id float64 1.55k 110k ⌀ | title stringlengths 1 256 ⌀ | template_id float64 0 6 ⌀ | doi stringlengths 39 49 ⌀ | url stringlengths 40 92 ⌀ | authors stringlengths 1 933 ⌀ | protocol_text stringlengths 34 1.08M | steps_list stringlengths 2 269k |
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null | null | null | dx.doi.org/10.17504/protocols.io.grubv6w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 1">
<div class="layoutArea">
<div class="column">
<p><strong>Developed for:</strong></p>
<p> </p>
<p>Aerius,<br /> Odyssey® Classic,</p>
<p>Odyssey CLx, and</p>
<p>Odyssey Sa</p>
<p>Imaging Systems</p>
</div>
</div>
</div>
[GUIDELINES]
<p><strong>R... | [] |
68,121 | Use of flow cytometry (Novocyte Advanteon) to monitor the complete life cycle of the parasite Amoebophrya ceratii infecting its dinoflagellate host | 4 | dx.doi.org/10.17504/protocols.io.ewov1nrq2gr2/v1 | https://www.protocols.io/view/use-of-flow-cytometry-novocyte-advanteon-to-monito-cerztd76 | Jeremy Szymczak, Estelle Bigeard, Laure Guillou | TITLE: Use of flow cytometry (Novocyte Advanteon) to monitor the complete life cycle of the parasite Amoebophrya ceratii infecting its dinoflagellate host
AUTHORS: Jeremy Szymczak, Estelle Bigeard, Laure Guillou
[DESCRIPTION]
The parasite belongs to Amoebophrya ceratii (Amoebophryidae or MALVII, which stands for Marin... | ["[Flow cytometer startup procedure] Press the power button located on the front of the flow cytometer to switch it on. The flow cytometer will initiate a series of fluidics steps automatically, which typically takes approximately 5 minutes.\nSwitch on the computer.\nLaunch the cytometer software (NovoExpress).\nLog in... |
73,340 | Hepatitis C Virus (HCV) subtype 1b sequencing protocol v.1 | 4 | dx.doi.org/10.17504/protocols.io.5qpvorkkzv4o/v1 | https://www.protocols.io/view/hepatitis-c-virus-hcv-subtype-1b-sequencing-protoc-cju4unyw | Alí F Ruiz-Higareda, Kame Galan, Julio C Garza-Cabello, Ana G. Rivas-Estilla | TITLE: Hepatitis C Virus (HCV) subtype 1b sequencing protocol v.1
AUTHORS: Alí F Ruiz-Higareda, Kame Galan, Julio C Garza-Cabello, Ana G. Rivas-Estilla
[DESCRIPTION]
Amplicon sequencing protocol for Hepatitis C virus subtype 1b using Oxford Nanopore Technologies.
[STEPS]
SECTION: cDNA synthesis
1. Prepare the RNA-p... | ["[cDNA synthesis] Prepare the RNA-primer Mix following these instructions:", "[cDNA synthesis] Prepare the RT reaction mix following the next steps:", "Incubate the reaction as follows:\n10 min at 55 °C \n10 min at 80 °C", "[cDNA synthesis] Combine and the RNA-primer and RT reaction mixes in a 0.2 mL tube, mix by p... |
71,332 | Assembly of pAOXHygR vector for protein expression in the yeast Pichia pastoris | 4 | dx.doi.org/10.17504/protocols.io.kxygx9pdzg8j/v1 | https://www.protocols.io/view/assembly-of-paoxhygr-vector-for-protein-expression-chwct7aw | Kaia Kukk | TITLE: Assembly of pAOXHygR vector for protein expression in the yeast Pichia pastoris
AUTHORS: Kaia Kukk
[DESCRIPTION]
The protocol describes assembly of an Pichia pastoris expression vector composed of the following building blocks: alcohol oxidase 1 (AOX1) promoter, multiple cloning site, myc epitope, 6xHis tag, AO... | ["The sequences of the vectors pPICZ A (Thermo Fisher), pUDP082 (Addgene, plasmid #103875) and pJET1.2 (CloneJET PCR Cloning Kit,Thermo Fisher) were stored in the Benchling R&D cloud. The pPICZ A vector was used as a source for the sequence encoding AOX1 promoter followed by multiple cloning site (MCS), myc epitope, 6x... |
16,967 | Set of quality indicators for physiotherapy care process of patients with Whiplash-Associated Disorders (WAD) | 1 | dx.doi.org/10.17504/protocols.io.utfewjn | https://www.protocols.io/view/set-of-quality-indicators-for-physiotherapy-care-p-utfewjn | Rob A B Oostendorp | TITLE: Set of quality indicators for physiotherapy care process of patients with Whiplash-Associated Disorders (WAD)
AUTHORS: Rob A B Oostendorp
[DESCRIPTION]
Quality indicators for physiotherapy care process of patients with Whiplash-Associated Disorders (WAD):
. steps of clinical reasoning
. number of indicators
. t... | [] |
91,220 | Protocol for infection of Hymenochirus boettgeri with Batrachochytrium dendrobatidis (Bd) and Ranavirus (Rv) | 1 | dx.doi.org/10.17504/protocols.io.kqdg3xyqzg25/v1 | https://www.protocols.io/view/protocol-for-infection-of-hymenochirus-boettgeri-w-c5buy2nw | Tamilie Carvalho, Evelyn Faust, Francisco De Jesus Andino, Jacques Robert, Timothy Y. James | TITLE: Protocol for infection of Hymenochirus boettgeri with Batrachochytrium dendrobatidis (Bd) and Ranavirus (Rv)
AUTHORS: Tamilie Carvalho, Evelyn Faust, Francisco De Jesus Andino, Jacques Robert, Timothy Y. James
[DESCRIPTION]
This protocol outlines the procedures for exposing H. boettgeri specimens to the pathoge... | ["[Production of pathogens] Preparation of Bd inoculum", "[Production of pathogens] Inoculate several 10 cm Petri dishes containing 1% tryptone media with Bd liquid culture by adding 500 µL with a 1000 pipetman. Usually, one plate per 2 frogs is sufficient. Seal all Petri dishes with parafilm.", "[Production of pathoge... |
66,314 | Prima Weight Loss Reviews Latest Updated Reviews 2022-Does Prima Weight Loss Pills Work Or Scam? | 3 | dx.doi.org/10.17504/protocols.io.e6nvwky59vmk/v1 | https://www.protocols.io/view/prima-weight-loss-reviews-latest-updated-reviews-2-cczisx4e | Prima Weight Loss Pills Reviews | TITLE: Prima Weight Loss Reviews Latest Updated Reviews 2022-Does Prima Weight Loss Pills Work Or Scam?
AUTHORS: Prima Weight Loss Pills Reviews
[DESCRIPTION]
Prima Weight Loss Pills
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.rtbd6in | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><a href="https://www.creative-biolabs.com/phage-display-service.html" target="_blank" rel="noopener noreferrer">Phage display technology</a> is to insert the DNA sequence of a foreign protein or polypeptide into the proper position of the phage coat protein structural gene, s... | [] |
21,193 | Recordings of cervical vagus nerve activity | 1 | dx.doi.org/10.17504/protocols.io.yxhfxj6 | https://www.protocols.io/view/recordings-of-cervical-vagus-nerve-activity-yxhfxj6 | Vitaly Napadow, Ilknur Ay, Catherine Morello | TITLE: Recordings of cervical vagus nerve activity
AUTHORS: Vitaly Napadow, Ilknur Ay, Catherine Morello
[DESCRIPTION]
The goal of this work is to evaluate laterality of vagus nerve efference evoked by unilateral auricular branch of the vagus nerve (ABVN) stimulation by performing bilateral recordings of cervical vagu... | ["CVNA was recorded using hook electrodes from the right and/or left cervical vagus nerve in response to left auricular vagus nerve stimulation.", "[fromNewSection] Ten-to-12 week old male and female Wistar rats ranging in weight from 232-400g were anesthesized.", "[fromNewSection] ABVN stimulation protocol was as foll... |
27,807 | 622.2 URMC HTC Rapid Clearing of Thick Human Lung Tissue Sections | 1 | dx.doi.org/10.17504/protocols.io.7d7hi9n | https://www.protocols.io/view/622-2-urmc-htc-rapid-clearing-of-thick-human-lung-7d7hi9n | Cory Poole, Gloria Pryhuber | TITLE: 622.2 URMC HTC Rapid Clearing of Thick Human Lung Tissue Sections
AUTHORS: Cory Poole, Gloria Pryhuber
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Purpose and Scope of the Procedure: </span></div><div class = "text-block">Provide a relatively rapid clea... | ["[Preparing Reagents]\n1X Phosphate Buffered SalineAdd of 10X Phosphate Buffered Saline to ultrapure water and mix the solution well. Store at room temperature.100% CUBIC-LAdd 16g of ultrapure water to a 50mL conical followed by of Triton X-100. Swirl the tube until the Triton X-100 completely dissolves into soluti... |
36,257 | LR Clonase | null | dx.doi.org/10.17504/protocols.io.bfm9jk96 | https://www.protocols.io/view/lr-clonase-bfm9jk96 | Invitrogen | TITLE: LR Clonase
AUTHORS: Invitrogen
[STEPS]
?. Add the following components to a 1.5-mL microcentrifuge tube at room temperature and mix: • 1–7 μL entry clone (50–150 ng) • 1 μL destination vector (150 ng/μL) • TE bufferǰ pH 8.0, to 8 μL
?. Thaw on ice the LR Clonase™ II enzyme mix for about 2 minutes. Vortex the LR... | ["Add the following components to a 1.5-mL microcentrifuge tube at room temperature and mix: • 1–7 μL entry clone (50–150 ng) • 1 μL destination vector (150 ng/μL) • TE bufferǰ pH 8.0, to 8 μL", "Thaw on ice the LR Clonase™ II enzyme mix for about 2 minutes. Vortex the LR Clonase™ II enzyme mix brefl¢ twice (2 seconds... |
33,941 | High Efficiency Transformation Protocol using NEB 10-beta Competent E. coli (C3019) | 1 | dx.doi.org/10.17504/protocols.io.zewov12ogr24/v6 | https://www.protocols.io/view/high-efficiency-transformation-protocol-using-neb-bddvi266 | New England Biolabs | TITLE: High Efficiency Transformation Protocol using NEB 10-beta Competent E. coli (C3019)
AUTHORS: New England Biolabs
[DESCRIPTION]
This is the High Efficiency Transformation Protocol for C3019H and C3019I cells.
[GUIDELINES]
Transformation Protocol Variables
Thawing: Cells are best thawed on ice and DNA added... | ["Please select whether you have C3019H or C3019I cells.", "Add 1 µL-5 µL containing 1 pg-100 ng to the cell mixture.", "Carefully flick the tube 4-5 times to mix cells and DNA. Do not vortex.", "Place the mixture on ice for 30 min. Do not mix.", "Heat shock at exactly 42 °C for exactly 30 s. Do not mix.", "Place on ic... |
51,641 | Comparative transcriptomics of Oenothera | 4 | dx.doi.org/10.17504/protocols.io.bwnzpdf6 | https://www.protocols.io/view/comparative-transcriptomics-of-oenothera-bwnzpdf6 | Eunice Kariñho-Betancourt, David Carlson | TITLE: Comparative transcriptomics of Oenothera
AUTHORS: Eunice Kariñho-Betancourt, David Carlson
[DESCRIPTION]
We present the comparative transcriptomics protocol employed for evolutionary analysis in the genus Oenothera. We examined genome-wide patterns and functional diversification by searching for orthologous g... | ["[Orthology, phylogenomics and gene family evolution] Transcriptome assembly and functional annotation\n\nRNA-seq reads of 32 Oenothera taxa (63 samples that included replicates for some species) were trimmed and filtered for quality using fastp v.20.0, set to an average PHRED quality score of 20. We employed Trinity ... |
null | null | null | dx.doi.org/10.17504/protocols.io.quxdwxn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><span style="font-weight: 400;">This protocol has been optimized for </span><a href=""https://www.thermofisher.com/us/en/home/life-science/cell-culture/transfection/transfection---selection-misc/neon-transfection-system.html?c" target="_blank" rel="noopener noreferrer"><... | [] |
49,650 | The TARGET System: Rapid Identification of Direct Targets of Transcription Factors by Gene Regulation in Plant Cells | 4 | dx.doi.org/10.17504/protocols.io.buqsnvwe | https://www.protocols.io/view/the-target-system-rapid-identification-of-direct-t-buqsnvwe | Matthew D. Brooks, Kelsey M. Reed, Gabriel Krouk, Gloria M. Coruzzi, Bastiaan O. R. Bargmann | TITLE: The TARGET System: Rapid Identification of Direct Targets of Transcription Factors by Gene Regulation in Plant Cells
AUTHORS: Matthew D. Brooks, Kelsey M. Reed, Gabriel Krouk, Gloria M. Coruzzi, Bastiaan O. R. Bargmann
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The TARGET system allows f... | [] |
53,084 | Multiplexed Iterative FISH Experimental Protocol SOP002.v3.5 | 4 | null | https://www.protocols.io/view/multiplexed-iterative-fish-experimental-protocol-s-bx34pqqw | Rory Kruithoff, Lei Zhou, Douglas Shepherd | TITLE: Multiplexed Iterative FISH Experimental Protocol SOP002.v3.5
AUTHORS: Rory Kruithoff, Lei Zhou, Douglas Shepherd
[DESCRIPTION]
This document, SOP002 - Multiplexed Iterative FISH Experimental Protocol, describes the process for in-situ fluorescence labeling of RNA transcripts in cells and tissues using a layer... | ["[Part 1 - Tissue or Cell-Based Experiment Preparation] Part 1 of this protocol describes the steps to setup a multiplexed iterative FISH experiment for tissue or cell-based samples. These steps are focused on the biochemical requirements for tissue or cell preparation, probe hybridization and imaging.This protocol do... |
81,604 | AAV DNA library generation | 4 | dx.doi.org/10.17504/protocols.io.5jyl8jy89g2w/v1 | https://www.protocols.io/view/aav-dna-library-generation-ctxcwpiw | Sripriya Ravindra Kumar, Timothy F. Shay, Xinhong Chen, David Brown, Tatyana Dobreva, Qin Huang, Xiaozhe Ding, Yicheng Luo, Pétur H. Einarsson, Alon Greenbaum, Min J. Jang, Benjamin E. Deverman, Viviana Gradinaru | TITLE: AAV DNA library generation
AUTHORS: Sripriya Ravindra Kumar, Timothy F. Shay, Xinhong Chen, David Brown, Tatyana Dobreva, Qin Huang, Xiaozhe Ding, Yicheng Luo, Pétur H. Einarsson, Alon Greenbaum, Min J. Jang, Benjamin E. Deverman, Viviana Gradinaru
[DESCRIPTION]
This protocol describes how to generate a DNA lib... | ["[Generation of Library Fragments] Design primers for the randomized insertion.", "[Generation of Library Fragments] Generate the AAV capsid library fragments by PCR using the AAV9 cap gene as template with and forward and reverse primers.", "[Library Assembly] Linearize the rAAV-ΔCap-in-cis-Lox plasmid by restricti... |
65,264 | Immunohistochemistry of liver tissue sections | 4 | dx.doi.org/10.17504/protocols.io.5qpvob1k9l4o/v1 | https://www.protocols.io/view/immunohistochemistry-of-liver-tissue-sections-cbyqspvw | Presha Rajbhandari, Taruna V. Neelakantan, Brent R. Stockwell | TITLE: Immunohistochemistry of liver tissue sections
AUTHORS: Presha Rajbhandari, Taruna V. Neelakantan, Brent R. Stockwell
[DESCRIPTION]
This protocol outlines the steps used to perform standard immunohistochemistry for antibody validation in frozen human liver tissue samples, performed at Molecular Pathology Cor... | ["Cryosection the frozen liver tissue at 5µm thickness and place it on charged slide", "Air dry the sections for 3 minutes 180 min", "Fix the tissue sections in cold acetone for 15 minutes 15 min", "Air dry the sections at room temperature for 2 minutes 2 min", "Incubate the slides in 0.3% hydrogen peroxide in PBS for ... |
95,791 | Delay Discounting Task | 1 | dx.doi.org/10.17504/protocols.io.4r3l22dqql1y/v1 | https://www.protocols.io/view/delay-discounting-task-c9spz6dn | Xiaowen Zhuang, Alexandra Nelson | TITLE: Delay Discounting Task
AUTHORS: Xiaowen Zhuang, Alexandra Nelson
[DESCRIPTION]
This protocol details the Delay discounting task.
[GUIDELINES]
This protocol can be used after following the Basic Operant Training protocol listed separately. That protocol includes information about operant box design and implemen... | ["[Setup] Refer to Basic Operant Training Protocol.", "[Phase 4/Delay Discounting (10 - 15 sessions)] Each session contains three trial types: forced choice delayed/large, forced choice immediate/small, and free choice.", "[Phase 4/Delay Discounting (10 - 15 sessions)] Each session contains four blocks, each using a di... |
76,216 | Adult mouse skin dissociation protocol (on ice) | 1 | dx.doi.org/10.17504/protocols.io.n92ld391og5b/v3 | https://www.protocols.io/view/adult-mouse-skin-dissociation-protocol-on-ice-cnnyvdfw | Andrew Potter | TITLE: Adult mouse skin dissociation protocol (on ice)
AUTHORS: Andrew Potter
[DESCRIPTION]
This protocol was developed to dissociate adult (8-10 wk) mouse skin "on ice". It utilizes two layers of digestion with a Bacillus licheniformis protease cocktail, combined with mechanical disruption from a dounce homogenizer. ... | ["[Isolating tissue] After euthanizing mouse, remove hair using Nair: dab with Nair, wait 30 secs, wipe with wet paper towel.", "[Isolating tissue] Isolate tissue and place in ice-cold hypothermosol.", "[Isolating tissue] Scrape off underlying layer of fatty / connective tissue using scalpel before proceeding.", "[Isol... |
24,772 | Fabrication of DNA constructs by Gibson Assembly and Golden Gate reactions | null | dx.doi.org/10.17504/protocols.io.4fcgtiw | null | Tamara Matute, Isaac Nuñez, Peter Von Dassow, Fernan Federici | TITLE: Fabrication of DNA constructs by Gibson Assembly and Golden Gate reactions
AUTHORS: Tamara Matute, Isaac Nuñez, Peter Von Dassow, Fernan Federici
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>We used this protocol to build a series of codon optimized BFP expressing vectors in the c... | ["[Introduction and rationale]\nGolden Gate assembly creates vectors by combining vectors containing level 0 parts (e.g. promoters, CDSes, terminators) and an acceptor vector. The first step involves the creation of libraries of level 0 parts by 'domesticating' DNA sequences of interest (e.g a promoter or a new fluore... |
99,108 | Test for admin publication | 0 | dx.doi.org/10.17504/protocols.io.kxygxyzmol8j/v1 | https://www.protocols.io/view/test-for-admin-publication-dc2c2yaw | Joanna Sendecka | TITLE: Test for admin publication
AUTHORS: Joanna Sendecka
[DESCRIPTION]
This protocol is created to test the process of publishing by admins and possible curation possibilities. We want to see possible notifications to admins and how the process works.
[GUIDELINES]
This protocol is created to test the process of pub... | ["[Section one and only] This is step one", "[Section one and only] This is sub-step two", "[Section one and only] This is sub-step two", "[Section one and only] Step two"] |
null | null | null | dx.doi.org/10.17504/protocols.io.t2aeqae | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Endozoicomonas are gram-negative bacteria widely and often abundantly associated with marine invertebrates and fish (Yang et al., 2010; Bayer et al., 2013; Nishijima et al., 2013; Hyun et al., 2014; Katharios et al., 2015; Ding et al., 2016; Neave et al., 2017a; Schreiber et al.... | ["Collect coral fragment(s) (approx. finger-sized) in a sterile zip-lock bag. Take notes on sampling conditions (site, sampling depth, habitat).", "It is recommended to process coral fragment(s) right away. If not feasible, maintain at ambient reef water temperatures in flow-through aquaria (Temperature 28°C, salinity ... |
87,629 | Sanger Tree of Life HMW DNA Fragmentation: Diagenode Megaruptor®3 for PacBio HiFi | 4 | dx.doi.org/10.17504/protocols.io.8epv5x2zjg1b/v1 | https://www.protocols.io/view/sanger-tree-of-life-hmw-dna-fragmentation-diagenod-cztmx6k6 | Maja Todorovic, Filipa Sampaio, Caroline Howard | TITLE: Sanger Tree of Life HMW DNA Fragmentation: Diagenode Megaruptor®3 for PacBio HiFi
AUTHORS: Maja Todorovic, Filipa Sampaio, Caroline Howard
[DESCRIPTION]
This protocol describes the fragmentation of HMW DNA from either the MagAttract v.1, Plant MagAttract v.1, or Plant MagAttract v.2 Sanger Tree of Life HMW DNA ... | ["[Laboratory protocol] Label the required number of Diagenode Hydro Tube for each DNA sample that will be sheared; ensure to label the tubes both on the lid and on the side.", "[Laboratory protocol] Prior to transferring the DNA sample from its original tube, first mix the DNA sample by pipetting carefully with wide-b... |
54,394 | Growth Curves of S. elongatus under salt stress and high carbon | 4 | dx.doi.org/10.17504/protocols.io.bzc2p2ye | https://www.protocols.io/view/growth-curves-of-s-elongatus-under-salt-stress-and-bzc2p2ye | Akashdutta | TITLE: Growth Curves of S. elongatus under salt stress and high carbon
AUTHORS: Akashdutta
[DESCRIPTION]
When liquid media is inoculated with bacteria and the cell population is counted at intervals, it is possible to plot a typical bacterial growth curve that shows the increase in the number of cells over time. Suc... | ["Grow 100 mL of culture in a 250 mL flask in CoBG-11 medium.", "To this add bicarbonate equivalent to 0.6% carbon dioxide., or 2 g/L of sodium bicarbonate in CoBG-11", "12 hours later, take 3 1 mL samples from each flask in 2 microcentrifuge tubes", "Use one set of samples to take the OD measurements", "Take the othe... |
60,261 | Genomic RNA extraction by TRIzol method by using Drosophila melanogaster gut | 4 | dx.doi.org/10.17504/protocols.io.dm6gpb92plzp/v1 | https://www.protocols.io/view/genomic-rna-extraction-by-trizol-method-by-using-d-b64drgs6 | Mohamed Sabeelil Islam | TITLE: Genomic RNA extraction by TRIzol method by using Drosophila melanogaster gut
AUTHORS: Mohamed Sabeelil Islam
[DESCRIPTION]
Simple method followed for RNA extraction of Drosophila melanogaster larval(3rd instar) gut for CDNA
[GUIDELINES]
ware gloves while extraction
[STEPS]
1. Dissection was used to isolate... | ["Dissection was used to isolate the larval gut of Drosophila 3rd Instar.\n(around 10-15 gut was taken)", "The dissected gut was taken in a 1.5ml ependorf tube which contained 200μL of TRIzol.\n\n(For a total of 800μL or 0.8 mL of TRIzol needed for the extraction)\nTo avoid spurt, 200μL were taken.", "Homogenize by usi... |
38,311 | Animal Room (Covid-19 Shutdown Re-Entry, Srivastava Lab) | 1 | dx.doi.org/10.17504/protocols.io.bhnfj5bn | https://www.protocols.io/view/animal-room-covid-19-shutdown-re-entry-srivastava-bhnfj5bn | Srivastava Lab | TITLE: Animal Room (Covid-19 Shutdown Re-Entry, Srivastava Lab)
AUTHORS: Srivastava Lab
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Disclaimer: </span><span>The SOP presented here has been designed by the Srivastava Lab at Harvard University and is being shared ... | ["Wash hands before entering the animal room.\nIf you choose to wear gloves, be cognizant not to touch sea water that will come in contact with the animals", "Turn on water", "Wash hands", "Dry hands with paper towel", "Turn off faucet with paper towel", "Turn on the HEPA filter", "Wipe surfaces (bench, incubator handl... |
64,299 | Immunohistochemistry | 4 | dx.doi.org/10.17504/protocols.io.14egn7yyzv5d/v1 | https://www.protocols.io/view/immunohistochemistry-ca2jsgcn | Beatriz E Nielsen | TITLE: Immunohistochemistry
AUTHORS: Beatriz E Nielsen
[DESCRIPTION]
This protocol describes the steps for performing immunohistochemistry.
[STEPS]
SECTION: Cardiac Perfusion
1. Prepare solutions and tools.
SECTION: Brain Harvesting and Storage
8. Remove brain.
SECTION: Tissue Sectioning (Cryostat)
12. Prepare cryost... | ["[Cardiac Perfusion] Prepare solutions and tools.", "[Brain Harvesting and Storage] Remove brain.", "[Tissue Sectioning (Cryostat)] Prepare cryostat:\nTemperature in the chamber and at the chuck holder set to -20 °C \nReplace blade if needed", "[Immunostaining and Mounting Sections] Wash sections three times in 1X PBS... |
72,946 | Sample preparation for genome wide DNA methylation analysis | 4 | dx.doi.org/10.17504/protocols.io.x54v9dpo1g3e/v1 | https://www.protocols.io/view/sample-preparation-for-genome-wide-dna-methylation-cjgsujwe | Shyaron Poudel, Asela Wijeratne | TITLE: Sample preparation for genome wide DNA methylation analysis
AUTHORS: Shyaron Poudel, Asela Wijeratne
[DESCRIPTION]
Background: DNA methylation, the most common epigenetic modification, is defined as the removal or addition of methyl groups to cytosine bases. Studying DNA methylation provides insight into the r... | ["[Plant growth and DNA isolation] a)\tGrow seeds of soybean genotype Williams 82 in a Miracle-Gro Moisture Control potting medium at 25°°C, 16 h d−1 light at 230 to 365 μM m−2 s−1, and 90% relative humidity in a growth chamber.", "[Plant growth and DNA isolation] b)\tCollect a trifoliate leaf at the V2 developmental s... |
50,630 | SRB viability assay for Acanthamoeba castellanii | 4 | dx.doi.org/10.17504/protocols.io.bvpen5je | https://www.protocols.io/view/srb-viability-assay-for-acanthamoeba-castellanii-bvpen5je | Carrie A. Flynn, Rebecca Colon-Rios, Barbara Kazmierczak | TITLE: SRB viability assay for Acanthamoeba castellanii
AUTHORS: Carrie A. Flynn, Rebecca Colon-Rios, Barbara Kazmierczak
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Viability assay for </span><span style = "font-style:italic;">Acanthamoeba castellanii </span><span>trophozoites and cysts,... | ["[Cell preparation]\nGrow Acanthamoeba castellanii trophozoites in in vented tissue culture-treated 75 cm2 cell culture flasks at without shaking. Passage 1:80 every 3-4 days.\n[PYG media]\n25 °C", "[Cell preparation]\nAdd to flasks and close lids tightly. Gently tap all surfaces of flasks on benchtop to dislodge t... |
84,902 | Bulk RNA sequencing | 4 | dx.doi.org/10.17504/protocols.io.rm7vzx362gx1/v1 | https://www.protocols.click/view/bulk-rna-sequencing-cw6exhbe | Connor Monahan | TITLE: Bulk RNA sequencing
AUTHORS: Connor Monahan
[DESCRIPTION]
This protocol details bulk RNA sequencing from the mouse small intestine.
[STEPS]
SECTION: Procedure
1. Collect the ileum from a PBS-perfused mouse.
SECTION: Procedure
2. Thoroughly flush the ileum sample with cold 1x PBS.
SECTION: Procedure
3. Incubate... | ["[Procedure] Collect the ileum from a PBS-perfused mouse.", "[Procedure] Thoroughly flush the ileum sample with cold 1x PBS.", "[Procedure] Incubate samples in TRIzol reagent (Thermo Fisher Scientific, Cat #15596026; Waltham, MA) and store at -80 °C until ready for bulk RNA sequencing.", "[Procedure] Extract RNA and c... |
34,907 | s3-WGS | 1 | dx.doi.org/10.17504/protocols.io.beb3jaqn | https://www.protocols.io/view/s3-wgs-beb3jaqn | Andrew Adey | TITLE: s3-WGS
AUTHORS: Andrew Adey
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">s3WGS (symmetrical strand single-cell combinatorial indexing; whole genome sequencing) protocol for the capture of genomic reads in single-cells.</div><div class = "text-block"><span>See </span><a href="https://mul... | ["[Prepare oligoes and transposases]\nAttached is a s3 molecular layout per step. As well as oligonucleotides used in the protocol. Prior to starting, iTSM plate should be prepared following the protocols listed within this step.Tabs with oligonucleotides to be ordered and prepared:iTSM sci_WGA14_ME_LNAPCR_i5 primersPC... |
84,389 | Fluorescent in situ hybridisation for juvenile Fasciola hepatica | 4 | dx.doi.org/10.17504/protocols.io.3byl4q7xjvo5/v1 | https://www.protocols.io/view/fluorescent-in-situ-hybridisation-for-juvenile-fas-cwndxda6 | Duncan Wells, Paul McCusker, Rebecca Armstrong, Emily Robb | TITLE: Fluorescent in situ hybridisation for juvenile Fasciola hepatica
AUTHORS: Duncan Wells, Paul McCusker, Rebecca Armstrong, Emily Robb
[DESCRIPTION]
This FISH protocol has been adapted for use in Fasciola hepatica, specifically 4-week-old juveniles, grown in vitro in 50% Chicken Serum, 50% RPMI culture medium. Th... | ["[Worm Preparation] Carry out excystment (see McVeigh et al., 2014), transfer newly excysted juveniles to 96-well round-bottomed plates, in groups of <25 NEJs per well. Add 200μl of pre-warmed, pre-mixed 50:50 chicken serum (New Zealand Origin, 16110082, Thermo) and RPMI (11835030, Thermo). Replace this every other da... |
43,012 | PBMC Thawing Protocol | 4 | dx.doi.org/10.17504/protocols.io.bm9ck92w | https://www.protocols.io/view/pbmc-thawing-protocol-bm9ck92w | Fang Zhang | TITLE: PBMC Thawing Protocol
AUTHORS: Fang Zhang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details methods for thawing peripheral blood mononuclear cells (PBMC). </div><br/><div class = "text-block"><span>For a protocol detailing Culture and Stimulation, please view the following... | ["Warm Washing buffer and medium to in a water bath.\n37 °C", "Remove vials from liquid nitrogen and transport them to the lab on dry ice.", "Thaw frozen vials, only 1 vial at a time, in a water bath. When cells are nearly completely thawed, carry the vials to the hood and swab them with 70% EtOH.\n37 °C", "Gently re... |
96,525 | Strawberry Hermit Crabs & Pisonia Leaves | 0 | dx.doi.org/10.17504/protocols.io.j8nlko76xv5r/v1 | https://www.protocols.io/view/strawberry-hermit-crabs-amp-pisonia-leaves-dahm2b46 | Marcella Welter, Eva Louise Gibbs-Zehnder, Kat Osborn, Melissa Andico Murphy | TITLE: Strawberry Hermit Crabs & Pisonia Leaves
AUTHORS: Marcella Welter, Eva Louise Gibbs-Zehnder, Kat Osborn, Melissa Andico Murphy
[DESCRIPTION]
The Strawberry Hermit Crab experiment is useful to understand more about the repercussions of nutrient depletion on motus in Tetiaroa with invasive species- particula... | ["[Introduction] What is the problem? \nRepercussions of nutrient depletion on atolls (Tiaraunu and Tahuna Iti) with invasive species like rats \n\nWhy is that a problem we care about? \nStrawberry Hermit Crabs are a vital species on Tetiaroa and it is important that they get enough nutrients to support a stable popula... |
54,517 | Protocolo do experimento - CPBL/MA/FGAD (Projeto: Elaborar seminário de Biodiversidade) | 1 | dx.doi.org/10.17504/protocols.io.bzgvp3w6 | https://www.protocols.io/view/protocolo-do-experimento-cpbl-ma-fgad-projeto-elab-bzgvp3w6 | Geiser Chalco Challco | TITLE: Protocolo do experimento - CPBL/MA/FGAD (Projeto: Elaborar seminário de Biodiversidade)
AUTHORS: Geiser Chalco Challco
[DESCRIPTION]
Main protocol in portugues used to conduct a quasi-experimental study of group formation of high performance in Collaborative-Learning-Projects with Agile Methods
[STEPS]
SECTI... | ["[Pré-teste] Aplicar um questionário para medir o conhecimento prévio do estudante no assunto de Biodiversidade.\nO questionário será disponibilizado através do microsoft forms, com 15 questões de múltipla escolha (com 5 alternativas em cada questão). O questionário será acerca de Biodiversidade (tema do seminário) e ... |
78,361 | Adverse Event Reporting (Part 7 of "Effects of Online Exercise Intervention on Physical and Mental Conditions in Young Adults with Chronic Neck Pain") | 1 | dx.doi.org/10.17504/protocols.io.dm6gpjm88gzp/v1 | https://www.protocols.io/view/adverse-event-reporting-part-7-of-34-effects-of-on-cqrzvv76 | Yiting Lin | TITLE: Adverse Event Reporting (Part 7 of "Effects of Online Exercise Intervention on Physical and Mental Conditions in Young Adults with Chronic Neck Pain")
AUTHORS: Yiting Lin
[DESCRIPTION]
This is Part 7 of "Effects of Online Exercise Intervention on Physical and Mental Conditions in Young Adults with Chron... | [] |
65,175 | PUMP/probe experiment | 1 | dx.doi.org/10.17504/protocols.io.14egn71zyv5d/v1 | https://www.protocols.io/view/pump-probe-experiment-cbvxsn7n | Alison E E. Malcolm | TITLE: PUMP/probe experiment
AUTHORS: Alison E E. Malcolm
[DESCRIPTION]
Run a PUMP/probe experiment as described by Gallot, T., et al. "Characterizing the nonlinear interaction of S-and P-waves in a rock sample." Journal of Applied Physics 117.3 (2015): 034902.
[GUIDELINES]
It is best to run the experiment once with ... | ["[Pre-Experiment Steps] Gather equipment and attach transducers to samples. (Typically P traveling perpendicular to S with the polarization of the S-wave aligned with the polarization of the P-wave.)", "[Pre-Experiment Steps] Measure pump and probe velocities using the 'measuring velocities' protocol.", "[Pre-Experim... |
37,997 | Flash Freezing Unclaimed Islets | 4 | dx.doi.org/10.17504/protocols.io.bhcmj2u6 | https://www.protocols.io/view/flash-freezing-unclaimed-islets-bhcmj2u6 | Integrated Islet Distribution Program | TITLE: Flash Freezing Unclaimed Islets
AUTHORS: Integrated Islet Distribution Program
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The objective of the Integrated Islet Distribution Program (IIDP) is to develop a standardized procedure for the freezing and storage of unclaimed islet tissue ... | ["[Materials]\nLaboratory Supplies:The following supplies are necessary for the preparation of human islets prior to flash freezing for distribution.Islet preparation and distributionSterile pipettes, pipettors, and other appropriate sterile labware for manipulation of islet preparations.Hanks Buffered Salt Solution (H... |
55,423 | Immunofluorescence | 4 | dx.doi.org/10.17504/protocols.io.b2c7qazn | https://www.protocols.io/view/immunofluorescence-b2c7qazn | Daehun Park, Pietro De Camilli | TITLE: Immunofluorescence
AUTHORS: Daehun Park, Pietro De Camilli
[DESCRIPTION]
This protocol details methods for the immunofluorescence staining of neurons.
[STEPS]
SECTION: Protocol
1. Wash cultured hippocampal neurons with pre-warmed tyrode.
SECTION: Protocol
2. Fix the cells with fixative solution for 15 min at R... | ["[Protocol] Wash cultured hippocampal neurons with pre-warmed tyrode.", "[Protocol] Fix the cells with fixative solution for 15 min at Room temperature.", "[Protocol] After fixation, wash the cells with PBS.", "[Protocol] Wash the cells briefly with PBS and incubate the cells with primary antibodies (1:500 ~ 1:2000) i... |
75,102 | LEGACY01: QUALITY ASSURANCE AND CONTROL | 1 | null | https://www.protocols.io/view/legacy01-quality-assurance-and-control-cmj6u4re | Katrina M Pollock, Calliope Dendrou | TITLE: LEGACY01: QUALITY ASSURANCE AND CONTROL
AUTHORS: Katrina M Pollock, Calliope Dendrou
[DESCRIPTION]
This protocol details quality assurance and control in an experimental medicine study of seasonal influenza vaccination responses in Lymph nodE single-cell Genomics in AnCestrY (LEGACY01).
[GUIDELINES]
QUALITY AS... | [] |
62,978 | Uncaged Male Enhancement Reviews, Benefits, Shocking Price, *Restore Sex Drive Level* | 3 | dx.doi.org/10.17504/protocols.io.261gen9rog47/v1 | https://www.protocols.io/view/uncaged-male-enhancement-reviews-benefits-shocking-b9rar52e | macpaqtus | TITLE: Uncaged Male Enhancement Reviews, Benefits, Shocking Price, *Restore Sex Drive Level*
AUTHORS: macpaqtus
[DESCRIPTION]
Uncaged Male Enhancement reviews, benefits, and shocking price, give the best results for bigger penis size 100% safe & risk-free. It is loaded with many crucial vitamins and min... | [] |
44,341 | Calculation_and_Normalization_of_Relative_Gene_Abundance | 5 | dx.doi.org/10.17504/protocols.io.bpivmke6 | https://www.protocols.io/view/calculation-and-normalization-of-relative-gene-abu-bpivmke6 | Fan Wei, Fan Jiang | TITLE: Calculation_and_Normalization_of_Relative_Gene_Abundance
AUTHORS: Fan Wei, Fan Jiang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Calculate the relative abundance of gene for metagenome analysis.</div></div>
[STEPS]
?. Mapping the clean reads (abc.clean.read1.fq.gz, abc.clean.read2.fq.gz)... | ["Mapping the clean reads (abc.clean.read1.fq.gz, abc.clean.read2.fq.gz) of each sample to all sequences of the indexed gene catalog", "Construction of the bwa index for the gene catalog (MGCA_gene_Catalog.fasta)", "Selecting the first and last columns from the output file (abc.clean.fq.gz.sam.gz..mapping.abundance), ... |
21,490 | Protocol for publishing | null | dx.doi.org/10.17504/protocols.io.y8sfzwe | null | Andrew Khramchenkov | TITLE: Protocol for publishing
AUTHORS: Andrew Khramchenkov
[STEPS]
?. [Section 1]
?. [Section 1]
?. [Section 2] | ["[Section 1]", "[Section 1]", "[Section 2]"] |
92,195 | Automated 96 well plate based protein reduction and alkylation using a Beckman Biomek™ NxP workstation | 1 | dx.doi.org/10.17504/protocols.io.eq2lyj4delx9/v1 | https://www.protocols.io/view/automated-96-well-plate-based-protein-reduction-an-c6abzaan | ronan.ocualain | TITLE: Automated 96 well plate based protein reduction and alkylation using a Beckman Biomek™ NxP workstation
AUTHORS: ronan.ocualain
[DESCRIPTION]
Sample preparation for mass spectrometry analysis involves numerous liquid transfer steps.
These include
sample lysis,
protein extraction,
solubilisation,
estimation... | ["[Preparation] Double click the software icon.", "[Preparation] Under the Method tab, select home all axes to orient and prepare the automated liquid handler.", "[Preparation] Under File, select Open/Method. Select the ProteinLysateReductionAlkylationV01 method.", "[Preparation] To the deck of the NxP, add two p20 tip... |
98,913 | kpoint Inhibitors Combined with Radiotherapy or Chemoradiotherapy for Advanced Non-Small Cell Lung Cancer: A Systematic Review and Single-Arm Meta-Analysis | 0 | dx.doi.org/10.17504/protocols.io.261ge54njg47/v2 | https://www.protocols.io/view/kpoint-inhibitors-combined-with-radiotherapy-or-ch-dct92wr6 | ran cui, ran cui | TITLE: kpoint Inhibitors Combined with Radiotherapy or Chemoradiotherapy for Advanced Non-Small Cell Lung Cancer: A Systematic Review and Single-Arm Meta-Analysis
AUTHORS: ran cui, ran cui
[DESCRIPTION]
Background: The recent usage of immunotherapy combined with chemoradiotherapy has improved survival in advanced non-... | ["[steps] Develop a research question and hypothesis:Clearly define the research question and hypothesis for the meta-analysis, focusing on the efficacy and safety of concurrent immune checkpoint inhibitors combined with radiotherapy or chemoradiotherapy for advanced non-small cell lung cancer.", "[steps] Register the ... |
86,355 | Labyrinthulomycete total RNA extraction protocol - hot phenol | 4 | null | https://www.protocols.io/view/labyrinthulomycete-total-rna-extraction-protocol-h-cyjtxunn | Jackie Collier | TITLE: Labyrinthulomycete total RNA extraction protocol - hot phenol
AUTHORS: Jackie Collier
[DESCRIPTION]
Modified from Lippmeier et al. 2009; developed as part of the labyrinthulomycete JGI Community Sequencing Project and Gordon and Betty Moore Foundation Marine Microbial Eukaryote Transcriptome Sequencing Project ... | ["[Preparing biomass and reagents] Grow up cells, collect, and freeze rapidly - preferably in liquid nitrogen. Store biomass at -80C if not extracting immediately. \nThis protocol has worked so far for two different thraustochytrids (Aurantiochytrium limacinum ATCC MYA-1381, Schizochytrium aggregatum ATCC 28920) and tw... |
null | null | null | dx.doi.org/10.17504/protocols.io.ssceeaw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for extraction of tissue RNA by Qiagen Mini Kit.</p>
[BEFORE_START]
<p>Clean the benches and all the material that you will use with alcohol 70.<br />Use tips with filter.</p>
<p> </p>
<p>Add 4 volumes of ethanol 100 to 4 volume RPE buffer.</p>
<p>To lyse your sampl... | [] |
55,410 | High-throughput and cost effective pan trap DNA extraction | 4 | dx.doi.org/10.17504/protocols.io.b2csqawe | https://www.protocols.io/view/high-throughput-and-cost-effective-pan-trap-dna-ex-b2csqawe | Jordan P Cuff, James JN Kitson | TITLE: High-throughput and cost effective pan trap DNA extraction
AUTHORS: Jordan P Cuff, James JN Kitson
[DESCRIPTION]
This protocol is designed for extracting DNA from pan trap-collected invertebrates for biomonitoring and community metabarcoding. The reagents and methods proposed offer a cost effective and high-thr... | ["[Preparation and homogenisation of samples] Vortex each sample to mix and incubate at 37 °C overnight (12-16 hours).", "[DNA extraction and purification] Add all of the sample solution (~ 600 μL) to a well in a 96-well silica membrane spin-column plate and cover with a breathable seal.", "[DNA extraction and purifica... |
64,460 | Open Eye Hemp Relief Helps To Vanish Joint Pains (Anxiety Killer) | 3 | dx.doi.org/10.17504/protocols.io.yxmvmnmr6g3p/v1 | https://www.protocols.io/view/open-eye-hemp-relief-helps-to-vanish-joint-pains-a-ca7kshkw | Open Eye Hemp Relief | TITLE: Open Eye Hemp Relief Helps To Vanish Joint Pains (Anxiety Killer)
AUTHORS: Open Eye Hemp Relief
[DESCRIPTION]
https://www.mynewsdesk.com/iexponet/pressreleases/open-eye-hemp-roller-reviews-how-does-oeh-reliefx-roller-helps-to-relieve-chronic-pain-3188258
[STEPS] | [] |
37,812 | Immunofluorescent staining of pancreatic sections | 4 | dx.doi.org/10.17504/protocols.io.bg6ujzew | https://www.protocols.io/view/immunofluorescent-staining-of-pancreatic-sections-bg6ujzew | Caroline CT Tremblay, Valentine Moullé, Bader Zarrouki, Julien Ghislain, Vincent Poitout | TITLE: Immunofluorescent staining of pancreatic sections
AUTHORS: Caroline CT Tremblay, Valentine Moullé, Bader Zarrouki, Julien Ghislain, Vincent Poitout
[DESCRIPTION]
This protocol describes the steps for performing fluorescence immunohistochemistry on fixed-frozen pancreatic tissue sections. It is suitable for p... | ["[Preparation of cryosections] Preparing cryosections \nSet the cryostat and the pedestal temperature at -20 °C. \nGather all of the needed material (OCT, slides, pencil, blades, paintbrushes, aluminium foil, slide box, tissues). \nCut cryosections at 0.8 µm thickness and collect on Superfrost Plus microscopic slides.... |
49,277 | Antibody Conjugation and CODEX Multiplexed Immunofluorescence of Fresh Frozen Tissue | 1 | dx.doi.org/10.17504/protocols.io.buc5nsy6 | https://www.protocols.io/view/antibody-conjugation-and-codex-multiplexed-immunof-buc5nsy6 | Elizabeth Neumann, Carrie Romer, Nathan Heath Patterson, Jamie Allen, Jeff Spraggins | TITLE: Antibody Conjugation and CODEX Multiplexed Immunofluorescence of Fresh Frozen Tissue
AUTHORS: Elizabeth Neumann, Carrie Romer, Nathan Heath Patterson, Jamie Allen, Jeff Spraggins
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes antibody conjugation, tissue preparation,... | ["[Antibody Conjugation for Custom Antibody Markers]\nStart with purified antibodies (no BSA, azides, glycerol, etc.). If BSA is present, remove with ab173231.", "[Antibody Conjugation for Custom Antibody Markers]\nBlock 50 kDa molecular weight cut off filters with of filter blocking solution.\n500 µl", "[Antibody Co... |
87,499 | E.Z.N.A.® Plasmid DNA Maxi Kit Centrifugation Protocol (modified) | 4 | null | https://www.protocols.io/view/e-z-n-a-plasmid-dna-maxi-kit-centrifugation-protoc-czpjx5kn | Bettina Ergün | TITLE: E.Z.N.A.® Plasmid DNA Maxi Kit Centrifugation Protocol (modified)
AUTHORS: Bettina Ergün
[DESCRIPTION]
Describes a modified protocol to use the E.Z.N.A.® Plasmid DNA Maxi Kit # D6922 from Omega Bio-Tek without Ultracentrifuge.
For additionally information read the manufacturer's manual (attached)
[STEPS]
SECT... | ["[Extraction and purification] Transfer 50-200 mL overnight culture to an appropriate centrifuge tube\n\nNote: The optimal volume to use depends on the culture density and plasmid copy number. The optimal cell mass (OD600 x mL culture) for the HiBind‱ DNA Maxi Column is 300-400. For example, if the OD600 of a culture ... |
87,005 | CUTAC for FFPEs | 1 | dx.doi.org/10.17504/protocols.io.14egn292zg5d/v2 | https://www.protocols.io/view/cutac-for-ffpes-cy75xzq6 | Steven Henikoff | TITLE: CUTAC for FFPEs
AUTHORS: Steven Henikoff
[DESCRIPTION]
For more than a century, Formalin Fixed Paraffin Embedded (FFPE) sample preparation has been the preferred method for long-term preservation of biological material. However, the use of FFPE samples for epigenomic studies has been difficult because of chroma... | ["[REAGENT SETUP (for up to 16 samples)] Cross-link reversal buffer Mix 800 µL 1 M Tris-HCl pH8.0, 200 µL dH2O.\n\nRinse buffer Mix 1 mL 1 M HEPES pH 7.5 and 1.5 mL 5 M NaCl, 250 µl Triton-X100 and bring the final volume to 50 mL with dH2O.\n\nTriton-Wash buffer Mix 1 mL 1 M HEPES pH 7.5, 1.5 mL 5 M NaCl, 250 µl Triton... |
88,521 | PCR Clean-up | 4 | dx.doi.org/10.17504/protocols.io.ewov1q212gr2/v1 | https://www.protocols.io/view/pcr-clean-up-c2phydj6 | NUS iGEM | TITLE: PCR Clean-up
AUTHORS: NUS iGEM
[DESCRIPTION]
2023 NUS-Singapore iGEM team followed this protocol to isolate the known DNA fragments from the PCR product without running the gel electrophoresis.
[STEPS]
1. Add 5 times the sample's volume of into the PCR tube with the PCR product.
3. Centrifuge the tube at 1... | ["Add 5 times the sample's volume of into the PCR tube with the PCR product.", "Centrifuge the tube at 13 rpm, 1 min.", "Discard the flow-through and place the QIAquick column back into the same tube.", "Add 700 µL of into the QIAquick column.", "Discard the flow-through and place the QIAquick column back into the ... |
79,597 | selSeq: A method for the enrichment of non-polyadenylated RNAs including enhancer and long non-coding RNAs for sequencing | 4 | dx.doi.org/10.17504/protocols.io.j8nlkwpk6l5r/v1 | https://www.protocols.io/view/selseq-a-method-for-the-enrichment-of-non-polyaden-crymv7u6 | Jason D Limberis, Joel Ernst, John Metcalfe, Alina Nalyvayko | TITLE: selSeq: A method for the enrichment of non-polyadenylated RNAs including enhancer and long non-coding RNAs for sequencing
AUTHORS: Jason D Limberis, Joel Ernst, John Metcalfe, Alina Nalyvayko
[DESCRIPTION]
Non-polyadenylated RNA includes a large subset of crucial regulators of RNA expression and constitutes a s... | ["[poly-A tailed cDNA synthesis] Mix the following in a 0.2ml tube\n COMPONENT Volume Total RNA 1 Oligo dTs 1.5 10 mM dNTP 1.5 Nuclease-free H2O 10", "[poly-A tailed cDNA synthesis] Spin tube briefly and add the following and mix by pipetting\n COMPON... |
78,067 | Isolation of NeuN+ cells from brain tissue (for CUT and RUN) | 4 | dx.doi.org/10.17504/protocols.io.4r3l27pejg1y/v1 | https://www.protocols.io/view/isolation-of-neun-cells-from-brain-tissue-for-cut-cqgtvtwn | anita.adami | TITLE: Isolation of NeuN+ cells from brain tissue (for CUT and RUN)
AUTHORS: anita.adami
[DESCRIPTION]
This protocol describes the steps to isolate NeuN+ cells from brain tissue in preparation for CUT and RUN
[STEPS]
SECTION: Isolation of NeuN+ cells
1. Nuclei were isolated from frozen tissue as described here.
SECT... | ["[Isolation of NeuN+ cells] Nuclei were isolated from frozen tissue as described here.", "[Isolation of NeuN+ cells] Before FACSing, nuclei were incubated with Recombinant Alexa Fluor® 488 Anti-NeuN antibody [EPR12763] - Neuronal Marker (Abcam, Cat# ab190195, RRID:AB_2716282) at a concentration of 1:500 for 30 min on ... |
92,389 | Whole-genome CRISPR Screening of stably expressing Cas9 Cancer Organoid Lines | 4 | dx.doi.org/10.17504/protocols.io.3byl4q6zrvo5/v1 | https://www.protocols.io/view/whole-genome-crispr-screening-of-stably-expressing-c6gdzbs6 | Tessa Fowler, Jade Smith, Adam Jackson, Agnieszka Andres, Emily Souster, Hazel Rogers, Alexandra Beck, Charlotte Beaver, Mathew Garnett | TITLE: Whole-genome CRISPR Screening of stably expressing Cas9 Cancer Organoid Lines
AUTHORS: Tessa Fowler, Jade Smith, Adam Jackson, Agnieszka Andres, Emily Souster, Hazel Rogers, Alexandra Beck, Charlotte Beaver, Mathew Garnett
[DESCRIPTION]
This protocol is for whole-genome CRISPR screening of stably expressing Cas... | ["[Puromycin titration] Day 1: Titration plate set up", "[Puromycin titration] Pre-warm organoid specific culture media to room temperature.", "[Puromycin titration] Aspirate media from each well of the organoid culture plate plate and add 2 mL TrypLE to each well.", "[Puromycin titration] Using a cell-scraper detach B... |
92,342 | Neuromelanin quantification in formalin-fixed substantia nigra and locus coeruleus | 4 | dx.doi.org/10.17504/protocols.io.14egn29bpg5d/v2 | https://www.protocols.io/view/neuromelanin-quantification-in-formalin-fixed-subs-c6ewzbfe | Dipshay Avi Chand, Miriam Scadeng, Birger Victor Dieriks | TITLE: Neuromelanin quantification in formalin-fixed substantia nigra and locus coeruleus
AUTHORS: Dipshay Avi Chand, Miriam Scadeng, Birger Victor Dieriks
[DESCRIPTION]
There are limited methods for absolute quantification of neuromelanin in brain regions such as the substantia nigra and locus coeruleus. While stereo... | ["[Neuromelanin synthesis] Add 50 mL phosphate buffer, 630 μL dopamine stock solution, 61 μL L-cysteine stock solution, and 250 μL mushroom tyrosinase stock to an Erlenmeyer flask", "[Neuromelanin synthesis] Wrap the flask with aluminium foil and make small holes on top; this protects the reaction from light but allo... |
42,096 | ATAC-seq from nuclei from frozen tissue | 4 | dx.doi.org/10.17504/protocols.io.bp2l6b4nkgqe/v1 | https://www.protocols.io/view/atac-seq-from-nuclei-from-frozen-tissue-bmcqk2vw | Eric RA Pederson | TITLE: ATAC-seq from nuclei from frozen tissue
AUTHORS: Eric RA Pederson
[DESCRIPTION]
Modified ATAC-seq method for frozen tissue, in this case brain tissue.
[BEFORE_START]
The pre-experimentation steps are important
Also it is important that all the primers have been ordered and reconstituted beforehand.
[GUIDELIN... | ["[Pre-experimentation] All steps should be performed on ice or at 4 °C.", "[Nuclei extraction and filtration] Materials for the cutting of tissue on dry ice.", "[Nuclei extraction and filtration] Place 20 mg frozen tissue into a pre-chilled 2 ml Dounce containing 1 ml cold 1x HB and let thaw for 5 min.", "[Pre-experim... |
46,259 | Population Structure and Phylogenetics | 5 | dx.doi.org/10.17504/protocols.io.bretm3en | https://www.protocols.io/view/population-structure-and-phylogenetics-bretm3en | Graham Etherington | TITLE: Population Structure and Phylogenetics
AUTHORS: Graham Etherington
[DESCRIPTION]
The European polecat (Mustela putorius) is a mammalian predator which breeds across much of Europe east to central Asia. In Great Britain, following years of persecution the European polecat has recently undergone a population incr... | ["[Structure analysis] To create ADMIXTURE plots for our data, we used the following pipeline:\nBCFTOOLS prune for linkage, reformat the into Plink format, run Structure over a sensible range of K, chooseK and plot with Structure", "[Structure analysis] Take the linkage pruned dataset from 'Phylogenetics, Step 3.2, and... |
20,327 | U Mass - Protein metabolism | null | dx.doi.org/10.17504/protocols.io.x4ffqtn | null | Jason Kim | TITLE: U Mass - Protein metabolism
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Hyperinsulinemic-euglycemic clamp is the gold-standard method to assess insulin sensitivity. The hyperinsulinemic-e... | ["Mice are fasted overnight (~15 hours) prior to the start of experiment.", "Chronic indwelling catheter is placed 5~6 days prior to experiment for intravenous infusion. (methods can be referred to M1023: Surgery-jugular vein cannulation)", "Place a mouse in a rat-size restrainer with its tail tape-tethered at one end.... |
45,487 | Transfection with PEI | 1 | null | https://www.protocols.io/view/transfection-with-pei-bqnpmvdn | JCPrice | TITLE: Transfection with PEI
AUTHORS: JCPrice
[STEPS]
?. Cells should be 50-70% confluency and have a healthy morphology
?. In a clean biosafety cabinet, remove serum media from cells (DO NOT TRYPSINIZE!)
?. Add 1.5 mL of serum-free cell culture media (DMEM or similar)
?. In a sterile tube dilute total plasmid DNA (... | ["Cells should be 50-70% confluency and have a healthy morphology", "In a clean biosafety cabinet, remove serum media from cells (DO NOT TRYPSINIZE!)", "Add 1.5 mL of serum-free cell culture media (DMEM or similar)", "In a sterile tube dilute total plasmid DNA (µg) in serum-free DMEM. 6 well plate: 200 µl + 3 µg of tot... |
82,388 | HEK3/LINC01509 Library Preparation | 4 | dx.doi.org/10.17504/protocols.io.5qpvorjxzv4o/v1 | https://www.protocols.io/view/hek3-linc01509-library-preparation-cupuwvnw | Mathew Chu | TITLE: HEK3/LINC01509 Library Preparation
AUTHORS: Mathew Chu
[DESCRIPTION]
Library preparation for HEK3 recording site (LINC01509) using PCR and digestion.
[STEPS]
SECTION: HEK293T Cell Lysis
1. Make up 1:50 Thermolabile Proteinase K (NEB) in Viagen (cell).
2. Resuspend cells in 25 µL of Viagen/Proteinase K.
Quick... | ["[HEK293T Cell Lysis] Make up 1:50 Thermolabile Proteinase K (NEB) in Viagen (cell).", "Resuspend cells in 25 µL of Viagen/Proteinase K. \n\nQuickly transfer cells into a PCR strip to avoid viscosity.", "Perform lysis in a PCR machine:\n\n37 °C 60 min \n55 °C 30 min \non ice \n\nStore lysates at -20 °C in the pre-PCR ... |
95,631 | Rotarod (40 RPM and 20 RPM with docking) | 4 | dx.doi.org/10.17504/protocols.io.3byl4qo5zvo5/v2 | https://www.protocols.io/view/rotarod-40-rpm-and-20-rpm-with-docking-c9mpz45n | daniel.dautan daniel, Per Svenningsson | TITLE: Rotarod (40 RPM and 20 RPM with docking)
AUTHORS: daniel.dautan daniel, Per Svenningsson
[DESCRIPTION]
This protocol describes motor function testing in mice using the rotarod by the Svenningsson lab.
Two options for the protocol are included: 1) 40 RPM constant speed after habituation and 2) 20 RPM with dock... | ["Using a paper tube, transfer each mouse of the same cage onto the rotarod (Ugo Basile, 47650). Always maintain order, mice one into line one, mice 2 into line 2 etc…", "Lift the collecting platform and set up the protocol: either max speed of constant 40 RPM or 20 RPM docking.", "The time to fall is defined as the mo... |
null | null | null | dx.doi.org/10.17504/protocols.io.gv9bw96 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
57,221 | mPSM protocol | 4 | null | https://www.protocols.io/view/mpsm-protocol-b35dqq26 | Takehito Tomita | TITLE: mPSM protocol
AUTHORS: Takehito Tomita
[DESCRIPTION]
Protocol to perform 2D ex vivo segmentation assay (Lauschke et al. 2013).
[STEPS]
1. Coat dishes/plates with fibronectin.
1.1. Dilute fibronectin (Sigma, Cat.No: F1141) with PBS to 50ug/mL (20 fold dilution).
1.2. Fill each well of 8-well plate (NuncTMLab-T... | ["Coat dishes/plates with fibronectin.", "Dilute fibronectin (Sigma, Cat.No: F1141) with PBS to 50ug/mL (20 fold dilution).", "Fill each well of 8-well plate (NuncTMLab-TekTMII Chambered Coverglass, Cat.No: 155409PK) with ~160μl of fibronectin solution and incubate for 1 hour in 37°C.", "Remove all fibronectin solution... |
99,193 | RAFT Based Synthesis of In-house Polymers | 0 | dx.doi.org/10.17504/protocols.io.ewov19noylr2/v1 | https://www.protocols.io/view/raft-based-synthesis-of-in-house-polymers-dc4z2yx6 | Caroline Brown, Snehasish Ghosh, Kallol Gupta | TITLE: RAFT Based Synthesis of In-house Polymers
AUTHORS: Caroline Brown, Snehasish Ghosh, Kallol Gupta
[DESCRIPTION]
The protocol gives details for synthesizing the ChloroSMA series of membrane active polymers.
[STEPS]
SECTION: Chemicals and reagents
1. All reagents were purchased from Sigma-Aldrich and used without... | ["[Chemicals and reagents] All reagents were purchased from Sigma-Aldrich and used without further purification unless specified \notherwise.", "[Synthesis of ChloroSMA20] To a 50 mL add 1.52 millimolar (mM) ,1.52 millimolar (mM) , and 0.076 millimolar (mM) .", "[Synthesis of ChloroSMA 40] To a 50 mL add 3.1 millimolar... |
67,005 | STICR Barcode Library Amplification Protocol | 1 | dx.doi.org/10.17504/protocols.io.8epv598r4g1b/v1 | https://www.protocols.io/view/sticr-barcode-library-amplification-protocol-cdn5s5g6 | Ryan N. Delgado, Denise E. Allen, Matthew G. Keefe | TITLE: STICR Barcode Library Amplification Protocol
AUTHORS: Ryan N. Delgado, Denise E. Allen, Matthew G. Keefe
[DESCRIPTION]
Barcode amplification protocol for SNICR libraries based on:
Delgado, R.N., Allen, D.E., Keefe, M.G.et al.Individual human cortical progenitors can produce excitatory and inhibitory neurons.Nat... | ["[PCR] Following cDNA amplification in 10X workflow, bead purify as directed in instructions and set aside 10ul of cDNA to use in the following reaction. This should leave you with 30 µL of bead purified cDNA to complete the rest of the standard 10X whole transcriptome library with. \n\nPrimers: Reverse primer (P5-Rea... |
94,893 | Bulk tissue RNA-sequencing - hiPSC-derived astrocytes, neurons and co-cultures | 4 | dx.doi.org/10.17504/protocols.io.ewov1q6kpgr2/v1 | https://www.protocols.io/view/bulk-tissue-rna-sequencing-hipsc-derived-astrocyte-c8wmzxc6 | Karishma D'Sa | TITLE: Bulk tissue RNA-sequencing - hiPSC-derived astrocytes, neurons and co-cultures
AUTHORS: Karishma D'Sa
[DESCRIPTION]
Bulk tissue RNA-sequencing of hiPSC-derived astrocytes, neurons and co-cultures using the Illumina TruSeq Stranded mRNA Library Prep kit
[STEPS]
SECTION: Bulk tissue RNA-sequencing
1. Libraries ... | ["[Bulk tissue RNA-sequencing] Libraries for sequencing were prepared using the Illumina TruSeq Stranded mRNA Library Prep kit by loading 50 ng of total RNA into the initial reaction; fragmentation and PCR steps were undertaken as per the manufacturer’s instructions.", "[Bulk tissue RNA-sequencing] Final library concen... |
59,401 | Measurement of activity-related impedance changes in porcine subdiaphragmatic nerve | 1 | dx.doi.org/10.17504/protocols.io.b59hq936 | https://www.protocols.io/view/measurement-of-activity-related-impedance-changes-b59hq936 | Ilya Tarotin, Svetlana Mastitskaya, Enrico Ravagli, Justin D Perkins, David S Holder, Kirill Aristovich | TITLE: Measurement of activity-related impedance changes in porcine subdiaphragmatic nerve
AUTHORS: Ilya Tarotin, Svetlana Mastitskaya, Enrico Ravagli, Justin D Perkins, David S Holder, Kirill Aristovich
[DESCRIPTION]
This experimental protocol covers the preparation and execution of ex-vivo experiments for the meas... | ["Prepare nerve Ringer’s solution. \n\nPlace the glass beaker with 1L of distilled water on the magnetic stirrer, switch the medium speed stirring and put the following ingredients to the water (per 1L): 6.604 g , 0.357 g , 0227 g , 0.163 g ,0.144 g ,2.1 g ,0.901 g .", "Pour the solution into a dedicated reservoir co... |
23,347 | Parasitological diagnosis of American Tegumentary Leishmaniasis - Isolation of Leishmania in Culture | null | dx.doi.org/10.17504/protocols.io.22tggen | null | Luciana F. Miranda, Aline Fagundes da Silva, Marcela Xavier de Mello, Célia de Fatima Moreira Venâncio, Andreia Alves Marcolini, Cíntia Xavier de Mello, Maria de Fátima Madeira | TITLE: Parasitological diagnosis of American Tegumentary Leishmaniasis - Isolation of Leishmania in Culture
AUTHORS: Luciana F. Miranda, Aline Fagundes da Silva, Marcela Xavier de Mello, Célia de Fatima Moreira Venâncio, Andreia Alves Marcolini, Cíntia Xavier de Mello, Maria de Fátima Madeira
[DESCRIPTION]
<div class ... | ["[Section 1: Preparing Schneider´s Insect Medium - protocol based on the manufacturer's instructions S9895 - SIGMA]\nApplicationOriginally developed for the culture of Drosophila; suitable for culture of other dipteran cell lines.When supplemented with 5-20% heat-inactivated fetal bovine serum, Schneider′s medium has ... |
50,459 | Media Preparation for E. coli growth for Cell-free Protein Synthesis | 1 | dx.doi.org/10.17504/protocols.io.bvh3n38n | https://www.protocols.io/view/media-preparation-for-e-coli-growth-for-cell-free-bvh3n38n | Weston Kightlinger | TITLE: Media Preparation for E. coli growth for Cell-free Protein Synthesis
AUTHORS: Weston Kightlinger
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Cell-free protein synthesis reactions require cell-free extract derived from rapidly dividing E. coli cells to produce high yields of protein therap... | ["[Media Preparation for E. coli growth for Cell-free Protein Synthesis]\nMix ingredients except for glucose with water below the amount of volume of MilliQ water needed using a plastic beaker and a stir-bar. Once dissolved (you can use a spatula to help break up clumps), pour into a big plastic graduated cylinder and ... |
null | null | null | dx.doi.org/10.17504/protocols.io.dib4am | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol is an update of the Metatranscriptomics protocol from DeLong lab 2012 which incorporates ScriptSeq v2 RNA library preparation.<br /><br />Part A: RNA extraction, DNase treatment, purification, and quantification.<br />Part B: rRNA subtraction<br />Part C: cDNA synt... | [] |
63,982 | POSTDRAFTED PROTOCOL 001 | 1 | null | https://www.protocols.io/view/postdrafted-protocol-001-caqnsdve | rober | TITLE: POSTDRAFTED PROTOCOL 001
AUTHORS: rober
[DESCRIPTION]
6TH OF JUNE, TESTING
[STEPS]
1. TEST 001
2. TEST 002
3.
| ["TEST 001", "TEST 002"] |
98,681 | Sequencing Bacterial Isolates from Contaminated Food Samples with ONT | 0 | dx.doi.org/10.17504/protocols.io.81wgbz7zogpk/v1 | https://www.protocols.io/view/sequencing-bacterial-isolates-from-contaminated-fo-dckz2ux6 | Sarah Fletcher | TITLE: Sequencing Bacterial Isolates from Contaminated Food Samples with ONT
AUTHORS: Sarah Fletcher
[DESCRIPTION]
In this protocol, we aim to sequence multiple bacterial isolates from 1 contaminated food sample. The goal is to obtain long-read sequences for food-borne pathogens to provide information regarding their... | ["[Part 1: Colony PCR DNA Extraction] Enriching for plasmid DNA only: If you are interested in the genomic DNA, proceed straight to step 2.3. If you are interested in the plasmid DNA, transfer the 50 μl cell suspension to a 0.2 ml thin-walled PCR tube and incubate at 95°C for 5 minutes.\nNote: It is observed that pre-t... |
98,161 | Assessing the post-nuclear testing genetic health of Pacific Islanders on Mo'orea, French Polynesia | 0 | dx.doi.org/10.17504/protocols.io.dm6gpzry8lzp/v1 | https://www.protocols.io/view/assessing-the-post-nuclear-testing-genetic-health-db4r2qv6 | Kedhar Bartlett | TITLE: Assessing the post-nuclear testing genetic health of Pacific Islanders on Mo'orea, French Polynesia
AUTHORS: Kedhar Bartlett
[DESCRIPTION]
The atrocities of imperial nuclear testing in the Pacific Ocean have gone without widespread recognition or addressing for too long. Health effects caused by radiation e... | ["[Collecting DNA Sample] Lay out all materials", "[Sequencing DNA] Isolate DNA", "[DNA Analysis] Paste DNA sequence into NCBI BLAST software", "[Contacting Participants] Contact participant by email and (if phone number provided) phone, attempting to set up a time and location to meet for data collection", "[Contactin... |
51,080 | Tn5 based tagmentation library prep protocol, high throughput | 1 | dx.doi.org/10.17504/protocols.io.bv5gn83w | https://www.protocols.io/view/tn5-based-tagmentation-library-prep-protocol-high-bv5gn83w | Charlotte Grace Sprehn, Erik Enbody, Yanjun Zan, Leif Andersson | TITLE: Tn5 based tagmentation library prep protocol, high throughput
AUTHORS: Charlotte Grace Sprehn, Erik Enbody, Yanjun Zan, Leif Andersson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>A very cost effective library preparation for whole-genome Illumina-based sequencing was previously dem... | ["[Transposon Assembly]\nRemove primers Tn5ME-A, Tn5ME-B, Tn5ME-Arev, Tn5ME-Brev, DF buffer, and Tn5 from freezer. Melt primers and buffer, mix by vortexing and spin. Leave Tn5 to melt on bench. Turn on incubator.\n70 °C", "[Transposon Assembly]\nPrepare primers A and B in tube: primer Tn5ME-A + primer Tn5ME-rev = p... |
74,909 | Sanger sequencing of SARS-CoV-2 Spike protein | 4 | dx.doi.org/10.17504/protocols.io.5qpvoyzkbg4o/v2 | https://www.protocols.io/view/sanger-sequencing-of-sars-cov-2-spike-protein-cmd5u286 | Tiago S. Salles*, Andrea Cony Cavalcanti*, Fabio Burack da Costa, Renata Campos Azevedo | TITLE: Sanger sequencing of SARS-CoV-2 Spike protein
AUTHORS: Tiago S. Salles*, Andrea Cony Cavalcanti*, Fabio Burack da Costa, Renata Campos Azevedo
[DESCRIPTION]
The SARS-CoV-2 responsible for the ongoing COVID pandemic reveals particular evolutionary dynamics and an extensive polymorphism, mainly in Spike protein... | ["RT-PCR\n\nProgram the thermal cycler before setting up the reaction. The thermal cycler should be preheated to 45–60°C.\nKeep all components, reaction mixes, and samples on ice. After preparation of the samples, transfer them to the preheated thermal cycler and immediately start the RT–PCR program.\nReaction mix shou... |
44,979 | Dilution of the Cell Suspension | 4 | dx.doi.org/10.17504/protocols.io.bp6tmren | https://www.protocols.io/view/dilution-of-the-cell-suspension-bp6tmren | Nicolas Giguère | TITLE: Dilution of the Cell Suspension
AUTHORS: Nicolas Giguère
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the requirements for successful dilution of cell suspension.</div></div>
[STEPS]
?. [Dilution of the Cell Suspension]
Re-suspend the cell pellet in .
[trituration s... | ["[Dilution of the Cell Suspension]\nRe-suspend the cell pellet in .\n[trituration solution]", "[Dilution of the Cell Suspension]\nTake of the suspension and dilute it in .\n10 µl\n[Trypan Blue Solution (Gibco 15250061)]", "[Dilution of the Cell Suspension]\nTake of this mix to count on the hematocytometer.\n10 µl", ... |
null | null | null | dx.doi.org/10.17504/protocols.io.hsib6ce | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Establishment and transfer of classical eyeblink conditioning using electrical microstimulation of the hippocampus as the conditioned stimulus</p>
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.rpfd5jn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
20,783 | UC Davis - Ex vivo assessment of barrier function-gut permeability | null | dx.doi.org/10.17504/protocols.io.yipfudn | null | Amy Ehrlich, Trina Knotts | TITLE: UC Davis - Ex vivo assessment of barrier function-gut permeability
AUTHORS: Amy Ehrlich, Trina Knotts
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Gut tissue (by region- e.g ileum & colon) will be opened alon... | ["Tip Preparation1. Make 3% solution of agar in Ringers or KRB solution*. Place 0.75g agar and 25 ml Ringers/KRB into 50 ml conical. Use orange conical lid attached to 30ml syringe for degassing agar. Fill a 500ml beaker halfway with dH²O and place conical inside. Heat on hot plate. 2. When the solution thickens, us... |
22,594 | A Randomized Trial of a Pilot Behavioral Support Intervention After Bariatric Surgery | null | dx.doi.org/10.17504/protocols.io.2bagaie | null | Michelle Lent | TITLE: A Randomized Trial of a Pilot Behavioral Support Intervention After Bariatric Surgery
AUTHORS: Michelle Lent
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Bariatric surgery patients may experience significant psychosocial changes after surgery, but little</div><div class = "text-block">psyc... | [] |
62,599 | https://www.facebook.com/Kelly-Clarkson-CBD-Gummies-105983145436466/ | 1 | dx.doi.org/10.17504/protocols.io.14egn7er6v5d/v1 | https://www.protocols.io/view/https-www-facebook-com-kelly-clarkson-cbd-gummies-b9dfr23n | kellybealy | TITLE: https://www.facebook.com/Kelly-Clarkson-CBD-Gummies-105983145436466/
AUTHORS: kellybealy
[DESCRIPTION]
https://www.facebook.com/Kelly.Clarkson.CBD.Gummies.official/
https://www.facebook.com/KellyClarksonCBDGummies2022/
https://www.facebook.com/Kelly-Clarkson-CBD-Gummies-105983145436466/
[STEPS]
1.
Kelly C... | ["Kelly Clarkson CBD Gummies - The Gummy to a Complete Bone Health Regime!\n\nThe idea of torment is developing to a bigger scope consistently. Many individuals, are occupied with life nowadays and depend much on pain relievers for even the smallest or moderate agony. Such a clinical pill isn't alluring, which is the r... |
88,828 | 13329A - Shoot Maturation Medium | 4 | null | https://www.protocols.io/view/13329a-shoot-maturation-medium-c2y4yfyw | leiboffs | TITLE: 13329A - Shoot Maturation Medium
AUTHORS: leiboffs
[DESCRIPTION]
This is part of the Leiboff Lab maize transformation protocol for somatic embryogenesis of B104 immature embryos. This protocol is a combination of Chen et al. 2022 and Kang et al. 2022 with some modifications based on material availability. This ... | ["[Planning] Estimate the volume of 13329A you will need based on the following:\n\n \n\nMake sure to round up! Check the table below to plan your media", "[Mixing Heat-Stable Ingredients] Retrieve the following heat-stable ingredients:\nMurashige & Skoog Basal Salt Mixture, 'Basal MS' - Stored in Main Lab, 4C Refrige... |
102,298 | Implementing the learning from training in Open Research Practices | 0 | null | https://www.protocols.io/view/implementing-the-learning-from-training-in-open-re-df523q8e | Joseph Angus Corneli, L.Saul, tim.newton | TITLE: Implementing the learning from training in Open Research Practices
AUTHORS: Joseph Angus Corneli, L.Saul, tim.newton
[DESCRIPTION]
To establish the perceptions of individuals who have attended training in Open Research practices on the implementation of their learning at their host institution using the perspec... | ["[Phase 1: Post-only questionnaire surveys of individuals who participated in UKRN-ORP training] Recruiting T3 participants to join the study when they are invited to join the community of practice", "[Phase 2: Follow-up focus groups with members of the Training Community of Practice] Recruit members of the Training C... |
49,952 | Small Object and Artefact Photography - 'SOAP' Protocol | 5 | dx.doi.org/10.17504/protocols.io.buz8nx9w | https://www.protocols.io/view/small-object-and-artefact-photography-39-soap-39-p-buz8nx9w | Jacopo Niccolo Cerasoni, Felipe Do Nascimento Rodrigues | TITLE: Small Object and Artefact Photography - 'SOAP' Protocol
AUTHORS: Jacopo Niccolo Cerasoni, Felipe Do Nascimento Rodrigues
[DESCRIPTION]
Photography is among one of the most widely used methods in scientific publications to efficiently and objectively communicate morphological, technological and aesthet... | ["[Setting Camera Functions] Select image raw format.\n\nRAW image formats (CR2, CRW, NEF, PEF...) are always preferred as they are the least processing, with little to no loss of visual details.\n\nOther formats can also be used if very high resolution photos are not necessary, and they are:\n\nTagged Image Files (TIF... |
81,824 | NCEM Drop - Tissue Dounce Homogenisation (TM-014) | 4 | dx.doi.org/10.17504/protocols.io.bp2l69j4dlqe/v1 | https://www.protocols.io/view/ncem-drop-tissue-dounce-homogenisation-tm-014-ct58wq9w | sandra.crameri | TITLE: NCEM Drop - Tissue Dounce Homogenisation (TM-014)
AUTHORS: sandra.crameri
[DESCRIPTION]
cell pellet dounce homogenisation
[STEPS]
SECTION: HEADER
1. SAN:
SPEC No:
OPERATOR:
SECTION: Conventional
9. Adsorb 10 µL sample to grid 10 min , inspect to ensure sample does not dry out.
SECTION: Conventional... | ["[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... |
39,710 | 703.3 URMC HTC_Cryopreservation_of_Isolated_Cells_061220 | 4 | dx.doi.org/10.17504/protocols.io.biz6kf9e | https://www.protocols.io/view/703-3-urmc-htc-cryopreservation-of-isolated-cells-biz6kf9e | Gloria Pryhuber, Ravi Misra, Heidie Huyck, Gautam Bandyopadhyay | TITLE: 703.3 URMC HTC_Cryopreservation_of_Isolated_Cells_061220
AUTHORS: Gloria Pryhuber, Ravi Misra, Heidie Huyck, Gautam Bandyopadhyay
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left"><span style = "font-weight:bold;">Lung MAP HTC - BioRepository for... | ["[Procedure for Freezing]\nAfter Centrifugation at 800Xg for 10min at 40C pour off supernatant and resuspend cell pellet by gently tapping the tube by hand (with fingers) before adding the appropriate amount of freezing medium to tube to yield a cell concentration/vial as indicated in the following table. Immediately... |
null | null | null | dx.doi.org/10.17504/protocols.io.e2sbgee | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The cells targeted by the Nanobeads are either selected or depleted by incubating your sample with the directly conjugated magnetic particles. The magnetically labeled fraction is retained by the use of a magnetic separator. After collection of the targeted cells, downstream ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.eqwbdxe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Western blotting uses specific antibodies to identify proteins that have been separated based on size by gel electrophoresis. The immunoassay uses a membrane made of nitrocellulose or PVDF (polyvinylidene fluoride). The gel is placed next to the membrane and application of an el... | [] |
90,948 | Morphological plasticity of African cichlid as a model in Ecology and Biodiversity | 1 | null | https://www.protocols.io/view/morphological-plasticity-of-african-cichlid-as-a-m-c43cyyiw | Elena L. Peredo | TITLE: Morphological plasticity of African cichlid as a model in Ecology and Biodiversity
AUTHORS: Elena L. Peredo
[DESCRIPTION]
Morphological plasticity of African cichlid as model in Ecology and Biodiversity
[STEPS] | [] |
67,398 | Prima Weight Loss UK (Tablets And Pills Reviews UK) Reviews – Does these Capsules work? | 1 | dx.doi.org/10.17504/protocols.io.rm7vzyzmxlx1/v1 | https://www.protocols.io/view/prima-weight-loss-uk-tablets-and-pills-reviews-uk-cd3es8je | roxylilo | TITLE: Prima Weight Loss UK (Tablets And Pills Reviews UK) Reviews – Does these Capsules work?
AUTHORS: roxylilo
[DESCRIPTION]
➢ Product Name —Prima Weight loss uk
➢ Composition—NATURAL
➢ Side-Effects— NA
➢ Availability—Online
➢ Rating— ⭐⭐⭐⭐⭐
➢ Official Website (Sale Is Live) —Prima Weight loss uk.com
➢VISIT THE OFF... | ["[Prima Weight loss uk] Prima weight loss capsules are created to burn fat that is hard to lose with exercise or diet. According to its manufacturers, these pills are a safe choice to consider, and unlike other fat burners, they have no side effects. Read this Prima Weight loss uk review and understand how they work."... |
94,427 | Plant RNA purification using TRIzol (TRI reagent) | 4 | dx.doi.org/10.17504/protocols.io.36wgq4enyvk5/v2 | https://www.protocols.io/view/plant-rna-purification-using-trizol-tri-reagent-c8f3ztqn | Diep R Ganguly | TITLE: Plant RNA purification using TRIzol (TRI reagent)
AUTHORS: Diep R Ganguly
[DESCRIPTION]
Extraction of total RNA from plant tissue using TRIzol (or TRI reagent) followed by DNA nuclease treatment.
[BEFORE_START]
Ensure benches and equipment are RNase free.
For RNase-Free DNase Set (Qiagen): Prepare DNase I sto... | ["[RNA purification] Collect 50-100 mg of plant tissue and freeze immediately in liquid N2.", "[RNA purification] Invert each tube by hand ~20x and incubate at room temperature for 5 minutes (DO NOT vortex samples as it may result in RNA degradation).", "[RNA purification] Centrifuge at 14,000 rcf for 10 minutes at 4°C... |
56,743 | Benchmarking missing-values approaches for predictive models on health databases | 1 | dx.doi.org/10.17504/protocols.io.b3nfqmbn | https://www.protocols.io/view/benchmarking-missing-values-approaches-for-predict-b3nfqmbn | Alexandre Perez-Lebel, Gaël Varoquaux, Marine Le Morvan, Julie Josse, Jean-Baptiste Poline | TITLE: Benchmarking missing-values approaches for predictive models on health databases
AUTHORS: Alexandre Perez-Lebel, Gaël Varoquaux, Marine Le Morvan, Julie Josse, Jean-Baptiste Poline
[DESCRIPTION]
BACKGROUND
As databases grow larger, it becomes harder to fully control their collection, and they frequently come w... | ["[Introduction] This protocol details the experiments run in the GigaScience article Benchmarking missing-values approaches for predictive models on health databases, Perez-Lebel et al. 2022. The code used for running the experiments and plotting the results is available on GitHub:\n \nAnd can be installed through the... |
58,415 | Post mortem human substantial nigra TH staining | 4 | dx.doi.org/10.17504/protocols.io.n2bvj68d5lk5/v1 | https://www.protocols.io/view/post-mortem-human-substantial-nigra-th-staining-b5apq2dn | Waijiao Kai, Xiqun Chen | TITLE: Post mortem human substantial nigra TH staining
AUTHORS: Waijiao Kai, Xiqun Chen
[DESCRIPTION]
This protocol is standardized for postmortem (frozen) SN tissue from pathologically diagnosed PD patients and control individuals for Immunofluorescence staining.
[STEPS]
1. Deparaffinization
Wash slides in 2 change... | ["Deparaffinization\nWash slides in 2 changes of 300 mL ml of xylene – 6 min each at room temperature.", "Rehydration\nWash slides in 300 mL of 100% alcohol –9 min at Room temperature.\nWash slides in300 mL of 95% alcohol – 6 min at Room temperature.\nWash slides in 300 mL of 80% alcohol – 3 min at Room temperature.\nR... |
null | null | null | dx.doi.org/10.17504/protocols.io.u2weyfe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Steroids are important organic compounds based on the fundamental saturated tetracyclic hydrocarbon.Steroidal compounds are solid alcohols that shoulder very important biological functions in the cells, which are widely distributed in plants, animals and fungi.
[STEPS] | [] |
34,530 | Quantification of Total Biomass in Ground Coral Samples | null | dx.doi.org/10.17504/protocols.io.bdyai7se | https://www.protocols.io/view/quantification-of-total-biomass-in-ground-coral-sa-bdyai7se | Rowan Mclachlan, Kerri Dobson, Andrea Grottoli | TITLE: Quantification of Total Biomass in Ground Coral Samples
AUTHORS: Rowan Mclachlan, Kerri Dobson, Andrea Grottoli
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines a method for quantifying the total biomass of Scleractinian coral samples which have been ground into a homoge... | ["[Grind coral fragments into a homogenous paste]\nLabel pans. Using an unleaded mechanical pencil, engrave the base of a pre-baked aluminum weighing pan with the coral sample ID (Fig. 1). This pan is hereafter referred to as \"pan A\".", "[Grind coral fragments into a homogenous paste]\nPrepare equipment for grinding ... |
94,824 | Wholemount immunolabeling and stereological quantification of autophagosomes in Arabidopsis thaliana root epidermal cells | 4 | dx.doi.org/10.17504/protocols.io.bp2l6x5yklqe/v1 | https://www.protocols.io/view/wholemount-immunolabeling-and-stereological-quanti-c8ugzwtw | Michal Danek, Katerina Eliasova, Daniela Kocourková | TITLE: Wholemount immunolabeling and stereological quantification of autophagosomes in Arabidopsis thaliana root epidermal cells
AUTHORS: Michal Danek, Katerina Eliasova, Daniela Kocourková
[DESCRIPTION]
The workflow enables the quantification of autophagosomes in Arabidopsis thaliana root epidermal cells in 3D. It co... | ["[Microtubule-stabilizing buffer preparation] Microtubule-stabilizing buffer (MTSB) [1] is used throughout the procedure. \nComposition: 50 mM PIPES, 5 mM EGTA, 5 mM MgSO4.7H2O, pH = 6.8 (5M KOH). \n\nNote: PIPES will not dissolve in water unless the solution is alkalized.", "[Root tissue fixation] PFA [2] is depolyme... |
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