id float64 1.55k 110k ⌀ | title stringlengths 1 256 ⌀ | template_id float64 0 6 ⌀ | doi stringlengths 39 49 ⌀ | url stringlengths 40 92 ⌀ | authors stringlengths 1 933 ⌀ | protocol_text stringlengths 34 1.08M | steps_list stringlengths 2 269k |
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95,843 | General Media Recipes: WA, PDA, LB, CMA, V8 | 4 | null | https://www.protocols.io/view/general-media-recipes-wa-pda-lb-cma-v8-c9ubz6sn | rebecca.bennett, Nimalka Weerasuriya | TITLE: General Media Recipes: WA, PDA, LB, CMA, V8
AUTHORS: rebecca.bennett, Nimalka Weerasuriya
[DESCRIPTION]
These are current general media recipes for (acidified) water agar, (acidified) potato dextrose agar, LB broth, cornmeal agar, and clarified V8 juice agar.
[BEFORE_START]
Prepare the following:
Turn on wate... | ["[Making Media] Select media types from below:", "[Preparation] Autoclave liquid setting for 20 minutes to sterilize.", "[Preparation] Add stir bar and stir contents well. \nPlace a loose orange cap. Label cap with autoclave tape (1.5% WA) and date.", "[Preparation] Water Agar preparation:\n \n500 mL ~ 1.5 sleeves of ... |
49,232 | Stone Tools Illustrations with Vector Art: The 'STIVA' Method | 1 | dx.doi.org/10.17504/protocols.io.bubqnsmw | https://www.protocols.io/view/stone-tools-illustrations-with-vector-art-the-39-s-bubqnsmw | Jacopo Niccolo Cerasoni | TITLE: Stone Tools Illustrations with Vector Art: The 'STIVA' Method
AUTHORS: Jacopo Niccolo Cerasoni
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">Lithic illustrations are often used in scientific publications to efficiently communicate the... | ["[Photograph Artefact]\nLock camera on a tripod (ideally use a macro lens with a focal length of between 90mm to 105mm) and place in light box (if available).", "[Photograph Artefact]\nPlace artefact flat onto the workspace.", "[Photograph Artefact]\nIf the artefact does not sit flat due to its irregular shape, use an... |
82,289 | Whole Brain Embedding for SmartSPIM - EasyIndex with 2% Agarose | 1 | dx.doi.org/10.17504/protocols.io.3byl4jpn8lo5/v1 | https://www.protocols.io/view/whole-brain-embedding-for-smartspim-easyindex-with-cukrwuv6 | Holly Myers, Daphne Toglia | TITLE: Whole Brain Embedding for SmartSPIM - EasyIndex with 2% Agarose
AUTHORS: Holly Myers, Daphne Toglia
[DESCRIPTION]
This modified LifeCanvas embedding protocol is intended to prepare cleared mouse brains for imaging on the SmartSPIM (see Imaging cleared mouse brains on SmartSPIM). It details mixing and degassing ... | ["[Setup] Preheat the water bath to 90 °C and preheat the vacuum oven to 80 °C Preheating typically takes 60 min .", "[De-gas agarose solution in vacuum oven] Remove glass vial of homogenized agarose solution from water bath, uncap vial, and place in the vacuum oven preheated to 80 °C", "De-gas the agarose solution us... |
null | null | null | dx.doi.org/10.17504/protocols.io.dc52y5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Minimal growth medium for fission yeast. Very useful when performing transformations and needing to create dropout media. This protocol creates medium that yeast can grow on natively. To create dropout medium, simply omit whichever amino acid you are using as a marker.
[S... | [] |
23,887 | Neuropathy Phentoyping Protocols - Cryoembedding | null | dx.doi.org/10.17504/protocols.io.3jpgkmn | null | Eva Feldman | TITLE: Neuropathy Phentoyping Protocols - Cryoembedding
AUTHORS: Eva Feldman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block"><span style = "font-weight:bold;">Phenotyping of Rodents for the Presence of Diabetic Neuropat... | ["Procedure: Fixed Tissue 1. Following fixation (immersion or perfusion), rinse tissue in phosphate buffer (PB, 0.1M, pH 7.3) containing 5, 10, and 20% sucrose for 24 hours per step or until the tissue \"sinks” to the bottom of the container or tube. The final sucrose concentration in the tissue may vary from 5-30% dep... |
58,488 | Midbrain-like Organoids generation from hiPSCs | 4 | dx.doi.org/10.17504/protocols.io.5qpvobr8xl4o/v1 | https://www.protocols.io/view/midbrain-like-organoids-generation-from-hipscs-b5cyq2xw | Hariam Raji, michela.deleidi | TITLE: Midbrain-like Organoids generation from hiPSCs
AUTHORS: Hariam Raji, michela.deleidi
[DESCRIPTION]
In this protocol we describe the differentiation of human induced pluripotent stem cells (hiPSCs) into human midbrain-like organoids (hMLOs). This protocol has been developed based from several published protocols... | ["[Day 0] Dissociate iPSC colonies to single cells with Accutase for 7 min at 37 °C.", "[Day 0] Re-suspend cells in day0 medium and plate 8.000 cells/well in 96-Wells Plate U-round-Bottom Low Attachment.", "[Day 4] Carefully exchange the medium, without touching the EBs.", "[Day 7: Matrigel embedding] Dilute Matrigel i... |
33,534 | DNA extraction protocol for the eastern banjo frog using the Gentra Puregene Tissue Kit | 1 | dx.doi.org/10.17504/protocols.io.bcy6ixze | https://www.protocols.io/view/dna-extraction-protocol-for-the-eastern-banjo-frog-bcy6ixze | Qiye Li, Qunfei Guo, Yang Zhou, Huishuang Tan, Terry Bertozzi, Yuanzhen Zhu, Ji Li, Stephen Donnellan, Guojie Zhang | TITLE: DNA extraction protocol for the eastern banjo frog using the Gentra Puregene Tissue Kit
AUTHORS: Qiye Li, Qunfei Guo, Yang Zhou, Huishuang Tan, Terry Bertozzi, Yuanzhen Zhu, Ji Li, Stephen Donnellan, Guojie Zhang
[DESCRIPTION]
Genomic DNA was extracted from the liver of an adult female Limnodynastes dumerilii d... | [". \n20 s \n5 min", "-20 °C \n120 min", "Room temperature \n60 min", "The following protocol is a modification of the protocol for \"DNA purification from 5-10mg fresh or frozen solid tissue\" using the Gentra Puregene Genomic DNA Purification Kit. \n\nThe amounts listed in this protocol are for a single extraction. ... |
70,342 | Fluorescent false neurotransmitter (FFN) live-cell DAT imaging | 1 | dx.doi.org/10.17504/protocols.io.36wgqj55xvk5/v1 | https://www.protocols.io/view/fluorescent-false-neurotransmitter-ffn-live-cell-d-cgxetxje | gurvir.virdi | TITLE: Fluorescent false neurotransmitter (FFN) live-cell DAT imaging
AUTHORS: gurvir.virdi
[DESCRIPTION]
This protocol describes how to measure the rate of uptake of FFN102, a fluorescent DAT substrate inside midbrain dopaminergic neurons.
[STEPS]
1. To measure the presence and activity of the DAT, we utilised the ... | ["To measure the presence and activity of the DAT, we utilised the commercially available fluorescent DAT and VMAT2 substrate FFN102 (Abcam, ab120866).", "To measure the uptake of the FFN102 dye, a field of view was first found using the brightfield settings on a Zeiss LSM 880 confocal microscope.", "Cells were washed ... |
105,004 | HMW gDNA purification and ONT ultra-long-read data generation | 1 | dx.doi.org/10.17504/protocols.io.81wgbpnrnvpk/v4 | https://www.protocols.io/view/hmw-gdna-purification-and-ont-ultra-long-read-data-disk4ecw | Glennis Logsdon, Shu-Cheng Chuang | TITLE: HMW gDNA purification and ONT ultra-long-read data generation
AUTHORS: Glennis Logsdon, Shu-Cheng Chuang
[DESCRIPTION]
This protocol describes the purification of high-molecular-weight genomic DNA from mammalian cells and the generation of ultra-long (N50 >100 kbp) Oxford Nanopore data using the PromethION. It ... | ["[Cell collection and lysis] Freeze down ~2 x 10^7 cells as a cell pellet, and store at -80°C.", "[Cell collection and lysis] When you are ready to purify the DNA, thaw the cell pellet on ice (usually takes ~30 mins).", "[Cell collection and lysis] While the cells are thawing, add RNase A to the lysis buffer at a fina... |
50,167 | Overall survival of non-small cell lung cancer with spinal metastasis: a protocol for systematic review | 1 | dx.doi.org/10.17504/protocols.io.bu8xnzxn | https://www.protocols.io/view/overall-survival-of-non-small-cell-lung-cancer-wit-bu8xnzxn | Chung Liang Chai, Fon-yih Tsuang, Jin Pyeong Jeon | TITLE: Overall survival of non-small cell lung cancer with spinal metastasis: a protocol for systematic review
AUTHORS: Chung Liang Chai, Fon-yih Tsuang, Jin Pyeong Jeon
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Our study aimed at deriving a summary survival curve in the population of non-sm... | ["Review TitleOverall survival of non-small cell lung cancer with spinal metastasis: a systematic review and meta-analysis", "Anticipated or actual start date07 June 2021", "Anticipated completion date31 August 2021", "Stage of review at time of this submissionPreliminary searchesYesNoPiloting of the study selection pr... |
30,349 | Protocol for a reproducible circRNA analysis using Docker4Circ | null | dx.doi.org/10.17504/protocols.io.9vmh646 | null | Giulio Ferrero, Nicola Licheri, Lucia Coscujuela Tarrero, Carlo De Intinis, Valentina Miano, Raffaele Adolfo Calogero, Francesca Cordero, Marco Beccuti, Michele De Bortoli | TITLE: Protocol for a reproducible circRNA analysis using Docker4Circ
AUTHORS: Giulio Ferrero, Nicola Licheri, Lucia Coscujuela Tarrero, Carlo De Intinis, Valentina Miano, Raffaele Adolfo Calogero, Francesca Cordero, Marco Beccuti, Michele De Bortoli
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">D... | ["[Softwares and datasets preparation]\nInstallation of the docker4seq R package.In the R environment digit the following command to install and run the docker4seq pipeline", "[Softwares and datasets preparation]\nCreation of the analysis folders.Before running the analyses, create the following directories in the work... |
65,907 | Multi-scale optimization of fermentation process | 4 | null | https://www.protocols.io/view/multi-scale-optimization-of-fermentation-process-ccktsuwn | BOC Sciences | TITLE: Multi-scale optimization of fermentation process
AUTHORS: BOC Sciences
[DESCRIPTION]
Combining fermentation and organic synthesis capabilities, BOC Sciences supports scale-up process from the early stages through commercial production. It provides services for strain development, process optimization, and... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.mr9c596 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
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?.
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43,136 | Protcol 3: Design on Genious Prime | 5 | null | https://www.protocols.io/view/protcol-3-design-on-genious-prime-bnc8mazw | TITLE: Protcol 3: Design on Genious Prime
AUTHORS:
[STEPS]
?. [Manual Primer entry]
Insert desired sequenceGo to file -> New -> Sequence. This will direct you to the new sequence window. From this window, you will be able to enter the sequence manually. You will be asked what type of sequence it is that you are desi... | ["[Manual Primer entry]\nInsert desired sequenceGo to file -> New -> Sequence. This will direct you to the new sequence window. From this window, you will be able to enter the sequence manually. You will be asked what type of sequence it is that you are designing. Press the dropdown menu and select the option for prime... | |
65,051 | BAF_Protocol_001 In-gel Digestion | 1 | dx.doi.org/10.17504/protocols.io.14egn7r5mv5d/v1 | https://www.protocols.io/view/baf-protocol-001-in-gel-digestion-cbr3sm8n | nesf | TITLE: BAF_Protocol_001 In-gel Digestion
AUTHORS: nesf
[DESCRIPTION]
This protocol is for in-gel digestion of proteins, including large mixtures, to produce peptides for mass spectrometry analysis. The gel method can be useful for getting rid of detergents or small molecules that might interfere with minimal loss. The... | ["[DAY 1:] Cut gel band into small pieces (~2 mm).", "[DAY 1:] Add the pieces in a pre-cleaned 1.5 mL polypropylene tube.", "[DAY 1:] Destain the pieces in 0.5 mL destain solution for ~2hrs.", "[DAY 1:] Remove destain (using 1 gel load tip for all tubes in batch) and replace with 0.5 mL destain solution for 30min. It’s... |
null | null | null | dx.doi.org/10.17504/protocols.io.cqrvv5 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?. | [] |
93,168 | Stringency wash buffer | 3 | dx.doi.org/10.17504/protocols.io.kqdg3xndeg25/v1 | https://www.protocols.io/view/stringency-wash-buffer-c68qzhvw | Anna Schmidt, Sarah Nagel, Matthias Meyer | TITLE: Stringency wash buffer
AUTHORS: Anna Schmidt, Sarah Nagel, Matthias Meyer
[DESCRIPTION]
Protocol for the preparation of Stringency wash buffer for automated single-stranded DNA library preparation using the ssDNA2.0 method (Gansauge et al. 2020).
References
Gansauge, M.-T., Aximu-Petri, A., Nagel, S., & Meyer,... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ezqbf5w | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p><strong>Reagent List:</strong></p>
<ul>
<li>Sterile PBS</li>
<li>Cell culture medium (RPMI 1640 supplemented with 10% FBS)</li>
<li>Sterile plastic petri dishes</li>
<li>Sterile T-75 culture flask</li>
<li>RBC Lysis Buffer (Cat. No. 420301)</li>
<li>Concanavalin A (Con A) (Sig... | [] |
29,024 | MoClo reaction | null | dx.doi.org/10.17504/protocols.io.8j8hurw | null | Laura Sánchez | TITLE: MoClo reaction
AUTHORS: Laura Sánchez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Molecular cloning system </div></div>
[STEPS]
?. Fill in Setup Sheet (tab below)
?. Dilutions for Parts and Destination VectorsFollow instructions on "Dilutions_PRINT" sheetIf dilutions are already done, sk... | ["Fill in Setup Sheet (tab below)", "Dilutions for Parts and Destination VectorsFollow instructions on \"Dilutions_PRINT\" sheetIf dilutions are already done, skip to \"Reaction Set-up\" below.", "Reaction Set-up", "Turn on PCR machineThaw DNA samplesThaw 10x NEB ligase buffer on ice", "___ uL of each part___ uL desti... |
48,574 | Mixotrophy - Quantification of the percent of phytoplankton cells with preys (e.g. fluorescent microspheres or fluorescently labeled bacteria) | 1 | dx.doi.org/10.17504/protocols.io.rm7vz3oj4gx1/v1 | https://www.protocols.io/view/mixotrophy-quantification-of-the-percent-of-phytop-btn6nmhe | Valeria Jimenez | TITLE: Mixotrophy - Quantification of the percent of phytoplankton cells with preys (e.g. fluorescent microspheres or fluorescently labeled bacteria)
AUTHORS: Valeria Jimenez
[DESCRIPTION]
This methodology describes a protocol modified from Sherr and Sherr (1993) to determine phytoplankton prey uptake using flow cytom... | ["[Experiment Set up and Fixation] Prepare your prey (YG-beads or FLBs) stock solution. Vortex vigorously and sonicate the solution for ~60 seconds.", "[Experiment Set up and Fixation] Take the phytoplankton flasks under different culture conditions (e.g. phytoplankton incubated in the dark and under nutrient limitatio... |
null | null | null | dx.doi.org/10.17504/protocols.io.pvbdn2n | null | null | TITLE: No Title
AUTHORS:
[STEPS]
SECTION: Prepare the nucleic acid samples
?.
SECTION: Prepare the nucleic acid samples
?.
SECTION: Prepare the nucleic acid samples
?.
SECTION: Assay design and chip ordering by Thermo Fisher
?.
SECTION: Perform the Quant Studio™ 12K Flex system
?.
SECTION: Perform the Quant Stud... | ["[Prepare the nucleic acid samples] Extract high-molecular-weight genomic DNA was from 2 ml venous blood using the QuickGene 610L Automatic DNA/RNA Extraction System (Fijifilm, Tokyo, Japan).", "[Prepare the nucleic acid samples] The quantitative detection of gDNA by NanoDrop 8000, the ratio of ultraviolet (UV) spectr... |
97,832 | Automated BioID sample preparation | 0 | dx.doi.org/10.17504/protocols.io.kxygxymdwl8j/v1 | https://www.protocols.io/view/automated-bioid-sample-preparation-dbsg2nbw | 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... |
88,855 | Lifeplan Camera Trapping Protocol | 1 | null | https://www.protocols.io/view/lifeplan-camera-trapping-protocol-c2zxyf7n | Hanna M.K. Rogers, Gaia Giedre Banelyte, Arielle M Farrell, Bess Hardwick, Tommi Mononen, Deirdre Kerdraon | TITLE: Lifeplan Camera Trapping Protocol
AUTHORS: Hanna M.K. Rogers, Gaia Giedre Banelyte, Arielle M Farrell, Bess Hardwick, Tommi Mononen, Deirdre Kerdraon
[DESCRIPTION]
Lifeplan is a global biodiversity monitoring project with the aim of assessing the current state of biodiversity worldwide, and using this knowledge... | ["[Preparations]", "[Preparations] Preparing equipment\n\n\n•\tLabel cameras with QR codes on the inside. Choose stickers marked “urban” or “natural” depending on which place you are sampling in the first year.\n\n•\tLabel SD cards with QR codes\n\n\n•\tCheck camera ID and change the Night Mode setting:\n\no\tInsert 6 ... |
95,857 | PERTURB SEQ PROTOCOL FOR EARLY POST-MITOTIC DOPAMINERGIC NEURONS | 0 | null | https://www.protocols.io/view/perturb-seq-protocol-for-early-post-mitotic-dopami-c9urz6v6 | Renuka Ravi Gupta, n.farbehi, hendersa, Vikram Khurana, Gist Croft, Lorenz Studer, Joseph Powell | TITLE: PERTURB SEQ PROTOCOL FOR EARLY POST-MITOTIC DOPAMINERGIC NEURONS
AUTHORS: Renuka Ravi Gupta, n.farbehi, hendersa, Vikram Khurana, Gist Croft, Lorenz Studer, Joseph Powell
[DESCRIPTION]
We have developed a protocol where genetic perturbations via CRISPRi machinery are introduced into early post mitotic dopaminer... | ["[Day -1: Coating wells with Poly - L ornithine(PO)] Coat 500 ul per well in a 48-well plate with 15 ug/ml PO in DPBS.", "[Day -1: Coating wells with Poly - L ornithine(PO)] Incubate the plate overnight at 37ºC with 5% CO2 and 20.9% O2.", "[Day 0: Coating wells with Laminin and Fibronectin] Thaw Fibronectin and Lamini... |
20,906 | MRI and Biomarkers in Prostate Cancer (Multi-IMPROD) | null | dx.doi.org/10.17504/protocols.io.ynifvce | null | Ivan Jambor | TITLE: MRI and Biomarkers in Prostate Cancer (Multi-IMPROD)
AUTHORS: Ivan Jambor
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>MULTI-IMPROD clinical trial (</span><a style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">ClinicalTrials.gov Identifier NCT02241122</s... | [] |
76,506 | CUT & RUN | 4 | dx.doi.org/10.17504/protocols.io.261ge32b7l47/v1 | https://www.protocols.io/view/cut-amp-run-cnx2vfqe | Yunkyeong Lee | TITLE: CUT & RUN
AUTHORS: Yunkyeong Lee
[DESCRIPTION]
CUT & RUN protocol
[STEPS]
1. EpiCypher CUTANATM ChIC/CUT&RUN kit (Kit Version 2.0, User Manual Version 2.1)
Catalog No. 14-1048, 48 ChIC/CUT&RUN samples
Overview of the CUTANA CUT&RUN protocol
1. Immobilize & permeabilize cells (or nuclei)
2. Add antibody... | ["EpiCypher CUTANATM ChIC/CUT&RUN kit (Kit Version 2.0, User Manual Version 2.1)\nCatalog No. 14-1048, 48 ChIC/CUT&RUN samples\n\n\nOverview of the CUTANA CUT&RUN protocol\n\n\n1. Immobilize & permeabilize cells (or nuclei)\n2. Add antibody to histone PTM or chromatin-interacting protein\n3. Add & activate pAG-MNase to... |
80,978 | Preparation of Proteins from Whole Body Larval Zebrafish Tissue for Proteomics | 4 | dx.doi.org/10.17504/protocols.io.36wgqj843vk5/v1 | https://www.protocols.io/view/preparation-of-proteins-from-whole-body-larval-zeb-ctbswine | Abigail Henke | TITLE: Preparation of Proteins from Whole Body Larval Zebrafish Tissue for Proteomics
AUTHORS: Abigail Henke
[DESCRIPTION]
This protocol describes the steps needed to prepare proteins from whole body larval zebrafish tissue for bottom-up shotgun proteomics via high resolution liquid chromatography mass spectrometry. ... | ["[Solution Preparation For Protein Extraction Steps] Phosphate Buffered Saline (PBS, 1X, 1L)\nObtain a clean 1L glass media bottle, 1000mL graduated cylinder, sodium chloride (NaCl), potassium chloride (KCl), disodium phosphate (Na2HPO4), potassium phosphate (KH2PO4), a mass balance capable handling milligram scale m... |
61,546 | The role of mutuals in social protection policies: innovative experiences around the world | 3 | dx.doi.org/10.17504/protocols.io.x54v9y1x1g3e/v1 | https://www.protocols.io/view/the-role-of-mutuals-in-social-protection-policies-b8cirsue | Marietou Niang, Émilie Gélinas, Oumar Mallé Samb, Valery Ridde | TITLE: The role of mutuals in social protection policies: innovative experiences around the world
AUTHORS: Marietou Niang, Émilie Gélinas, Oumar Mallé Samb, Valery Ridde
[DESCRIPTION]
The objective of this scoping review is to produce a state of knowledge on the experiences of countries that have used community-ba... | [] |
45,273 | Easy Covid LAMP | 4 | dx.doi.org/10.17504/protocols.io.bqfzmtp6 | https://www.protocols.io/view/easy-covid-lamp-bqfzmtp6 | ahmet , ayten | TITLE: Easy Covid LAMP
AUTHORS: ahmet , ayten
[STEPS]
?. Collect sample into 1.5ml eppendorf tube.
?. Insert sample transfer plastic into the sample tube, mix for 5 seconds, then insert into pre-filled 0.2ml master mix PCR tube, mix for 5 seconds, discard.
?. Place PCR tube on the pre-heated heat block device and run... | ["Collect sample into 1.5ml eppendorf tube.", "Insert sample transfer plastic into the sample tube, mix for 5 seconds, then insert into pre-filled 0.2ml master mix PCR tube, mix for 5 seconds, discard.", "Place PCR tube on the pre-heated heat block device and run .\n[(Heat block is pre-set)]", "Check the color of the P... |
60,886 | C. elegans worm size measurement | 4 | dx.doi.org/10.17504/protocols.io.e6nvwke4wvmk/v1 | https://www.protocols.io/view/c-elegans-worm-size-measurement-b7pwrmpe | Laura Breimann | TITLE: C. elegans worm size measurement
AUTHORS: Laura Breimann
[DESCRIPTION]
Protocol to detect the size (length + width) of worms using a stereoscope and a camera.
The protocol was used in the publication:
[STEPS]
SECTION: Preparing worms for imaging
1. Select worm line(s) and prepare the worms for size mea... | ["[Preparing worms for imaging] Select worm line(s) and prepare the worms for size measurement.", "[Imaging worms] Use a microscope calibration ruler and take an image with the same settings. This will allow you later to give the results a unit.\n\n \n\nMicroscope calibration rulers can be found here.", "[Imaging worm... |
45,715 | How to Determine Isoelectric Point | 4 | null | https://www.protocols.io/view/how-to-determine-isoelectric-point-bqvtmw6n | 181830691 | TITLE: How to Determine Isoelectric Point
AUTHORS: 181830691
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Isoelectric Point, the pH of a molecule without charge on its surface, is mentioned for things that are charged, including but not limited to amphoteric electrolytes, such as amino acids and... | [] |
69,104 | Applied GPU Computing in Computational Biology to Study Disparate Multicellularity Scenarios | 3 | dx.doi.org/10.17504/protocols.io.3byl47z2zlo5/v2 | https://www.protocols.io/view/applied-gpu-computing-in-computational-biology-to-cfqqtmvw | Avimanyu Bandyopadhyay | TITLE: Applied GPU Computing in Computational Biology to Study Disparate Multicellularity Scenarios
AUTHORS: Avimanyu Bandyopadhyay
[DESCRIPTION]
A prethesis in partial fulfilment for a PhD in Bioinformatics at Heritage Institute of Technology under Maulana Abul Kalam Azad University of Technology (formerly West Benga... | ["{\"blocks\":null,\"entityMap\":null}"] |
null | null | null | dx.doi.org/10.17504/protocols.io.e86bhze | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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55,172 | Surgical versus non-surgical treatment for thoracolumbar burst fractures without neurological deficit: A systematic review and meta-analysis | 1 | dx.doi.org/10.17504/protocols.io.bz5cp82w | https://www.protocols.io/view/surgical-versus-non-surgical-treatment-for-thoraco-bz5cp82w | Tzu-Yi Chou, Fon-yih Tsuang, Chung Liang Chai | TITLE: Surgical versus non-surgical treatment for thoracolumbar burst fractures without neurological deficit: A systematic review and meta-analysis
AUTHORS: Tzu-Yi Chou, Fon-yih Tsuang, Chung Liang Chai
[DESCRIPTION]
The aim of this systematic review is to compare the outcomes of burst fracture between non-operativ... | ["Review Title\n\nSurgical versus non-surgical treatment for thoracolumbar burst fractures without neurological deficit: A systematic review and meta-analysis", "Anticipated or actual start date\n\n16 November 2021", "Anticipated completion date\n\n31 January 2022", "Review team members and their organisational affilia... |
68,423 | Examples of protocols on protocols.io from different disciplines | 1 | dx.doi.org/10.17504/protocols.io.4r3l2odzpv1y/v2 | https://www.protocols.io/view/examples-of-protocols-on-protocols-io-from-differe-ce3ftgjn | protocols.io team | TITLE: Examples of protocols on protocols.io from different disciplines
AUTHORS: protocols.io team
[DESCRIPTION]
We warmly welcome all research methods. While the origin of the platform was more biology/wetlab, we expanded to support all fields when we partnered with PLOS ONE in 2017.
There is now a diverse spectrum ... | ["[Molecular Biology] Micropatterning EM grids for cryo-electron tomography of cells\nEngineering brain assembloids to interrogate human neural circuits\nHigh quality DNA from Fungi for long read sequencing e.g. PacBio V.11\nmcSCRB-seq protocol V.2\nMonkeypox virus multiplexed PCR amplicon sequencing (PrimalSeq) V.2. ... |
107,158 | SOD2 and human alpha-synuclein immunofluorescence staining | 0 | dx.doi.org/10.17504/protocols.io.6qpvr8zxblmk/v1 | https://www.protocols.io/view/sod2-and-human-alpha-synuclein-immunofluorescence-dkvw4w7e | Pietro La Vitola | TITLE: SOD2 and human alpha-synuclein immunofluorescence staining
AUTHORS: Pietro La Vitola
[DESCRIPTION]
This protocol is designed for SOD2 and human alpha-synuclein staining using the anti-SOD2 (RRID:AB_2636921) and MJFR1-Alexa 488 (RRID:AB_2537217) antibodies. Tissue stained with this protocol include 35 μm free-fl... | ["[Day 1] Rinse brain slices (35µ) in TBS (0.05M Trizma base and 0.15M NaCl; pH: 7.6) 3X 10 min", "[Day 1] Quench brain slices in a solution containing 3%H2O2 and 10% Methanol in TBS 20 min", "[Day 1] Rinse brain slices in TBS (0.05M Trizma base and 0.15M NaCl; pH: 7.6) 3X 10 min", "[Day 1] Incubate in blocking buffer ... |
98,231 | Histology Protocol | 0 | dx.doi.org/10.17504/protocols.io.q26g71bdqgwz/v1 | https://www.protocols.io/view/histology-protocol-db6x2rfn | Sasha Burwell | TITLE: Histology Protocol
AUTHORS: Sasha Burwell
[DESCRIPTION]
This protocol details the histological processing of a mouse brain.
[STEPS]
SECTION: Histology Pro31hocol
1. Prepare 4% paraformaldehyde in 0.1 Molarity (M) PB, and pH 7.4. Let chill to 4 °C.
SECTION: Histology Pro31hocol
2. Deeply anesthetize mouse with... | ["[Histology Pro31hocol] Prepare 4% paraformaldehyde in 0.1 Molarity (M) PB, and pH 7.4. Let chill to 4 °C.", "[Histology Pro31hocol] Deeply anesthetize mouse with isofluorane until completely under (no toe pinch response, low to no breathing).", "[Histology Pro31hocol] If the mouse has an electrode bundle implanted, q... |
71,213 | ONT Basecalling, Demultiplexing, and Analysis for Fungal Barcodes | 5 | dx.doi.org/10.17504/protocols.io.dm6gpbm88lzp/v2 | https://www.protocols.io/view/ont-basecalling-demultiplexing-and-analysis-for-fu-chsmt6c6 | Stephen Douglas Russell | TITLE: ONT Basecalling, Demultiplexing, and Analysis for Fungal Barcodes
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
This protocol assumes that your MinION run has been completed and the data from the run has been saved. It should take you from raw data to useable FASTA files containing consensus sequences fo... | ["[Initial Post-Run Preparation] This protocol assumes the experiment name is \"FirstRun.\"\n\nCreate a new working folder on the desktop. Ex - FirstRun. Within that create a new folder called \"fast5,\" another called \"Programs,\" and a final one called \"NGSpeciesID.\"\n\nI will start by copying all of the fast5 fil... |
21,190 | Vandy - Hyperglycemic clamp | null | dx.doi.org/10.17504/protocols.io.yxefxje | null | Li Kang | TITLE: Vandy - Hyperglycemic clamp
AUTHORS: Li Kang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">
Mice with catheters implanted in the jugular vein (infusions) and carotid artery (sampling) are used for this procedur... | ["Surgical catheterization of the carotid artery and jugular vein in mice at least 5 days prior to the day of the study (refer to protocol for Surgical Catheterization of the Carotid Artery and Jugular Vein).", "Weigh mouse and start fast (suggested starting time between 7:00 and 8:00 AM) by placing mouse in a plastic ... |
98,285 | In vitro preparation of single filamentous microtubules optimized for dynamic and electrophoretic light scattering measurements. | 0 | dx.doi.org/10.17504/protocols.io.dm6gpzrqjlzp/v1 | https://www.protocols.io/view/in-vitro-preparation-of-single-filamentous-microtu-db8m2ru6 | Annitta George, Ernesto Alva, Lorenzo Brancaleon, Marcelo Marucho | TITLE: In vitro preparation of single filamentous microtubules optimized for dynamic and electrophoretic light scattering measurements.
AUTHORS: Annitta George, Ernesto Alva, Lorenzo Brancaleon, Marcelo Marucho
[DESCRIPTION]
The lack of essential information on sample preparation and the need to characterize and under... | ["[First-day procedure: Stock preparations]", "[First-day procedure: Stock preparations] 100 mM PIPES:\n\nAdd 302.4 mg of PIPES to a 15 mL polypropylene centrifuge tube.", "[First-day procedure: Stock preparations] Add 13-15 drops of 5 Molarity (M) KOH solution to the tube.", "[First-day procedure: Stock preparations] ... |
71,728 | 城市微生物相調查計畫—採集土壤教學 | 1 | dx.doi.org/10.17504/protocols.io.n92ldpyj9l5b/v2 | https://www.protocols.io/view/protocol-ciaquadw | Hsin-Mao Wu | TITLE: 城市微生物相調查計畫—採集土壤教學
AUTHORS: Hsin-Mao Wu
[DESCRIPTION]
吳昕懋
[STEPS]
SECTION: 採土與iNaturalist紀錄教學
1. 移除表土，取距離土表5~7公分之處的土，裝入塑膠夾鏈袋中
SECTION: 採土與iNaturalist紀錄教學
2. 將塑膠袋中的土均勻混合，倒入採集罐之中
SECTION: 採土與iNaturalist紀錄教學
3. 在採集紀錄紙上勾選採樣地點、採樣種類，以及填寫日期、城市、鄉鎮、地點、採集者等資訊
SECTION: 採土與iNaturalist紀錄教學
4. 最後拍兩張照片
... | ["[採土與iNaturalist紀錄教學] 移除表土，取距離土表5~7公分之處的土，裝入塑膠夾鏈袋中", "[採土與iNaturalist紀錄教學] 將塑膠袋中的土均勻混合，倒入採集罐之中", "[採土與iNaturalist紀錄教學] 在採集紀錄紙上勾選採樣地點、採樣種類，以及填寫日期、城市、鄉鎮、地點、採集者等資訊", "[採土與iNaturalist紀錄教學] 最後拍兩張照片", "[採土與iNaturalist紀錄教學] 接著打開iNaturalist app", "[採土與iNaturalist紀錄教學] 如圖所示，點選右下角的加號", "[採土與iNaturalist紀錄教學] 如下圖所示接著需選擇觀察類型，請點「選擇... |
80,543 | Forage and Range Research Laboratory Standard Operating Procedures (SOP) and Protocols | 1 | dx.doi.org/10.17504/protocols.io.4r3l27jzjg1y/v2 | https://www.protocols.io/view/forage-and-range-research-laboratory-standard-oper-csv7we9n | Blair L Waldron, B Shaun Bushman, Alexander J Hernandez, Kevin B Jensen, Thomas A Jones, Steven R Larson, Thomas A Monaco, Michael D Peel, Matthew D Robbins, Joseph G. Robins, Richard R-C Wang | TITLE: Forage and Range Research Laboratory Standard Operating Procedures (SOP) and Protocols
AUTHORS: Blair L Waldron, B Shaun Bushman, Alexander J Hernandez, Kevin B Jensen, Thomas A Jones, Steven R Larson, Thomas A Monaco, Michael D Peel, Matthew D Robbins, Joseph G. Robins, Richard R-C Wang
[DESCRIPTION]
The Unite... | ["[Breeding Nursery and Plant Trait Measurements] Field Plots/Spaced-Plant\nRandomize plot assignments using a randomized complete block design with three to four complete blocks, unless otherwise specified. Spaced-plant nurseries are comprised of 5 to 10 plants plot-1 and established by hand or mechanically transplant... |
52,690 | Measuring photophysiological traits of diatoms from Rapid Light Curves using a Water-PAM | 4 | dx.doi.org/10.17504/protocols.io.36wgq4zmovk5/v1 | https://www.protocols.io/view/measuring-photophysiological-traits-of-diatoms-fr-bxpspmne | Phoebe Argyle, Jana Hinners, Nathan G. Walworth, Sinead Collins, Naomi M. Levine, Martina A. Doblin | TITLE: Measuring photophysiological traits of diatoms from Rapid Light Curves using a Water-PAM
AUTHORS: Phoebe Argyle, Jana Hinners, Nathan G. Walworth, Sinead Collins, Naomi M. Levine, Martina A. Doblin
[DESCRIPTION]
This is a brief protocol for how to measure ETRmax, alpha (α) and Ik for microalgae cultures using... | ["[Prepare culture] Take a 2 mL aliquot of microalgae culture into a glass cuvette compatible with the WATER-PAM instrument. \n\nWhen the overall culture volume is limited (i.e. <2 mL of culture available for the measurement), take 0.5-1 mL and dilute with sterile seawater to a final volume of 2 mL.\n\nNotes:\n The opt... |
69,998 | In vivo reduction of age-dependent neuromelanin accumulation mitigates features of Parkinson’s disease | 2 | dx.doi.org/10.17504/protocols.io.rm7vzbno2vx1/v1 | https://www.protocols.io/view/in-vivo-reduction-of-age-dependent-neuromelanin-ac-cgkntuve | miquel.vila | TITLE: In vivo reduction of age-dependent neuromelanin accumulation mitigates features of Parkinson’s disease
AUTHORS: miquel.vila
[DESCRIPTION]
Methodological collection for In vivo reduction of age-dependent neuromelanin accumulation mitigates features of Parkinson’s disease
[STEPS] | [] |
46,312 | Nucleic acid precipitation | 4 | null | https://www.protocols.io/view/nucleic-acid-precipitation-brggm3tw | Elizabeth Fozo | TITLE: Nucleic acid precipitation
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Precipitation of nucleic acids</div></div>
[STEPS]
?. [Steps]
Bring volume of reaction/nucleic acid mixture to 200µL with sterile, clean water
?. [Steps]
Add 20µL of 3M sodium acetate (NaOAc), ... | ["[Steps]\nBring volume of reaction/nucleic acid mixture to 200µL with sterile, clean water", "[Steps]\nAdd 20µL of 3M sodium acetate (NaOAc), 1µL glycogen, and 550µL ethanol (99%).", "[Steps]\nPlace in -20°C freezer for approximately 30-60 minutes or store there indefinitely.", "[Steps]\nSpin samples at 4°C, 13000 RPM... |
86,937 | Qaigen RNEasy RNA extration protocol | 4 | dx.doi.org/10.17504/protocols.io.dm6gp337dvzp/v1 | https://www.protocols.io/view/qaigen-rneasy-rna-extration-protocol-cy5zxy76 | Jessica Pardy, Michael Dan Siemon, Dilan Joseph, Justin Donovan, christopher.degroot, Richard Gibson | TITLE: Qaigen RNEasy RNA extration protocol
AUTHORS: Jessica Pardy, Michael Dan Siemon, Dilan Joseph, Justin Donovan, christopher.degroot, Richard Gibson
[DESCRIPTION]
This protocol was employed by Western University for RNA extraction of wastewater samples for wastewater-based epimelogy in London, Ontario, Canada and... | ["[Protocol modified from QIAamp® Viral RNA Mini Handbook] Thoroughly mix wastewater sample then aliquot 40 mL into 50 mL Falcon tube. Centrifuge at 12000 RPM for 90 min. Decant supernatant, assume 280 µl pellet.", "[Protocol modified from QIAamp® Viral RNA Mini Handbook] Pipet 1120 µl prepared Buffer AVL into Falcon t... |
93,169 | ssDNA2.0: Klenow mix | 3 | dx.doi.org/10.17504/protocols.io.ewov1qkbygr2/v1 | https://www.protocols.io/view/ssdna2-0-klenow-mix-c68rzhv6 | Sarah Nagel, Anna Schmidt, Matthias Meyer | TITLE: ssDNA2.0: Klenow mix
AUTHORS: Sarah Nagel, Anna Schmidt, Matthias Meyer
[DESCRIPTION]
Protocol for the preparation of Klenow mix for automated single-stranded DNA library preparation using the ssDNA2.0 method (Gansauge et al. 2020).
References
Gansauge, M.-T., Aximu-Petri, A., Nagel, S., & Meyer, M. (2020). M... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.vqbe5sn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol outline steps to detect Mycobacterium ulcerans from insect samples. Extraction of DNA is conducted by using FastDNA kit.
[STEPS]
?. | [] |
78,000 | Coastal Environmental DNA Sampling & Gravity Filtration Protocol | 1 | null | https://www.protocols.click/view/coastal-environmental-dna-sampling-amp-gravity-fil-cqeqvtdw | Meghan M. Shea | TITLE: Coastal Environmental DNA Sampling & Gravity Filtration Protocol
AUTHORS: Meghan M. Shea
[DESCRIPTION]
This is a protocol for collecting coastal environmental DNA (eDNA) samples and gravity filtering them on site, using a set-up developed by Gold et al. 2021 with single-use enteral feeding pouches.
[STEPS]... | ["[Pre-Sampling Preparation] Sterilize luer lock to hose barb adapters, male-female luer lock caps, and silicone rubber cap", "[Pre-Sampling Preparation] Clean 1000 mL Nalgene bottles (as many as field blanks needed) with a 10% bleach rinse (leave for 10 minutes), then three rinses of DI water", "[Pre-Sampling Preparat... |
103,750 | A method for RNA extraction, cDNA synthesis and and quantitative PCR from NIH-3T3 fibroblasts | 0 | dx.doi.org/10.17504/protocols.io.rm7vzjo84lx1/v1 | https://www.protocols.io/view/a-method-for-rna-extraction-cdna-synthesis-and-and-dhje34je | Sreeja V Nair, Suzanne R Pfeffer | TITLE: A method for RNA extraction, cDNA synthesis and and quantitative PCR from NIH-3T3 fibroblasts
AUTHORS: Sreeja V Nair, Suzanne R Pfeffer
[DESCRIPTION]
Here we describe a protocol for RNA extraction, cDNA synthesis and quantitative PCR from NIH-3T3 fibroblasts. This method has also been used with mouse embryonic... | ["[RNA extraction, cDNA synthesis and and quantitative PCR from NIH-3T3 fibroblasts] RNA extraction", "[RNA extraction, cDNA synthesis and and quantitative PCR from NIH-3T3 fibroblasts] Plate 0.3 X 106 cells NIH-3T3 fibroblasts or MEF cells in individual wells of a 6-well plate.", "[RNA extraction, cDNA synthesis and a... |
48,475 | Chloroform-Methanol Protein Extraction with Bead Beating for Yeast | 1 | dx.doi.org/10.17504/protocols.io.btj3nkqn | https://www.protocols.io/view/chloroform-methanol-protein-extraction-with-bead-b-btj3nkqn | Leanne Chan, Christopher Petzold | TITLE: Chloroform-Methanol Protein Extraction with Bead Beating for Yeast
AUTHORS: Leanne Chan, Christopher Petzold
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We adapted a high-throughput sample preparation workflow for Gram-negative bacteria to work with yeast. It consists of a bead-beating st... | ["[Bead-beating treatment]\nThaw cells at\n0 Room temperature\nNote: If transferring directly from active cultures, omit this step. Adapt as needed for your specific organism and culturing conditions.", "[Bead-beating treatment]\nTransfer 2-4 OD*mLs of cells to 8-Strip PCR tubes (Axygen, Cat.#14-222-251) or a 96-well P... |
41,536 | Practice Protocols for PBI | 4 | dx.doi.org/10.17504/protocols.io.bks8kwhw | https://www.protocols.io/view/practice-protocols-for-pbi-bks8kwhw | Holly Rumery | TITLE: Practice Protocols for PBI
AUTHORS: Holly Rumery
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the steps of a Practice Protocol.</div></div>
[STEPS]
?. [Set 1]
AIf you click the box beside the one, that is the checklist functionality.
[reagent]
?. [Set 1]
B Automa... | ["[Set 1]\nAIf you click the box beside the one, that is the checklist functionality.\n[reagent]", "[Set 1]\nB Automatically turns into a 3 min timer.To create, type 3:00, highlight 3:00, and then select duration component.", "This is used to showcase a sidenote.", "- Insert images or videos by using the tool bar - You... |
90,941 | eDNA extraction from buffer EtOH 100% using DNeasy Blood and Tissue Kit (QIAGEN) | 6 | dx.doi.org/10.17504/protocols.io.3byl4qrojvo5/v1 | https://www.protocols.io/view/edna-extraction-from-buffer-etoh-100-using-dneasy-c425yyg6 | delphine.vanhaecke | TITLE: eDNA extraction from buffer EtOH 100% using DNeasy Blood and Tissue Kit (QIAGEN)
AUTHORS: delphine.vanhaecke
[DESCRIPTION]
This is a protocol for extracting eDNA from the buffer EtOH 100% in which Millipore filters are stored.
[STEPS]
1. Clean the laminar flow hood and micropipettes with DNAZAP (solution 1 an... | ["Clean the laminar flow hood and micropipettes with DNAZAP (solution 1 and 2) and rinse with ddH2O.", "Place disposable gloves, sleeves and 1.5ml sterilized tubes (as many as the number of samples to process + 1 negative extraction control) in the laminar flow hood and submit to UV light for 10 minutes.", "In the mean... |
null | null | null | dx.doi.org/10.17504/protocols.io.mguc3ww | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Background: Natural disasters increase the level population stress, including pregnant women, who can experience prenatal maternal stress, affecting to the fetus and trigger perinatal complications, such as low birth weight, smaller head circumference, etc. However, little is... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.igxcbxn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Please contact Dr. Steven Wilhelm (wilhelm@utk.edu) for additional information regarding this protocol.</p>
[STEPS]
?.
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null | null | null | dx.doi.org/10.17504/protocols.io.hmeb43e | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?. | [] |
80,957 | Archival DNA extraction protocol for insect specimens from museum collections | 4 | dx.doi.org/10.17504/protocols.io.81wgbybqyvpk/v1 | https://www.protocols.io/view/archival-dna-extraction-protocol-for-insect-specim-cta5wig6 | Fernando Lopes | TITLE: Archival DNA extraction protocol for insect specimens from museum collections
AUTHORS: Fernando Lopes
[DESCRIPTION]
This protocol can be used to dry specimens from natural history collections to obtain DNA for UCE-seq.
[BEFORE_START]
The protocol can be performed in two days
On the first day, you prepare your ... | ["[Fundamental reading before starting] From museum drawers to a tree: phylogenomics of historical DNA sheds light on the systematics of rare dung beetles (Coleoptera: Scarabaeinae) from museum collections\nAuthors: Fernando Lopes, Nicole Gunter, Giulio Montanaro, Michele Rossini, Federica Losacco,\nConrad P.D.T. Gille... |
93,106 | Collect and Extract Biomass Cyanobacteria (English) | 1 | dx.doi.org/10.17504/protocols.io.261ged18wv47/v1 | https://www.protocols.io/view/collect-and-extract-biomass-cyanobacteria-english-c66szhee | Ricardo M. Borges, Fernanda Chagas | TITLE: Collect and Extract Biomass Cyanobacteria (English)
AUTHORS: Ricardo M. Borges, Fernanda Chagas
[DESCRIPTION]
It is crucial to pay meticulous attention to high-quality materials, including HPLC-grade solvents, pristine microtubes, and never-before-used Eppendorf Quality tips. Stringent quality controls encompas... | ["[Biomass Collection] After 28 days, extract ~80-90% of biomass from each Erlenmeyer flask (quantity determined visually only)\n\nAllow the specimens to grow until a good amount of biomass is formed, with a tentative empirical limit of four months per specimen.\n\nEach specimen will be allowed to continue growing unti... |
null | null | null | dx.doi.org/10.17504/protocols.io.hhdb326 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><span style="color: #000339; font-family: Raleway, sans-serif; font-size: 14px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; w... | [] |
48,528 | Testing and validation of a Patient-Reported Outcome Measure for Older People with frailty and Acute Care needs (PROM-OPAC). | 1 | dx.doi.org/10.17504/protocols.io.btmqnk5w | https://www.protocols.io/view/testing-and-validation-of-a-patient-reported-outco-btmqnk5w | James van Oppen | TITLE: Testing and validation of a Patient-Reported Outcome Measure for Older People with frailty and Acute Care needs (PROM-OPAC).
AUTHORS: James van Oppen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Aim: To refine, validate, and evaluate the early impact of a novel PROM instrument, the Patient... | ["[Preparatory work]\nSemi-structured interviews with 15-30 older people living with frailty with recent experience of UK emergency and acute care.Qualitative analysis using blended approach of framework and comparative methods.Outcome: a framework to define outcome goals for acute healthcare among older people living ... |
95,606 | NGGDPP Collection Metadata Submission Guide | 5 | dx.doi.org/10.17504/protocols.io.6qpvr321bvmk/v2 | https://www.protocols.io/view/nggdpp-collection-metadata-submission-guide-c9kwz4xe | darthur Arthur | TITLE: NGGDPP Collection Metadata Submission Guide
AUTHORS: darthur Arthur
[DESCRIPTION]
The Registry of Scientific Collections (ReSciColl) is a metadata catalog administered by the National Geological and Geophysical Data Preservation Program (NGGDPP). The catalog includes essential metadata describing scientific col... | ["[Contacts - Importing] In mdEditor, Contacts are created and maintained as separate records from metadata records. This enables a contact to be used many times in a single metadata record or across multiple metadata records without requiring a user to reenter the contact's information. Rather than entering a contact'... |
null | null | null | dx.doi.org/10.17504/protocols.io.frkbm4w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Cas9 nuclease may be used <em>in vivo</em> to create targeted genome modifications. There are several ways in which to introduce Cas9-guide RNA complexes into cells. Here we present a method for the introduction of Cas9 RNP’s into HEK293 FT cells using the Thermo Fisher Neo... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.fvabn2e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for cleaning new and old teflon products.</p>
[GUIDELINES]
<p><span class="TextRun SCX158040763" lang="EN-US" style="font-size: 12pt;" xml:lang="EN-US"><span class="NormalTextRun SCX158040763" style="background-color: inherit;">All acid soaking is done HOT but not b... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ihfcb3n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>DNA is extracted from peripheral blood using QIAamp DNA mini kit (Qiagen) in accordance to the blood and body fluid protocol of the user manual supplied with the kit.</p>
[STEPS]
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73,537 | Halo assay to assess mitophagy | 4 | dx.doi.org/10.17504/protocols.io.dm6gpjzm8gzp/v1 | https://www.protocols.io/view/halo-assay-to-assess-mitophagy-cj29uqh6 | nguyen.tha | TITLE: Halo assay to assess mitophagy
AUTHORS: nguyen.tha
[DESCRIPTION]
This protocol describes how to assess mitophagy using Halo assay developed by Mizushima lab (DOI: 10.7554/eLife.78923).
[STEPS]
SECTION: Procedures
1. Generating cells expressing mitochondrially targeted Halo-GFP using pSu9-Halo-mGFP from Mizushi... | ["[Procedures] Generating cells expressing mitochondrially targeted Halo-GFP using pSu9-Halo-mGFP from Mizushima lab (Addgene #184905; DOI: 10.7554/eLife.78923).", "[Procedures] Seed HeLa cells the day before the treatment day in 6 well plates. \nEach well contained 2 mL of growth media; \nSeed 350,000 cells for penta ... |
53,811 | Nucleic acid & protein electrophoresis | 4 | dx.doi.org/10.17504/protocols.io.bystpwen | https://www.protocols.io/view/nucleic-acid-amp-protein-electrophoresis-bystpwen | Shuning Guo | TITLE: Nucleic acid & protein electrophoresis
AUTHORS: Shuning Guo
[DESCRIPTION]
This protocol concludes two types of the electrophoresis used to detect target DNA or protein.
[BEFORE_START]
Prepare 50 x TAE, 1.5 mol/L Tris-Gly (pH 8.8), 1.0 mol/L Tris-Gly (pH 6.8), 5× Tris-Gly electrophoresis solution, coomas... | ["Choose suitable electrophoresis method depends on the type of the sample.", "Weigh appropriate agarose depends on the concentration of the gel (1% agarose gel for detection and 1% or 2% for gel extraction).", "Add 1X TAE to a conical flask. Need to prepare 1X TAE with 50X TAE.", "Heat up by microwave until the soluti... |
58,952 | Overall protocol for top-down LC-MS/MS of human spleen tissue | 1 | dx.doi.org/10.17504/protocols.io.b5tgq6jw | https://www.protocols.io/view/overall-protocol-for-top-down-lc-ms-ms-of-human-sp-b5tgq6jw | Jeannie Camarillo, Bryon Drown, Neil Kelleher | TITLE: Overall protocol for top-down LC-MS/MS of human spleen tissue
AUTHORS: Jeannie Camarillo, Bryon Drown, Neil Kelleher
[DESCRIPTION]
Overview description of the process for acquiring top-down LC-MS/MS data on human spleen tissue
[STEPS]
SECTION: Tissue Collection
1. Spleen tissue was provided by University of... | ["[Tissue Collection] Spleen tissue was provided by University of Florida TMC. Tissue was collected and prepared according to the following:", "[Sample Preparation] Perform LC based Proteomics on adjacent tissue sections:", "[Data Acquisition]", "[Data Analysis]"] |
null | null | null | dx.doi.org/10.17504/protocols.io.h58b89w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a modification of the origianl Chelex 100 extraction described by Walsh, Metzger and Higuchi (1991 BioTechniques 10(4):506). Adding PVPP facilitates working with environmental samples as well as pure cultures hi in phenolics or other contaminants. </p>
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.q78dzrw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol counts the number of pollen and evaluate their maturity by lactophenol blue staining. This protocol is adjusted for the flower of citrus.</p>
[STEPS]
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86,350 | ChAT Immunofluorescent Staining | 1 | dx.doi.org/10.17504/protocols.io.rm7vzxbz4gx1/v1 | https://www.protocols.io/view/chat-immunofluorescent-staining-cyjnxume | Haley Geertsma | TITLE: ChAT Immunofluorescent Staining
AUTHORS: Haley Geertsma
[DESCRIPTION]
This protocol is designed for 3-day choline acetyltransferase (ChAT) staining using the EMD Millipore AB144P (RRID:AB_2079751) antibody. Tissue stained with this protocol include 40μm free-floating mouse brain and spinal cord sections, and 20... | ["[ChAT Immunofluorescent Staining] Wash tissue slices in 1X phosphate buffered saline (PBS) for 5 minutes. Repeat x2.", "[ChAT Immunofluorescent Staining] Incubate in blocking buffer (10% horse serum, 0.5% gelatin, 0.1% triton X-100 in 1X PBS) for 2 hours at room temperature.", "[ChAT Immunofluorescent Staining] Incub... |
80,214 | How the Metaverse will be used to preserve the culture of Tuvalu? | 1 | dx.doi.org/10.17504/protocols.io.e6nvwjyddlmk/v1 | https://www.protocols.io/view/how-the-metaverse-will-be-used-to-preserve-the-cul-csjwwcpe | Kalani Alcala | TITLE: How the Metaverse will be used to preserve the culture of Tuvalu?
AUTHORS: Kalani Alcala
[DESCRIPTION]
To research the preservation of culture and sovereignty into a digital space I will be taking a social science approach. I plan on interviewing key actors, including but not limited to: government officials, t... | ["[Interview Protocol] Find people to interview. To do so, get in contact with community leaders and ask them to spread the word. \n- Make sure to offer compensation for people's time if possible.", "[Interview Protocol] Create a list of questions. \n Tell a story about your favorite childhood memory in Tuvalu\nWalk me... |
62,532 | Brain slicing | 1 | dx.doi.org/10.17504/protocols.io.kxygxzo1ov8j/v1 | https://www.protocols.io/view/brain-slicing-b9bcr2iw | rabdelha | TITLE: Brain slicing
AUTHORS: rabdelha
[DESCRIPTION]
This protocol details brain slicing.
[GUIDELINES]
Vibratome Protocol Notes
Sectioning notes from the literature
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE35723
https://www.cell.com/molecular-therapy-family/nucleic-acids/pdfExtended/S2162-2531(17)30... | ["[Embedding the brain:] Perform a gross coronal cut using the 1 mm matrix at a site either anterior or posterior of the region of interest, ~2mm distal from the region of interest.", "[Embedding the brain:] Dry the flat part of the brain repeatedly on a kimwipe.", "[Embedding the brain:] Place in the plastic square mo... |
46,650 | Adipose depot innervation: whole mount staining, imaging, quantification | 1 | dx.doi.org/10.17504/protocols.io.brs2m6ge | https://www.protocols.io/view/adipose-depot-innervation-whole-mount-staining-ima-brs2m6ge | Jake Willows, Kristy Townsend, Magdalena Blaszkiewicz | TITLE: Adipose depot innervation: whole mount staining, imaging, quantification
AUTHORS: Jake Willows, Kristy Townsend, Magdalena Blaszkiewicz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Abstract</div><div class = "text-block">Little is known about the diversity and function of adipose tissue ne... | ["See attachments under Abstract for PDF copies of protocols."] |
63,771 | NanoString GeoMx DSP TMA-TNP protein assay | 1 | dx.doi.org/10.17504/protocols.io.eq2lyn25pvx9/v1 | https://www.protocols.io/view/nanostring-geomx-dsp-tma-tnp-protein-assay-cah3sb8n | Jinho Lee, Jose Ceja Navarro, Koei Chin, Heidi S Feiler, Christopher Corless | TITLE: NanoString GeoMx DSP TMA-TNP protein assay
AUTHORS: Jinho Lee, Jose Ceja Navarro, Koei Chin, Heidi S Feiler, Christopher Corless
[DESCRIPTION]
This protocol outlines the NanoString GeoMx DSP protein assay that was applied in the Human Tumor Atlas Network (HTAN) Tissue MicroArrary (TMA) -TransNetwork Project (T... | ["[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... |
95,546 | Planktoscope protocol for plankton imaging | 1 | dx.doi.org/10.17504/protocols.io.bp2l6bq3zgqe/v3 | https://www.protocols.io/view/planktoscope-protocol-for-plankton-imaging-c9i2z4ge | Pierre Kostyrka, Lombard Fabien | TITLE: Planktoscope protocol for plankton imaging
AUTHORS: Pierre Kostyrka, Lombard Fabien
[DESCRIPTION]
This protocol is for using PlanktoScope and collecting usable results for quantitative imaging of plankton.
This project has received funding from the European Union’s Horizon 2020 research and innovation programm... | ["[Table of Contents] Table of Contents \nIntroduction \nQuick usage version \nAssemble the PlanktoScope \nUser Interface and initial connexion \nHow to export data \nWhite Balance calibration \nPump calibration \nSize calibration \nGet your sample \nPass the sample on the PlanktoScope \nSegment the Acquisit... |
null | null | null | dx.doi.org/10.17504/protocols.io.jh2cj8e | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
66,329 | ProDentim Rviews - Does It Work or Scam? Read Shocking Side Effects 2022 | 1 | dx.doi.org/10.17504/protocols.io.8epv59qz5g1b/v1 | https://www.protocols.io/view/prodentim-rviews-does-it-work-or-scam-read-shockin-cczzsx76 | prodentim | TITLE: ProDentim Rviews - Does It Work or Scam? Read Shocking Side Effects 2022
AUTHORS: prodentim
[DESCRIPTION]
dental health
[STEPS]
1. ProDentim Dental wellbeing is a significant part of day to day existence. Dealing with your teeth is fundamental. Clinical specialists say that anybody who neglects to clean thei... | ["ProDentim Dental wellbeing is a significant part of day to day existence. Dealing with your teeth is fundamental. Clinical specialists say that anybody who neglects to clean their teeth consistently could have dental issues. This is because of the absence of dental consideration for individuals who have unfortunate o... |
30,834 | True-Nuclear™ Transcription Factor Staining Protocol for 5 mL Tubes | null | dx.doi.org/10.17504/protocols.io.bacsiawe | null | Sam Li | TITLE: True-Nuclear™ Transcription Factor Staining Protocol for 5 mL Tubes
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Perform cell surface staining as described in BioLegend's Cell Surface Immunofluorescence Staining Protocol.
?. Add 1mL of the True-Nuclear™ 1X Fix Concentrate to each ... | ["Perform cell surface staining as described in BioLegend's Cell Surface Immunofluorescence Staining Protocol.", "Add 1mL of the True-Nuclear™ 1X Fix Concentrate to each tube, vortex and incubate at room temperature in the dark for 45-60 minutes. If necessary, the protocol can be suspended at this point. After discardi... |
102,259 | Spatial Gene Expression for Formalin-Fixed Paraffin-Embedding (FFPE)-Lung Tissue using 10x Genomics Visium Spatial Transcriptomics | 0 | dx.doi.org/10.17504/protocols.io.n92ld852xv5b/v1 | https://www.protocols.io/view/spatial-gene-expression-for-formalin-fixed-paraffi-df4t3qwn | Natalia-Del Pilar Vanegas, Lorena Rosas, Ana L. Mora, Mauricio Rojas | TITLE: Spatial Gene Expression for Formalin-Fixed Paraffin-Embedding (FFPE)-Lung Tissue using 10x Genomics Visium Spatial Transcriptomics
AUTHORS: Natalia-Del Pilar Vanegas, Lorena Rosas, Ana L. Mora, Mauricio Rojas
[DESCRIPTION]
We present a method to map gene expression in formalin-fixed paraffin-embedded (FFPE) lun... | ["[Preservation of the samples:] Store formalin-fixed paraffin-embedded (FFPE) lung tissue blocks at 4 degrees Celsius to preserve RNA integrity.", "[Tissue Quality Assessment:] RNA quality: High quality FFPE sections will have well-preserved RNA for accurate measurement.", "[Tissue Quality Assessment:] For Visium Spat... |
19,576 | SPARC_Duke_Grill_OT2-OD025340_HumanVagusNerve_Collection_Histology_Microscopy | null | dx.doi.org/10.17504/protocols.io.xcyfixw | null | Nicole A. Pelot, J. Ashley Ezzell, Kara A. Clissold, Warren M. Grill | TITLE: SPARC_Duke_Grill_OT2-OD025340_HumanVagusNerve_Collection_Histology_Microscopy
AUTHORS: Nicole A. Pelot, J. Ashley Ezzell, Kara A. Clissold, Warren M. Grill
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for collection, histological processing, and imaging of human vagus nerves.</div... | ["[Collect human vagus nerve samples.]\nWe collected vagus nerve samples from embalmed human cadavers. The study was deemed exempt by the Duke University Institutional Review Board. The bodies were donated to the Duke Anatomical Gifts Program and we accessed them after they were used for medical training courses. The c... |
58,384 | Methods for culturing the freshwater sponge Ephydatia muelleri: Growing sponges on agarose and priming gemmules | 4 | dx.doi.org/10.17504/protocols.io.yxmvmn29bg3p/v1 | https://www.protocols.io/view/methods-for-culturing-the-freshwater-sponge-ephyda-b49qqz5w | Shunsuke Sogabe, Taitum Cornish, April Hill, Ana Riesgo, Sally P Leys | TITLE: Methods for culturing the freshwater sponge Ephydatia muelleri: Growing sponges on agarose and priming gemmules
AUTHORS: Shunsuke Sogabe, Taitum Cornish, April Hill, Ana Riesgo, Sally P Leys
[DESCRIPTION]
The freshwater sponge Ephydatia muelleri is an emerging sponge model system. This species has clonal asexu... | ["[Preparing agarose plates (2% in 1x Strekal's medium)] Make 2% agarose plates and allow to cool.", "[Cleaning and plating gemmules] Clean gemmules for plating, or rinse gemmules stored at -80°C following the protocol - \"Hatching and freezing gemmules from the freshwater sponge Ephydatia muelleri\" by Sally P Le... |
21,274 | Vandy – Oral glucose tolerance test | null | dx.doi.org/10.17504/protocols.io.yz2fx8e | null | Louise Lantier | TITLE: Vandy – Oral glucose tolerance test
AUTHORS: Louise Lantier
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">The glucose tolerance test measures the clearance of an oral glucose load from the body. It is used to ... | ["Weigh the mice. For mice of differing fat mass, we recommend dosing the bolus of glucose on lean mass. This requires body composition.", "Fast mice for 5 hours by transferring mice to individual cages or containers (7am to 12pm).", "Prepare an experiment record sheet, sticks for glucose measurement and syringe for or... |
52,399 | Long-range correlation character Investigation of SARS-CoV-2 Genbanks | 5 | null | https://www.protocols.io/view/long-range-correlation-character-investigation-of-bxeppjdn | Sid Ali Ouadfeul | TITLE: Long-range correlation character Investigation of SARS-CoV-2 Genbanks
AUTHORS: Sid Ali Ouadfeul
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The main goal of this propotoc is to use the 1D Wavelet Transform Modulus Maxima lines (WTMM) method to investigate the Long-Range Correlation (L... | ["1-Gathering SARS-Cov-2 Genbanks", "DNA Coding using the Knucleotidic, Purine, Pyrimidine, Ameno, Keto and GC methods1) The Knucleotidic DNA coding: T=2, G=-2, A=1, C=-12) Purine coding A=G=1 , C=T=-1 3) Pyrimidine C=T=1, A=G=-1. 4) Ameno groupe: A=C=1, G=T=-1. 5) Keto coding G=T=1, A=C=-1. 6) GC coding G=C=1, A=T=-1.... |
106,416 | UDA-Multiome-protocol | 0 | dx.doi.org/10.17504/protocols.io.5qpvokd4xl4o/v1 | https://www.protocols.io/view/uda-multiome-protocol-dj6q4rdw | Yun Li | TITLE: UDA-Multiome-protocol
AUTHORS: Yun Li
[DESCRIPTION]
Droplet microfluidics-based single-cell combinatorial indexing sequencing represents an attractive way to balance cost, scalability, robustness, and accessibility. However, current methods need a tailored protocol for specific modality respectively, which may ... | ["[Transposition] Prepare Transposition Mix (7ul ATAC Buffer B (2000193); 3ul ATAC Buffer B (2000193) each sample) on ice. Pipette mix 10x and centrifuge briefly.", "[Transposition] Add 10 µl Transposition Mix to a tube of a PCR 8-tube strip for each sample.", "[Transposition] Refer to Nuclei Concentration Guidelines... |
28,462 | ChroPack - Protein G | null | dx.doi.org/10.17504/protocols.io.72nhqde | null | Alexandra Ehl, David Frommholz, Nadine Stefanczyk | TITLE: ChroPack - Protein G
AUTHORS: Alexandra Ehl, David Frommholz, Nadine Stefanczyk
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Purification Guide for the Isolation of Antibodies with ChroPack Columns by DALEX Biotech.</span></div><div class = "text-block">Wi... | ["[What do you want to do?]\nDo you want to purify antibodies or sanitize your column?Please choose below.", "[Equilibration]\nConnect the column to your FPLC system. Set the flow rate to 1 bed volume per minute. Wash the column with 5 volumes deionized water (bed volume is written on the column).\nA dry column can be ... |
63,395 | Live Well CBD Gummies *100% Effectiveness Record* Offers Body Significant Boost In Health! | 3 | dx.doi.org/10.17504/protocols.io.eq2lyn2devx9/v1 | https://www.protocols.io/view/live-well-cbd-gummies-100-effectiveness-record-off-b96br9an | jerritdsuza | TITLE: Live Well CBD Gummies *100% Effectiveness Record* Offers Body Significant Boost In Health!
AUTHORS: jerritdsuza
[DESCRIPTION]
Live Well CBD Gummies *Effective* Curing All Your Health Issues In Very Little Time
[STEPS] | [] |
71,231 | Guanidine-based DNA extraction with silica-coated beads or silica spin columns | 4 | dx.doi.org/10.17504/protocols.io.eq2ly73mmlx9/v2 | https://www.protocols.io/view/guanidine-based-dna-extraction-with-silica-coated-chs7t6hn | Dominik Buchner | TITLE: Guanidine-based DNA extraction with silica-coated beads or silica spin columns
AUTHORS: Dominik Buchner
[DESCRIPTION]
This protocol describes how to extract DNA from samples lysed as described in
using guanidine hydrochloride and ethanol-based buffer combined with silica-coated magnetic beads or silica spin ... | ["To clear the lysates 11.000 x g, 3 min, 20 °C", "[Bead-based protocol] Prepare 240 µL and 20 µL per sample in a 1.2 mL", "[Bead-based protocol] Add 100 µL", "[Bead-based protocol]", "[Bead-based protocol] Place the plate on a magnet to pellet the beads for 2 min", "[Bead-based protocol] Discard the supernatant by pip... |
103,591 | Plant Sample Preparation for ICP-AES Analysis of Salt-Stressed Plants | 0 | dx.doi.org/10.17504/protocols.io.4r3l2q3kql1y/v1 | https://www.protocols.io/view/plant-sample-preparation-for-icp-aes-analysis-of-s-dhef33bn | Maryam Rahmati Ishka | TITLE: Plant Sample Preparation for ICP-AES Analysis of Salt-Stressed Plants
AUTHORS: Maryam Rahmati Ishka
[DESCRIPTION]
This procedure outlines the preparation of plant samples exposed to salt stress. For plants grown under treatments other than salt, a special buffer is needed to remove surface chemicals during the ... | ["[Plant Sample Preparation for ICP-AES Analysis of Salt-Stressed Plants:] Record the fresh weight of roots and shoots separately for each seedling.", "[Plant Sample Preparation for ICP-AES Analysis of Salt-Stressed Plants:] Quickly dip the roots and shoots in deionized sterile water for approximately 30 seconds.", "[P... |
33,913 | Diagnostic accuracy of a radiographic device to assess cranial tibial translation in dogs: validation protocol | null | dx.doi.org/10.17504/protocols.io.bdczi2x6 | null | Adolfo Maria Tambella, Stefano Martin, Luca Omini, Cecilia Vullo, Anna Rita Attili | TITLE: Diagnostic accuracy of a radiographic device to assess cranial tibial translation in dogs: validation protocol
AUTHORS: Adolfo Maria Tambella, Stefano Martin, Luca Omini, Cecilia Vullo, Anna Rita Attili
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align... | ["OBJECTIVE This study was designed to objectively quantify the in vivo cranial canine stifle translation using a radiolucent translator device keeping fixed the joint angle during the thrust. The hypothesis was that changes in cranial cruciate ligament (CrCL) integrity would result in detectable changes in tibial tran... |
99,730 | PDUS- Swelling_SOP_V3 | 0 | null | https://www.protocols.io/view/pdus-swelling-sop-v3-ddms246e | Daniel Rohde | TITLE: PDUS- Swelling_SOP_V3
AUTHORS: Daniel Rohde
[DESCRIPTION]
This protocol details the study of standard operating procedures of swelling by Power Doppler ultrasonography (PDUS).
[GUIDELINES]
Template instructions (to be deleted upon use):
This template has all necessary styles embedded. Please use only t... | ["[Consent] Print a paper copy of the Informed Consent for the PDUS Swelling Study found on IRIS and hand it to the study participant. Go over the Informed Consent with the participant and have them and the study representative both sign and date the paper copy.", "[Consent] Ensure to explain the purpose, procedures, r... |
75,096 | LEGACY01: PARTICIPANT ENTRY | 1 | null | https://www.protocols.io/view/legacy01-participant-entry-cmjyu4pw | Katrina M Pollock, Calliope Dendrou | TITLE: LEGACY01: PARTICIPANT ENTRY
AUTHORS: Katrina M Pollock, Calliope Dendrou
[DESCRIPTION]
This protocol details participant entry in an experimental medicine study of seasonal influenza vaccination responses in Lymph nodE single-cell Genomics in AnCestrY (LEGACY01).
[GUIDELINES]
PRE-REGISTRATION EVALUATIONS
Part... | [] |
70,103 | Brain processing, slicing and immunohistochemistry protocol | 4 | dx.doi.org/10.17504/protocols.io.14egn2xrpg5d/v1 | https://www.protocols.io/view/brain-processing-slicing-and-immunohistochemistry-cgpxtvpn | Andrew Hunter | TITLE: Brain processing, slicing and immunohistochemistry protocol
AUTHORS: Andrew Hunter
[DESCRIPTION]
This is a step by step procedure from collecting brain samples to immunohistochemical staining and mounting brain slices.
[STEPS]
SECTION: Perfusion fixation
1. While wearing proper PPE, set up surgical area in fu... | ["[Perfusion fixation] While wearing proper PPE, set up surgical area in fume hood", "[Perfusion fixation] Once a suitable period post-surgery has occurred (3+ weeks) the animal can be perfused", "[Perfusion fixation] Set up surgical area", "[Perfusion fixation] Load ketamine-xylazine cocktail into injection syringe (0... |
21,525 | PEI Transfection | null | dx.doi.org/10.17504/protocols.io.y9vfz66 | null | Nobody | TITLE: PEI Transfection
AUTHORS: Nobody
[STEPS]
?. [Day 1]
Split cells into wells - see relevant protocol
?. [Day 2]
Make a solution of - 500ng transfection DNA - 2.5ul PET - Serum Free Media (OptiMEM) up to 50ul
?. [Day 2]
Vortex solution twice for 5 secondsLeave solution to incubate in hood for 15 minutes... | ["[Day 1]\nSplit cells into wells - see relevant protocol", "[Day 2]\nMake a solution of - 500ng transfection DNA - 2.5ul PET - Serum Free Media (OptiMEM) up to 50ul", "[Day 2]\nVortex solution twice for 5 secondsLeave solution to incubate in hood for 15 minutes Add 50ul of solution per well (500ul) Incubate ... |
37,738 | Cas9 transduction of cancer cell lines | 1 | dx.doi.org/10.17504/protocols.io.bg4ijyue | https://www.protocols.io/view/cas9-transduction-of-cancer-cell-lines-bg4ijyue | Emily Souster, Verity Goodwin, Adam Jackson, Charlotte Beaver, Rizwan Ansari, Fiona Behan, Mathew Garnett | TITLE: Cas9 transduction of cancer cell lines
AUTHORS: Emily Souster, Verity Goodwin, Adam Jackson, Charlotte Beaver, Rizwan Ansari, Fiona Behan, Mathew Garnett
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The creation of stably Cas9 expressing cancer cell lines allows targeted and genome-wide ge... | ["[Day 1: Transduction]\nDetach, collect and count cells by following Steps 1-8 of protocol: Passaging adherent cancer cell lines.", "[Day 1: Transduction]\nUsing the cell count from the source labware, determine the appropriate flask size for transduction. This will be the flask size that is best able to accomodate 2.... |
93,170 | Differentiation of Astrocytes from Human iPSC-derived NPCs | 4 | dx.doi.org/10.17504/protocols.io.x54v9pb4mg3e/v1 | https://www.protocols.io/view/differentiation-of-astrocytes-from-human-ipsc-deri-c68szhwe | Balazs Szeky, Anita Feher, Melinda Zana, Radek Kucera, Jan Lochman, Andras Dinnyes | TITLE: Differentiation of Astrocytes from Human iPSC-derived NPCs
AUTHORS: Balazs Szeky, Anita Feher, Melinda Zana, Radek Kucera, Jan Lochman, Andras Dinnyes
[DESCRIPTION]
Astrocytes are multifunctional glial cells of the central nervous system (CNS). They play essential roles in the metabolic support of neurons, sy... | ["[Neural Progenitor Cell Expansion] Thawing NPCs", "[Astroglial Progenitor Cell Induction] Starting astrocyte induction at Day 0. Next day after the second NPC passaging, replace completed NMM intro AIM, (2mL/well for 6-well plates). Change the medium every other day at least for 21 days. Passage the APCs upon reachin... |
26,742 | Chemical Inventory for Wilhelm Lab 624 | null | dx.doi.org/10.17504/protocols.io.6cwhaxe | null | Steven Wilhelm, Gary LeCleir | TITLE: Chemical Inventory for Wilhelm Lab 624
AUTHORS: Steven Wilhelm, Gary LeCleir
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This document serves as a reference for chemicals used and stored in room 624 in the Science and Engineering Building at The University of Tennessee. For more informati... | ["AB1CAS numberCompound Name (no abbreviations or\n formulas)2125572-95-4(1,2-CYCLOHEXYLENEDINITRILO)TETRAACETIC\n ACID3 (DL)\n METHIONINE46381-92-6[ETHYLENEDIAMINE]TETRAACETATE\n DISODIUM55144-89-81,10-PHENANTHROLINE\n MONOHYDRATE63829-86-51,10-PHENANTHROLINE\n MONOHYDROCHLORIDE, MONOHYDRATE7110-18-91,2-BIS(DIME... |
28,806 | Total RNA Isolation from Bulk Tissue or Isolated Cells | null | dx.doi.org/10.17504/protocols.io.8dehs3e | null | Brad Godfrey | TITLE: Total RNA Isolation from Bulk Tissue or Isolated Cells
AUTHORS: Brad Godfrey
[STEPS]
?. [Procedures]
Transfer biopsy in cryotube (polypropylene) in RNAlater
1.8 ml
1 ml
?. [Procedures]
Use color coding cap inserts to indicate biopsy origin
?. [Procedures]
Store at until RNA extraction
-20 °C
?. [Procedures]... | ["[Procedures]\nTransfer biopsy in cryotube (polypropylene) in RNAlater\n1.8 ml\n1 ml", "[Procedures]\nUse color coding cap inserts to indicate biopsy origin", "[Procedures]\nStore at until RNA extraction\n-20 °C", "[Procedures]\nPerform microdissection of glomeruli / tubulointerstitium", "[Procedures]\nStore disse... |
36,583 | Citrate Buffer | null | dx.doi.org/10.17504/protocols.io.bfyfjptn | https://www.protocols.io/view/citrate-buffer-bfyfjptn | Neilier Junior | TITLE: Citrate Buffer
AUTHORS: Neilier Junior
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A buffer solution has the function of resisting changes in pH even when adding powerful acids or bases. However, in the physiological environment the buffered system also provides cofactors for enzymatic re... | ["[Citrate Buffer]\nMix citric acid and sodium citrate solutions in the proportions indicated and adjust the final volume to with deionized water. ABCDEFGHIJ1mL of Citric acid46.540.035.031.525.520.516.011.87.22mL of Sodium citrate3.51015.018.524.529.534.038.242.83pH3.03.43.84.24.65.05.45.86.2\npH range: to \n(a) ... |
70,364 | Stranded Transcript Count Table Generation from Long Reads | 1 | dx.doi.org/10.17504/protocols.io.5qpvonn2bl4o/v17 | https://www.protocols.io/view/stranded-transcript-count-table-generation-from-lo-cgx4txqw | David A Eccles | TITLE: Stranded Transcript Count Table Generation from Long Reads
AUTHORS: David A Eccles
[DESCRIPTION]
This protocol is for generating count tables for different samples at the transcript level, using long reads that are mapped to transcripts.
Input(s): demultiplexed and oriented fastq files (see protocol Preparing... | ["[Demultiplex Reads] Demultiplex and orient reads as per the protocol Preparing Reads for Stranded Mapping. It is expected that these demultiplexed reads will be split up in the current directory, and coupled with a 'barcode_counts.txt' file. If that's the case, the following should work:\n \nExample expected output:\... |
38,381 | Lipoxygenase activity determination | 1 | dx.doi.org/10.17504/protocols.io.bhqmj5u6 | https://www.protocols.io/view/lipoxygenase-activity-determination-bhqmj5u6 | Neilier Junior | TITLE: Lipoxygenase activity determination
AUTHORS: Neilier Junior
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Lipoxygenase activity on linoleic acid was determined according to the method described by Axelrod et al. (1981). This method determines the increase in absorbance at 234 nm, resulting ... | ["[Reagent Preparation]\n10 mM sodium linoleate stock solution\n\n\nIn a 150 mL Erlenmeyer add:\n\n\n10 mL distilled water (previously boiled)\n78 μL linoleic acid\n90 μL of tween 20\n\nKeep the solution protected from light by wrapping the Erlenmeyer in aluminum foil.\n\n\nMix the solution with the aid of a pipette, t... |
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