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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41,124 | Precompute Node Rankings | 5 | dx.doi.org/10.17504/protocols.io.bkecktaw | https://www.protocols.io/view/precompute-node-rankings-bkecktaw | Lillian Thistlethwaite | TITLE: Precompute Node Rankings
AUTHORS: Lillian Thistlethwaite
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how probability diffusion algorithm informs the path a network walker takes in a disease-specific network as described in Thistlethwaite et al. (2020). Briefly, usi... | ["[wrapper_ranks.r]\nThis Protocol should be completed on a computing cluster, ideally. Running node ranks in serial takes a much longer amount of time, depending on the size of the network and the number of starting nodes you want to precompute node ranks for. If you launch a job for each starting node you want node r... |
34,648 | Viral Sequencing, from Gunk to Graph | null | dx.doi.org/10.17504/protocols.io.bd3yi8pw | null | David Eccles | TITLE: Viral Sequencing, from Gunk to Graph
AUTHORS: David Eccles
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a fast "gunk to graph" protocol for analysing viral RNA from nasopharyngeal swabs. The approach involves swab lysis and inactivation at the point of sampling, uses a cellulose bi... | ["[Swab Lysis]\nPrepare a centrifuge tube with heated lysis buffer and a cellulose disc\n1.5 ml", "[Swab Lysis]\nCollect sample using a sterile polystyrene swab with a 30mm breakpoint (e.g. Puritan 25-3606-U; PurFlock Ultra 6\" Sterile Elongated Flock Swab w/Polystryene Handle, 30mm Breakpoint).", "[Swab Lysis]\nAdd l... |
100,182 | IRIS Software Protocol | 0 | dx.doi.org/10.17504/protocols.io.3byl497wjgo5/v3 | https://www.protocols.io/view/iris-software-protocol-dd3w28pe | Leonardo Zilli, Erica Andreose, Salvatore Di Marzo | TITLE: IRIS Software Protocol
AUTHORS: Leonardo Zilli, Erica Andreose, Salvatore Di Marzo
[DESCRIPTION]
We present a step-by-step methodology for tracking the coverage of the IRIS dataset in the OpenCitations Corpus.
The methodology filters the original IRIS dataset and the OpenCitations Meta and Index dumps, produci... | ["[IRIS Dataset Preparation] Make sure that the IRIS dump is present in the work directory.", "[Create iris_in_meta dataset] This step will create a version of the OpenCitations Meta dump that is transformed and filtered according to the elements in the IRIS dump. This new dataset is stored in a parquet format that mak... |
44,761 | PMN- 02 - MTT Assay in Human PMN | 4 | dx.doi.org/10.17504/protocols.io.bpxzmpp6 | https://www.protocols.io/view/pmn-02-mtt-assay-in-human-pmn-bpxzmpp6 | Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino | TITLE: PMN- 02 - MTT Assay in Human PMN
AUTHORS: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Published work using this protocol:</div><div class = "text-block"><span>- </span><s... | ["Isolate PMN according to the protocol PMN-01a for buffy coats or PMN-01b for fresh whole blood.", "Resuspend PMN at 1x106cells/ml in RPMI 1640 medium supplemented with 10% Fetal Bovine Serum (FBS) and 1% penicillin/streptomycin (SOLUTION- 13).", "Add of cell suspension per well in a 96-well round bottom plate and in... |
19,152 | Painting Neuropixels probes and other silicon probes for electrophysiological recordings | null | dx.doi.org/10.17504/protocols.io.wxqffmw | null | Liu Liu | TITLE: Painting Neuropixels probes and other silicon probes for electrophysiological recordings
AUTHORS: Liu Liu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is for consistently applying fluorescent dyes to Neuropixels probes and other types of silicon probes, which allows imaging a... | ["Secure Neuropixels probes (shown) or other silicon probes onto a micromanipulator. The side with eletrode sites should face up.", "Secure a microscope slide onto a holder, and a clean coverslip at the end of the microscope slide. Place the coverslip attached to the microscope slide near to the Neuropixels probe (2-3 ... |
25,206 | RNA Isolation from Plant Tissue Protocol 17: Invitrogen PureLink-Qiagen RNeasy Hybrid | null | dx.doi.org/10.17504/protocols.io.4uwgwxe | null | null | TITLE: RNA Isolation from Plant Tissue Protocol 17: Invitrogen PureLink-Qiagen RNeasy Hybrid
AUTHORS:
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Implemented by: Patrick Edger and J. Chris Pires</div><div class = "text-block"><span>For a small number of samples the Invitrogen </span><a href="ht... | [] |
93,189 | Dopaminergic neuron differentiation | 4 | dx.doi.org/10.17504/protocols.io.3byl4q8yovo5/v1 | https://www.protocols.io/view/dopaminergic-neuron-differentiation-c69dzh26 | Khaja Mohieddin Syed, Oriol Busquets, Frank Soldner, Dirk Hockemeyer | TITLE: Dopaminergic neuron differentiation
AUTHORS: Khaja Mohieddin Syed, Oriol Busquets, Frank Soldner, Dirk Hockemeyer
[DESCRIPTION]
This protocol has been used to differentiate dopaminergic neurons from hPSC adapted to feeder free culture systems.
Protocol overview
A. Plate preparation
B. Media recipes
C. Dopamin... | ["[Plate preparation] Plate preparation:", "[Plate preparation] Matrigel/Geltrex coating: Prepare matrigel/geltrex (1:30) in cold DMEM/F12 or DPBS in a 15 ml tube as described by the manufacturer. Coat each well with 1-1.5 ml (6 well plate size) or 0.5 ml (12w plate size) of solution and incubate at 37 °C incubator fo... |
57,441 | Total RNA extraction from frozen placenta tissue | 4 | dx.doi.org/10.17504/protocols.io.b4b9qsr6 | https://www.protocols.io/view/total-rna-extraction-from-frozen-placenta-tissue-b4b9qsr6 | Scott Lindsay-Hewett | TITLE: Total RNA extraction from frozen placenta tissue
AUTHORS: Scott Lindsay-Hewett
[DESCRIPTION]
This protocol describes the isolation of high-quality total RNA from frozen placenta tissue. Tissue is disrupted using a bead beater, and total RNA is isolated using the mirVana miRNA Isolation Kit from Ambion.
Writ... | ["[Preparation] Heat nuclease-free water to 95 °C.", "[Preparation] Pre-cool microcentrifuge to 4 °C.", "[Cell lysis and tissue disruption] Add approximately 1 mL of 1.0mm zirconia/silica beads to each frozen placenta sample, and 700 µL mirVana Lysis/Binding Buffer.", "[Cell lysis and tissue disruption] Load samples i... |
103,075 | DEVELOPMENT OF A QUESTIONNAIRE OF COMMITMENT TO NEW PHYSICAL INTERVENTIONS FOR ATHLETES: DELPHI RESEARCH | 0 | dx.doi.org/10.17504/protocols.io.14egn6w5ql5d/v1 | https://www.protocols.io/view/development-of-a-questionnaire-of-commitment-to-ne-dgwb3xan | Rybakova Polina Denisovna, Miroshnikov Alexander Borisovich, Shevtsov Alexey Victorovich | TITLE: DEVELOPMENT OF A QUESTIONNAIRE OF COMMITMENT TO NEW PHYSICAL INTERVENTIONS FOR ATHLETES: DELPHI RESEARCH
AUTHORS: Rybakova Polina Denisovna, Miroshnikov Alexander Borisovich, Shevtsov Alexey Victorovich
[DESCRIPTION]
In the context of exercise, commitment is the correct level of a person's performance of a reco... | [] |
58,988 | Agrobacterium-mediated transformation of Zymoseptoria tritici | 4 | dx.doi.org/10.17504/protocols.io.b5ukq6uw | https://www.protocols.io/view/agrobacterium-mediated-transformation-of-zymosepto-b5ukq6uw | Harry T Child, Nicolas Helmstetter | TITLE: Agrobacterium-mediated transformation of Zymoseptoria tritici
AUTHORS: Harry T Child, Nicolas Helmstetter
[DESCRIPTION]
This protocol describes the procedure for transforming plasmids into the plant pathogenic fungus Zymoseptoria tritici by Agrobacterium tumefaciens-mediated transformation. It is based on the ... | ["[1.\tMedia Recipes] Induction Media (IM)\nMake stock solutions in deionised water (diH20) according to Table 1, with K2HPO4/KH2PO4/NaCl combined to make ‘Stock A’, which can be autoclaved and used in a sterile environment to make IM for mutliple transformations.\nTo prepare fresh for each transformation, dissolve the... |
28,871 | IPTG-induced Overexpression in E. coli | null | dx.doi.org/10.17504/protocols.io.8ffhtjn | null | iGEM Dusseldorf | TITLE: IPTG-induced Overexpression in E. coli
AUTHORS: iGEM Dusseldorf
[STEPS]
?. [Protein Expression (optimised for inclusion bodies)]
Protein Expression (optimised for inclusion bodies)Take volume (100 ml) LB+ampicillinAdd 1 ml of the overnight cultureLet the culture grow to an OD600 of 0.6 at 37°C/180 rpmInduce wit... | ["[Protein Expression (optimised for inclusion bodies)]\nProtein Expression (optimised for inclusion bodies)Take volume (100 ml) LB+ampicillinAdd 1 ml of the overnight cultureLet the culture grow to an OD600 of 0.6 at 37°C/180 rpmInduce with 0.5 mM IPTG (1M Stock) --> 50 µlIncubate for 2 hours at 37°C/ 180 rpmCentrifug... |
40,206 | MGH COVID-19 Effort Blood Processing Protocol for PBMC, Neutrophils and Plasma Isolation | 4 | dx.doi.org/10.17504/protocols.io.bjhnkj5e | https://www.protocols.io/view/mgh-covid-19-effort-blood-processing-protocol-for-bjhnkj5e | Moshe Sade-Feldman, Miguel Reyes, Alexandra-Chloe Villani | TITLE: MGH COVID-19 Effort Blood Processing Protocol for PBMC, Neutrophils and Plasma Isolation
AUTHORS: Moshe Sade-Feldman, Miguel Reyes, Alexandra-Chloe Villani
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the steps and methods for blood processing for PBMC to assist the... | ["[PBMC Isolation]\nFollow the steps detailed in the \"Before Start\" section prior to moving forward in this protocol.", "[PBMC Isolation]\nInvert vacutainer 5x to mix blood.\nDo not shake.", "[PBMC Isolation]\nFor transferring blood to the different tubes, proceed ONLY one patient sample set at a time and avoid openi... |
44,886 | Protocols for "The female urinary microbiota in relation to the reproductive tract microbiota." | 2 | dx.doi.org/10.17504/protocols.io.bp3wmqpe | https://www.protocols.io/view/protocols-for-34-the-female-urinary-microbiota-in-bp3wmqpe | Chen Chen, Lilan Hao, Weixia Wei, Fei Li, Liju Song, Xiaowei Zhang, Juanjuan Dai, Zhuye Jie, Jiandong Li, Xiaolei Song, Zirong Wang, Zhe Zhang, Liping Zeng, Hui Du, Huiru Tang, Tao Zhang, Huanming Yang, Jian Wang, Susanne Brix, Karsten Kristiansen, Xun Xu, Ruifang Wu, Huijue Jia | TITLE: Protocols for "The female urinary microbiota in relation to the reproductive tract microbiota."
AUTHORS: Chen Chen, Lilan Hao, Weixia Wei, Fei Li, Liju Song, Xiaowei Zhang, Juanjuan Dai, Zhuye Jie, Jiandong Li, Xiaolei Song, Zirong Wang, Zhe Zhang, Liping Zeng, Hui Du, Huiru Tang, Tao Zhang, Huanming Yang, Jian ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.fbdbii6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
60,956 | LRRK2RCKW Widefield fluorescence microtubule binding assay | 4 | dx.doi.org/10.17504/protocols.io.kxygxz7bdv8j/v1 | https://www.protocols.io/view/lrrk2rckw-widefield-fluorescence-microtubule-bindi-b7r4rm8w | David M. Snead | TITLE: LRRK2RCKW Widefield fluorescence microtubule binding assay
AUTHORS: David M. Snead
[DESCRIPTION]
This assay uses TMR labeled LRRK2 or LRRK1 RCKW to measure binding to microtubules in vitro.
Created by David Snead. Adapted to protocols.io by Mariusz Matyszewski.
As used in Snead, Matyszewski, Dickey et al. 202... | ["[Create microscope slides:] Adhere Biotin-PEG-functionalized coverslips (Microsurfaces) to a microscope slide using double-sided scotch tape, creating 4 channels per slide.", "[Prepare LRRK2:] Make sure to use TMR labelled protein. See https://dx.doi.org/10.17504/protocols.io.ewov1nq5ogr2/v1 for labeling protocol.", ... |
103,788 | Characterizing qPCR Assays Using Different Software Tools. | 0 | dx.doi.org/10.17504/protocols.io.5qpvok7b7l4o/v1 | https://www.protocols.io/view/characterizing-qpcr-assays-using-different-softwar-dhkk34uw | Jonathan Phillips, Gregor Blaha | TITLE: Characterizing qPCR Assays Using Different Software Tools.
AUTHORS: Jonathan Phillips, Gregor Blaha
[DESCRIPTION]
This protocol aims to assist those new to qPCR data analysis and those who seek to escape the closed-source, proprietary software tied to their qPCR instrumentation.
Here we describe how to assess ... | [] |
52,636 | Day 2: DNA Extraction | 1 | dx.doi.org/10.17504/protocols.io.bxm4pk8w | https://www.protocols.io/view/day-2-dna-extraction-bxm4pk8w | Tom Little | TITLE: Day 2: DNA Extraction
AUTHORS: Tom Little
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"> DAY 2: ADE field practical instructions for DNA extraction</div></div>
[STEPS]
?. You will be assigned a single SEQUENCING IDENTIFIER, a number from 01 to 96. Your tubes must be labelled with this SEQ... | ["You will be assigned a single SEQUENCING IDENTIFIER, a number from 01 to 96. Your tubes must be labelled with this SEQUENCING IDENTIFIER. Write down what SEQUENCING IDENTIFIER you have been assigned. Do not lose this. \n\t\t\t\t\t\t\t .justify:after {\n\t\t\t\t\t\t\t content: \"\";\n\t\t\t\t\t\t\t display:i... |
49,299 | Nucleic acid extraction - RNeasy PowerMicrobiome Kit (Qiagen) | 4 | dx.doi.org/10.17504/protocols.io.budtns6n | https://www.protocols.io/view/nucleic-acid-extraction-rneasy-powermicrobiome-kit-budtns6n | Adélaïde Roguet, Shuchen Feng | TITLE: Nucleic acid extraction - RNeasy PowerMicrobiome Kit (Qiagen)
AUTHORS: Adélaïde Roguet, Shuchen Feng
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Total nucleic extraction from wastewater using RNeasy PowerMicrobiome kit (qiagen)</div></div>
[STEPS]
?. [Nucleic acid extraction (in the chem... | ["[Nucleic acid extraction (in the chemical safety cabinet)]\nFor HA filter extraction, add 6.5 µL of beta-Mercaptoethanol to each of the 2-mL ZR BashingBead Lysis tubes. Go to step 2. For BCoV/BRSV extraction, add 5 µL of BCoV/BRSV solution to the 2-mL tube containing the warmed PM1 + beta-Mercaptoethanol solution. Vo... |
16,405 | Single-cell suspensions from primary human esophagus tissue | 1 | dx.doi.org/10.17504/protocols.io.t9ver66 | https://www.protocols.io/view/single-cell-suspensions-from-primary-human-esophag-t9ver66 | Annette Hayden, Rob Walker, Jack Harrington, Lucy Kimbley, Sara Waise, Chris Hanley, Gareth Thomas, Peter Johnson, Jonathan West, Matthew Rose Zerilli, TIm Underwood | TITLE: Single-cell suspensions from primary human esophagus tissue
AUTHORS: Annette Hayden, Rob Walker, Jack Harrington, Lucy Kimbley, Sara Waise, Chris Hanley, Gareth Thomas, Peter Johnson, Jonathan West, Matthew Rose Zerilli, TIm Underwood
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A protocol... | ["Wash tissue in PBSA.", "Mince tissue with scalpel.", "Transfer the minced tissue to the Collagenase/DNAse solution in a 50ml Falcon.", "Shake the suspension at 110-150 rpm for 60 mins at 37°C (with the tube on its side to increase agitation of the tissue).", "After 15, 30, and 60 mins – pipette up and down with desce... |
42,802 | Data Processing of Nano-DESI IMS data | 1 | dx.doi.org/10.17504/protocols.io.bm2sk8ee | https://www.protocols.io/view/data-processing-of-nano-desi-ims-data-bm2sk8ee | yang1832 , Julia Laskin | TITLE: Data Processing of Nano-DESI IMS data
AUTHORS: yang1832 , Julia Laskin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Scope:</div><div class = "text-block">Process a mass spectrometry imaging data into a final imzML file.</div></div>
[STEPS]
?. Import the raw data folder into PeakByPeak Im... | ["Import the raw data folder into PeakByPeak Imaging software under \"Process Raw folder\"", "Set \"Number of Processes\" to 10.", "Choose \"File Format\" as imzML.", "Run."] |
46,544 | Operating of the Torion® T-9 portable gas chromatograph-mass spectrometer (PerkinElmer) for the analysis of animal scent samples | 1 | dx.doi.org/10.17504/protocols.io.brpqm5mw | https://www.protocols.io/view/operating-of-the-torion-t-9-portable-gas-chromatog-brpqm5mw | Alice C. Poirier, John S. Waterhouse, Mrinalini Watsa, Gideon A. Erkenswick, Laís A. A. Moreira, Jia Tang, Jacob C. Dunn, Amanda D. Melin, Andrew C. Smith | TITLE: Operating of the Torion® T-9 portable gas chromatograph-mass spectrometer (PerkinElmer) for the analysis of animal scent samples
AUTHORS: Alice C. Poirier, John S. Waterhouse, Mrinalini Watsa, Gideon A. Erkenswick, Laís A. A. Moreira, Jia Tang, Jacob C. Dunn, Amanda D. Melin, Andrew C. Smith
[DESCRIPTION]
<div... | ["SAMPLE COLLECTION", "Material:Individually numbered clean glass vials with screw-top and silicone septa lids in a cardboard boxBag of sterile cotton bud swabsEppendorf tubes filled with distilled waterTwo Thermos® flasks filled with ice packs", "Before each animal is processed, prepare:20 vials on a tray20 swabs read... |
null | null | null | dx.doi.org/10.17504/protocols.io.iapcadn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
98,407 | Descending Platform | 4 | dx.doi.org/10.17504/protocols.io.14egn3ko6l5d/v3 | https://www.protocols.io/view/descending-platform-dccf2stn | daniel.dautan daniel, Per Svenningsson | TITLE: Descending Platform
AUTHORS: daniel.dautan daniel, Per Svenningsson
[DESCRIPTION]
Behavioral test to assess motor function.
The test is using a custom made 45-degree grid path with a width of 5cm and a length of 45cm. The 15cm one side is oriented with a 45-degree angle. The grid is formed by metal mesh with a ... | ["Place the custom-made, metal mesh grid to have an angle of 45 degrees with the floor.", "At the end of the platform, place the animal cage to provide a safe target.", "Place a camera above the grid to record the entire procedure. Here we use the Logitech C920 webcam and windows camera software.", "Using the video, re... |
93,203 | Multi-color fiber array imaging | 1 | dx.doi.org/10.17504/protocols.io.14egn31qml5d/v1 | https://www.protocols.io/view/multi-color-fiber-array-imaging-c69tzh6n | Mai-Anh Vu, mwhowe | TITLE: Multi-color fiber array imaging
AUTHORS: Mai-Anh Vu, mwhowe
[DESCRIPTION]
We have developed a new micro-fiber array approach capable of chronically measuring and optogenetically manipulating local dynamics across over 100 targeted locations simultaneously in head-fixed and freely moving mice, enabling investiga... | ["[Imaging setup] Fiber bundle imaging for head-fixed experiments was performed with a custom microscope mounted on a 4’ x 8’ x 12’’ vibration isolation table (Newport). The setup is detailed in the substeps below.", "[Imaging setup] Excitation light (470nm, 405nm, 415nm, and 570nm) for fluorescent sensors was provided... |
43,607 | Specificity test of toehold | 4 | null | https://www.protocols.io/view/specificity-test-of-toehold-bntxmepn | Hung Liang Pai, Cheng-Ruei Yang | TITLE: Specificity test of toehold
AUTHORS: Hung Liang Pai, Cheng-Ruei Yang
[STEPS]
?. [Preparation]
Sterilize the bench, and put on a labmat
?. [Preparation]
Thaw the reagents including 1. DNase/ RNase free water (store in -20°C) 2. solution A (store in -80°C) 3. solution B (store in -80°C) 4. RNase inhibitor (store ... | ["[Preparation]\nSterilize the bench, and put on a labmat", "[Preparation]\nThaw the reagents including 1. DNase/ RNase free water (store in -20°C) 2. solution A (store in -80°C) 3. solution B (store in -80°C) 4. RNase inhibitor (store in -20°C) 5.toehold switches with invertase DNA (store in 4°C) 6.miRNA as the trigge... |
null | null | null | dx.doi.org/10.17504/protocols.io.ffwbjpe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol is from:<br /><br />Satinsky, Brandon M., et al. "<a href="http://www.sciencedirect.com/science/article/pii/B9780124078635000125" target="_blank">Use of internal standards for quantitative metatranscriptome and metagenome analysis.</a>" Methods in enzymology 531 (2... | [] |
24,446 | MOVAT Pentachrome Staining | null | dx.doi.org/10.17504/protocols.io.346gqze | null | Charles Alpers | TITLE: MOVAT Pentachrome Staining
AUTHORS: Charles Alpers
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">The following table describes the staining color for various structures.</div><div class = "text-block">Results:... | ["Deparaffinize and hydrate to distilled water", "Preheat Alkaline Alcohol in 60 degree oven", "Mordant in Bouins in microwave, covered, at Med power for 45 seconds. Let sit for 10 mins. (Do Not Dump)", "Rinse in cold running water for 10 minutes", "Sodium Thiosulfate for 5 minutes, wash for 5 minutes under cold runnin... |
68,832 | Protocol for Data Independent Acquisition - Mass spectrometry analysis – a DIA-based Organelle Proteomics | 1 | dx.doi.org/10.17504/protocols.io.kxygxzrokv8j/v1 | https://www.protocols.io/view/protocol-for-data-independent-acquisition-mass-spe-cff8tjrw | Raja Sekhar Nirujogi, Rotimi Fasimoye, Toan K Phung, Dario R Alessi | TITLE: Protocol for Data Independent Acquisition - Mass spectrometry analysis – a DIA-based Organelle Proteomics
AUTHORS: Raja Sekhar Nirujogi, Rotimi Fasimoye, Toan K Phung, Dario R Alessi
[DESCRIPTION]
Purification of intact organelles by previously described methods (dx.doi.org/10.17504/protocols.io.bybjpskn; dx.do... | ["[High-pH Reversed-phase Liquid Chromatography fractionation of pooled Golgi-tag IP peptides to generate Spectral library:] Take ~5 µg of peptide digest from each of the Golgi-tag IP and Control-IP sample.", "[High-pH Reversed-phase Liquid Chromatography fractionation of pooled Golgi-tag IP peptides to generate Spectr... |
null | null | null | dx.doi.org/10.17504/protocols.io.j6pcrdn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?. | [] |
37,211 | Gel Slice Sample Preparation for Proteomics | 1 | dx.doi.org/10.17504/protocols.io.bgj3juqn | https://www.protocols.io/view/gel-slice-sample-preparation-for-proteomics-bgj3juqn | Jennifer Gin, Leanne Chan, Christopher Petzold | TITLE: Gel Slice Sample Preparation for Proteomics
AUTHORS: Jennifer Gin, Leanne Chan, Christopher Petzold
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol details steps for gel slice sample preparation for proteomic data acquisition. It was adapted from Shevchenko et al. "In-gel ... | ["[Day 1: Washing the gel slices]\nWash gel slice with in a tube (Eppendorf Centrifuge, Cat.#022363204). Incubate for then remove liquid.\n[Water]", "[Day 1: Washing the gel slices]\nWash gel slice withand incubate for then remove liquid.\n[50 mM AMBIC/ACN]\nDiscard used buffers and solvents in appropriate waste co... |
53,878 | Preparation of electrocompetent cells | 4 | dx.doi.org/10.17504/protocols.io.byuwpwxe | https://www.protocols.io/view/preparation-of-electrocompetent-cells-byuwpwxe | Shuning Guo | TITLE: Preparation of electrocompetent cells
AUTHORS: Shuning Guo
[DESCRIPTION]
This protocol is used to prepare electrocompetent cells with high transformation efficiency.
[BEFORE_START]
All the medium and containers used in the protocol should be sterilized by high temperature autoclave.
All the steps that expos... | ["Line the E. coli strain on a solid LB medium without resistance and culture at 37℃ for 12h.", "Pick monoclonal cells from the medium and culture them in 5 ml LB medium at 37℃ for 12h.", "Inoculate 100 ml of LB medium with 1% volume of E. coli culture from step 2.", "Grow the cells at 37℃ shaking at 200 rpm to an OD60... |
92,126 | Applications based on Artificial Intelligence for swallowing analysis described in the literature: Scope Review | 1 | dx.doi.org/10.17504/protocols.io.rm7vzxq42gx1/v1 | https://www.protocols.io/view/applications-based-on-artificial-intelligence-for-c576y9re | maiara tomanchieviez, Rafaela Soares Rech, Fernando Neves Hugo | TITLE: Applications based on Artificial Intelligence for swallowing analysis described in the literature: Scope Review
AUTHORS: maiara tomanchieviez, Rafaela Soares Rech, Fernando Neves Hugo
[DESCRIPTION]
Introduction: Considering the growing number of articles involving artificial intelligence strategies for analyzin... | [] |
63,858 | Simplihealth ACV+Keto Gummies Where To Buy? | 1 | dx.doi.org/10.17504/protocols.io.6qpvr625zvmk/v1 | https://www.protocols.io/view/simplihealth-acv-keto-gummies-where-to-buy-caksscwe | bayleysbalorr | TITLE: Simplihealth ACV+Keto Gummies Where To Buy?
AUTHORS: bayleysbalorr
[DESCRIPTION]
✔️Product Name - Simplihealth ACV+Keto Gummies
✔️Category - Health
✔️Side-Effects - NA
✔️Price for Sale - Best Price
✔️Availability - Online
✔️Rating -⭐⭐⭐⭐⭐
✔️Official Website - [SALE IS LIVE] Hurry Get Your “Simplihealt... | ["[Simplihealth ACV+Keto Gummies Where To Buy?]"] |
42,041 | covid 19 indirect detection thru rise of 100nm filter fluid resistance | 4 | dx.doi.org/10.17504/protocols.io.bmazk2f6 | https://www.protocols.io/view/covid-19-indirect-detection-thru-rise-of-100nm-fil-bmazk2f6 | Ladislav Nevery | TITLE: covid 19 indirect detection thru rise of 100nm filter fluid resistance
AUTHORS: Ladislav Nevery
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">By passing saliva sample thru 150nm filter to remove particles larger than avg 125nm sized covid 19 virus particles and concentrating resulting fluid... | ["3d print all required parts", "place 25mm ideally 110nm pc or nylon membrane filter between blue parts. I used what I had piece", "place 25mm ideally 150nm membrane filter in green saliva holder bellow red rubber gasket. I used what I had piece", ".attach empty 2L soda bottle and squeze until all saliva passes thru b... |
99,143 | Wake Forest University Health Sciences Manual of Procedures Biospecimen Collection and Processing V2 | 1 | dx.doi.org/10.17504/protocols.io.4r3l2qo8xl1y/v1 | https://www.protocols.io/view/wake-forest-university-health-sciences-manual-of-p-dc3f2yjn | Kim Kennedy, Heather Gregory | TITLE: Wake Forest University Health Sciences Manual of Procedures Biospecimen Collection and Processing V2
AUTHORS: Kim Kennedy, Heather Gregory
[DESCRIPTION]
This includes the methods associated with obtaining muscle, blood, and urine along with demographic, clinical, health, and functional data from younger and old... | [] |
44,022 | The Protocol of Adachi Rehabilitation Programme, Version1.0 | 1 | dx.doi.org/10.17504/protocols.io.bn8wmhxe | https://www.protocols.io/view/the-protocol-of-adachi-rehabilitation-programme-ve-bn8wmhxe | Yoshihiko Baba, Chika Ooyama, Yasushi Tazawa, Masahiro Kohzuki | TITLE: The Protocol of Adachi Rehabilitation Programme, Version1.0
AUTHORS: Yoshihiko Baba, Chika Ooyama, Yasushi Tazawa, Masahiro Kohzuki
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Objectives</span></div><div class = "text-block">We have developed Adachi Rehab... | ["ARP is a weekly exercise and occupational therapy that facilitated participation with low (In the first week, participants visit a shopping street to purchase the items for park cleaning and gardening. The total duration of transportation and shopping is approximately three hours. In weeks two to four, participants g... |
62,970 | (SCAM LEGIT)Tamra Judge CBD Gummies Reviews, Benefits, Price, Offers, Where To Buy? | 3 | dx.doi.org/10.17504/protocols.io.x54v9yw24g3e/v1 | https://www.protocols.io/view/scam-legit-tamra-judge-cbd-gummies-reviews-benefi-b9q2r5ye | Tamra Judge CBD Gummies | TITLE: (SCAM LEGIT)Tamra Judge CBD Gummies Reviews, Benefits, Price, Offers, Where To Buy?
AUTHORS: Tamra Judge CBD Gummies
[DESCRIPTION]
Tamra Judge CBD Gummies Reviews [Customer Reviews 2022] It Is a Great Product
Tamra Judge CBD Gummies is a chewable gummy supplement that offers a variety of natural health benefit... | [] |
43,290 | 1M KPO4 pH6.0 | 1 | dx.doi.org/10.17504/protocols.io.bnh2mb8e | https://www.protocols.io/view/1m-kpo4-ph6-0-bnh2mb8e | Ida Barlow | TITLE: 1M KPO4 pH6.0
AUTHORS: Ida Barlow
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for making phosphate salt solution for adding to NGM</div></div>
[STEPS]
?. [Make 1M solutions of monobasic and dibasic salts]
Prepare 1M solution dibasic salt: K2HPO4 water
174.18 g
1 L
?. [Make 1M so... | ["[Make 1M solutions of monobasic and dibasic salts]\nPrepare 1M solution dibasic salt: K2HPO4 water\n174.18 g\n1 L", "[Make 1M solutions of monobasic and dibasic salts]\nPrepare 1M solutions of monobasic salt: KH2PO4 water\n136.09 g\n1 L", "[Make 1M solutions of monobasic and dibasic salts]\nAutoclave both solutions ... |
94,228 | Preparation of Free Floating Coronal Mouse Brain Sections | 4 | dx.doi.org/10.17504/protocols.io.5jyl8pzk9g2w/v1 | https://www.protocols.io/view/preparation-of-free-floating-coronal-mouse-brain-s-c79uzr6w | madalynn.erb Erb | TITLE: Preparation of Free Floating Coronal Mouse Brain Sections
AUTHORS: madalynn.erb Erb
[DESCRIPTION]
Protocol to prepare free floating mouse brain sections for immunostaining or in situ hybridization.
[STEPS]
SECTION: Collect Mouse Brain Tissue
1. Deeply anesthetize mice via intraperitoneal injection of 2X Averti... | ["[Collect Mouse Brain Tissue] Deeply anesthetize mice via intraperitoneal injection of 2X Avertin solution", "[Collect Mouse Brain Tissue] Perform transcardial perfusion using chilled saline solution", "[Collect Mouse Brain Tissue] Switch from saline solution to chilled PFA", "[Collect Mouse Brain Tissue] Remove brain... |
21,812 | Contact testing doc | null | dx.doi.org/10.17504/protocols.io.ziuf4ew | null | Monika Hassan | TITLE: Contact testing doc
AUTHORS: Monika Hassan
[STEPS]
?. | [] |
95,133 | Mouse stereotaxic surgery | 1 | dx.doi.org/10.17504/protocols.io.81wgbx373lpk/v1 | https://www.protocols.io/view/mouse-stereotaxic-surgery-c855zy86 | madalynn.erb | TITLE: Mouse stereotaxic surgery
AUTHORS: madalynn.erb
[DESCRIPTION]
This protocol details the mouse stereotaxic surgery.
[STEPS]
SECTION: Procedure
1. Turn on the heating pad to and set to 36.9 °C.
SECTION: Procedure
2. Weigh mouse and record weight before starting surgery.
SECTION: Procedure
3. Place mouse in isofl... | ["[Procedure] Turn on the heating pad to and set to 36.9 °C.", "[Procedure] Weigh mouse and record weight before starting surgery.", "[Procedure] Place mouse in isoflurane chamber (3% isoflurane).", "[Procedure] Place mouse back into isoflurane chamber (3% isoflurane) until fully anesthetized.", "[Procedure] Transfer m... |
null | null | null | dx.doi.org/10.17504/protocols.io.r69d9h6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
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?. | ["10 Larvae were disseted on ice and placed in 100uL of ice-cold mitochondrial isolation buffer", "The larvae were homogenized by 80 strokes up and down using sterile kontes pellet pestles", "The homogenate was pipette into the syringe (with 2cm2 of gauze pad), followed by 400uL of isolation buffer", "Gently press thro... |
33,745 | TCA protein extraction from diatoms | null | dx.doi.org/10.17504/protocols.io.bc7rizm6 | null | Anna Santin, Antonella Ruggiero, Francesco Manfellotto, Mariella Ferrante | TITLE: TCA protein extraction from diatoms
AUTHORS: Anna Santin, Antonella Ruggiero, Francesco Manfellotto, Mariella Ferrante
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protein extraction from diatoms using TCA</div></div>
[STEPS]
?. Pellet of around 50 ml of culture in exponential phase (2 mi... | ["Pellet of around 50 ml of culture in exponential phase (2 million of cells)", "Wash pellet with 1 ml of TCA 20%", "Centrifuge at maximum speed for 1 minute", "Pour off the supernatant and dilute in 100 µl of TCA 20%", "Add Glass-Beads till meniscus and vortex for 7 minutes", "Add 400 µl of TCA 5% and transfer the sup... |
96,033 | 10x Genomics Xenium for FFPE User Guides | 0 | dx.doi.org/10.17504/protocols.io.81wgbxjonlpk/v1 | https://www.protocols.io/view/10x-genomics-xenium-for-ffpe-user-guides-c9z9z796 | Andrew Houston | TITLE: 10x Genomics Xenium for FFPE User Guides
AUTHORS: Andrew Houston
[DESCRIPTION]
Xenium allows for in situ transcript detection of selected probe set of RNA targets revealing spatially resolved expression patterns at nearly single-cell resolution.
[STEPS]
SECTION: Tissue processing and QC
1. Determine suitable ... | ["[Tissue processing and QC] Determine suitable samples of interest by performing a test described in CG000578, sectioning guidelines described in Step 1 pgs. 18-25 and H&E staining in Appendix pgs. 38-45", "[Tissue processing and QC] Evaluate section and staining quality, only choose samples or regions free of detachm... |
57,741 | Standard operating procedure for the isolation of genetically engineered hPSCs clones in a high-throughput way | 2 | dx.doi.org/10.17504/protocols.io.b4mmqu46 | https://www.protocols.io/view/standard-operating-procedure-for-the-isolation-of-b4mmqu46 | Hanqin Li, Yogendra Verma, Dirk Hockemeyer, Frank Soldner | TITLE: Standard operating procedure for the isolation of genetically engineered hPSCs clones in a high-throughput way
AUTHORS: Hanqin Li, Yogendra Verma, Dirk Hockemeyer, Frank Soldner
[DESCRIPTION]
This collection describes a standard procedure for isolating single human pluripotent stem cell (hPSC) clones in a high... | [] |
51,841 | PBMC surface flow staining | 1 | dx.doi.org/10.17504/protocols.io.bwu9pez6 | https://www.protocols.io/view/pbmc-surface-flow-staining-bwu9pez6 | cecilia , Alessandro Sette | TITLE: PBMC surface flow staining
AUTHORS: cecilia , Alessandro Sette
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is about Flow staining.</div></div>
[STEPS]
?. [Day 1 - THAWING of PBMC]
Add per donor vial being thawed to a labeled 50 ml tube.
[cell culture media]
?. [Day 1 - THA... | ["[Day 1 - THAWING of PBMC]\nAdd per donor vial being thawed to a labeled 50 ml tube.\n[cell culture media]", "[Day 1 - THAWING of PBMC]\nAdd per 10 ml media of Benzonase to the 50 ml tube.\n20 µl", "[Day 1 - THAWING of PBMC]\nGet as many vials of PBMC as needed.", "[Day 1 - THAWING of PBMC]\nPlace the vials in wate... |
54,866 | FPCount protocol - Full protocol | 4 | dx.doi.org/10.17504/protocols.io.bztsp6ne | https://www.protocols.io/view/fpcount-protocol-full-protocol-bztsp6ne | Eszter Csibra, Guy-Bart Stan | TITLE: FPCount protocol - Full protocol
AUTHORS: Eszter Csibra, Guy-Bart Stan
[DESCRIPTION]
FPCount is a complete protocol for fluorescent protein calibration, consisting of:
1. FP expression/purification using Thermo's HisPur Cobalt Resin.
2. FP concentration determination in a microplate reader.
3. FP fluoresc... | ["[Harvesting and Washing] [ Day 2 ]\n\nBuffers:\nWash buffer = T50N150\n 50 mM Tris-Cl pH 7.5, 150 mM NaCl\n Doesn’t need protease inhibitors\n Can be substituted by T50N300\nResuspension buffer = T50N300+pi\n 50 mM Tris-Cl pH 7.5, 300 mM NaCl\n protease inhibitors (pi; 1 tablet/10ml) \n filter steri... |
49,131 | Data Processing and Image Registration | 1 | dx.doi.org/10.17504/protocols.io.bt8jnrun | https://www.protocols.io/view/data-processing-and-image-registration-bt8jnrun | Elizabeth Neumann, Nathan Heath Patterson, Lukasz Migas, Jamie Allen, Carrie Romer, Jeff Spraggins, Danielle Gutierrez | TITLE: Data Processing and Image Registration
AUTHORS: Elizabeth Neumann, Nathan Heath Patterson, Lukasz Migas, Jamie Allen, Carrie Romer, Jeff Spraggins, Danielle Gutierrez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Scope: </div><div class = "text-block">Annotate lipid species detected by MAL... | ["[Data Processing]\nExtract peak intensity from the calibrated dataset using one of the available options: 1a. Extract ion images based on an untargeted feature list that has not been narrowed down by the previous step. 1b. Extract ion images based on the identified feature list generated using the previous step. Note... |
70,330 | PARENTING AND SELF CRITICISM AMONG OFFSPRING: A SYSTEMATIC REVIEW | 1 | dx.doi.org/10.17504/protocols.io.261ge3oowl47/v1 | https://www.protocols.io/view/parenting-and-self-criticism-among-offspring-a-sys-cgw2txge | Mafia Shahzadi | TITLE: PARENTING AND SELF CRITICISM AMONG OFFSPRING: A SYSTEMATIC REVIEW
AUTHORS: Mafia Shahzadi
[DESCRIPTION]
Background:Self-criticism is the drill of negative self-appraisal and a tendency in which the individual reacts critically towards the self and points out one's own beliefs, actions, and thoughts that make th... | ["[PARENTING AND SELF CRITICISM AMONG OFFSPRING: A SYSTEMATIC REVIEW]"] |
37,780 | 30% Sucrose for Cryoprotection of brains after Perfusions | 1 | dx.doi.org/10.17504/protocols.io.bg5ujy6w | https://www.protocols.io/view/30-sucrose-for-cryoprotection-of-brains-after-perf-bg5ujy6w | Allen Institute for Brain Science | TITLE: 30% Sucrose for Cryoprotection of brains after Perfusions
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to prepare 30% Sucrose Solution in 0.1M phosphate buffer. 30% Sucrose in 0.1M phosphate buffer is used for the cryoprotect... | [] |
68,500 | Scoping Review Protocol: Instruments to Measure Information Searching Strategies of Health Professions Education Students | 1 | dx.doi.org/10.17504/protocols.io.bp2l61jj1vqe/v1 | https://www.protocols.io/view/scoping-review-protocol-instruments-to-measure-inf-ce5utg6w | Noviarina Kurniawati, Widyandana, Gandes Retno Rahayu | TITLE: Scoping Review Protocol: Instruments to Measure Information Searching Strategies of Health Professions Education Students
AUTHORS: Noviarina Kurniawati, Widyandana, Gandes Retno Rahayu
[DESCRIPTION]
Introduction: Health professionals are expected to be lifelong independent learners. Evidence-based medicine unde... | ["[Protocol and Registration] Author develops protocols and made it public by registering it in protocols.io.", "[Identifying the Research Question] The author identifies the research questions as follows:\nWhat is known from the literature about healthcare professions students’ online information searching strategies?... |
73,361 | Oligonucleotide-polymer conjugation for imaging mass cytometry | 4 | null | https://www.protocols.io/view/oligonucleotide-polymer-conjugation-for-imaging-ma-cjvrun56 | Danielschulz | TITLE: Oligonucleotide-polymer conjugation for imaging mass cytometry
AUTHORS: Danielschulz
[DESCRIPTION]
This protocol describes the procedures to label 5'-thiol modified oligonucleotides with maleimide carrying polymers which are also chelated with metal-ions.
This is the basis to perform RNAscope with Imaging Mas... | ["[Oligonucleotide resuspension and reduction] Resuspend lyophilized oligos in ddH20 (RNAase and DNAse free water) to a final concentration of 250 µM in 1.5 mL eppendorf tubes", "[Polymer metal chelation] Note: This part comes from the Fluidigm protocol \"Lanthanide Labeling of antibodies – PRD002 Version 11\"\n\nSpin... |
14,715 | Examine the relationship between expertise, performance, and gaze behavior | null | dx.doi.org/10.17504/protocols.io.sk3ecyn | null | Stephanie Brams1, Ignace Hooge2, Gal Ziv3, Siska Dauwe1, Ken Evens4, Tony De Wolf4, Oron Levin1, Johan Wagemans5, Werner F Helsen1 | TITLE: Examine the relationship between expertise, performance, and gaze behavior
AUTHORS: Stephanie Brams1, Ignace Hooge2, Gal Ziv3, Siska Dauwe1, Ken Evens4, Tony De Wolf4, Oron Levin1, Johan Wagemans5, Werner F Helsen1
[DESCRIPTION]
<p>To examine the relationship between expertise, performance, and gaze behavior, e... | ["The error-detection cockpit task (1st day): Participant scores on the RPE Borg scale his or her rate of perceived exertion at that moment.", "The participant receives instructions about the error-detection cockpit task: Monitor the instruments of the cockpit and click with the computer mouse on the instrument that sh... |
80,045 | Vidyadhara et al., 2023 “Dopamine transporter…Parkinson’s Disease" (L-DOPA treatment, IHC, HPLC, Microscopy Imaging and Analysis, Western Blotting, and FSCV) | 4 | dx.doi.org/10.17504/protocols.io.ewov1obeolr2/v1 | https://www.protocols.io/view/vidyadhara-et-al-2023-dopamine-transporter-parkins-csemwbc6 | Vidyadhara DJ | TITLE: Vidyadhara et al., 2023 “Dopamine transporter…Parkinson’s Disease" (L-DOPA treatment, IHC, HPLC, Microscopy Imaging and Analysis, Western Blotting, and FSCV)
AUTHORS: Vidyadhara DJ
[DESCRIPTION]
This protocol details L-DOPA treatment, Immunohistochemistry, HPLC, and electron microscopy tissue preparation an... | ["[L-DOPA treatment] Prepare the L-DOPA treatment solution by dissolving L-DOPA powder in 0.85% saline solution to achieve a concentration of 15 mg/kg body weight.", "[L-DOPA treatment] Select adult mice for the study and divide them into pre-treatment and post-treatment groups.", "[L-DOPA treatment] Conduct behavior t... |
86,799 | Synthetic COI spike-ins for use in metabarcoding-based insect biodiversity surveys | 1 | null | https://www.protocols.io/view/synthetic-coi-spike-ins-for-use-in-metabarcoding-b-cyzpxx5n | ela.iwaszkiewicz, Monika Prus-Frankowska, Piotr Łukasik | TITLE: Synthetic COI spike-ins for use in metabarcoding-based insect biodiversity surveys
AUTHORS: ela.iwaszkiewicz, Monika Prus-Frankowska, Piotr Łukasik
[DESCRIPTION]
We have designed two synthetic spike-ins, called Callio-synth and tp53-synth, for use in metabarcoding arthropod surveys. As the starting point for d... | ["[Sequence synthesizing, plasmid production and transformation into E. coli] Download FASTA file with the spike-in sequences from GitHub: https://github.com/ela-iwaszkiewicz/Synthetic_COI_spike-ins", "[Plasmid isolation from E. coli] The plasmids were isolated from E. coli using a GeneMATRIX PLASMID\nMINIPREP (EURx) k... |
106,114 | Splitting Adherent Cell Lines | 4 | dx.doi.org/10.17504/protocols.io.x54v9p51qg3e/v2 | https://www.protocols.io/view/splitting-adherent-cell-lines-djva4n2e | Carolina Lopez | TITLE: Splitting Adherent Cell Lines
AUTHORS: Carolina Lopez
[DESCRIPTION]
This protocol describes how to split and maintain adherent cell lines in culture. Examples of these cells are: A549 cells, LLCMK2 cells, and MDCK cells.
[STEPS]
SECTION: Protocol
1. Splitting Adherent cells
Wash flask 2x with sterile PBS.
Add ... | ["[Protocol] Splitting Adherent cells\nWash flask 2x with sterile PBS.\nAdd 2mL of trypsin/T75. Incubate at 37ºC for 2-3 mins or until cells are detached from the flask.\nAdd 8mL of cell culture media and pipette up and down. Transfer all the media to a 15mL tube. \nCentrifuge at 1200 rpm for 5 min. \nDiscard media and... |
69,589 | Detection of Tau ubiquitylation | 4 | dx.doi.org/10.17504/protocols.io.3byl4je4rlo5/v1 | https://www.protocols.io/view/detection-of-tau-ubiquitylation-cf7vtrn6 | Itika Saha, F. Ulrich Hartl, Mark S. Hipp | TITLE: Detection of Tau ubiquitylation
AUTHORS: Itika Saha, F. Ulrich Hartl, Mark S. Hipp
[DESCRIPTION]
This protocol describes the detection of ubiquitylated Tau from HEK293 cells stably expressing and propagating aggregates of Tau repeat domain fused to YFP (Sanders et al. Neuron, 2014; Saha et al, BioRxiv, 2022).
... | ["Harvest cells from 2 confluent wells of a 6 well plate.", "Lyse aggregate-containing cells by vortexing in cold RIPA buffer (Thermo) supplemented with protease inhibitor cocktail (Roche) and DNase. 20 mM N-ethylmalemide should be included in the lysis buffer to inhibit the activity of deubiquitinating enzymes.", "Bri... |
40,300 | Preparation of horseradish peroxidate (HRP) conjugated Peptostreptococcal protein-L by the periodate method. | 6 | dx.doi.org/10.17504/protocols.io.bjkkkkuw | https://www.protocols.io/view/preparation-of-horseradish-peroxidate-hrp-conjugat-bjkkkkuw | Angel Justiz-Vaillant | TITLE: Preparation of horseradish peroxidate (HRP) conjugated Peptostreptococcal protein-L by the periodate method.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This reagent can be used in ELISA, Western blotting and Dot blot to detect antigens and antibodies. It ... | ["Horseradish peroxidase (500 µg in 50 µl NaCO3 , pH 9.6) is mixed with freshly made sodium periodate solution (1.71 mg/ml) followed by incubation in the dark for 2 h.", "Mix 500 µg of protein-L (SpL) with an equal amount (500 micrograms) of a mix of horseradish peroxidase-sodium periodate.", "The mixture is incubated ... |
null | null | null | dx.doi.org/10.17504/protocols.io.feqbjdw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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91,116 | Photostimulation for optogenetics or uncaging | 1 | dx.doi.org/10.17504/protocols.io.rm7vzx2nrgx1/v2 | https://www.protocols.io/view/photostimulation-for-optogenetics-or-uncaging-c48kyzuw | enrico.zampese | TITLE: Photostimulation for optogenetics or uncaging
AUTHORS: enrico.zampese
[DESCRIPTION]
Protocol for photostimulation, to be combined with any other electrophysiology/imaging recording approach.
Once the desired patch clamp recording (e.g., cell attached, whole cell, perforated patch) and/or imaging (e.g., genetica... | ["[Preliminary steps] Obtain brain slices of region of interest according to existing protocols", "[Preliminary steps] Identify/patch neurons of interest and adjust settings according to the desired experimental protocol .", "[Preliminary steps] Once a recording on a cell of interest is established, set up the stimulat... |
70,982 | Protocol for Safe, Affordable, and Reproducible Isolation of SARS-CoV-2 RNA from Wastewater | 4 | dx.doi.org/10.17504/protocols.io.x54v9jrqzg3e/v3 | https://www.protocols.io/view/protocol-for-safe-affordable-and-reproducible-isol-chjet4je | Monica Trujillo, Kristen Cheung, Anna Gao, Irene Hoxie, Sherin Kannoly, Kaung Myat San, Davida S. Smyth, John Dennehy | TITLE: Protocol for Safe, Affordable, and Reproducible Isolation of SARS-CoV-2 RNA from Wastewater
AUTHORS: Monica Trujillo, Kristen Cheung, Anna Gao, Irene Hoxie, Sherin Kannoly, Kaung Myat San, Davida S. Smyth, John Dennehy
[DESCRIPTION]
The following protocol describes our workflow for processing wastewater ... | ["[Day 1 - Pasteurization and Solids removal] Sample handling\n\nThe samples must be kept at 4°C at all times after collection. Keep wastewater sample containers closed throughout the entire procedure except where noted.", "[Day 1 - Pasteurization and Solids removal] Pasteurization\n\nIn our protocol, samples are paste... |
67,919 | Keto Super Burn Gummies Reviews | Weight Loss Pills That Actually Work | 3 | dx.doi.org/10.17504/protocols.io.4r3l2owwxv1y/v1 | https://www.protocols.io/view/keto-super-burn-gummies-reviews-weight-loss-pills-cejptcmn | Keto Super Burn Gummies | TITLE: Keto Super Burn Gummies Reviews | Weight Loss Pills That Actually Work
AUTHORS: Keto Super Burn Gummies
[DESCRIPTION]
Keto Super Burn Gummies
[STEPS] | [] |
92,511 | ASAP protocol: Crystallization of Enterovirus D68 3C protease (PDB code 8CNX) | 1 | dx.doi.org/10.17504/protocols.io.n92ldm6jnl5b/v1 | https://www.protocols.io/view/asap-protocol-crystallization-of-enterovirus-d68-3-c6j7zcrn | ryan.lithgo, Peter Marples, daren.fearon, Lizbé Koekemoer | TITLE: ASAP protocol: Crystallization of Enterovirus D68 3C protease (PDB code 8CNX)
AUTHORS: ryan.lithgo, Peter Marples, daren.fearon, Lizbé Koekemoer
[DESCRIPTION]
The crystallization protocol and buffer conditions used to obtain Enterovirus D68 3C protease crystals suitable for XChem fragment screening. The crystal... | ["[Crystallization experiment] Protein and buffer requirements:\n32 µL1 millimolar (mM) \n2.88 mL \n16 µL seeds, dilution 1:100 000", "[Crystallization experiment] Dispense 30 µL into SwissCI 3 lens plate reservoir wells using a 100 µl multi-channel pipette.\nDispense 100 nL1 millimolar (mM) to each lens using th... |
65,257 | Condor CBD Gummies (ALERT FRAUD) Does This Condor CBD Gummies Formula Really Works? Read Shocking Report! | 3 | dx.doi.org/10.17504/protocols.io.81wgb6oz1lpk/v1 | https://www.protocols.io/view/condor-cbd-gummies-alert-fraud-does-this-condor-cb-cbyhspt6 | Working Health Supplements | TITLE: Condor CBD Gummies (ALERT FRAUD) Does This Condor CBD Gummies Formula Really Works? Read Shocking Report!
AUTHORS: Working Health Supplements
[DESCRIPTION]
Condor CBD Gummies is a CBD solution that claims to increase focus, reduce anxiety issues and also support better chronic issues. It is using Hemp plant-b... | [] |
66,307 | Plasmid construction | 4 | null | https://www.protocols.io/view/plasmid-construction-cczbsx2n | Adam Yokom | TITLE: Plasmid construction
AUTHORS: Adam Yokom
[DESCRIPTION]
plasmid construction
[STEPS]
5. Purify the DNA from gel using a Gel extraction kit (Bio Basic).
2. Linearize the backbone with restriction enzymes (NEB).
1. Amplify the insert gene fragment by PCR with primers including 21 nt of overlapping sequence with... | ["Purify the DNA from gel using a Gel extraction kit (Bio Basic).", "Linearize the backbone with restriction enzymes (NEB).", "Amplify the insert gene fragment by PCR with primers including 21 nt of overlapping sequence with the target gene.", "Run PCR products and linearized backbone in an agarose gel to confirm the ... |
60,198 | Injection of cholera toxin subunit B in the interscapular brown adipose fat and Stellate Ganglion dissection | 4 | dx.doi.org/10.17504/protocols.io.rm7vzykoxlx1/v1 | https://www.protocols.io/view/injection-of-cholera-toxin-subunit-b-in-the-inters-b62ergbe | Seoeun Lee, Daniele Neri, Lori Zeltser | TITLE: Injection of cholera toxin subunit B in the interscapular brown adipose fat and Stellate Ganglion dissection
AUTHORS: Seoeun Lee, Daniele Neri, Lori Zeltser
[DESCRIPTION]
Protocol to deliver cholera toxin subunit B into the interscapular brown fat of mice
[STEPS]
SECTION: Preparation
2. Anesthetize the anim... | ["[Preparation] Anesthetize the animal under isoflurane until there's no toe pinch reflex", "[Preparation] Prepare the surgery area by placing a clean paper towel on top of a heat pad", "[Preparation] Transfer the mouse to the surgery area, flat on its stomach on the heatpad. Place the nose cone to maintain anesthesia"... |
28,741 | Faktorová_et_al_2019_pTpPuc3_TpSil3p-eGFP | null | dx.doi.org/10.17504/protocols.io.8bdhsi6 | null | Jernej Turnsek | TITLE: Faktorová_et_al_2019_pTpPuc3_TpSil3p-eGFP
AUTHORS: Jernej Turnsek
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Details of the conjugation episome used to generate the TpSil3p-EGFP expressing </span><span style = "font-style:italic;">Thalassiosira pseudonana</span><span> strain as rep... | [] |
86,086 | Induction of starvation stress | 1 | null | https://www.protocols.io/view/induction-of-starvation-stress-cybexsje | Louise Uoselis | TITLE: Induction of starvation stress
AUTHORS: Louise Uoselis
[DESCRIPTION]
Induction of starvation stress using EBSS in HeLa cells
[STEPS]
SECTION: Day 1
1. Seed cells, aiming for a confluency of 90 – 100%
at the time of treatment the next day.
SECTION: Day 2
2. Feed cells for 1 h in an appropriate volume of stand... | ["[Day 1] Seed cells, aiming for a confluency of 90 – 100%\nat the time of treatment the next day.", "[Day 2] Feed cells for 1 h in an appropriate volume of standard growth media.", "[Day 2] Remove the media, and wash each well 3 times with an ample amount of room temperature PBS (eg. Wash with 3 mL of PBS per well of ... |
28,484 | RNA precipitation | null | dx.doi.org/10.17504/protocols.io.73chqiw | null | Liz Hughes | TITLE: RNA precipitation
AUTHORS: Liz Hughes
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol can be used to precipitate RNA to clean it up after extraction or to concentrate it. </div><div class = "text-block">Sodium acetate is highly efficient at precipitating nucleic acids and is th... | ["Make up the volume of your RNA solution to 500μl with RNase free water.", "Add 50 μl of room temperature 3M Sodium Acetate (pH 5.2-5.5)", "Add 500 μl of room temperature Propan-2-ol. Mix by inverting a few times.Leave at room temperature for 15-20 mins.", "Pellet the precipitated RNA by centrifugation at 12,000 g for... |
45,743 | Direct-lysis Saliva SARS-CoV-2 Detection | 4 | dx.doi.org/10.17504/protocols.io.bqwpmxdn | https://www.protocols.io/view/direct-lysis-saliva-sars-cov-2-detection-bqwpmxdn | Suzie Alarcon, Hannah Dose, Arturo Hernandez, Kyle Tanguay, Stephen Wilson | TITLE: Direct-lysis Saliva SARS-CoV-2 Detection
AUTHORS: Suzie Alarcon, Hannah Dose, Arturo Hernandez, Kyle Tanguay, Stephen Wilson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A One-Step RT-qPCR assay based on the CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel ha... | ["[Saliva Collection]\nPrepare saliva collection packetsInclude:Large RNase, DNase-free tube into which participant can deposit saliva2ml Safe-Lock Eppendorf tube containing 1.5 ml TE pH 82ml screw-cap gasketed cryo-safe tubeTransfer pipette (plastic bulb type)Barcodes for tubes, or human readable labelsAlcohol wipesBi... |
20,072 | U Mass - Chronic high-fat feeding | null | dx.doi.org/10.17504/protocols.io.xugfntw | null | Jason Kim | TITLE: U Mass - Chronic high-fat feeding
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">A high-fat diet of varying composition and percent fat is administered to induce obesity in mice. High-fat die... | ["High-fat diet is given ad libitum in mice.", "A stock bag of high-fat diet should be stored in a refrigerator.", "High-fat diet placed in cages should be replaced 2~3 times a week to avoid spoilage."] |
96,406 | Exposure to Bisphenol-A and Melatonin altered the Expression of Estrogen and Androgen Receptors in Neonatal Female rats | 0 | dx.doi.org/10.17504/protocols.io.261gedqryv47/v1 | https://www.protocols.io/view/exposure-to-bisphenol-a-and-melatonin-altered-the-dadw2a7e | Eniola Risikat Kadir | TITLE: Exposure to Bisphenol-A and Melatonin altered the Expression of Estrogen and Androgen Receptors in Neonatal Female rats
AUTHORS: Eniola Risikat Kadir
[DESCRIPTION]
This protocol details about grouping and breeding of animals, sample collection and processing, hormonal assay, biochemical assay and quantitative r... | ["[Grouping and breeding of animals] Cage adult male wistar rats of proven fertility overnight with females in proestrous phase of the cycle.", "[Grouping and breeding of animals] Gestational Day 1 (GD 1) is the day detect sperm cells in the vagina. Once pregnancy is confirmed, isolate the pregnant rat in a cage to st... |
26,063 | CRAC Analysis in Budding Yeast with HTP Tagged Proteins | 1 | dx.doi.org/10.17504/protocols.io.5ppg5mn | https://www.protocols.io/view/crac-analysis-in-budding-yeast-with-htp-tagged-pro-5ppg5mn | Rosey Bayne, Stefan Bresson, David Tollervey, Edward Wallace | TITLE: CRAC Analysis in Budding Yeast with HTP Tagged Proteins
AUTHORS: Rosey Bayne, Stefan Bresson, David Tollervey, Edward Wallace
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>CRAC (Cross-linking and cDNA Analysis) is a method that uses UV-crosslinking to identify which RNAs bind to an R... | ["[Yeast Culture Day 1]\nAutoclave milliQ water per CRAC sample in 5 litre flasks. For each flask prepare each of sterile 10x Yeast Nitrogen Base without Amino Acids (YNB-aas; Formedium), 10x Complete Synthetic Medium - Tryptophan (CSM -TRP; Formedium) and 20% glucose. These will be combined at Step 3 to make Syntheti... |
36,224 | Fish eDNA: DNA extraction from water samples filtered through Sterivex filter unit and preserved in buffer | 1 | dx.doi.org/10.17504/protocols.io.bfk8jkzw | https://www.protocols.io/view/fish-edna-dna-extraction-from-water-samples-filter-bfk8jkzw | Marine Vautier, Cécile Chardon, Isabelle Domaizon | TITLE: Fish eDNA: DNA extraction from water samples filtered through Sterivex filter unit and preserved in buffer
AUTHORS: Marine Vautier, Cécile Chardon, Isabelle Domaizon
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left"><span>The objective of this... | ["[Prepare the sample]\nNote : If the samples have been stored at RT or at 4°C, proceed directly to step 2. If the samples have been frozen, proceed to step 1.Defrost the sample at (about )Note : during this step heat the incubator at\n4 °C\n37 °C", "[Sample Lysis]\nFix the Sterivex cartriges on the vortex and vorte... |
null | null | null | dx.doi.org/10.17504/protocols.io.nb6dare | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes a step-by-step procedure for the production of autologous platelet-rich plasma for topical application in dogs.</p>
<p>This protocol was used in the following publication:</p>
<p>Tambella AM, Attili AR, Dini F, Palumbo Piccionello A, Vullo C, Serri E, ... | [] |
21,154 | UC Davis - ß hydroxy butyrate Protocol | null | dx.doi.org/10.17504/protocols.io.ywafxae | null | Peter Havel | TITLE: UC Davis - ß hydroxy butyrate Protocol
AUTHORS: Peter Havel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">When a sample is mixed with R1, AcAc in the sample is broken down to acetone by AADC. Upon addition of ... | ["Reconstitute R1 and R2 using the buffers provided.", "Add 4 µl of calibrator and sample to each well.", "Add 270 µl of R1 to each well. Incubate at 37°C for 5 minutes.", "Add 90 µl of R2 to each well. Incubate at 37°C for 2 minutes. Read at 405 nm. Then continue reading every 30 seconds for 2 minutes.", "Calculate th... |
null | null | null | dx.doi.org/10.17504/protocols.io.ibncame | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Please contact Dr. Steven Wilhelm (wilhelm@utk.edu) for additional information regarding this protocol.</p>
<p> </p>
<p>Modified from Wilhelm SW and CG Trick. 1995. Physiological profiles of <em>Synechococcu</em>s (Cyanophyceae) in iron-limiting continuous cultures. Journal... | [] |
101,138 | SCRMshaw: supervised cis-regulatory module prediction for insect genomes | 0 | dx.doi.org/10.17504/protocols.io.e6nvw1129lmk/v1 | https://www.protocols.io/view/scrmshaw-supervised-cis-regulatory-module-predicti-dezs3f6e | Hasiba Asma, Luna Liu, Marc S. Halfon | TITLE: SCRMshaw: supervised cis-regulatory module prediction for insect genomes
AUTHORS: Hasiba Asma, Luna Liu, Marc S. Halfon
[DESCRIPTION]
As the number of sequenced insect genomes continues to grow, there is a pressing need for rapid and accurate annotation of their regulatory component. SCRMshaw is a computational... | ["[Create Project directory] Create a Project Directory and subdirectories", "[Create Project directory] Under the project directory create subdirectories for saving input and output files respectively, for training data, and for scripts", "[Install SCRMshaw] From the project directory, clone the SCRMshaw_HD software f... |
72,745 | MTT assay | 4 | dx.doi.org/10.17504/protocols.io.ewov1oq9ylr2/v1 | https://www.protocols.io/view/mtt-assay-cjahuib6 | PMAT0001 | TITLE: MTT assay
AUTHORS: PMAT0001
[DESCRIPTION]
The MTT assay is based on the conversion of MTT (3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide into purple formazan crystals by LIVINGcells, which determines the mitochondrial activity of these cells. Viable cells contain NADPH-dependent oxidoreducta... | ["[Day 0] Passage cells which are at 80-90% confluence. Perform the usual trypsinization procedure.", "[Day 0] Seed 15,000 cells well (100uL) in complete DMEM (using 1X DMEM) in a 96 well plate. Make sure to fill the peripheral wells with 100uL of water. Only use the inner 60 wells for test wells. Seed cells in one pla... |
84,761 | RT-PCR amplification for the discrimination between wild type and mutation alleles in SARS-CoV-2 genomes from wastewater | 4 | dx.doi.org/10.17504/protocols.io.dm6gp3ww1vzp/v1 | https://www.protocols.click/view/rt-pcr-amplification-for-the-discrimination-betwee-cwzzxf76 | Ana C Reis, Daniela Pinto, Mónica V. Cunha | TITLE: RT-PCR amplification for the discrimination between wild type and mutation alleles in SARS-CoV-2 genomes from wastewater
AUTHORS: Ana C Reis, Daniela Pinto, Mónica V. Cunha
[DESCRIPTION]
This protocol describes the procedure of RT-PCR for the allelic discrimination between wild type and mutation alleles in spec... | ["[RT-PCR amplification] Prepare the amplification mixture as follows:\n\n \nTo the 15 μl of reaction mix, add 5 μl of wastewater RNA sample, or no-template control (DNAse/RNAse free water), or a wild-type AcroMetrix Coronavirus 2019 (COVID-19) RNA control, to complete 20 μl of reaction volume.", "Thermocycling conditi... |
6,453 | Typing E. coli ATCC 11303 with fluorescently stained virus. | null | dx.doi.org/10.17504/protocols.io.iivcce6 | null | Dr. Steven Wilhelm | TITLE: Typing E. coli ATCC 11303 with fluorescently stained virus.
AUTHORS: Dr. Steven Wilhelm
[DESCRIPTION]
<p>Please contact Dr. Steven Wilhelm (wilhelm@utk.edu) with any additional information regarding this protocol.</p>
[STEPS]
?. Grow a 4 hour culture of ATCC 11303 in Fe-free LB by inoculating ATCC 11303 from a... | ["Grow a 4 hour culture of ATCC 11303 in Fe-free LB by inoculating ATCC 11303 from an overnight culture grown in Fe-Free media into fresh media.\n[ATCC 11303 culture]", "Add 4 hour ATCC 11303 culture into a sterile 1.5 mL tube.\n[of 4 hour ATCC 11303 culture]", "Add YO-PRO stained T5.\n[YO-PRO]\nadd 10 ul DAPI, if need... |
50,569 | Overnight culture in Round-bottomed tubes | 4 | null | https://www.protocols.io/view/overnight-culture-in-round-bottomed-tubes-bvmhn436 | Wolfram Moebius | TITLE: Overnight culture in Round-bottomed tubes
AUTHORS: Wolfram Moebius
[DESCRIPTION]
This protocol describes how to produce an overnight bacterial culture.
[STEPS]
SECTION: Prepare overnight culture
1. Create a streak plate and incubate at 37 °C .
SECTION: Prepare overnight culture
2. Label a 14 mL round-bott... | ["[Prepare overnight culture] Create a streak plate and incubate at 37 °C .", "[Prepare overnight culture] Label a 14 mL round-bottom falcon tube with name, date, strain and any other contents. Transfer 5 mL LB media into the falcon tube.", "[Prepare overnight culture] Using an inoculation loop, pick an E.coli isolat... |
28,449 | MojoSort™ Selection Kits Protocol - 5 | null | dx.doi.org/10.17504/protocols.io.7z9hp96 | null | Sam Li | TITLE: MojoSort™ Selection Kits Protocol - 5
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Product description and procedure summary:</span></div><div class = "text-block">Target cells are either selected or depleted by incubating the sample with t... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes.", "In the final wash of your sample preparation, resuspend the cells in MojoSort™ Buffer by adding up to 4 mL in a 5 mL (12 x 75 mm) polypropylene tube.Note: Keep MojoSort™ Buffer on ice throughout the procedure.", "Filter the cells with... |
90,949 | protocols.io academic and non-profit contract | 1 | dx.doi.org/10.17504/protocols.io.e6nvwk5j7vmk/v6 | https://www.protocols.io/view/protocols-io-academic-and-non-profit-contract-c43dyyi6 | protocols.io team | TITLE: protocols.io academic and non-profit contract
AUTHORS: protocols.io team
[DESCRIPTION]
Template Contract
This contract is hereby made between the UNIVERSITY/ORGANIZATION (Univ) and ZappyLab, Inc. (DBA “protocols.io”).
DATE:December 13, 2021START DATE:December 27, 2021END DATE:December 26, 2022DESCRIPTION OF S... | ["[Activation] Within thirty (30) days from the Start Date, Univ will provide to protocols.io a list of IP addresses for on-campus user notification about free Premium workspaces.", "[Activation] Within two (2) weeks from the Start Date, protocols.io will enable free Premium workspaces accounts to be created by any Uni... |
20,647 | Case - Intraperitoneal Insulin Tolerance Test | null | dx.doi.org/10.17504/protocols.io.yefftbn | null | Henri Brunengraber | TITLE: Case - Intraperitoneal Insulin Tolerance Test
AUTHORS: Henri Brunengraber
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This is the standard protocol for routine insulin tolerance testing. It is performed on a... | ["Fast mice for overnight or for 6 hours. Remove mouse from cage and put into a clean cage with water and no food.", "Label the mice using a marker on their tail to quickly tell them apart", "Weigh each mouse and record weight. Calculate the amount of insulin needed for 0.75U to 1.0 U /kg body weight. Record the volume... |
null | null | null | dx.doi.org/10.17504/protocols.io.u26eyhe | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
Make sure you have all necessary equipment, reagents and PCR primers before begining the protocol.
For preparation of multiple samples please, use 'START EXPERIMENT' then 'SCALE PROTOCOL'.
[GUIDELINES]
Workflow was designed and optimised for sample preparation of 16S rRNA gen... | ["[PCR amplification of 16S rRNA gene] {\"blocks\":[{\"key\":\"24q86\",\"text\":\" Master Mix - combine the following reagents using volumes below:\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"7rn5f\",\"text\":\" \",\"type\":\"unstyled\",\"depth\":0,\"inlineSt... |
86,707 | CAMbank: cfDNA BCT Field Processing v1 | 4 | null | https://www.protocols.io/view/cambank-cfdna-bct-field-processing-v1-cywtxxen | Eliah G Overbey, Krista A Ryon, jak, Christopher E Mason | TITLE: CAMbank: cfDNA BCT Field Processing v1
AUTHORS: Eliah G Overbey, Krista A Ryon, jak, Christopher E Mason
[DESCRIPTION]
Field processing of cfDNA BCTs for the Cornell Aerospace Medicine Biobank (CAMbank).
Instructions for preserving: plasma and RBC Pellets.
[STEPS]
SECTION: Perform Venipuncture
1. After venipu... | ["[Perform Venipuncture] After venipuncture, invert the tubes gently 8 to 10 times to fully mix tube anticoagulant with blood sample.\n\nStore the tube upright at room temperature until centrifugation.\n\nNote: The tube stabilizes cell-free DNA for up to 14 days at 6 °C to 37 °C and CTCs for up to 7 days at 15 °C to 30... |
84,804 | Phylogenetic analyses | 5 | dx.doi.org/10.17504/protocols.io.5jyl8p5j6g2w/v1 | https://www.protocols.click/view/phylogenetic-analyses-cw3cxgiw | elizabeth fay, matthew daugherty | TITLE: Phylogenetic analyses
AUTHORS: elizabeth fay, matthew daugherty
[DESCRIPTION]
Original protocol by Matthew Daugherty and Elizabeth Fay.
[STEPS]
1. Human LRRK1 (accession NP_078928.3) and LRRK2 (accession NP_940980.4) were used as a BLASTp (Altschul et al., 1990)(http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM... | ["Human LRRK1 (accession NP_078928.3) and LRRK2 (accession NP_940980.4) were used as a BLASTp (Altschul et al., 1990)(http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome) search query against the Reference Sequence (RefSeq) (http://www.ncbi.nlm.nih.gov/RefSeq/) protein databa... |
69,463 | protocols.io academic and non-profit contract | 1 | dx.doi.org/10.17504/protocols.io.e6nvwk5j7vmk/v2 | https://www.protocols.io/view/protocols-io-academic-and-non-profit-contract-cf3xtqpn | protocols.io team | TITLE: protocols.io academic and non-profit contract
AUTHORS: protocols.io team
[DESCRIPTION]
Template Contract
This contract is hereby made between the UNIVERSITY/ORGANIZATION (Univ) and ZappyLab, Inc. (DBA “protocols.io”).
DATE:December 13, 2021START DATE:December 27, 2021END DATE:December 26, 2022DESCRIPTION OF S... | ["[Activation] Within thirty (30) days from the Start Date, Univ will provide to protocols.io a list of IP addresses for on-campus user notification about free Premium workspaces.", "[Activation] Within two (2) weeks from the Start Date, protocols.io will enable free Premium workspaces accounts to be created by any Uni... |
101,851 | Sonication of PFFs for use in vitro | 1 | dx.doi.org/10.17504/protocols.io.14egn69qql5d/v1 | https://www.protocols.io/view/sonication-of-pffs-for-use-in-vitro-dfp33mqn | Vijay Singh, Marta Castellana-Cruz, Nunilo Cremades, Laura Volpicelli-Daley | TITLE: Sonication of PFFs for use in vitro
AUTHORS: Vijay Singh, Marta Castellana-Cruz, Nunilo Cremades, Laura Volpicelli-Daley
[DESCRIPTION]
Animal models that accurately recapitulate the accumulation of alpha-synuclein (α-syn) inclusions, progressive neurodegeneration of the nigrostriatal system and motor deficits c... | ["[PFF Sonication] Transfer to within cell culture hood", "[PFF Sonication] Fill Qsonica water reservoir with about 900 mL.", "[PFF Sonication] Turn on sonicator and recirculating chiller. Set the temperature at 10 °C and allow to cool.", "[PFF Sonication] Transfer tube to Qsonica tube holder for placement within the... |
64,956 | Topical Application of Insecticidal Active Ingredients | 1 | dx.doi.org/10.17504/protocols.io.kxygxz4xov8j/v1 | https://www.protocols.io/view/topical-application-of-insecticidal-active-ingredi-cbn4smgw | Edmund J. Norris, Joel R. Coats | TITLE: Topical Application of Insecticidal Active Ingredients
AUTHORS: Edmund J. Norris, Joel R. Coats
[DESCRIPTION]
The development of new insecticidal formulations is important to overcome the burgeoning hurdle of insecticide resistance in field populations of mosquitoes and other pest arthropods. In order to standa... | ["[Anesthetize Mosquitoes] Take a container of all female mosquitoes and gently introduce carbon dioxide gas to anesthetizeindividuals. From a gas cylinder equiped with a regulator and a hose, slowly increase the rate of flowing CO2 to a gentle stream. Flow CO2 into container with mosquitoes (cover hand over container ... |
101,126 | Purification of BCL2L13-GST | 0 | dx.doi.org/10.17504/protocols.io.rm7vzjj12lx1/v1 | https://www.protocols.io/view/purification-of-bcl2l13-gst-deze3f3e | Elias Adriaenssens | TITLE: Purification of BCL2L13-GST
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol details the purification of BCL2L13-GST.
[STEPS]
SECTION: Purification - BCL2L13-GST
1. To purify BCL2L13-GST, fuse the cytosol-exposed domain of BCL2L13 (1-463aa) to a C-terminal GST-tag through cloning into a pET-DUET1 vector... | ["[Purification - BCL2L13-GST] To purify BCL2L13-GST, fuse the cytosol-exposed domain of BCL2L13 (1-463aa) to a C-terminal GST-tag through cloning into a pET-DUET1 vector (available on Addgene).", "[Purification - BCL2L13-GST] Introduce the point mutants by in vitro mutagenesis to generate \nBCL2L13 W275A/I278A (ΔLIR1)... |
90,725 | Expression and Purification of RH proteins via MBP affinity tag | 4 | dx.doi.org/10.17504/protocols.io.j8nlko6nwv5r/v1 | https://www.protocols.io/view/expression-and-purification-of-rh-proteins-via-mbp-c4udyws6 | Dan Tudorica | TITLE: Expression and Purification of RH proteins via MBP affinity tag
AUTHORS: Dan Tudorica
[DESCRIPTION]
Affinity purification followed by size exclusion chromatography.
[STEPS]
SECTION: Expression
1. Transform relevant bacterial expression constructs of the Rubicon/ Pacer RH domains into BL21 start (DE3) E. coli e... | ["[Expression] Transform relevant bacterial expression constructs of the Rubicon/ Pacer RH domains into BL21 start (DE3) E. coli expressing MBP or GST fusions. Expression constructs should be in pET-based, IPTG-inducible expression vectors. Select colonies via antibiotic screening, and pick individual colonies. Grow 20... |
81,243 | Total nucleic acid extraction - NucleoMag® DNA/RNA Water Kit (MACHEREY-NAGEL Inc.) | 4 | dx.doi.org/10.17504/protocols.io.q26g7yjq9gwz/v2 | https://www.protocols.io/view/total-nucleic-acid-extraction-nucleomag-dna-rna-wa-ctj3wkqn | Adélaïde Roguet, Melissa Schussman | TITLE: Total nucleic acid extraction - NucleoMag® DNA/RNA Water Kit (MACHEREY-NAGEL Inc.)
AUTHORS: Adélaïde Roguet, Melissa Schussman
[DESCRIPTION]
Total nucleic acid extraction from wastewater using NucleoMag® DNA/RNA Water Kit (Catalog no. 744220.1, MACHEREY-NAGEL Inc., Duren, Germany).
[BEFORE_START]
1. Clean the ... | ["[Total nucleic acid extraction] For HA filter extraction, let the sample thaw on ice and go to step 2. \n\nFor BCoV/BRSV extraction (in duplicate), add 5 µL of BCoV/BRSV solution to the 2-mL tube containing 475 µL MWA1. Vortex for 15 seconds (speed 7 out of 10) and flash freeze the tube. Go to step 4.\n\nFor Direct e... |
57,917 | Identification of the different phylogroups from the Klebsiella pneumoniae species complex by real-time PCR | 4 | dx.doi.org/10.17504/protocols.io.b4s5qwg6 | https://www.protocols.io/view/identification-of-the-different-phylogroups-from-t-b4s5qwg6 | Elodie Barbier, Carla Rodrigues, Sylvain Brisse, Pascal Piveteau | TITLE: Identification of the different phylogroups from the Klebsiella pneumoniae species complex by real-time PCR
AUTHORS: Elodie Barbier, Carla Rodrigues, Sylvain Brisse, Pascal Piveteau
[DESCRIPTION]
KpSC phylogroup ID
We developed and optimized a real-time PCR for the identification of the different phylogr... | ["[Primers and Probes] The KpSC phylogroup ID : Primers, Probes and Amplicon length\n\n \n PhG -Target Forward (5‘ – 3‘) Reverse (5‘ – 3‘) Probe Quencher Reporter Amplicon length (bp) Kp1 - group_8970 CCTCAAACACGCCAATATGC TACCGCGACGAGTAAAGTGG GATCCATTGATTCCATTCGA... |
54,210 | Augur/Auspice/UShER SARS-CoV-2 Cluster Detection Workflow for the Terra Platform | 5 | null | https://www.protocols.io/view/augur-auspice-usher-sars-cov-2-cluster-detection-w-by7apzie | Anusha Ginni, Jill V Hagey, Michael Weigand, Technical Outreach and Assistance for States Team | TITLE: Augur/Auspice/UShER SARS-CoV-2 Cluster Detection Workflow for the Terra Platform
AUTHORS: Anusha Ginni, Jill V Hagey, Michael Weigand, Technical Outreach and Assistance for States Team
[DESCRIPTION]
The Titan_Augur workflow processes concatenated assembly fasta data for SARS-CoV-2 phylogenetic analysis and ... | ["[Setup Terra and Google Cloud Accounts]", "[Import Augur workflows from Dockstore] Importing the Titan_Augur Workflows from Dockstore to the Terra User Workspace\n\nNote: The Augur workflow includes two steps: Titan_Augur_Prep and Titan_Augur_Run.\n\nThe Titan_Augur_Prep workflow prepares the metadata and assembly fa... |
102,152 | Microwave synthesis of low molecular weigth deacylated chitosan | 6 | dx.doi.org/10.17504/protocols.io.x54v9d6w4g3e/v3 | https://www.protocols.io/view/microwave-synthesis-of-low-molecular-weigth-deacyl-dfzg3p3w | Maria J Torres, Eric S McLamore, Geisianny AM Moreira | TITLE: Microwave synthesis of low molecular weigth deacylated chitosan
AUTHORS: Maria J Torres, Eric S McLamore, Geisianny AM Moreira
[DESCRIPTION]
This protocol describes the synthesis of low molecular weight deacylated chitosan using microwave irradiation. The process requires approximately 2.5 hours (including base... | ["[SECTION 1) Materials and solution preparation] Prepare reaction vials\n\nCheck the vial cap and Teflon liner to make sure neither is damageddamage to the cap and both are clean (Fig 1A-B)", "[SECTION 1) Materials and solution preparation] Add solution to the reaction vial.\n\nPipette 8000 µL of 1% deacylated chitosa... |
104,320 | Laser Capture Microdissection Assisted Spatial Proteomics | 0 | dx.doi.org/10.17504/protocols.io.kqdg32b51v25/v1 | https://www.protocols.io/view/laser-capture-microdissection-assisted-spatial-pro-dh4838zw | Zhenda Wang, Yuexin Chen, Janine Gote-Schniering, Herbert Schiller | TITLE: Laser Capture Microdissection Assisted Spatial Proteomics
AUTHORS: Zhenda Wang, Yuexin Chen, Janine Gote-Schniering, Herbert Schiller
[DESCRIPTION]
This protocol was used to generate spatial proteomics dataset from pediatric lung, as a part of the CZI-MPII project.
For more information: Mapping the Pediatric In... | ["[Tissue sectioning] Prepare consecutive FFPE tissue sections series on PEN slides and SuperFrost Plus slides according to the experiment design.", "[Tissue sectioning] Ideally, cut all slides from the same FFPE block in one sitting (no extra trimming in between). Sections should be thick on PEN slides for LCM, and ... |
54,941 | RNA extraction from wastewater for detection of SARS-CoV-2 | 4 | dx.doi.org/10.17504/protocols.io.bzv5p686 | https://www.protocols.io/view/rna-extraction-from-wastewater-for-detection-of-sa-bzv5p686 | David Findlay, Julie Bolland, Brindusa Cerghizan, Kirsty Campbell, David Thomson, Alexander Corbishley, David Gally, Stephen Fitzgerald, Alison Tidswell, Sean McAteer, Livia C T Scorza | TITLE: RNA extraction from wastewater for detection of SARS-CoV-2
AUTHORS: David Findlay, Julie Bolland, Brindusa Cerghizan, Kirsty Campbell, David Thomson, Alexander Corbishley, David Gally, Stephen Fitzgerald, Alison Tidswell, Sean McAteer, Livia C T Scorza
[DESCRIPTION]
As part of the global response to the 2019 n... | ["[Sample preparation] Remove solid matter from wastewater samples by centrifugation at 4669 x g, 10 min, 4 °C", "[RNA Concentration] Concentrate samples ~ by centrifugation (1500 x g, 10 min, 4 °C)", "[RNA Concentration] Check the level of the concentrate in the filter device by transferring the concentrate to a pre-w... |
48,736 | HT2-280 Sorting Protocol | 4 | null | https://www.protocols.io/view/ht2-280-sorting-protocol-btt8nnrw | Morrisey Lab | TITLE: HT2-280 Sorting Protocol
AUTHORS: Morrisey Lab
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">HT2-280 Sorting Protocol</div></div>
[STEPS] | [] |
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