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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32,174 | The molecular neuropathology of amyotrophic lateral sclerosis: protocol for systematic review and meta-analysis | 1 | dx.doi.org/10.17504/protocols.io.bbnnimde | https://www.protocols.io/view/the-molecular-neuropathology-of-amyotrophic-latera-bbnnimde | Elizabeth Elliott, Jenna M Gregory, Arpan R Mehta, Siddharthan Chandran, Colin Smith. | TITLE: The molecular neuropathology of amyotrophic lateral sclerosis: protocol for systematic review and meta-analysis
AUTHORS: Elizabeth Elliott, Jenna M Gregory, Arpan R Mehta, Siddharthan Chandran, Colin Smith.
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A significant body of neuropathologica... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.hhrb356 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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27,970 | DNA Purification from a PCR Product (Protocol for NucleoSpin® PCR clean-up Gel Extraction Kit) | null | dx.doi.org/10.17504/protocols.io.7jahkie | null | Alba Balletbó | TITLE: DNA Purification from a PCR Product (Protocol for NucleoSpin® PCR clean-up Gel Extraction Kit)
AUTHORS: Alba Balletbó
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The following protocol is suitable for PCR clean-up as well as DNA concentration and removal of salts, enzymes, etc. from enzym... | ["Adjust DNA binding condition, For very small sample volumes 'Note': For removal of small fragments like primer dimers dilutions of Buffer NTI can be used instead of 100 % Buffer NTI. Incubate the mixture at 50ºC for 5-10 minutes or until the gel has completely melted.", "Place a NucleoSpin® PCR clean-up Gel column in... |
33,860 | Phylogenetic analyses of the JEV gene sequence | 1 | dx.doi.org/10.17504/protocols.io.bdbci2iw | https://www.protocols.io/view/phylogenetic-analyses-of-the-jev-gene-sequence-bdbci2iw | Wenjing Liu, Shihong Fu | TITLE: Phylogenetic analyses of the JEV gene sequence
AUTHORS: Wenjing Liu, Shihong Fu
[DESCRIPTION]
The E gene was amplified by semi-nested PCR.
[STEPS]
SECTION: Nucleic acid extraction
1. Use Tianlong nucleic acid extraction instrument (automatic nucleic acid extraction instrument, model: np968. C, manufacturer: ... | ["[Nucleic acid extraction] Use Tianlong nucleic acid extraction instrument (automatic nucleic acid extraction instrument, model: np968. C, manufacturer: Suzhou Tianlong Biotechnology Co., Ltd.), and supporting nucleic acid extraction kit: Tianlong nucleic acid extraction kit (magnetic bead method EX-RNA/DNAvirus), man... |
35,853 | Sectioning of Mouse Proximal Thoracic Aorta | null | dx.doi.org/10.17504/protocols.io.be9mjh46 | https://www.protocols.io/view/sectioning-of-mouse-proximal-thoracic-aorta-be9mjh46 | Jeff Z. Chen, Deborah A. Howatt, Jessica J. Moorleghen, Michael K. Franklin, Hisashi Sawada, Yanxiang Gao, Hong S. Lu, Alan Daugherty | TITLE: Sectioning of Mouse Proximal Thoracic Aorta
AUTHORS: Jeff Z. Chen, Deborah A. Howatt, Jessica J. Moorleghen, Michael K. Franklin, Hisashi Sawada, Yanxiang Gao, Hong S. Lu, Alan Daugherty
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used for generation of ascending aortic s... | ["[Collection of thoracic aorta]\nEuthanize mouse with ketamine : xyalazine cocktail", "[Collection of thoracic aorta]\nOpen thoracic cavity and expose heart", "[Collection of thoracic aorta]\nNick right atrium with sharp scissors", "[Collection of thoracic aorta]\nFlush vasculature with cold saline (>5 mL) introduced ... |
43,449 | Agarose Gel Casting Protocol | 3 | null | https://www.protocols.io/view/agarose-gel-casting-protocol-bnnzmdf6 | TITLE: Agarose Gel Casting Protocol
AUTHORS:
[STEPS] | [] | |
98,430 | 10x Protocols: Chromium Next GEM Single Cell 3ʹ -- University of Minnesota TMCs (CG000315 Rev E) | 0 | dx.doi.org/10.17504/protocols.io.261ge5ozdg47/v1 | https://www.protocols.io/view/10x-protocols-chromium-next-gem-single-cell-3-univ-dcc62sze | Laura J Niedernhofer, David A Bernlohr | TITLE: 10x Protocols: Chromium Next GEM Single Cell 3ʹ -- University of Minnesota TMCs (CG000315 Rev E)
AUTHORS: Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
Following single-cell dissociation or nuclei isolation, the Next GEM 3' assay uses microfluidics to partition and assign cell- or nuclei-specific barcode... | ["[Library Preparation]", "[FASTQ Generation] BCL data from Illumina sequencer is demultiplexed and converted into FASTQ format using bcl2fastq version 2.20.0", "[Tissue Preparation] Complete single cell or nuclei isolation prior to starting this protocol"] |
68,929 | Fluorescent Immunolabelling for endogenous ChAT in mice striatum | 4 | dx.doi.org/10.17504/protocols.io.8epv59wk6g1b/v1 | https://www.protocols.io/view/fluorescent-immunolabelling-for-endogenous-chat-in-cfi9tkh6 | Roberta Marongiu | TITLE: Fluorescent Immunolabelling for endogenous ChAT in mice striatum
AUTHORS: Roberta Marongiu
[DESCRIPTION]
This immunohistochemistry protocol has been designed and adjusted specifically for ChAT immunolabelling in the mice striatum
[STEPS]
2. Wash: 3 x 10 min gently on a shaker, in TBST at Room temperature .
... | ["Wash: 3 x 10 min gently on a shaker, in TBST at Room temperature .", "Blocking step: Incubate the slides with blocking solution on the shaker for 60 min at Room temperature .", "Primary antibody: incubate the slides with the blocking solution/Antibody on a shaker at 4 °C for 1440 min 2880 min.", "Washes: 3 x 10... |
98,602 | Enterovirus coxsackievirus A16 2A protease small scale expression and purification protocol | 1 | dx.doi.org/10.17504/protocols.io.rm7vzj3y5lx1/v1 | https://www.protocols.io/view/enterovirus-coxsackievirus-a16-2a-protease-small-s-dcii2uce | Korvus Wang, michael fairhead, Eleanor Williams | TITLE: Enterovirus coxsackievirus A16 2A protease small scale expression and purification protocol
AUTHORS: Korvus Wang, michael fairhead, Eleanor Williams
[DESCRIPTION]
This protocol details the expression and purification of coxsackievirus A16 2A protease construct bearing a N-terminal His-SUMO tag at small scale (<... | ["[Plasmid Transformation] Transform the coxsackievirus A16 2A protease plasmid into BL21(DE3) and store a glycerol stock of this at -80 °C\nThe coxsackievirus A16 2A protease plasmid encodes the 2A protease with an N-terminal His6-SUMO tag on a kanamycin resistant backbone with a T7 promoter.", "[Protein expression] W... |
null | null | null | dx.doi.org/10.17504/protocols.io.mdic24e | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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35,386 | SPRI beads preparation | null | dx.doi.org/10.17504/protocols.io.bes2jege | null | Daniel Kitsberg, Miriam Adam, Naomi Habib | TITLE: SPRI beads preparation
AUTHORS: Daniel Kitsberg, Miriam Adam, Naomi Habib
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">SPRI is a technique for extracting nucleic acids from liquid mixtures.</div><div class = "text-block"><span>This is a quick and cheap alternative to commerical SPRI beads ... | ["[SPRI buffer preparation]\nPrepare 50 ml RNA Wash Buffer:1 mM Trisodium citrate, 0.05% Tween 20, pH 6.4 @ 25 °CAdd nuclease free waterAdd 1M Trisodium citrateAdd 10% Tween 20Add 1N HClComplete volume to with nuclease free water\n30 ml\n50 µl\n250 µl\n21 µl\n50 ml", "[SPRI buffer preparation]\nBead PreparationVor... |
56,688 | Bogus Data Acquisition Protocol III | 1 | dx.doi.org/10.17504/protocols.io.b3kqqkvw | https://www.protocols.io/view/bogus-data-acquisition-protocol-iii-b3kqqkvw | Abby Moore | TITLE: Bogus Data Acquisition Protocol III
AUTHORS: Abby Moore
[DESCRIPTION]
The purpose of this protocol is to demo protocol development.
[BEFORE_START]
Know before you start.
[GUIDELINES]
My guidelines.
[STEPS]
1. I'll display an image using embed code retrieved from Box.
2. I'll show a command usi... | ["I'll display an image using embed code retrieved from Box.", "I'll show a command using the Command component:"] |
83,682 | A protocol of application of medicament testing method based on the electrodermal measurement of acupuncture points in diagnosis of SARS-CoV-2 infection | 4 | dx.doi.org/10.17504/protocols.io.6qpvr3e3zvmk/v1 | https://www.protocols.click/view/a-protocol-of-application-of-medicament-testing-me-cvyaw7se | naila.djumaeva | TITLE: A protocol of application of medicament testing method based on the electrodermal measurement of acupuncture points in diagnosis of SARS-CoV-2 infection
AUTHORS: naila.djumaeva
[DESCRIPTION]
This protocol details application of medicament testing method based on the electrodermal measurement of acupuncture po... | ["[Application of medicament testing method] Medication testing is carried out with a Voll electroacupuncture diagnostic device (EAV) equipped with software containing information about nosodes (homeopathic preparations consisting of potentiated antigens and their components of various viruses, bacteria, fungi and ot... |
14,114 | IPTG | 1 | dx.doi.org/10.17504/protocols.io.r2ad8ae | https://www.protocols.io/view/iptg-r2ad8ae | Erçağ Pinçe | TITLE: IPTG
AUTHORS: Erçağ Pinçe
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Preparation of Inducer IPTG for expression of CFP and YFP </div></div>
[STEPS]
?. [Dissolving IPTG]
Dissolve 2.383 g of IPTG in 8 mL double distilled water(milliQ)
?. [Complete the volume of water to 10mL]
Add more ddH... | ["[Dissolving IPTG]\nDissolve 2.383 g of IPTG in 8 mL double distilled water(milliQ)", "[Complete the volume of water to 10mL]\nAdd more ddH2O to bring the total volume to 10mL", "[Filter sterilize ]\nFilter sterilize with a 0.22 μ- syringe filter.", "[Aliquot and store]\nStore in 1mL aliquots at -20 °C."] |
null | null | null | dx.doi.org/10.17504/protocols.io.dnq5dv | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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93,840 | ECIS Data Analysis for Stimulation of Human Pulmonary Microvascular Endothelial Cells (HPMECs) with Human Serum | 4 | dx.doi.org/10.17504/protocols.io.bp2l69erklqe/v4 | https://www.protocols.io/view/ecis-data-analysis-for-stimulation-of-human-pulmon-c7vqzn5w | Michael Bokoch | TITLE: ECIS Data Analysis for Stimulation of Human Pulmonary Microvascular Endothelial Cells (HPMECs) with Human Serum
AUTHORS: Michael Bokoch
[DESCRIPTION]
Sera from patients in our UCSF Liver Transplant Biobank are used to stimulate human pulmonary microvascular endothelial cells (HPMECs) grown to confluency on ECIS... | ["[ECIS Data Analysis for HPMEC stimulation by Liver Biobank Sera] Determine Difference in Area-under-the-Curve (Normalized Resistance at 4000 Hz)\nTo be calculated after recording full ECIS curve after stimulation with human serum from liver transplant (LT) patients.\n\nGoal: To calculate the difference in AUC between... |
101,106 | Purification of BNIP3-GST | 0 | dx.doi.org/10.17504/protocols.io.261ge5527g47/v1 | https://www.protocols.io/view/purification-of-bnip3-gst-deys3fwe | Elias Adriaenssens | TITLE: Purification of BNIP3-GST
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol details the purification of BNIP3-GST.
[STEPS]
SECTION: Purification - BNIP3-GST
1. To purify BNIP3-GST, we purchase the gene-synthesized codon-optimized cytosol-exposed domain of BNIP3 (1-158aa) fused to a C-terminal GST-tag in ... | ["[Purification - BNIP3-GST] To purify BNIP3-GST, we purchase the gene-synthesized codon-optimized cytosol-exposed domain of BNIP3 (1-158aa) fused to a C-terminal GST-tag in a pFastBac-Dual vector from Genscript (available from Addgene).", "[Purification - BNIP3-GST] Introduce the point mutants by in vitro mutagenesis ... |
95,889 | 605CefTB - Resting Medium (basta selection) | 4 | null | https://www.protocols.io/view/605ceftb-resting-medium-basta-selection-c9vrz656 | leiboffs | TITLE: 605CefTB - Resting Medium (basta selection)
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 availabi... | ["[Planning] Estimate the volume of 605CefTB 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:\n605 Medium - Stored in Main Lab, 4C Refrigerator, Top Shelf\nCasin Hydrolysate ... |
null | null | null | dx.doi.org/10.17504/protocols.io.j6fcrbn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes the recipe for a standard sugar-agar food source for fruit flies</p>
[GUIDELINES]
<p>This protocol describes how to make enough sugar-agar solution for approximatley 60 Drosophila storage vials (23ml; Sarstedt 58.490). </p>
<p>Once the sugar-agar food... | [] |
94,537 | Tau aggregation monitored by thioflavin-T (ThT) fluorescence in a plate reader | 1 | dx.doi.org/10.17504/protocols.io.dm6gp3nw8vzp/v1 | https://www.protocols.io/view/tau-aggregation-monitored-by-thioflavin-t-tht-fluo-c8jhzuj6 | Patricia Yuste-Checa, F Ulrich Hartl | TITLE: Tau aggregation monitored by thioflavin-T (ThT) fluorescence in a plate reader
AUTHORS: Patricia Yuste-Checa, F Ulrich Hartl
[DESCRIPTION]
This protocol details how to efficiently monitor Tau aggregation by thioflavin T fluorescence in a plate reader.
[STEPS]
SECTION: Tau aggregation monitored by thioflavin-T ... | ["[Tau aggregation monitored by thioflavin-T (ThT) fluorescence in a plate reader] Mix reagents to a final concentration of 10 micromolar (µM) Tau (TauRD), 2.5 micromolar (µM) Heparin, 2 millimolar (mM) MgCl2, 10 micromolar (µM) ThT in 1x PBS pH 7.2. Prepare a mix for 4.5 reactions per condition (per condition, four te... |
78,510 | Genome-wide mapping of nucleosomes is improved by using a more appropriate reference genome. | 4 | dx.doi.org/10.17504/protocols.io.6qpvr4w83gmk/v1 | https://www.protocols.io/view/genome-wide-mapping-of-nucleosomes-is-improved-by-cqwnvxde | Paula Beati, Milena Massimino Stepñicka, Salomé C. Vilchez Larrea, Guillermo Daniel Alonso, Josefina Ocampo | TITLE: Genome-wide mapping of nucleosomes is improved by using a more appropriate reference genome.
AUTHORS: Paula Beati, Milena Massimino Stepñicka, Salomé C. Vilchez Larrea, Guillermo Daniel Alonso, Josefina Ocampo
[DESCRIPTION]
InTrypanosoma cruzi, an early divergent eukaryote, DNA is packaged into chromatin by... | ["[MNase digestion of T. cruzi epimastigote chromatin] Pellet 10e8 late exponentially growing epimastigotes per reaction (normally 7) by centrifugation at 1700 xg for 5 minutes at Room temperature. Wash the cells with 10 ml Incomplete Lysis Solution (1 mM L-glutamine, 250 mM sucrose, 2.5 mM CaCl2, 1 mM phenylmethylsulf... |
86,713 | Standard cell-based assays for cytokine release and cellular proliferation of murine CAR T cells. | 4 | dx.doi.org/10.17504/protocols.io.dm6gp3358vzp/v1 | https://www.protocols.io/view/standard-cell-based-assays-for-cytokine-release-an-cywzxxf6 | Tamer B Shabaneh, Andrew R Stevens | TITLE: Standard cell-based assays for cytokine release and cellular proliferation of murine CAR T cells.
AUTHORS: Tamer B Shabaneh, Andrew R Stevens
[DESCRIPTION]
Two standard cell-based assay to assess the function of murine CAR T cells, which we regularly performed at the end of the process of generating those CAR T... | ["[Procedure for the preparation of adherent tumor cells (target cells) for ELISA and CellTrace assays] Aspirate media from T75 flasks; wash with 10ml PBS to remove complete DMEM media (cDMEM).\nAdd 5mL of Cell Dissociation Media (0.5mM EDTA in PBS); incubate at 37C for 10-20 mins.\n\nPipet vigorously to dissociate the... |
67,670 | Annealing Oligonucleotides (Instructor Protocol) | 4 | null | https://www.protocols.io/view/annealing-oligonucleotides-instructor-protocol-cebwtape | Brian Teague | TITLE: Annealing Oligonucleotides (Instructor Protocol)
AUTHORS: Brian Teague
[DESCRIPTION]
This is the instructor protocol for
[STEPS]
SECTION: Lab Setup
1. Prepare 15 ml conicals with 5 mL in each. Prepare one tube for each 4 students (2 groups of 2).
SECTION: Instructor Tips & Common Student Errors
3.... | ["[Lab Setup] Prepare 15 ml conicals with 5 mL in each. Prepare one tube for each 4 students (2 groups of 2).", "[Instructor Tips & Common Student Errors] Instructor Tips\nThis is the first \"real\" lab. I generally start the class explaining what annealing is and why we're doing it, point out where the materials... |
96,603 | Extracellular fluid extraction in zebrafish brain tissue and samples | 0 | dx.doi.org/10.17504/protocols.io.14egn3p1zl5d/v1 | https://www.protocols.io/view/extracellular-fluid-extraction-in-zebrafish-brain-daj32cqn | Caio Maximino | TITLE: Extracellular fluid extraction in zebrafish brain tissue and samples
AUTHORS: Caio Maximino
[DESCRIPTION]
This protocol is used to extract the contents of the extracellular fluid of the adult zebrafish brain, allowing quantification of analytes such as neurotransmitter (e.g., Maximino et al., 2013) or proteins ... | ["[Euthanasia and dissection] Sacrifice animals in ice-cold water.", "[ECF extraction] In a 1.5 mL microtube filled with extraction fluid, add one brain (or fraction). Keep the microtube on ice or on the fridge, maintaining the temperature at 4 ºC. Incubate for 30 min.\n4 °C \n30 min", "[Quantification] Samples can be ... |
90,661 | QuPath Visualization/Segmentation | 4 | dx.doi.org/10.17504/protocols.io.dm6gp35d5vzp/v1 | https://www.protocols.io/view/qupath-visualization-segmentation-c4sdywa6 | Michael X. Henderson | TITLE: QuPath Visualization/Segmentation
AUTHORS: Michael X. Henderson
[DESCRIPTION]
This protocol describes QuPath visualization/segmentation.
[GUIDELINES]
QuPath is a visualization and segmentation platform optimized for whole slide images. This the place where you can visualize all your slides, and create the outp... | ["[QuPath Visualization/Segmentation] Open QuPath. Click “Create Project.”", "[QuPath Visualization/Segmentation] Select your QuPath folder for this project and upload images by pressing “Add Images.” Navigate to full slide scans and add slides for this project.", "[QuPath Visualization/Segmentation] Upload series of i... |
26,439 | Admission for substance-induced disorders in refugee and migrant groups in Sweden | null | dx.doi.org/10.17504/protocols.io.53fg8jn | null | James B. Kirkbride, Samantha Harris, Jennifer Dykxhoorn, Christina Dalman, Anna-Clara Hollander | TITLE: Admission for substance-induced disorders in refugee and migrant groups in Sweden
AUTHORS: James B. Kirkbride, Samantha Harris, Jennifer Dykxhoorn, Christina Dalman, Anna-Clara Hollander
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Background</span></div><... | [] |
43,291 | Navigating in UNIX | 5 | null | https://www.protocols.io/view/navigating-in-unix-bnh3mb8n | Anthony Underwood | TITLE: Navigating in UNIX
AUTHORS: Anthony Underwood
[DESCRIPTION]
<div class = "text-blocks"><div style = "text-align :; float : ;"><img style = "" src = "https://s3.amazonaws.com/protocols-files/private/01a7878d3c622e9c4d27343721a1b5c5559e4cb768b63015146659aa9ec62085/cns4bgvt7.png" /></div><div class = "text-block">... | ["[Basic Navigation]\nWhere on earth am I?Short for 'present working directory'. This will show you your current location as an absolute (more on what this means below). For example:/home/anthony/data", "[Basic Navigation]\nWhat's in my current location?", "[Basic Navigation]\nGet me out of here!This will change your l... |
null | null | null | dx.doi.org/10.17504/protocols.io.jqvcmw6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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84,439 | Mitophagy experiments | 4 | dx.doi.org/10.17504/protocols.io.n2bvj3yjnlk5/v1 | https://www.protocols.io/view/mitophagy-experiments-cwpxxdpn | Elias Adriaenssens | TITLE: Mitophagy experiments
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol describes how to induce mitophagy in HeLa cells.
[STEPS]
SECTION: Mitophagy experiments
1. To induce mitophagy, treat cells with 10 micromolar (µM) Oligomycin and 4 micromolar (µM) Antimycin A.
SECTION: Mitophagy experiments
2. In ca... | ["[Mitophagy experiments] To induce mitophagy, treat cells with 10 micromolar (µM) Oligomycin and 4 micromolar (µM) Antimycin A.", "[Mitophagy experiments] In case cells are treated for more than 480 min, add 10 micromolar (µM) Q-VD-OPh to suppress apoptosis.", "[Mitophagy experiments] Analyze the samples by SDS-PAGE a... |
null | null | null | dx.doi.org/10.17504/protocols.io.hgyb3xw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<header>We analyzed the recently available whole genome sequences from two thraustochytrids (Aurantiochytrium limacinum ATCC MYA-1381, Schizochytrium aggregatum ATCC 28209) and one aplanochytrid (Aplanochytrium PBS07) We then calculated the genome-wide relative synonymous codon ... | [] |
22,269 | Trace Metals Solution | 1 | null | https://www.protocols.io/view/trace-metals-solution-zy5f7y6 | Adrien Assie, Buck Samuel | TITLE: Trace Metals Solution
AUTHORS: Adrien Assie, Buck Samuel
[DESCRIPTION]
Large quantities of C. elegans can be grown in a liquid medium. Liquid cultures of C. elegans are usually grown on S Medium using concentrated E. coliOP50 as a food source. This is the Trace Metals solution recipe to complement the S complet... | ["Start with700 mL", "10 mLof *500 mM EDTA, pH 8.0 or 1.86 gNa2EDTA.2H2O (5 mM)", "0.69 gFeSO4 ∙7H2O (2.5 mM)", "0.20 gMnCl2 ∙ 4H2O (1 mM)", "0.29 g ZnSO4 ∙7H2O (1 mM)", "0.016 gCuSO4 (0.1 mM)", "Adjust to 1000 mL", "Autoclave and store in the dark"] |
null | null | null | dx.doi.org/10.17504/protocols.io.gz3bx8n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Now that we've learned how to assemble our sequences, we'll next learn how to identify genes (or open reading frames) on our new assemblies. We'll do that using a software program called Prodigal. After we've identified ORFs, we will compare those ORFs to other sequences usin... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.eh5bb86 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol outlines the analysis used to plot contig coverage statistics, as well as sequence count and length stats. We begin with visualizing contig length vs coverage. We then visualize the distributions of sequence counts per sample as a probability density plot (similar ... | [] |
105,044 | Highly Amplified Multiplexed Fluorescence In Situ Hybridization (hamFISH) | 0 | dx.doi.org/10.17504/protocols.io.kqdg32yqzv25/v1 | https://www.protocols.io/view/highly-amplified-multiplexed-fluorescence-in-situ-ditu4enw | Mathew Edwards, Yoh Isogai | TITLE: Highly Amplified Multiplexed Fluorescence In Situ Hybridization (hamFISH)
AUTHORS: Mathew Edwards, Yoh Isogai
[DESCRIPTION]
This is the protocol associated with Combined transcriptomic, connectivity, and activity profiling of the medial amygdala using highly amplified multiplexed in situ hybridization (hamFISH)... | ["[Gene selection and probe design] A panel of up to 32 genes should be selected based on your area of interest. Once this has been determined, cDNA sequences of these genes can be used to design 30 nucleotide (nt) antisense probes. To do this we used a custom R script to BLAST 30mer sequences from each transcript agai... |
55,755 | Nextera XT protocol for MiSeq HIVPR-RT sequencing | 1 | dx.doi.org/10.17504/protocols.io.b2pjqdkn | https://www.protocols.io/view/nextera-xt-protocol-for-miseq-hivpr-rt-sequencing-b2pjqdkn | Paula Aulicino | TITLE: Nextera XT protocol for MiSeq HIVPR-RT sequencing
AUTHORS: Paula Aulicino
[DESCRIPTION]
The protocol allows amplification and NGS sequencing of a PR-RT HIV-1 sequence using tagmentation strategy and Illumina MiSeq equipment, followed by analysis of drug-resistance associated mutations by HyDRA
[STEPS]
1. Prep... | ["Prepare the sample in BSL2 laboratory. This protocol can be used to amplify and sequence HIV-1 from plasma or culture supernatants, as well as from cell-associated HIV-1. In the latter, skip the step of reverse transcription and go straight to PCR amplification.", "Perform reverse transcription of HIV-1 and PCR ampli... |
null | null | null | dx.doi.org/10.17504/protocols.io.jhacj2e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>In this study, we investigate the effects of using smart wearables by patients undergoing cardiac rehabilitation. A field experiment involving 29 patients was designed and participants were either assigned to the study group (N=13 patients who finished the study and used a se... | [] |
96,058 | Modified Promega Wizard Extraction for Barcoding Macrofungi | 1 | dx.doi.org/10.17504/protocols.io.rm7vzb3p4vx1/v3 | https://www.protocols.io/view/modified-promega-wizard-extraction-for-barcoding-m-c922z8ge | Stephen Douglas Russell | TITLE: Modified Promega Wizard Extraction for Barcoding Macrofungi
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
'This protocol is best used when preparing macrofungal specimens for Sanger sequencing or as a secondary extraction protocol for ONT nanopore barcoding.
The quality of a DNA extraction method is a primar... | ["Add 600uL of to 1.5mL eppi tubes containing your tissue.", "Place tissue from your specimens into each tube using tweezers. Utilize a piece about the size of a grain of rice or smaller. It should easily drop to the bottom of the tube. The tissue can be either fresh or dried. Label the tube with the appropriate numb... |
54,673 | Planaria 2021 Environmental Summary, Reptile & Aquatics, Stowers Institute for Medical Research | 3 | dx.doi.org/10.17504/protocols.io.bzmrp456 | https://www.protocols.io/view/planaria-2021-environmental-summary-reptile-amp-aq-bzmrp456 | Shane C. Miller, M. Shane Merryman, Diana P Baumann | TITLE: Planaria 2021 Environmental Summary, Reptile & Aquatics, Stowers Institute for Medical Research
AUTHORS: Shane C. Miller, M. Shane Merryman, Diana P Baumann
[DESCRIPTION]
Planaria are an emerging model organism, and we have maintained a colony of asexual and sexual worms at the Stowers Institute for Medic... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.dbp2mm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<strong>Purpose:</strong> This protocol describes how to pellet bacterial cells onto grids and stain them so that viruses can be visualized within the cells using transmission electron microscopy. Data obtained from these grids can be used to calculate the frequency of visibly i... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ifwcbpe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Please contact Dr. Steven Wilhelm (wilhelm@utk.edu) for additional information regarding this protocol.</p>
<p> </p>
<p>Modified from <span style="font-family: 'Segoe UI', sans-serif; font-size: small;">Schwyn, B. & Neilands, J. B. Universal chemical assay for the detecti... | [] |
44,246 | ID16A measurements on pollen samples | 1 | dx.doi.org/10.17504/protocols.io.bpfwmjpe | https://www.protocols.io/view/id16a-measurements-on-pollen-samples-bpfwmjpe | Alexandra Pacureanu, Ruxandra Cojocaru, Oonagh Mannix | TITLE: ID16A measurements on pollen samples
AUTHORS: Alexandra Pacureanu, Ruxandra Cojocaru, Oonagh Mannix
[DESCRIPTION]
X-ray Phase-contrast nano-tomography and X-ray fluorescence microscopy was performed on modern Pinaceae (pine) pollen at the ID16A nano-imaging beamline of the European Synchrotron (ESRF), in Fr... | ["[Experimental setup] Beamline: European Synchrotron Radiation Facility (ESRF) ID16A\n\n185 m long nano-imaging beamline that provides nano-focused beams.\nBeam size between 30x30 nm to 400x400 um.\nCan perform X-ray phase-contrast nano-tomography and X-ray fluorescence microscopy (XRF)\nHard X-ray photon energies ava... |
83,248 | AFOG | 4 | dx.doi.org/10.17504/protocols.io.bp2l6xkrzlqe/v1 | https://www.protocols.click/view/afog-cviqw4dw | Joana G Antunes | TITLE: AFOG
AUTHORS: Joana G Antunes
[DESCRIPTION]
Staining technique largely used to diagnose ischemic cardiac lesions and kidney diseases, in particular the regeneration or scarring of the lesion. The selectivity in this method is due to the different affinity degrees between dyes and the macromolecules of the tissu... | ["[Preparation] Warm the cryosections from the -80º freezer toRoom temperature 30 min ;", "[Preparation] If gelatin embedded tissue, incubate in 15 min 37 °C ;", "[Preparation] Fix the slides in 4% PFA for 5 minRoom temperature", "[Preparation] Wash 1x in 5 min", "[Preparation] Wash 2x in 5 min", "[Preparation] ... |
84,426 | Tissue biopsy FFPE preparation | 4 | dx.doi.org/10.17504/protocols.io.rm7vzx81rgx1/v1 | https://www.protocols.click/view/tissue-biopsy-ffpe-preparation-cwpixdke | kyu sang han, peihsun.wu | TITLE: Tissue biopsy FFPE preparation
AUTHORS: kyu sang han, peihsun.wu
[DESCRIPTION]
Creating human tissue FFPE block from excisional biopsy, and sectioning to create H&E slides.
[STEPS]
SECTION: Tissue biopsy collection
1. Take excisional biopsy of human skin in abdomen or scalp
SECTION: Tissue biopsy collection
2.... | ["[Tissue biopsy collection] Take excisional biopsy of human skin in abdomen or scalp", "[Tissue biopsy collection] After excisional biopsy from a operating room (OR), place the skin tissue into a tissue container prefilled with buffered formalin for 12-24 hours at room temperature (RT)", "[Tissue biopsy collection] Di... |
30,661 | Whole Mouse Brain Processing for Microglia Isolation, Cell Separation, and Flow Cytometry | null | dx.doi.org/10.17504/protocols.io.97dh9i6 | null | Sam Li | TITLE: Whole Mouse Brain Processing for Microglia Isolation, Cell Separation, and Flow Cytometry
AUTHORS: Sam Li
[STEPS]
?. [Harvesting the brain]
If the mouse is >2 weeks old, perfuse the mouse with 10 mL 1X PBS through the left ventricle prior to brain harvest.
?. [Harvesting the brain]
Beginning from the brain stem... | ["[Harvesting the brain]\nIf the mouse is >2 weeks old, perfuse the mouse with 10 mL 1X PBS through the left ventricle prior to brain harvest.", "[Harvesting the brain]\nBeginning from the brain stem, cut upward along the sagittal suture as to not damage the brain. Note: Sagittal Suture is a connective joint that split... |
105,309 | hPSC Passaging and Propagation on laminin521 | 0 | dx.doi.org/10.17504/protocols.io.81wgbz9e3gpk/v1 | https://www.protocols.io/view/hpsc-passaging-and-propagation-on-laminin521-di354gq6 | Gist Croft, Regine Tipon, Niraj Sawarkar, Sigi Benjamin | TITLE: hPSC Passaging and Propagation on laminin521
AUTHORS: Gist Croft, Regine Tipon, Niraj Sawarkar, Sigi Benjamin
[DESCRIPTION]
hPSC Passaging and propagation using Laminin521 and EDTA. Laminin actively supports survival, prevents spontaneous differentiation, and increases plating efficiency, thus net expansion, ... | ["[Plate Coating] PREPARE LAMININ WORKING SOLUTION: Dilute laminin521 stock (100ug/ml) to 5 ug/mL in PBS with Mg2+ and Ca2+, (1:20 dilution). IMPORTANT: Mg and Ca cations in PBS required for laminin function, do not use PBS without Mg2+ and Ca2+", "[Plate Coating] VOLUMES OF WORKING SOLUTIONS REQUIRED FOR DIFFERENT P... |
18,825 | "Globalization, Cooperation & Social Identity" project | null | dx.doi.org/10.17504/protocols.io.wmhfc36 | null | Nancy R. Buchan, Gianluca Grimalda, Marilynn Brewer, Enrique Fatas, Margaret Foddy, Rick Wilson | TITLE: "Globalization, Cooperation & Social Identity" project
AUTHORS: Nancy R. Buchan, Gianluca Grimalda, Marilynn Brewer, Enrique Fatas, Margaret Foddy, Rick Wilson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We present the protocol of international economics experiments conducted to study the... | ["Country selection aimed to maximise dispersion across the 3 dimensions (economic, social and political) of a country-level globalisation scale.", "We targeted samples of 200 adults in each country (US, Italy, Russia, Argentina, South Africa, Iran), equally distributed across 18 demographic categories. Such categories... |
49,660 | Synthesis and Characterization of Silver Nanoparticles using Sodium Borohydride as a Reducing Agent | 1 | dx.doi.org/10.17504/protocols.io.buq4nvyw | https://www.protocols.io/view/synthesis-and-characterization-of-silver-nanoparti-buq4nvyw | Sean Byrne McDonnell, Sebnem Gunes, Alan Casey, James Curtin, Eline Manaloto | TITLE: Synthesis and Characterization of Silver Nanoparticles using Sodium Borohydride as a Reducing Agent
AUTHORS: Sean Byrne McDonnell, Sebnem Gunes, Alan Casey, James Curtin, Eline Manaloto
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Silver nanoparticles (AgNP) have a multitude of uses,... | ["[Synthesis]\nAdd of to an Erlenmeyer flask.\n30 mL", "[Synthesis]\nInsert the Erlenmeyer flask containing of sodium borohydride into the previously set up ice bath containing the stir plate and allow to cool for\n30 mL", "[Synthesis]\nPlace a magnetic mixing rod into the Erlenmeyer flask and start the stir plate ... |
93,934 | Sonication-induced fragmentation analysis of α-synuclein fibrils | 4 | dx.doi.org/10.17504/protocols.io.6qpvr3nebvmk/v1 | https://www.protocols.io/view/sonication-induced-fragmentation-analysis-of-synuc-c7ynzpve | Arpine Sokratian | TITLE: Sonication-induced fragmentation analysis of α-synuclein fibrils
AUTHORS: Arpine Sokratian
[DESCRIPTION]
This protocol is designed to quantify the fragmentation pattern of full-length α-synuclein fibrils, induced by ultrasonic frequencies through sonication. To ensure consistency, we have adopted the indirect
... | ["[Amplification of α-synuclein fibrils] Prepare α-synuclein fibrils according to the protocol attached", "[Concentration measurements] Measure concentration of fibrils according to the protocol step #5", "[Concentration measurements] Dilute fibrils to the concentration 5 mg/mL in PBS\n \nUse protein-low binding tubes... |
62,212 | Rebel Wilson Keto Reviews - Is It Fake Or Trusted Pills? | 1 | dx.doi.org/10.17504/protocols.io.yxmvmn5ong3p/v1 | https://www.protocols.io/view/rebel-wilson-keto-reviews-is-it-fake-or-trusted-pi-b8zcrx2w | rebelwilsonketoreviews | TITLE: Rebel Wilson Keto Reviews - Is It Fake Or Trusted Pills?
AUTHORS: rebelwilsonketoreviews
[DESCRIPTION]
Rebel Wilson Keto Reviews - Is It Fake Or Trusted Pills?
[STEPS]
1. Rebel Wilson Keto Reviews - Is It Fake Or Trusted Pills?
Drink to the Revolutionary Wilson Keto Capsules inspection. Nearly everyone is f... | ["Rebel Wilson Keto Reviews - Is It Fake Or Trusted Pills?\nDrink to the Revolutionary Wilson Keto Capsules inspection. Nearly everyone is facing weight loss problems moment. Latterly, the request for weight loss supplements is roaring each over the world. Out of nowhere, your overabundant peers get in shape and post t... |
53,683 | Homology modeling using SWISS-Model for Biochemistry I | 1 | dx.doi.org/10.17504/protocols.io.byntpven | https://www.protocols.io/view/homology-modeling-using-swiss-model-for-biochemist-byntpven | Michael Friedman, Chris Berndsen | TITLE: Homology modeling using SWISS-Model for Biochemistry I
AUTHORS: Michael Friedman, Chris Berndsen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for homology modeling proteins for use in Biochemistry I at James Madison University. Protocol guides students to use the SWISS-Model web s... | ["[NCBI BLAST]\nNavigate to NCBI BLAST (Basic Local Sequence Alignment Tool) and paste your sequence into the \"Enter Query Sequence\" box.", "[NCBI BLAST]\nThe standard settings for the search are shown in the table. ABC1Default SettingWhat it does2Enter Query Sequence3Query Subrange(Blank)Limits search to a part of ... |
101,667 | Transcriptome assembly | 0 | dx.doi.org/10.17504/protocols.io.4r3l2q9e4l1y/v1 | https://www.protocols.io/view/transcriptome-assembly-dfib3kan | Rafael Rodrigues Ferrari, Thiago Mafra Batista | TITLE: Transcriptome assembly
AUTHORS: Rafael Rodrigues Ferrari, Thiago Mafra Batista
[DESCRIPTION]
This protocol provides detailed, step-by-step instructions for students and researchers to assemble transcriptomes from short reads generated by Illumina technology. In this tutorial, we will check the quality of the se... | ["[SEQUENCING QUALITY CHECK] ****FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)****", "[CROSS-SPECIES CONTAMINATION FILTERING] ****Magic-BLAST (https://ncbi.github.io/magicblast/)****\n\n***Prepare a .pbs file to run the analysis remotely on Sagarana***\n \n**Convert output file**", "[ASSEMBLY] ///... |
62,709 | *CUSTOMER REVIEWS* Willie Nelson CBD Gummies Relief Pain 100% Natural & Risk-Free! | 3 | dx.doi.org/10.17504/protocols.io.81wgb62b3lpk/v1 | https://www.protocols.io/view/customer-reviews-willie-nelson-cbd-gummies-relief-b9gvr3w6 | Willie Nelson CBD Gummies | TITLE: *CUSTOMER REVIEWS* Willie Nelson CBD Gummies Relief Pain 100% Natural & Risk-Free!
AUTHORS: Willie Nelson CBD Gummies
[DESCRIPTION]
TIREDNESS PEOPLE Willie Nelson CBD Gummies *Read 8 Facts*100% Clinically Certified Reduce Chronic Pain!
[STEPS] | [] |
29,321 | Protocol used in the comparison of balance changes after inspiratory muscle or Otago exercise training. | null | dx.doi.org/10.17504/protocols.io.8vhhw36 | null | Francesco FVF. Ferraro, James Gavin, Tom Wainwright, Alison McConnell | TITLE: Protocol used in the comparison of balance changes after inspiratory muscle or Otago exercise training.
AUTHORS: Francesco FVF. Ferraro, James Gavin, Tom Wainwright, Alison McConnell
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The following protocol has been used in the research title: Co... | ["[Participants]\nWritten informed consent to take part in the study and to use photographs for scientific publication, was obtained from all participants before testing. Participants were familiarised with all test procedures before testing by verbal explanation, with the aid of participant information sheets. On test... |
21,886 | Biolistic Transfection in Euplotes crassus (provisional) | null | dx.doi.org/10.17504/protocols.io.zk6f4ze | null | Angela Piersanti | TITLE: Biolistic Transfection in Euplotes crassus (provisional)
AUTHORS: Angela Piersanti
[STEPS]
?. 105 vegetative Euplotes crassus cells or 105 mating DP1 and DP3 E. crassus strains (50 h after mixing) were placed on a filter paper soaked with 10 mM HEPES pH 7.4.
?. Shooting conditions were set as follows in the Bio... | ["105 vegetative Euplotes crassus cells or 105 mating DP1 and DP3 E. crassus strains (50 h after mixing) were placed on a filter paper soaked with 10 mM HEPES pH 7.4.", "Shooting conditions were set as follows in the Bio-Rad Biolistic PDS-1000/He Particle Delivery System : rupture disk 1550 psi, helium pressure 1750 ps... |
86,415 | CNO Preparation and Consumption Monitoring | 4 | null | https://www.protocols.io/view/cno-preparation-and-consumption-monitoring-cympxu5n | Victoria Vance, Katerina Rademacher, Ken Nakamura | TITLE: CNO Preparation and Consumption Monitoring
AUTHORS: Victoria Vance, Katerina Rademacher, Ken Nakamura
[DESCRIPTION]
Chemogenetic models utilize the consumption of clozapine N-oxide (CNO) to activate Designer Receptors Activated Only by Designer Drugs (DREADDs) in order to modulate neuronal activity. This protoc... | ["[Materials and Solutions] Materials:\nClozapine N-oxide \nSucrose \nAutoclaved water", "[Materials and Solutions] Making CNO and vehicle water stock stolutions", "[Materials and Solutions] CNO Water (2% sucrose, 200 mg/L CNO):\n20g sucrose and 300mg CNO in 1L autoclaved water\nCarefully weigh CNO to the nearest ... |
95,846 | LENTIVIRAL PRODUCTION FOR PCRISPRi DUAL GUIDE mDA NEURON LIBRARY | 0 | null | https://www.protocols.io/view/lentiviral-production-for-pcrispri-dual-guide-mda-c9uez6te | Renuka Ravi Gupta, Nona Farbehi, Helaine Graziele Santos Vieira, Helen E. King, hendersa, Vikram Khurana, Gist Croft, Robert J Weatheritt, Lorenz Studer, Joseph Powell | TITLE: LENTIVIRAL PRODUCTION FOR PCRISPRi DUAL GUIDE mDA NEURON LIBRARY
AUTHORS: Renuka Ravi Gupta, Nona Farbehi, Helaine Graziele Santos Vieira, Helen E. King, hendersa, Vikram Khurana, Gist Croft, Robert J Weatheritt, Lorenz Studer, Joseph Powell
[DESCRIPTION]
This protocol outlines the production of lentiviral su... | ["[Day 0: Seeding HEK 293T] Seed HEK 293T cells into T25 flasks in 5ml of HEK culture media at a cell seeding density of 1.5x10^6 cells/flask.", "[Day 1: Transfection OF CRISPRi plasmid pool] After 24 hours, check whether the HEK293T cells are at least 60% confluent and proceed with transfection and bring the Opti-MEM ... |
21,416 | Culturing THP-1 Cells | null | dx.doi.org/10.17504/protocols.io.y6gfzbw | null | Teesha Luehr | TITLE: Culturing THP-1 Cells
AUTHORS: Teesha Luehr
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">THP-1 cells are a human monocyte suspension cell line from peripheral blood of a 1 year old infant who had acute mnocytic leukemia. </div></div>
[STEPS]
?. [Preparing Media]
The base medium for this c... | ["[Preparing Media]\nThe base medium for this cell line is RMPI-1640", "[Preparing Media]\nReguired supplements:\n[L-glutamine]\n[Fetal Bovine Serum]\nMost catalog numbers of RMPI-1640 contain L-glutamine, however, some do not. Ensure that it is in the media before using it for culturing.", "[Preparing Media]\nOptional... |
48,923 | Assembly Instructions for colosseum | 1 | dx.doi.org/10.17504/protocols.io.btz3np8n | https://www.protocols.io/view/assembly-instructions-for-colosseum-btz3np8n | Sina Booeshaghi, Yeokyoung Kil, Kyung Hoi Min, Jase Gehring, Lior Pachter | TITLE: Assembly Instructions for colosseum
AUTHORS: Sina Booeshaghi, Yeokyoung Kil, Kyung Hoi Min, Jase Gehring, Lior Pachter
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>We present colosseum, a low-cost, modular, and automated fluid sampling device for scalable fluidic applications. The co... | ["[Preparation]\nPrepare 3D-printed components and parts.", "[Base and Base Plate Assembly]\nAssemble the base and motor.", "[Base and Base Plate Assembly]\nInsert M5 screws into the narrower ends of the rubber feet. Two M5 screws should be 20 mm long, and the other three screws should be shorter (16 mm works fine).", ... |
34,651 | Environmental Exposures and Craniofacial Birth Defects: A Scoping Review Protocol. | null | dx.doi.org/10.17504/protocols.io.bd33i8qn | https://www.protocols.io/view/environmental-exposures-and-craniofacial-birth-def-bd33i8qn | Maira Alejandra Moreno Castillo, João Victor Leite Dias, Sarah Alves Auharek | TITLE: Environmental Exposures and Craniofacial Birth Defects: A Scoping Review Protocol.
AUTHORS: Maira Alejandra Moreno Castillo, João Victor Leite Dias, Sarah Alves Auharek
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left"><span style = "font-weight:... | [] |
86,055 | SenNet Participant Selection Criteria for Breast Tissue | 4 | dx.doi.org/10.17504/protocols.io.q26g7py59gwz/v1 | https://www.protocols.io/view/sennet-participant-selection-criteria-for-breast-t-cyafxsbn | kschneider | TITLE: SenNet Participant Selection Criteria for Breast Tissue
AUTHORS: kschneider
[DESCRIPTION]
SenNet Participant Selection Criteria for Breast Tissue. Tissue was acquired from the Komen Tissue Bank: https://komentissuebank.iu.edu/donate-tissue/donation-procedure.php based on H&E slide from the KTB study (https://d... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.rujd6un | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Lipid peroxidation (LP) is determined by quantifying the malondialdehyde (MDA) content in the homogenate supernatant in the caudal adjacent segment to epicenter by colorimetric reaction with thiobarbituric acid (TBA) at high temperatures. Malondialdehyde is the principal and ... | [] |
31,401 | Plasmid Cloning by PCR | null | dx.doi.org/10.17504/protocols.io.bawhifb6 | null | Addgene the nonprofit plasmid repository | TITLE: Plasmid Cloning by PCR
AUTHORS: Addgene the nonprofit plasmid repository
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes plasmid cloning by </span><a href="https://www.addgene.org/protocols/pcr/" style = "text-decoration:underline;color:blue;cursor:pointer;"><spa... | ["[Designing primers for PCR based cloning:]\nThe basic PCR primers for molecular cloning consist of:Leader Sequence: Extra base pairs on the 5' end of the primer assist with restriction enzyme digestion (usually 3-6bp)Restriction Site: Your chosen restriction site for cloning (usually 6-8bp)Hybridization Sequence: The... |
40,129 | Screening of compounds for inhibition of Sporothix spp. growth | 3 | dx.doi.org/10.17504/protocols.io.bje9kjh6 | https://www.protocols.io/view/screening-of-compounds-for-inhibition-of-sporothix-bje9kjh6 | luanaborba | TITLE: Screening of compounds for inhibition of Sporothix spp. growth
AUTHORS: luanaborba
[STEPS] | [] |
56,615 | cDNA library preparation from total RNA extracts of Single-cell marine protists (e.g. Acantharia, Strombidium basimorphum, and Prymnesium parvum) for transcriptome sequencing | 4 | dx.doi.org/10.17504/protocols.io.b3ifqkbn | https://www.protocols.io/view/cdna-library-preparation-from-total-rna-extracts-o-b3ifqkbn | Joost S Mansour, Konstantinos Anestis, Fabrice Not, Uwe John | TITLE: cDNA library preparation from total RNA extracts of Single-cell marine protists (e.g. Acantharia, Strombidium basimorphum, and Prymnesium parvum) for transcriptome sequencing
AUTHORS: Joost S Mansour, Konstantinos Anestis, Fabrice Not, Uwe John
[DESCRIPTION]
Many marine protists are not culturable and therefo... | ["[cDNA synthesis preparations] Label for each sample a tube .", "[cDNA synthesis preparations] Prepare a 72°C incubator (e.g. a thermocycler)", "[cDNA synthesis preparations] Thaw other reagents on ice – except SmartScribe Reverse Transcriptase, take that from the freezer only once needed.", "[cDNA synthesis preparat... |
62,975 | visisharp | 1 | dx.doi.org/10.17504/protocols.io.14egn7n6pv5d/v1 | https://www.protocols.io/view/visisharp-b9q7r5zn | Dr. Ali | TITLE: visisharp
AUTHORS: Dr. Ali
[DESCRIPTION]
VisiSharp claims to be a nutritional supplement that targets the real cause of eyesight loss.
[STEPS]
SECTION: VisiSharp Review - Is it the Real Cause of Eye Sight Loss?
1.
Well, this sounds interesting! Let’s find out more... VisiSharp is a nutritional suppleme... | ["[VisiSharp Review - Is it the Real Cause of Eye Sight Loss?] Well, this sounds interesting! Let’s find out more... VisiSharp is a nutritional supplement that targets the real cause of eyesight loss and can potentially cure it as well! It’s made from natural herbs and extracts that help strengthen your eyesight, prote... |
86,660 | CAMbank: CPT Field Processing v1 | 4 | null | https://www.protocols.io/view/cambank-cpt-field-processing-v1-cyvcxw2w | Eliah G Overbey, Krista A Ryon, jak, chm2042 | TITLE: CAMbank: CPT Field Processing v1
AUTHORS: Eliah G Overbey, Krista A Ryon, jak, chm2042
[DESCRIPTION]
Field processing of CPT vacutainers for the Cornell Aerospace Medicine Biobank (CAMbank).
Instructions for preserving: Plasma, PBMCs, and RBC Pellets.
[STEPS]
SECTION: Perform Venipuncture
1. After venipunctur... | ["[Perform Venipuncture] After venipuncture, invert the tubes 8 to 10 times to fully mix in the sodium heparin anticoagulant.\n\nStore the tube upright at room temperature until centrifugation.\n\nTo ensure proper barrier formation, blood samples should be centrifuged within 2 hours of blood collection. Centrifugation ... |
null | null | null | dx.doi.org/10.17504/protocols.io.getbten | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Fe-EDTA Stock Solution for ESAW Media for Marine Phytoplankton</p>
[STEPS]
?.
?.
?. | [] |
52,334 | Bulk RNA sequencing (mRNA seq) | 4 | dx.doi.org/10.17504/protocols.io.bxcnpive | https://www.protocols.io/view/bulk-rna-sequencing-mrna-seq-bxcnpive | Klaus H. Kaestner Lab, Suzanne Shapira | TITLE: Bulk RNA sequencing (mRNA seq)
AUTHORS: Klaus H. Kaestner Lab, Suzanne Shapira
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Bulk RNA sequencing (RNA-seq) is a quantitative method used to interrogate the transcriptome of a biological sample at a given point... | ["[Steps in pre-processing]\n1. 250,000 to 500,000 cells for use in Qiagen DNA/RNA AllPrep kit: for >500,000 cells, use DNA/RNA Universal AllPrep kit; for a. Centrifuge cells, then carefully remove all supernatant by aspiration.b. Loosen pellet by flicking and add RLT Plus buffer (prepared with Beta-mercaptoethanol)6... |
67,431 | Is Growth Matrix Male Enhancement Effective Long Term? | 3 | dx.doi.org/10.17504/protocols.io.q26g742r9gwz/v1 | https://www.protocols.io/view/is-growth-matrix-male-enhancement-effective-long-t-cd4fs8tn | saksemahiano | TITLE: Is Growth Matrix Male Enhancement Effective Long Term?
AUTHORS: saksemahiano
[DESCRIPTION]
https://bumppy.com/tm/read-blog/103390
[STEPS] | [] |
57,531 | Isolation of Symbiodiniaceae from scleractinian coral hosts suitable for cryopreservation and laser-warming | 4 | dx.doi.org/10.17504/protocols.io.b4e3qtgn | https://www.protocols.io/view/isolation-of-symbiodiniaceae-from-scleractinian-co-b4e3qtgn | Jessica Bouwmeester, Jonathan Daly, Mariko Quinn, and Mary Hagedorn | TITLE: Isolation of Symbiodiniaceae from scleractinian coral hosts suitable for cryopreservation and laser-warming
AUTHORS: Jessica Bouwmeester, Jonathan Daly, Mariko Quinn, and Mary Hagedorn
[DESCRIPTION]
This protocol is used to obtain a clean isolate of Symbiodiniaceae extracted from their coral hosts. The freshly... | ["[Isolation of Symbiodiniaceae Day 1] Select 3-5 genotypes for each target species to ensure a sample representative of the Symbiodiniaceae commonly found in that coral species.", "[Isolation of Symbiodiniaceae Day 1] Take a photosynthetic yield measurement of each genotype using a PAM fluorometer to use as reference ... |
37,057 | Effects of singing bowl exposure on Karolinska sleepiness scale and pupillographic sleepiness test: A randomised crossover study. | null | dx.doi.org/10.17504/protocols.io.bge9jth6 | https://www.protocols.io/view/effects-of-singing-bowl-exposure-on-karolinska-sle-bge9jth6 | Melanie Bergmann , Stefan Riedinger , Ambra Stefani, Thomas Mitterling, Evi Holzknecht, Peter Grassmayr, Birgit Högl | TITLE: Effects of singing bowl exposure on Karolinska sleepiness scale and pupillographic sleepiness test: A randomised crossover study.
AUTHORS: Melanie Bergmann , Stefan Riedinger , Ambra Stefani, Thomas Mitterling, Evi Holzknecht, Peter Grassmayr, Birgit Högl
[DESCRIPTION]
<div class = "text-blocks"><div class = ... | ["[Identify participants]\nInclusion criteria Participants can be included in this study if they:", "[Identify participants ]\nExclusion criteria Participants cannot be included in the study if they:have a body mass index > 30 kg/m2,report less than six hours of sleep the night before the assessment,report insomnia, de... |
81,174 | PHYTOMap in Arabidopsis root tips | 4 | null | https://www.protocols.io/view/phytomap-in-arabidopsis-root-tips-cthwwj7e | Tatsuya Nobori, Joseph Ecker | TITLE: PHYTOMap in Arabidopsis root tips
AUTHORS: Tatsuya Nobori, Joseph Ecker
[DESCRIPTION]
Retrieving the complex responses of individual cells in the native three-dimensional tissue context is crucial for a complete understanding of tissue functions. Here, we present PHYTOMap (Plant HYbridization-based Targeted Obs... | ["[Sampling] Cut Arabidopsis root tips (approximately 1 cm) with razor blade and place them on a Poly-D-Lysine coated dish. The tissue should adhere to the dish well.", "[Tissue Permeabilization] Rehydrate the tissue by 5 min successive washes with 100 µL 75%, 50%, 25% MeOH in DPBST.", "[Gene Specific Probe Hybridizati... |
null | null | null | dx.doi.org/10.17504/protocols.io.gipbudn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol was standarized in our lab based on the publication of Ahn T et al (2001): <strong> Polyacrylamide Gel Electrophoresis without a stacking Gel: Use of Amino Acids as Electrolytes. DOI:<a href="https://dx.doi.org/10.1006/abio.2001.5038" target="_blank">10.1006/abi... | [] |
92,707 | Economical Nanopore LSK Sequencing: Adapted Protocols with Homebrew Reagents | 1 | null | https://www.protocols.io/view/economical-nanopore-lsk-sequencing-adapted-protoco-c6sbzean | Jie Hao Ou, Yin-Tse Huang | TITLE: Economical Nanopore LSK Sequencing: Adapted Protocols with Homebrew Reagents
AUTHORS: Jie Hao Ou, Yin-Tse Huang
[DESCRIPTION]
This protocol introduces a cost-effective alternative for end repair and dA-tailing in DNA library preparation, particularly tailored for PCR samples with an N50 of 3 kb. By employing a ... | ["[Homebrew End Repair/dA-Tailing] Add the materials in the following table sequentially.\nMaterialsQuantityDNA800 – 1600 ngH2OBring up to a volume of 43 ul2X PNK/Taq Buffer50 ulATP (25 mM)1 uldNTP (10 mM)5 ulTaq polymerase0.5 ul (2.5 U)T4 PNK0.5 ul (5 U)", "[Homebrew End Repair/dA-Tailing] Incubate at 37 °C for30 min"... |
94,411 | Elevated plus maze test for mice | 1 | dx.doi.org/10.17504/protocols.io.n92ldmxkxl5b/v1 | https://www.protocols.io/view/elevated-plus-maze-test-for-mice-c8fjztkn | Csilla Novák, Andrés Mauricio Jaramillo Flautero, Matthias Prigge | TITLE: Elevated plus maze test for mice
AUTHORS: Csilla Novák, Andrés Mauricio Jaramillo Flautero, Matthias Prigge
[DESCRIPTION]
The elevated plus maze is a classical test to screen anxiety-like behaviors in laboratory animals. This protocol is optimized to mice. The protocol also describes the use of Biobserve Viewe... | ["[Biobserve Viewer] Open Biobserve Viewer.", "[Biobserve Viewer] Make sure that the arena is well positioned in the middle of the view of the webcam.", "[Biobserve Viewer] Go to Configuration and Experiment. Set “stop experiment after: “ to 10 minutes. If you are alone, it is best to tick “Delayed start”, so you can s... |
46,022 | Isolation of Nuclei from Adult Mouse Brain Tissue Protocol | 1 | dx.doi.org/10.17504/protocols.io.bq7emzje | https://www.protocols.io/view/isolation-of-nuclei-from-adult-mouse-brain-tissue-bq7emzje | Allen Institute for Brain Science | TITLE: Isolation of Nuclei from Adult Mouse Brain Tissue Protocol
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for isolation of nuclei from microdissected mouse brain tissue sections for FPCR and/or RNA-seq analysis. </div><div class = "text-blo... | [] |
40,092 | Photomap of the polythenic chromosomes of Drosophila and in situ mapping | 4 | dx.doi.org/10.17504/protocols.io.bjd4ki8w | https://www.protocols.io/view/photomap-of-the-polythenic-chromosomes-of-drosophi-bjd4ki8w | Pierre Teodosio | TITLE: Photomap of the polythenic chromosomes of Drosophila and in situ mapping
AUTHORS: Pierre Teodosio
[STEPS]
?. Making the photomap of polythenic chromosomes
?. 1 The slides of politenic chromosomes of D. malerkotliana of the population of Parque Dois Irmãos (Recife) were prepared by crushing the dissected saliva... | ["Making the photomap of polythenic chromosomes", "1 The slides of politenic chromosomes of D. malerkotliana of the population of Parque Dois Irmãos (Recife) were prepared by crushing the dissected salivary glands of zero-hour pre pupae, fixed with a solution of acetic acid, water and lactic acid, in a 3:2:1 ratio. The... |
40,657 | Direct ELISA for investigating the binding of Protein-G to immunoglobulins. | 6 | dx.doi.org/10.17504/protocols.io.bjxrkpm6 | https://www.protocols.io/view/direct-elisa-for-investigating-the-binding-of-pro-bjxrkpm6 | Angel Justiz-Vaillant, Monica F. Smikle | TITLE: Direct ELISA for investigating the binding of Protein-G to immunoglobulins.
AUTHORS: Angel Justiz-Vaillant, Monica F. Smikle
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Streptococcal protein G is an immunoglobulin-binding protein that interacts with the Fc region of many mammalian imm... | ["This ELISA is used to study the interaction of Streptococcal protein-G (SpG) with diverse immunoglobulins.", "The 96 well microtitre plate is coated overnight at 4°C with 1 µg/µl per well of purified immunoglobulins or 50 µl of any animal sera in carbonate-bicarbonate buffer pH 9.6.", "Then plate is treated with bovi... |
81,111 | DToL Taxon-specific Standard Operating Procedures for Marine Metazoa | 2 | dx.doi.org/10.17504/protocols.io.n92ldpdxnl5b/v1 | https://www.protocols.click/view/dtol-taxon-specific-standard-operating-procedures-ctfxwjpn | Kesella Scott-Somme, John Bishop, Chris Fletcher, Patrick Adkins, Nova Mieszkowska , Rebekka Uhl, Freja Azzopardi, Dominic Phillips, Inez Januszczak | TITLE: DToL Taxon-specific Standard Operating Procedures for Marine Metazoa
AUTHORS: Kesella Scott-Somme, John Bishop, Chris Fletcher, Patrick Adkins, Nova Mieszkowska , Rebekka Uhl, Freja Azzopardi, Dominic Phillips, Inez Januszczak
[DESCRIPTION]
These Standard Operating Procedures (SOPs) contain guidance on how to p... | [] |
96,882 | Systematic Literature Review for operational research on humanitarian cause | 0 | null | https://www.protocols.io/view/systematic-literature-review-for-operational-resea-daus2ewe | Leonardo Rocha, Rodrigo Clemente Thom de Souza, Alan Cesar | TITLE: Systematic Literature Review for operational research on humanitarian cause
AUTHORS: Leonardo Rocha, Rodrigo Clemente Thom de Souza, Alan Cesar
[DESCRIPTION]
This systematic review investigates the use of artificial intelligence (AI) algorithms in locating facilities for humanitarian causes, focusing on issues ... | ["[Context] Human mobility is one of the most intriguing phenomena of the present days. The movement of people around the world has increased in recent years. This has placed groups around the globe in adverse situations. Known as refugees and stateless persons, these are individuals who find themselves forced for some... |
102,705 | Device Fabrication Using Soft Lithography Technique V2 | 0 | dx.doi.org/10.17504/protocols.io.5qpvokpydl4o/v2 | https://www.protocols.io/view/device-fabrication-using-soft-lithography-techniqu-dgir3ud6 | Jann Gamboa, Freeman Lan | TITLE: Device Fabrication Using Soft Lithography Technique V2
AUTHORS: Jann Gamboa, Freeman Lan
[DESCRIPTION]
Standard Operating Procedure
Institute of Biomedical Engineering
University of Toronto
Name of the procedures: Device Fabrication using Soft Lithography Technique
Location: MB308A
PI: Dr. Freeman Lan
Instruct... | ["[Equipment Preparation] Hot Plates and Oven", "[Equipment Preparation] The first step consists of turning one hot plate to 95 °C and another hot plate to ~200 °C", "[Potential Hazards] is a reproductive toxin and goes through gloves!\n\n2. Wear cut resistant gloves when using the razor!\n\n3. Always put the lid on wh... |
44,581 | Introduction to PCR | 3 | dx.doi.org/10.17504/protocols.io.bpsdmna6 | https://www.protocols.io/view/introduction-to-pcr-bpsdmna6 | TITLE: Introduction to PCR
AUTHORS:
[STEPS] | [] | |
69,115 | Nanopore Influenza A Virus WGS using one step RT/PCR with RBK barcoding | 4 | dx.doi.org/10.17504/protocols.io.n2bvj655wlk5/v1 | https://www.protocols.click/view/nanopore-influenza-a-virus-wgs-using-one-step-rt-p-cfq3tmyn | Tom Williams | TITLE: Nanopore Influenza A Virus WGS using one step RT/PCR with RBK barcoding
AUTHORS: Tom Williams
[DESCRIPTION]
A protocol to generate Influenza A Virus sequences from RNA extracts in under 24 hours with less than two hours of hands on time.
Based on:
King, J., Harder, T., Beer, M., & Pohlmann, A. (2020). Rapid mu... | ["[Combined RT/PCR] Prepare up to 20 RNA extracts from samples plus:\nNegative control of nuclease-free water \nPositive control of H1N1\nPositive control of H3N2\n\nIf samples previously frozen, mix by briefly vortexing and pulse spin to collect liquid. Keep samples on cool block at all times.", "[Combined RT/PCR] In ... |
49,883 | DNBSEQ-T7RS Sequencing protocol | 4 | dx.doi.org/10.17504/protocols.io.bux3nxqn | https://www.protocols.io/view/dnbseq-t7rs-sequencing-protocol-bux3nxqn | Hongfang Zhang | TITLE: DNBSEQ-T7RS Sequencing protocol
AUTHORS: Hongfang Zhang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>DNBSEQ-T7 is a high throughput sequencer developed by MGI (part of BGI Group). It can generate 1-6Tb of high quality data per day, for a wide range of applications including Whole Gen... | ["Make DNB: use reagents from the DNB Making Kit and DNA library from user to make DNBs (DNA nanoballs) .", "Load DNB: load DNBs onto the flow cell using reagents from the DNB Load Reagent Kit via the MGIDL-T7RS loader.", "Prepare sequencing reagent kit: inspect, thaw the reagent kit and then add the required reagents,... |
null | null | null | dx.doi.org/10.17504/protocols.io.fcabise | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Purpose:</strong> To reproducibly generate fresh preparations of virus for independent experiments.</p>
<p><strong>Summary:</strong> Fresh virus sample for an experiment is generated by a primary infection of exponentially growing host cells from a master stock of vir... | [] |
22,324 | Stable isotopes in avian research: a step by step protocol to feather sample preparation for stable isotope analysis of carbon (δ13C), nitrogen (δ15N), and hydrogen (δ2H). Version 1.1 | null | dx.doi.org/10.17504/protocols.io.z2uf8ew | null | Brian Chew, Jeff Kelly, Andrea Contina | TITLE: Stable isotopes in avian research: a step by step protocol to feather sample preparation for stable isotope analysis of carbon (δ13C), nitrogen (δ15N), and hydrogen (δ2H). Version 1.1
AUTHORS: Brian Chew, Jeff Kelly, Andrea Contina
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style =... | ["[Preparation of Cleaning Solution: 2:1 Chloroform Methanol Solution]\nUnder fume hood, pour 100mL chloroform into clean 250 mL beaker.", "[Preparation of Cleaning Solution: 2:1 Chloroform Methanol Solution]\nPour 50mL methanol into beaker.", "[Preparation of Cleaning Solution: 2:1 Chloroform Methanol Solution]\nStir ... |
41,583 | Bacterial 16S-V4V5 rRNA amplification for NGS Illumina sequencing (Metabarcoding) | 4 | dx.doi.org/10.17504/protocols.io.n92ld9bzng5b/v1 | https://www.protocols.io/view/bacterial-16s-v4v5-rrna-amplification-for-ngs-illu-bkupkwvn | Estelle Bigeard, Julie Dinasquet | TITLE: Bacterial 16S-V4V5 rRNA amplification for NGS Illumina sequencing (Metabarcoding)
AUTHORS: Estelle Bigeard, Julie Dinasquet
[DESCRIPTION]
For metabarcoding purpose, the first step involves the amplification by PCR of a given gene region (for example V3 or V5 region of 16S rRNA gene) or gene itself if its size... | ["[Samples : Acid nucleic extraction and quantification] Extract DNA/RNA from the samples using the method/kit appropriate to the specific samples. \n\nWhen working with RNA, another step to transform the RNA in cDNA is necessary. \n\nQuantify and quality-check the final DNA via NanoDrop or Qubit/PicoGreen Method. \n\n... |
41,072 | COOMASSIE COLLOIDAL STAIN - CHEM 584 | 4 | dx.doi.org/10.17504/protocols.io.bkcqksvw | https://www.protocols.io/view/coomassie-colloidal-stain-chem-584-bkcqksvw | Ken Christensen | TITLE: COOMASSIE COLLOIDAL STAIN - CHEM 584
AUTHORS: Ken Christensen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Staining polyacrylamide gels using a colloidal Coomassie Blue stain. Adapted from a JoVE article.</div></div>
[STEPS]
?. Wash gel with ~50 mL ddH2O 3x for ~ for each wash on a shaker... | ["Wash gel with ~50 mL ddH2O 3x for ~ for each wash on a shaker NOTE: insufficient washing causes poor sensitivity because the remaining SDS on the gels disturbs the bounding of the dye to the protein", "Shake the colloidal Coomassie solution before use to disperse particles evenly.", "Incubate the gels with the Coomas... |
90,472 | C-SOP-601: Operation of the Illumina MiSeq for Whole Genome Sequencing (WGS) | 4 | null | https://www.protocols.io/view/c-sop-601-operation-of-the-illumina-miseq-for-whol-c4kgyutw | Mihir Kekre, Ben Pascoe | TITLE: C-SOP-601: Operation of the Illumina MiSeq for Whole Genome Sequencing (WGS)
AUTHORS: Mihir Kekre, Ben Pascoe
[DESCRIPTION]
The Illumina® MiSeq™ system combines proven sequencing by synthesis (SBS) technology with a revolutionary workflow that lets you go from DNA to analysed data in as few as 48 hours. The MiS... | ["[Before Starting] Prior to initiating the protocol, ensure that all active workbenches are cleaned with 80% ethanol, all relevant personal protective clothing is worn and the work area is prepared according to local GLP guidelines for molecular methods.\n\nCreate an organised bench space by clearing away all clutter ... |
98,227 | In vivo Electrophysiology Protocol | 0 | dx.doi.org/10.17504/protocols.io.14egn68eql5d/v1 | https://www.protocols.io/view/in-vivo-electrophysiology-protocol-db6t2ren | Sasha Burwell | TITLE: In vivo Electrophysiology Protocol
AUTHORS: Sasha Burwell
[DESCRIPTION]
This protocol details the procedure used to collect extracellular single unit dopamine recordings for this paper.
[STEPS]
SECTION: In vivo Electrophysiology Protocol
1. Headfix mouse on a treadmill.
SECTION: In vivo Electrophysiology Proto... | ["[In vivo Electrophysiology Protocol] Headfix mouse on a treadmill.", "[In vivo Electrophysiology Protocol] Attach prepared internal cannula (see DART Infusion protocol for details on how to set this up) to the implanted guide cannula.", "[In vivo Electrophysiology Protocol] Attach implanted electrode bundle to the Op... |
70,674 | Isolating non-axenic monoclonal Symbiodinium cultures from Aiptasia pallida | 4 | dx.doi.org/10.17504/protocols.io.rm7vzb89rvx1/v1 | https://www.protocols.io/view/isolating-non-axenic-monoclonal-symbiodinium-cultu-cg9stz6e | Emily Aguirre | TITLE: Isolating non-axenic monoclonal Symbiodinium cultures from Aiptasia pallida
AUTHORS: Emily Aguirre
[DESCRIPTION]
To isolate non-axenic, monoclonal Symbiodinium from the anemone Aiptasia pallida (CC7). Although there is no guarantee that all bacterial associates will be conserved using this method, 16S rDNA sequ... | ["[INITIAL ISOLATION FROM ANEMONE] Rinse an anemone (preferably ~ 1cm + ) with 0.2 µm FSW at least 3x, prior to disruption with a homogenizer. Place the anemone in a 15 mL Eppendorf tube with ~ 5mL of 0.2 µm FSW and homogenize at \"medium\" speed for >30 seconds or until all visible anemone tissue has been completely d... |
103,941 | An ImageJ macro for the quantification of ciliary accessible cholesterol | 0 | dx.doi.org/10.17504/protocols.io.q26g71d88gwz/v2 | https://www.protocols.io/view/an-imagej-macro-for-the-quantification-of-ciliary-dhrd3526 | Jonas Nikoloff, Sreeja V Nair, Suzanne R Pfeffer | TITLE: An ImageJ macro for the quantification of ciliary accessible cholesterol
AUTHORS: Jonas Nikoloff, Sreeja V Nair, Suzanne R Pfeffer
[DESCRIPTION]
ALOD4, a toxin-based probe, can be used to visualize the accessible pool of cholesterol (1). Here we describe an algorithm for segmenting fluorescently-labeled cilia u... | ["[Description of the Macro: Four basic steps] Step 1: Drag and drop the macro to ImageJ/Fiji", "[Description of the Macro: Four basic steps] Step 2: Click “Run’’. The macro requests the user for a folder containing .tif files of images to be analyzed. Choose the folder, click ‘Open’.", "[Description of the Macro: Four... |
99,842 | HiDEF-seq | 0 | dx.doi.org/10.17504/protocols.io.kxygxy9mwl8j/v1 | https://www.protocols.io/view/hidef-seq-ddra252e | Mei Hong Liu, Benjamin M. Costa, Emilia C. Bianchini, Una Choi, Rachel C. Bandler, Emilie Lassen, Marta Grońska-Pęski, Adam Schwing, Zachary R. Murphy, Daniel Rosenkjær, Shany Picciotto, Vanessa Bianchi, Lucie Stengs, Melissa Edwards, Nuno Miguel Nunes, Caitlin A. Loh, Tina K. Truong, Randall E. Brand, Tomi Pastinen, J... | TITLE: HiDEF-seq
AUTHORS: Mei Hong Liu, Benjamin M. Costa, Emilia C. Bianchini, Una Choi, Rachel C. Bandler, Emilie Lassen, Marta Grońska-Pęski, Adam Schwing, Zachary R. Murphy, Daniel Rosenkjær, Shany Picciotto, Vanessa Bianchi, Lucie Stengs, Melissa Edwards, Nuno Miguel Nunes, Caitlin A. Loh, Tina K. Truong, Randall ... | ["[Reagent Preparation] If necessary, create 75% PB Ampure Bead dilution as follows:\n\n \n\nVortex mix", "[Reagent Preparation] Create fresh 80% Ethanol as follows:\n\n \n\nVortex mix", "[E. Coli Nick Ligation] Prepare E. Coli Nick Ligation reaction as follows:\n \n\nPipette mix and spin down", "[A-Tailing] Prepare A-... |
71,172 | Immunocytochemical analysis | 4 | dx.doi.org/10.17504/protocols.io.bp2l69bmrlqe/v1 | https://www.protocols.io/view/immunocytochemical-analysis-chrct52w | Felix Kraus | TITLE: Immunocytochemical analysis
AUTHORS: Felix Kraus
[DESCRIPTION]
Protocol for the immunocytochemical analysis of cell culture cells.
[STEPS]
SECTION: Seeding of HeLa
1. Wash HeLa cells with 1x PBS
SECTION: Seeding of HeLa
2. Add Trypsin to cells for 5 min and incubate at 37°C to dissociate cells from plastic we... | ["[Seeding of HeLa] Wash HeLa cells with 1x PBS", "[Seeding of HeLa] Add Trypsin to cells for 5 min and incubate at 37°C to dissociate cells from plastic well", "[Seeding of HeLa] Resuspend cells in 1 mL DMEM media", "[Seeding of HeLa] Count cells", "[Seeding of HeLa] Seed appropriate number of cells into 6-/12-/24-wel... |
79,514 | protocols.io academic and non-profit contract | 1 | dx.doi.org/10.17504/protocols.io.e6nvwk5j7vmk/v5 | https://www.protocols.io/view/protocols-io-academic-and-non-profit-contract-crv2v68e | protocols.io team | TITLE: protocols.io academic and non-profit contract
AUTHORS: protocols.io team
[DESCRIPTION]
Template Contract
This contract is hereby made between the UNIVERSITY/ORGANIZATION (Univ) and ZappyLab, Inc. (DBA “protocols.io”).
DATE:December 13, 2021START DATE:December 27, 2021END DATE:December 26, 2022DESCRIPTION OF S... | ["[Activation] Within thirty (30) days from the Start Date, Univ will provide to protocols.io a list of IP addresses for on-campus user notification about free Premium workspaces.", "[Activation] Within two (2) weeks from the Start Date, protocols.io will enable free Premium workspaces accounts to be created by any Uni... |
61,654 | Quantification of SARS-CoV-2 variant mutations (HV69-70, E484K/N501Y, del156-157/R158G, del143-145, and LPPA24S) in settled solids using digital RT-PCR | 1 | dx.doi.org/10.17504/protocols.io.14egnzrrzg5d/v5 | https://www.protocols.io/view/quantification-of-sars-cov-2-variant-mutations-hv6-b8fwrtpe | 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, and LPPA24S) in settled solids using digital RT-PCR
AUTHORS: Bridgette Hughes, Bradley J. White, Marlene K. Wolfe, Alexandria B B Boehm
[DESCRIPTION]
This process instruction describes the steps for quantitativ... | ["[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... |
109,359 | Development of a machine-learning model to predict chronic postsurgical pain in patients undergoing cardiac surgery: a case-control study | 0 | dx.doi.org/10.17504/protocols.io.n92ld8kdnv5b/v1 | https://www.protocols.io/view/development-of-a-machine-learning-model-to-predict-dn2p5gdn | Ying Zhang, Xi Wang, Feng Xiao, Hui Liu, Hequan Zhu, Qing Liu, Xin | TITLE: Development of a machine-learning model to predict chronic postsurgical pain in patients undergoing cardiac surgery: a case-control study
AUTHORS: Ying Zhang, Xi Wang, Feng Xiao, Hui Liu, Hequan Zhu, Qing Liu, Xin
[DESCRIPTION]
ABSTRACT
Background: Chronic postsurgical pain is common, affecting more than 30% of... | ["[Clarify the research theme and content] Type of study: retrospective, case-control, machine learning, clinical predictive modeling", "[Clarify the research theme and content] Title: Development of a machine-learning model to predict chronic postsurgical pain in patients undergoing cardiac surgery: a case-control stu... |
null | null | null | dx.doi.org/10.17504/protocols.io.g29byh6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Defined Medium for Aureococcus anophagefferens</p>
[GUIDELINES]
<table>
<tbody>
<tr style="text-align: center;">
<td colspan="7">
<p><strong>Anhydrous Salts</strong></p>
</td>
</tr>
<tr style="text-align: center;">
<td>
<p><strong>Constituent</strong></p>
</td>
<td>
<p><stro... | [] |
49,179 | SAHDA: Sequence Alignment from Haplotype De Novo Assembly | 5 | dx.doi.org/10.17504/protocols.io.q26g78w58lwz/v1 | https://www.protocols.io/view/sahda-sequence-alignment-from-haplotype-de-novo-as-bt93nr8n | Joseph C Blackwell, Megan Mcdonald | TITLE: SAHDA: Sequence Alignment from Haplotype De Novo Assembly
AUTHORS: Joseph C Blackwell, Megan Mcdonald
[DESCRIPTION]
SAHDA is a Snakemake based workflow tool designed identify and analyse genes/features of interest within small haplotype genomes. The workflow will assemble haploid genomes de novo from short pai... | ["[Overview] The following is an overview of the workflow. When run, the workflow will automatically take inputs and perform subsequent steps. Each step can act as an input for files and generates an intermediary output that can be extracted from the workflow. The software used in each step is linked and the inputs and... |
24,145 | Preparation of XL1-Blue competent cells using MgCl2 and CaCl2 | null | dx.doi.org/10.17504/protocols.io.3trgnm6 | null | Rashmi Karki, Monica Rieth | TITLE: Preparation of XL1-Blue competent cells using MgCl2 and CaCl2
AUTHORS: Rashmi Karki, Monica Rieth
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Preparation of chemically competent Xl1-Blue cells using MgCl</span><span style = "vertical-align:sub;">2</span><span> and CaCl</span><span ... | ["[Day 1]\nInoculate a 5 mL culture of liquid LB media from a glycerol stock (-80ºC) of XL1-Blue competent cells", "[Day 1]\nIncubate it for 16-20 hours at 37°C at 220-225 rpm", "[Day 2]\nRemove the culture tubes from incubator", "[Day 2]\nMake four dilutions of the culture in liquid broth", "[Day 2]\nDilution 1: 20μl ... |
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