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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null | null | null | dx.doi.org/10.17504/protocols.io.ib3caqn | 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 the Handbook of Methods in Aquatic Microbial Ecology (p. 220)</p>
[STEPS]
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28,596 | Insert + Vector DNA Ligation | null | dx.doi.org/10.17504/protocols.io.76uhrew | null | iGEM Dusseldorf | TITLE: Insert + Vector DNA Ligation
AUTHORS: iGEM Dusseldorf
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Pipette mix the following components:</div><table border><tr style = "text-align:center;"><td> </td><td>A</td><td>B</td><td>C</td><td>D</td><td>E</td><td>F</td><td>G</td><td>H</td></tr><tr><... | [] |
51,469 | Data review | 5 | dx.doi.org/10.17504/protocols.io.bwhmpb46 | https://www.protocols.io/view/data-review-bwhmpb46 | Alise J. Ponsero | TITLE: Data review
AUTHORS: Alise J. Ponsero
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocols aims to details the steps necessary to review new data points for the "Database Justice League" project.</div></div>
[STEPS]
?. [Data download]
Once you have received the link to download you... | ["[Data download]\nOnce you have received the link to download your dataset, download the csv file locally.Make sure to save it on your computer in a convenient folder!The goal of this review process is to Ensure a quality control for the dataset collected by peersDiscuss and document potential choices that have to be ... |
18,300 | Sample preparation for single nuclei sequencing of brain | null | dx.doi.org/10.17504/protocols.io.v44e8yw | null | Anna Martinez Casals, Nicholas Mitsios | TITLE: Sample preparation for single nuclei sequencing of brain
AUTHORS: Anna Martinez Casals, Nicholas Mitsios
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Sample preparation for single nuclei sequencing using fresh frozen tissue from human postmortem brain. The protocol is a combination o... | ["[Nuclei isolation]\nPlace a Petri dish on dry ice and transfer the tissue there, cut it using a chilled scalpel. Transfer the tissue into the precooled Dounce homogenizer and keep the homogenizer on ice during the rest of the protocol ( to reduce heat caused by friction).", "[Nuclei isolation]\nHomogenize the tissue ... |
104,953 | Determination of free and protein-bound DA and NE, 5HT and Ach and their metabolites and oxidation products by UPLC-MS/MS method | 6 | dx.doi.org/10.17504/protocols.io.8epv5rmj6g1b/v1 | https://www.protocols.io/view/determination-of-free-and-protein-bound-da-and-ne-diqz4dx6 | Miquel Vila, Marta Gonzalez-Sepulveda | TITLE: Determination of free and protein-bound DA and NE, 5HT and Ach and their metabolites and oxidation products by UPLC-MS/MS method
AUTHORS: Miquel Vila, Marta Gonzalez-Sepulveda
[DESCRIPTION]
Protocol for the determination of free and protein-bound DA and NE, 5HT and Ach and their metabolites and oxidation produc... | ["[Preparation of the aminochrome (AC) external standard] Mix 500 µL of 1 millimolar (mM) with 500 µLof 2 millimolar (mM) disolved in 100 micromolar (µM) aqueous ammonium acetate buffer pH 5.8 at RT with vigorous shaking for 1 min.", "[Preparation of calibration curves] Prepare a stock solution of the IS in 25 millim... |
73,823 | Advanced Dynamic Weight Bearing system for mice | 4 | null | https://www.protocols.io/view/advanced-dynamic-weight-bearing-system-for-mice-ckb7usrn | Fanglin Lu | TITLE: Advanced Dynamic Weight Bearing system for mice
AUTHORS: Fanglin Lu
[DESCRIPTION]
We can assess spontaneous limb pain-like behaviors using advanced DWB apparatus, wherein changes in the postural equilibrium of each freely moving animal were tracked and analyzed.
This protocol outlines the procedures from calib... | ["[Calibration] Connect the sensor and the camera to the PC.", "[Data acquisition] Place the mouse in the chamber.\nAdjust the camera aperture and focus to get a bright and clear image.\nClick \"Capture\" to lauch the acquisition.\nInput the weight and click \"OK\".\n\n \nThe mouse is allowed to move freely in the cham... |
95,332 | Hydrogen peroxide decontamination of eDNA dedicated material | 1 | dx.doi.org/10.17504/protocols.io.kxygx36ozg8j/v1 | https://www.protocols.io/view/hydrogen-peroxide-decontamination-of-edna-dedicate-c9ccz2sw | Marine Vautier, Cyrielle Galiegue | TITLE: Hydrogen peroxide decontamination of eDNA dedicated material
AUTHORS: Marine Vautier, Cyrielle Galiegue
[DESCRIPTION]
The purpose of this protocol is to detail the material decontamination steps to be performed to remove all traces of DNA from environmental DNA (eDNA) dedicated material.
The use of concentrate... | ["[Material preparation] Pre and post equipment cleaning.\n\nPreparation of all material to be decontaminated.\n\nProvide a waste container to dispose of the hydrogen peroxide solution.\n\nPersonal protective equipment (gloves and protective gown and goggles) and ventilated hood.", "[Material decontamination] The aim o... |
null | null | null | dx.doi.org/10.17504/protocols.io.dr659d | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Protocol for labeling Gambierdiscus cells with FISH probes in PIG.
[BEFORE_START]
Turn on the incubator and set to correct temperature according to probe.<br />Get probes and Poly A out of freezer to thaw in dark location.<br /><br />
[STEPS]
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?.... | [] |
81,984 | Analysis of paracetamol and AT7519 in serum using LC-MS/MS | 6 | null | https://www.protocols.click/view/analysis-of-paracetamol-and-at7519-in-serum-using-cua8wshw | Natalie ZM Homer, Joanna Simpson | TITLE: Analysis of paracetamol and AT7519 in serum using LC-MS/MS
AUTHORS: Natalie ZM Homer, Joanna Simpson
[DESCRIPTION]
This protocol describes the extraction and targeted mass spectrometry analysis of two drugs - paracetamol and AT7519, a CKDI inhibitor, following enrichment with isotopically labelled internal stan... | ["[Extract calibration standard & Quality Control and samples by PPT] Complete a plate map for standards, quality controls and samples (MAKE SURE TO PLACE THEM COLUMN-WISE!) using the design as shown below. The attached excel can be downloaded and filled in with sample specific detail for a real plate map and real ... |
100,933 | LungMAP2 URMC cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) protocol | 1 | dx.doi.org/10.17504/protocols.io.81wgbzzyqgpk/v1 | https://www.protocols.io/view/lungmap2-urmc-cellular-indexing-of-transcriptomes-detd3ei6 | Jeffrey Malik, Gloria S Pryhuber, John Ashton, Ravi Misra, Cameron Baker, Gautam Bandyopadhyay, Heidie Huyck | TITLE: LungMAP2 URMC cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) protocol
AUTHORS: Jeffrey Malik, Gloria S Pryhuber, John Ashton, Ravi Misra, Cameron Baker, Gautam Bandyopadhyay, Heidie Huyck
[DESCRIPTION]
The LungMAP program has been working for over a decade to provide the lung communit... | ["[GEM Generation and Barcoding] Prepare Reagents for use \nEquilibrate gel beads to room temperature for 30 min. \nThaw, vortex, and centrifuge RT Reagent, Template Switch Oligo, and Reducing Agent B. Verify no precipitate in Reducing Agent B. \nCentrifuge RT Enzyme C before adding to Master Mix.", "[GEM Generation an... |
36,887 | Targeted proteomic LC-MS/MS analysis | 1 | dx.doi.org/10.17504/protocols.io.bf9xjr7n | https://www.protocols.io/view/targeted-proteomic-lc-ms-ms-analysis-bf9xjr7n | Yan Chen, Jennifer Gin, Christopher Petzold | TITLE: Targeted proteomic LC-MS/MS analysis
AUTHORS: Yan Chen, Jennifer Gin, Christopher Petzold
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details steps in targeted proteomic data acquisition with a standard-flow UHPLC-QQQ system. It was adapted from Chen, Y. et al. “A rapid meth... | ["[Proteomics: HPLC and Mass Spectromtery]\nThaw peptide samples, and transfer of each sample to LC autosampler vials (Agilent, Cat.# 5182-0567, 5182-0564) or 96-well plate (Bio-Rad, Cat.# HSP9655).\non ice\n30 µl", "[Proteomics: HPLC and Mass Spectromtery]\nLiquid chromatography tandem-mass spectrometry (LC-MS/MS) ana... |
70,004 | Perfusion-fixation procedure for adult rhesus monkeys | 1 | dx.doi.org/10.17504/protocols.io.5jyl8jn67g2w/v1 | https://www.protocols.io/view/perfusion-fixation-procedure-for-adult-rhesus-monk-cgkutuww | Yoland Smith | TITLE: Perfusion-fixation procedure for adult rhesus monkeys
AUTHORS: Yoland Smith
[DESCRIPTION]
This protocol details Perfusion-fixation procedure for adult rhesus monkeys.
[STEPS]
SECTION: Perfusion-fixation procedure for adult rhesus monkeys
1. Add glutaraldehyde to the fixative solution.
SECTION: Perfusion-fixati... | ["[Perfusion-fixation procedure for adult rhesus monkeys] Add glutaraldehyde to the fixative solution.", "[Perfusion-fixation procedure for adult rhesus monkeys] Start oxygenation of the Ringer’s solution.", "[Perfusion-fixation procedure for adult rhesus monkeys] Anesthetize the animal with Ketamine (10 mg/kg, i.m.) o... |
108,397 | A CellProfiler computational pipeline to quantify localization of PPM1H on mitochondria | 0 | dx.doi.org/10.17504/protocols.io.j8nlk8qk6l5r/v1 | https://www.protocols.io/view/a-cellprofiler-computational-pipeline-to-quantify-dm4m48u6 | Ebsy Jaimon, Suzanne R Pfeffer | TITLE: A CellProfiler computational pipeline to quantify localization of PPM1H on mitochondria
AUTHORS: Ebsy Jaimon, Suzanne R Pfeffer
[DESCRIPTION]
Here we present a CellProfiler (1) software pipeline to quantify the localization of PPM1H on mitochondria. In this work, we have fragmented the mitochondria by hypotoni... | ["[Batch process images and import files into CellProfiler] Use the FIJI macro as described in dx.doi.org/10.17504/protocols.io.3byl4bpo8vo5/v1 to maximum intensity Z project the images. Open the folder with the images that need to be processed, choose the channel and the output folder, run code for maximum intensity Z... |
33,585 | CODEX Preparation of Reporter 96-Well Plates | null | dx.doi.org/10.17504/protocols.io.bc2riyd6 | null | Jerelyn Nick, Marda Jorgensen | TITLE: CODEX Preparation of Reporter 96-Well Plates
AUTHORS: Jerelyn Nick, Marda Jorgensen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A CODEX® Reporter is a fluorescent dye conjugated to an oligonucleotide that is complementary to a specific oligonucleotide barcoded antibody. This protocol desc... | ["Prepare the Reporter Stock Solution (Based on the number of cycles and coverslips to be run ): ABCDEFGHIJ1 Prepare Reporter Stock Solution 2Number of cycles (wells) 5 9 10 15 18 20 27 36 45 3 cycles (wells)4 Nuclease Free Water 1220 2196 2440 3660 4392 4880 6588... |
103,283 | qPCR based multipathogen detection for SARS-CoV-2, CrAssphage and Hepatitis E virus from wastewater samples. | 0 | dx.doi.org/10.17504/protocols.io.n92ld8787v5b/v1 | https://www.protocols.io/view/qpcr-based-multipathogen-detection-for-sars-cov-2-dg4t3ywn | Dilip Abraham, Blossom Benny, Nirmal Kumar, Karthikeyan Govindan, Venkata Raghava Mohan | TITLE: qPCR based multipathogen detection for SARS-CoV-2, CrAssphage and Hepatitis E virus from wastewater samples.
AUTHORS: Dilip Abraham, Blossom Benny, Nirmal Kumar, Karthikeyan Govindan, Venkata Raghava Mohan
[DESCRIPTION]
This protocol outlines the steps for detecting multiple viral gene targets for the pathogen... | ["[Primer-Probe Panel] The following primers and probes are employed for the detection of SARS-CoV-2, CrAssphage and HEV gene targets.", "[Primer-Probe Reconstitution] To reconstitute the lyophilized primers/probes use the nmole information on the specification sheet received with the primers and probes.", "[Primer-Pro... |
54,644 | DNA Extraction from Bacteriophages - 96 well format | 1 | dx.doi.org/10.17504/protocols.io.bzkup4ww | https://www.protocols.io/view/dna-extraction-from-bacteriophages-96-well-format-bzkup4ww | Frej Larsen | TITLE: DNA Extraction from Bacteriophages - 96 well format
AUTHORS: Frej Larsen
[DESCRIPTION]
Extraction of viral DNA/RNA from culture lysate or filtered samples free from bacteria. The protocol is based on the Qiagen kit QIAamp Viral RNA Mini kit for 96 well plates and uses consumables from this kit as well as the ... | ["Pipet 1 µL 100x diluted Pierce Universal Nuclease (2.5units/uL) to each well of a Qiagen S-block", "Transfer 140 µL of each sample from the outer chamber of the CentrisArt filter tube to the S-block. Mix by pipetting", "Incubate for 5 min at room temperature", "Add 540 µL AVL buffer to inactivate nucleases and lyse... |
null | null | null | dx.doi.org/10.17504/protocols.io.tqbemsn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Isolated astrocyte cell culture preparation. Dissociation, preparation and plating of mice cortex neurons and glia cells on MEA. Isolatioin process of the culture from neurons, to obtain an isolated astrocyte culture.
[STEPS]
SECTION: Sample collection
?.
SECTION: Cell lysis
?... | ["[Sample collection] Dissect and place on ice cortices from pups (post natal day 0 or 1 mice).", "[Cell lysis] {\"blocks\":[{\"key\":\"euvce\",\"text\":\"1. Chop with scissors in a papain-based dissociation buffer (2.5 mM CaCl2, 0.83 mM EDTA, 137 U papain (Sigma-Aldrich)), 100 \\u03bcl DNAse (Sigma-Aldrich), 3\\u20135... |
33,664 | Radiographic protocol to quantify cranial tibial translation in dogs | null | dx.doi.org/10.17504/protocols.io.bc48iyzw | null | Adolfo Maria Tambella, Stefano Martin, Anna Rita Attili, Cecilia Vullo, Luca Omini | TITLE: Radiographic protocol to quantify cranial tibial translation in dogs
AUTHORS: Adolfo Maria Tambella, Stefano Martin, Anna Rita Attili, Cecilia Vullo, Luca Omini
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify"><span>This protocol describes a ... | ["BACKGROUND Canine cranial cruciate ligament (CrCL), in addition to other biomechanical functions, prevents cranial tibial translation [1-4]. The detection of tibial translation can aid revealing stifle joint instability as a result of CrCL injury. However, clinical diagnosis of CrCL insufficiency is subjective and di... |
38,739 | Bilateral Adeno-associated virus (AAV) injection into interscapular brown adipose tissue | 1 | dx.doi.org/10.17504/protocols.io.bh3tj8nn | https://www.protocols.io/view/bilateral-adeno-associated-virus-aav-injection-int-bh3tj8nn | Heike Muenzberg | TITLE: Bilateral Adeno-associated virus (AAV) injection into interscapular brown adipose tissue
AUTHORS: Heike Muenzberg
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol details how to inject AAV virus into each interscapular brown adipose tissue fat pad in the mouse. </div></div>
[STEPS]
?... | ["[Surgery]\nPlace a sterile towel on the surgery platform over the heating mat, another sterile towel in the anesthesia induction chamber.", "[Surgery]\nRecord the mouse’s body weight to prepare syringes for saline and analgesia treatment.\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... |
94,718 | A method to prepare Sera-Mag SpeedBeads for purification and size selection of nucleic acids | 4 | dx.doi.org/10.17504/protocols.io.x54v9p7b1g3e/v2 | https://www.protocols.io/view/a-method-to-prepare-sera-mag-speedbeads-for-purifi-c8q6zvze | John B. Ridenour, Rafal Donczew | TITLE: A method to prepare Sera-Mag SpeedBeads for purification and size selection of nucleic acids
AUTHORS: John B. Ridenour, Rafal Donczew
[DESCRIPTION]
In this protocol, we describe a method to prepare Sera-Mag Speedbeads for purification and size selection of nucleic acids. We additionally describe a method to va... | ["[Preparation of 10% (v/v) Tween 20] Place a 50 ml conical tube on a balance and tare the balance.", "[Preparation of 10% (v/v) Tween 20] Slowly add 5.475 g of Tween 20 to the conical tube using a serological pipette.", "[Preparation of 10% (v/v) Tween 20] Remove the conical tube from the balance and add 45 ml of Mill... |
45,242 | Using the Confocal Microscope with Enterococcus faecalis and NAO dye. | 4 | null | https://www.protocols.io/view/using-the-confocal-microscope-with-enterococcus-fa-bqe2mtge | Elizabeth Fozo | TITLE: Using the Confocal Microscope with Enterococcus faecalis and NAO dye.
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Using the Confocal Microscope with </span><span style = "font-style:italic;">Enterococcus faecalis </span><span>and NAO dye.</span></div></div>
... | ["[Steps]\nPrepare an Enterococcus faecalis overnight culture.", "[Steps]\nNext morning, dilute overnight E. faecalis to an OD600 of 0.01 in fresh BHI.", "[Steps]\nCheck OD600 after 3 hours.", "[Steps]\nIsolate 4mL of log phase culture and place in BD Facs tube.", "[Steps]\nCentrifuge 3500 RPM 5 to10 minutes.", "[Steps... |
77,372 | SOP - Routine SARS-CoV-2 sequencing data administration | 5 | dx.doi.org/10.17504/protocols.io.kxygx91zzg8j/v1 | https://www.protocols.io/view/sop-routine-sars-cov-2-sequencing-data-administrat-cps4vngw | Mateusz Jundzill, Riccardo Spott, Mara Lohde, Martin Hölzer, Adrian Viehweger, Christian Brandt | TITLE: SOP - Routine SARS-CoV-2 sequencing data administration
AUTHORS: Mateusz Jundzill, Riccardo Spott, Mara Lohde, Martin Hölzer, Adrian Viehweger, Christian Brandt
[DESCRIPTION]
This is a step-by-step standard operating protocol (SOP) for data administration using the MongoDB database for routine SARS-CoV-2 seque... | ["[Creating New Entries] Sample arrives from external or internal partner.", "[Creating New Entries] Sample entry creation. Fill the template CSV file with the given information and import it through MongoDB Compass. \n\nExample of a template CSV:\n \n \nSelect Import File and choose a file for data upload. Pick CSV i... |
null | null | null | dx.doi.org/10.17504/protocols.io.jprcmm6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Atrial fibrillation (AF) is the most common arrhythmia. The most common diagnostic method, 12-lead ECG, can record episodes of arrhythmia from which the type and severity can be determined. The Heart Spectrum Blood Pressure Monitor (P2, OSTAR Meditech Corp.) is used to measur... | [] |
22,521 | Validity of screening instruments for the detection of dementia and mild cognitive impairment in hospital inpatients: A systematic review of diagnostic accuracy studies - Study protocol | null | dx.doi.org/10.17504/protocols.io.z8zf9x6 | null | Aljoscha Benjamin Hwang, Stefan Boes, Thomas Nyffeler, Guido Schuepfer | TITLE: Validity of screening instruments for the detection of dementia and mild cognitive impairment in hospital inpatients: A systematic review of diagnostic accuracy studies - Study protocol
AUTHORS: Aljoscha Benjamin Hwang, Stefan Boes, Thomas Nyffeler, Guido Schuepfer
[DESCRIPTION]
<div class = "text-blocks"><div ... | ["[INTRODUCTION]\nRationaleDespite the absence of a cure for dementia, numerous dementia strategies emphasize earlier diagnosis and intervention. This drive toward earlier diagnosis and intervention has been accompanied by a debate about the value of arriving at a diagnosis of dementia earlier in the disease process. S... |
42,193 | Protocols for Bioinformatic Tools | 5 | null | https://www.protocols.io/view/protocols-for-bioinformatic-tools-bmfrk3m6 | TITLE: Protocols for Bioinformatic Tools
AUTHORS:
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In this lab, students will work through BLAST and the UCSC Genome browser to find and analyze information about their genes of interest. </div></div>
[STEPS]
?. [BLAST]
BLASTDo a BLAST search of a ge... | ["[BLAST]\nBLASTDo a BLAST search of a gene of interest.", "[UCSC Genome Browser]\nWhat diseases are associated with this gene?", "[UCSC Genome Browser]\nWhat Biochemical and Signaling Pathways is this gene involved in? Again, what is the signficance?", "[UCSC Genome Browser]\nWhat orthologs does this gene have? What i... | |
27,236 | Isolation of nuclei from frozen tissue for snMultiome, snATAC-seq, snRNA-seq, and other epigenomic/transcriptomic assays | 1 | dx.doi.org/10.17504/protocols.io.kxygxmr34l8j/v2 | https://www.protocols.io/view/isolation-of-nuclei-from-frozen-tissue-for-snmulti-6uchesw | Adam Turner, Fiorella Grandi, alia.johnson, Heather Chang, Shreya Menon, Serena Chang, Aayushi Shah, Hailey Modi, courtney.colston, Vitto Resnick, Ryan Corces | TITLE: Isolation of nuclei from frozen tissue for snMultiome, snATAC-seq, snRNA-seq, and other epigenomic/transcriptomic assays
AUTHORS: Adam Turner, Fiorella Grandi, alia.johnson, Heather Chang, Shreya Menon, Serena Chang, Aayushi Shah, Hailey Modi, courtney.colston, Vitto Resnick, Ryan Corces
[DESCRIPTION]
This prot... | ["[Before you start the protocol:] All steps should be performed on ice or at 4 °C. Pre-chill a swinging bucket centrifuge and a fixed angle centrifuge to 4 °C .", "[Before you start the protocol:] Pre-chill all Dounces and pestles to 4 °C in a fridge.", "[Before you start the protocol:] Pre-chill all tubes. For each s... |
75,991 | Stereologic Cell Population Estimates in Cleared Human Brain Tissue | 5 | dx.doi.org/10.17504/protocols.io.4r3l273dqg1y/v1 | https://www.protocols.io/view/stereologic-cell-population-estimates-in-cleared-h-cnfxvbpn | Bridget Wicinski, Patrick.hof | TITLE: Stereologic Cell Population Estimates in Cleared Human Brain Tissue
AUTHORS: Bridget Wicinski, Patrick.hof
[DESCRIPTION]
We provide a step-by-step protocol for stereologic assessment in the human cerebral cortex using cleared postmortem specimens with a laminar level of analysis for distinct neuronal population... | [] |
14,573 | Conidial production from M. fijiensis mycelium | null | dx.doi.org/10.17504/protocols.io.sgmebu6 | null | Leticia Peraza, Cecilia Rodríguez, Dalia Zapata | TITLE: Conidial production from M. fijiensis mycelium
AUTHORS: Leticia Peraza, Cecilia Rodríguez, Dalia Zapata
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Continuous </span><span style = "font-style:italic;">in vitro</span><span> conidial production from </span><span style = "font-style:it... | ["V8 juice\n[per litre]", "[V8 sporulation (V8S) medium]\nCalcium carbonate\n[per litre]", "Add Agar-agar\n[per litre]", "Mix step 1 and 2 in 1 L of distiller water for 15 min", "Measure pH and adjut to pH 6", "Sterilize at 1 pressure atmosphere and 120° C for 15 min", "Pour 25 mL of V8 sporulation medium into each Pet... |
null | null | null | dx.doi.org/10.17504/protocols.io.nz3df8n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is the protocol for the preparation of denaturing polyacrylamide gels and silver staining</p>
[BEFORE_START]
<p>Prepare:</p>
<p> </p>
<p>FORMAMIDE for Acrylamyde (10mL)</p>
<p> </p>
<ul>
<li>Formamide 9,8mL<br />EDTA 0,5M pH 8,0 125µL<br />Azul de Bromofenol 1µL<br />Xi... | [] |
89,019 | Plasma/serum sample preparation for untargeted MS-based metabolomic | 6 | null | https://www.protocols.io/view/plasma-serum-sample-preparation-for-untargeted-ms-c263yhgn | Carole MIGNÉ, charlotte JOLY, Stéphanie DURAND, Estelle Pujos-Guillot | TITLE: Plasma/serum sample preparation for untargeted MS-based metabolomic
AUTHORS: Carole MIGNÉ, charlotte JOLY, Stéphanie DURAND, Estelle Pujos-Guillot
[DESCRIPTION]
The following protocol describes the preparation of serum and plasma samples for non-targeted analysis by mass spectrometry coupled to liquid or gas ch... | ["[Sample preparation] Thaw the samples according to these conditions depending on the analysis to be carried out :", "[Sample preparation] Extract protein by adding ice-cold methanol to each sample under the following conditions :", "[Sample preparation] Mix and placed the samples at -20 °C for 30 min.", "[Sample pre... |
77,696 | Western blot - alpha-synuclein | 4 | dx.doi.org/10.17504/protocols.io.bp2l69pqdlqe/v1 | https://www.protocols.io/view/western-blot-alpha-synuclein-cp48vqzw | Michael J Hurley | TITLE: Western blot - alpha-synuclein
AUTHORS: Michael J Hurley
[DESCRIPTION]
This protocol describes how to detect alpha-synuclein in protein derived from STC-1 cells by western blot using DAB/peroxidase or ECL to visualise the bands.
[STEPS]
SECTION: Sample preparation
1. Sample preparation using either protein pel... | ["[Sample preparation] Sample preparation using either protein pellet from an extraction (step 1.1) or direct lysis (step 1.2)", "[Electrophoresis and transfer] Separate samples (~ 10 ug total protein) by polyacrylamide gel electrophoresis using precast Bolt™ or NuPAGE™ 12%, Bis-Tris, 1.0 mm, Mini Protein Gels at 180 ... |
95,111 | Modified RNeasy Mini Kit protocol for filter extractions - USF edition | 4 | dx.doi.org/10.17504/protocols.io.8epv59qd6g1b/v3 | https://www.protocols.io/view/modified-rneasy-mini-kit-protocol-for-filter-extra-c85fzy3n | Margaret M. Brisbin | TITLE: Modified RNeasy Mini Kit protocol for filter extractions - USF edition
AUTHORS: Margaret M. Brisbin
[DESCRIPTION]
RNA extraction protocol for filters - modification of RNeasy mini kit protocol
[STEPS]
SECTION: Prep
1. Wipe all surfaces inside the RNA hood with:
1. RNAase ZAP (this is a detergent so do not use ... | ["[Prep] Wipe all surfaces inside the RNA hood with:\n1. RNAase ZAP (this is a detergent so do not use much as it can leave a soapy residue)\n2. RNAse AWAY (this is a weak base, it can be used liberally but does not evaporate quickly)\n3. 70% ethanol (etOH), this can be used liberally and evaporates quickly \n\nuse lar... |
69,176 | Fluorescence intensity analyses | 1 | dx.doi.org/10.17504/protocols.io.5jyl8jrmdg2w/v1 | https://www.protocols.io/view/fluorescence-intensity-analyses-cfsytnfw | Ayse Ulusoy, Sinead O'Sullivan, Michael Helwig, Angela Rollar, Shirley Lee, Michael Klinkenberg, Rita Pinto-Costa, Donato Di Monte | TITLE: Fluorescence intensity analyses
AUTHORS: Ayse Ulusoy, Sinead O'Sullivan, Michael Helwig, Angela Rollar, Shirley Lee, Michael Klinkenberg, Rita Pinto-Costa, Donato Di Monte
[DESCRIPTION]
Fluorescence intensity analyses
[STEPS]
1.
Collect confocal z-stack images from fluorescent-labeled tissue samples. Here we ... | ["Collect confocal z-stack images from fluorescent-labeled tissue samples. Here we used DHE-treated mice tissue counter-stained with human alpha-synuclein or tissue co-immunolabeled with a human alpha-synuclein and SynO2 antibodies.", "[Ox-DHE fluorescent signal measurement] Create a 3D surface rendering model of h-alp... |
29,632 | Starvation & washing protocol for anaerobic ciliates | null | dx.doi.org/10.17504/protocols.io.868hzhw | null | Roxanne Beinart, Johana Rotterova | TITLE: Starvation & washing protocol for anaerobic ciliates
AUTHORS: Roxanne Beinart, Johana Rotterova
[STEPS]
?. [Cell picking]
To pick ciliate cells, use a sterile drawn glass Pasteur pipette, a sterile depression slide with multiple wells, and inverted microscope. Transfer several hundred live cells into clean medi... | ["[Cell picking]\nTo pick ciliate cells, use a sterile drawn glass Pasteur pipette, a sterile depression slide with multiple wells, and inverted microscope. Transfer several hundred live cells into clean media (0.22 μm filtered).", "[Cell washing]\nThen, pass the cells through 3 wells of 0.22 μm filtered clean media.",... |
null | null | null | dx.doi.org/10.17504/protocols.io.g2abyae | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Preparation of 1.5 mg/mL Sera-mag magnetic particles for DNA purification, a low cost Agencourt Ampure XP reagent substitute</p>
<p> </p>
<p>Adapted from B. Faircloth & T. Glenn, 11.19.11, Ecology and Evolutionary Biology, UCLA</p>
<p><br />https://ethanomics.files.wordpr... | [] |
43,704 | Microplate reader operating procedure V.2 | 1 | dx.doi.org/10.17504/protocols.io.bnwymffw | https://www.protocols.io/view/microplate-reader-operating-procedure-v-2-bnwymffw | Zhujun Wei | TITLE: Microplate reader operating procedure V.2
AUTHORS: Zhujun Wei
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We use Tecan Spark® multimode microplate reader to measure absorbance.</div></div>
[STEPS]
?. 10mTurn on the power and warm up for 10 minutes.
?. Open the program and select "New" to... | ["10mTurn on the power and warm up for 10 minutes.", "Open the program and select \"New\" to create a new process.", "Select \"Absorbance\" in the left column. There is a schematic of a 96-well plate in the middle of the screen.", "You can select the hole to be used according to the spotting hole, and the selected hole... |
null | null | null | dx.doi.org/10.17504/protocols.io.hagb2bw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.j8ccrsw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The human umbilical vein endothelial cell line EA.hy926 (ATCC; Mannasas, VA, USA) was cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum (FCS) in an atmosphere of 5% CO2/95% air and 37°C.</p>
<p>EA.hy926 cells (10<sup>5</sup>cells/plate... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.qjjdukn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A protocol for the making of 1M Propionic Acid for the use in Drosophila food. </p>
[BEFORE_START]
<p>Be sure to have the following materials: </p>
<ul>
<li>Propionic Acid, Sodium Salt</li>
<li>Hydrochloric Acid</li>
<li>Distilled water</li>
<li>Deionized water</li>
</ul>
[... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ht7b6rn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?. | [] |
103,561 | ATG9A-vesicle isolation protocol | 0 | dx.doi.org/10.17504/protocols.io.dm6gpzok8lzp/v1 | https://www.protocols.io/view/atg9a-vesicle-isolation-protocol-dhdh3236 | Daniel Bernklau, Justyna Sawa-Makarska, Julia Romanov | TITLE: ATG9A-vesicle isolation protocol
AUTHORS: Daniel Bernklau, Justyna Sawa-Makarska, Julia Romanov
[DESCRIPTION]
This protocol details about the ATG9-vesicle isolation.
[BEFORE_START]
Hap1 cells were previously CRISPR engineered in our lab to contain ATG9A endogenously tagged on the
C-terminus with mEGFP-3C-FLAG.... | ["[Day1: Cell lysis and binding to Flag beads] Equilibrate Flag beads\nAlways pellet the beads with 4000 rcf, 4 °C cooled 5415R centrifuge for 3’.", "[Day1: Cell lysis and binding to Flag beads] Wash 3x with MilliQ water", "[Day1: Cell lysis and binding to Flag beads] Wash 3x with Vesicle Isolation Buffer.", "[Day1: Ce... |
25,441 | RNA Isolation from Plant Tissue | null | dx.doi.org/10.17504/protocols.io.439gyr6 | null | Marc T. J. Johnson, Eric J. Carpenter, Zhijian Tian, Richard Bruskiewich, Jason N. Burris, Charlotte T. Carrigan, Mark W. Chase, Neil D. Clarke, Sarah Covshoff, Claude W. dePamphilis, Patrick P. Edger, Falicia Goh, Sean Graham, Stephan Greiner, Julian M. Hibberd, Ingrid Jordon-Thaden, Toni M. Kutchan, James Leebens-Mac... | TITLE: RNA Isolation from Plant Tissue
AUTHORS: Marc T. J. Johnson, Eric J. Carpenter, Zhijian Tian, Richard Bruskiewich, Jason N. Burris, Charlotte T. Carrigan, Mark W. Chase, Neil D. Clarke, Sarah Covshoff, Claude W. dePamphilis, Patrick P. Edger, Falicia Goh, Sean Graham, Stephan Greiner, Julian M. Hibberd, Ingrid J... | [] |
92,698 | Protocols for assembly of a serine integrase-based platform for functional validation of genetic switch controllers in eukaryotic cells | 2 | dx.doi.org/10.17504/protocols.io.rm7vzx945gx1/v1 | https://www.protocols.io/view/protocols-for-assembly-of-a-serine-integrase-based-c6r2zd8e | Marco A. de Oliveira, Lilian H. Florentino, Thais T. Sales, Rayane N. Lima, Luciana R. C. Barros, Cintia G. Limia, Mariana S. M. Almeida, Maria L. Robledo, Leila M. G. Barros, Eduardo O. Melo, Daniela M. Bittencourt, Stevens K. Rehen, Martín H. Bonamino, Elibio Rech | TITLE: Protocols for assembly of a serine integrase-based platform for functional validation of genetic switch controllers in eukaryotic cells
AUTHORS: Marco A. de Oliveira, Lilian H. Florentino, Thais T. Sales, Rayane N. Lima, Luciana R. C. Barros, Cintia G. Limia, Mariana S. M. Almeida, Maria L. Robledo, Leila M. G. ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.grhbv36 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div title="Page 2">
<div>
<div>
<p>The independent channels of the LI-COR MPX (Multiplex) Blotter make it possible to optimize blocking buffer, primary antibody dilution, and secondary antibody dilution on a single Western blot. Western blotting procedures that generate a blot ... | [] |
63,377 | Exipure Weight Loss Reviews 2022: Does It Work In 2022 ?? | 3 | dx.doi.org/10.17504/protocols.io.8epv59m75g1b/v1 | https://www.protocols.io/view/exipure-weight-loss-reviews-2022-does-it-work-in-2-b95rr856 | Exipure Reviews | TITLE: Exipure Weight Loss Reviews 2022: Does It Work In 2022 ??
AUTHORS: Exipure Reviews
[DESCRIPTION]
Exipure Reviews 2022: Does It Work In 2022 ??
[STEPS] | [] |
21,103 | Illumina metabarcoding protocol for the study of fungi in marine sediments | null | dx.doi.org/10.17504/protocols.io.yupfwvn | null | Lluvia Vargas, Jennyfers Chong-Robles, Asunción Lago-Lestón, Meritxell Riquelme | TITLE: Illumina metabarcoding protocol for the study of fungi in marine sediments
AUTHORS: Lluvia Vargas, Jennyfers Chong-Robles, Asunción Lago-Lestón, Meritxell Riquelme
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The study of fungi in marine sediments has received a growing attention in the re... | ["[Preparation of syringes]\nGrab a sterile syringe package and open it by the end, where the syringe tip is localized. Avoid moving the plunger.\nControl #1: Keep a microcentrifuge tube containing 1 mL of sterile HPLC grade water open during the syringe preparation. The tube has to be close to the working area, where ... |
18,542 | Protein interaction analysis of KaiC3 with various Kai homologs via yeast two-hybrid experiments (Growth Assay) | null | dx.doi.org/10.17504/protocols.io.wcnfave | null | Anika Wiegard, Christin Köbler, Katsuaki Oyama, Anja K. Dörrich, Chihiro Azai, Kazuki Terauchi, Annegret Wilde, Ilka Maria Axmann | TITLE: Protein interaction analysis of KaiC3 with various Kai homologs via yeast two-hybrid experiments (Growth Assay)
AUTHORS: Anika Wiegard, Christin Köbler, Katsuaki Oyama, Anja K. Dörrich, Chihiro Azai, Kazuki Terauchi, Annegret Wilde, Ilka Maria Axmann
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-b... | ["[Preparation of buffers and media]\nPrepareCSM ‑Leu ‑Trp agar (complete supplement mixture lacking leucine and tryptophan) CSM ‑Leu ‑Trp -His agar (complete supplement mixture lacking leucine, tryptophan and histidine) 3-AT solution, 1M", "[Transformation of yeast cells]\nPerform the transformation of yeast cells acc... |
71,446 | Measuring leaf carbon fractions with the ANKOM2000 Fiber Analyzer | 1 | dx.doi.org/10.17504/protocols.io.x54v9dyeqg3e/v1 | https://www.protocols.io/view/measuring-leaf-carbon-fractions-with-the-ankom2000-chzwt77e | Jocelyne Ayotte, Etienne Laliberté | TITLE: Measuring leaf carbon fractions with the ANKOM2000 Fiber Analyzer
AUTHORS: Jocelyne Ayotte, Etienne Laliberté
[DESCRIPTION]
Here we describe the standardized protocol used by the Canadian Airborne Biodiversity Observatory (CABO) to measure carbon fractions in leaf samples, using the ANKOM2000 Fiber Analyzer. Pr... | ["[Sample preparation] Use a solvent resistant marker to label the filter bags to be used in the analysis.", "[Sample preparation] Weigh and record the weight of each empty filter bag to the nearest 0.0001 g (in Fulcrum). Zero the balance.", "[Sample preparation] Place 0.45–0.50 g of prepared sample in up to 23 of the ... |
81,357 | A NEW ACQUISITION PROTOCOL FOR CONDUCTING STUDIES WITH CHILDREN: THE SCIENCE CAMP RESEARCH EXPERIENCE | 1 | dx.doi.org/10.17504/protocols.io.81wgby3y3vpk/v1 | https://www.protocols.click/view/a-new-acquisition-protocol-for-conducting-studies-ctpmwmk6 | Amparo V. Marquez-Garcia, Sam M. Doesburg, Grace Iarocci, Justine R. Magnuson, Sylvain Moreno | TITLE: A NEW ACQUISITION PROTOCOL FOR CONDUCTING STUDIES WITH CHILDREN: THE SCIENCE CAMP RESEARCH EXPERIENCE
AUTHORS: Amparo V. Marquez-Garcia, Sam M. Doesburg, Grace Iarocci, Justine R. Magnuson, Sylvain Moreno
[DESCRIPTION]
In the last 50 years, the study of brain development has brought major discoveries to educati... | ["Prior to the event:\nphone or email all event information to parents or guardians,\nemail consent forms and list with recommendations for the day of the event,\nhold information sessions with all the assistants,\ncompleting criminal background checks for all the assistants,\ntraining workshops for all assistants.", "... |
51,914 | Express Protocol NEBNext® ARTIC SARS-CoV-2 Library Prep Kit (Illumina®) (NEB #E7650S/L) without PCR Bead Cleanup | 1 | dx.doi.org/10.17504/protocols.io.bwxipfke | https://www.protocols.io/view/express-protocol-nebnext-artic-sars-cov-2-library-bwxipfke | Isabel Gautreau | TITLE: Express Protocol NEBNext® ARTIC SARS-CoV-2 Library Prep Kit (Illumina®) (NEB #E7650S/L) without PCR Bead Cleanup
AUTHORS: Isabel Gautreau
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details methods for the NEBNext® ARTIC SARS-CoV-2 Library Prep Kit (Illumina®), NEB #E7650S/L... | ["[cDNA Synthesis]\nGently mix and spin down the LunaScript RT SuperMix reagent. Prepare the cDNA synthesis reaction as described below:COMPONENT VOLUMERNA Sample8 µl(lilac) LunaScript RT SuperMix2 µlTotal Volume10 µlFor no template controls, mix the following components:COMPONENTVOLUME(white) Nuclease-free Water8 µl(l... |
98,134 | SARS-CoV-2 Mpro fluorescence dose response | 1 | dx.doi.org/10.17504/protocols.io.81wgbye9nvpk/v4 | https://www.protocols.io/view/sars-cov-2-mpro-fluorescence-dose-response-db3w2qpe | Haim Barr, Noa Lahav | TITLE: SARS-CoV-2 Mpro fluorescence dose response
AUTHORS: Haim Barr, Noa Lahav
[DESCRIPTION]
This is a functional, biochemical assay used to identify treatments for viral infectious disease that target SARS-COV-2 Main Protease (MPro).
Utilizing a direct enzyme activity measurement method, the experiment was perform... | ["[Prepare 384 Well Plate] PRIME Multi-Drop Combi Tube Dispensing Cassette with Assay Buffer by selecting the PRIME button on the Combi Dispenser until the tubes are filled completely.", "[Prepare 384 Well Plate] DISPENSE 10 µL to Columns 1 and 23 of assay plate\nNote: These will represent the inhibitor control column... |
101,144 | HTBE ALI System Infection & Sample Collections | 0 | null | https://www.protocols.io/view/htbe-ali-system-infection-amp-sample-collections-dezy3f7w | Briana L McGovern | TITLE: HTBE ALI System Infection & Sample Collections
AUTHORS: Briana L McGovern
[DESCRIPTION]
HTBE ALI System
[STEPS]
SECTION: Background on the HTBE ALI System
1. The air liquid interface (ALI) system provides a life-like experimental set up for human tracheal/bronchial epithelial cells. Cells are cultured (by ... | ["[Background on the HTBE ALI System] The air liquid interface (ALI) system provides a life-like experimental set up for human tracheal/bronchial epithelial cells. Cells are cultured (by Mattek) in a small circular insert. This insert is then gently placed, or optionally suspended, in a 6-well/12-well/24-well plate dep... |
45,008 | Triaxial mechanical testing of dog colon samples | 1 | dx.doi.org/10.17504/protocols.io.bp7qmrmw | https://www.protocols.io/view/triaxial-mechanical-testing-of-dog-colon-samples-bp7qmrmw | Bhavesh Patel, Yanmin Wang | TITLE: Triaxial mechanical testing of dog colon samples
AUTHORS: Bhavesh Patel, Yanmin Wang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the step followed to conduct ex vivo triaxial mechanical testing (inflation, extension, torsion) of dog colon samples on our custom buil... | ["[Collect tissue]\n1. At termination of the animal, open the abdominal cavity to expose the colon. 2. Identify a ~20 cm colon segment and isolate it with sutures or clamps at both ends. 3. Take a picture with a scale (Pic.1). 4. Dissect the segment. 5. Gently remove luminal content by squeezing it out, and clean rema... |
67,074 | Protocol for counting pathogen spores on hemocytometer | 3 | null | https://www.protocols.io/view/protocol-for-counting-pathogen-spores-on-hemocytom-cdras52e | Meghan Duffy | TITLE: Protocol for counting pathogen spores on hemocytometer
AUTHORS: Meghan Duffy
[DESCRIPTION]
This is a protocol to quantify the number of pathogen spores you have in a sample using a hemocytometer.
[STEPS] | [] |
28,109 | Preparation of Chemicals | null | dx.doi.org/10.17504/protocols.io.7pmhmk6 | null | NUS iGEM | TITLE: Preparation of Chemicals
AUTHORS: NUS iGEM
[STEPS]
?. Weigh x grams of desired chemical
?. Dissolve in sterile deionized water for IPTG and arabinose or DMSO for ATC
?. Syringe filter chemical solution using a 0.22-μm filter | ["Weigh x grams of desired chemical", "Dissolve in sterile deionized water for IPTG and arabinose or DMSO for ATC", "Syringe filter chemical solution using a 0.22-μm filter"] |
6,388 | Site directed mutagenesis by PCR | null | dx.doi.org/10.17504/protocols.io.igucbww | null | Tobias von der Haar | TITLE: Site directed mutagenesis by PCR
AUTHORS: Tobias von der Haar
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Design four primers in the following way: Primer 1 anneals upstream of the region to be mutatedPrimer 2 anneals downstream of the region to be mutated, in reverse direction, and has a 6 nt m... | ["Design four primers in the following way: Primer 1 anneals upstream of the region to be mutatedPrimer 2 anneals downstream of the region to be mutated, in reverse direction, and has a 6 nt mismatch to the target at its 3'-end.Primer 3 anneals downstream of primer 2 (not overlapping with the primer 2 site).Primer M an... |
98,956 | Imaging of cholinergic interneurons in post-mortem rodent tissue to identify striatal satellite astrocytes | 1 | dx.doi.org/10.17504/protocols.io.j8nlkkq31l5r/v1 | https://www.protocols.io/view/imaging-of-cholinergic-interneurons-in-post-mortem-dcvk2w4w | Shinil Raina, Stephanie J Cragg | TITLE: Imaging of cholinergic interneurons in post-mortem rodent tissue to identify striatal satellite astrocytes
AUTHORS: Shinil Raina, Stephanie J Cragg
[DESCRIPTION]
This protocol details confocal image acquisition steps and the analysis pipeline used to calculate inter-soma distance between cholinergic interneuron... | ["[Confocal Imaging Acquisition] Turn on the Leica LSM980 confocal microscope and Zen Blue imaging acquisition software.", "[Confocal Imaging Acquisition] Using a 10x objective, identify anatomical landmarks using the DAPI or ChAT/NeuN signal in the region of interest. This would include the corpus callosum for the dor... |
61,982 | Titan XL Male Enhancement | 1 | dx.doi.org/10.17504/protocols.io.6qpvr6m22vmk/v1 | https://www.protocols.io/view/titan-xl-male-enhancement-b8r6rv9e | Com SBMGame | TITLE: Titan XL Male Enhancement
AUTHORS: Com SBMGame
[DESCRIPTION]
Titan XL Male Enhancement (#1 Titan XL Testosterone Enhancer) - Does It Work for Male Testosterone?
Weaknesses among accomplices connected with their sexual exhibition are developing to an ever increasing extent. It is more normal in the male accompl... | [] |
49,623 | Protocol of the benchmark for designing and developing the National Edition of Aldo Moro's works | 1 | dx.doi.org/10.17504/protocols.io.bupxnvpn | https://www.protocols.io/view/protocol-of-the-benchmark-for-designing-and-develo-bupxnvpn | Sebastian Barzaghi | TITLE: Protocol of the benchmark for designing and developing the National Edition of Aldo Moro's works
AUTHORS: Sebastian Barzaghi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">This work aims to define a series of reference models that would se... | ["[Data analysis]\nA Jupyter Notebook has been created to document the whole benchmark process, including the code snippets used to produce visualizations.", "[Data collection]\nA sample of 30 editions has been selected for their analysis and evaluation on the basis of certain criteria. The evaluation criteria that hav... |
61,485 | Guion de entrevista en profundidad para profesorado sobre el impacto del método ECO en la docencia | 1 | dx.doi.org/10.17504/protocols.io.dm6gpby1plzp/v1 | https://www.protocols.io/view/guion-de-entrevista-en-profundidad-para-profesorad-b8amrsc6 | Juan Jesus Torres-Gordillo, Nazaret Tomé Miranda | TITLE: Guion de entrevista en profundidad para profesorado sobre el impacto del método ECO en la docencia
AUTHORS: Juan Jesus Torres-Gordillo, Nazaret Tomé Miranda
[DESCRIPTION]
El propósito de esta entrevista es conocer el impacto de la implementación del método ECO en la docencia universitaria desde la perspectiva... | [] |
47,142 | Discontinuation of mass azithromycin distribution for trachoma: a systematic review | 1 | dx.doi.org/10.17504/protocols.io.bsaenabe | https://www.protocols.io/view/discontinuation-of-mass-azithromycin-distribution-bsaenabe | hamidah.mahmud , Catherine Oldenburg | TITLE: Discontinuation of mass azithromycin distribution for trachoma: a systematic review
AUTHORS: hamidah.mahmud , Catherine Oldenburg
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The WHO recommends continuing azithromycin mass drug administration (MDA) for trachoma until endemic regions... | ["[Review questions ]\n1. What is the prevalence of clinical trachoma (TF) and ocular chlamydia infection pre-MDA and post MDA?", "[Review questions ]\n2. Is there a correlation between pre-treatment trachoma prevalence and return of trachoma infection prevalence after discontinuing oral azithromycin treatment?", "[Sea... |
54,754 | GCaMP6F Fluorescence in Ex Vivo Intestinal Preparation | 4 | dx.doi.org/10.17504/protocols.io.bzqap5se | https://www.protocols.io/view/gcamp6f-fluorescence-in-ex-vivo-intestinal-prepara-bzqap5se | Bryan Yoo, Jessica Griffiths, Sarkis Mazmanian | TITLE: GCaMP6F Fluorescence in Ex Vivo Intestinal Preparation
AUTHORS: Bryan Yoo, Jessica Griffiths, Sarkis Mazmanian
[DESCRIPTION]
Protocol for GCaMP6F imaging in ex vivo intestinal tissue used in Yoo et al 2021
[STEPS]
1.
Small intestinal tissue was quickly harvested from ChAT-Cre mice, flushed and placed in ox... | ["Small intestinal tissue was quickly harvested from ChAT-Cre mice, flushed and placed in oxygenated (95% O2, 5% CO2), ice cold Krebs-Henseleit solution for 1 hour followed by 15 min at room temperature.", "A segment was cut along the mesenteric attachment, and pinned flat (mucosa facing down) on a Sylgard-lined record... |
28,168 | Biochemical Measures of Neuropathy - Hydrogen Peroxide Assay | null | dx.doi.org/10.17504/protocols.io.7rghm3w | null | Eva Feldman | TITLE: Biochemical Measures of Neuropathy - Hydrogen Peroxide Assay
AUTHORS: Eva Feldman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">Oxidative stress is highly correlated with the metabolic changes caused by hypergl... | ["[Sample Preparation:]\nPrepare stock solutions above for Amplex Red Reagent, Reaction Buffer, HRP, 20 mM H²O² and Resorufin, sodium salt.", "Prepare H²O² standard curve. Label tubes 1-5. Add 999 µL 1X Reaction Buffer to tube 2. Add 100 µL 1X Reaction Buffer to tubes 2 – 5. Add 1 µL of 20 mM H²O² working dilution prep... |
37,755 | 0.1M Phosphate Buffer | 1 | dx.doi.org/10.17504/protocols.io.bg43jyyn | https://www.protocols.io/view/0-1m-phosphate-buffer-bg43jyyn | Allen Institute for Brain Science | TITLE: 0.1M Phosphate Buffer
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to prepare 0.1M Phosphate Buffer. 0.1M Phosphate Buffer is used in the preparation of Sucrose solutions for cryoprotection.</div><div class = "text-block"><sp... | [] |
40,646 | Comparative efficacy of statin and antihypertensive agent combinations: a network meta-analysis of randomized controlled trials | 1 | dx.doi.org/10.17504/protocols.io.bjxekpje | https://www.protocols.io/view/comparative-efficacy-of-statin-and-antihypertensiv-bjxekpje | Ioannis Bellos | TITLE: Comparative efficacy of statin and antihypertensive agent combinations: a network meta-analysis of randomized controlled trials
AUTHORS: Ioannis Bellos
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Hypertension and dyslipidemia often co-occur, significantly increasing the risk of cardiovasc... | ["Background: Hypertension often occurs concomitantly with dyslipidemia, increasing the risk of adverse cardiovascular outcomes. These two entities both contribute on endothelial dysfunction and insulin resistance and thus can act synergistically in promoting atherosclerotic disease. For this reason, lipid-lowering dr... |
49,240 | Self Pollinating Tobacco | 1 | dx.doi.org/10.17504/protocols.io.bubynspw | https://www.protocols.io/view/self-pollinating-tobacco-bubynspw | Lynn Doran | TITLE: Self Pollinating Tobacco
AUTHORS: Lynn Doran
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for self pollination of tobacco. Validated on Petite Havana and Samsun varieties.</div></div>
[STEPS]
?. Grow tobacco plants to flowering.
?. Trim off lower florets of the chose inflorescen... | ["Grow tobacco plants to flowering.", "Trim off lower florets of the chose inflorescence to create a clean section of stalk to attach the pollination bag to.", "Choose an inflorescence to self pollinate. Tobacco tillers and will generate multiple inflorescences per plant. Any inflorescence will produce seed but the p... |
30,818 | NCBI data curation protocol | null | dx.doi.org/10.17504/protocols.io.bacaiase | null | Ruth Timme, Maria Balkey, Sai Laxmi Gubbala Venkata, Robyn Randolph, William Wolfgang, Errol Strain | TITLE: NCBI data curation protocol
AUTHORS: Ruth Timme, Maria Balkey, Sai Laxmi Gubbala Venkata, Robyn Randolph, William Wolfgang, Errol Strain
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">PURPOSE: </span><span>After data are submitted to NCBI submitters often en... | ["[BioProject Curation ]\nThe BioProject protocol details how to check if your BioProjects were submitted correctly and how to track and update them once they are live.", "[BioSample curation]\nThe BioSample protocol details how to check if your metadata was submitted correctly and how to track, update, or retract them... |
42,651 | Audiovisual stimuli creation | 1 | dx.doi.org/10.17504/protocols.io.bmv3k68n | https://www.protocols.io/view/audiovisual-stimuli-creation-bmv3k68n | HansRutger.Bosker | TITLE: Audiovisual stimuli creation
AUTHORS: HansRutger.Bosker
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes three ways of creating audiovisual stimuli that include (1) manipulations of the suprasegmental cues to lexical stress and (2) two different gestural alignments. Th... | ["[Experiment 1A (+2)]\nFor Experiment 1A, we created 12 disyllabic pseudowords that are phonotactically legal in Dutch (e.g., \"wasol\" /ʋa.sɔl/; see Table below). In Dutch, lexical stress is cued by three suprasegmental cues: amplitude, fundamental frequency (F0), and duration (Rietveld & Van Heuven, 2009). We create... |
107,691 | Development of mRNA-Based Vaccination for BRCA1-Mutated Cancers | 0 | dx.doi.org/10.17504/protocols.io.4r3l2qrx4l1y/v1 | https://www.protocols.io/view/development-of-mrna-based-vaccination-for-brca1-mu-dmej43cn | Roy Cohen | TITLE: Development of mRNA-Based Vaccination for BRCA1-Mutated Cancers
AUTHORS: Roy Cohen
[DESCRIPTION]
Title: A Phase I/II Clinical Trial of mRNA-Encoded BRCA1 Therapy in BRCA1-Mutated Cancers: Assessing Safety, Efficacy, and Tumor Suppression
Background: BRCA1 mutations are associated with a significantly increased ... | ["[Headline] Research Proposal: Development of mRNA-Based Vaccination for BRCA1-Mutated Cancers, Including BRCA1 Glioblastoma Cell Lines", "[Introduction] BRCA1 is a critical tumor suppressor gene involved in homologous recombination (HR) repair of DNA double-strand breaks, with mutations leading to higher susceptibili... |
48,196 | Chimeric Protein-LAG and Streptococcal protein G sandwich ELISA | 1 | dx.doi.org/10.17504/protocols.io.btbcniiw | https://www.protocols.io/view/chimeric-protein-lag-and-streptococcal-protein-g-s-btbcniiw | Angel Justiz-Vaillant | TITLE: Chimeric Protein-LAG and Streptococcal protein G sandwich ELISA
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This ELISA was used to study the interactions between protein-LAG (PLAG) and streptococcal protein-G (SpG) with different immunoglobulin preparations... | ["This ELISA was used to study the interactions between protein-LAG (PLAG) and streptococcal protein-G (SpG) with different immunoglobulin preparations of mammalian and avian species. The 96 well microtiter plate was coated overnight at 4°C with 2 µg/µl per well of PLAG in carbonate-bicarbonate buffer pH 9.6.", "The pl... |
null | null | null | dx.doi.org/10.17504/protocols.io.qz9dx96 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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86,040 | CD8 Cell Density In Substantia Nigra And Cerebral Peduncle Image Analysis | 1 | dx.doi.org/10.17504/protocols.io.5qpvo3roxv4o/v1 | https://www.protocols.io/view/cd8-cell-density-in-substantia-nigra-and-cerebral-cx9yxr7w | Hemanth Ramesh Nelvagal, Toby J Curless, Zane Jaunmuktane | TITLE: CD8 Cell Density In Substantia Nigra And Cerebral Peduncle Image Analysis
AUTHORS: Hemanth Ramesh Nelvagal, Toby J Curless, Zane Jaunmuktane
[DESCRIPTION]
QuPath is a bioimage analysis software designed for digital pathology and whole slide image analysis. This protocol describes how to measure CD8 density in t... | ["[Annotation] Manually annotate the substantia nigra and cerebral peduncle on NZConnect (Hamamatsu), a web-based whole-slide image (WSI) viewer.", "[Annotation] Download the annotations using a Python script then import into QuPath [1] using a Groovy script.", "[QuPath Deconvolution and CD8 Density Measurement] In QuP... |
null | null | null | dx.doi.org/10.17504/protocols.io.etfbejn | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<strong>Supplemental notes:</strong><br /><br />An A<sub>260</sub> may be determined on a UV spectrophotometer (usually a 1:100 dilution works well).<br />1 A<sub>260</sub> unit of PBCV-1 routinely yields 1.5-2.5 X 10<sup>10</sup> PFU/ml of virus.<br /><br />For critical work, a ... | [] |
45,333 | Protein Transfer | 4 | null | https://www.protocols.io/view/protein-transfer-bqhvmt66 | Steven Burgess | TITLE: Protein Transfer
AUTHORS: Steven Burgess
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is based on the assumption that TGX pre-cast gels have been used, the procedure is very similar for self-made gels, just that the running time is longer. Using the transfer packs is economic... | ["Place the membrane and bottom stack in the middle of the cassette base", "Place pre-cast gel in the middle of the membrane and roll to remove air-bubbles", "Place the top stack on top of the gel, gently roll", "Close the cassette lid, taking care not to disturb the gel", "Place the cassette in the Trans-Blot Turbo an... |
90,671 | ONT Library Prep for Split-seq cDNA | 1 | null | https://www.protocols.io/view/ont-library-prep-for-split-seq-cdna-c4spywdn | Jasmine Sakr | TITLE: ONT Library Prep for Split-seq cDNA
AUTHORS: Jasmine Sakr
[DESCRIPTION]
This protocol outlines the preparation of single-cell barcoded cDNA for Oxford Nanopore long-read sequencing. The input cDNA was initially barcoded using the Parse Biosciences Evercode platform for single-nucleus or single-cell RNA-seq (ref... | ["[Preparation] Thaw the following reagents:", "[End-prep] End-prep Reaction", "[End-prep] Clean-Up", "[Preparation] Prepare the following:", "[Preparation] Set heat block to 65°C.", "[End-prep] In a 1.5 mL tube, mix the following for each sample:", "[End-prep] Thoroughly mix by pipetting and avoid creating bubbles.", ... |
80,968 | Fabrication of fluid-walled dumbbells and generation of the human corticostriatal pathway | 1 | dx.doi.org/10.17504/protocols.io.kqdg39zb1g25/v1 | https://www.protocols.io/view/fabrication-of-fluid-walled-dumbbells-and-generati-ctbgwijw | Quyen Do, Federico Nebuloni, Richard Wade-Martins | TITLE: Fabrication of fluid-walled dumbbells and generation of the human corticostriatal pathway
AUTHORS: Quyen Do, Federico Nebuloni, Richard Wade-Martins
[DESCRIPTION]
This protocol described the generation of fluid-walled dumbbells for culturing of induced pluripotent stem cell-derived neurons with directional conn... | ["[Fabrication of Fluid-Walled Dumbbells] Preparation of petri dishes (Day -7)", "[Fabrication of Fluid-Walled Dumbbells] Pre-coat 6 cm petri dishes with 7 mL of Poly-D-lysine overnight.", "[Fabrication of Fluid-Walled Dumbbells] Remove Poly-D-lysine and wash with PBS twice.", "[Fabrication of Fluid-Walled Dumbbells] R... |
48,880 | High Throughput pre-analytical processing of wastewater settled solids for SARS-CoV-2 RNA analyses | 1 | dx.doi.org/10.17504/protocols.io.btyqnpvw | https://www.protocols.io/view/high-throughput-pre-analytical-processing-of-waste-btyqnpvw | Aaron Topol, Marlene Wolfe, Brad White, Krista Wigginton, Alexandria Boehm | TITLE: High Throughput pre-analytical processing of wastewater settled solids for SARS-CoV-2 RNA analyses
AUTHORS: Aaron Topol, Marlene Wolfe, Brad White, Krista Wigginton, Alexandria Boehm
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This process instruction describes the steps for pre-analytica... | ["[Preparation]\nProcess fresh samples stored at if possible. If analyzing a frozen sample, thaw at overnight. Set centrifuge temperature to .Set oven temperature to .Remove an aliquot of BCoV from the freezer and thaw .\n4 °C\n4 °C\n4 °C\n110 °C\non ice", "[Aliquot and Sample Storage]\nApply a label for each sample ... |
null | null | null | dx.doi.org/10.17504/protocols.io.fmnbk5e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Growth medium used at the Technical University Munich, Phytopathology, for cultivation of Fusarium spp.</p>
<p> </p>
<p>Note, we use 1/4 concentration.</p>
[STEPS]
?.
?.
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64,980 | Germination and seedling establishment for deep-flow hydroponics: The benefit of slant boards | 4 | dx.doi.org/10.17504/protocols.io.5jyl89b86v2w/v2 | https://www.protocols.io/view/germination-and-seedling-establishment-for-deep-fl-cbpusmnw | noah.langenfeld, Bruce Bugbee | TITLE: Germination and seedling establishment for deep-flow hydroponics: The benefit of slant boards
AUTHORS: noah.langenfeld, Bruce Bugbee
[DESCRIPTION]
Germination and seedling establishment for transplanting into hydroponics often uses porous substrates, but fine roots grow into these substrates, and they cannot be... | ["[Seeding] Clean a rigid plastic slant board and lay flat on a clean surface.", "[Seeding] Cut a piece of germination paper 10 cm in height and the same length as the slant board.", "[Seeding] Place germination paper on top of slant board.", "[Seeding] Place seeds on top of germination paper (about 9 cm from the botto... |
28,310 | Ancient Proteins Extraction Protocol | 1 | dx.doi.org/10.17504/protocols.io.7vwhn7e | https://www.protocols.io/view/ancient-proteins-extraction-protocol-7vwhn7e | Ashley Scott, Christina Warinner | TITLE: Ancient Proteins Extraction Protocol
AUTHORS: Ashley Scott, Christina Warinner
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a protocol for extracting total proteins from archaeological dental calculus. It is based on the filter-aided sample preparation (FASP) protocol first publish... | ["[Sample Prep]\nWeigh samples (aim for 5-10 mg per sample) and place within a 1.5 mL Safelock Eppendorf tube.", "[Sample Prep]\nAlso prepare empty tubes for blank extractions that should be processed alongside your samples to monitor for lab contamination", "[Demineralization]\nAdd 500 µL of 0.5 M EDTA to each sample,... |
34,000 | DNA extraction and Nanopore library prep from 15-30 whole flies | 1 | dx.doi.org/10.17504/protocols.io.bdfqi3mw | https://www.protocols.io/view/dna-extraction-and-nanopore-library-prep-from-15-3-bdfqi3mw | Bernard Kim, Danny E. Miller, Jeremy Wang | TITLE: DNA extraction and Nanopore library prep from 15-30 whole flies
AUTHORS: Bernard Kim, Danny E. Miller, Jeremy Wang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>We have been assembling the genomes of many </span><span style = "font-style:italic;">Drosophila</span><span> species. With ... | ["[(Optional) Hydration of ethanol-fixed tissue]\nPlace flies on a sheet of filter paper and briefly dab with a Kimwipe to remove excess ethanol, then transfer the flies to a 1.5 mL tube.", "[(Optional) Hydration of ethanol-fixed tissue]\nAdd Buffer STE to the tube with the flies.\n1 mL", "[(Optional) Hydration of eth... |
20,103 | Tracking acute response of C elegans to cocaine | null | dx.doi.org/10.17504/protocols.io.xvffn3n | null | Priota Islam | TITLE: Tracking acute response of C elegans to cocaine
AUTHORS: Priota Islam
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Our aim is to study addiction in C elegans with cocaine being the drug choice of abuse. This short experiment is done to check how the worms react instantaneously upon exposur... | ["[Preparing worms]\nChunk WT N2 on 3 maintenance plates Bleach the plates after 2 days following the protocol for Bleach synchronization of c elegans Refeed the starved L1s on 4 different plates that are OP50 seeded, 72hr prior to the experiment day", "[Preparing Imaging plates]\nPrepare and pour Low peptone NGM on 3... |
101,064 | Statistics analysis plan for evaluation of the safety and efficacy of 99mTc-3PRGD2 SPECT/CT for integrin αVβ3-targeted imaging of lung cancer and the lymph node metastases: a prospective, multicenter, self-controlled phase 3 clinical trial | 0 | null | https://www.protocols.io/view/statistics-analysis-plan-for-evaluation-of-the-saf-dexg3fjw | Zhaohui Zhu, Fan Wang | TITLE: Statistics analysis plan for evaluation of the safety and efficacy of 99mTc-3PRGD2 SPECT/CT for integrin αVβ3-targeted imaging of lung cancer and the lymph node metastases: a prospective, multicenter, self-controlled phase 3 clinical trial
AUTHORS: Zhaohui Zhu, Fan Wang
[DESCRIPTION]
This is the statistics anal... | ["[Study protocol] Introduction\n1.1 Background\nLung cancer affects 2.5 million new cases and leads to 1.8 million deaths each year around the world, ranking the most frequently diagnosed cancer and also the leading cause of cancer death of all cancers globally. With an increasing number of patients being diagnosed at... |
23,031 | Mayaro virus real-time RT-PCR - 2016 method | null | dx.doi.org/10.17504/protocols.io.2qxgdxn | null | Judy Northill, Ian Mackay | TITLE: Mayaro virus real-time RT-PCR - 2016 method
AUTHORS: Judy Northill, Ian Mackay
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Mayaro virus (MAYV) is an Alphavirus, transmitted by mosquitos in south and central America.</div><div class = "text-block">This assay is designed to detect a portion... | ["[Oligonucleotide sequences]\nAB1Name \n5'-3'\n2MAYV2016TM-FGCATCAGGHGAAGTCGTTG3MAYV2016TM-RCTGATCTGTGTGAAGGCAAA4MAYV2016TM-P6FAM-AGACGACCTGCAGTCAGTGATGGC-BHQ1\nAB1Name \n5'-3'\n2MAYV2016TM-FGCATCAGGHGAAGTCGTTG3MAYV2016TM-RCTGATCTGTGTGAAGGCAAA4MAYV2016TM-P6FAM-AGACGACCTGCAGTCAGTGATGGC-BHQ1", "[Reaction set-up]\nAssay ... |
49,461 | Microalgal culture | 4 | null | https://www.protocols.io/view/microalgal-culture-buivnue6 | Victoria Jackson | TITLE: Microalgal culture
AUTHORS: Victoria Jackson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A brief guide to subculturing marine eukaryotic microalgae such as prasinophytes, diatoms and dinoflagellates.</div></div>
[STEPS]
?. [Media preparation]
Microalgal culture media are comprised of mac... | ["[Media preparation]\nMicroalgal culture media are comprised of macronutrients (nitrates, phosphates, sulphates), micronutrients (trace metals) and vitamins.\nFor media preparation, it is best to prepare stock solutions of the macro- and micronutrients and vitamins at concentrations higher than those needed in the fin... |
94,296 | Protocol for α-synuclein (αSyn) proximity ligation assay (PLA) for detecting α-synuclein oligomers in rodents | 1 | dx.doi.org/10.17504/protocols.io.bp2l6x6eklqe/v1 | https://www.protocols.io/view/protocol-for-synuclein-syn-proximity-ligation-assa-c8byzspw | alba.nicolau, Thais Cuadros, Miquel Vila | TITLE: Protocol for α-synuclein (αSyn) proximity ligation assay (PLA) for detecting α-synuclein oligomers in rodents
AUTHORS: alba.nicolau, Thais Cuadros, Miquel Vila
[DESCRIPTION]
Protocol for α-synuclein (αSyn) proximity ligation assay (PLA) for detecting α-synuclein oligomers in rodents.
[STEPS]
SECTION: Antibody ... | ["[Antibody conjugation with Duolink Probes] Add 2 µL of Conjugation buffer from the Duolink PLUS (Merck, DUO92009-1KT) or Duolink MINUS (Merck, DUO92010-1KT) probes to rabbit anti-alpha-synuclein polyclonal antibody (Merck, AB5038P).\nNOTE: Consider that primary antibody should be made in goat, rabbit or mouse and sho... |
53,725 | Nuclei:Cytoplasm EKC Quantification Script (FIJI Macro) | 5 | null | https://www.protocols.io/view/nuclei-cytoplasm-ekc-quantification-script-fiji-ma-byp5pvq6 | Condon ND | TITLE: Nuclei:Cytoplasm EKC Quantification Script (FIJI Macro)
AUTHORS: Condon ND
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes how to download, install, and run the ImageJ/Fiji macro for quantifying the ratio fluorescence intensity of EKC in both the nuclei and cyto... | ["[Downloading & installing the macro]\nRetrieve a copy of the macro file from either the GitHub repo or from the Software Heritige archive", "[Downloading & installing the macro]\nDownload the .ZIP copy of the entire repo to your computer, and extract the compressed file.", "[Downloading & installing the macro]\nLaun... |
28,881 | pIgNAT vector | null | dx.doi.org/10.17504/protocols.io.8frhtm6 | null | Glen Wheeler, Andrea Highfield, Rowena Stern | TITLE: pIgNAT vector
AUTHORS: Glen Wheeler, Andrea Highfield, Rowena Stern
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">pIgNAT vector</div><div class = "text-block"><span>contains nourseothricin-resistance gene (NAT) codon-optimised for expression in </span><span style = "font-style:italic;">Isoc... | [] |
67,420 | Alpha Extracts Pure Hemp Oil Reviews & How to Order It? | 3 | dx.doi.org/10.17504/protocols.io.kqdg3pj4pl25/v1 | https://www.protocols.io/view/alpha-extracts-pure-hemp-oil-reviews-amp-how-to-or-cd34s8qw | karenbauers | TITLE: Alpha Extracts Pure Hemp Oil Reviews & How to Order It?
AUTHORS: karenbauers
[DESCRIPTION]
Alpha Extracts Pure Hemp Oil
[STEPS] | [] |
107,203 | High-throughput assay for quantifying bacterial biofilm formation | 0 | dx.doi.org/10.17504/protocols.io.14egn6o8ql5d/v1 | https://www.protocols.io/view/high-throughput-assay-for-quantifying-bacterial-bi-dkxb4xin | Lisa Bowers | TITLE: High-throughput assay for quantifying bacterial biofilm formation
AUTHORS: Lisa Bowers
[DESCRIPTION]
Biofilms are assemblages of single-celled organisms attached to a surface and encased in a sticky extracellular polymeric substance that the cells produce. Difficult to eradicate, they can have profound effects ... | ["[Set-up biofilms] Dilute overnight bacterial culture to an optical density (OD600) of 0.01 with fresh media.", "[Set-up biofilms] For the blank samples, pipette 100 uL of sterile media into at least 8 wells of a 96 well plate. These wells have media but no cells and no treatment. Purpose: account for the effect of me... |
7,730 | Survival analyses protocol: Killing wolves to prevent predation on livestock may protect one farm but harm
neighbors | 1 | dx.doi.org/10.17504/protocols.io.jsscnee | https://www.protocols.io/view/survival-analyses-protocol-killing-wolves-to-preve-jsscnee | Francisco Santiago-Ávila, Adrian Treves, Ari Cornman | TITLE: Survival analyses protocol: Killing wolves to prevent predation on livestock may protect one farm but harm
neighbors
AUTHORS: Francisco Santiago-Ávila, Adrian Treves, Ari Cornman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"> Large carnivores, such as wolves Canis lupus, are difficult to p... | ["Variables and Sample STATA 14 .Do file used for survival analyses at each spatial scale", "Here, we make available basic sample code for the statistical survival analyses employed in our manuscript. This code should allow for replication of analyses at all spatial scales for all datasets involved.*", "1. VARIABLES US... |
57,496 | Simple electroporation for efficient CRISPR/Cas9 genome editing in murine zygotes | 1 | dx.doi.org/10.17504/protocols.io.b4dyqs7w | https://www.protocols.io/view/simple-electroporation-for-efficient-crispr-cas9-g-b4dyqs7w | Simon E. Tröder, Branko Zevnik | TITLE: Simple electroporation for efficient CRISPR/Cas9 genome editing in murine zygotes
AUTHORS: Simon E. Tröder, Branko Zevnik
[DESCRIPTION]
Electroporation of zygotes represents a rapid alternative to the elaborate pronuclear injection procedure for CRISPR/Cas9-mediated genome editing in mice. However, current prot... | ["[guide RNA annealing] Resuspend lyophilized crRNA, tracrRNA and ssODN in T10E0.1 buffer to 100 µM (e.g., 5 nmol in 50 µl)\n(Store at -80 °C until use)", "[guide RNA annealing] Combine 5 µl crRNA (100 µM) and 5 µl tracrRNA (100 µM) in a nuclease-free PCR tube to yield an equimolar crRNA:tracrRNA duplex solution of 50 ... |
null | null | null | dx.doi.org/10.17504/protocols.io.drb52m | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in "<a href="https://www.protocols.io/view/One-step-growth-experiments-cyanophages-dra52d" target="_blank">One-step growth experiments (cyanophages)</a>"
[STEPS]
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18,769 | Retrograde labeling of brown adipose tissue (BAT)-projecting sympathetic neurons with cholera toxin B (CTB) | null | dx.doi.org/10.17504/protocols.io.wjrfcm6 | null | Seoeun Lee, Lori Zeltser | TITLE: Retrograde labeling of brown adipose tissue (BAT)-projecting sympathetic neurons with cholera toxin B (CTB)
AUTHORS: Seoeun Lee, Lori Zeltser
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to retrogradely label the Brown Adipose Tissue (BAT) - projecting sympathet... | ["[Survival surgery for CTB injection into BAT]\nAnesthetize the animal with isoflurane, and keep it anesthetized for the whole procedure", "[Survival surgery for CTB injection into BAT]\nOnce animal is unconscious (check with toe pinch), place it on heating pad and lubricate the eyes with ophthalamic ointment", "[Surv... |
92,395 | hsqc-tocsy_metab.nan | 5 | dx.doi.org/10.17504/protocols.io.8epv5x2rng1b/v2 | https://www.protocols.io/view/hsqc-tocsy-metab-nan-c6gjzbun | NAN KB, John Glushka, Mario Uchimiya, Saraa Al Jawad, Christopher Esselman, Leandro I Ponce, Laura Morris, Arthur Edison | TITLE: hsqc-tocsy_metab.nan
AUTHORS: NAN KB, John Glushka, Mario Uchimiya, Saraa Al Jawad, Christopher Esselman, Leandro I Ponce, Laura Morris, Arthur Edison
[DESCRIPTION]
This is a protocol for running the Bruker pulse program "hsqcdietgpsisp.2".
[BEFORE_START]
This protocol assumes:
Your sample is loaded, locked, t... | ["[Create a new dataset]", "[Create a new dataset] On the menu bar on TopSpin, click on\nStart → Create Dataset", "[Create noesypr1d experiment file] When Lock, Tune, Shim are complete proceed to the specific protocol for your desired pulseprogram(s).", "[Acquire a spectrum]", "[Acquire a spectrum] Click on\nAcquire → ... |
null | null | null | dx.doi.org/10.17504/protocols.io.iatcaen | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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62,598 | Limitless Glucose 1 | 3 | dx.doi.org/10.17504/protocols.io.rm7vzyo9xlx1/v1 | https://www.protocols.io/view/limitless-glucose-1-b9der23e | Limitless Glucose | TITLE: Limitless Glucose 1
AUTHORS: Limitless Glucose
[DESCRIPTION]
Limitless Glucose 1
[STEPS] | [] |
39,169 | Fluorescent mutants screening in 96 well plates - Chlamydomonas reinhardtii | 4 | null | https://www.protocols.io/view/fluorescent-mutants-screening-in-96-well-plates-ch-big9kbz6 | Joao Vitor Molino | TITLE: Fluorescent mutants screening in 96 well plates - Chlamydomonas reinhardtii
AUTHORS: Joao Vitor Molino
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is intended for screening experiments with algae cells. Nevertheless, with modifications, it can be used for other microrganims.... | ["[Plate preparation]\nFor 96 well plates, the usual max volume is ~ . Clean and desinfect a biological cabinetPlace all materials inside. (e.g: sterile tips, media, sterile 96 well plates with lids, pipettes)Add per well (Or another media) on the choosen plate. (For fluorescent experiments, black plates are recommed... |
104,229 | HIV-PULSE Wet-lab Protocol | 0 | dx.doi.org/10.17504/protocols.io.8epv5rby4g1b/v1 | https://www.protocols.io/view/hiv-pulse-wet-lab-protocol-dh2d38a6 | Laurens Lambrechts, Sofie De Braekeleer, Basiel Cole, Linos Vandekerckhove | TITLE: HIV-PULSE Wet-lab Protocol
AUTHORS: Laurens Lambrechts, Sofie De Braekeleer, Basiel Cole, Linos Vandekerckhove
[DESCRIPTION]
Protocols.io for HIV-PULSE assay, including an updated protocol from the work published in NAR.
[BEFORE_START]
The HIV-PULSE assay consists of six different PCR steps followed by sequenc... | ["[Pre-amplification: PCR using PrimeSTAR GXL] Prepare the master mix according to this principle (if doing replicates, add DNA to master mix, mix well and then divide per sample to ensure ‘even’ input), beware to adapt the mix according to the required DNA input volume: \na. x µL DNA input \nb. 33- x µL NFW", "[Pre-am... |
96,957 | Myco-Ed Module: Using iNaturalist - Create a Course Project | 0 | dx.doi.org/10.17504/protocols.io.81wgbzdz3gpk/v1 | https://www.protocols.io/view/myco-ed-module-using-inaturalist-create-a-course-p-daw52fg6 | Andrew W. Wilson | TITLE: Myco-Ed Module: Using iNaturalist - Create a Course Project
AUTHORS: Andrew W. Wilson
[DESCRIPTION]
This protocol is for instructors. Follow the steps for making a Traditional Project. This type of project will make it easier for instructors to control the observations that are included in the project and insur... | ["[Create a Traditional Project] We want to use a Traditional Project as opposed to a Collections Project on iNaturalist because the Traditional Project allows you and the students to have more control over which observations are included.\n\nHOWEVER, iNaturalist requires that users have a minimum of 50 verifiable obse... |
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