgette Hughes, Bradley J. White, Marlene K. Wolfe, Alexandria B B Boehm
[DESCRIPTION]
This process instruction descr... | ["[Preparation] Retrieve all kit components from the One-Step RT-ddPCR advanced kit for probes from the -20 °C freezer and thaw the components on ice.", "[Preparation] Retrieve ddPCR positive control aliquots (50 copies per uL gRNA) from the -80 °C freezer and thaw on ice", "[Preparation] For re-running frozen plates o... |
21,146 | UC Davis - Radial Arm Water Maze | null | dx.doi.org/10.17504/protocols.io.yv2fw8e | null | Mari Golub | TITLE: UC Davis - Radial Arm Water Maze
AUTHORS: Mari Golub
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">The radial arm water maze (RAWM) measures spatial learning by combining both a water maze and radial arm maze ... | ["Scheduling and Design: Time of day: Time of day strongly affects performance. For any experiment, testing should take place during the same 2-3 hour period on each day. Morning or afternoon testing at least one hour prior to dark cycle onset are appropriate. Testing after “lights out” in the vivarium is not appropria... |
65,406 | In vitro germination of Austropuccinia psidii urediniospores | 4 | dx.doi.org/10.17504/protocols.io.3byl4b73jvo5/v2 | https://www.protocols.io/view/in-vitro-germination-of-austropuccinia-psidii-ure-cb46sqze | Alyssa M Martino, Rebecca M Degnan | TITLE: In vitro germination of Austropuccinia psidii urediniospores
AUTHORS: Alyssa M Martino, Rebecca M Degnan
[DESCRIPTION]
Optimisation of Austropuccinia psidii urediniospore germination for use in RNA extraction and cytogenetics.
[STEPS]
SECTION: Spore collection, desiccation, and storage
1. Harvest fresh spo... | ["[Spore collection, desiccation, and storage] Harvest fresh spores from heavily infected leaves by shaking into a paper bag.", "[Spore collection, desiccation, and storage] Move fresh spores to a glass petri dish with no lid. Transfer petri dish to a desiccator with silica gel beads for 24 - 48 hours to dry the spores... |
27,228 | Golden Gate Protocol | null | dx.doi.org/10.17504/protocols.io.6t4heqw | null | N.J. Hillson | TITLE: Golden Gate Protocol
AUTHORS: N.J. Hillson
[STEPS]
?. Measure the DNA concentration (ng/ml) of each assembly piece.
?. Add 100 ng of the linearized vector backbone and equimolar amounts of the other assembly pieces to a 15 ml total volume assembly reaction mixture as follows:linearized vector backbone (100 ng)+... | ["Measure the DNA concentration (ng/ml) of each assembly piece.", "Add 100 ng of the linearized vector backbone and equimolar amounts of the other assembly pieces to a 15 ml total volume assembly reaction mixture as follows:linearized vector backbone (100 ng)+ each additional assembly piece (to equimolar with backbone)... |
57,856 | Soft agar for yeast imaging | 4 | null | https://www.protocols.io/view/soft-agar-for-yeast-imaging-b4q8qvzw | leonhard.bandilla | TITLE: Soft agar for yeast imaging
AUTHORS: leonhard.bandilla
[DESCRIPTION]
The here described medium can be used to image yeast without immobilization or compression while allowing for growth in all directions. The medium constists of YPD with agar added at a very low concentration to form a soft gel that allows f... | ["To an autoclavable bottle add per 1l:\n10 g Yeast extract\n20 g Peptone\n1 g Agar", "Invert the bottle to dissolve everything apart from the agar", "Autoclave or heat up sufficiently to dissolve the agar and insure sterility", "Per 1l add 50 mL of sterile 40% glucose and mix, avoid introducing air bubbles", "Let the... |
32,849 | Fresh Frozen Mouse Brain Preparation (for Single Nuclei Sequencing) | null | dx.doi.org/10.17504/protocols.io.bcbrism6 | null | Chuck Vanderburg, Carly Martin, Velina Kozareva, Naeem Nadaf, Nehal Patel, Evan Macosko | TITLE: Fresh Frozen Mouse Brain Preparation (for Single Nuclei Sequencing)
AUTHORS: Chuck Vanderburg, Carly Martin, Velina Kozareva, Naeem Nadaf, Nehal Patel, Evan Macosko
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Mice are anesthetized with 3% isoflourane prior to cardiac perfusion with ice cold HEPE... | ["Mice are anesthetized with 3% isoflourane prior to cardiac perfusion with ice cold HEPES-Sucrose Cutting Solution:", "Their head is removed by bisecting between c2 and c3 with large scissors. The brain is removed immediately as follows:", "The cranial and facial skin and fat pads are peeled forward and the splenius ... |
35,354 | TissueCyte Installation And Alignment Guide | null | dx.doi.org/10.17504/protocols.io.ber2jd8e | null | Allen Institute for Brain Science | TITLE: TissueCyte Installation And Alignment Guide
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines some of the steps that are required to align a TissueCyte 1000 serial two-photon imaging system and install commonly replaced parts.</d... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.izucf6w | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
26,726 | Protocol to determine seed dormancy, imbibition, viability, longevity and germination responses to temperature | null | dx.doi.org/10.17504/protocols.io.6cehate | null | Corrine Duncan, Nick Schultz, Wolfgang Lewandrowski, Megan Good, Simon Cook | TITLE: Protocol to determine seed dormancy, imbibition, viability, longevity and germination responses to temperature
AUTHORS: Corrine Duncan, Nick Schultz, Wolfgang Lewandrowski, Megan Good, Simon Cook
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>We study the seed traits and germination st... | ["[Seed viability]\nTest for seed viability: Place seeds in a petri dish, soak with a 1% solution of 2,3,5-triphenyl tetrazolium chloride (TZ), and incubate seeds under diurnal temperatures for at least 48 hours. Extract seeds from the incubator and perform longitudinal dissections under a microscope to record seed via... |
52,534 | STRIP: Systematic Testing using Robotics and Innovation during Pandemics | 2 | null | https://www.protocols.io/view/strip-systematic-testing-using-robotics-and-innova-bxiwpkfe | Peter H L Krijger, Tim A Hoek, Sanne Boersma, Lieke I P M Donders, Maaike M C Broeders, Mark Pieterse, Pim W Toonen, Ive Logister, Bram M P Verhagen, Marjon J A M Verstegen, Thomas W van Ravesteyn, Rene J T M Roymans, Francesca Mattiroli, Jo Vandesompele, Monique Nijhuis, Stefan Meijer, Anton van Weert, Edwin Dekker, F... | TITLE: STRIP: Systematic Testing using Robotics and Innovation during Pandemics
AUTHORS: Peter H L Krijger, Tim A Hoek, Sanne Boersma, Lieke I P M Donders, Maaike M C Broeders, Mark Pieterse, Pim W Toonen, Ive Logister, Bram M P Verhagen, Marjon J A M Verstegen, Thomas W van Ravesteyn, Rene J T M Roymans, Francesca Mat... | [] |
39,064 | Ancient DNA Extraction from Dental Calculus | 1 | dx.doi.org/10.17504/protocols.io.bidyka7w | https://www.protocols.io/view/ancient-dna-extraction-from-dental-calculus-bidyka7w | Franziska Aron, Courtney Hofman, Zandra Fagernäs, Irina Velsko, Eirini Skourtanioti, Guido Brandt, Christina Warinner | TITLE: Ancient DNA Extraction from Dental Calculus
AUTHORS: Franziska Aron, Courtney Hofman, Zandra Fagernäs, Irina Velsko, Eirini Skourtanioti, Guido Brandt, Christina Warinner
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Silica-based total DNA extraction protocol optimised for the recover... | ["[Day 1: Preparation of reagents (Buffer Prep Room)]\nPrepare cleaned workspace with all necessary reagents and equipment.\nIf lab-wide large-batch pre-prepared reagent stores are used, ensure to have made personal stock-aliquot of reagents such as UV-Water, EDTA, sodium acetate, and proteinase K in amounts sufficient... |
101,997 | Chromatographic separation of strontium in archaeological cremated remains for Thermal Ionisation Mass Spectrometry (TIMS) analysis | 0 | dx.doi.org/10.17504/protocols.io.j8nlk8d5xl5r/v1 | https://www.protocols.io/view/chromatographic-separation-of-strontium-in-archaeo-dfum3nu6 | Maura De Coster, Lisette M. Kootker | TITLE: Chromatographic separation of strontium in archaeological cremated remains for Thermal Ionisation Mass Spectrometry (TIMS) analysis
AUTHORS: Maura De Coster, Lisette M. Kootker
[DESCRIPTION]
This protocol describes in great detail all the steps that must be taken for strontium isotope analysis on archaeological... | ["[Cleaning and leaching] Mechanically clean the cremated bone samples using a handheld drill (e.g., PROXXON or Dremel) to remove the outer layer of the bone, so all soil residue is removed. If present, also remove all of the trabecular bone (but see De Coster et al. 2024 paragraph 4.1). \n\nNext, following the protoc... |
48,313 | Building An Enhanced Flight Mill for the Study of Tethered Insect Flight | 1 | dx.doi.org/10.17504/protocols.io.bteznjf6 | https://www.protocols.io/view/building-an-enhanced-flight-mill-for-the-study-of-bteznjf6 | Anastasia Bernat | TITLE: Building An Enhanced Flight Mill for the Study of Tethered Insect Flight
AUTHORS: Anastasia Bernat
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Makerspaces have a high potential of enabling researchers to develop new techniques and to work with novel species in ecological research. This pr... | ["Build the Flight Mill in a Makerspace", "[Laser cut and assemble the acrylic plastic support structure.]\nUse 8 (304.8 mm x 609.6 mm x 3.175 mm) thick transparent acrylic sheets to construct the acrylic plastic support structure. Ensure that the material is not polycarbonate, which looks similar to acrylic but will m... |
95,137 | Preparation of Free Floating Coronal Mouse Brain Sections | 1 | dx.doi.org/10.17504/protocols.io.dm6gp3pb8vzp/v1 | https://www.protocols.io/view/preparation-of-free-floating-coronal-mouse-brain-s-c859zy96 | madalynn.erb | TITLE: Preparation of Free Floating Coronal Mouse Brain Sections
AUTHORS: madalynn.erb
[DESCRIPTION]
This protocol details the preparation of free floating coronal mouse brain sections.
[STEPS]
SECTION: Collect Mouse Brain Tissue
1. Deeply anesthetize mice via intraperitoneal injection of 2X Avertin solution.
SECTION... | ["[Collect Mouse Brain Tissue] Deeply anesthetize mice via intraperitoneal injection of 2X Avertin solution.", "[Collect Mouse Brain Tissue] Perform transcardial perfusion using chilled saline solution", "[Collect Mouse Brain Tissue] Keep 0.9% NaCl on ice.", "[Collect Mouse Brain Tissue] Use approximately 60 mL saline ... |
106,837 | ImageJ Analyses of Mitochondria (HSP60) in TH+ cells | 0 | dx.doi.org/10.17504/protocols.io.6qpvr8y83lmk/v2 | https://www.protocols.io/view/imagej-analyses-of-mitochondria-hsp60-in-th-cells-dkjv4un6 | Chiara Pavan, Stefano Frausin, Wai Kit (Leo) Lam, Clare Parish | TITLE: ImageJ Analyses of Mitochondria (HSP60) in TH+ cells
AUTHORS: Chiara Pavan, Stefano Frausin, Wai Kit (Leo) Lam, Clare Parish
[DESCRIPTION]
This protocol explains how to use Fiji to analyse mitochondria in iPSC derived dopaminergic neurons in culture for parameters such as network branching, sphericity and mean ... | ["[Image acquisition] Images analysed with this protocol were taken with Leica Stellaris 8 confocal (for mitochondrial morphology and ATG13-HSP60 co-localization, with FLIM 40x/1.30 oil immersion objective, HC PL\nAPO, CS2, using Leica Power HyD detector S and HyD detector X).\n\nAll mitochondria morphology images were... |
92,637 | Materials and assembly for a portable soil greenhouse gas flux collection case | 1 | null | https://www.protocols.io/view/materials-and-assembly-for-a-portable-soil-greenho-c6p5zdq6 | Rachel E. Clarkson, David Walla, Robert Harrison, Myron Coleman, Marty Schmer, VIRGINIA.JIN | TITLE: Materials and assembly for a portable soil greenhouse gas flux collection case
AUTHORS: Rachel E. Clarkson, David Walla, Robert Harrison, Myron Coleman, Marty Schmer, VIRGINIA.JIN
[DESCRIPTION]
The collection of soil nitrous oxide, carbon dioxide, and methane greenhouse gas (GHG) flux measurements utilizing sta... | ["[Plumbing the Flux Case] Flip orientation of solenoid valves", "[Plumbing the Flux Case] Insert and tighten the plastic plug in all five of the solenoid valves", "Cut the Teflon tape in half lengthwise to create two thin strips.", "[Plumbing the Flux Case] Remove the top screw from the solenoid valve using a medium P... |
50,568 | a-commands and Allas | 5 | null | https://www.protocols.io/view/a-commands-and-allas-bvmgn43w | Alise Ponsero | TITLE: a-commands and Allas
AUTHORS: Alise Ponsero
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Main interactions between Puhti and the Allas storage service at CSC using the a-command tools.</div><div class = "text-block"><span>For more detailed documentations on Allas and a-commands: </span><a ... | ["[Connecting to Allas]\nIn order to interact with Allas, especially to push and pull large files, it is best to request an interactive node.After login into Puthi, type the following to request an interactive node.sinteractiveFollow the instructions (choice of a project for the billing) and get an interactive node!", ... |
22,186 | Zebrafish Immunofluorescence Protocol | null | dx.doi.org/10.17504/protocols.io.zwif7ce | null | Kim Kobar | TITLE: Zebrafish Immunofluorescence Protocol
AUTHORS: Kim Kobar
[STEPS]
?. [Day 1]
Dechorionate embryos with two pairs of forceps.
Under a dissecting microscope, pinch an embryo’s chorion using a pair of forceps held in one of your hands. With the forceps in your other hand, pinch the chorion near to the original pinc... | ["[Day 1]\nDechorionate embryos with two pairs of forceps.\nUnder a dissecting microscope, pinch an embryo’s chorion using a pair of forceps held in one of your hands. With the forceps in your other hand, pinch the chorion near to the original pinch and gently tear the chorion by separating your hands. Repeat pinching ... |
15,982 | Protocol for use with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760, E7765) | null | dx.doi.org/10.17504/protocols.io.tunenve | null | New England Biolabs | TITLE: Protocol for use with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760, E7765)
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The NEBNext Ultra II Directional RNA Library Prep K... | ["[mRNA Isolation, Fragmentation and Priming Starting with Total RNA]\nDilute the total RNA with nuclease-free water to a final volume of in a nuclease-free 0.2 ml PCR tube and keep on ice.\n50 µl", "[mRNA Isolation, Fragmentation and Priming Starting with Total RNA]\nTo wash the Oligo dT Beads, add the following to a... |
48,394 | Protocol for Using the Microfluidizer Lysis Apparatus | 1 | null | https://www.protocols.io/view/protocol-for-using-the-microfluidizer-lysis-appara-bthinj4e | Clark Fritsch | TITLE: Protocol for Using the Microfluidizer Lysis Apparatus
AUTHORS: Clark Fritsch
[DESCRIPTION]
The Microfluidizer Lysis apparatus is used to efficiently lyse bacterial and yeast cells using high pressure sheering against a ceramic cone inside the machine. Unlike conventional approaches for cell lysis such as sonica... | ["Begin by filling the red tray next to the Microfluidizer with a ice. Pack the ice densely around the sheering vessel/compartment, as shown in Figure 1. The sheering vessel flows your cells at ultrasonic speeds against a pointed ceramic cone. This quickly and efficiently sheers your cells, but it also heats your sampl... |
19,868 | U Cinn - Triglyceride Assay | null | dx.doi.org/10.17504/protocols.io.xm4fk8w | null | Patrick Tso, Dana Lee | TITLE: U Cinn - Triglyceride Assay
AUTHORS: Patrick Tso, Dana Lee
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Determinations of triglycerides in plasma/serum/lymph will be made using a Randox Triglycerides colorim... | ["Prepare Working Standards by making a serial dilution of the stock 200mg/dl standard. (See diagram below) *Stock standard is included in kit", "Prepare Working Reagent by reconstituting one vial of Enzyme Reagent R1b with a portion of Buffer R1a and then transfer entire contents to bottle R1a, rinsing vial R1b severa... |
92,197 | Modular automated sample processing of biological samples using ultrasonication and a workstation for high-throughput proteomics | 2 | dx.doi.org/10.17504/protocols.io.j8nlkoy56v5r/v1 | https://www.protocols.io/view/modular-automated-sample-processing-of-biological-c6adzaa6 | ronan.ocualain | TITLE: Modular automated sample processing of biological samples using ultrasonication and a workstation for high-throughput proteomics
AUTHORS: ronan.ocualain
[DESCRIPTION]
Sample preparation for mass spectrometry analysis involves numerous liquid transfer steps.
These include
sample lysis,
protein extraction,
so... | [] |
39,454 | CARD-FISH/VirusFISH PROTOCOL | 4 | dx.doi.org/10.17504/protocols.io.bir6kd9e | https://www.protocols.io/view/card-fish-virusfish-protocol-bir6kd9e | Dolors Vaqué, Marta Sebastian | TITLE: CARD-FISH/VirusFISH PROTOCOL
AUTHORS: Dolors Vaqué, Marta Sebastian
[STEPS]
?. [Virus probes design and synthesis]
The VirusFISH method requires that we design, synthetize and label the probes that will hybridize to our virus of interest. In this section we explain what is needed for this purpose.
?. [Buffers p... | ["[Virus probes design and synthesis]\nThe VirusFISH method requires that we design, synthetize and label the probes that will hybridize to our virus of interest. In this section we explain what is needed for this purpose.", "[Buffers preparation for CARD-FISH and VirusFISH]\nIn this step we explain how to prepare the ... |
28,615 | Cloning and mutagenesis | 1 | dx.doi.org/10.17504/protocols.io.77fhrjn | https://www.protocols.io/view/cloning-and-mutagenesis-77fhrjn | Federico Herrera | TITLE: Cloning and mutagenesis
AUTHORS: Federico Herrera
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>We generated a human-GFAP-EGFP fusion construct by randomly inserting the coding region of EFGP into the coding region of hGFAP (A). Briefly, in the presence of a transposase protein, a 190... | [] |
21,736 | FLAVONOID PROFILING BY LIQUID CHROMATOGRAPHY COUPLED TO MASS SPECTROMETRY (LC/MS) | null | dx.doi.org/10.17504/protocols.io.zggf3tw | null | Camilo E. Vital, Jenny D. Gómez, Pedro M. Vidigal, Edvaldo Barros, Claudia S.L. Pontes, Nívea M. Vieira, Maria G. A. Oliveira, Humberto J. O. Ramos | TITLE: FLAVONOID PROFILING BY LIQUID CHROMATOGRAPHY COUPLED TO MASS SPECTROMETRY (LC/MS)
AUTHORS: Camilo E. Vital, Jenny D. Gómez, Pedro M. Vidigal, Edvaldo Barros, Claudia S.L. Pontes, Nívea M. Vieira, Maria G. A. Oliveira, Humberto J. O. Ramos
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Flavon... | ["[3.1 FLAVONOIDS 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 ... |
52,063 | Preparation of biological monolayers for producing high-resolution scanning electron micrographs Code: PLOS2021 [PONE-D-21-26669] - [EMID:f8569bc7b537f6e4] | 3 | dx.doi.org/10.17504/protocols.io.bw37pgrn | https://www.protocols.io/view/preparation-of-biological-monolayers-for-producin-bw37pgrn | Shireen Mentor, Franscious Cummings, David Fisher, shireen.mentor | TITLE: Preparation of biological monolayers for producing high-resolution scanning electron micrographs Code: PLOS2021 [PONE-D-21-26669] - [EMID:f8569bc7b537f6e4]
AUTHORS: Shireen Mentor, Franscious Cummings, David Fisher, shireen.mentor
[DESCRIPTION]
Scanning electron microscopy (SEM) provides a technical pl... | [] |
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