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 |
|---|---|---|---|---|---|---|---|
31,499 | 4-methylumbelliferyl heptanoate (MUH) - Cell Viability Assay | null | dx.doi.org/10.17504/protocols.io.bazjif4n | null | Peter Vangheluwe, Shaun Martin, Mujahid Azfar | TITLE: 4-methylumbelliferyl heptanoate (MUH) - Cell Viability Assay
AUTHORS: Peter Vangheluwe, Shaun Martin, Mujahid Azfar
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The 4-methylumbelliferyl heptanoate (</span><span style = "font-style:italic;">MUH</span><span>) assay is a A fluorimetric ... | [] |
96,507 | Adverse Outcomes of Combined Cochlear Implant and Hearing Aid Use: A Scoping Review | 0 | dx.doi.org/10.17504/protocols.io.dm6gp37xdvzp/v2 | https://www.protocols.io/view/adverse-outcomes-of-combined-cochlear-implant-and-dag32byn | augustina.noel, Jithin Raj Balan, Priyanka Jaisinghani | TITLE: Adverse Outcomes of Combined Cochlear Implant and Hearing Aid Use: A Scoping Review
AUTHORS: augustina.noel, Jithin Raj Balan, Priyanka Jaisinghani
[DESCRIPTION]
Relevant articles highlighting adverse outcomes with the combination of hearing aid and cochlear implant published between 2000 and 2023 will be searc... | ["[Review Demographic details] Title: Adverse Outcomes of Combined Cochlear Implant and Hearing Aid Use: A Scoping Review.", "[Review Demographic details] Original language title: English", "[Review Demographic details] Start Date: 25/02/2024", "[Review Demographic details] End Date: 25/02/25", "[Review Demographic det... |
11,050 | E7805 NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina® Protocol for Large Fragment Sizes (> 550 bp) (Chapter 3) | 1 | dx.doi.org/10.17504/protocols.io.n2idgce | https://www.protocols.io/view/e7805-nebnext-ultra-ii-fs-dna-library-prep-kit-for-n2idgce | New England Biolabs | TITLE: E7805 NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina® Protocol for Large Fragment Sizes (> 550 bp) (Chapter 3)
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The NEBNext Ultra II FS DNA Library Prep Kit for Illumina contains the enzymes and buffers requ... | ["[Fragmentation/End Prep]\nStarting Material: 100–500 ng purified, genomic DNA. We recommend that the DNA be in 1X TE (10 mM Tris pH 8.0, 1 mM EDTA), however, 10 mM Tris pH 7.5–8, low EDTA TE or H2O are also acceptable. If the input DNA is less than 26 µl, add TE (provided) to a final volume of 26 µl.Ensure that the U... |
63,864 | Microbial Metabolite Profiling | 4 | dx.doi.org/10.17504/protocols.io.5qpvob2mxl4o/v1 | https://www.protocols.io/view/microbial-metabolite-profiling-cakyscxw | contact.microbialtec | TITLE: Microbial Metabolite Profiling
AUTHORS: contact.microbialtec
[DESCRIPTION]
Microorganisms and in particular actinomycetes and microfungi are known to produce a vast number of bioactive secondary metabolites. Natural product research needs to continually improve the efficiency of the selection, screening, dere... | [] |
90,959 | SAVE imaging of protein aggregates in cerebrospinal fluid | 4 | dx.doi.org/10.17504/protocols.io.n92ldmqkol5b/v1 | https://www.protocols.io/view/save-imaging-of-protein-aggregates-in-cerebrospina-c43pyymn | mathew.horrocks | TITLE: SAVE imaging of protein aggregates in cerebrospinal fluid
AUTHORS: mathew.horrocks
[DESCRIPTION]
This protocol describe the procedures used to clean a coverglass surface and perform ThT detection of protein aggregates in CSF (SAVE imaging) on a TIRF microscope.
[STEPS]
SECTION: Preparation of ThT solution
12.... | ["[Preparation of ThT solution] Add 70 uL of PLL to each chamber and incubate for 30 minutes.", "[Preparation of ThT] Prepare approx. 4 mM stock of ThT in 100% ethanol and vortex extensively (approx. 1 hour).", "[Preparation of ThT] Prepare approx. 200 uM ThT dilution in PBS, vortex thoroughly (approx. 20 mins) and fil... |
84,415 | Nuclei isolation and permeabilisation of fresh frozen human brain samples for 10X Genomics Multiome | 1 | null | https://www.protocols.click/view/nuclei-isolation-and-permeabilisation-of-fresh-fro-cwn7xdhn | Koen Theunis, Suresh Poovathingal, Sarah Geurs | TITLE: Nuclei isolation and permeabilisation of fresh frozen human brain samples for 10X Genomics Multiome
AUTHORS: Koen Theunis, Suresh Poovathingal, Sarah Geurs
[DESCRIPTION]
This protocol details the procedure of nuclei isolation and debris removal from fresh frozen brain tissue in preparation for the 10X Genomics ... | ["[Preparation] Prepare the 2X salt-Tris solution and aliquot to 1 ml tube and freeze at -20°C", "[Preparation] Prepare the BSA in PBS and filter through 0.2um filter.", "[Preparation] Prepare the Tween-20 Homogenization lysis buffer fresh for each preperations", "[Preparation] Filter sucrose 2M solution through 0.2um/... |
92,483 | SOP: cell culture methods for non-model organisms | 3 | dx.doi.org/10.17504/protocols.io.n92ldm6q7l5b/v1 | https://www.protocols.io/view/sop-cell-culture-methods-for-non-model-organisms-c6jbzcin | Ana Riesgo, María Conejero, C.DiNizo, Jonas Astrin, Cira Martínez, Tomàs Marqués | TITLE: SOP: cell culture methods for non-model organisms
AUTHORS: Ana Riesgo, María Conejero, C.DiNizo, Jonas Astrin, Cira Martínez, Tomàs Marqués
[DESCRIPTION]
Acquisition of somatic cells from vertebrates for cell cultures is well stablished in the literature. However, some vertebrate taxa like amphibians prove to... | [] |
44,915 | OG1RF_genomic_DNA | 4 | null | https://www.protocols.io/view/og1rf-genomic-dna-bp4tmqwn | Elizabeth Fozo | TITLE: OG1RF_genomic_DNA
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">OG1RF genomic DNA isolation</div></div>
[STEPS]
?. [Steps]
Generate an overnight culture in 10 mL of BHI
?. [Steps]
Spin down culture in morning for 10 min at 3500 RPM and pour off supernatant.
?. [Step... | ["[Steps]\nGenerate an overnight culture in 10 mL of BHI", "[Steps]\nSpin down culture in morning for 10 min at 3500 RPM and pour off supernatant.", "[Steps]\nMake 50 mM EDTA (500 µL 0.5M EDTA stock in 4.5 mL water).", "[Steps]\nAdd 960 µL of 50 mM EDTA to OG1RF pellet, then aliquot 480 µL of 50 mM EDTA/cells to a 1.5 ... |
80,434 | Nanopore Sequencing for Apicomplexan Haemoparasite 18S rRNA Gene Metabarcoding | 4 | dx.doi.org/10.17504/protocols.io.6qpvr4nqpgmk/v1 | https://www.protocols.io/view/nanopore-sequencing-for-apicomplexan-haemoparasite-csssweee | hugginsl | TITLE: Nanopore Sequencing for Apicomplexan Haemoparasite 18S rRNA Gene Metabarcoding
AUTHORS: hugginsl
[DESCRIPTION]
Here we report the methodology for a novel nanopore sequencing based method for the unbiased characterisation of apicomplexan haemoparasites from mammalian blood, validated on field samples from canine... | ["[DNA Extraction] Whole blood was collected via venepuncture into ethylenediaminetetraacetic acid (EDTA) tubes. Samples were temporarily kept at 4 °C in the field before being couriered at -20 °C to the processing laboratory where 200 µl of thawed whole blood was extracted using the DNeasy Blood & Tissue Kit (Qiagen, ... |
19,476 | SEM Sample Prep | null | dx.doi.org/10.17504/protocols.io.w9ufh6w | null | Tim D'Angelo, Beth Orcutt | TITLE: SEM Sample Prep
AUTHORS: Tim D'Angelo, Beth Orcutt
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The SEM can be used to directly image biofilms on solid surfaces such as polished rock chips or collected crustal samples. Seawater or fluid bacteria can be imaged after filtering the sample ont... | ["[Fixation of Sample]\nUsing sterile forceps, submerge sample in an appropriate amount of 4°C 4% PFA in PBS in a 1.5 ml eppitube", "[Fixation of Sample]\nIncubate in a 4°C refrigerator for 1 - 3 hours.", "[Fixation of Sample]\nRinse briefly in 1xPBS", "[Fixation of Sample]\nDispose of PFA waste in the G2 waste contain... |
40,932 | ELISA for quantification of human C5 in serum or plasma. | 6 | dx.doi.org/10.17504/protocols.io.bj8ckrsw | https://www.protocols.io/view/elisa-for-quantification-of-human-c5-in-serum-or-bj8ckrsw | Angel Justiz-Vaillant, Belkis Ferrer-Cosme | TITLE: ELISA for quantification of human C5 in serum or plasma.
AUTHORS: Angel Justiz-Vaillant, Belkis Ferrer-Cosme
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. An anti-human C5 coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.
?.... | ["An anti-human C5 coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.", "Add 50 µl of human serum or plasma. Human C5 present in the serum or plasma binds to antibodies adsorbed into the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buf... |
106,766 | JAX-Sen: Collection and shipment of specimen for Bulk RNA-sequencing (Bulk RNA-seq) | 0 | dx.doi.org/10.17504/protocols.io.4r3l2qz5ql1y/v2 | https://www.protocols.io/view/jax-sen-collection-and-shipment-of-specimen-for-bu-dkhn4t5e | Laura Robinson, Susan Sheehan, Gaven Garland, Ron Korstanje | TITLE: JAX-Sen: Collection and shipment of specimen for Bulk RNA-sequencing (Bulk RNA-seq)
AUTHORS: Laura Robinson, Susan Sheehan, Gaven Garland, Ron Korstanje
[DESCRIPTION]
These samples are part of the JAX-Sen project in the SenNet Consortium. Here we provide details on specimen collection and shipment to the Robson... | ["[Reagents and Materials:] 2mL Eppendorf tubes or 5 ml Eppendorf tubes\nRNA Later solution\nWet Ice\nTweezers (clean, sterile)", "[Quality Key Points:] The tissue specimen should be always kept at 4 degrees Celsius and RNase-free. \nIt is crucial to not store the tissue specimen at RT to avoid any cell death, and tiss... |
91,666 | FlowFISH with PrimeFlow | 1 | dx.doi.org/10.17504/protocols.io.36wgq3q4olk5/v1 | https://www.protocols.io/view/flowfish-with-primeflow-c5rsy56e | Ronghao Zhou, Jesse Engreitz | TITLE: FlowFISH with PrimeFlow
AUTHORS: Ronghao Zhou, Jesse Engreitz
[DESCRIPTION]
Detect RNA expression in single cell with PrimeFlow
[STEPS]
SECTION: Before start:
1. Make sure the heat block temp is set to 40ºC using the digital monitor. The heat block should be ON at least a day in advance to stabilize temperatur... | ["[Before start:] Make sure the heat block temp is set to 40ºC using the digital monitor. The heat block should be ON at least a day in advance to stabilize temperature", "[Before start:] Turn on Hyb oven (use to pre-warm target probe diluent)", "[Before start:] Make FACS staining buffer: 0.5% BSA in PBS, filter steril... |
28,121 | DNA quantification using the Quantus fluorometer | null | dx.doi.org/10.17504/protocols.io.7pzhmp6 | null | Josh Quick | TITLE: DNA quantification using the Quantus fluorometer
AUTHORS: Josh Quick
[STEPS]
?. Set up the required number of tubes for the number of DNA samples to be quantified.
0.5 ml
Use only thin-wall, clear, 0.5mL PCR tubes such as Axygen #PCR-05-C
?. Label the tubes on the lids, avoid marking the sides of the tube as ... | ["Set up the required number of tubes for the number of DNA samples to be quantified.\n0.5 ml\nUse only thin-wall, clear, 0.5mL PCR tubes such as Axygen #PCR-05-C", "Label the tubes on the lids, avoid marking the sides of the tube as this could interfere with the sample reading.", "Add ONE dsDNA dye solution to each ... |
null | null | null | dx.doi.org/10.17504/protocols.io.d7m9k5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Overview:</p>
<p>1. Filter DNA reads by quality and host (e.g. for mouse gut bacteria we would filter low-quality reads AND reads that belong to mice)</p>
<p>2. Align DNA reads (fastq, fasta) to <a href="https://www.patricbrc.org/" target="_blank">Patric</a> database (bacteri... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.jz2cp8e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The aim of this study was to analyze the trend in mortality from uterine neoplasms and their risk factors, specified by the International Classification of Diseases - 10th Edition (ICD-10): C53, C54 and C55. This is an ecological study of a cross-sectional cohort and time ser... | [] |
96,518 | ISP Fish Biodiversity Survey | 0 | dx.doi.org/10.17504/protocols.io.36wgq32eylk5/v1 | https://www.protocols.io/view/isp-fish-biodiversity-survey-dahe2b3e | Stephanie Gay, Kylie Ren, Charlotte Wiggins | TITLE: ISP Fish Biodiversity Survey
AUTHORS: Stephanie Gay, Kylie Ren, Charlotte Wiggins
[DESCRIPTION]
This survey addresses the marine biodiversity present off the coast of the Onetahi motu in Tetiaroa, French Polynesia. Researchers conducted transects observing present fish species and their interactions in order to... | ["[Belt Transect Survey] Split into teams of 2 (with additional team member(s) to assist with securing the transect tape)", "[Species Identification] Export photos from camera to laptop", "[Species Interaction] Photograph distinct interactions between individuals of different species", "[Survey Site Selection] From nor... |
69,131 | HTTM : gDNA extraction | 4 | dx.doi.org/10.17504/protocols.io.q26g7yzz3gwz/v2 | https://www.protocols.io/view/httm-gdna-extraction-cfrjtm4n | Antoine Champie | TITLE: HTTM : gDNA extraction
AUTHORS: Antoine Champie
[DESCRIPTION]
Part of the HTTM protocol dedicated to the extraction of gDNA from transposon mutated cell pellets.
[STEPS]
SECTION: DNA extraction
2. Add 600 µLof lysis solution to each well of the deep-well plate and resuspend the pellet.
SECTION: DNA extracti... | ["[DNA extraction] Add 600 µLof lysis solution to each well of the deep-well plate and resuspend the pellet.", "[DNA extraction] Prepare the lysis solution by adding 165 µL of proteinase K to 66 mL of homemade lysis buffer and mix well.", "[DNA extraction] Cover with an adhesive aluminum foil and incubate at 55 °C for ... |
90,318 | Single-molecule pulldown for immunodetection of protein aggregates | 4 | dx.doi.org/10.17504/protocols.io.36wgq3bz3lk5/v1 | https://www.protocols.io/view/single-molecule-pulldown-for-immunodetection-of-pr-c4fnytme | Rebecca Saleeb, Craig Leighton, Ji-Eun Lee, Mathew Horrocks | TITLE: Single-molecule pulldown for immunodetection of protein aggregates
AUTHORS: Rebecca Saleeb, Craig Leighton, Ji-Eun Lee, Mathew Horrocks
[DESCRIPTION]
This protocol describe the procedures used to clean and passivate a coverglass surface, functionalise it with biotin and specifically immobilise proteins of inter... | ["[Coverslip passivation and functionalisation] Treat coverslips with argon plasma for 45 mins", "[Coverslip passivation and functionalisation] Immerse coverslips in 0.22 micron-filtered 1M potassium hydroxide for 20mins", "[Coverslip passivation and functionalisation] Rinse coverslips in ultrapure deionised water and ... |
39,372 | Croprological flotation techniques Tibor-Kassai, 1998 | 1 | dx.doi.org/10.17504/protocols.io.bipkkdkw | https://www.protocols.io/view/croprological-flotation-techniques-tibor-kassai-19-bipkkdkw | Javier Antonio Benavides-Montaño, Javier Antonio Benavides | TITLE: Croprological flotation techniques Tibor-Kassai, 1998
AUTHORS: Javier Antonio Benavides-Montaño, Javier Antonio Benavides
[STEPS]
?. Prepare a Sheather's Sucrose Solution. Density = 1.20-1.27. Preparation: dissolve over indirect heat (to avoid caramelization) approximately 500 g of granulated sugar (sucrose) in... | ["Prepare a Sheather's Sucrose Solution. Density = 1.20-1.27. Preparation: dissolve over indirect heat (to avoid caramelization) approximately 500 g of granulated sugar (sucrose) in 1 liter of boiling water; add 6 ml of 37% formaldehyde or crystallized phenol to prevent microbial growth (mold).", "Immerse 3-5 g of fece... |
52,918 | DNA/RNA extraction and qPCR protocol to assess bacterial abundance in the sponge Halichondria panicea | 1 | dx.doi.org/10.17504/protocols.io.bxwwppfe | https://www.protocols.io/view/dna-rna-extraction-and-qpcr-protocol-to-assess-bac-bxwwppfe | Lara Schmittmann, Lucia Pita | TITLE: DNA/RNA extraction and qPCR protocol to assess bacterial abundance in the sponge Halichondria panicea
AUTHORS: Lara Schmittmann, Lucia Pita
[DESCRIPTION]
This protocol summarizes experience and recommendations regarding DNA and RNA extractions from the sponge Halichondria panicea and qPCR to quantify bacterial ... | ["[RNA extraction] Extract RNA from sponge samples fixed in RNAlater (stored at -80°C)\n\nClean all surfaces and instruments with ethanol and subsequently RNase-Away\nThe manufacturers protocol for the RNeasy Mini Kit have been optimized for Halichondria tissue. For more details please refer to the manufacturers protoc... |
83,802 | iPSC to Motor Neuron Differentiation Various Protocols | 1 | dx.doi.org/10.17504/protocols.io.rm7vzxn7rgx1/v1 | https://www.protocols.click/view/ipsc-to-motor-neuron-differentiation-various-proto-cv32w8qe | jwaligor | TITLE: iPSC to Motor Neuron Differentiation Various Protocols
AUTHORS: jwaligor
[DESCRIPTION]
iPSC to Motor Neuron Differentiation Various Protocols
[STEPS]
SECTION: iPSC/MNP Passaging TrypLE Protocol
1. Aspirate media off
SECTION: iPSC/MNP Passaging TrypLE Protocol
2. Rinse with DPBS-/-
SECTION: iPSC/MNP Passaging T... | ["[iPSC/MNP Passaging TrypLE Protocol] Aspirate media off", "[iPSC/MNP Passaging TrypLE Protocol] Rinse with DPBS-/-", "[iPSC/MNP Passaging TrypLE Protocol] Add 1X TrypLE, 1ml per 6 well, 2ml per T-25, 3ml per T-75 (can use as low as 0.75X TrypLE according to GESC, dilute in 0.5mM EDTA pH 8)", "[iPSC/MNP Passaging Tryp... |
58,476 | A reproducibility protocol and dataset on the biomedical sentence similarity | 5 | dx.doi.org/10.17504/protocols.io.b5ckq2uw | https://www.protocols.io/view/a-reproducibility-protocol-and-dataset-on-the-biom-b5ckq2uw | Alicia Lara Clares, Juan J. Lastra-Díaz, Ana Garcia-Serrano | TITLE: A reproducibility protocol and dataset on the biomedical sentence similarity
AUTHORS: Alicia Lara Clares, Juan J. Lastra-Díaz, Ana Garcia-Serrano
[DESCRIPTION]
This protocol introduces a set of reproducibility resources with the aim of allowing the exact replication of the experiments introduced by our main pa... | ["[Installing Docker on Ubuntu] If Docker is not installed in your machine, instructions below install latest version of Docker CE. For further details, we refer the reader to the official Docker setup page https://docs.docker.com/install/linux/docker-ce/ubuntu/\n\nFirst, we update the system:\n \nWe install the depend... |
32,764 | 7-trial RAWM protocol | 1 | dx.doi.org/10.17504/protocols.io.bb84iryw | https://www.protocols.io/view/7-trial-rawm-protocol-bb84iryw | Teresa Macheda, Kelly Roberts, Adam Bachstetter | TITLE: 7-trial RAWM protocol
AUTHORS: Teresa Macheda, Kelly Roberts, Adam Bachstetter
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Cognitive impairments can be a significant problem after a traumatic brain injury (TBI), which affects millions worldwide each year. There is a need for establish re... | ["Experimental Design and Recommendations:Housing: Behavior is affected by the housing mode. Singly housed mice could perform differently than group housed mice. Blinding: Experimental groups of mice should be coded while the operator is testing the mice.Test order: Mice should be randomized in test order, to avoid con... |
69,881 | Artificial seawater medium | 1 | dx.doi.org/10.17504/protocols.io.81wgby1zovpk/v1 | https://www.protocols.io/view/artificial-seawater-medium-cggzttx6 | Shaaijer, l.kop, h.koch, Sluecker | TITLE: Artificial seawater medium
AUTHORS: Shaaijer, l.kop, h.koch, Sluecker
[DESCRIPTION]
This artificial seawater medium was adapted from the Synthetic Crenarchaeota Medium described in Könneke et al. 2005 (10.1038/nature03911).
[STEPS]
SECTION: SCMU medium
2. Dissolve in 900 ml demineralized water:
SECTION: SCM... | ["[SCMU medium] Dissolve in 900 ml demineralized water:", "[SCMU medium] Autoclave at 121°C for 20 min at 15 psi.", "[SCMU medium] After cooling to room temperature add (in the flow cabinet) from sterile stocks:", "[SCMU medium] Adjust the pH to 7.8 using sterile 1M NaHCO3 solution.", "[Thauer's vitamin solution] ... |
90,421 | DatsenkoWannerCportucalensis | 4 | dx.doi.org/10.17504/protocols.io.ewov1q5e7gr2/v1 | https://www.protocols.io/view/datsenkowannercportucalensis-c4ivyue6 | Dianne K Newman, Lev Tsypin, Scott Saunders, Allen W Chen | TITLE: DatsenkoWannerCportucalensis
AUTHORS: Dianne K Newman, Lev Tsypin, Scott Saunders, Allen W Chen
[DESCRIPTION]
Protocol for performing Datsenko-Wanner deletions of C. portucalensis MBL genes based on https://doi.org/10.1073/pnas.120163297
[STEPS]
SECTION: Amplify the resistance cassette for knocking out a genet... | ["[Amplify the resistance cassette for knocking out a genetic region of interest using the appropriate primer pairs. Use a high-fidelity polymerase, such as Q5, KAPA, or Phusion according to manufacturer instructions.] Design primers for replacing the gene locus of interest with a Kanamycin resistance casette via homol... |
92,877 | M9 minimal medium | 6 | dx.doi.org/10.17504/protocols.io.8epv5x5j4g1b/v1 | https://www.protocols.io/view/m9-minimal-medium-c6xmzfk6 | Isaac Núñez, Tamara Matute | TITLE: M9 minimal medium
AUTHORS: Isaac Núñez, Tamara Matute
[DESCRIPTION]
M9 minimal medium is a classical bacterial growth broth (Miller, et al., 1972) characterized by its low autofluorescence.
As it is minimal, it can be supplemented with defined carbon sources or amino acids acord the custom experimental setups.... | ["[Recipe] This is the recipe for 500 mL total medium.\nIt is assembled from sterile reagents in sterile conditions (in a laminar flow or flame, and using a sterille glass bottle). They have to be added in this order and mixed well after incopore each component.\n\n250 mL Sterile Molecular grade water\n100 mL 5X M9 Sal... |
null | null | null | dx.doi.org/10.17504/protocols.io.iuxcexn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a RNA extraction protocol adapted from Byron Crump's lab, which was developed from both Zhou et al. 1996 and Crump et al. 2003. It is intended to be used with 47 mm 0.22 um PES filters or a 0.22 uM Sterivex filter, both preserved with RNALater after sample collection.... | [] |
38,626 | Advancements and Critical Steps for Statistical Analyses in Blood Pressure Response to Resistance Training in Hypertensive Older Women: A Methodological Approach | 3 | dx.doi.org/10.17504/protocols.io.bhyaj7se | https://www.protocols.io/view/advancements-and-critical-steps-for-statistical-an-bhyaj7se | Dahan Cunha Nascimento | TITLE: Advancements and Critical Steps for Statistical Analyses in Blood Pressure Response to Resistance Training in Hypertensive Older Women: A Methodological Approach
AUTHORS: Dahan Cunha Nascimento
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This document represents a supplemental appe... | [] |
61,874 | POSTDRAFTED PROTOCOL 001 | 1 | null | https://www.protocols.io/view/postdrafted-protocol-001-b8nsrvee | rober | TITLE: POSTDRAFTED PROTOCOL 001
AUTHORS: rober
[DESCRIPTION]
test
[STEPS]
1. test
2. test 002
3. test 003 | ["test", "test 002", "test 003"] |
79,799 | Animal housing and ethical concerns | 1 | dx.doi.org/10.17504/protocols.io.14egn2oepg5d/v1 | https://www.protocols.click/view/animal-housing-and-ethical-concerns-cr6xv9fn | michela.deleidi, Bianca Marchetti, Federico Bertoli, Carmela Giachino | TITLE: Animal housing and ethical concerns
AUTHORS: michela.deleidi, Bianca Marchetti, Federico Bertoli, Carmela Giachino
[DESCRIPTION]
This protocol details animal housing and ethical concerns.
[STEPS]
SECTION: Animal housing and ethical concerns
1. Males C57BL/6J wild type (WT) and C57BL/6J LRRK2*G2019S 2AMjff/J tr... | ["[Animal housing and ethical concerns] Males C57BL/6J wild type (WT) and C57BL/6J LRRK2*G2019S 2AMjff/J transgenic (TG-G2019S) (stock 018785) mice purchased from Jackson Laboratory (Bar Harbor, ME, USA) at 8-12 weeks of age were housed at the animal facilities unit (C.A.Pi.R. Via Santa Sofia 97, Catania 13/2017-UT) an... |
105,297 | Acidified 0.5x Potato Dextrose Agar (APDA) | 0 | dx.doi.org/10.17504/protocols.io.j8nlk82jdl5r/v1 | https://www.protocols.io/view/acidified-0-5x-potato-dextrose-agar-apda-di3r4gm6 | Gabriela Paredes | TITLE: Acidified 0.5x Potato Dextrose Agar (APDA)
AUTHORS: Gabriela Paredes
[DESCRIPTION]
Acidified 0.5x Potato Dextrose Agar (APDA) is a specialized culture medium used in microbiology for the selective cultivation of fungi, particularly in environments where lower pH is required to inhibit bacterial growth. This med... | ["[Prepare the Medium:] In a 1-liter Erlenmeyer flask with a stir bar, dissolve the following components in 1 liter of distilled water (dH2O):\n10 g of potato dextrose broth.\n18 g of agar.\nStir the mixture thoroughly until all components are fully dissolved.", "[Sterilize:] Autoclave the solution at 121 °C for 20m... |
23,889 | Neuropathy Phentoyping Protocols - Dosages of Analgesics for Rats and Mice | null | dx.doi.org/10.17504/protocols.io.3jrgkm6 | null | Eva Feldman | TITLE: Neuropathy Phentoyping Protocols - Dosages of Analgesics for Rats and Mice
AUTHORS: Eva Feldman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block"><span style = "font-weight:bold;">Phenotyping of Rodents for the Pre... | [] |
101,459 | Anotação de genomas de fungos | 0 | dx.doi.org/10.17504/protocols.io.n92ld8r97v5b/v1 | https://www.protocols.io/view/anota-o-de-genomas-de-fungos-dfbt3inn | Thiago Mafra Batista | TITLE: Anotação de genomas de fungos
AUTHORS: Thiago Mafra Batista
[DESCRIPTION]
Este tutorial guiará estudantes e pesquisadores a realizarem a anotação (estrutural e funcional) de genomas de fungos com o software Maker2. Iniciamos com a identificação e mascaramento das regiões repetitivas com o RepeatModeler e Repeat... | ["[Identificação e mascaramento das regiões repetitivas] Antes de realizar a predição gênica, vamos identificar as famílias de repetições com o RepeatModeler e depois mascará-las no genoma com o RepeatMasker. No exemplo abaixo estou utilizando um arquivo fasta com nome contigs_Y6065_v1.fasta, os softwares instalados em... |
86,425 | Free floating immunofluorescent staining protocol on mouse brain sections | 4 | dx.doi.org/10.17504/protocols.io.j8nlkoo55v5r/v1 | https://www.protocols.io/view/free-floating-immunofluorescent-staining-protocol-cymzxu76 | Giselle Sagredo, YuHong Fu | TITLE: Free floating immunofluorescent staining protocol on mouse brain sections
AUTHORS: Giselle Sagredo, YuHong Fu
[DESCRIPTION]
This protocol describes our multiplex fluorescent immunohistochemistry protocol used to identify pathological signatures in human iPSC-derived cells within thin, fixed mouse brain tissue s... | ["[Day 1 - Tissue preparation] 30 um mouse brain sections were stored in anti-freeze solution at -20 °C until required. \nRemove samples from freezer and equilibrate at Room temperature for 10 min - 20 min\nPour sections into a well insert in a 6-well plate to separate storage solution from section\n Move the well inse... |
92,472 | 801.1.HTC_H&E Stain (Paraffin or Cryosections) | 1 | dx.doi.org/10.17504/protocols.io.36wgqjnq3vk5/v4 | https://www.protocols.io/view/801-1-htc-h-amp-e-stain-paraffin-or-cryosections-c6iyzcfw | Jeffrey Purkerson, Luis Colon, Cory Poole, Anthony Corbett, Gloria S Pryhuber | TITLE: 801.1.HTC_H&E Stain (Paraffin or Cryosections)
AUTHORS: Jeffrey Purkerson, Luis Colon, Cory Poole, Anthony Corbett, Gloria S Pryhuber
[DESCRIPTION]
Hematoxylin and Eosin staining is the standard chemical stain used on slides to be reviewed for assessment of general histopathology and the generation of a pat... | ["[Staining Procedure] Verify that all slides are completely dry. Slides can be dried in an 55C oven for one hour or more prior to use to prevent loss of tissue.", "[Staining Procedure] If sections were from tissue block embedded in paraffin, deparaffinize slides with 3 changes of Xylene for 5 minutes each.", "[Staini... |
32,385 | Lipids in microalgae: The Extraction by modified Folch solvent | 1 | null | https://www.protocols.io/view/lipids-in-microalgae-the-extraction-by-modified-fo-bbu9inz6 | Yingyu Hu, Zoe V Finkel | TITLE: Lipids in microalgae: The Extraction by modified Folch solvent
AUTHORS: Yingyu Hu, Zoe V Finkel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>In this protocol, lipids in miroalgae is extracted with 2 ml Folch solvent (2:1 chloroform-methanol v/v) after frozen and thawed with the addi... | ["[Prepare reagent]\nFolch solvent (CHCl3: MeOH=2:1 v/v)", "[Prepare reagent]\nKCl solution ( )", "[Extraction]\nTransfer sample into muffled centrifuge tube, use precombusted filter as blank.", "[Filtration]", "[Separation]\nCalculate the volume of 0.88% KCl by multiplying (V+2) by 4/21.\nIn order to obtain a biphase ... |
76,058 | Assessment of Knowledge, Attitude and Practice toward Hepatitis B virus infection among Healthcare Providers working at sixty Public and Private Hospitals in Khartoum State Sudan 2023 | 1 | dx.doi.org/10.17504/protocols.io.6qpvr4reogmk/v1 | https://www.protocols.io/view/assessment-of-knowledge-attitude-and-practice-towa-cnh2vb8e | essam.abuobaida | TITLE: Assessment of Knowledge, Attitude and Practice toward Hepatitis B virus infection among Healthcare Providers working at sixty Public and Private Hospitals in Khartoum State Sudan 2023
AUTHORS: essam.abuobaida
[DESCRIPTION]
Introduction: Hepatitis B infection is a major public health problem worldwide, accordin... | ["[Research Steps] Writing the study protocol", "[Research Steps] Data collection and analysis", "[Research Steps] Writing the manuscript", "[Research Steps] Publishing"] |
null | null | null | dx.doi.org/10.17504/protocols.io.ijccciw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Contact Dr. Alison Buchan (abuchan@utk.edu) with any questions.</p>
[STEPS]
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103,037 | Albendazole plus Praziquantel versus Albendazole Alone in the Treatment of Neurocysticercosis: A Systematic Review and Meta-Analysis | 0 | dx.doi.org/10.17504/protocols.io.dm6gpzypjlzp/v1 | https://www.protocols.io/view/albendazole-plus-praziquantel-versus-albendazole-a-dgu53wy6 | Luísa Menegaz, Gabriela Oliveira Caetano, Jade Lingiardi Altoé, Laíse Lênin Leodoro Silva, Maria Eduarda Silva, Artur Menegaz de Almeida, Ítalo Barros Andrade, Michele Kreuz MD, Davi Tanajura Costa | TITLE: Albendazole plus Praziquantel versus Albendazole Alone in the Treatment of Neurocysticercosis: A Systematic Review and Meta-Analysis
AUTHORS: Luísa Menegaz, Gabriela Oliveira Caetano, Jade Lingiardi Altoé, Laíse Lênin Leodoro Silva, Maria Eduarda Silva, Artur Menegaz de Almeida, Ítalo Barros Andrade, Michele Kre... | ["[Abstract] Review title:\nAlbendazole plus Praziquantel versus Albendazole Alone in the Treatment of Neurocysticercosis: A Systematic Review and Meta-Analysis", "PICO: \nP - patients with neurocysticercosis;\nI - treatment with albendazole and praziquentel associated;\nC - placebo, praziquentel alone or with an incre... |
null | null | null | dx.doi.org/10.17504/protocols.io.c77zrm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Supplement to seawater for growth of cyanobacteria.
[GUIDELINES]
<strong>Note:</strong> <br />Matt suggested higher concentrations of NH<sub>4</sub>Cl so only need to use 0.5 ml per 1 L seawater:<br />1.6 M NH<sub>4</sub>Cl 2.14g/25ml or 8.56g/100ml<br />Use 500µl per 1L sea... | [] |
21,872 | Quantification of salt-induced changes in Root System Architecture in Arabidopsis | null | dx.doi.org/10.17504/protocols.io.zkqf4vw | null | Magdalena Julkowska, Christa Testerink | TITLE: Quantification of salt-induced changes in Root System Architecture in Arabidopsis
AUTHORS: Magdalena Julkowska, Christa Testerink
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The protocol was developed for observing salt-induced changes in Root System Architecture of Arabidopsis and ... | ["Prepare germination media.Per 1L of media: 2.2 g Murashi-Skoog, 5 g sucrose, 1 g MES Monohydrate, pH at 5.8 with KOH. After adjusting the pH add 10g Dashin agar directly into the bottle. Make sure you add it AFTER measuring pH - it can clog the pH meter otherwise.Autoclave using liquid sterilization cycle.Pour 40 ml ... |
63,295 | A novel laboratory method to simulate climatic stress with successful application to experiments with medically relevant ticks | 4 | dx.doi.org/10.17504/protocols.io.rm7vzyo8rlx1/v2 | https://www.protocols.io/view/a-novel-laboratory-method-to-simulate-climatic-str-b927r8hn | Sang Hyo Kim, Caleb Nielebeck, Lauren Dedmon, Mark Pangilinan, Jahred Quan, William Ota, Javier D. Monzón | TITLE: A novel laboratory method to simulate climatic stress with successful application to experiments with medically relevant ticks
AUTHORS: Sang Hyo Kim, Caleb Nielebeck, Lauren Dedmon, Mark Pangilinan, Jahred Quan, William Ota, Javier D. Monzón
[DESCRIPTION]
This protocol details a novel method to isolate indivi... | ["[Set up] Place a single tick with one wooden skewer in each tube and seal with a cap, labelling each tube with an individual identifier", "[Set up] Place six tubes in each airtight container along with a humidity pack, labelling each container", "[Set up] Confirm the humidity in one container of each RH level with th... |
48,874 | Correlative Light-Electron Microscopy of α-synuclein Aggregates in Primary Neurons | 4 | dx.doi.org/10.17504/protocols.io.btyinpue | https://www.protocols.io/view/correlative-light-electron-microscopy-of-synuclein-btyinpue | Felix Kraus, vtrinkaus , Ruben Fernandez Busnadiego | TITLE: Correlative Light-Electron Microscopy of α-synuclein Aggregates in Primary Neurons
AUTHORS: Felix Kraus, vtrinkaus , Ruben Fernandez Busnadiego
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details methods for correlative light-electron microscopy of α-synuclein aggregates in ... | ["[Correlative Light-Electron Microscopy of α-synuclein Aggregates in Primary Neurons]\nGrow primary neurons on EM grids (SiO2, R1/4 or 1.2/20, Quantifoil):\nCarbon Au grids may also be used, but they should be coated with an additional layer of carbon to stabilize the grids and to allow the neurons attach better on th... |
61,959 | Work Or Hoax? Are there any adverse effects of the Power Keto Gummies? | 1 | dx.doi.org/10.17504/protocols.io.n92ldz7qnv5b/v1 | https://www.protocols.io/view/work-or-hoax-are-there-any-adverse-effects-of-the-b8rfrv3n | Menemora | TITLE: Work Or Hoax? Are there any adverse effects of the Power Keto Gummies?
AUTHORS: Menemora
[DESCRIPTION]
Power Keto Gummies
[STEPS]
1. (Huge Savings) Click Here To Get Power Keto Gummies For A Discounted Price Today!
What’s Power Keto Gummies Diet?Power Keto Gummies is an effective dietary supplement that c... | ["(Huge Savings) Click Here To Get Power Keto Gummies For A Discounted Price Today!\n\nWhat’s Power Keto Gummies Diet?Power Keto Gummies is an effective dietary supplement that claims to help people with weight loss. If they are taking ketogenic diets then they also need dietary supplements. Why…? The fact is this i... |
40,870 | Isolation and Characterization of Enteric Bacteria from Oysters | 4 | dx.doi.org/10.17504/protocols.io.bj6ekrbe | https://www.protocols.io/view/isolation-and-characterization-of-enteric-bacteria-bj6ekrbe | Sade Aisha Folashade John, Patrick E. Akpaka, Chandrashekhar Unakal, Arvind Kurhade, Angel Justiz-Vaillant | TITLE: Isolation and Characterization of Enteric Bacteria from Oysters
AUTHORS: Sade Aisha Folashade John, Patrick E. Akpaka, Chandrashekhar Unakal, Arvind Kurhade, Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Enterobacteriaceae the leading cause of gastroenteritis. These gr... | ["Study Design: This cross sectional study was carried out over a five-month period during the rainy season (22 May - 09 September). The study evaluated the total and fecal coliform of the oyster cocktails including the water used by the vendors. Additionally, the enteric organisms present were isolated and characteriz... |
57,764 | Measuring ammonium (NH4+) concentrations in water samples | 1 | dx.doi.org/10.17504/protocols.io.b4ncqvaw | https://www.protocols.io/view/measuring-ammonium-nh4-concentrations-in-water-sam-b4ncqvaw | Jacob Waldbauer, Amy Amy Zimmerman | TITLE: Measuring ammonium (NH4+) concentrations in water samples
AUTHORS: Jacob Waldbauer, Amy Amy Zimmerman
[DESCRIPTION]
Fluorometric assay for precise measurements of ammonium from 0.3 to 50 µmol•L-1 concentrations. Reaction reaches maximum fluorescence after ~2 hours and remains stable for several more hours. Si... | ["1. Prepare 200 µM stock solution: Dilute 1:500 from 0.1 M solution => 20 µL + 9.980 mL nanopure water.", "Dilute the stock solution to the following concentrations ( µM) in nanopure water: 0, 0.5, 1.25, 2.5, 5, 7.5, 10. NOTE: 1 mL of each standard is necessary for triplicate reactions.", "Prepare Reagents and Solutio... |
80,596 | ISP Research Proposal | 1 | dx.doi.org/10.17504/protocols.io.bp2l696j1lqe/v1 | https://www.protocols.io/view/isp-research-proposal-csxuwfnw | Erica Garibay | TITLE: ISP Research Proposal
AUTHORS: Erica Garibay
[DESCRIPTION]
The island of Mo’orea is the heart of French Polynesia’s pineapple production. Ever since farmers advocated for the opening of the Rotui Juice Factory in 1981, production has increased to support growing demand for the factory’s tropical fruit juices. T... | ["[Identifying Plant Species For Field Buffers] Meet with the participating pineapple producers and the agricultural school officials to listen and discuss which plant species they think may be suitable to use as a mulch, cover crop, or field buffer on their farm.", "[Identifying Plant Species For Field Buffers] Conduc... |
66,253 | Crystallization of ATG9 HDIR-ATG101:ATG13 complex | 4 | null | https://www.protocols.io/view/crystallization-of-atg9-hdir-atg101-atg13-complex-ccxmsxk6 | Adam Yokom | TITLE: Crystallization of ATG9 HDIR-ATG101:ATG13 complex
AUTHORS: Adam Yokom
[DESCRIPTION]
Crystallization protocol for the ATG9 HDIR-ATG101:ATG13 complex
[STEPS]
SECTION: Crystallization
1. ATG9 HDIR (828-839) fused ATG101 (1-198):ATG13 (1-197) complex was concentrated to 6 mg/ml in 25 mM HEPES pH 7.5, 150mM NaCl, ... | ["[Crystallization] ATG9 HDIR (828-839) fused ATG101 (1-198):ATG13 (1-197) complex was concentrated to 6 mg/ml in 25 mM HEPES pH 7.5, 150mM NaCl, 1mM MgCl2, 1mM TCEP", "[Crystallization] Crystallization was carried out by sitting-drop vapor diffusion using an automated liquid-handling system (Mosquito, TTP LabTech, UK)... |
null | null | null | dx.doi.org/10.17504/protocols.io.s5teg6n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes an immunoassay, originally developed to quantitate ubiquitin in mouse tissues (Oh et al., Anal. Biochem. 443, 153–155), which we adapted to <em>Drosophila melanogaster</em>. The method is suitable for the simultaneous determination of total, free and c... | [] |
87,415 | LRRK2-RCKW:E11DARPin:MLi-2 image processing | 5 | dx.doi.org/10.17504/protocols.io.n2bvj3nmnlk5/v1 | https://www.protocols.io/view/lrrk2-rckw-e11darpin-mli-2-image-processing-czkxx4xn | Marta Sanz Murillo, Andres Leschziner | TITLE: LRRK2-RCKW:E11DARPin:MLi-2 image processing
AUTHORS: Marta Sanz Murillo, Andres Leschziner
[DESCRIPTION]
Protocol for data processing of 8000 to 12000 micrographs for LRRK2-RCKW:E11 DARPin:MLi-2 complexes. Datasets are collected with an electron microscope equipped with a direct detector. It focused primarily ... | ["After movie alignment and CTF estimation (Patch Motion Correction and Patch CTF Estimation jobs in CryoSPARC), discard the micrographs with an estimated resolution worse than 3.5 Å.", "Pick your particles with Cryosparc’s Blob picker.", "Set particle diameter to 240-300 Å. This range diameter willl include from monom... |
63,433 | Steve Harvey CBD Gummies Shark TankReviews Benefits,Ingredients,side effects and Is it legitor Does it Really Work [HOAX OR SCAM]{Update 2022}-, What To Know Before Using It?? | 1 | dx.doi.org/10.17504/protocols.io.81wgb6971lpk/v1 | https://www.protocols.io/view/steve-harvey-cbd-gummies-shark-tankreviews-benefit-b97hr9j6 | Steve Harvey CBD Gummies | TITLE: Steve Harvey CBD Gummies Shark TankReviews Benefits,Ingredients,side effects and Is it legitor Does it Really Work [HOAX OR SCAM]{Update 2022}-, What To Know Before Using It??
AUTHORS: Steve Harvey CBD Gummies
[DESCRIPTION]
Steve Harvey CBD Gummies - You plan to recuperate just as truly feel over and above anyo... | ["Steve Harvey CBD Gummies\n\n➢Product Name —Steve Harvey CBD Gummies Reviews\n➢Main Benefits —Improve Metabolism & Help in Pain Relief\n➢ Composition —NaturalOrganic Compound\n➢ Side-Effects —NA\n➢ Rating : —⭐⭐⭐⭐⭐\n➢ Availability —Online\n➢Price (for Sale) Buy Now Here —Click HereSteve Harvey CBD Gu... |
101,886 | Teeth Steroid Extraction for "Steroid profiling in human primary teeth via liquid chromatography-tandem mass spectrometry for long-term retrospective steroid measurement" | 0 | dx.doi.org/10.17504/protocols.io.e6nvw1b3dlmk/v1 | https://www.protocols.io/view/teeth-steroid-extraction-for-34-steroid-profiling-dfq63mze | Ruolan S. Wu, hamden@zoology.ubc.ca, Melody Salehzadeh, Michael X. Li, Asmita Poudel, Kim L. Schmidt, Michael S. Kobor, Kiran K. Soma | TITLE: Teeth Steroid Extraction for "Steroid profiling in human primary teeth via liquid chromatography-tandem mass spectrometry for long-term retrospective steroid measurement"
AUTHORS: Ruolan S. Wu, hamden@zoology.ubc.ca, Melody Salehzadeh, Michael X. Li, Asmita Poudel, Kim L. Schmidt, Michael S. Kobor, Kiran... | ["[First Day] Put 5 1.4mm beads in a 2mL Bead ruptor tube", "[First Day] Label bead ruptor tubes", "[2nd Day] Preheat speed vac to 60C", "[First Day] Label 0.6mL polypropelene microcentrifuge tubes to\ncorrespond with bead ruptor tubes", "[First Day] Label LC-MS/MS vials to corresond with bead ruptor tubes and\nput gl... |
27,402 | CD200 and CD200R levels in psoriasis patients | null | dx.doi.org/10.17504/protocols.io.6zihf4e | null | Carmen Farid, Aisha A. Mahmoud, Hanaa M. Donia, Hafsa M. Ghatesh | TITLE: CD200 and CD200R levels in psoriasis patients
AUTHORS: Carmen Farid, Aisha A. Mahmoud, Hanaa M. Donia, Hafsa M. Ghatesh
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Serum soluble CD200 levels in psoriasis patients was measured by ELISA (Human CD200 PicoKine™ ELISA Kit, Boster Biological ... | [] |
31,410 | Colony Formation Titering Assay for Lentivirus | null | dx.doi.org/10.17504/protocols.io.bawsifee | null | Addgene the nonprofit plasmid repository | TITLE: Colony Formation Titering Assay for Lentivirus
AUTHORS: Addgene the nonprofit plasmid repository
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is for running a colony formation titering assay for Lentivirus. To see the full abstract and additional resources, visit the </... | ["[Procedure]\nBefore beginning a colony formation assay, the dose of antibiotic required to kill your target cell line needs to be empirically determined. Treat the target cells with a range of doses of antibiotic. Determine the minimum concentration required to kill all of the cells. Use this dose for the colony form... |
30,336 | Quantitative Real‐Time Polymerase Chain Reaction (qRT‐PCR) | 1 | null | https://www.protocols.io/view/quantitative-real-time-polymerase-chain-reaction-q-9u8h6zw | Yingchao Xue, Xiping Zhan, Shisheng Sun, Senthilkumar S. Karuppagounder, Shuli Xia, Valina L Dawson, Ted M Dawson, John Laterra, Jianmin Zhang, Mingyao Ying | TITLE: Quantitative Real‐Time Polymerase Chain Reaction (qRT‐PCR)
AUTHORS: Yingchao Xue, Xiping Zhan, Shisheng Sun, Senthilkumar S. Karuppagounder, Shuli Xia, Valina L Dawson, Ted M Dawson, John Laterra, Jianmin Zhang, Mingyao Ying
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol ... | ["[RNA Extraction]\nExtract total RNA using a RNeasy Mini Kit.", "[qRT-PCR]\nReverse transcribe using murine leukemia virus reverse transcriptase and oligo(dT) primers.", "[qRT-PCR]\nSet up qRT-PCR using SYBR green PCR Master Mix in the IQ5 RT‐PCR detection system. Primer sequences are listed in \"Guidelines\".", "[qRT... |
19,605 | CONNECTOR, fitting and clustering of longitudinal data. | 1 | dx.doi.org/10.17504/protocols.io.8epv56e74g1b/v1 | https://www.protocols.io/view/connector-fitting-and-clustering-of-longitudinal-d-xdvfi66 | Simone Pernice, Roberta Sirovich, Elena Grassi, Marco Viviani, Martina Ferri, Francesco Sassi, Luca Alessandri', Dora Tortarolo, Raffaele A. Calogero, Livio Trusolino, Andrea Bertotti, Marco Beccuti, Martina Olivero, Francesca Cordero | TITLE: CONNECTOR, fitting and clustering of longitudinal data.
AUTHORS: Simone Pernice, Roberta Sirovich, Elena Grassi, Marco Viviani, Martina Ferri, Francesco Sassi, Luca Alessandri', Dora Tortarolo, Raffaele A. Calogero, Livio Trusolino, Andrea Bertotti, Marco Beccuti, Martina Olivero, Francesca... | ["[Data Reading]", "[Data Reading] GrowDataFile: the name of the excel file storing the growth evolution data. The description of the file format is reported in the Input data section.", "[Data Reading] AnnotationFile: the name of a csv file storing the annotation data. The description of the file format is reported in... |
null | null | null | dx.doi.org/10.17504/protocols.io.ri9d4h6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Socioeconomic status (SES) predicts health, wellbeing, and cognitive ability, including executive function (EF). A body of recent work has shown that childhood SES is positively related to EF, but it is not known whether this disparity grows, diminishes or holds steady over d... | [] |
98,408 | Glucose Tolerance Test | 4 | dx.doi.org/10.17504/protocols.io.261geddodv47/v2 | https://www.protocols.io/view/glucose-tolerance-test-dccg2stw | Sabina Marciano, Roberta Marongiu | TITLE: Glucose Tolerance Test
AUTHORS: Sabina Marciano, Roberta Marongiu
[DESCRIPTION]
The glucose tolerance test is performed to determine how quickly the glucose is cleared from the blood. It is used to test for diabetes or insulin resistance.
[STEPS]
1. Single cage the mice for 1 week in advance
2. Weight the mic... | ["Single cage the mice for 1 week in advance", "Weight the mice", "Fast mice for 360 min", "After fasting, measure glucose with a glucose meter", "Perform an intraperitoneal injection of 2g / kg body weight of glucose (20% D-glucose stock solution dissolving 2g of glucose in 10ml saline and give 10ul per gram of body w... |
46,713 | Prepare and run test on available dataset | 1 | dx.doi.org/10.17504/protocols.io.bruzm6x6 | https://www.protocols.io/view/prepare-and-run-test-on-available-dataset-bruzm6x6 | Stepan Orlov, Alexey Zhuravlev, Егор Усик, Alexey Kuzin | TITLE: Prepare and run test on available dataset
AUTHORS: Stepan Orlov, Alexey Zhuravlev, Егор Усик, Alexey Kuzin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol shows how to perform tests whose results are presented in the manuscript dedicated to the ReVisE open source visualization s... | ["[Prepare to measure ReVisE visualization performance]\nDownload and build the ReVisE system if it is not built.\n{\"blocks\":[{\"key\":\"8vgnr\",\"text\":\"Current protocol is intended to show how to build visualization system which is called ReVisE. Such system is aimed to provide interactive visualization of large ... |
97,054 | Sample vitrification for cryo-ET | 0 | dx.doi.org/10.17504/protocols.io.261ge5pxyg47/v1 | https://www.protocols.io/view/sample-vitrification-for-cryo-et-daz62f9e | Dorothy zhao | TITLE: Sample vitrification for cryo-ET
AUTHORS: Dorothy zhao
[DESCRIPTION]
Aggregation
of proteins containing expanded polyglutamine (polyQ) repeats is the
cytopathologic hallmark of a group of dominantly inherited neurodegenerative
diseases, including Huntington's disease (HD). Huntingtin (Htt), the disease
protein ... | ["[vitrification for cells grown on the grids] Cells were seeded on holey carbon-coated 200 mesh gold EM grids (Quantifoil Micro Tools, Jena, Germany) in 35 mm cell culture dishes.", "[vitrification for cells grown on the grids] Allow to properly attach before transfection with GFP-polyQ and RFP-reporters. Cells were i... |
18,674 | Protocol for DNA Extraction from Urine | null | dx.doi.org/10.17504/protocols.io.wgsfbwe | null | A. Lenore Ackerman, Jennifer Tash Anger, Muhammad Umair Khalique, James E. Ackerman, Jie Tang, Jayoung Kim, David M. Underhill, Michael R. Freeman | TITLE: Protocol for DNA Extraction from Urine
AUTHORS: A. Lenore Ackerman, Jennifer Tash Anger, Muhammad Umair Khalique, James E. Ackerman, Jie Tang, Jayoung Kim, David M. Underhill, Michael R. Freeman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify... | ["Spin 30 ml for 15 minutes at 1500 X G at room temperature", "Pour off supernatant into a separate, 50 ml tube and store at -80 c.Enzymatic Disruption", "Resuspend pellets in 500 uL Enzyme buffer (0.5 M Tris, 1 mM EDTA, 0.2% 2-mercaptoethanol, pH 7.5) in a 1.5 ml Eppendorf tube", "Add Enzymes: 100 uL Lyticase (2000 U... |
93,679 | Direct Detection of poliovirus and Nanopore Sequencing (DDNS) - Stool | 4 | dx.doi.org/10.17504/protocols.io.rm7vzbyyxvx1/v2 | https://www.protocols.io/view/direct-detection-of-poliovirus-and-nanopore-sequen-c7qpzmvn | Alex Shaw, Catherine Troman, Manasi Majumdar, Erika Bujaki, Joyce Akello, Shannon Fitz, Ben Bellekom, Aine.OToole, c.ansley, rachel.colquhoun, arshady, khurshida, alammu, Andrew Rambaut, Javier Martin, Nick Grassly | TITLE: Direct Detection of poliovirus and Nanopore Sequencing (DDNS) - Stool
AUTHORS: Alex Shaw, Catherine Troman, Manasi Majumdar, Erika Bujaki, Joyce Akello, Shannon Fitz, Ben Bellekom, Aine.OToole, c.ansley, rachel.colquhoun, arshady, khurshida, alammu, Andrew Rambaut, Javier Martin, Nick Grassly
[DESCRIPTION]
This... | ["[Nested PCR First Round (PanEV)] Prepare a master mix using the reaction volumes detailed in the table below for the number of samples you have plus negative controls. The reaction mix and SSIII enzyme are provided in \n\n\nForward primer: 5'NTR [TGGCGGAACCGACTACTTTGGGTG] (Arita et al. 2015)\n\nReverse Primers: Cre... |
96,524 | ONETAHI PLANT DISCOVERY PROTOCOL | 0 | dx.doi.org/10.17504/protocols.io.bp2l6xom5lqe/v1 | https://www.protocols.io/view/onetahi-plant-discovery-protocol-dahk2b4w | Flynn Ryan Dartland, Leilani Villasenor, Alexander Ferrera, Jacob Yinger | TITLE: ONETAHI PLANT DISCOVERY PROTOCOL
AUTHORS: Flynn Ryan Dartland, Leilani Villasenor, Alexander Ferrera, Jacob Yinger
[DESCRIPTION]
Invasive Plant Identification On Onetahi Motu, Tetiaroa Within French Polynesia
This protocol describes a means of sampling plant species on Tetiaroa's Onetahi Motu in order to identi... | ["[Protocol] Analyze the data to see which plants are native or nonnative to Tetiaroa. If there's a need for clarification, utilize the help of local experts such as Dr. Jean-Yves Meyer.", "[Protocol] Distinguish which plants are most invasive, overcrowding the rest, and even potentially harmful.", "[Protocol] Determin... |
67,073 | Immunofluorescent Labelling of Post-Mortem Rodent Brain Tissue | 1 | dx.doi.org/10.17504/protocols.io.j8nlkkq31l5r/v1 | https://www.protocols.io/view/immunofluorescent-labelling-of-post-mortem-rodent-cdq9s5z6 | Jeffrey Stedehouder, Shinil Raina, Stephanie J Cragg | TITLE: Immunofluorescent Labelling of Post-Mortem Rodent Brain Tissue
AUTHORS: Jeffrey Stedehouder, Shinil Raina, Stephanie J Cragg
[DESCRIPTION]
This protocol is to label one or several targets using a two-step immunofluorescent approach in PFA perfusion-fixed, 50-µm thick, post-mortem rodent brain tissue.
[GUI... | ["[Washes] Place 50 µm thick brain slices in a jar (or well). The jar or well should be able to hold ~2-5 ml Phosphate Buffered Saline (PBS) for proper washing.", "[Washes] Place the jar or well on an orbital shaker for ~10-15 mins.", "[Preincubation] Prepare preincubation solution containing PBS with 10% Normal Bovine... |
null | null | null | dx.doi.org/10.17504/protocols.io.dh238d | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Combine:<br />150mls Ethanol<br />150mls distilled water<br />3mls Glacial Acetic Acid<br /><br />Split into 4 beakers (approx 75mls each) and add a stir bar.<br /><br />Beaker 1 - Add: 0.5g Acid Fuchsin and 1.0g Ponceau 2R<br />Beaker 2 - Add: 0.45g Light green, SF, yellowish<b... | [] |
68,471 | Disposal of Samples from Water Bodies with Zebra Mussels | 4 | null | https://www.protocols.io/view/disposal-of-samples-from-water-bodies-with-zebra-m-ce4xtgxn | Malcolm A Barnard, Stephen Powers | TITLE: Disposal of Samples from Water Bodies with Zebra Mussels
AUTHORS: Malcolm A Barnard, Stephen Powers
[DESCRIPTION]
Zebra Mussels (Dreissena polymorpha) are a highly invasive species that have been invading water bodies around the United States and beyond. This protocol for sample disposal for sample collected fr... | ["[Sample Killing] Pour all sample water into a dish pan.", "[Sample Killing] Add 50 mL of bleach per 1 L of sample water.", "[Sample Killing] Save the bottles for acid washing (do not bleach as acid and bleach produce chlorine gas).", "[Sample Disposal] Dispose of bleached sample down drain with excess water.", "Let t... |
null | null | null | dx.doi.org/10.17504/protocols.io.sw3efgn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Purpose: The immediate purpose is to determine the maximum number of tube voltages which are useful for acquiring information in medical computed tomography (CT) along with specific linear combinations of quantities of chemical elements which are observable with the current g... | [] |
58,450 | AD BONCAT-FCM Screening & Coupled SYBR+ FCM Cell-Counting - 2022 | 4 | dx.doi.org/10.17504/protocols.io.rm7vzyb75lx1/v1 | https://www.protocols.io/view/ad-boncat-fcm-screening-amp-coupled-sybr-fcm-cell-b5bsq2ne | Maxwell Madill | TITLE: AD BONCAT-FCM Screening & Coupled SYBR+ FCM Cell-Counting - 2022
AUTHORS: Maxwell Madill
[DESCRIPTION]
This protocol provides a detailed description of all steps required to label, analyze and quantify the absolute abundances of BONCAT-labelled (i.e. translationally active) cells within samples collected fr... | ["[Reagent and Materials Preparation] Long-Term Stored BONCAT Reagents \n\n 20mM Copper sulfate solution: \nPrepare 500 mL of stock by adding 2.4968 g of CuSO4*5H2O to a 500 mL volumetric flask, rinsing the weigh boat and funnel thoroughly with DI water, and filling the flask to just above the neck with DI wate... |
null | null | null | dx.doi.org/10.17504/protocols.io.d2q8dv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Comeau, A. M., and R. T. Noble. 2010. Preparation and application of fluorescently labeled virus particles, p. 19–29. In S. W. Wilhelm, M. G. Weinbauer, and C. A. Suttle [eds.], Manual of Aquatic Viral Ecology. ASLO.<br /><br />Please see the <a href="http://www.aslo.org/books/m... | [] |
20,584 | Glutaraldehyde fixation | null | dx.doi.org/10.17504/protocols.io.ycgfstw | null | Veronika Cencen | TITLE: Glutaraldehyde fixation
AUTHORS: Veronika Cencen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Fixation of adherent mammalian cells for AFM imaging </div></div>
[STEPS]
?. Rinse cells 3 times with appropriate buffer, such as PBS or Ringer's
?. Prepare concentration glutaraldehyde in KMgH... | ["Rinse cells 3 times with appropriate buffer, such as PBS or Ringer's", "Prepare concentration glutaraldehyde in KMgH buffer (or other buffer used for your application). Pipette just enough of the dilution on top of the rinsed cells to cover the area. Let sit for\n2 Mass/Volume Percent", "Rinse at least 3 times with ... |
null | null | null | dx.doi.org/10.17504/protocols.io.e52bg8e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a magnetic bead-based protocol enables the generation of high quality Illumina miRNA libraries without the need of PAGE-gel size selection.</p>
<p> </p>
<p>Our protocol enables the discovery and profiling of miRNAs from various organisms and tissues via the Illumina s... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.c7jzkm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Version 3<br /><br />This protocol describes the use of Cesium Chloride to purify viruses with an optional dialysis step to remove the CsCl. DNase I treatment, CsCl purification, and sucrose purification methods were compared using replicated viral metagenomics in Hurwitz et al.... | [] |
26,222 | Counting worms / C. elegans / nematodes | null | dx.doi.org/10.17504/protocols.io.5ung6ve | null | Cristian Riccio | TITLE: Counting worms / C. elegans / nematodes
AUTHORS: Cristian Riccio
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Count worms, e.g. arrested L1s after an overnight starvation in M9 on a rotating wheel.</div></div>
[STEPS]
?. Shake your wormy solution to make the concentration of worms in it m... | ["Shake your wormy solution to make the concentration of worms in it more homogeneous.", "Pipet 10 microlitres of wormy solution in a streak onto a glass slide. Don't pipet the 10 ul in a blob. That would make it harder to count.", "From left to right, or right to left, follow the streak under the microscope and count ... |
45,663 | Spatial Transfer of Oligonucleotides and Imaging | 4 | null | https://www.protocols.io/view/spatial-transfer-of-oligonucleotides-and-imaging-bqt7mwrn | Sanjay Srivatsan, Mary Regier | TITLE: Spatial Transfer of Oligonucleotides and Imaging
AUTHORS: Sanjay Srivatsan, Mary Regier
[STEPS]
?. [Prep work]
Prepare the following reagents prior to beginning the protocolNuclei Buffer (NB)Indexed Cold Lysis Buffer (CLB)5% PFA solution Nuclei Buffer + SuperaseIn + BSA (NSB)
?. [Spatial Transfer of Oligonuc... | ["[Prep work]\nPrepare the following reagents prior to beginning the protocolNuclei Buffer (NB)Indexed Cold Lysis Buffer (CLB)5% PFA solution Nuclei Buffer + SuperaseIn + BSA (NSB)", "[Spatial Transfer of Oligonucleotide]\nA single mouse embryo section (stored at -80C) and a single sci-Space grid (stored at -20C) were... |
52,912 | MicroCT protocols for scanning and 3D analysis of adult Hexaplex trunculus | 4 | dx.doi.org/10.17504/protocols.io.bxwqppdw | https://www.protocols.io/view/microct-protocols-for-scanning-and-3d-analysis-of-bxwqppdw | Eva Chatzinikolaou, Kleoniki Keklikoglou | TITLE: MicroCT protocols for scanning and 3D analysis of adult Hexaplex trunculus
AUTHORS: Eva Chatzinikolaou, Kleoniki Keklikoglou
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Micro-computed tomography (micro-CT) is a high-resolution 3D-imaging technique which is now increasingly applied ... | ["[Sample preparation]\nAnesthetization of gastropods with 7% MgCl2", "[Sample preparation]\nStorage in -20°C", "[Sample preparation]\nSample placement inside a custom-made felisol holder without any scanning medium (in the air)", "[microCT scanning]", "[Images reconstruction]\nProjection images were reconstructed into... |
36,918 | Purification of 2,3-bisphosphate-dependent phosphoglycerate mutase (dPGM) | 1 | dx.doi.org/10.17504/protocols.io.bgawjsfe | https://www.protocols.io/view/purification-of-2-3-bisphosphate-dependent-phospho-bgawjsfe | Cristina Rodrigues Gabriel Sales, Anabela Silva, Elizabete Carmo-Silva | TITLE: Purification of 2,3-bisphosphate-dependent phosphoglycerate mutase (dPGM)
AUTHORS: Cristina Rodrigues Gabriel Sales, Anabela Silva, Elizabete Carmo-Silva
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">This protocol describes the purification ... | ["[REAGENTS & SOLUTIONS]\nREAGENTS & SOLUTIONS TO PREPARE BEFOREHAND", "[REAGENTS & SOLUTIONS]\nLB mediumTryptone Yeast extractAdd ultrapure H2O and mix until dissolved; check if and adjust with NaOH if required.\nAdd agar if making solid LB agar.\nTo pour LB agar plates:Melt agar in the microwave if required (loos... |
80,342 | BAF_Protocol_003 Desalting | 1 | dx.doi.org/10.17504/protocols.io.36wgqjzmyvk5/v1 | https://www.protocols.io/view/baf-protocol-003-desalting-cspwwdpe | nesf | TITLE: BAF_Protocol_003 Desalting
AUTHORS: nesf
[DESCRIPTION]
The procedure is used to desalt and purify peptides from solution or in-gel digestion. This step results in minimal losses but increases analytical column life on the mass spectrometer. At the end of the procedure salts and small molecules should be washed ... | ["[Procedure for the 10 μL C18 Tips] Set the micropipette to 10 μL and secure the pipette tip tightly to the end for optimum tip-to-micropipette seal and sample aspiration.", "[Procedure for the 10 μL C18 Tips] Resuspend the sample with 0.1% FA (formic acid) or adjust sample to 0.1-1.0% FA using 2.5% FA to 12 µL total ... |
65,186 | nCoV-2019 McGill Artic PCR Protocol, V4.1 at 63C | 1 | dx.doi.org/10.17504/protocols.io.ewov18e4ygr2/v2 | https://www.protocols.io/view/ncov-2019-mcgill-artic-pcr-protocol-v4-1-at-63c-cbwaspae | Sarah J Reiling, Kayleigh Loranger, Anne-Marie Roy, Shu-Huang Chen, Ioannis Ragoussis | TITLE: nCoV-2019 McGill Artic PCR Protocol, V4.1 at 63C
AUTHORS: Sarah J Reiling, Kayleigh Loranger, Anne-Marie Roy, Shu-Huang Chen, Ioannis Ragoussis
[DESCRIPTION]
This is the updated SARS-Cov-2 PCR Protocol, with the ARTIC V4.1 primers, that is currently being used at the McGill Genome Center.
[STEPS]
SE... | ["[Primer pool preparation] PRIMER POOL PREPARATION\n\nIf required resuspend lyophilised primers at a concentration of 100 µM each", "[Primer pool preparation] The V4.1 pre-pooled primers in 1.5 mL Eppendorf labelled tubes are labelled “Pool 1 (100µM)” or “Pool 2 (100µM)\". The primers do not require additional prepara... |
36,226 | Manual Silane magnetic bead-based high throughput protocol for SARS-CoV-2 RNA extraction | null | dx.doi.org/10.17504/protocols.io.bfmajk2e | https://www.protocols.io/view/manual-silane-magnetic-bead-based-high-throughput-bfmajk2e | Ainhoa Goñi-Salaverri, Jose A. Rodriguez, Nicholas Weber, Juan Pablo Unfried, Josepmaria Argemi, , David Lara Astiaso, | TITLE: Manual Silane magnetic bead-based high throughput protocol for SARS-CoV-2 RNA extraction
AUTHORS: Ainhoa Goñi-Salaverri, Jose A. Rodriguez, Nicholas Weber, Juan Pablo Unfried, Josepmaria Argemi, , David Lara Astiaso,
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The COVID-19 pandemic has... | ["[Sample collection]\nFollowing oropharyngeal and/or nasopharyngeal swab collection, place the swab directly into a 2 mL safe-lock tube containing 800 l of RLT-plus buffer (Qiagen).* When collected in RLT plus the viral particles become inactive. This provides further biosafety for the process. However, samples shoul... |
54,164 | Sepiolite - Chitosan Biocompatible Foams | 6 | dx.doi.org/10.17504/protocols.io.by5upy6w | https://www.protocols.io/view/sepiolite-chitosan-biocompatible-foams-by5upy6w | celiamm | TITLE: Sepiolite - Chitosan Biocompatible Foams
AUTHORS: celiamm
[DESCRIPTION]
The foams are biohybrid, resistant, biocompatible, biodegradable materials that allow cyanobacteria to survive inside them and produce the desired biofuel. It is a macroporous material with high porosity.
Its synthesis is relatively sim... | ["[Solutions preparation] Having different options to do the chitosan: sepiolite solutions:\n\n To make a 1:1 mix chitosan:sepiolite:\n\nFirst, produce a 4% solution of chitosan(that after doing the mix will be a 2%). It is IMPORTANT to mention that it is difficult to disolve it. To do it: \n -Take a glass (r... |
42,155 | Early versus delayed feeding after endoscopic submucosal dissection: a systematic review and meta-analysis (protocol) | 1 | dx.doi.org/10.17504/protocols.io.bmejk3cn | https://www.protocols.io/view/early-versus-delayed-feeding-after-endoscopic-subm-bmejk3cn | Jun Watanabe, Joji Watanabe, Kazuhiko Kotani | TITLE: Early versus delayed feeding after endoscopic submucosal dissection: a systematic review and meta-analysis (protocol)
AUTHORS: Jun Watanabe, Joji Watanabe, Kazuhiko Kotani
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Background</span><span>: Endoscopic sub... | [] |
44,820 | Cerulenin experiment | 4 | null | https://www.protocols.io/view/cerulenin-experiment-bpzump6w | Elizabeth Fozo | TITLE: Cerulenin experiment
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Rescue from Cerulenin Inhibition</div><div class = "text-block">Based on Saito, et al., 2018</div></div>
[STEPS]
?. [Steps]
Grow strain of interest overnight in 5 ml BHI
?. [Steps]
The next day, set ... | ["[Steps]\nGrow strain of interest overnight in 5 ml BHI", "[Steps]\nThe next day, set up the following tubes:Tube with no ceruleninTube with cerulenin + solvent control (for fatty acid)Tube with cerulenin + fatty acid of interest\nFor current studies, use 5mg/ml of cerulenin (note, can dissolve stock in 10 mg/ml ethan... |
null | null | null | dx.doi.org/10.17504/protocols.io.n3edgje | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><em>The MELD Project is an international collaboration aiming to create open-access, robust and generalisable tools for FCD detection. To this end, we will train a neural network classifier on MRI features from FCD patients from multiple centres worldwide.</em></p>
<p><strong... | [] |
44,702 | Cell DIVE™ Platform | Antibody Staining & Imaging | 4 | dx.doi.org/10.17504/protocols.io.bpv6mn9e | https://www.protocols.io/view/cell-dive-platform-antibody-staining-amp-imaging-bpv6mn9e | Liz McDonough, Chrystal Chadwick, Fiona Ginty, Christine Surrette, Anup Sood | TITLE: Cell DIVE™ Platform | Antibody Staining & Imaging
AUTHORS: Liz McDonough, Chrystal Chadwick, Fiona Ginty, Christine Surrette, Anup Sood
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This document outlines the workflow for antibody staining, dye inactivation, and imaging as per the Cell DIVE... | ["[Background Imaging]\nRefer to Cell DIVE Imaging Manual.", "[Decoverslipping]\nCoverslips are removed from slides to prepare them for the next slide processing step.", "[Decoverslipping]\nTake a plastic slide box and place it in secondary containment.", "[Decoverslipping]\nFill the plastic slide box with 1x PBS.", "[... |
55,420 | Standard-S: PCR barcoding of SARS-CoV-2 S gen amplicons for Nanopore sequencing | 1 | dx.doi.org/10.17504/protocols.io.kqdg3pe9pl25/v1 | https://www.protocols.io/view/standard-s-pcr-barcoding-of-sars-cov-2-s-gen-ampli-b2c4qayw | Cecilia Salazar | TITLE: Standard-S: PCR barcoding of SARS-CoV-2 S gen amplicons for Nanopore sequencing
AUTHORS: Cecilia Salazar
[DESCRIPTION]
Most of the defining mutations of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants of concern (VOCs) have been identified in the S gene sequence. For this reason, S-bas... | ["[Reverse transcription] Keeping the SARS-CoV-2 extracted RNA samples on ice all the time and spin down the tubes.", "[S gene tiled amplification] Set up the first round PCR reaction in a pre-PCR cabinet for primer pool A and primer pool B", "[Pooling and clean-up] Spin down the tubes and pool all samples in a 1.5 mL ... |
null | null | null | dx.doi.org/10.17504/protocols.io.vgie3ue | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Protocolos da equipe de anestesiologia do Instituto Castro e Santos (Distrito Federal)
[STEPS] | [] |
36,622 | SPARC Cat - Sham Control Chronic Cat 2, Day 14 | 1 | dx.doi.org/10.17504/protocols.io.bfznjp5e | https://www.protocols.io/view/sparc-cat-sham-control-chronic-cat-2-day-14-bfznjp5e | Brett Hanzlicek, Anna Rietsch, Margot Damaser | TITLE: SPARC Cat - Sham Control Chronic Cat 2, Day 14
AUTHORS: Brett Hanzlicek, Anna Rietsch, Margot Damaser
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a procedure for a sham control chronic cat experiment (Day 14) for cystotomy (bladder surgery). The cystotomy is performed without... | ["[Transport Cat]\nTransport cat from housing site to surgery site.", "[Animal Prep and catheter placement]\nAnimal is anesthetized and abdomen is shaved by the vet team. The cat is then moved into the surgery room and attached to monitors by the vet team.", "[Animal Prep and catheter placement]\nDrape animal and perf... |
80,426 | Rice recipe | 1 | null | https://www.protocols.io/view/rice-recipe-cssiwece | Jessica Coolidge | TITLE: Rice recipe
AUTHORS: Jessica Coolidge
[DESCRIPTION]
Test recipe
[STEPS] | [] |
55,488 | Total RNA and DNA in Microalgae | 1 | null | https://www.protocols.io/view/total-rna-and-dna-in-microalgae-b2e8qbhw | Yingyu Hu, Zoe V Finkel | TITLE: Total RNA and DNA in Microalgae
AUTHORS: Yingyu Hu, Zoe V Finkel
[DESCRIPTION]
Here we describe a protocol for extracting and quantifying bulk RNA and DNA from microalgae, which is adapted from Berdalet E. et al. (2005).
RNA and DNA are extracted from microalgae samples and then quantified by fluorochrome SY... | ["[Day 1: Freeze-dry samples] Freeze dry samples and blank filters. Freeze at -80 °C until processed.", "[Day 1: Prepare primary solutions] Turn on UV light in biosafety cabinet for 15 min and clean working surface with decontamination solution.", "[Day 1: Prepare primary solutions] Prepare Tris buffer 5 mM pH 8.0", ... |
103,033 | T cell purification and activation | 0 | dx.doi.org/10.17504/protocols.io.81wgbz431gpk/v1 | https://www.protocols.io/view/t-cell-purification-and-activation-dguz3wx6 | Moustafa Nouh Elemeery, Salix Boulet | TITLE: T cell purification and activation
AUTHORS: Moustafa Nouh Elemeery, Salix Boulet
[DESCRIPTION]
This protocol details the purification and activation of Mouse Naïve CD8+ T Cell using an isolation kit from STEMCELL. This kit is designed to isolate naïve CD62L+CD44-CD8+ T cells from single-cell suspensions of sple... | ["[Purification and activation] Dilute CD3 antibody (145-2C11) (clone KT3 can also be used) to 1 1621 in PBS.", "[Purification and activation] Coat plates with anti-CD3 antibody.", "[Purification and activation] Use 24 or 96 wells flat bottom suspension plates. If these plates are not used, there is a risk of partial s... |
88,226 | Opentrons Pipeline: PCR Preparation | 4 | dx.doi.org/10.17504/protocols.io.rm7vzx6y8gx1/v1 | https://www.protocols.io/view/opentrons-pipeline-pcr-preparation-c2eaybae | Jhakelin Reyes Vasquez, P. Sánchez-Vendizú, thalia.silvestre, Gideon Erkenswick, Alexandra Sacco, Mrinalini Watsa | TITLE: Opentrons Pipeline: PCR Preparation
AUTHORS: Jhakelin Reyes Vasquez, P. Sánchez-Vendizú, thalia.silvestre, Gideon Erkenswick, Alexandra Sacco, Mrinalini Watsa
[DESCRIPTION]
This protocol is a general automated pipeline to prepare mastermix at the plate level in a sterile way. The protocol volumes can be edited... | ["[Materials and reagents] Reagents List\n \nPrimers Forward and Reverse 10 micromolar (µM) or specific for each primer.", "[Materials and reagents] Materials List\n2 X Opentrons 20µL Filter Tips\n1 X Opentrons Thermocycler Module - GEN2*\n1 X Nest skirted PCR Plate\n1 X 96-well Opentrons Aluminum Block\n1 X P20 Gen 2... |
46,087 | Hydrophobicity Protocol | 4 | null | https://www.protocols.io/view/hydrophobicity-protocol-bq9fmz3n | Elizabeth Fozo | TITLE: Hydrophobicity Protocol
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">P-Xylene Hydrophobicity Assay</div><div class = "text-block">Note that I have written this before doing it. Changes most likely will be made.</div></div>
[STEPS]
?. [Steps]
Grow 10mls OG1RF in BHI... | ["[Steps]\nGrow 10mls OG1RF in BHI using short-term or long-term supplementation", "[Steps]\nAt 0.3 OD for long-term or 30 minutes after supplementation for short-term, spin cells and wash twice using PUM buffer", "[Steps]\nAliquot 1 ml 6 times into glass tubes and mix with a range of P-xylene volumes", "[Steps]\nVorte... |
77,465 | UAB-VU BIOMIC Preparation of Left Fresh Frozen Eye | 4 | dx.doi.org/10.17504/protocols.io.3byl4jd38lo5/v1 | https://www.protocols.io/view/uab-vu-biomic-preparation-of-left-fresh-frozen-eye-cpvzvn76 | David Anderson, Jeffrey D. Messinger, Angela Kruse, Jamie Allen, Melissa Farrow, Christine Curcio, Jeff Spraggins, Kevin Schey | TITLE: UAB-VU BIOMIC Preparation of Left Fresh Frozen Eye
AUTHORS: David Anderson, Jeffrey D. Messinger, Angela Kruse, Jamie Allen, Melissa Farrow, Christine Curcio, Jeff Spraggins, Kevin Schey
[DESCRIPTION]
Scope:
This protocol describes the process of procuring donor eyes from Advancing Sight Network, the pro... | ["[Positioning and Marking Globe] Whole donor globes on wet ice are received within less than 6 hours’ time of death (TOD) from the Advancing Sight Network (500 Robert Jemison Rd Birmingham, AL 35209).", "[Positioning and Marking Globe] Laterality is verified using extraocular anatomy.", "[Positioning and Marking Globe... |
null | null | null | dx.doi.org/10.17504/protocols.io.d8u9wv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol gives an introduction to running VirSorter in the iPlant Discovery Environment.
[BEFORE_START]
To access VirSorter on iPlant, you will first need to create a (free) account. This can be done at this address: <a href="https://user.iplantcollaborative.org/register/"... | [] |
58,472 | FLASH-seq UMI protocol (V1) | 4 | dx.doi.org/10.17504/protocols.io.b5cgq2tw | https://www.protocols.io/view/flash-seq-umi-protocol-v1-b5cgq2tw | Simone Picelli, Vincent Hahaut | TITLE: FLASH-seq UMI protocol (V1)
AUTHORS: Simone Picelli, Vincent Hahaut
[DESCRIPTION]
The single-cell RNA-sequencing (scRNA-seq) field has evolved tremendously since the first paper was published back in 2009. While the first methods analysed just a handful of cells, the throughput and performance rapidly increa... | ["[Prepare lysis mix] Prepare the following lysis mix:\n ReagentReaction concentrationVolume (µl)384-well plateTriton-X100 (10% v/v)0.2%0.0208.448dNTP mix (25 mM each)6 mM0.240101.376STRT-P1-T31 oligo (100 µM)1.8 mM0.0187.603RNAse inhibitor (40 U/µl)1.2 U/µl0.03012.672DTT (100 mM)1.2 mM0.0125.069dCTP (100 µM)9 mM0.0... |
43,329 | Plaque PCR | 1 | dx.doi.org/10.17504/protocols.io.bni9mch6 | https://www.protocols.io/view/plaque-pcr-bni9mch6 | Jiaxin Li | TITLE: Plaque PCR
AUTHORS: Jiaxin Li
[STEPS]
?. Mark independent plaques on the back of the Petri dish with a black pen. Take 6 points in a plate and try to take points randomly and evenly.
?. Take 24 1.5 ml EP tubes.A) Add 200 μl SM Buffer per tubeB) Add 2 μl chloroform to each tube
?. [Sampling]
Suck out the plaque ... | ["Mark independent plaques on the back of the Petri dish with a black pen. Take 6 points in a plate and try to take points randomly and evenly.", "Take 24 1.5 ml EP tubes.A) Add 200 μl SM Buffer per tubeB) Add 2 μl chloroform to each tube", "[Sampling]\nSuck out the plaque just spotted with the pipette", "[Sampling]\nP... |
50,531 | COPAS wormsorter v.2 | 1 | dx.doi.org/10.17504/protocols.io.bvkbn4sn | https://www.protocols.io/view/copas-wormsorter-v-2-bvkbn4sn | Saul Moore, Ida Barlow | TITLE: COPAS wormsorter v.2
AUTHORS: Saul Moore, Ida Barlow
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for dispensing adult worms using the COPAS 500 flowpilot</div></div>
[STEPS]
?. [Prepare equipment]
Turn on equipment in the following ordera.Sorter (left side of unit near bottom)b... | ["[Prepare equipment]\nTurn on equipment in the following ordera.Sorter (left side of unit near bottom)b.Computer and monitorc.Laser, located under computerd.Vacuum pump (switch on wall to right of sorter)", "[Prepare equipment]\nDiscard waste contents that are in the recovery cup (small shallow cup on the left-hand si... |
48,632 | Immunofluorescence staining of Collagen Type XVIII in islet beta cells of formalin-fixed mouse pancreas | 1 | dx.doi.org/10.17504/protocols.io.btqynmxw | https://www.protocols.io/view/immunofluorescence-staining-of-collagen-type-xviii-btqynmxw | Sarah Popp, Charmaine Simeonovic | TITLE: Immunofluorescence staining of Collagen Type XVIII in islet beta cells of formalin-fixed mouse pancreas
AUTHORS: Sarah Popp, Charmaine Simeonovic
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Paraffin sections of formalin-fixed mouse pancreas were treated with 0.05% pronase for antigen ret... | ["Deparaffinize slides in each xylene for 1 min (see Guidelines). Rehydrate slides in graded alcohols beginning in absolute ethanol (10 dips)/ container of absolute ethanol), followed by 90% ethanol (10 dips) and 70% ethanol (10 dips). Wash well in running tap water for 5 min.", "Wipe around sections using tissue and c... |
84,011 | Membrane and cytosol fractionation | 4 | dx.doi.org/10.17504/protocols.io.n92ldm3d7l5b/v1 | https://www.protocols.io/view/membrane-and-cytosol-fractionation-cwajxacn | wusj, schekman | TITLE: Membrane and cytosol fractionation
AUTHORS: wusj, schekman
[DESCRIPTION]
This protocol describes membrane and cytosol fractionation of cells expressing different DNAJC5 isoforms
[STEPS]
SECTION: Cytosol fractionation
1. Cells (one 10 cm dish) were cultured to 70% confluence and transfected with different const... | ["[Cytosol fractionation] Cells (one 10 cm dish) were cultured to 70% confluence and transfected with different constructs\nof DNAJC5", "[Cytosol fractionation] One day after transfection, we harvested the transfected cells by scraping in 1 ml B88 (20 mM HEPES-KOH, pH 7.2, 250 mM sorbitol, 150 mM potassium acetate, and... |
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