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 |
|---|---|---|---|---|---|---|---|
62,974 | Maximum Keto Gummies | 1 | dx.doi.org/10.17504/protocols.io.rm7vzy1j4lx1/v1 | https://www.protocols.io/view/maximum-keto-gummies-b9q6r5ze | Maximum Keto Gummies | TITLE: Maximum Keto Gummies
AUTHORS: Maximum Keto Gummies
[DESCRIPTION]
Maximum Keto Gummies
[STEPS]
1. Maximum Keto Gummies: Reviews, Burn Fat Quick, Weight Loss Supplements, Where To Buy?
👉DEAL IS LIVE CLICK HERE TO PURCHASE NOW👈
✔️Product Name - Maximum Keto Gummies
✔️Category - Health
✔️Side-Effects - NA
... | ["Maximum Keto Gummies: Reviews, Burn Fat Quick, Weight Loss Supplements, Where To Buy?\n\n\n👉DEAL IS LIVE CLICK HERE TO PURCHASE NOW👈\n\n\n✔️Product Name - Maximum Keto Gummies\n✔️Category - Health \n✔️Side-Effects - NA \n✔️Price for Sale - Best Price \n✔️Availability - Online\n✔️Rating -⭐⭐⭐⭐⭐\n\n\nMaximum Keto Gumm... |
108,928 | Immunocytochemistry | 0 | dx.doi.org/10.17504/protocols.io.5jyl82ym8l2w/v1 | https://www.protocols.io/view/immunocytochemistry-dnk85czw | Michael Henderson, Naman Vatsa | TITLE: Immunocytochemistry
AUTHORS: Michael Henderson, Naman Vatsa
[DESCRIPTION]
This is a protocol for immunocytochemistry for 24 and 96 well cell culture plates.
[STEPS]
SECTION: Preparation
1. Prepare 1x phosphate buffer saline (PBS)
SECTION: Preparation
2. Prepare fixation solution: 4% paraformaldehyde/4% sucros... | ["[Preparation] Prepare 1x phosphate buffer saline (PBS)", "[Preparation] Prepare fixation solution: 4% paraformaldehyde/4% sucrose in PBS", "[Preparation] Prewarm the fixative solution to 37 degrees Celsius", "[Preparation] Prepare blocking buffer: 3% Bovine Serum Albumin (BSA) in PBS\nSeal the conical with parafilm t... |
79,364 | Confocal microscopy of intracellular components within NK cells | 1 | dx.doi.org/10.17504/protocols.io.5qpvor14zv4o/v1 | https://www.protocols.click/view/confocal-microscopy-of-intracellular-components-wi-crrcv52w | Philippa R Kennedy | TITLE: Confocal microscopy of intracellular components within NK cells
AUTHORS: Philippa R Kennedy
[DESCRIPTION]
NK cells are small cells and their organelles e.g. mitochondria are consequently harder to visualize than those in larger cells. We have found that imaging NK cells that are stretched out across fibronectin... | ["[Coat a plate with fibronectin] Coat chambered coverglass (µ-Slide 8 well polymer bottom 1.5, Ibidi, Cat. 80826) with fibronectin (10μg/mL in PBS, Sigma-Aldrich, Cat. F1141) to allow NK cells to stretch out across the coverglass.\n\nCoating options:\n30 min at 37°C\n45 min at room temperature\novernight at 4°C", "[Al... |
null | null | null | dx.doi.org/10.17504/protocols.io.hm2b48e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>While dinoflagellate transformation tool is not yet ready, transforming dinoflagellate genes into a model alga such as a diatom is a viable option.</p>
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
58,789 | Extraction and determination by fluorescence of Phycocyanin | 3 | null | https://www.protocols.io/view/extraction-and-determination-by-fluorescence-of-ph-b5ndq5a6 | Kristel Sanchez | TITLE: Extraction and determination by fluorescence of Phycocyanin
AUTHORS: Kristel Sanchez
[DESCRIPTION]
This protocol details the chemical extraction of phycocyanin from phytoplankton cells and the quantification of phycocyanin by fluorescence using the Turner Trilogy Laboratory Fluorometer.
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.dq65zd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in "<a href="https://www.protocols.io/view/Obtaining-pure-cyanophage-stocks-liquid-assay-dqm5u5" target="_blank">Obtaining pure cyanophage stock: plaque purification</a>"
[GUIDELINES]
Use either the liquid amplification method (A) or the plate amplification method (B) i... | [] |
38,315 | SNPscan protocol for genotyping | 4 | dx.doi.org/10.17504/protocols.io.bhnjj5cn | https://www.protocols.io/view/snpscan-protocol-for-genotyping-bhnjj5cn | Guangming Jiang, Meng Wu, Rui Liu, Mengya Chen, Renfang Han | TITLE: SNPscan protocol for genotyping
AUTHORS: Guangming Jiang, Meng Wu, Rui Liu, Mengya Chen, Renfang Han
[STEPS]
?. Pipet 20 µl QIAGEN Protease (or proteinase K) into the bottom of a 1.5 ml microcentrifuge tube.
?. Add 200 µl whole-blood samples to the microcentrifuge tube.
?. Add 200 µl Buffer AL to the sample. Mi... | ["Pipet 20 µl QIAGEN Protease (or proteinase K) into the bottom of a 1.5 ml microcentrifuge tube.", "Add 200 µl whole-blood samples to the microcentrifuge tube.", "Add 200 µl Buffer AL to the sample. Mix by pulse-vortexing for 15 s.", "Incubate at 56 °C for 10 min.", "Briefly centrifuge the 1.5 ml microcentrifuge tube ... |
95,745 | Extract-N-Amp Equivalent DNA Extraction Protocol | 0 | dx.doi.org/10.17504/protocols.io.5jyl8p458g2w/v2 | https://www.protocols.io/view/extract-n-amp-equivalent-dna-extraction-protocol-c9q9z5z6 | Stephen Douglas Russell | TITLE: Extract-N-Amp Equivalent DNA Extraction Protocol
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
This extraction protocol uses an Extract-N-Amp equivalent solution to quickly and cheaply perform DNA extractions. This protocol has been widely used for dried specimens of macrofungi, but will work for other organis... | ["[Create the Extraction Solution] Add 10mL of 1 M Tris stock into a 100mL Erlenmeyer flask. \n\nFor larger batches:\n25mL for 250mL of end product in a 250mL flask\n50mL for 500mL of end product in a 500mL flask.\n1000mL for 1000mL of end product in a 1000mL flask.", "[Create the Extraction Solution] Add 1.86g of KCl.... |
61,230 | EPMotion - Normalization and Randomization | 4 | dx.doi.org/10.17504/protocols.io.261genw5dg47/v1 | https://www.protocols.io/view/epmotion-normalization-and-randomization-b72nrqde | Katarina A Cohen, Khai-Minh H Nguyen, Oksana Polesskaya, Abraham Palmer | TITLE: EPMotion - Normalization and Randomization
AUTHORS: Katarina A Cohen, Khai-Minh H Nguyen, Oksana Polesskaya, Abraham Palmer
[DESCRIPTION]
This protocol normalizes and randomizes samples on the EPmotion for the Twist 96-Plex (Formerly riptide) library prep protocol. The procedure outlines how to complete normal... | ["[Excel Calculations] Enter sample information and values into the \"Riptide Library Template\" Excel worksheet:\n \n \n\nOnly use Low-Concentration Template when average concentration is lower than 90ng/ul.\nEnter all information under the \"Sample_Information\" tab (all information should be filled in from the Goo... |
99,588 | NanoString GeoMx DSP TMA-TNP Phase 4 Protein assay | 1 | dx.doi.org/10.17504/protocols.io.5qpvokbm7l4o/v1 | https://www.protocols.io/view/nanostring-geomx-dsp-tma-tnp-phase-4-protein-assay-ddhc232w | Jinho Lee, Gabriel Zangirolani, Koei Chin, Heidi S Feiler, Christopher Corless | TITLE: NanoString GeoMx DSP TMA-TNP Phase 4 Protein assay
AUTHORS: Jinho Lee, Gabriel Zangirolani, Koei Chin, Heidi S Feiler, Christopher Corless
[DESCRIPTION]
This protocol outlines the NanoString GeoMx DSP phase 4 protein assay that was applied in the Human Tumor Atlas Network (HTAN) Tissue MicroArrary (TMA)-TransN... | ["[FFPE slide sample preparation] FFPE slide preparation", "[FFPE slide sample preparation] Bake FFPE slides at 60 °C for 60 min .", "[FFPE slide sample preparation] Deparaffinize by sequential incubation with Xylene (3 min twice), 100% EtOH (1 min), 95% EtOH (1 min ) and 70% EtOH (1 min ).", "[FFPE slide sample prepa... |
42,129 | Moistube™ Irrigation (MTI) Discharge Under Variable Evaporative Demand | 3 | dx.doi.org/10.17504/protocols.io.bmdrk256 | https://www.protocols.io/view/moistube-irrigation-mti-discharge-under-variable-e-bmdrk256 | Tinashe Lindel Dirwai, Aidan Senzanje, Tafadzwanashe Mabhaudhi | TITLE: Moistube™ Irrigation (MTI) Discharge Under Variable Evaporative Demand
AUTHORS: Tinashe Lindel Dirwai, Aidan Senzanje, Tafadzwanashe Mabhaudhi
[STEPS] | [] |
76,737 | Glucose Concentration assay (Hexokinase/G6PDH method) | 4 | dx.doi.org/10.17504/protocols.io.dm6gpj5jdgzp/v1 | https://www.protocols.io/view/glucose-concentration-assay-hexokinase-g6pdh-metho-cn69vhh6 | Daniel T Hass, James Hurley | TITLE: Glucose Concentration assay (Hexokinase/G6PDH method)
AUTHORS: Daniel T Hass, James Hurley
[DESCRIPTION]
The assay I describe measures glucose concentration in a sample. The principle of the assay is to consume glucose from the sample with hexokinase and excess ATP in the buffer, then to oxidize the resulting g... | ["[Generate glucose standards] Make a D-glucose stock solution (for me, normally 500 mM), and dilute to make standards. My typical standards are 0-10 mM (10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 0 mM). The composition of standards may of course be adapted to your needs. \n\nNote:\nThe range of the standard curve must exceed the ... |
59,656 | Plant assemble - Plant de novo genome assembly: scaffolding | 5 | dx.doi.org/10.17504/protocols.io.ewov14bz7vr2/v2 | https://www.protocols.io/view/plant-assemble-plant-de-novo-genome-assembly-scaff-b6hgrb3w | Scott Ferguson, Ashley Jones, Justin Borevitz | TITLE: Plant assemble - Plant de novo genome assembly: scaffolding
AUTHORS: Scott Ferguson, Ashley Jones, Justin Borevitz
[DESCRIPTION]
With the advancement of long-read sequencing technologies and associated bioinformatics tools, it has now become possible to de novo assemble complex plant genomes with unrivalled ... | ["[Genome scaffolding] Currently your genome will not exist as full chromosomes, rather as fragmented sections of chromosomes. To increase the utility of your genome scaffolding is performed. Scaffolding attempts to find how your sequences should be joined to form full chromosomes and joins them. There are a number of ... |
49,731 | A SARS-CoV-2 Surveillance Sequencing Protocol Optimized for Oxford Nanopore PromethION | 4 | dx.doi.org/10.17504/protocols.io.butbnwin | https://www.protocols.io/view/a-sars-cov-2-surveillance-sequencing-protocol-opti-butbnwin | Jannatul Ferdous, Torri Weathers, Visva Bharati Barua, Erin Stiers, Adam France, Kevin C Lambirth, Cynthia Gibas, Jessica A Schlueter | TITLE: A SARS-CoV-2 Surveillance Sequencing Protocol Optimized for Oxford Nanopore PromethION
AUTHORS: Jannatul Ferdous, Torri Weathers, Visva Bharati Barua, Erin Stiers, Adam France, Kevin C Lambirth, Cynthia Gibas, Jessica A Schlueter
[DESCRIPTION]
To identify and monitor SARS-CoV-2 variant evolution, UNC Charlot... | ["[cDNA Synthesis] Reagents : \n10x Random Primer \n25x dNTPs Mix \n10x RT Buffer\n50mM MgCl2\nMultiScribe RT\n\nThaw everything except MultiScribe RT at room temperature. Mix each of the tubes by vortexing. After that spin down and place on ice.", "[cDNA Synthesis] Prepare master mix 1 (MM1) in a 1.5ml Lobind tube ... |
36,706 | Human Post Mortem Brain Processing | null | dx.doi.org/10.17504/protocols.io.bf4ajqse | https://www.protocols.io/view/human-post-mortem-brain-processing-bf4ajqse | Allen Institute for Brain Science | TITLE: Human Post Mortem Brain Processing
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the steps for processing post-mortem human brain, starting from whole brain or a single hemisphere.</div><div class = "text-block"><span style ... | [] |
83,806 | Converting ssDNA oligos to dsDNA with T4 DNA polymerase | 4 | dx.doi.org/10.17504/protocols.io.261ged6xyv47/v1 | https://www.protocols.click/view/converting-ssdna-oligos-to-dsdna-with-t4-dna-polym-cv36w8re | Alex N Nguyen Ba | TITLE: Converting ssDNA oligos to dsDNA with T4 DNA polymerase
AUTHORS: Alex N Nguyen Ba
[DESCRIPTION]
This protocol allows one to convert ssDNA to dsDNA oligos. In principle, one can buy two complementary oligos and anneal them. However, there are a few cases where randomized bases are desired, and therefore compleme... | ["[Primer design] Design your target single-stranded DNA oligo such that the 3' end contains the reverse complement of an extending oligonucleotide. For example, appending \"GTCATAGCTGTTTCCTG\" to the end of your oligo will allow an oligonucleotide matching the M13 Reverse (-27) primer to extend it (5'-CAGGAAACAGCTATGA... |
40,713 | Comparison of Two Fat Emulsions on Interleukin-1β, Interleukin-8 and Fatty Acid Composition in Infants Post Gastrointestinal Surgery: A Randomized Trial Protocol | 1 | dx.doi.org/10.17504/protocols.io.bjzhkp36 | https://www.protocols.io/view/comparison-of-two-fat-emulsions-on-interleukin-1-i-bjzhkp36 | Meta Herdiana Hanindita | TITLE: Comparison of Two Fat Emulsions on Interleukin-1β, Interleukin-8 and Fatty Acid Composition in Infants Post Gastrointestinal Surgery: A Randomized Trial Protocol
AUTHORS: Meta Herdiana Hanindita
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left... | [] |
82,893 | Posted Draft Test | 1 | null | https://www.protocols.click/view/posted-draft-test-cu7mwzk6 | Emma Ganley | TITLE: Posted Draft Test
AUTHORS: Emma Ganley
[DESCRIPTION]
test
[STEPS]
1. | [] |
67,633 | Single Cell Isolation of Human Lung Organoids | 1 | dx.doi.org/10.17504/protocols.io.3byl4b7orvo5/v3 | https://www.protocols.io/view/single-cell-isolation-of-human-lung-organoids-ceartad6 | Morris Baumgardt, Maren Hülsemann, Anna Löwa, Benedikt Obermayer, Emanuel Wyler, Stefan Hippenstiel, Andreas C. Hocke, Katja Hönzke | TITLE: Single Cell Isolation of Human Lung Organoids
AUTHORS: Morris Baumgardt, Maren Hülsemann, Anna Löwa, Benedikt Obermayer, Emanuel Wyler, Stefan Hippenstiel, Andreas C. Hocke, Katja Hönzke
[DESCRIPTION]
This protocol describes the single cell isolation of infected human alveolar-like organoids in order to perform... | ["[Single cell dissociation] Remove organoid medium from two wells and add 1 mL cold base medium per well (300,000 cells per well is a good amount to have sufficient cells even after the dissociation process.", "[Single cell dissociation] Transfer organoids with a 1000 µL pipette to a 2 mL reagent tube and spin down at... |
null | null | null | dx.doi.org/10.17504/protocols.io.h78b9rw | null | null | TITLE: No Title
AUTHORS:
[STEPS] | [] |
70,922 | protocol 10/06 1 | 1 | null | https://www.protocols.io/view/protocol-10-06-1-chhit34e | Maria Gul | TITLE: protocol 10/06 1
AUTHORS: Maria Gul
[DESCRIPTION]
Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Integer in sapien. Praesent id justo in neque elementum ultrices. Cras elementum. Sed ac dolor sit amet purus malesuada congue. Nunc auctor. Quis autem vel eum iure reprehenderit qui in ea voluptate velit... | ["Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Integer in sapien. Praesent id justo in neque elementum ultrices. Cras elementum. Sed ac dolor sit amet purus malesuada congue. Nunc auctor. Quis autem vel eum iure reprehenderit qui in ea voluptate velit esse quam nihil molestiae consequatur, vel illum qui do... |
null | null | null | dx.doi.org/10.17504/protocols.io.g8dbzs6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div title="Page 2">
<div title="Page 3">
<div>
<div>
<p>QWB is often used for relative analysis of protein phosphorylation and other post- translational modifications (PTMs). This method combines two primary antibodies raised in different hosts: a phospho-specific or other PTM-... | [] |
103,200 | Tile Scan Imaging and Cell Counting | 0 | dx.doi.org/10.17504/protocols.io.bp2l6231kgqe/v1 | https://www.protocols.io/view/tile-scan-imaging-and-cell-counting-dgz83x9w | Shiyi Wang | TITLE: Tile Scan Imaging and Cell Counting
AUTHORS: Shiyi Wang
[DESCRIPTION]
Tile Scan Imaging and Cell Counting
[STEPS]
1. **Sample Preparation**
1.1. - Prepare 30 μm thick coronal sections containing the anterior cingulate cortex (ACC) and primary motor cortex (MOp) from P21 WT and LRRK2 G2019Ski/ki; Aldh1l1-eGFP m... | ["**Sample Preparation**", "- Prepare 30 μm thick coronal sections containing the anterior cingulate cortex (ACC) and primary motor cortex (MOp) from P21 WT and LRRK2 G2019Ski/ki; Aldh1l1-eGFP mice.", "**Confocal Microscopy**", "- Acquire tile scan images using a confocal Leica SP8 STED microscope equipped with a galvo... |
44,639 | Dip-C (Part 1: Chromosome Conformation Capture, for Fixed Nuclei) | 4 | dx.doi.org/10.17504/protocols.io.bpt7mnrn | https://www.protocols.io/view/dip-c-part-1-chromosome-conformation-capture-for-f-bpt7mnrn | Longzhi Tan | TITLE: Dip-C (Part 1: Chromosome Conformation Capture, for Fixed Nuclei)
AUTHORS: Longzhi Tan
[STEPS]
?. [Digestion]
Thaw a tube of fixed nuclei .
on ice
?. [Digestion]
Prepare 0.5% SDS ( per sample; recipe below for ): (final: ) water
50 µl
100 µl
5 µl
95 µl
?. [Digestion]
Resuspend nuclei in 0.5% SDS.
50 µl
?. [Dig... | ["[Digestion]\nThaw a tube of fixed nuclei .\non ice", "[Digestion]\nPrepare 0.5% SDS ( per sample; recipe below for ): (final: ) water\n50 µl\n100 µl\n5 µl\n95 µl", "[Digestion]\nResuspend nuclei in 0.5% SDS.\n50 µl", "[Digestion]\nIncubate at for .\n62 °C", "[Digestion]\nAdd: water\n145 µl\n25 µl", "[Digestion]\nRo... |
99,098 | How to extract cyanobacterial genome | 0 | dx.doi.org/10.17504/protocols.io.rm7vzjyn8lx1/v1 | https://www.protocols.io/view/how-to-extract-cyanobacterial-genome-dcz22x8e | Leonardo Ken Okumura | TITLE: How to extract cyanobacterial genome
AUTHORS: Leonardo Ken Okumura
[DESCRIPTION]
This protocol describes how to extract cyanobacterial genomes. The main treatments are carried out by sodium iodide, lysozyme, proteinase K and SDS.
[STEPS]
SECTION: Extracting cyanobacteria genome
1. Centrifuge the cyanobacteria ... | ["[Extracting cyanobacteria genome] Centrifuge the cyanobacteria culture at 16,000 x g for 10 minutes and remove the supernatant.", "[Extracting cyanobacteria genome] Add 400 µL of Extraction Buffer and 100 µL of Saturated NaI Solution to the pellet, and mix well.", "[Extracting cyanobacteria genome] Incubate at 37°C f... |
35,047 | Hello | null | dx.doi.org/10.17504/protocols.io.begfjbtn | https://www.protocols.io/view/hello-begfjbtn | Yaju Pradhan | TITLE: Hello
AUTHORS: Yaju Pradhan
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. | [] |
19,098 | Create a class Github repository | null | dx.doi.org/10.17504/protocols.io.wv2fe8e | null | Bonnie Hurwitz, Ken Youens-Clark | TITLE: Create a class Github repository
AUTHORS: Bonnie Hurwitz, Ken Youens-Clark
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The github repository will serve as a location for you to turn-in your homework, and allow the instructors to push back code modifications and suggestions.</div></div>
[... | ["Login to http://github.com", "Fork (or \"copy\") the class repository into your own Github account. This creates a copy of the repository in your own account that you can edit and update. Select your Github account as the place to \"fork\" the repository.", "Click on your \"biosys-analytics\" repository. Click on the... |
null | null | null | dx.doi.org/10.17504/protocols.io.jvqcn5w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>L1 trace element solution, modified from Bigelow: NCMAM Center. Components to prepare 1 L of trace element solution.</p>
[BEFORE_START]
<p>Prepare primary stock solutions (in dH<sub>2</sub>O) of the following:</p>
<ul>
<li>MnCl<sub>2</sub>·4H<sub>2</sub>O: 178.10 g/L</li>
<l... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.cjhuj5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is the Double Digest Protocol with Standard Restriction Enzymes, using a common reaction and same incubation temperature for both enzymes.
[BEFORE_START]
NEB's online tools, <a href="https://www.neb.com/tools-and-resources/interactive-tools/double-digest-finder" ... | [] |
55,418 | Plasma Ultracentrifugation Protocol | 1 | null | https://www.protocols.io/view/plasma-ultracentrifugation-protocol-b2c2qaye | Dakota Gustafson | TITLE: Plasma Ultracentrifugation Protocol
AUTHORS: Dakota Gustafson
[DESCRIPTION]
This protocol is intended to isolate a holistic population of extracellular vesicles from human plasma using input volumes of at least 1mL. Note, there are a number of nuances for the isolation of 'extracellular vesicles' including the... | ["[Sample Thawing and Set Up] Prepare all materials needed for the protocol, including an ice bucket with wet ice.", "[Sample Thawing and Set Up] Annotate samples and tubes with corresponding sample IDs.", "[Sample Thawing and Set Up] Thaw samples on ice for two hours with inversion of tubes every thirty minutes. Sampl... |
48,774 | Fluorescent In Situ Hybridization (FISH - RNAscope) in mouse brain sections | 4 | dx.doi.org/10.17504/protocols.io.btvenn3e | https://www.protocols.io/view/fluorescent-in-situ-hybridization-fish-rnascope-in-btvenn3e | Yu Lin Tan, Oriol Pavon Arocas, Lucille Duquenoy, Tiago Branco | TITLE: Fluorescent In Situ Hybridization (FISH - RNAscope) in mouse brain sections
AUTHORS: Yu Lin Tan, Oriol Pavon Arocas, Lucille Duquenoy, Tiago Branco
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Here we describe a protocol to perform multiplex fluorescent in situ hybridization (FISH) in thin... | ["[Day 0 | Brain extraction]\n[Preparation ~ 15 min]\nYou can extract and freeze several brains on the same day and then store them at -80°C until sectioning. You can do the brain extraction either in the PFA perfusion room (with tools from there) or in the slice electrophysiology area where you prepare acute brain sli... |
31,455 | A simple, non-invasive approach to detect vagal nerve response patterns that predict a positive treatment response to gastric electrical stimulation therapy for gastroparesis | 1 | dx.doi.org/10.17504/protocols.io.bax7ifrn | https://www.protocols.io/view/a-simple-non-invasive-approach-to-detect-vagal-ner-bax7ifrn | Matthew Ward, Bartek Rajwa, John M Wo, Anita Gupta, John Furness, Terry Powley, Thomas V Nowak | TITLE: A simple, non-invasive approach to detect vagal nerve response patterns that predict a positive treatment response to gastric electrical stimulation therapy for gastroparesis
AUTHORS: Matthew Ward, Bartek Rajwa, John M Wo, Anita Gupta, John Furness, Terry Powley, Thomas V Nowak
[DESCRIPTION]
<div class = "text-... | ["[Preparation]\nReview the nature of the study and the informed consent document with the prospective subject. Be sure to answer any questions that s/he may have. Move to Step 2 if the subject understands the nature of the study and agrees to enroll into the study by signing the informed consent document.", "[Sympto... |
98,522 | A General Guide To Generate Different Humanized Mouse Models | 4 | dx.doi.org/10.17504/protocols.io.eq2lyp4zwlx9/v2 | https://www.protocols.io/view/a-general-guide-to-generate-different-humanized-mo-dcf22tqe | Mohsen Khosravi-Maharlooei, Markus Holzl, Austin Chen, Megan Sykes | TITLE: A General Guide To Generate Different Humanized Mouse Models
AUTHORS: Mohsen Khosravi-Maharlooei, Markus Holzl, Austin Chen, Megan Sykes
[DESCRIPTION]
This protocol details how to create humanized mouse models from NSG mice. Four different variants of humanized mice can be generated based on whether or not the ... | ["NOD-scid common gamma chain knockout (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) (NSG) and NSG-(Kb Db)null (IA)null(NSG MHC KO) mice are obtained from the Jackson Laboratory or bred in-house and housed in a specific pathogen-free microisolator environment. Adult mice are used at 6–10 wk of age.", "Discarded human fetal thymus... |
79,749 | WC Medium | 1 | null | https://www.protocols.io/view/wc-medium-cr5dv826 | Richard W Lambrecht | TITLE: WC Medium
AUTHORS: Richard W Lambrecht
[DESCRIPTION]
Protocoll description to prepare WC medium.
[STEPS]
SECTION: Stock Solution preparation
1. The stock solutions don't need to be autoclaved after preparation. Make sure to use volumetric flasks to ensure the right concentrations of the salts and transfer the ... | ["[Stock Solution preparation] The stock solutions don't need to be autoclaved after preparation. Make sure to use volumetric flasks to ensure the right concentrations of the salts and transfer the solution to autoclavable flasks and store it in the fridge. Remember to start the preparation with less than 1L of MilliQ ... |
80,056 | Reproducible protocol for the extraction and semi-automated quantification of macroscopic charcoal from soil | 1 | dx.doi.org/10.17504/protocols.io.kxygx9xr4g8j/v1 | https://www.protocols.io/view/reproducible-protocol-for-the-extraction-and-semi-cseywbfw | Javier Ruiz-Pérez, Julie C. Aleman, Joseph W. Veldman | TITLE: Reproducible protocol for the extraction and semi-automated quantification of macroscopic charcoal from soil
AUTHORS: Javier Ruiz-Pérez, Julie C. Aleman, Joseph W. Veldman
[DESCRIPTION]
Charcoal fragments preserved in soils or sediments are used by scientists to reconstruct fire histories and thereby improve o... | ["[Charcoal extraction] Preparation of samples\n1.A. Oven-dry soil samples to constant weight at 40 ºC.\n\n1.B. Label ≥200 mL beakers.\n\n1.C. Place 20 g of each soil sample in a beaker and record weight (after taring the weight of the beaker).", "[Charcoal extraction] Dispersion and digestion of soils\n2.A. To each be... |
83,944 | Whole-cell proteomics and Analysis by Tandem Mass Tagging-based proteomics | 4 | dx.doi.org/10.17504/protocols.io.kqdg3x4n1g25/v1 | https://www.protocols.io/view/whole-cell-proteomics-and-analysis-by-tandem-mass-cv8gw9tw | Felix Kraus, Sharan Swarup, Vinay V. Eapen, J. Wade Harper wade_harper@hms.harvard.edu | TITLE: Whole-cell proteomics and Analysis by Tandem Mass Tagging-based proteomics
AUTHORS: Felix Kraus, Sharan Swarup, Vinay V. Eapen, J. Wade Harper wade_harper@hms.harvard.edu
[DESCRIPTION]
The analysis of relative protein abundance has emerged as an important tool in cell biology. Typically, it is possible to quant... | ["[Harvest, precipitation and digestion] For whole proteome analysis, 50 µg is required for each replicate. Lyse cells in lysis buffer and pass them through a 21G needle 10 times. Alternatively, lyse cells by\nsonication as per manufactures instructions.", "[Harvest, precipitation and digestion] Centrifugate suspensio... |
100,061 | BAF_Protocol_011 Metabolomics: Database Search MS-DIAL and Analysis using Metaboanalyst 6.0 | 0 | dx.doi.org/10.17504/protocols.io.dm6gpzj1jlzp/v1 | https://www.protocols.io/view/baf-protocol-011-metabolomics-database-search-ms-d-ddx527q6 | Nicholas Sherman | TITLE: BAF_Protocol_011 Metabolomics: Database Search MS-DIAL and Analysis using Metaboanalyst 6.0
AUTHORS: Nicholas Sherman
[DESCRIPTION]
These steps represent a starting point for analysis of metabolomics data. Other data analysis and/or packages may be used.
[STEPS]
SECTION: MS-DIAL V 4.9.221218 starting
1. Thermo... | ["[MS-DIAL V 4.9.221218 starting] Thermo RAW files are organized in two folders - one for all positive mode raw files and another for all negative mode raw files. These files will be loaded into MS-DIAL in two separate searches. Download MSP library files for Positive and Negative mode and save them in a folder in the ... |
null | null | null | dx.doi.org/10.17504/protocols.io.dah2b5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Mounting Media<br /><br /><br />
[STEPS]
?. | [] |
29,468 | Drug tracking on hydra | null | dx.doi.org/10.17504/protocols.io.8z4hx8w | null | Ida Barlow, Adam McDermott-Rouse, Luigi Feriani | TITLE: Drug tracking on hydra
AUTHORS: Ida Barlow, Adam McDermott-Rouse, Luigi Feriani
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for preparing worms, preparing drug plates, dispensing worms with wormsorter and tracking on Hydra rigs</div></div>
[STEPS]
?. [Prepare tracking plates and... | ["[Prepare tracking plates and worms (-2 days)]\nRefeed bleach synchronised worms onto 4 x 150mm plates by pipette 4 small droplets around the plate 2.5 days prior to tracking (eg 5pm on Monday for Thursday tracking)", "[Prepare drugs onto plates (-1 days)]\nGet low peptone 96WP out of the fridge, weigh three plates a... |
33,952 | Gibson Assembly® Master Mix – Assembly (E2611) | 1 | dx.doi.org/10.17504/protocols.io.bdd8i29w | https://www.protocols.io/view/gibson-assembly-master-mix-assembly-e2611-bdd8i29w | New England Biolabs | TITLE: Gibson Assembly® Master Mix – Assembly (E2611)
AUTHORS: New England Biolabs
[DESCRIPTION]
This protocol explains methods for the Gibson Assembly using the Gibson Assembly® Master Mix (E2611).
[GUIDELINES]
Optimal Quantities
NEB recommends a total of 0.02–0.5 pmols of DNA fragments when 1 or 2 fragments are... | ["Set up the following reaction on ice:\n 2-3 Fragment", "Incubate samples in a thermocycler at 50 °C for 15 min when 2 or 3 fragments are being assembled or 60 min when 4-6 fragments are being assembled.", "Store samples on ice or at -20 °C for subsequent transformation."] |
64,383 | An analysis of Relative Telomere Length (RTL) during chemotherapy in patients with advanced gastro-oesophageal adenocarcinoma | 1 | dx.doi.org/10.17504/protocols.io.n92ldznenv5b/v1 | https://www.protocols.io/view/an-analysis-of-relative-telomere-length-rtl-during-ca47sgzn | Jeff Evans, Nicol Keith | TITLE: An analysis of Relative Telomere Length (RTL) during chemotherapy in patients with advanced gastro-oesophageal adenocarcinoma
AUTHORS: Jeff Evans, Nicol Keith
[DESCRIPTION]
OBJECTIVES
The primary objective of this study is:
(a) To analyse Relative Telomere Length (RTL) in blood samples taken from patients durin... | [] |
92,470 | Motor behavioral evaluation of mice | 4 | null | https://www.protocols.io/view/motor-behavioral-evaluation-of-mice-c6iwzcfe | Tae-Un Han | TITLE: Motor behavioral evaluation of mice
AUTHORS: Tae-Un Han
[DESCRIPTION]
This is a general protocol to test motor coordination of mice used models of neurological disorder
[STEPS]
SECTION: Rotarod test
1. On first day, mice are acclimated to standing on a non-rotating rod (Rotamex 5, Columbus Instrument) for thre... | ["[Rotarod test] On first day, mice are acclimated to standing on a non-rotating rod (Rotamex 5, Columbus Instrument) for three 1 min trials with 10 min interval.", "[Rotarod test] Three hours later, mice are acclimated to walking on the rod over three 90 s trials at a speed of 4 rpm", "[Rotarod test] On next day, lat... |
null | null | null | dx.doi.org/10.17504/protocols.io.k9acz2e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is our ‘one-pot ligation’ protocol for Oxford Nanopore ligation libraries. It benefits from increased recovery of library and faster preparation time by using the Ultra II ligation module in conjunction with the Ultra II end repair/dA-tailing module therefore removing a ... | [] |
51,443 | Mitogenome Assembly with GetOrganelle | 1 | dx.doi.org/10.17504/protocols.io.4r3l24zq3g1y/v1 | https://www.protocols.io/view/mitogenome-assembly-with-getorganelle-bwgtpbwn | Dakota Betz | TITLE: Mitogenome Assembly with GetOrganelle
AUTHORS: Dakota Betz
[DESCRIPTION]
Basic instructions for assembling mitogenomes with the GetOrganelle Program
[STEPS]
SECTION: Installation
1.
Before installation, activate your python environment (example code below for python3 environment):
SECTION: Installation... | ["[Installation] Before installation, activate your python environment (example code below for python3 environment):", "[Installation] Install GetOrganelle with the following code:\n\n \n\nYou may need to install updates, be sure to say yes (type y and hit enter) when prompted to update any conda-related programs.", "[... |
null | null | null | dx.doi.org/10.17504/protocols.io.rf7d3rn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>We performed a considerate prediction of intact protein-coding gene models using three independent approaches, i.e.,de novoprediction, homology-based method, and RNA-Seq approach.</p>
[STEPS]
?.
?.
?.
?. | [] |
40,207 | Seek & Blastn Standard Operating Procedure | 5 | dx.doi.org/10.17504/protocols.io.bjhpkj5n | https://www.protocols.io/view/seek-amp-blastn-standard-operating-procedure-bjhpkj5n | Jennifer A. Byrne, Yasunori Park, Amanda Capes-Davis, Bertrand Favier, Guillaume Cabanac, Cyril Labbé | TITLE: Seek & Blastn Standard Operating Procedure
AUTHORS: Jennifer A. Byrne, Yasunori Park, Amanda Capes-Davis, Bertrand Favier, Guillaume Cabanac, Cyril Labbé
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Seek & Blastn is a semi-automated tool that automatically extracts gene identifiers and nuc... | ["[Upload publication to Seek & Blastn]\nUpload the publication of interest in pdf format to Seek & Blastn", "[Upload publication to Seek & Blastn]\nFor Seek & Blastn, click here.Click on the above link and upload the publication of interest by selecting browse, then submit. In this procedure, the retracted article: PM... |
79,989 | Bulk FLASH-seq | 4 | dx.doi.org/10.17504/protocols.io.3byl4jynolo5/v1 | https://www.protocols.io/view/bulk-flash-seq-cscvwaw6 | Vincent Hahaut, Simone Picelli, Rebecca A Siwicki | TITLE: Bulk FLASH-seq
AUTHORS: Vincent Hahaut, Simone Picelli, Rebecca A Siwicki
[DESCRIPTION]
Bulk RNA sequencing has revolutionized the study of transcriptomes, enabling the analysis of gene expression in complex tissues and heterogenous cell populations. While single cell RNA sequencing (scRNA-seq) has gained popul... | ["[Prepare Lysis Mix] Prepare the following Lysis Mix:\n \nABC Reagent Final Concentration Volume 96 rxn Triton-X100 (10% v/v) 0.02 2.208 dNTP mix (25 mM each) 0.24 26.496 SMART dT30VN (100uM) 0.018 1.9872 RNase Inhibitor (40 U/ul) 0.03 3.312 DTT (100 mM) 0.012 1.3248... |
58,761 | Metsch farms protocol | 3 | null | https://www.protocols.io/view/metsch-farms-protocol-b5mhq436 | Meghan Duffy, Katherine Hunsberger, Rebecca Bilich | TITLE: Metsch farms protocol
AUTHORS: Meghan Duffy, Katherine Hunsberger, Rebecca Bilich
[DESCRIPTION]
This is a protocol to infect and maintain Daphnia with Metschnikowia bicuspidata for use in laboratory experiments.
[STEPS] | [] |
54,884 | Eukaryotes 18S-V4 rRNA Metabarcoding PCR protocol for NGS Illumina sequencing | 4 | dx.doi.org/10.17504/protocols.io.bzucp6sw | https://www.protocols.io/view/eukaryotes-18s-v4-rrna-metabarcoding-pcr-protocol-bzucp6sw | Sarah Romac | TITLE: Eukaryotes 18S-V4 rRNA Metabarcoding PCR protocol for NGS Illumina sequencing
AUTHORS: Sarah Romac
[DESCRIPTION]
Nowadays metabarcoding approaches allow to explore the diversity of different communities using next-generation sequencing (NGS).
Here we describe the 18S-V4 DNA amplification method applied for e... | ["[Tagged Primer Design and preparation] We use the eukaryotic 18SV4 primer set TAReukF1- TAReukR3 from Stoeck et al. 2010.", "[PCR] PCR reactions are performed using the Taq polymerase Phusion High-Fidelity Master Mix with GC buffer (Thermofisher, Cat No F-532 L).\nThis Taq has a good proof-reading and its buffer all... |
null | null | null | dx.doi.org/10.17504/protocols.io.iadcaa6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol provides an efficient DNA extraction and purification of ancient bones.</p>
[BEFORE_START]
<p>Clean</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.cifubm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
PCR Protocol for Taq DNA Polymerase with ThermoPol® Buffer (M0267)
[GUIDELINES]
<strong>OVERVIEW</strong><br /><br />The Polymerase Chain Reaction (PCR) is a powerful and sensitive technique for DNA amplification (1). Taq DNA Polymerase is an enzyme... | [] |
44,322 | Agarose Gel Electrophoresis and Size-Selection of Library | 4 | dx.doi.org/10.17504/protocols.io.bpiamkae | https://www.protocols.io/view/agarose-gel-electrophoresis-and-size-selection-of-bpiamkae | Eric L. Van Nostrand, Thai B. Nguyen, Chelsea Gelboin-Burkhart, Ruth Wang, Steven M. Blue, Gabriel A. Pratt, Ashley L. Louie, Gene W. Yeo | TITLE: Agarose Gel Electrophoresis and Size-Selection of Library
AUTHORS: Eric L. Van Nostrand, Thai B. Nguyen, Chelsea Gelboin-Burkhart, Ruth Wang, Steven M. Blue, Gabriel A. Pratt, Ashley L. Louie, Gene W. Yeo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Profiling of RNA binding protein targets... | ["Prepare 3% low-melting temp agarose gel with 1:10,000 SybrSafe in 1× TBE.", "[Prepare Samples and Run Gel]\nAdd to each sample (18 μL of sample), mix.\n[6× Orange G buffer]", "[Prepare Samples and Run Gel]\nLoad on gel, leave one empty well between samples, 50 bp ladder on both sides of the gel.", "[Prepare Samples ... |
21,775 | Polymerase Chain Reaction - Comparative genomics of Staphylococcus aureus associated with subclinical and clinical bovine mastitis (Rocha et al., 2019) | null | dx.doi.org/10.17504/protocols.io.zhpf35n | null | Lis Rocha | TITLE: Polymerase Chain Reaction - Comparative genomics of Staphylococcus aureus associated with subclinical and clinical bovine mastitis (Rocha et al., 2019)
AUTHORS: Lis Rocha
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Comparative genomics of </span><span style = "font-style:italic;">St... | ["[primers cl3309sub F/R]\n35 cycles of denaturation at 95.0 °C for 45 s,", "[primers cl3309sub F/R]\nAnealing: 55 °C for 45s", "[primers cl3309sub F/R]\nExtension: 72 °C for 45 s", "[primers cl3309sub F/R]\nfinal extension at 72.0 °C for 10 min", "[primers cl3316F/R]\ninitial denaturation: 95.0 °C for 5 min;", "[prime... |
83,300 | 2-step PCR mixture and conditions (Barcoded-head primers for seqs pooling) | 4 | dx.doi.org/10.17504/protocols.io.yxmvm263og3p/v3 | https://www.protocols.click/view/2-step-pcr-mixture-and-conditions-barcoded-head-pr-cvkcw4sw | 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 m... | ["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... |
null | null | null | dx.doi.org/10.17504/protocols.io.rj8d4rw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Results of CTTI Pregnanacy Testing Project Survey</p>
[STEPS]
?. | ["{\"blocks\":[{\"key\":\"48m15\",\"text\":\" \",\"type\":\"atomic\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[{\"offset\":0,\"length\":1,\"key\":0}],\"data\":[]}],\"entityMap\":[{\"type\":\"dataset\",\"mutability\":\"MUTABLE\",\"data\":{\"id\":\"140\",\"guid\":\"930BAFC89DE341D686D23DE62F61D68B\",\"name\"... |
75,986 | The Selfish Reasons for Practicing Open Research | 1 | dx.doi.org/10.17504/protocols.io.e6nvwj8w9lmk/v1 | https://www.protocols.io/view/the-selfish-reasons-for-practicing-open-research-cnfsvbne | Lenny Teytelman | TITLE: The Selfish Reasons for Practicing Open Research
AUTHORS: Lenny Teytelman
[DESCRIPTION]
Champions and practitioners of open research and FAIR data practices are realizing significant benefits to their research along with the impactful bonus of making the whole research enterprise better for everyone. In additi... | ["[Introduction] Cancer Bio Reproducibility Project\n\nAs part of the background on why we created protocols.io, we like to talk about the Cancer Biology Reproducibility Project, which was a $1.5 million dollar initiative coordinated by the Center for Open Science and by Science Exchange with the goal of trying to inde... |
25,197 | How to Prepare a Single Cell Suspension from a Frozen Cell Sample | null | dx.doi.org/10.17504/protocols.io.4umgwu6 | null | STEMCELL Technologies | TITLE: How to Prepare a Single Cell Suspension from a Frozen Cell Sample
AUTHORS: STEMCELL Technologies
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Preparing a single cell suspension from a frozen starting sample is critical for optimizing cell isolations by avoiding additional cell loss and ena... | ["[Preparation of a Single Cell Suspension]\nThaw the vial of cells quickly by swirling it in a water bath.\n37 °C", "[Preparation of a Single Cell Suspension]\nTransfer thawed cells into a sterile 50 mL conical tube.\nOptional: Add 0.25 to 0.5 mL of a 1 mg/mL DNase I solution directly to the tube prior to transferrin... |
82,542 | iPSC Cell Culture Protocol | 4 | dx.doi.org/10.17504/protocols.io.36wgqj2n3vk5/v1 | https://www.protocols.click/view/ipsc-cell-culture-protocol-cuunwwve | Isabelle J Fisher, Sally Salomonsson, Claire D Clelland | TITLE: iPSC Cell Culture Protocol
AUTHORS: Isabelle J Fisher, Sally Salomonsson, Claire D Clelland
[DESCRIPTION]
This protocol describes regular maintenance of induced pluripotent stem cell (iPSC) cultures.
[STEPS]
SECTION: Thawing iPSCs
1. Coat four wells of a six-well plate with matrigel solution and incubate at 3... | ["[Thawing iPSCs] Coat four wells of a six-well plate with matrigel solution and incubate at 37°C for at least 30 minutes.", "[Thawing iPSCs] To make matrigel solution, resuspend matrigel 1:in KnockOut DMEM.", "[Thawing iPSCs] Make thawing medium:", "[Thawing iPSCs] Add ROCK inhibitor (RI) 1:1000 to mTeSR Plus media (e... |
78,155 | Choanoflagellate Ciliogenesis Live Imaging | 4 | null | https://www.protocols.io/view/choanoflagellate-ciliogenesis-live-imaging-cqjjvukn | Maxwell C Coyle | TITLE: Choanoflagellate Ciliogenesis Live Imaging
AUTHORS: Maxwell C Coyle
[DESCRIPTION]
This protocol removes the cilia/flagella from choanoflagellate cells and sets up the cells for live imaging of ciliogenesis. It has been developed for the species Salpingoeca rosetta, but may be portable into other choanoflagellat... | ["[Concentrate cells and remove cilia] Grow choanoflagellate cells in High Nutrient Media to a density of 1-2 x 106 cells/ml", "[Concentrate cells and remove cilia] Aliquot and pellet 6 x 106 cells 2000 x g, 10 min", "[Concentrate cells and remove cilia] Corona treat a fluorodish 5-10 seconds", "[Concentrate cells and ... |
92,528 | Generation of Gba L444P mutant mouse | 4 | null | https://www.protocols.io/view/generation-of-gba-l444p-mutant-mouse-c6kqzcvw | Tae-Un Han, Edward Ginns | TITLE: Generation of Gba L444P mutant mouse
AUTHORS: Tae-Un Han, Edward Ginns
[DESCRIPTION]
This protocol was used to generate of mutant mouse carrying Gba L444P point mutation.
The protocol was also described in a previous literature (Mol Genet Metab. 2014 Feb;111(2):152-62. doi: 10.1016)
[STEPS]
1. The replacement ... | ["The replacement targeting vector enabling positive/negative selection contained a neomycin resistance (neoR) cassette flanked by loxP sequences inserted into the intergenic regions between murine metaxin (mtx) and glucocerebrosidase (gba).", "The L444P was introduced into a genomic clone of murine gba by PCR mutagene... |
19,746 | Mussel Spawning Protocol | 3 | dx.doi.org/10.17504/protocols.io.xiafkae | https://www.protocols.io/view/mussel-spawning-protocol-xiafkae | Estefania Paredes | TITLE: Mussel Spawning Protocol
AUTHORS: Estefania Paredes
[DESCRIPTION]
Mussel spawning protocol
[STEPS]
1. {"blocks":null,"entityMap":null} | ["{\"blocks\":null,\"entityMap\":null}"] |
86,088 | Mitochondrial isolation | 1 | null | https://www.protocols.io/view/mitochondrial-isolation-cybgxsjw | Louise Uoselis | TITLE: Mitochondrial isolation
AUTHORS: Louise Uoselis
[DESCRIPTION]
Mitochondrial isolation and quantification from HeLa cells
[STEPS]
SECTION: Mitochondrial isolation
1. Thaw cell pellets that have been frozen at -80 deg C for at least 15 min, on ice
SECTION: Mitochondrial isolation
2. Aliquot out an amount ... | ["[Mitochondrial isolation] Thaw cell pellets that have been frozen at -80 deg C for at least 15 min, on ice", "[Mitochondrial isolation] Aliquot out an amount of Solution B assuming for5 mL of Solution B per sample (if samples have been collected from 10cm plates), and add PMSF at a final concentration of 0.5 mM. Kee... |
95,581 | Lysosome analysis with confocal microscopy_V2 | 4 | dx.doi.org/10.17504/protocols.io.81wgbx3jqlpk/v1 | https://www.protocols.io/view/lysosome-analysis-with-confocal-microscopy-v2-c9j5z4q6 | Sjors Maassen | TITLE: Lysosome analysis with confocal microscopy_V2
AUTHORS: Sjors Maassen
[DESCRIPTION]
This protocol provides an overview of lysosomal analysis using confocal microscopy and Fiji
[STEPS]
SECTION: Sterilize glass cover slips
1. Put the glass coverslips in a 24-well plate, submerge the coverslips in 70% ethanol, and... | ["[Sterilize glass cover slips] Put the glass coverslips in a 24-well plate, submerge the coverslips in 70% ethanol, and then expose them to UV light in a tissue culture hood for between 20 and 30 minutes.", "[Sterilize glass cover slips] Remove the ethanol, wash the wells containing coverslips three times with sterile... |
18,368 | Electrophysiological studies | null | dx.doi.org/10.17504/protocols.io.v68e9hw | null | Kiichi Hirota, Yoshiyuki Matsuo, Mikio Hayashi | TITLE: Electrophysiological studies
AUTHORS: Kiichi Hirota, Yoshiyuki Matsuo, Mikio Hayashi
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. MIN6 cells were incubated in an extracellular bath solution containing 2 mM glucose for 30 min at 37 °C before patch-clamp experiments.
?. Membrane potential and whole... | ["MIN6 cells were incubated in an extracellular bath solution containing 2 mM glucose for 30 min at 37 °C before patch-clamp experiments.", "Membrane potential and whole-cell current were recorded using the EPC 800 patch-clamp amplifier (HEKA Elektronik Inc. Holliston, MA, USA). The amplifier was driven by Clampex 9 (A... |
82,638 | Fixing hippo neurons to assess endogenous NEMO during oxidative stress | 1 | dx.doi.org/10.17504/protocols.io.e6nvwjx8dlmk/v1 | https://www.protocols.io/view/fixing-hippo-neurons-to-assess-endogenous-nemo-dur-cuxnwxme | OLIVIA HARDING | TITLE: Fixing hippo neurons to assess endogenous NEMO during oxidative stress
AUTHORS: OLIVIA HARDING
[DESCRIPTION]
We altered a previously developed method (dx.doi.org/10.17504/protocols.io.bxpfpmjn) in order to investigate the interaction of endogenous NEMO with damaged mitochondria in Hippocampal rat neurons. M... | ["[Plating and maintenance of hippocampal neurons] Plate primary hippocampal Sprague Dawley rat neurons (embryonic day 18) on 35 mm glass-bottomed, PLL-coated dishes at 250,00 cells per dish in MEM supplemented with 10% horse serum, 33 mM D-glucose, and 1 mM sodium pyruvate. This is day 0.", "[Plating and maintenance o... |
null | null | null | dx.doi.org/10.17504/protocols.io.htwb6pe | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?. | [] |
63,346 | An optimised protocol for the detection of lipofuscin in cells cultured in vitro | 1 | dx.doi.org/10.17504/protocols.io.x54v9yw91g3e/v1 | https://www.protocols.io/view/an-optimised-protocol-for-the-detection-of-lipofus-b94sr8we | Camilla SA Davan-Wetton, Trinidad Montero-Melendez | TITLE: An optimised protocol for the detection of lipofuscin in cells cultured in vitro
AUTHORS: Camilla SA Davan-Wetton, Trinidad Montero-Melendez
[DESCRIPTION]
Lipofuscin is a complex material that accumulates in lysosomes and it is considered a marker of cellular senescence and ageing. This substance can be detecte... | ["[Saturated Sudan Black B solution preparation] Dissolve 1.2 g Sudan Black B in 80 mL 70% ethanol in a glass bottle and stir on a magnetic stirrer.", "[Saturated Sudan Black B solution preparation] Before use, filter the solution three times as follows:\n - first through a 70μm cell strainer\n - then through ... |
null | null | null | dx.doi.org/10.17504/protocols.io.n74dhqw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>We present a lab-in-the-field experiment to demonstrate how individual behavior in the lab predicts their ability to identify phishing attempts. Using the business and finance staff members from a large public university in the U.S., we find that participants who are intolera... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.q9ndz5e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A single prospective cohort of women submitted to cesarean section who received spinal anesthesia will be assessed for the proposed risk factors and the incidence of nausea or vomiting will be observed during the first 48 hours.</p>
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
69,308 | Sterivex DNA Extraction with PowerSoil Kit | 1 | null | https://www.protocols.io/view/sterivex-dna-extraction-with-powersoil-kit-cfw4tpgw | Molly A Moynihan | TITLE: Sterivex DNA Extraction with PowerSoil Kit
AUTHORS: Molly A Moynihan
[DESCRIPTION]
Adapted from: Jacobs, J., Rhodes, M., Sturgis, B. & Wood, B. 2009. Influence of environmental gradients on the abun- dance and distribution of Mycobacterium spp. in a coastal lagoon estuary. Appl. Environ. Microbiol., 73787384, D... | ["[DNA extraction of sterivex filter using PowerSoil kit] Thaw sterivex samples and remove any RNAlater or excess water from filter using a syringe.", "[DNA extraction of sterivex filter using PowerSoil kit] Using sterile pliers, break open sterivex by applying pressure along the seam of the casing. Do so over a steril... |
43,098 | 1 Preparation of Mica Substrate | 1 | dx.doi.org/10.17504/protocols.io.bnb2maqe | https://www.protocols.io/view/1-preparation-of-mica-substrate-bnb2maqe | Philip J. Haynes, Kavit H. S. Main, Alice Pyne | TITLE: 1 Preparation of Mica Substrate
AUTHORS: Philip J. Haynes, Kavit H. S. Main, Alice Pyne
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is part 1 of the "Atomic Force Microscopy of DNA and DNA-Protein Interactions" collection of protocols.</div><div class = "text-block"><span style = "fo... | ["[Preparation of Mica Substrate]\nCut the adhesive PTFE into circles of the same size as the steel sample discs (15 mm), using either a punch or scalpel (see Note 7).", "[Preparation of Mica Substrate]\nPeel off the backing of the PTFE cut-out and adhere to the steel disc.", "[Preparation of Mica Substrate]\nMix the A... |
101,945 | Hematoxylin and Eosin (H&E) Staining | 0 | dx.doi.org/10.17504/protocols.io.ewov19deklr2/v1 | https://www.protocols.io/view/hematoxylin-and-eosin-h-amp-e-staining-dfsz3nf6 | Núria Peñuelas, Ariadna Laguna, Miquel Vila | TITLE: Hematoxylin and Eosin (H&E) Staining
AUTHORS: Núria Peñuelas, Ariadna Laguna, Miquel Vila
[DESCRIPTION]
Hematoxylin and Eosin (H&E) Staining for histological sections
[STEPS]
SECTION: DEPARAFFINIZE
1. Xylene - 5 minutes
SECTION: HYDRATE
3. 100º alcohol - 6 quick immersions
SECTION: DEPARAFFINIZE
2. Xylene... | ["[DEPARAFFINIZE] Xylene - 5 minutes", "[HYDRATE] 100º alcohol - 6 quick immersions", "[DEPARAFFINIZE] Xylene - 6 quick immersions", "[HYDRATE] 70º alcohol - 6 quick immersions", "[HYDRATE] 96º alcohol - 6 quick immersions", "[HYDRATE] 100º alcohol - 6 quick immersions", "[HYDRATE] 50º alcohol - 6 quick immersions", "[... |
null | null | null | dx.doi.org/10.17504/protocols.io.e25bgg6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Anti-Neu5Gc Antibody Kit Protocols for Flow Cytometry, ELISA, and Western blot.</p>
[STEPS] | [] |
38,576 | SARS-CoV2 EBI assembly submission protocol | 1 | dx.doi.org/10.17504/protocols.io.bhwqj7dw | https://www.protocols.io/view/sars-cov2-ebi-assembly-submission-protocol-bhwqj7dw | Nabil-Fareed Alikhan, Emma Griffiths, Ruth Timme, Duncan MacCannell | TITLE: SARS-CoV2 EBI assembly submission protocol
AUTHORS: Nabil-Fareed Alikhan, Emma Griffiths, Ruth Timme, Duncan MacCannell
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">PURPOSE: </span></div><div class = "text-block"><span style = "font-weight:bold;">This pro... | ["The Webin-CLI program is described as the only way to upload assembled sequences. This includes consensus sequences of SARS-COV2. Generally, you should follow the guidance here: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli.htmlThe process, briefly, is as follows: Download the Webin-cli too... |
75,214 | FastDNA SPIN Kit for Soil | 4 | null | https://www.protocols.io/view/fastdna-spin-kit-for-soil-cmpnu5me | leighton.r.king | TITLE: FastDNA SPIN Kit for Soil
AUTHORS: leighton.r.king
[DESCRIPTION]
The FastDNATM SPIN Kit for Soil quickly and efficiently isolates PCR-ready genomic DNA directly from soil samples in less than 30 minutes. Designed for use with the FastPrep® instruments from MP Biomedicals, plant and animal tissues, bacteria, alg... | ["[PREPARE the sample] ADD up to 500 mg of soil sample,\n978 µL Sodium Phosphate Buffer, and 122 µL MT Buffer to Lysing Matrix E tube", "[HOMOGENIZE with the FastPrep] LOAD tube in FastPrep instrument. \n\nPROCESS 40 s at a speed setting of 6.0 m/s. \n\nCENTRIFUGE at 14000 x g, 10 min to pellet debris", "[PRECIPITATE p... |
76,692 | Preparation and transformation of chemically super-competent Escherichia coli | 4 | null | https://www.protocols.io/view/preparation-and-transformation-of-chemically-super-cn5uvg6w | Andreas Sagen | TITLE: Preparation and transformation of chemically super-competent Escherichia coli
AUTHORS: Andreas Sagen
[DESCRIPTION]
Based on a method produced by Inoue, et al.
Inoue, Nojima, H., & Okayama, H. (1990). High efficiency transformation of Escherichia coli with plasmids.Gene,96(1), 23–28. https://doi.org/10.1016/037... | ["[Preparation of Inoue transformation buffer] In a sterile flask, add 200 mL distilled water", "[Transformation] Quickly thaw a single reaction tube with 100 µL hyper-competent cells in Inoue-DMSO", "[Preparation of Inoue transformation buffer] Measure 2.5 mL (1 Molarity (M)) PIPES, 2.177 g Manganese(II) chloride tetr... |
94,739 | DNA extraction from infected or not wheat leaf tissue | 4 | dx.doi.org/10.17504/protocols.io.n2bvj34pplk5/v1 | https://www.protocols.io/view/dna-extraction-from-infected-or-not-wheat-leaf-tis-c8rtzv6n | Benjamin Schwessinger | TITLE: DNA extraction from infected or not wheat leaf tissue
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... | ["[Week 2: Sampling of representative leaf tissue and tissue rupture] Label each 2ml Eppendorf tube containing 2-3 steal beads with the treatment group name and your research group name. Label both the top and the side of each tube clearly.", "[Week 2: Sampling of representative leaf tissue and tissue rupture] Carefull... |
79,763 | A laboratory study using a split-tooth design to analyze the micromorphology of the resin-dentin interface when combining the internal/external resin infiltration of proximal caries lesions and the internal tunnel technique | 4 | dx.doi.org/10.17504/protocols.io.n2bvj8mppgk5/v1 | https://www.protocols.io/view/a-laboratory-study-using-a-split-tooth-design-to-a-cr5tv86n | Prof Dr med dent Dr h c Andrej M. Kielbassa, Sabrina Summer, Julia_batzer | TITLE: A laboratory study using a split-tooth design to analyze the micromorphology of the resin-dentin interface when combining the internal/external resin infiltration of proximal caries lesions and the internal tunnel technique
AUTHORS: Prof Dr med dent Dr h c Andrej M. Kielbassa, Sabrina Summer, Julia_batzer
[DESC... | ["[Methods] Ethical approval, sample size calculation, and tooth selection\nWith the current report, we will adhere to the modified CONSORT guidelines for reporting pre-clinical studies on dental materials15,16. This study protocol was approved by the Institutional Ethical Review Board of the Danube Private University ... |
99,196 | Intracellular and extracellular MHC-II immunostaining and microscopy on peritoneal macrophages | 0 | dx.doi.org/10.17504/protocols.io.bp2l62191gqe/v1 | https://www.protocols.io/view/intracellular-and-extracellular-mhc-ii-immunostain-dc442yyw | Rebecca Wallings | TITLE: Intracellular and extracellular MHC-II immunostaining and microscopy on peritoneal macrophages
AUTHORS: Rebecca Wallings
[DESCRIPTION]
Staining of intracellular and extracellular MHCII in peritoneal macrophages in 96 well plate using EVOS fluorescent microscope and analysis on CellProfiler
[STEPS]
1. After har... | ["After harvesting and plating pMacs from mouse, plate in 96-well plate at 50,000 cells/well in 200uL as described in pMac harvesing protocol. Once cells have adhered, aspirate media and replace with fresh growth media containing vehicle or 100U of IFNy for 18", "Retrieve cells from 37 degrees. Aspirate media and wash ... |
86,981 | Protocol to isolate and fix nuclei from flash frozen mouse adrenal glands for IGVF | 4 | null | https://www.protocols.io/view/protocol-to-isolate-and-fix-nuclei-from-flash-froz-cy7dxzi6 | Elisabeth Rebboah | TITLE: Protocol to isolate and fix nuclei from flash frozen mouse adrenal glands for IGVF
AUTHORS: Elisabeth Rebboah
[DESCRIPTION]
This protocol describes isolation of nuclei from 10 week old mouse adrenal glands from 8 founder strains (B6J, AJ, 129S1J, NZOJ, WSBJ, NODJ, PWKJ, and CASTJ), preparation of a single nucle... | ["[Setup] Label tubes.", "[Setup] Pre-chill centrifuge to 4C.", "[Setup] Prepare ice buckets.", "[Setup] Prepare lysis buffer in a 50 ml conical tube on ice. Distribute 2 ml into 8 gentleMACS C Tubes on ice. Add RNase inhibitor to the lysis buffer aliquot the day of the experiment.", "[Setup] Prepare NB + BSA + RNase i... |
52,360 | Finalizing Mitogenome Annotation in Geneious | 1 | dx.doi.org/10.17504/protocols.io.yxmvmkjrbg3p/v1 | https://www.protocols.io/view/finalizing-mitogenome-annotation-in-geneious-bxdgpi3w | Dakota Betz | TITLE: Finalizing Mitogenome Annotation in Geneious
AUTHORS: Dakota Betz
[DESCRIPTION]
Our protocols are constantly evolving and old versions will be deleted.
The documents here are not intended to be cited in publications
[STEPS]
SECTION: Opening Geneious and Setting Up Workspace
2. Log into Geneious - (or, if you h... | ["[Opening Geneious and Setting Up Workspace] Log into Geneious - (or, if you have your own version, just open that) Use the floating license server. IT IS VERY IMPORTANT YOU DO NOT UPDATE GENEIOUS - the floating license will not work with newer versions.", "[Importing Sequences] Importing Your Data", "[Importing Seque... |
98,806 | USDA LTAR Common Experiment measurement: Soil water content | 0 | dx.doi.org/10.17504/protocols.io.261ge542yg47/v1 | https://www.protocols.io/view/usda-ltar-common-experiment-measurement-soil-water-dcqw2vxe | Michael H. Cosh, Claire Baffaut | TITLE: USDA LTAR Common Experiment measurement: Soil water content
AUTHORS: Michael H. Cosh, Claire Baffaut
[DESCRIPTION]
Soil water content, also known as soil moisture, is commonly defined as the volume of water per volume of soil (volumetric soil water content). Gravimetric soil water content is the weight of water... | ["[Data collection] Equipment\n\nVarious technologies are available for monitoring soil water content, many using the dielectric nature of water to provide an estimate. Others are based on capacitance, cosmic ray neutron counting, time domain reflectometry, transmission line oscillators, time domain transmission, lysim... |
34,321 | Identification of interacting proteins using proximity-dependent biotinylation with BioID2 in Trypanosoma brucei | 1 | dx.doi.org/10.17504/protocols.io.bdrri556 | https://www.protocols.io/view/identification-of-interacting-proteins-using-proxi-bdrri556 | Jan Pyrih, Julius Lukeš | TITLE: Identification of interacting proteins using proximity-dependent biotinylation with BioID2 in Trypanosoma brucei
AUTHORS: Jan Pyrih, Julius Lukeš
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>A range of recently developed techniques that take advantage of proximity biotinylation, such... | ["[Hypotonic mitochondria isolation]\nresuspend cell pellets in 50 ml of SBG and spin again at same condition", "[Hypotonic mitochondria isolation]\nresuspend cell pellet in 3 ml of DTE", "[Hypotonic mitochondria isolation]\nAdd 0,5 ml of 60% Sucrose, mix the sample in dounce and transfer it into 3 eppendorf tubes", "[... |
95,342 | Do, Q. B. et al. (2023) Early deficits in an in vitro striatal microcircuit model carrying the Parkinson’s GBA-N370S mutation | 2 | dx.doi.org/10.17504/protocols.io.x54v9dw61g3e/v2 | https://www.protocols.io/view/do-q-b-et-al-2023-early-deficits-in-an-in-vitro-st-c9cnz2ve | Quyen Do, Humaira Noor, Ricardo Marquez Gomez, Kaitlyn M L Cramb, Bryan Ng, Ajantha Abbey, Naroa Ibarra-Aizpura, Maria-Claudia Caiazza, Parnaz Sharifi, Charmaine Lang, Dayne Beccano-Kelly, Jimena Baleriola, Nora Bengoa-Vergniory, Richard Wade-Martins | TITLE: Do, Q. B. et al. (2023) Early deficits in an in vitro striatal microcircuit model carrying the Parkinson’s GBA-N370S mutation
AUTHORS: Quyen Do, Humaira Noor, Ricardo Marquez Gomez, Kaitlyn M L Cramb, Bryan Ng, Ajantha Abbey, Naroa Ibarra-Aizpura, Maria-Claudia Caiazza, Parnaz Sharifi, Charmaine Lang, Dayne Becc... | [] |
23,856 | Making LB Agar Plate | null | dx.doi.org/10.17504/protocols.io.3iqgkdw | null | Kenneth Schackart | TITLE: Making LB Agar Plate
AUTHORS: Kenneth Schackart
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">How to make LB Agar Broth plates for bacterial quantification.</div><div class = "text-block"><span>*Protocol image used is from Wikimedia commons [</span><a href="https://commons.wikimedia.org/wik... | ["[Mix Broth]\nAdd Miller's LB Agar Powder and agarose to Deionized Water.\n2.5 g\n1.5 g\n100 ml", "[Mix Broth]\nSwirl powder in DIW until dissolved.", "[Sterilize Broth]\nCover top of glassware containing broth solution with aluminum foil, and add a small piece of thermal indicator tape.", "[Sterilize Broth]\nAutoc... |
51,498 | H&E Staining for Pancreas Cryosections | 1 | dx.doi.org/10.17504/protocols.io.bwiipcce | https://www.protocols.io/view/h-amp-e-staining-for-pancreas-cryosections-bwiipcce | Diane Saunders, Angela Kruse, Jamie Allen, Carrie Romer, Danielle Gutierrez, Alvin Powers, Jeff Spraggins | TITLE: H&E Staining for Pancreas Cryosections
AUTHORS: Diane Saunders, Angela Kruse, Jamie Allen, Carrie Romer, Danielle Gutierrez, Alvin Powers, Jeff Spraggins
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol for H&E staining can be applied to either fixed or unfixed frozen cryosectio... | ["Air dry sections for .", "Incubate in 95% alcohol for , then wash, dipping until clear.", "Incubate in hematoxylin for , then wash until clear.", "Dip 3-4x in bluing solution, then wash for", "Dip 3-4x in 95% alcohol.", "Dip 1-2x in eosin.", "Dip 5-10x in 95% alcohol, then repeat using 2nd aliquot.", "Dip 5-10x in... |
80,829 | Estimating the prevalence, quality of life, economic and societal impact of arthritis in Tanzania: Protocol for a mixed methods study | 2 | dx.doi.org/10.17504/protocols.io.8epv5j8r4l1b/v1 | https://www.protocols.io/view/estimating-the-prevalence-quality-of-life-economic-cs65whg6 | Kajiru Gad Kilonzo, Stefanie J. Krauth, Jo Halliday, Clive Kelly, Stefan Siebert, Gloria Temu, Christopher Bunn, Nateiya M Yongolo, Sally Wyke, Emma McIntosh, Blandina Mmbaga | TITLE: Estimating the prevalence, quality of life, economic and societal impact of arthritis in Tanzania: Protocol for a mixed methods study
AUTHORS: Kajiru Gad Kilonzo, Stefanie J. Krauth, Jo Halliday, Clive Kelly, Stefan Siebert, Gloria Temu, Christopher Bunn, Nateiya M Yongolo, Sally Wyke, Emma McIntosh, Blandina Mm... | [] |
46,686 | Preparation of Carbon Sources for Possible Heterotrophic Feedstock for O. tauri | 4 | null | https://www.protocols.io/view/preparation-of-carbon-sources-for-possible-heterot-brt6m6re | Lynn Doran, Steven Burgess | TITLE: Preparation of Carbon Sources for Possible Heterotrophic Feedstock for O. tauri
AUTHORS: Lynn Doran, Steven Burgess
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Instructions for preparing stock carbon source solutions as experimental heterotrophic feedstocks for Ostreococcus tauri. </div><... | ["Determine amount of carbon source solution that is needed. Take into account both the amount needed, concentration needed, dilution factor, and the smallest amount that can be made while still accurately weighing solids and measuring liquids.C SourceStock C Source Vol Solid (g)Stock C Source to Vol with ASW (mL)Stoc... |
88,037 | Opentrons Pipeline: DNA Extraction with the Omega Biotek Stool Kit | 5 | dx.doi.org/10.17504/protocols.io.dm6gp39njvzp/v1 | https://www.protocols.io/view/opentrons-pipeline-dna-extraction-with-the-omega-b-cz8dx9s6 | Kristina Vsevolodova, Gideon Erkenswick, Mrinalini Watsa | TITLE: Opentrons Pipeline: DNA Extraction with the Omega Biotek Stool Kit
AUTHORS: Kristina Vsevolodova, Gideon Erkenswick, Mrinalini Watsa
[DESCRIPTION]
This protocol is an automated pipeline to extract a full 96-well plate of DNA from stool lysates prepared in two separate plates. Lysing of the stool can be perform... | ["[Before starting] Materials\n\n5x Nest 50mL Falcon Tubes for holding accurate reagent amounts before starting protocol.\n4x Opentrons 200µL Filter Tips\n1x VWR 96 Deep Well Plates 1mL for 300µL of lysate.\n2x NEST 1-Well Reservoirs, 195 mL for extraction waste collection during protocol.\n2x NEST 12-Well Reservoirs, ... |
null | null | null | dx.doi.org/10.17504/protocols.io.f3ebqje | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is the suggested protocol for clean-up using AMPure XP beads. It is recommended as part of the <a href="https://www.protocols.io/view/jetseq-dna-library-preparation-kit-fwgbpbw" target="_blank">JetSeq<sup>TM</sup> DNA Library Preparation Kit protocol</a> for post ligatio... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.eudbes6 | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<strong>MATERIALS:</strong><br /><br /> 1) NC64A <em>chlorella</em>, pelleted (fresh cells preferred)<br /> 2) 70% methanol<br /> 3) Centrifuge tubes, corex or polypropylene<br /> 4) 50 mM Tris-HCl, pH 7.8
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?. | [] |
91,746 | Assembling MAGs using KBase | 5 | dx.doi.org/10.17504/protocols.io.x54v9pop4g3e/v1 | https://www.protocols.io/view/assembling-mags-using-kbase-c5uay6se | John Beckley | TITLE: Assembling MAGs using KBase
AUTHORS: John Beckley
[DESCRIPTION]
This protocol describes the steps to run a KBase narrative to assemble MAGs from raw reads.
[STEPS]
1. Create an acount with KBase, login, and start a new narrative.
2. Import metagenomic data as SRA reads by selecting the “Import SRA File as Read... | ["Create an acount with KBase, login, and start a new narrative.", "Import metagenomic data as SRA reads by selecting the “Import SRA File as Reads from Web” app. Provide the SRA file URL, the sequencing technology, and an output name for the file to be generated. Run the app and locate output in My Data.", "To assess ... |
44,785 | Transplantation of Chicken Egg-White Extract-Induced Rabbit PBMCs as a Treatment for Renal Ischemia-Reperfusion Injury in Rabbits | 1 | dx.doi.org/10.17504/protocols.io.bpyrmpv6 | https://www.protocols.io/view/transplantation-of-chicken-egg-white-extract-induc-bpyrmpv6 | ruangp | TITLE: Transplantation of Chicken Egg-White Extract-Induced Rabbit PBMCs as a Treatment for Renal Ischemia-Reperfusion Injury in Rabbits
AUTHORS: ruangp
[STEPS]
?. Identification of noninduced and induced PBMCs
?. Preparation of the rabbit renal ischemia-reperfusion injury model
?. Rabbit PBMC isolation, culture, ind... | ["Identification of noninduced and induced PBMCs", "Preparation of the rabbit renal ischemia-reperfusion injury model", "Rabbit PBMC isolation, culture, induction and labeling", "Kidney function test", "Changes in the urinary protein content", "Observation of labeled cells in frozen sections", "Histopathological assess... |
null | null | null | dx.doi.org/10.17504/protocols.io.q7bdzin | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for human small intestine cell dissociation, performed on ice to reduce artifact gene expression. </p>
[BEFORE_START]
<div title="Page 1">
<p><strong>Checklist prior to beginning:</strong><br />-Centrifuges, large and small, set to 4 C<br />-Make enzyme stock; place... | [] |
85,032 | Nuclei Isolation for 10X Multiome Sequencing | 4 | dx.doi.org/10.17504/protocols.io.kxygx3pqkg8j/v1 | https://www.protocols.click/view/nuclei-isolation-for-10x-multiome-sequencing-cxagxibw | Lakme Caceres | TITLE: Nuclei Isolation for 10X Multiome Sequencing
AUTHORS: Lakme Caceres
[DESCRIPTION]
This protocol is for isolating nuclei for 10X multiome sequencing.
[GUIDELINES]
Keep tissue/nuclei on ice as much as possible.
[STEPS]
SECTION: Prepare Fresh Solutions
4. Make 3 mL Homogenization Buffer per sample by adding 2.89... | ["[Prepare Fresh Solutions] Make 3 mL Homogenization Buffer per sample by adding 2.895 mL Nuclear Isolation Media (filtered via syringe) to a 5 mL eppendorf. Then add 3 μL 100 mM DTT and 30 μL 10% Triton X-100. Add 15 uL RNAsin and invert to mix. Store on ice.", "[Prepare Stock Solutions] Make 20 mL 10% BSA by combinin... |
null | null | null | dx.doi.org/10.17504/protocols.io.mwec7be | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>MASAM MASAM is a useful tool discerning between memories of self-experienced real - life events and fabricated or fictitious accounts.<br />The theoretical framework of MASAM are four assumptions. First, it is necessary to consider the fact that in each statement, truthful an... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.pgudjww | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Modified from one of the methods tested by Cox et al. 2009</p>
[STEPS]
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.g78bzrw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div title="Page 4">
<div>
<div>
<p>This collection contains protocols that explains how to use serial dilutions of sample protein to determine the linear ranges of detection for a target and internal loading control, and choose an appropriate amount of sample to load for QWB an... | [] |
64,519 | POSTDRAFTED FOR SHARING | 1 | null | https://www.protocols.io/view/postdrafted-for-sharing-ca9fsh3n | rober | TITLE: POSTDRAFTED FOR SHARING
AUTHORS: rober
[DESCRIPTION]
Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Integer imperdiet lectus quis justo. Aliquam ornare wisi eu metus. In laoreet, magna id viverra tincidunt, sem odio bibendum justo, vel imperdiet sapien wisi sed libero. In dapibus augue non sapien. ... | ["Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Integer imperdiet lectus quis justo. Aliquam ornare wisi eu metus. In laoreet, magna id viverra tincidunt, sem odio bibendum justo, vel imperdiet sapien wisi sed libero. In dapibus augue non sapien. Quisque tincidunt scelerisque libero. Etiam bibendum elit ege... |
38,526 | RNA extraction from Sterivex using phenol:chloroform | 4 | dx.doi.org/10.17504/protocols.io.bhu6j6ze | https://www.protocols.io/view/rna-extraction-from-sterivex-using-phenol-chlorofo-bhu6j6ze | Helena Pound, Steven Wilhelm | TITLE: RNA extraction from Sterivex using phenol:chloroform
AUTHORS: Helena Pound, Steven Wilhelm
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This extraction protocol uses bead-beating techniques within the Sterivex to dislodge biomass from the Sterivex filter. Biomass in solution is the... | ["[RNA extraction]\nRemove luer-lock cap from Sterivex and carefully pour beads from Bashing Bead Lysis tube into the Sterivex", "[RNA extraction]\nAdd 700 µL of solution A to Sterivex.", "[RNA extraction]\nReplace luer-lock cap and vortex for 20 min.", "[RNA extraction]\nReturn Sterivex to ice, luer-lock side down to ... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.