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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29,015 | Postex System User Guide | null | dx.doi.org/10.17504/protocols.io.8jxhupn | null | Anna Crofts | TITLE: Postex System User Guide
AUTHORS: Anna Crofts
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The </span><a href="http://www.haglofsweden.com/index.php/en/products/instruments/calipers/496-dp-postex" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">Poste... | ["[Set-up Tripod]\nAttach the two tripods (herein referred to as tripod) and unfold and extend all tripod legs/arms.Position the tripod so it is centred over the plot centre.Level the tripod - place the level in the centre of the tripod and adjust- so that the upper arms are on the same horizontal plane. Using a compas... |
98,087 | Automated BioID sample preparation | 0 | dx.doi.org/10.17504/protocols.io.kxygxymdwl8j/v2 | https://www.protocols.io/view/automated-bioid-sample-preparation-db2f2qbn | Emilio Cirri, Hannah Knaudt, Domenico Di Fraia, Nadine Pömpner, Norman Rahnis, Ivonne Heinze, Alessandro Ori, Therese Dau | TITLE: Automated BioID sample preparation
AUTHORS: Emilio Cirri, Hannah Knaudt, Domenico Di Fraia, Nadine Pömpner, Norman Rahnis, Ivonne Heinze, Alessandro Ori, Therese Dau
[DESCRIPTION]
We introduce an automated workflow for proximity dependent biotinylation on a liquid handler to process up to 96 samples at a time,c... | ["[Abbreviations] ACN - Acetonitrile,\nAmBic - Ammonium Bicarbonate,\nDIA – Data Independent\nAcquisition,\nDMEM - Dulbecco's Modified Eagle\nMedium,\nEDTA – Ethylene Diamine\nTetraacetic Acid,\nEGTA - (Ethylene Glycol-bis(β-aminoethyl\nether)-N,N,N′,N′-Tetraacetic Acid,\nFBS - Fetal Bovine Serum,\nHEPES -\n4-(2-hydrox... |
27,986 | LB Medium (1 Liter) | null | dx.doi.org/10.17504/protocols.io.7jshkne | null | Alba Balletbó | TITLE: LB Medium (1 Liter)
AUTHORS: Alba Balletbó
[STEPS]
?. Add LB medium components in a 1 L autoclavable. LB medium components (1 L): AB1NaCl10 gram2Tryptone10 gram3Yeast Extract5 gram
AB1NaCl10 gram2Tryptone10 gram3Yeast Extract5 gram
?. Add 1 L of distilled water into the bottle.
?. Vigorously shake the bottle.
... | ["Add LB medium components in a 1 L autoclavable. LB medium components (1 L): AB1NaCl10 gram2Tryptone10 gram3Yeast Extract5 gram\nAB1NaCl10 gram2Tryptone10 gram3Yeast Extract5 gram", "Add 1 L of distilled water into the bottle.", "Vigorously shake the bottle.", "Place the bottle into the autoclave and sterilize."] |
45,944 | Cytochrome C Assay_small_volume | 4 | null | https://www.protocols.io/view/cytochrome-c-assay-small-volume-bq4ymyxw | Elizabeth Fozo | TITLE: Cytochrome C Assay_small_volume
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Cytochrome C Assay --- Small volume</div></div>
[STEPS]
?. [Cytochrome C Assay -- Small volume]
Start ON cultures of the strain of interest
?. [Cytochrome C Assay -- Small volume]
The next... | ["[Cytochrome C Assay -- Small volume]\nStart ON cultures of the strain of interest", "[Cytochrome C Assay -- Small volume]\nThe next day, measure OD600 and calculate how much of your overnight culture you need for OD600 ~ 0.01", "[Cytochrome C Assay -- Small volume]\nAdd supplement if doing Long Term exposure or place... |
98,968 | 562V-MSM - Co-Cultivation Medium (+L-Methionine) | 4 | null | https://www.protocols.io/view/562v-msm-co-cultivation-medium-l-methionine-dcvy2w7w | Sam Leiboff | TITLE: 562V-MSM - Co-Cultivation Medium (+L-Methionine)
AUTHORS: Sam Leiboff
[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 ... | ["[Planning] Estimate the volume of 562V-MSM you will need based on the following:\n\n \n\nEach unique construct will need a round number of plates; make sure to round up! \nCheck the table below to plan your media", "[Mixing Heat-Stable Ingredients] Retrieve the following heat-stable ingredients:\nMS Basal Salts - St... |
null | null | null | dx.doi.org/10.17504/protocols.io.eyhbft6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Preparing data for use in vContact by using VirSorted <a href="https://github.com/MicroB3-IS/osd-analysis" target="_blank">Ocean Sampling Day (2014)</a> contigs, using tools available in <a href="https://www.protocols.io/view/cyverse.org" target="_blank">Cyverse</a>. This protoc... | [] |
29,943 | Double immunostaining for PIP2 and phosphorylated ERK | null | dx.doi.org/10.17504/protocols.io.9gxh3xn | null | Hiraku MIYAGI, Michio Hiroshima, Yasushi Sako | TITLE: Double immunostaining for PIP2 and phosphorylated ERK
AUTHORS: Hiraku MIYAGI, Michio Hiroshima, Yasushi Sako
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span> Immunofluorescence microscopy is used to determine molecular localization and to measure fluorescence intensity of activit... | ["[Cell culture]\nCultivation of cells on cover slipsSee \"Materials\" to sterilize cover slips.Wash cells in a 60-mm dish with 3 mL of DPBS.Add 300 µL of Accumax (Funakoshi) to the dish.Incubate 10 min at 37° C in an incubator with 5% CO2.Suspend cells in 0.9 mL of DPBS containing 0.5 mM EDTA.Transfer this suspension ... |
67,141 | Scaffold-free, size-controlled generation of spheroids for biochemical assays, drug screening and high-content imaging | 4 | dx.doi.org/10.17504/protocols.io.3byl4bnrrvo5/v1 | https://www.protocols.io/view/scaffold-free-size-controlled-generation-of-sphero-cdtds6i6 | Ralitsa R Madsen | TITLE: Scaffold-free, size-controlled generation of spheroids for biochemical assays, drug screening and high-content imaging
AUTHORS: Ralitsa R Madsen
[DESCRIPTION]
This protocol will allow the user to establish size-controlled, scaffold-free spheroid cultures suitable for drug screening, biochemical signalling assay... | ["[Elplasia plate preparation] Pre-wet all wells with 100 µl cell culture medium of choice", "[Elplasia plate preparation] Centrifuge for 1 min at 500 g to remove any air bubbles", "[Elplasia plate preparation] Place the plate in the incubator at 37 ºC & 5 % CO2 for medium equilibration while processing the cells.", "[... |
61,926 | Cell Penetrating Peptide Design and Synthesis | 6 | dx.doi.org/10.17504/protocols.io.rm7vzy7oxlx1/v1 | https://www.protocols.io/view/cell-penetrating-peptide-design-and-synthesis-b8qervte | Cathy Miller | TITLE: Cell Penetrating Peptide Design and Synthesis
AUTHORS: Cathy Miller
[DESCRIPTION]
Cell penetrating peptides (CPPs), also known as protein transduction domains (PTDs) or membrane transduction peptides (MTPs), are small molecular peptides that consist of 5-30 amino acid residues, which not only penetrate the cel... | [] |
75,078 | Enteric neuron activity in the mouse colon and responses to lumbosacral stimulation | 4 | dx.doi.org/10.17504/protocols.io.ewov1o817lr2/v2 | https://www.protocols.io/view/enteric-neuron-activity-in-the-mouse-colon-and-res-cmjeu4je | Kristen Smith-Edwards | TITLE: Enteric neuron activity in the mouse colon and responses to lumbosacral stimulation
AUTHORS: Kristen Smith-Edwards
[DESCRIPTION]
This protocol describes the steps for calcium imaging activity in the enteric nervous system (ENS) and interstitial cells of Cajal (ICC) in isolated colons and ex vivo lumbosacral spi... | ["[Isolated Colon Preparation] Euthanize EIIa-GCaMP mice (offspring from the pairing of B6.FVB-Tg(EIIa-cre)C5379Lmgd/J [RRID:IMSR_JAX:003724; cat. 003724; Jax Labs] and B6J.Cg-Gt(ROSA)26Sortm96(CAG-GCaMP6s)Hze/MwarJ [RRID:IMSR_JAX:028866; cat. 028865; Jax Labs]), by inhalation of isoflurane and thoracotomy. Remove the ... |
32,992 | Mapping and Counting High-Intensity Perineuronal Nets in the Somatosensory Cortex | null | dx.doi.org/10.17504/protocols.io.bcf8itrw | null | Dana Layo, Billy Y.B. Lau, Keerthi Krishnan | TITLE: Mapping and Counting High-Intensity Perineuronal Nets in the Somatosensory Cortex
AUTHORS: Dana Layo, Billy Y.B. Lau, Keerthi Krishnan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The purpose of this protocol is to outline the process by which we count high-intensity perineuronal net... | ["[Preparation]\nDownload ImageJ from the NIHHave 10x whole somatosensory cortex images containing the dentate gyrus and striatum (these are sagittal directions) -- Know measured equivalent of a pixel from the microscope using 10x objectiveHave the images that you will be analyzing downloaded to the computerHave a di... |
18,018 | ADBS Whole Genome Sequencing (WGS) analysis pipeline for Genomic-QC Report | null | dx.doi.org/10.17504/protocols.io.vuae6se | null | Ravi More | TITLE: ADBS Whole Genome Sequencing (WGS) analysis pipeline for Genomic-QC Report
AUTHORS: Ravi More
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Whole Genome Sequencing (WGS) analysis pipeline devloped for generating Genomic-QC Report in Accelerator Program for Discovery in Brain Disorder... | ["[Define paths and directories]", "[Unzip the raw reads files from .gz to fastq format]", "[QC check of R1 and R2 paired-end raw reads using FASTQC, Trimming poor quality reads using Prinseq-lite, and Adapter contimination removal using AfterQC]\nSoftware versions used: FASTQC version 0.10.1 Prinseq-lite version 0.20.... |
38,630 | Metal-antibody MIBItag conjugation kit | 4 | dx.doi.org/10.17504/protocols.io.bhyej7te | https://www.protocols.io/view/metal-antibody-mibitag-conjugation-kit-bhyej7te | Marc Bosse, Sean Bendall, Mike Angelo | TITLE: Metal-antibody MIBItag conjugation kit
AUTHORS: Marc Bosse, Sean Bendall, Mike Angelo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a "protocol IO" extended version of MIBItag conjugation kit protocol from Ionpath. </div></div>
[STEPS]
?. [Antibody buffer exchange]
Add 300 µL of B... | ["[Antibody buffer exchange]\nAdd 300 µL of Buffer 2 ( 100 mM phosphate buffer, 2.5 mM EDTA, pH 7.2) to a 50-kDa MWCO micro-filter device", "[Antibody buffer exchange]\nIf step 2 not performed and antibody solution volume is less than Add the 100 µg antibody solution volume\n200 µl", "[Antibody buffer exchange]\nor\nCe... |
79,299 | 2-step PCR mixture and conditions (Barcoded-head primers for seqs pooling) | 4 | dx.doi.org/10.17504/protocols.io.j8nlkky3xl5r/v2 | https://www.protocols.io/view/2-step-pcr-mixture-and-conditions-barcoded-head-pr-crpbv5in | Yin-Tse Huang, Tsu-Chun Hung | TITLE: 2-step PCR mixture and conditions (Barcoded-head primers for seqs pooling)
AUTHORS: Yin-Tse Huang, Tsu-Chun Hung
[DESCRIPTION]
PCR mixture and condition (2X SUPERGREEN PCR MASTER MIX)
[STEPS]
1. Wear glove, clean up the working bench w. 1% bleach
SECTION: For 1' PCR head-primers
2. Prepare 1' PCR master... | ["Wear glove, clean up the working bench w. 1% bleach", "[For 1' PCR head-primers] Prepare 1' PCR master mixutre for head-primers (prepare 1.2X of solutions for pipetting error if needed)\n \nPCR mixture for head-primers for each reaction", "[For 1' PCR head-primers] Mix the 1' PCR master mixture gently by pi... |
106,139 | Purification of FKBP8-GST | 0 | dx.doi.org/10.17504/protocols.io.n2bvjne3pgk5/v1 | https://www.protocols.io/view/purification-of-fkbp8-gst-djv34n8n | Elias Adriaenssens | TITLE: Purification of FKBP8-GST
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol describes the purification and analysis of FKBP8-GST by SDS-PAGE and Coomassie staining.
[STEPS]
SECTION: Purification procedure
1. To purify FKBP8-GST, fuse the cytosol-exposed domain of FKBP8 (1-391aa) to a C-terminal GST-tag ... | ["[Purification procedure] To purify FKBP8-GST, fuse the cytosol-exposed domain of FKBP8 (1-391aa) to a C-terminal GST-tag and clone into a pET-DUET1 vector.", "[Purification procedure] After the transformation of the pET-DUET1 vector encoding FKBP8-GST in E.coli Rosetta pLysS cells (Novagen Cat# 70956-4), grow cells i... |
null | null | null | dx.doi.org/10.17504/protocols.io.eyxbfxn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The following is a general procedure guide for preparation and staining of formalin-fixed, paraffin-embedded tissues using a purified, unconjugated primary antibody, biotinylated secondary antibody and streptavidin-horseradish peroxidase (Sav-HRP) and DAB detection system. Be... | [] |
95,375 | New trends in the minimally invasive repair of abdominal wall defects | 1 | dx.doi.org/10.17504/protocols.io.eq2lyjk3wlx9/v2 | https://www.protocols.io/view/new-trends-in-the-minimally-invasive-repair-of-abd-c9dpz25n | Francesco Ferrara | TITLE: New trends in the minimally invasive repair of abdominal wall defects
AUTHORS: Francesco Ferrara
[DESCRIPTION]
In the last years several authors have proposed different names to describe their minimally invasive approaches, other than the classic laparoscopic techniques like IPOM and IPOM plus, for the treatme... | ["[Methods] A literature search was performed by two reviewers in December 2023 including articles from the 01st January 2013 to the 15th December 2023 and using the following databases:\nScopus, MEDLINE/Pubmed, Cochrane Library, and Web of Science. The following Medical Subjects Heading (MeSH) terms were used: ((minim... |
null | null | null | dx.doi.org/10.17504/protocols.io.ci8uhv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
How to make a 1 M PMSF Stock Solution
[GUIDELINES]
PMSF is hygroscopic and is highly unstable in aqueous solutions. A typical working solution of PMSF is 1mM.<br /><br /><a href="http://store.p212121.com/pmsf/" target="_blank">PMSF</a> is an anti-protease! Do not allow to come ... | [] |
93,717 | OCT Embedding | 1 | dx.doi.org/10.17504/protocols.io.3byl4qy6ovo5/v1 | https://www.protocols.io/view/oct-embedding-c7rvzm66 | Joanna Bi | TITLE: OCT Embedding
AUTHORS: Joanna Bi
[DESCRIPTION]
OCT Embedding protocol
[STEPS]
1. Sample tissue is collected fresh.
2. Squeeze a thin layer of OCT compound (Sakura Tissue-Tek O.C.T. Compound, ref 4583) into a disposable mold.
3. Place the sample tissue in the center of the mold, with the side to be cut orient... | ["Sample tissue is collected fresh.", "Squeeze a thin layer of OCT compound (Sakura Tissue-Tek O.C.T. Compound, ref 4583) into a disposable mold.", "Place the sample tissue in the center of the mold, with the side to be cut oriented into the mold.", "Squeeze more OCT compound over the top to full cover the tissue.", "L... |
45,277 | BSCI:414--Lab 13 Western Blot of Spike and Spike(RBD) | 1 | null | https://www.protocols.io/view/bsci-414-lab-13-western-blot-of-spike-and-spike-rb-bqf5mtq6 | Harley King | TITLE: BSCI:414--Lab 13 Western Blot of Spike and Spike(RBD)
AUTHORS: Harley King
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We used an anti-histidine polyclonal rabbit antibody as a primary antibody. The secondary antibody was a goat anti-rabbit antibody with conjugated HRP. </div></div>
[STE... | ["Watch this video to understand the WB process.", "Download the WB and Coomassie images and save them to your lab notebook.", "Read about the primary antibody.Read about the secondary antibody."] |
75,382 | Quantify coral paling with grayscale-normalized color intensity values | 4 | dx.doi.org/10.17504/protocols.io.6qpvr4p5bgmk/v1 | https://www.protocols.io/view/quantify-coral-paling-with-grayscale-normalized-co-cmuwu6xe | Loreto Paulino Jr., Colin J Anthony, Colin Lock, Justin T Berg, Anela E K Duenas, Bastian Bentlage | TITLE: Quantify coral paling with grayscale-normalized color intensity values
AUTHORS: Loreto Paulino Jr., Colin J Anthony, Colin Lock, Justin T Berg, Anela E K Duenas, Bastian Bentlage
[DESCRIPTION]
Color normalization is crucial for accurate assessment of coral health in ecological studies. Color intensity has conve... | ["[Excel Marco Code Set Up for Mass Data Collection] Go to the \"Tools\" menu and select \"Macros\"", "[Excel Marco Code Set Up for Mass Data Collection] Select \"Visual Basic Editor\"", "[Excel Marco Code Set Up for Mass Data Collection] In the Visual Basic Editor, there will be two drop-down tabs: \"General\" and \"M... |
18,183 | Making electro-competent E. coli cells and transformation of them | null | dx.doi.org/10.17504/protocols.io.vzfe73n | null | Jasper Koehorst | TITLE: Making electro-competent E. coli cells and transformation of them
AUTHORS: Jasper Koehorst
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes a method to make</span><span style = "font-style:italic;">Escherichia coli</span><span>cells electro-competent. The method i... | ["[Day 2]\n+ overnight cultureOriginal:Next day, first thing in the morning, inoculate 400 ml LB w/o salt in a 1 l Erlenmeyer flask with enough of the overnight culture to reach OD600 of 0.2 and incubate for ~3 hours to OD600 0.5-1.0.\n[LB/ w/o salt in 1 Liter erlenmeyer flask]\n[OD600]", "[Day 2]\nOriginal:Transfer cu... |
76,478 | PCR protocol for gene COXI neo-caledonian freshwater micro-crustaceans | 4 | dx.doi.org/10.17504/protocols.io.261ge4y4jv47/v2 | https://www.protocols.io/view/pcr-protocol-for-gene-coxi-neo-caledonian-freshwat-cnw6vfhe | coline.royaux, Nicolas Rabet, Céline Bonillo | TITLE: PCR protocol for gene COXI neo-caledonian freshwater micro-crustaceans
AUTHORS: coline.royaux, Nicolas Rabet, Céline Bonillo
[DESCRIPTION]
This PCR protocol has been used to amplify the Cytochrome Oxydase I gene of neo-caledonian genera Boeckella, Lynceus, Eulimnadia and Streptocephalus with several primers.
[... | ["Prepare the mix for the PCR depending on the quantity of DNA samples you want to amplify", "For each well, mix 12.44 µL, 2 µL, 1 µL, 1 µL, 0.8 µL and 0.12 µL. This mix is hereafter named \"intermediary mix\".", "Add your primers to the mix, 0.32 µL 10 picomolar (pM) and 0.32 µL 10 picomolar (pM) for each well. This ... |
null | null | null | dx.doi.org/10.17504/protocols.io.cdus6v | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is the protocol accompanying the "pLKO.1 – TRC Cloning Vector". For information about the PLKO.1-TRC cloning vector and tips on designing shRNA oligos for pLKO.1 see Addgene's website: http://www.addgene.org/tools/protocols/plko/
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?... | [] |
46,629 | Deep-resolution plant phenotyping platform description. | 5 | dx.doi.org/10.17504/protocols.io.brsdm6a6 | https://www.protocols.io/view/deep-resolution-plant-phenotyping-platform-descrip-brsdm6a6 | Taras Pasternak, Ivan A.Paponov, Thorsten Falk | TITLE: Deep-resolution plant phenotyping platform description.
AUTHORS: Taras Pasternak, Ivan A.Paponov, Thorsten Falk
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">DRPPP (Deep-Resolution Plant Phenotyping Platform) is a combination of protocols for plant tissue preparation, labeling, scanning, an... | ["Image pre-processing pipeline:", "Image analysis (segmentation/nuclei detection).For the analysis, images must be imported to organ analysis software (https://lmb.informatik.uni-freiburg.de/lmbsoft/iRoCS/).Channel-> import channel-> OkFor better visualization, normalize button must be clicked and the signal should be... |
null | null | null | dx.doi.org/10.17504/protocols.io.racd2aw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>1)The partial E gene of dengue virus is amplified before sequencing by using four sets of serotype-specific <br /> oligonucleotides as referenced in the manuscript text.</p>
<p>2) The reaction mixture is prepared as the following:</p>
<p> 12.5ul of MyTaq RT-PCR (Bioline,... | [] |
62,965 | GlucoFreeze: Symptoms Of High Blood Sugar Level! | 1 | dx.doi.org/10.17504/protocols.io.3byl4br9rvo5/v1 | https://www.protocols.io/view/glucofreeze-symptoms-of-high-blood-sugar-level-b9qvr5w6 | kjdfgkoxsa | TITLE: GlucoFreeze: Symptoms Of High Blood Sugar Level!
AUTHORS: kjdfgkoxsa
[DESCRIPTION]
Product Name - GlucoFreeze
Category -Blood Sugar Support
Healthy Benefits - Help to maintain a healthy blood sugar level
Ingredients - Vitamin C, Vitamin E, Juniper Berries
Item Form - Capsules
Net Quantity - 60 Capsules
Age Ra... | [] |
55,177 | Spatial Transcriptomics Protocol | 4 | dx.doi.org/10.17504/protocols.io.bz5hp836 | https://www.protocols.io/view/spatial-transcriptomics-protocol-bz5hp836 | Michael Eadon, Ricardo Melo Ferreira, Ying-Hua Cheng, Tarek Ashkar | TITLE: Spatial Transcriptomics Protocol
AUTHORS: Michael Eadon, Ricardo Melo Ferreira, Ying-Hua Cheng, Tarek Ashkar
[DESCRIPTION]
The tissue in OCT undergoes cryosectioning, affixment to the cDNA capture slide, H+E staining, 20x Keyence imaging, tissue permeabilization, RNA capture, and cDNA synthesis. Data is anal... | ["[Cryosectioning Procedure] Specimens should be handled wearing clean gloves treated with RNAse Away or with a clean RNAse Away treated forceps.", "[Cryosectioning Procedure] Cool Cryostat to -22 °C. Clean the work surfaces with RNAse away and install a new cutting blade.", "[Cryosectioning Procedure] Place a clean sm... |
81,186 | Aureococcus anophagefferens Virus (AaV)/Kratosvirus quantuckense viral particle count by SYBR Green staining and flow cytometry (CytoFLEX S Flow Cytometer Beckman Coulter) | 1 | dx.doi.org/10.17504/protocols.io.dm6gpj331gzp/v2 | https://www.protocols.io/view/aureococcus-anophagefferens-virus-aav-kratosvirus-ctiawkae | Emily E. Chase, Alex Truchon, Samantha R Coy, Steven W Wilhelm | TITLE: Aureococcus anophagefferens Virus (AaV)/Kratosvirus quantuckense viral particle count by SYBR Green staining and flow cytometry (CytoFLEX S Flow Cytometer Beckman Coulter)
AUTHORS: Emily E. Chase, Alex Truchon, Samantha R Coy, Steven W Wilhelm
[DESCRIPTION]
A method for obtaining viral particle counts of Aureoc... | ["[CytoFLEX Experiment Setup] Create a new experiment with sample acquisition settings as follows: \nFSC 500\nSSC 200\nVioSSC 200\nFITC 2000\nPerCP 500\nPB450 40 [placeholder; this could be set for a different dye than Pacific Blue shown here, this will not change the results]\nThreshold: (manual) Violet SSC 3000\n\nSe... |
28,337 | MojoSort™ Human CD45 Nanobeads Protocols | null | dx.doi.org/10.17504/protocols.io.7wrhpd6 | null | Sam Li | TITLE: MojoSort™ Human CD45 Nanobeads Protocols
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Note: If the percentage of CD45+ cells in your sample is less than 50%, please follow Protocol 1. If it is higher than 50% then please follow protocol 2.<... | [] |
53,975 | Coverslip Functionalization SOP003.v2.2 | 1 | null | https://www.protocols.io/view/coverslip-functionalization-sop003-v2-2-byxxpxpn | Rory Kruithoff, Douglas Shepherd | TITLE: Coverslip Functionalization SOP003.v2.2
AUTHORS: Rory Kruithoff, Douglas Shepherd
[DESCRIPTION]
Document Summary:
This document, SOP003 – Coverslip Functionalization, describes the process for cleaning and modifying the coverslip surface for improved adhesion of a sample.This procedure describes two methods o... | ["[Part 1 - Clean coverslips] Wash for 30 min via immersion in 1:1 mix of 37 % (v/v) and methanol at Room temperature.", "[Part 1 - Clean coverslips] Rinse 3x in DI H2O.", "[Part 1 - Clean coverslips] Fill beaker with Rnase-free water and autoclave coverslips to sterilize.", "[Part 1 - Clean coverslips] Rinse 1x in 70 ... |
92,373 | Graph Neural Network Framework for Web-Based Prediction of Protein-Ligand Docking Scores across multiple organs | 5 | dx.doi.org/10.17504/protocols.io.j8nlkoy9xv5r/v1 | https://www.protocols.io/view/graph-neural-network-framework-for-web-based-predi-c6fvzbn6 | Anagha S Setlur, Vidya Niranjan, Arjun Balaji, Chandrashekar K | TITLE: Graph Neural Network Framework for Web-Based Prediction of Protein-Ligand Docking Scores across multiple organs
AUTHORS: Anagha S Setlur, Vidya Niranjan, Arjun Balaji, Chandrashekar K
[DESCRIPTION]
Estimating the docking score between proteins and drugs is very important in the application of structure-based dr... | ["[IMPORTING LIBRARIES] Import all necessary libraries\n\nEnsure the installation and importation of all the necessary libraries needed for both the data preprocessing and the model training and evaluation. Provided below is a screenshot of the required libraries to be imported.", "[DATASET CREATION] In the present sce... |
97,025 | Operant Conditioning | 0 | dx.doi.org/10.17504/protocols.io.j8nlk8b31l5r/v1 | https://www.protocols.io/view/operant-conditioning-day92fz6 | daniel.dautan daniel, Per Svenningsson | TITLE: Operant Conditioning
AUTHORS: daniel.dautan daniel, Per Svenningsson
[DESCRIPTION]
This protocol is for training mice operant conditioning to assess cognitive performance using the resources described in Matikainen-Ankney BA et al 2021.
[STEPS]
SECTION: "Follow the light" testing
9. The number of cor... | ["["Follow the light" testing] The number of correct, incorrect pokes and pellets collected within 10s\nof delivery were then extracted for further analyses.", "["Follow the light" testing] Finally, on the last day, switch the protocol to \"Follow the Light\" for 24 hours. \nAssociate the poke with... |
103,556 | DNA extraction from environmental size-fractionned plankton samples | 0 | dx.doi.org/10.17504/protocols.io.kxygxy5xdl8j/v1 | https://www.protocols.io/view/dna-extraction-from-environmental-size-fractionned-dhdc322w | Sarah Romac | TITLE: DNA extraction from environmental size-fractionned plankton samples
AUTHORS: Sarah Romac
[DESCRIPTION]
This protocol has been designed for total DNA extraction from environmental marine water samples. Samples from different plankton size fractions are collected by Niskin bottles (Step Case 1) or by plankton net... | ["Depending of the plankton size fraction samples you have, select :\n\n1 - DNA extraction using NucleoSpin Plant II MINI kits regarding [<20µ] size fractions (samples collected using Niskin bottles or pumping and filtered on polycarbonate filters, diameter 47mm) ;\n\n2 - DNA extraction using NucleoSpin Plant II MIDI... |
53,180 | Protocol for nuclei isolation from fresh and frozen tissues using Salty-Ez10 or Salty-Ez50 buffer: compatible with snRNA-Seq and Multiome workflows from 10x Genomics | 1 | dx.doi.org/10.17504/protocols.io.bx64prgw | https://www.protocols.io/view/protocol-for-nuclei-isolation-from-fresh-and-froze-bx64prgw | Luciano Martelotto | TITLE: Protocol for nuclei isolation from fresh and frozen tissues using Salty-Ez10 or Salty-Ez50 buffer: compatible with snRNA-Seq and Multiome workflows from 10x Genomics
AUTHORS: Luciano Martelotto
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a protocol in development, which means it h... | ["[Tissue Homogenization]\nMince/chop tissue with a razor blade to small pieces. The tissue may be as small as a grain of rice.\nFor mincing the tissue, you may take the tube out of ice, however, be quick and return it to ice.", "[Tissue Homogenization]\nAdd of chilled Salty-Ez10 or Salty-Ez50 Lysis Buffer (supplement... |
null | null | null | dx.doi.org/10.17504/protocols.io.utxewpn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Protocol for the expression and purification of Cas9 protein
[STEPS] | [] |
88,080 | Preparation of DEPC-treated water | 4 | null | https://www.protocols.io/view/preparation-of-depc-treated-water-cz9qx95w | Carlos Costas Insua | TITLE: Preparation of DEPC-treated water
AUTHORS: Carlos Costas Insua
[DESCRIPTION]
Diethyl pyrocarbonate (DEPC) is a wide-spectrum RNase inhibitor. DEPC-treated water is generally used when working with RNA
[STEPS]
1. Add 1 mL of fresh DEPC to 1 L of H2O. Shake well to disperse the DEPC through the H2O. Incubate at ... | ["Add 1 mL of fresh DEPC to 1 L of H2O. Shake well to disperse the DEPC through the H2O. Incubate at 37°C for at least 12 h and/or autoclave at 15 psi on liquid cycle for 20 min to inactivate the remaining DEPC."] |
72,690 | Immunohistochemical staining of heparan sulfate (HS) and collagen type XVIII (col18) core proteins in islet beta cells of formalin-fixed human pancreas and isolated human islets | 1 | dx.doi.org/10.17504/protocols.io.81wgbkn1gpko/v4 | https://www.protocols.io/view/immunohistochemical-staining-of-heparan-sulfate-hs-ci8suhwe | Lora Starrs, Debra Brown, Sarah Popp, Andrew Ziolkowski, Charmaine Simeonovic | TITLE: Immunohistochemical staining of heparan sulfate (HS) and collagen type XVIII (col18) core proteins in islet beta cells of formalin-fixed human pancreas and isolated human islets
AUTHORS: Lora Starrs, Debra Brown, Sarah Popp, Andrew Ziolkowski, Charmaine Simeonovic
[DESCRIPTION]
Paraffin sections (4 μm thickness... | ["See Guidelines, \"Before starting\".", "Deparaffinize slides in each xylene for 1 min. rehydrate slides in graded alcohols beginning in absolute ethanol (10 dips)/ container of absolute ethanol), followed by 90% ethanol (10 dips) and 70% ethanol (10 dips). Wash well in running tap water for 5 min.", "Wipe around sect... |
20,223 | U Mass - Hepatic gluconeogenesis | null | dx.doi.org/10.17504/protocols.io.xy7fpzn | null | Jason Kim | TITLE: U Mass - Hepatic gluconeogenesis
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">Hepatic gluconeogensis is estimated using pyruvate tolerance test that measures systemic elevation of glucose pa... | ["Mice are fasted overnight (~15 hours) prior to the start of experiment.", "Collect plasma sample (10 µl) before the start of experiment (basal-0 min) to measure basal glucose levels.", "Administer intraperitoneal injection of pyruvate (1 g/kg body weight) using an insulin syringe.", "Collect plasma samples (10 µl) at... |
14,843 | Mating assay | 1 | dx.doi.org/10.17504/protocols.io.sq3edyn | https://www.protocols.io/view/mating-assay-sq3edyn | Serena Ding | TITLE: Mating assay
AUTHORS: Serena Ding
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">For imaging drug-treated young adult C. elegans in liquids using the Multiworm tracker. Worms are synchronised by picking L4s, and then the young adults are exposed to drugs for 4 hours prior to imaging for 15 m... | ["[Generating male stock (if needed) (~ -3 days) eg Friday]\nPick males from the heat-shocked plates onto the male stock plates, set up crosses with L4 hermaphrodites. If there are enough males, then set up 3 plates of 5 males x 2 hermaphrodites.\nKeep repeating this step every 3-4 days to maintain male stocks througho... |
31,089 | Non-UDG treated double-stranded ancient DNA library preparation for Illumina sequencing | 1 | dx.doi.org/10.17504/protocols.io.bakricv6 | https://www.protocols.io/view/non-udg-treated-double-stranded-ancient-dna-librar-bakricv6 | Franziska Aron, Gunnar Neumann, Guido Brandt | TITLE: Non-UDG treated double-stranded ancient DNA library preparation for Illumina sequencing
AUTHORS: Franziska Aron, Gunnar Neumann, Guido Brandt
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for the preparation of double-stranded genomic libraries for Illumina sequencing, optimised f... | ["[Blunt End Repair (aDNA library preparation room)]\nPrepare a mastermix for the blunt end repair calculating . Use a new 1.5 ml LoBind tube to set up the mastermix. ABCD1ReagentStock concentrationFinal concentration1x Volume [µl]2NEB Buffer 210 x1 x53ATP10 mM1 mM54BSA20 mg/ml0.8 mg/ml25dNTPs25 mM each0.1 mM0.26T4 P... |
30,470 | Trimble GPS Protocol | null | dx.doi.org/10.17504/protocols.io.9zeh73e | null | Sabine St-Jean | TITLE: Trimble GPS Protocol
AUTHORS: Sabine St-Jean
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Here we describe the standardised protocol used by the </span><a href="http://www.caboscience.org/" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">Canadian Air... | ["[GPS Connection]\nConnect the Trimble antenna to your field cellphone, by plugging the cable coming out of the antenna into your cellphone charging port.", "[GPS Connection]\nConnect the external battery to the Trimble antenna, by plugging the USB port into the battery and the micro USB port into the antenna. Place t... |
19,262 | Processing Human Colon "Myenteric Plexus" for Single Nuclei RNA-seq | 1 | dx.doi.org/10.17504/protocols.io.w26fghe | https://www.protocols.io/view/processing-human-colon-quot-myenteric-plexus-quot-w26fghe | Christina M Wright, Robert O Heuckeroth | TITLE: Processing Human Colon "Myenteric Plexus" for Single Nuclei RNA-seq
AUTHORS: Christina M Wright, Robert O Heuckeroth
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">INTRODUCTION: The human enteric nervous system (ENS) is a complex network of neurons and glia that extends throughout the lengt... | ["[PREPARING SYLGARD DISH FOR PINNING TISSUE]\nPrepare Sylgard by combining curing agent with polymer as described in the kit.", "[PREPARING SYLGARD DISH FOR PINNING TISSUE]\nCarefully drip Sylgard into a 35x10 mm dish until the dish is halfway full.", "[PREPARING SYLGARD DISH FOR PINNING TISSUE]\nAllow to cure in a fu... |
39,973 | SOLUTION- 10 - TEFF/TREG isolation buffer | 3 | dx.doi.org/10.17504/protocols.io.bjadkia6 | https://www.protocols.io/view/solution-10-teff-treg-isolation-buffer-bjadkia6 | Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino | TITLE: SOLUTION- 10 - TEFF/TREG isolation buffer
AUTHORS: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
[STEPS] | [] |
54,766 | A reproducibility protocol and dataset on the biomedical sentence similarity | 5 | null | https://www.protocols.io/view/a-reproducibility-protocol-and-dataset-on-the-biom-bzqnp5ve | Alicia Lara Clares, Juan J. Lastra-Díaz, Ana Garcia-Serrano | TITLE: A reproducibility protocol and dataset on the biomedical sentence similarity
AUTHORS: Alicia Lara Clares, Juan J. Lastra-Díaz, Ana Garcia-Serrano
[DESCRIPTION]
This protocol introduces a set of reproducibility resources with the aim of allowing the exact replication of the experiments introduced by our main pa... | ["[Installing Docker on Ubuntu] If Docker is not installed in your machine, instructions below install latest version of Docker CE. For further details, we refer the reader to the official Docker setup page https://docs.docker.com/install/linux/docker-ce/ubuntu/\n\nFirst, we update the system:\n \nWe install the depend... |
null | null | null | dx.doi.org/10.17504/protocols.io.i6vche6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Extraction of high quality DNA for long read sequencing e.g. the Oxford Nanopore </p>
<p>Optimized for DNA extraction from eucalyptus grandis and eucalyptus pauciflora. </p>
<p> </p>
<p>This protocol contains an optional Chloroform clean up step which is necessary for eucalyp... | [] |
48,820 | General Lab SOP | 3 | null | https://www.protocols.io/view/general-lab-sop-btwunpew | USDA | TITLE: General Lab SOP
AUTHORS: USDA
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">General Lab SOP.</div></div>
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ss4eegw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is used to clarity the process of Hi-C library preparation for L.maculatus genome.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
61,664 | Amblyomma americanum parallel transcriptomics and proteomics workflow | 1 | null | https://www.protocols.io/view/amblyomma-americanum-parallel-transcriptomics-and-b8f8rtrw | Peter Thuy-Boun | TITLE: Amblyomma americanum parallel transcriptomics and proteomics workflow
AUTHORS: Peter Thuy-Boun
[DESCRIPTION]
This is a method that lets researchers perform mass spectrometry-based proteomics experiments and build a new reference protein database to help interpret that data in parallel work streams. In our case,... | ["[Proteomics Sample Preparation] Dissect salivary glands from 10 adult female Amblyomma americanum ticks into approximately 100 µL of sterile water and store at -20°C.60 min", "[Proteomics Sample Preparation] Thaw salivary glands on ice, dilute to 1 mL with water, then transfer into 2 mL bead beating tubes containing ... |
40,360 | SOP14v1_TGD_DNAExtraction(QiagenDNeasyBlood&TissueKit) | 4 | null | https://www.protocols.io/view/sop14v1-tgd-dnaextraction-qiagendneasyblood-amp-ti-bjngkmbw | Varsha Rajesh | TITLE: SOP14v1_TGD_DNAExtraction(QiagenDNeasyBlood&TissueKit)
AUTHORS: Varsha Rajesh
[DESCRIPTION]
Guidelines
Bench work should be completed on the pre-PCR/DNA bench.
Blue DNA-only labeled materials should be used for this protocol to avoid cross-contamination.
Lab attire: gloves, lab coat, and safety glasses/go... | ["OPTIONAL: Add 4 uL of 100 mg/mL RNase A and vortex to mix.\nIncubate for 2 min at RT. \n**If RNA-free genomic DNA is required", "Incubate at 56°C for 20 minutes.", "Then, add 200 uL of 96-100% ethanol to sample and vortex to mix. Use a p1000 pipet first then a p200 pipet to homogenize the solution. Solution should be... |
28,115 | Gel Extraction | null | dx.doi.org/10.17504/protocols.io.7pthmnn | null | NUS iGEM | TITLE: Gel Extraction
AUTHORS: NUS iGEM
[STEPS]
?. Add Buffer QG into 2ml tube containing gel slice
450 µl
?. Incubate at for
50 °C
?. Add isopropanol to the sample and mix
150 µl
?. Transfer entire volume into QIAquick spin column
?. Centrifuge at for
Centrifuge: 13000 33
?. Discard flow through
?. Add Buffer PE... | ["Add Buffer QG into 2ml tube containing gel slice\n450 µl", "Incubate at for\n50 °C", "Add isopropanol to the sample and mix\n150 µl", "Transfer entire volume into QIAquick spin column", "Centrifuge at for\nCentrifuge: 13000 33", "Discard flow through", "Add Buffer PE to QIAquick spin column\n750 µl", "Centrifuge... |
45,888 | Sample Collection: Primate Hair for RNA | 4 | null | https://www.protocols.io/view/sample-collection-primate-hair-for-rna-bq28myhw | Alicia Rich | TITLE: Sample Collection: Primate Hair for RNA
AUTHORS: Alicia Rich
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">All of the methods and protocols for this project have been reviewed and approved by the Otterbein University Institutional Animal Care and Use Committee, Otterbein University's Envir... | ["[Animal Handling]\nDuring routine handling procedures, fold one piece of masking tape around a tuft of ~20 hairs on the dorsal neck area of the subject. As swiftly and firmly as possible, pluck the tuft of hairs in the masking tape. The most important part of the sample is the hair root at the end of the shaft, which... |
null | null | null | dx.doi.org/10.17504/protocols.io.hpvb5n6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?. | [] |
28,407 | MojoSort™ Selection Kits Protocol - 1 | null | dx.doi.org/10.17504/protocols.io.7yxhpxn | null | Sam Li | TITLE: MojoSort™ Selection Kits Protocol - 1
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Product description and procedure summary:</span></div><div class = "text-block"><span>Target cells are depleted by incubating the sample with the biotin ant... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes. Kits for human samples have been optimized for PBMCs, please prepare the cells using a suitable method.", "In the final wash of your sample preparation, resuspend the cells in MojoSort™ Buffer by adding up to 4mL in a 5 mL (12 x 75 mm) p... |
19,680 | scTHS-seq | null | dx.doi.org/10.17504/protocols.io.xf8fjrw | null | Kun Zhang, Brandon Sos, Dinh Diep, Thu E Duong | TITLE: scTHS-seq
AUTHORS: Kun Zhang, Brandon Sos, Dinh Diep, Thu E Duong
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Single cell transposome hypersensitive site sequencing (scTHS-seq) combined transposome hypersensitive site sequencing (THS-seq) with combinatorial cellular indexing using custom... | ["[Tagmentation]\nGenerate 384 annealed transposonsCombine top and bottom strand oligos in a PCR tube. In a thermocycler, incubate for 2 minutes at then ramp to at a rate of per second.\n[Indexed Tn5 top strand (100uM)]\n[5' phosphorylated mosaic end sequence bottom strand (100uM)]", "[Tagmentation]\nLoad Tn5-059\n[4... |
null | null | null | dx.doi.org/10.17504/protocols.io.dre53d | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol is for the NEXTflex™ Small RNA Sequencing Kit v2, designed to prepare small RNA libraries for sequencing using Illumina® sequencers. This kit utilizes adapters with randomized ends to greatly reduce sequence bias in small RNA sequencing library construction.<br /><... | [] |
53,550 | Standard Cell Culture Practices | 4 | null | https://www.protocols.io/view/standard-cell-culture-practices-byinpude | Allan JW Lui | TITLE: Standard Cell Culture Practices
AUTHORS: Allan JW Lui
[DESCRIPTION]
Basic cell culture techniques
[BEFORE_START]
Cell culture numbers:
6-well1406759.60.3 x 1061.2 x 106111 to 312-well1506283.50.1 x 1060.5 x 1060.4 to 10.4 to 11 to 224-well1424751.90.05 x 1060.24 x 1060.2 to 0.30.2 to 0.30.5 to 1.048-well150687... | ["[Thaw cells] Request cells from RICS on or before 9am on the day of planned thaw", "[Thaw cells] Confirm items are in the hood pre-thaw:\nWarm media\n15ml centrifuge tube\n1ml pipette & tips\nWaste bin\nAspiration pipettes\nMotorised pipette controller", "[Cell culture prep] Pre-warm media (and reagents to make compl... |
44,735 | Holiday Recipes | 2 | null | https://www.protocols.io/view/holiday-recipes-bpw7mphn | Anita Broellochs, Diana Curcio, Monika Hassan, Lenny Teytelman | TITLE: Holiday Recipes
AUTHORS: Anita Broellochs, Diana Curcio, Monika Hassan, Lenny Teytelman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a collection of favorite holiday recipes from the protocols.io team. Enjoy! </div></div>
[STEPS] | [] |
54,691 | TIMSTOF Pro Crosslinking by Johannes Hevler; Albert Heck/ Richard Scheltema Labs | 1 | dx.doi.org/10.17504/protocols.io.bznbp5an | https://www.protocols.io/view/timstof-pro-crosslinking-by-johannes-hevler-albert-bznbp5an | Johannes Hevler | TITLE: TIMSTOF Pro Crosslinking by Johannes Hevler; Albert Heck/ Richard Scheltema Labs
AUTHORS: Johannes Hevler
[DESCRIPTION]
crosslinking.m:
Method to run cross-linking samples on TimsTof pro instrument. Method and energies are specifically
optimized for PhoX cross-linker reagent (by Richard Scheltema and Markus L... | ["crosslinking.m:\n\nMethod to run cross-linking samples on TimsTof pro instrument. Method and energies are specifically\noptimized for PhoX cross-linker reagent (by Richard Scheltema and Markus Lubeck (Brucker))\n\nStandard_DDA_PASEF_1.1sec_cycletime_2segm_1st_15min_nospectra.m:\n\nMethod for classical bottom-up (prot... |
58,207 | YAP1 mKate:BSD HDR Knock-in (via Cas9 RNP lipofection) | 4 | null | https://www.protocols.io/view/yap1-mkate-bsd-hdr-knock-in-via-cas9-rnp-lipofecti-b437qyrn | Emir Bora Akmeriç, katharina.koch | TITLE: YAP1 mKate:BSD HDR Knock-in (via Cas9 RNP lipofection)
AUTHORS: Emir Bora Akmeriç, katharina.koch
[DESCRIPTION]
s
[STEPS]
SECTION: RNP Complex Formation and Reverse RNP Transfection
3. Resuspend lyophilized crRNA and tracrRNA in nuclease-free TE buffer to stock concentrations of 100 μM.
SECTION: RNP Comple... | ["[RNP Complex Formation and Reverse RNP Transfection] Resuspend lyophilized crRNA and tracrRNA in nuclease-free TE buffer to stock concentrations of 100 μM.", "[RNP Complex Formation and Reverse RNP Transfection] To form crRNA:tracrRNA:Cas9 complexes in a tube and to start excision of homology casette, mix 6 μL of crR... |
null | null | null | dx.doi.org/10.17504/protocols.io.nxpdfmn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>RAW264.7 cells are a macrophage-like cell line derived from BALB/c mice. These cells are loosely adherant and can be detached from cell culture flasks by light shaking or use of TrypLE (or Trypsin/EDTA). </p>
[GUIDELINES]
<p>Only thaw cultures from frozen vials when there ... | [] |
67,409 | Growth Matrix Male Enhancement Online Program That Will Help You Get A Larger And Stronger Penis(REAL OR HOAX) | 3 | dx.doi.org/10.17504/protocols.io.81wgb63dolpk/v1 | https://www.protocols.io/view/growth-matrix-male-enhancement-online-program-that-cd3rs8m6 | Growth Matrix Male Enhancement | TITLE: Growth Matrix Male Enhancement Online Program That Will Help You Get A Larger And Stronger Penis(REAL OR HOAX)
AUTHORS: Growth Matrix Male Enhancement
[DESCRIPTION]
First Time Buyers – Get the Special Discount on Purchase of Growth Matrix Male Enhancement Supplement
[STEPS] | [] |
42,509 | Ookinete purification by centrifugation | 4 | dx.doi.org/10.17504/protocols.io.bmrmk546 | https://www.protocols.io/view/ookinete-purification-by-centrifugation-bmrmk546 | Benito Recio Totoro | TITLE: Ookinete purification by centrifugation
AUTHORS: Benito Recio Totoro
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The ookinetes, as they come from the ookinete culture, are suspended in a solution that also contains blood cells and other parasite stages. Often, it is necessary to purify th... | ["Take the ookinete culture form the incubator and mix well to re-suspend the sedimented cells.Transfer to a 50 ml conical-bottom tube and\nCentrifuge: 1500 1324, 3 min, 20 10", "Remove supernatant and add NH4Cl at a ratio of 1:40 in relation to the volume of the pellet.Transfer the solution into a 500 ml Erlenmeyer fl... |
37,005 | A single cell RNA sequencing protocol for the pig colon | null | dx.doi.org/10.17504/protocols.io.bgdmjs46 | https://www.protocols.io/view/a-single-cell-rna-sequencing-protocol-for-the-pig-bgdmjs46 | Tao Li, Pu-Qing Yuan, Yvette Tache | TITLE: A single cell RNA sequencing protocol for the pig colon
AUTHORS: Tao Li, Pu-Qing Yuan, Yvette Tache
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify"></div><style>
.justify:after {
content: "";
display:inline-blo... | [] |
82,925 | Model building, validation, and visualization | 5 | dx.doi.org/10.17504/protocols.io.j8nlkw77wl5r/v1 | https://www.protocols.io/view/model-building-validation-and-visualization-cu8mwzu6 | Minghao Chen | TITLE: Model building, validation, and visualization
AUTHORS: Minghao Chen
[DESCRIPTION]
Model building, validation, and visualization
[STEPS]
SECTION: Model building
1. Generate a model by
[1] existing model in PDB
[2] creating a homology model by SWISS-MODEL
[3] creating a ab-initial model by AlphaFold
SECTION: Mod... | ["[Model building] Generate a model by\n[1] existing model in PDB\n[2] creating a homology model by SWISS-MODEL\n[3] creating a ab-initial model by AlphaFold", "[Model building] Do the flexible model fitting by [ISOLDE]\nRoughly fit the secodary structures into the map", "[Validation] Validate the quality of the models... |
82,696 | Systematic review of user experience and trust improvement evaluations on healthcare oriented explainable artificial intelligence | 1 | dx.doi.org/10.17504/protocols.io.bp2l69omzlqe/v1 | https://www.protocols.click/view/systematic-review-of-user-experience-and-trust-imp-cuzgwx3w | Iñaki Soto-Rey, Samantha Cramer | TITLE: Systematic review of user experience and trust improvement evaluations on healthcare oriented explainable artificial intelligence
AUTHORS: Iñaki Soto-Rey, Samantha Cramer
[DESCRIPTION]
Many different AI systems have been developed in recent years. The field of explainable AI is designed to shed light on the bla... | ["[Background] The reviews subjective is to identify the amount of evaluations done on the usability, user satisfaction, user experience and trust of XAI. The domain of interest is the medical field.", "[Methodology - Literature Search] General search query: (\"XAI\" OR \"X-AI\" OR (\"Explainable\" AND \"AI\") OR (\"E... |
104,538 | Whole genome amplification and long read sequencing using ONT | 4 | dx.doi.org/10.17504/protocols.io.j8nlko5q5v5r/v2 | https://www.protocols.io/view/whole-genome-amplification-and-long-read-sequencin-dib24aqe | YiChien Lee, Huei-Mien Ke, Isheng Jason Tsai | TITLE: Whole genome amplification and long read sequencing using ONT
AUTHORS: YiChien Lee, Huei-Mien Ke, Isheng Jason Tsai
[DESCRIPTION]
A genome reference is a prerequisite for a complete understanding of the biology and evolution of a species. However, the major challenge remains to obtain high-quality DNA and RNA ... | ["[[Optional] extraction and denature of genomic DNA] Prepare DLB Lysis buffer: \n33 µL REPLI-g DLB buffer \n3 µL 1M DTT", "[Whole genome amplification] Prepare REPLI-g polymerase master mix\n9 µL Nuclease-free water\n29 µL REPLI-g Reaction Buffer\n2 µL REPLI-g DNA Polymerase", "[[Optional] extraction and denature of g... |
58,115 | Preparation of Polymeric Implants for the Sustained Release of Polychlorinated Biphenyls (PCBs) and Their Derivatives | 1 | dx.doi.org/10.17504/protocols.io.n2bvj667plk5/v1 | https://www.protocols.io/view/preparation-of-polymeric-implants-for-the-sustaine-b4zbqx2n | Amanda J. Bullert, Hui Wang, Hansjoachim Lehmler | TITLE: Preparation of Polymeric Implants for the Sustained Release of Polychlorinated Biphenyls (PCBs) and Their Derivatives
AUTHORS: Amanda J. Bullert, Hui Wang, Hansjoachim Lehmler
[DESCRIPTION]
Polymeric implants are a drug delivery system that can be grafted under the skin to allow for the continuous release of a ... | ["[1.\tFormulation of polymeric implant] Working in a hood, add 7 g of P-80 and 0.7 g of F127 in 20 mL of dichloromethane in a 125 mL glass beaker.", "[1.\tFormulation of polymeric implant] Add the test compound (i.e., biphenyl-4-ol or a hydroxylated PCB metabolite) to the P-80/F127 mixture in dichloromethane. \n\nNote... |
97,875 | Inexpensive DNA Extraction Protocol | 4 | null | https://www.protocols.io/view/inexpensive-dna-extraction-protocol-dbtt2nnn | Valerie Warhol | TITLE: Inexpensive DNA Extraction Protocol
AUTHORS: Valerie Warhol
[DESCRIPTION]
This is a protocol for doing extraction of DNA using inexpensive reagents rather than enzymes or kits. It can be used for plant, animal, or fungus samples.
[STEPS]
SECTION: Prepare sample and equipment
1. Make sure all instruments, such ... | ["[Prepare sample and equipment] Make sure all instruments, such as forceps and pestle, are clean and sterile. Make sure has been diluted 1:1 in 95% ethanol.", "[Lyse cells] Put sample in tube. Grind sample with pestle until broken up into tiny pieces.", "[Prepare sample and equipment] Prepare water bath at 65 °C.", ... |
92,810 | Generating stably-expressing Cas9 cancer organoid lines | 1 | dx.doi.org/10.17504/protocols.io.6qpvr3ydovmk/v1 | https://www.protocols.io/view/generating-stably-expressing-cas9-cancer-organoid-c6vize4e | Jade Smith, Tessa Fowler, Agnieszka Andres, Adam Jackson, Emily Souster, Hazel Rogers, Alexandra Beck, Charlotte Beaver, Mathew Garnett | TITLE: Generating stably-expressing Cas9 cancer organoid lines
AUTHORS: Jade Smith, Tessa Fowler, Agnieszka Andres, Adam Jackson, Emily Souster, Hazel Rogers, Alexandra Beck, Charlotte Beaver, Mathew Garnett
[DESCRIPTION]
This protocol aims to establish a robust Cas9 expression system in cancer organoids through a thr... | ["Day 4: Assess cell viability using CellTiter-Glo 2.0 assay", "Incubate the plate for 4320 min at 37 °C, 5% CO2.", "Add 100 µL of the blasticidin antibiotic stock into the corresponding wells in Fig.1.", "Make up blasticidin antibiotic solutions at 2x concentration in organoid specific culture media, containing no BME... |
36,592 | Buffers for Use in Biological Systems | null | dx.doi.org/10.17504/protocols.io.bfyqjpvw | https://www.protocols.io/view/buffers-for-use-in-biological-systems-bfyqjpvw | Neilier Junior | TITLE: Buffers for Use in Biological Systems
AUTHORS: Neilier Junior
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This collection contains all buffer protocols from Universidade Federal de Viçosa for use in Biological Systems.</div></div>
[STEPS] | [] |
49,918 | Gel electrophoresis | 4 | null | https://www.protocols.io/view/gel-electrophoresis-buy6nxze | Victoria Jackson | TITLE: Gel electrophoresis
AUTHORS: Victoria Jackson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Gel electrophoresis</div></div>
[STEPS]
?. [Making the gel]
For of a 1.2% agarose gel, add of agarose to TAE or TBE in a conical flask and mix by swirling the flask.
200 mL
2.4 g
200 mL
?. [Maki... | ["[Making the gel]\nFor of a 1.2% agarose gel, add of agarose to TAE or TBE in a conical flask and mix by swirling the flask.\n200 mL\n2.4 g\n200 mL", "[Making the gel]\nMicrowave on a high power for about , or until boiling, swirling the flask approximately every during heating to ensure all the agarose dissolves... |
53,372 | Protocol L2.3 (LIG fabrication) | 1 | dx.doi.org/10.17504/protocols.io.byc4psyw | https://www.protocols.io/view/protocol-l2-3-lig-fabrication-byc4psyw | Eric S McLamore, Diana Vanegas, dbahamo, kmccour, Yifan Tang | TITLE: Protocol L2.3 (LIG fabrication)
AUTHORS: Eric S McLamore, Diana Vanegas, dbahamo, kmccour, Yifan Tang
[DESCRIPTION]
This protocol describes the procedure for deposition of biotinylated aptamers on avidin-coated LIG electrodes. The complete process requires approximately 25 min to complete (Fig 1).
[BEF... | ["[LIG on polyimide film] Step 1) Prepare image file for processing and send to tool\nVerify that the Universal Control Panel (UCP) is running in the taskbar by looking for the square red icon with a diamond (Fig 1A)\nUsing CorelDraw, Open the image called “LIG working electrode_triple_COVID” and press Cntrl+P and sele... |
27,761 | Is Expired Air Carbon Monoxide Testing Effective for Screening of Cigarette Use in Orthopaedic Patients? | null | dx.doi.org/10.17504/protocols.io.7crhiv6 | null | Sean Sterrenberg, David Gallacher, Melissa Schmidt, Rebecca Rugel, Summer Gerke, Kenneth Gundle, Ryan Wallenberg | TITLE: Is Expired Air Carbon Monoxide Testing Effective for Screening of Cigarette Use in Orthopaedic Patients?
AUTHORS: Sean Sterrenberg, David Gallacher, Melissa Schmidt, Rebecca Rugel, Summer Gerke, Kenneth Gundle, Ryan Wallenberg
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "fon... | ["VISIT 1 (the day surgery is decided)The patients fill out a “Tobacco Use Questionnaire.”\nTobacco Use Questionnaire (If you answered yes, complete the questions below, if you answered no, skip to question #2)a. How frequently do you smoke? i. Daily ii. Weekly (intermittently) iii. Monthly (intermittently)... |
77,216 | General procedure for long-term cryopreservation of Bacteria | 4 | null | https://www.protocols.io/view/general-procedure-for-long-term-cryopreservation-o-cpm8vk9w | Andreas Sagen | TITLE: General procedure for long-term cryopreservation of Bacteria
AUTHORS: Andreas Sagen
[DESCRIPTION]
A simple and generalized procedure for freezing bacteria cells.
[STEPS]
SECTION: 50% Glycerol solution
1. Fill a 200 mL Duran bottle with 100 mL PBS
Materials:
SECTION: 50% Glycerol solution
2. Transfer 100 mL ... | ["[50% Glycerol solution] Fill a 200 mL Duran bottle with 100 mL PBS\n\nMaterials:", "[50% Glycerol solution] Transfer 100 mL 100% Glycerol to Duran bottle\n\nMaterials:", "[50% Glycerol solution] Sterilize by autoclave at 121 °C for 15 min", "Incubate a 20 mL batch of bacteria overnight", "Aliquot saturated culture in... |
30,939 | PCR protocol for MgSTS marker genotyping | null | dx.doi.org/10.17504/protocols.io.baf3ibqn | null | Matthew Farnitano, Andrea Sweigart | TITLE: PCR protocol for MgSTS marker genotyping
AUTHORS: Matthew Farnitano, Andrea Sweigart
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a standard PCR protocol used to amplify MgSTS markers from genomic DNA for genotyping. MgSTS markers were developed for use in Mimulus species and typic... | ["[Prepare PCR reaction]\nDetermine the amount of reagents needed. The following amounts are sufficient for a single reaction:\n[Molecular Biology Grade Water]\n[5X GoTaq Flexi Buffer, colorless]\n[MgCl2, 25mM stock]\n[dNTPs, 2.5mM stock]\n[BSA, 10 mg/mL stock]\n[Premixed F+R Primers, 5uM stock]\n[GoTaq G2 polymerase, ... |
null | null | null | dx.doi.org/10.17504/protocols.io.e9fbh3n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is part of the <a href="https://www.protocols.io/view/Collection-of-FOCUS-SubCell-Protocols-For-the-Enri-e9ebh3e" target="_blank">collection</a> of FOCUS™ SubCell protocols for the enrichment of subcellular fractions. Please refer to the appropriate protocol depending on... | [] |
76,859 | DNA Quality Control by Agarose Gel Electrophoresis | 4 | null | https://www.protocols.io/view/dna-quality-control-by-agarose-gel-electrophoresis-cpa3vign | Benjamin Schwessinger | TITLE: DNA Quality Control by Agarose Gel Electrophoresis
AUTHORS: Benjamin Schwessinger
[DESCRIPTION]
This protocols is part of the ANU Biosecurity mini-research project #1 "Plant Pathogen Diagnostics: Visuals, subcultures, and genomics".
You will be provided four pots of 3-4 week old wheat plants that have been i... | ["[Week 5: DNA agarose gel electrophoresis] You will load all DNA and PCR samples into one lane of a 1% agarose gel. You will share your gel with another research group as each gel has two rows.", "[Week 5: DNA agarose gel electrophoresis] You will receive two PCR strip tubes of 8 with 5ul of your PCR reaction from las... |
23,197 | RNA concentration measurement and non-denaturing agarose gel electrophoresis | null | dx.doi.org/10.17504/protocols.io.2v5ge86 | null | Lisa-Maria Rosenthal, Giang Tong, Katharina Schmitt | TITLE: RNA concentration measurement and non-denaturing agarose gel electrophoresis
AUTHORS: Lisa-Maria Rosenthal, Giang Tong, Katharina Schmitt
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">RNA concentration measurement and non-denaturing agarose gel electrophoresis</div></div>
[STEPS]
?. • Allo... | ["•\tAllow RNA to thaw on ice", "•\tDetermine RNA concentration using a NanoDropTM 2000/2000c Spectrophotometers (Nucleic Acids – RNA mode, 2 µL sample size)", "•\tDetermine RNA purity from protein contamination by assuring 260/280 ratio is 2.0", "•\tDetermine RNA integrity and purity from genomic DNA contamination by... |
47,170 | FastAmp Saliva Room Storage Powder for SARS-CoV-2 (Covid19) Testing. | 4 | null | https://www.protocols.io/view/fastamp-saliva-room-storage-powder-for-sars-cov-2-bsbanaie | Kazuhiro Kikuchi, Chengcang Charles Wu | TITLE: FastAmp Saliva Room Storage Powder for SARS-CoV-2 (Covid19) Testing.
AUTHORS: Kazuhiro Kikuchi, Chengcang Charles Wu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">FastAmp Saliva Room Storage Powder (Intact Genomics, Inc. Catalog #4607) enables the lysis of human cells and viral particles, ... | ["Saliva can either collected independently by the individual or with the assistance of a healthcare worker or technician.", "Before collection, clean hands using alcohol-based sanitizer or soap and water (no fragrance).", "Ensure all collection materials are labelled with the correct identifying information.", "Open t... |
47,748 | PROCEDURE TO INDUCE MITOCHONDRIAL DEPOLARISATION AND LYSING OF MOUSE CORTICAL NEURONS | 1 | dx.doi.org/10.17504/protocols.io.bsvcne2w | https://www.protocols.io/view/procedure-to-induce-mitochondrial-depolarisation-a-bsvcne2w | Odetta Antico, Miratul M. Muqit | TITLE: PROCEDURE TO INDUCE MITOCHONDRIAL DEPOLARISATION AND LYSING OF MOUSE CORTICAL NEURONS
AUTHORS: Odetta Antico, Miratul M. Muqit
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Mutations in PINK1 cause early-onset Parkinson’s disease. PINK1 becomes stabilised and active upon mitochondrial depo... | ["[Mitochondrial depolarisation]\nTo depolarize or uncouple mitochondrial membrane potential in neurons, cultures were treated for to with a combination of Antimycin A and Oligomycin dissolved in DMSO at .\n◊TIMING - , day of experiment in this section.\n10\n1\n37 °C", "[Lysing of mouse neuronal cultures]\nGently ... |
57,617 | Differential extraction of detergent-insoluble protein aggregates from cultured mammalian cells - a benchtop centrifuge method | 4 | null | https://www.protocols.io/view/differential-extraction-of-detergent-insoluble-pro-b4hrqt56 | S. BERGINK, W. HUITING | TITLE: Differential extraction of detergent-insoluble protein aggregates from cultured mammalian cells - a benchtop centrifuge method
AUTHORS: S. BERGINK, W. HUITING
[DESCRIPTION]
Protein aggregation is strongly associated with accelerated ageing and (neuro)degeneration, and considerable effort is directed towards stu... | ["[Fractionation] Take desired volume from supernatant to serve as Igepal soluble fraction (fraction I)\nAdd 4XSB into supernatant. Mix by brief vortexing.\nBoil (5 min, 95°C).\nStore samples at -20°C.", "[Fractionation] Prepare cell culture starting material according to your research question. \na. Harvest cells ... |
75,464 | Annonaceae DNA extraction protocol from silicagel dried and herbarium preserved leaves | 4 | dx.doi.org/10.17504/protocols.io.5qpvorqx9v4o/v1 | https://www.protocols.io/view/annonaceae-dna-extraction-protocol-from-silicagel-cmxgu7jw | Vincent Soulé, Thomas LP Couvreur, Cedric Mariac | TITLE: Annonaceae DNA extraction protocol from silicagel dried and herbarium preserved leaves
AUTHORS: Vincent Soulé, Thomas LP Couvreur, Cedric Mariac
[DESCRIPTION]
This protocol is used for DNA extraction of samples from the tropical plant family Annonaceae for leaves dried using silicagel or sampled from herbarium ... | ["[Leaf grinding] Prepare 48 2 mL Screw-Top tubes in rows of 8 in a 96 well rack. Add one 1/4'' ceramic beads (MP Biomedical REF 116540422).", "[Leaf grinding] Grind samples using a MP FastPrep grinder, twice for 40 s at 4m/second speed with a 2-minute pause in between each grind as not to over heat the samples.", "[Ly... |
null | null | null | dx.doi.org/10.17504/protocols.io.dps5nd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Phage lysis of host bacteria can be visualized by plaque formation on lawns of host cells in soft agar overlayed on agar plates (Adams, 1959; Sambrook et al. 1989). This principle can be used for the detection and subsequent isolation of specific lytic phages in environmental sa... | [] |
108,114 | QMask Hemispheric Separation | 4 | dx.doi.org/10.17504/protocols.io.n2bvj3qdblk5/v2 | https://www.protocols.io/view/qmask-hemispheric-separation-dmts46ne | Michael X. Henderson | TITLE: QMask Hemispheric Separation
AUTHORS: Michael X. Henderson
[DESCRIPTION]
This protocol describes QMask hemispheric separation.
[STEPS]
SECTION: QMask Hemispheric Separation
1. Open the Qmask tool and click “pick XML” and open the QuickN XML file generated in QuickNII.
SECTION: QMask Hemispheric Separation
2. ... | ["[QMask Hemispheric Separation] Open the Qmask tool and click “pick XML” and open the QuickN XML file generated in QuickNII.", "[QMask Hemispheric Separation] Enter the appropriate coordinates from the QMask Coordinates file.", "[QMask Hemispheric Separation] Click “Destination” and navigate to the QVN\\Mask folder. C... |
54,850 | QIAGEN DNeasy Power Water SOP | 4 | dx.doi.org/10.17504/protocols.io.rm7vz3wb5gx1/v1 | https://www.protocols.io/view/qiagen-dneasy-power-water-sop-bztap6ie | Andrea Ottesen, Brandon Kocurek | TITLE: QIAGEN DNeasy Power Water SOP
AUTHORS: Andrea Ottesen, Brandon Kocurek
[DESCRIPTION]
QIAGEN DNeasy PowerWater SOP
Purpose: For the isolation of genomic DNA from filter water samples, inculding turbid water
Introduction: The DNeasy PowerWater Kit can isolate genomic DNA from a variety of filtered water sam... | ["[Procedure] Filter water samples using a filter funnel attached to a vacuum source. The volume of water filtered will depend on the microbial load and turbidity of the water sample. See below for types of water samples.", "[Procedure] If using a reusable filter funnel, remove the upper portion of the apparatus.", "[P... |
92,767 | Bioanalyzer High Sensitivity DNA Kit | 4 | dx.doi.org/10.17504/protocols.io.4r3l22z5ql1y/v1 | https://www.protocols.io/view/bioanalyzer-high-sensitivity-dna-kit-c6t7zern | Ksenija Sabic | TITLE: Bioanalyzer High Sensitivity DNA Kit
AUTHORS: Ksenija Sabic
[DESCRIPTION]
This protocol explains how to use the Agilent High Sensitivity DNA Bioanalyzer Kit.
[STEPS] | [] |
82,258 | 9. Taxon Group: Gastropoda | 4 | dx.doi.org/10.17504/protocols.io.6qpvr4bnpgmk/v1 | https://www.protocols.io/view/9-taxon-group-gastropoda-cujswune | Nova Mieszkowska, Suzanne Williams, Chris Fletcher, Inez Januszczak | TITLE: 9. Taxon Group: Gastropoda
AUTHORS: Nova Mieszkowska, Suzanne Williams, Chris Fletcher, Inez Januszczak
[DESCRIPTION]
This is part of the collection "DToL Taxon-specific Standard Operating Procedures (SOPs) for Marine Metazoa", lead by the Other Metazoa Working Group. The SOP collection contains guidance on ho... | [] |
26,040 | Anesthetizing Sea Cucumbers | null | dx.doi.org/10.17504/protocols.io.5nyg5fw | null | Jon Eilers | TITLE: Anesthetizing Sea Cucumbers
AUTHORS: Jon Eilers
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is for anesthetizing sea cucumbers. After soaking the sea cucumber in the menthol/ethanol/saltwaer solution for 30-60 minutes the sea cucumber should be flacid and relatively unrespon... | ["Add .5 grams of menthol crystals to 100 ml of ethanol and stir/shake until dissolved", "Dilute to 10% menthol/ethanol solution by adding 900 ml of salt water", "In a separate container, add 400 ml diluted menthol/ethanol solution and 600 ml saltwater to create a 40% diluted solution", "Add sea cucumber to diluted sol... |
99,473 | Protein Extraction for Amyloid Beta Fractionation | 0 | dx.doi.org/10.17504/protocols.io.j8nlk8ky1l5r/v1 | https://www.protocols.io/view/protein-extraction-for-amyloid-beta-fractionation-dddr2256 | Lisa Blackmer-Raynolds, Tim Sampson | TITLE: Protein Extraction for Amyloid Beta Fractionation
AUTHORS: Lisa Blackmer-Raynolds, Tim Sampson
[DESCRIPTION]
This protocol can be used to isolate protein from murine brain tissue (volumes listed are for hippocampal samples) by solubility. It creates three protein fractions: tris soluble, triton soluble, and for... | ["[Preparation] 5x Homogenization Buffer (store 4oC):\n125 ml of 1.0 M Tris\n30 ml of 0.5 M MgCl2\n25 ml of 0.1 M EDTA (pH to 7.2 and store at 4°C for up to 6 months)\n20ml of MiliQ Water", "1x Homogenization Buffer (dilute day of):\nDilute 5x Homogenization buffer to 1x in MiliQ Water and add 1 tablet protease inhibit... |
87,938 | Cyanobacteria growth | 1 | dx.doi.org/10.17504/protocols.io.4r3l22o8xl1y/v2 | https://www.protocols.io/view/cyanobacteria-growth-cz5ax82e | Ricardo M. Borges, Gabriela de Assis Ferreira, Fernanda Chagas, pauloihc | TITLE: Cyanobacteria growth
AUTHORS: Ricardo M. Borges, Gabriela de Assis Ferreira, Fernanda Chagas, pauloihc
[DESCRIPTION]
Este documento tem como objetivo apresentar um protocolo abrangente para o cultivo de cianobactérias em meio aquático salino. O protocolo incorpora informações detalhadas sobre a composição das ... | ["[Material] Preparo do Meio de Cultivo F/2:\n Para 1 litro de água destilada, adicione:\n41,5 gramas de sal marinho para aquario (Reef Salt)\n1 mL de Solução Estoque de NaNO3 \n1 mL de Solução Estoque de NaH2PO4•H2O\n1 mL de Solução Estoque de Metais-Traço\nAutoclave: 15 minutos a 15 min a 121oC\nAguarde o resfriament... |
99,142 | Step-centrifugation Assay | 0 | dx.doi.org/10.17504/protocols.io.36wgqn75xgk5/v1 | https://www.protocols.io/view/step-centrifugation-assay-dc3e2yje | Caroline Brown, Snehasish Ghosh, Kallol Gupta | TITLE: Step-centrifugation Assay
AUTHORS: Caroline Brown, Snehasish Ghosh, Kallol Gupta
[DESCRIPTION]
This protocol details the protocol for conducting a step-centrifugation assay to determine the minimum required speed for full separation of vesicles from native nanodiscs.
[STEPS]
1. Resuspend cells in lysis buffer ... | ["Resuspend cells in lysis buffer (50 millimolar (mM), 150 millimolar (mM) , 10 % volume ) and lyse using nitrogen cavitation (750 PSI for 15 min minutes).", "Centrifuge lysed cells at 4000rpm for 10 minminutes to pellet cell debris.", "Spin the supernatant in a series of sequential ultracentrifugation steps at speeds ... |
40,987 | Determination of IgA concentration by the Mancini test. | 6 | dx.doi.org/10.17504/protocols.io.bj93kr8n | https://www.protocols.io/view/determination-of-iga-concentration-by-the-mancini-bj93kr8n | Angel Justiz-Vaillant | TITLE: Determination of IgA concentration by the Mancini test.
AUTHORS: Angel Justiz-Vaillant
[STEPS]
?. An appropriate anti-IgA antiserum (antibody) is poured in the center well of an agar-containing plate.
?. Carefully circular wells are cut and detached from the plates.
?. A series of standards containing known co... | ["An appropriate anti-IgA antiserum (antibody) is poured in the center well of an agar-containing plate.", "Carefully circular wells are cut and detached from the plates.", "A series of standards containing known concentrations of IgA are placed in separate wells, while “unknown” human serum samples and control are pla... |
100,257 | Clinical features and management of VEXAS syndrome in critical care: a scoping review protocol | 0 | dx.doi.org/10.17504/protocols.io.14egn621ql5d/v4 | https://www.protocols.io/view/clinical-features-and-management-of-vexas-syndrome-dd592896 | Kasumi Satoh, Yasushi Tsujimoto, Daisuke Kasugai, Kazuki Okura, Takao Ono, Yuki Miyamoto, Tasuku Matsuyama, Taketo Watase, Hajime Nakae, Tadahiro Goto | TITLE: Clinical features and management of VEXAS syndrome in critical care: a scoping review protocol
AUTHORS: Kasumi Satoh, Yasushi Tsujimoto, Daisuke Kasugai, Kazuki Okura, Takao Ono, Yuki Miyamoto, Tasuku Matsuyama, Taketo Watase, Hajime Nakae, Tadahiro Goto
[DESCRIPTION]
Objective: This study aims to understand th... | ["[Introduction] Vacuoles, E1 enzyme, X-linked, Autoinflammatory, Somatic (VEXAS) syndrome is an acquired autoinflammatory disorder that primarily affects men over 50 years of age and was identified in 2020 as a new disease concept associated with mutations in the Ubiquitin-like modifier activating enzyme 1 (UBA1) gene... |
13,380 | Keller's Band Counting Method with Chloroquine | 1 | dx.doi.org/10.17504/protocols.io.rbcd2iw | https://www.protocols.io/view/keller-s-band-counting-method-with-chloroquine-rbcd2iw | Salima Rüdiger, Rainer Machne | TITLE: Keller's Band Counting Method with Chloroquine
AUTHORS: Salima Rüdiger, Rainer Machne
[DESCRIPTION]
Supercoiling plays a major role in the regulation of bacterial growth, especially in the circadian rhythm of cyanobacteria. The Keller's Band Counting Method was modified with the use of intercalating substance ... | ["[Isolation of plasmid] The examined plasmid has to be isolated properly.\nFor a bigger topoisomer series, it is recommended to isolate a higher amount of bacterial culture. \nI use ZymoPURE™ Plasmid Maxiprep Kit, according to their Vacuum protocol.", "[Purification with T5 Exonuclease (optional)] The isolated plasmid... |
45,477 | SEM General Fixation | 4 | null | https://www.protocols.io/view/sem-general-fixation-bqndmva6 | Elizabeth Fozo | TITLE: SEM General Fixation
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">General SEM Fixation Procedure</div></div>
[STEPS]
?. [General SEM Fixation Procedure]
Grow 50mL cells to appropriate OD600 and wash in 1X PBS. Pour of supernatant.
?. [General SEM Fixation Procedure... | ["[General SEM Fixation Procedure]\nGrow 50mL cells to appropriate OD600 and wash in 1X PBS. Pour of supernatant.", "[General SEM Fixation Procedure]\nPrimary Fixation:3% Gultaraldehyde in 0.1M cacodylate (1X PBS)* = add 500uL and vortex brieflyFix for 1 hour at room temperature.*Any buffer should be fine = use 1X PBS"... |
null | null | null | dx.doi.org/10.17504/protocols.io.d9s96d | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>In this protocol we describe some approaches to graphically represent single profiled samples or a merged table of relative abundances.</p>
[BEFORE_START]
REQUIREMENTS: <a href="https://bitbucket.org/nsegata/graphlan" target="_blank">GraPhlAn</a> installed (and in the system... | [] |
52,452 | Method for detecting acetylated PD-L1 in cell lysates | 4 | dx.doi.org/10.17504/protocols.io.bxgcpjsw | https://www.protocols.io/view/method-for-detecting-acetylated-pd-l1-in-cell-lysa-bxgcpjsw | Frances Middleton-Davis, Ashley Davis, Kim Middleton | TITLE: Method for detecting acetylated PD-L1 in cell lysates
AUTHORS: Frances Middleton-Davis, Ashley Davis, Kim Middleton
[DESCRIPTION]
Here we present a method that allows detection of acetylated PD-L1 and is applicable to a wide range of cell lines. The method captures >90% of acetylated PD-L1 species, is semi-quan... | ["[IMMUNOPRECIPITATION ASSAY] Resuspend lyophilized Acetyl-Lysine affinity and Control beads in 500µl of 50% glycerol in MiliQ water and rotate for at least 1h at 4°C to rehydrate.60 min", "[ACETYL-LYSINE IMMUNOPRECIPITATION (IP)] ACETYL-LYSINE IP: BUFFERS AND EQUIPMENT\n\n\nBead Wash Buffer: 100 ml, store at room temp... |
22,900 | A simple approach to identify the influence of left vagal stimulus pulse parameters on vagal and gastric electrical activity in rat | null | dx.doi.org/10.17504/protocols.io.2kugcww | null | Matthew Ward, Thomas V Nowak, Zhenjun Tan, Bartek Rajwa, Robert Phillips, Terry L Powley | TITLE: A simple approach to identify the influence of left vagal stimulus pulse parameters on vagal and gastric electrical activity in rat
AUTHORS: Matthew Ward, Thomas V Nowak, Zhenjun Tan, Bartek Rajwa, Robert Phillips, Terry L Powley
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [A. Surgical Methods (... | ["[A. Surgical Methods (adapted from DOI:10.1109/TNSRE.2014.2351271)]\nThe surgical suite and instruments are sterilized prior to each procedure. Isoflurane gas anesthesia is used for the duration of surgery; it is set to the lowest level that will maintain a stable anesthetic plane (0.5%–3% isoflurane in 2 L/min O )",... |
null | null | null | dx.doi.org/10.17504/protocols.io.iizccf6 | 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> </p>
<p>Modified from: Watanabe, Makoto M. "Fresh-and salt-water forms of Spirulina platensis in axenic cultures." <em>Bull. Jpn. Soc. Phycol.</em> 25 (197... | [] |
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