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.c63zgm | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
** It is IMPORTANT to use a buffer that matches what the virus is resuspended in as it helps keep the virus heads intact. If you are looking at a CsCl gradient fraction that has not been dialyzed, we find that as the diluent using CsCl with a similar density helps keep the ... | [] |
18,458 | Measurement of cellular oxygen consumption and extracellular acidification | null | dx.doi.org/10.17504/protocols.io.v92e98e | null | Kiichi Hirota, Yoshiyuki Matsuo | TITLE: Measurement of cellular oxygen consumption and extracellular acidification
AUTHORS: Kiichi Hirota, Yoshiyuki Matsuo
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Cells were seeded on to the XFp Cell Culture microplate and incubated overnight.
?. The sensor cartridge of the XFp Analyzer was hydrate... | ["Cells were seeded on to the XFp Cell Culture microplate and incubated overnight.", "The sensor cartridge of the XFp Analyzer was hydrated at 37 °C in a non-CO2 incubator one day before the experiment.", "For the OCR assay, injection port A on the sensor cartridge was loaded with oligomycin (a complex V inhibitor, fin... |
89,662 | Free Floating IHC Fluorescent Staining | 4 | dx.doi.org/10.17504/protocols.io.e6nvwd8qwlmk/v1 | https://www.protocols.io/view/free-floating-ihc-fluorescent-staining-c3s6ynhe | Ashley Harms, Jhodi Webster | TITLE: Free Floating IHC Fluorescent Staining
AUTHORS: Ashley Harms, Jhodi Webster
[DESCRIPTION]
This protocol is optimized for to stain free floating sections for fluorescent labelling. Please note than each step must be done on a shaker.
[STEPS]
SECTION: Day 1
1. Using a 12-well plate with buckets, wash sections ... | ["[Day 1] Using a 12-well plate with buckets, wash sections 3x10min TBS", "[Day 1] Block in 5% serum in TBST for 1hour at RT (using approx 2mL per well)", "[Day 1] Using approx 500uL per well, let sections wash in primary antibody solution in TBST + 1% serum overnight in 4 °C", "[Day 2] Wash sections 3x10min in TBST", ... |
74,600 | ArchaeoScale Protocol: Inserting digital scale bars into scientific images – Full step-by-step guideline for anthropological and archaeological specimen photography | 1 | dx.doi.org/10.17504/protocols.io.8epv5j1p6l1b/v1 | https://www.protocols.io/view/archaeoscale-protocol-inserting-digital-scale-bars-ck4guytw | Dominik Göldner | TITLE: ArchaeoScale Protocol: Inserting digital scale bars into scientific images – Full step-by-step guideline for anthropological and archaeological specimen photography
AUTHORS: Dominik Göldner
[DESCRIPTION]
Geometric scale bars, also known as photography scales or photomacrographic rulers, are small but important ... | ["[Digital scale bar insertion using ImageJ] Take high-quality images according to your personal or project guidelines. For each session, take photos first with and then without the scale bar in the proper position and location. Make sure that you do not move the object before all the pictures have been taken.\n\nTake ... |
16,787 | Zymo Duet DNA/RNA MiniPrep Plus Extractions | null | dx.doi.org/10.17504/protocols.io.umteu6n | null | Amy Lyden | TITLE: Zymo Duet DNA/RNA MiniPrep Plus Extractions
AUTHORS: Amy Lyden
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Attached are detailed instructions for following the kit guidelines for the Zymo Duet DNA/RNA MiniPrep Plus.</div></div>
[STEPS]
?. [Sample Preparation for cultured isolates]
Add 1X... | ["[Sample Preparation for cultured isolates]\nAdd 1X DNA/RNA shield (2x concentrate diluted in nuclease-free water) to bead bashing tubesTissuelyse on Qiagen Tissuelyser II at a frequency of 1/30 s. Alternatively, vortex at the highest frequency for 2 minutes.Spin at 14000RCF.Add of DNA/RNA Lysis buffer. Proceed wit... |
97,021 | Dark Light Box | 0 | dx.doi.org/10.17504/protocols.io.ewov19jz7lr2/v1 | https://www.protocols.io/view/dark-light-box-day52fy6 | daniel.dautan daniel, Per Svenningsson | TITLE: Dark Light Box
AUTHORS: daniel.dautan daniel, Per Svenningsson
[DESCRIPTION]
Behavioral test for anxiety-like behaviors in mice.
[STEPS]
1. Set up the dark light box. See materials.
2. Place each mouse into the dark compartment before closing the lid and left to explore for 6
minutes.
3. Video record each ex... | ["Set up the dark light box. See materials.", "Place each mouse into the dark compartment before closing the lid and left to explore for 6\nminutes.", "Video record each experiments.", "Manually score for each animal the time in the light box as well as the number of times the mouse entered the light box."] |
null | null | null | dx.doi.org/10.17504/protocols.io.k5icy4e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><a href="https://www.promega.de/products/pcr/endpoint-pcr/gotaq-g2-master-mixes/?catNum=M7822" target="_blank">GoTaq® G2 Green Master Mix(a,b)</a> is a premixed ready-to-use solution containing GoTaq® G2 DNA Polymerase, dNTPs, MgCl2 and reaction buffers at optimal concentrati... | [] |
50,566 | Preparing a Bacterial Stock | 4 | null | https://www.protocols.io/view/preparing-a-bacterial-stock-bvmen43e | Wolfram Moebius, Dibyendu Dutta | TITLE: Preparing a Bacterial Stock
AUTHORS: Wolfram Moebius, Dibyendu Dutta
[DESCRIPTION]
This protocol describes how to create a glycerol bacterial stock for long-term storage at -70 °C.
[STEPS]
SECTION: Preparing Bacterial Stock
1. Produce an culture of the desired strain.
SECTION: Preparing Bacterial Stock
2... | ["[Preparing Bacterial Stock] Produce an culture of the desired strain.", "[Preparing Bacterial Stock] Label cryotube lid and side of tube with with strain, date. \n\nCreate 30 % glycerol (3 parts glycerol by volume, 7 parts Millipore H2O by volume) then autoclave.", "[Preparing Bacterial Stock] Store at -80 °C .", "... |
75,822 | Spatial Transcriptomics for OCT using 10x Genomics Visium | 1 | dx.doi.org/10.17504/protocols.io.x54v9d3opg3e/v1 | https://www.protocols.io/view/spatial-transcriptomics-for-oct-using-10x-genomics-cnanvade | Andrew Houston, Siqi Chen, Feng Chen | TITLE: Spatial Transcriptomics for OCT using 10x Genomics Visium
AUTHORS: Andrew Houston, Siqi Chen, Feng Chen
[DESCRIPTION]
To detect gene expression spatially mapped across a fresh-frozen tissue sample adapted from 10x Genomics Visium protocol.
[STEPS]
SECTION: Visium Fresh-Frozen
2. RNA extraction and assessment ... | ["[Visium Fresh-Frozen] RNA extraction and assessment is outlined in the above guide but not always necessary\nMost OCT blocks have preserved RNA quality well due to their preservation/storage", "[Visium Fresh-Frozen] Perform all fixation/H&E staining/imaging steps on the Visium Spatial Gene Expression Slide (PN-200023... |
66,149 | Protocol: HLA-DQB1*0301, HLA-DQB1*0501, and HLA-DQA1*0301 and Their Role in Scleroderma- A Systematic Review | 1 | dx.doi.org/10.17504/protocols.io.j8nlkkpqwl5r/v1 | https://www.protocols.io/view/protocol-hla-dqb1-0301-hla-dqb1-0501-and-hla-dqa1-ccudsws6 | Dylan Thibaut, Jared Lehman, Alexis Marquess, Kersten Schroeder | TITLE: Protocol: HLA-DQB1*0301, HLA-DQB1*0501, and HLA-DQA1*0301 and Their Role in Scleroderma- A Systematic Review
AUTHORS: Dylan Thibaut, Jared Lehman, Alexis Marquess, Kersten Schroeder
[DESCRIPTION]
Scleroderma remains a debilitating autoimmune condition with immunological linkage to HLA sequences remaining o... | ["[Administrative Information] Title\nProtocol: HLA-DQB1*0301, HLA-DQB1*0501, and HLA-DQA1*0301 and Their Role in Scleroderma- A Systematic Review", "[Administrative Information] Registration\nRegistration is via protocols.io", "[Administrative Information] Authors\n\nDylan Thibaut: Lake Erie College of Osteopathic Med... |
24,395 | Yeast growth profile analysis | null | dx.doi.org/10.17504/protocols.io.33jgqkn | null | Monica Rieth | TITLE: Yeast growth profile analysis
AUTHORS: Monica Rieth
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This method outlines a procedure for analyzing the growth curve of Baker's yeast, </span><span style = "font-style:italic;">Saccharomyces cerevisiae</span><span>, for the assessment of gr... | [] |
46,658 | Protocol for the detection of rare alleles in bulk seed samples | 4 | dx.doi.org/10.17504/protocols.io.brtam6ie | https://www.protocols.io/view/protocol-for-the-detection-of-rare-alleles-in-bulk-brtam6ie | Anthony Brusa, Eric Patterson | TITLE: Protocol for the detection of rare alleles in bulk seed samples
AUTHORS: Anthony Brusa, Eric Patterson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol was developed for the detection of </span><span style = "font-style:italic;">Amaranthus palmeri</span><span>seeds in mixed... | ["[Tissue Disruption]\nTissue disruption", "[Tissue Disruption]\nAssemble samples to be tested, partition into pools of an appropriate number of seeds (200 seeds for Amaranthus sp. testing).", "[Tissue Disruption]\nPlace seeds and grinding bead into a tube suitable for tissue disruption. Avoid conical bottom tubes as t... |
33,737 | Ectoplasmic Net (EN) formation in Aurantiochytrium limacinum (ATCC MYA-1381) | null | dx.doi.org/10.17504/protocols.io.bc7hizj6 | null | Anbarasu Karthikaichamy, Jackie Collier | TITLE: Ectoplasmic Net (EN) formation in Aurantiochytrium limacinum (ATCC MYA-1381)
AUTHORS: Anbarasu Karthikaichamy, Jackie Collier
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Protocol for ectoplasmic net (EN) formation in </span><span style = "font-style:italic;">Aurantiochytrium limacin... | ["[d-GPY plating]\nTake of 3 day old cells grown on GPY media and plate it on d-GPY plates. AB1ComponentsQuantity (%)2Yeast extract0.053Peptone0.14Glucose0.25Prepare 1/2 saline media by adding appropriate amount of instant ocean and water.6For agar plates1.5% agarIncubate the plates at\n150 µl\nAB1ComponentsQuantity ... |
16,027 | ChroSpin - IMAC | null | dx.doi.org/10.17504/protocols.io.tv3en8n | null | Alexandra Ehl, David Frommholz, Nadine Stefanczyk | TITLE: ChroSpin - IMAC
AUTHORS: Alexandra Ehl, David Frommholz, Nadine Stefanczyk
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Purification Guide for the Isolation of Histidine-tagged Proteins with ChroSpin Columns by DALEX Biotech.</span></div><div class = "text... | ["[Equilibration]\nAdd 500 µl of nickel or cobalt solution, close the lid, and incubate 1 minute with end-over-end mixing.\nApart from Ni2+ and Co2+, you can also use Cu2+ or Zn2+.The affinity of histidine towards the metal ions is in the order Cu > Ni > Zn > Co. However, the specificity is in the invers order, i.e. co... |
null | null | null | dx.doi.org/10.17504/protocols.io.erubd6w | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<strong>FIGURE OUT WHAT YOU NEED:</strong><br /><br /> A. Type of gel: regular agarose or low melting point (LMP) agarose<br /><br /> B. Concentration of gel<br /> 1. Mini gels (50 mL gels):<br /> 0.7% = 0.35 gm per 50 mL<br /> 0.8% = 0.40 gm per 5... | [] |
35,711 | Opentrons COVID-19 testing: Station B, Zymo kit, 24 samples | null | dx.doi.org/10.17504/protocols.io.be47jgzn | https://www.protocols.io/view/opentrons-covid-19-testing-station-b-zymo-kit-24-s-be47jgzn | Max Marrone | TITLE: Opentrons COVID-19 testing: Station B, Zymo kit, 24 samples
AUTHORS: Max Marrone
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Station B: Initial OT-2 setup]
Clean the OT-2.
?. [Station B: Initial OT-2 setup]
Place the following labware on the OT-2's deck:Slot 1: An Opentrons Temperature Module w... | ["[Station B: Initial OT-2 setup]\nClean the OT-2.", "[Station B: Initial OT-2 setup]\nPlace the following labware on the OT-2's deck:Slot 1: An Opentrons Temperature Module with an Opentrons 96 well aluminum block and an empty, sterile NEST 100 µL PCR plate.Slots 3 and 6: A full, sterile rack of Opentrons 200 µL filte... |
18,567 | 16S rRNA probe design for HCR-FISH | 1 | null | https://www.protocols.io/view/16s-rrna-probe-design-for-hcr-fish-wdffa3n | Kayley Hake | TITLE: 16S rRNA probe design for HCR-FISH
AUTHORS: Kayley Hake
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol outlines how to design HCR-FISH probes targeting 16S rRNA sequences. It covers downloading and installing software (ARB, MacPorts, XQuartz), importing SILVA 16S rRNA da... | ["[Installing ARB, MacPorts, and XQuartz Software]\nDownload zip file of ARB software for your operating system from the ARB website.Download the MacPorts software through the MacPorts website. Install MacPorts. (Requires Xcode for Mac which can be downloaded in the App store)Once MacPorts is installed, open a new Term... |
107,766 | AAV-Zombie on cultured cells | 0 | dx.doi.org/10.17504/protocols.io.36wgqnz53gk5/v1 | https://www.protocols.io/view/aav-zombie-on-cultured-cells-dmgw43xe | Gerard Michael Coughlin | TITLE: AAV-Zombie on cultured cells
AUTHORS: Gerard Michael Coughlin
[DESCRIPTION]
Detection of AAV genomes in situ can facilitate understanding of AAV transduction and processing. This protocol enables detection of AAV genomes in cultured cells and is based on the Zombie method published in Askary et al., Nat Biotech... | ["[Reagent set up] General note on reagents and consumables", "[Sample preparation] At time of collection, aspirate media and wash cells one time with 1 mL DPBS. Aspirate DPBS and add 1 mL ice-cold MAA fixation buffer. Transfer to -20 °C for 15 min .", "[Sample preparation] Transduce cells with AAVs carrying Zombie ba... |
82,328 | Postnatal astrocyte labeling by electroporation (PALE) | 3 | dx.doi.org/10.17504/protocols.io.5jyl8j44dg2w/v1 | https://www.protocols.io/view/postnatal-astrocyte-labeling-by-electroporation-pa-cumywu7w | Shiyi Wang | TITLE: Postnatal astrocyte labeling by electroporation (PALE)
AUTHORS: Shiyi Wang
[DESCRIPTION]
Postnatal astrocyte labeling by electroporation (PALE)
[STEPS] | [] |
47,276 | Teachers’ mental health during the first two waves of the COVID-19 pandemic in Poland. | 1 | dx.doi.org/10.17504/protocols.io.bseknbcw | https://www.protocols.io/view/teachers-mental-health-during-the-first-two-waves-bseknbcw | Tomasz Jakubowski, Magdalena Sitko-Dominik | TITLE: Teachers’ mental health during the first two waves of the COVID-19 pandemic in Poland.
AUTHORS: Tomasz Jakubowski, Magdalena Sitko-Dominik
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The aim of the research is to investigate the relation between distance education and teachers’ well-being... | ["Tomasz Jakubowski, Magdalena Sitko-Dominik\n\t\t\t\t\t\t\t .justify:after {\n\t\t\t\t\t\t\t content: \"\";\n\t\t\t\t\t\t\t display:inline-block;\n\t\t\t\t\t\t\t width: 100%;\n\t\t\t\t\t\t\t }\n\t\t\t\t\t\t\tDesign PlanThe project will be realized as observational cross-sectional study. It will not use any ... |
73,229 | Extraction of fungal DNA and PCR for identification using the Sigma-Aldrich REDExtract Plant PCR kit | 4 | null | https://www.protocols.io/view/extraction-of-fungal-dna-and-pcr-for-identificatio-cjrmum46 | Siouxsie Wiles, Shara Van De Pas | TITLE: Extraction of fungal DNA and PCR for identification using the Sigma-Aldrich REDExtract Plant PCR kit
AUTHORS: Siouxsie Wiles, Shara Van De Pas
[DESCRIPTION]
This protocol describes how we use the REDExtract Plant PCR kit (Sigma-Aldrich) to extract DNA from fungal mycelium and PCR from the ITS region.
[BEFORE_S... | ["[DNA Extraction] Place 30 ul extraction solution into PCR tubes. Using a small sterile pipette tip place a small piece of mycelium so its only just visible on the tip into the tube. Vortex and briefly centrifuge.", "[DNA Extraction] Place PCR tubes into the PCR machine and run a cell break protocol (95 °C for 10 minu... |
null | null | null | dx.doi.org/10.17504/protocols.io.exabfie | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>sgRNA template assembly, in vitro T7 transcription, and SPRI bead cleanup</p>
[GUIDELINES]
The primers used are: one long, variable oligo that carries the T7 promoter and desired guide sequence; an 82-nt constant oligo that carries the 3' end of the sgRNA; two short external... | [] |
96,965 | Processing of pediatric adenoid and tonsil samples for single cell analysis | 0 | dx.doi.org/10.17504/protocols.io.3byl49ewjgo5/v1 | https://www.protocols.io/view/processing-of-pediatric-adenoid-and-tonsil-samples-daxd2fi6 | Liam Gubbels, Shivanthan Shanthikumar, Melanie R Neeland | TITLE: Processing of pediatric adenoid and tonsil samples for single cell analysis
AUTHORS: Liam Gubbels, Shivanthan Shanthikumar, Melanie R Neeland
[DESCRIPTION]
This protocol describes the collection, processing, and cryopreservation of pediatric adenoid and tonsil samples for downstream single-cell analysis.
[GUID... | ["[COLLECTION OF ADENOID AND TONSIL TISSUE] Prepare specimen containers for adenoid and tonsil samples by adding 10mL pre-chilled RPMI supplemented with 2% heat-inactivated fetal calf serum (referred to as RPMI 2% FCS).", "[COLLECTION OF ADENOID AND TONSIL TISSUE] After obtaining informed consent from family and/or pat... |
101,268 | Fabrication of laser inscribed graphene (LIG) 3-electrode plug-and-play chip | 0 | dx.doi.org/10.17504/protocols.io.dm6gpze1dlzp/v2 | https://www.protocols.io/view/fabrication-of-laser-inscribed-graphene-lig-3-elec-de5u3g6w | Lisseth Casso-Hartmann, Geisianny AM Moreira, Yifan Tang, Diana Vanegas, Eric S McLamore | TITLE: Fabrication of laser inscribed graphene (LIG) 3-electrode plug-and-play chip
AUTHORS: Lisseth Casso-Hartmann, Geisianny AM Moreira, Yifan Tang, Diana Vanegas, Eric S McLamore
[DESCRIPTION]
Laser inscribed graphene (LIG) is a versatile material that is commonly used to prepare electrochemical sensors (Moreira et... | ["Step 1) Fabrication of USB-A Adapter \nHeat the soldering iron, and prepare a wet sponge and solder wick. \nSee the following for an introduction to soldering techniques (link)\nSolder one 28AWG jumper wire to each of the two outer contacts in the USB-A adapter. \nCreate an electrical connection (i.e., “jump”) the tw... |
48,922 | Waimea Field Sampling | 1 | dx.doi.org/10.17504/protocols.io.btz2np8e | https://www.protocols.io/view/waimea-field-sampling-btz2np8e | Anthony Amend | TITLE: Waimea Field Sampling
AUTHORS: Anthony Amend
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Detailed Sampling Methods for Waimea Watershed Sampling Project</span></div></div>
[STEPS] | [] |
62,008 | Selective Enrichment Protocol for Salmonella Isolation from Surface Water | 4 | dx.doi.org/10.17504/protocols.io.kxygxz5q4v8j/v1 | https://www.protocols.io/view/selective-enrichment-protocol-for-salmonella-isola-b8syrwfw | Autumn L. Kraft, Manan Sharma, Jonathan G Frye, James E Wells, Abasiofiok Mark Ibekwe, NARMS EWG | TITLE: Selective Enrichment Protocol for Salmonella Isolation from Surface Water
AUTHORS: Autumn L. Kraft, Manan Sharma, Jonathan G Frye, James E Wells, Abasiofiok Mark Ibekwe, NARMS EWG
[DESCRIPTION]
This protocol describes the selective enrichment of Salmonella from surface water samples AFTER non-selective e... | ["[Selective Enrichment – Day 1] Dispense 9 mL TT (Tetrathionate) broth into sterile test tubes.", "[Selective Enrichment – Day 1] Dispense 9 mL GN (Gram-negative Hajna broth) into sterile test tubes.", "[Selective Enrichment – Day 1] Hand massage UPB(Universal Pre-enrichment Broth)-enriched modified Moore swab (MMS), ... |
37,784 | DAB Detection of Biocytin Labeled Tissue | 1 | dx.doi.org/10.17504/protocols.io.bg5yjy7w | https://www.protocols.io/view/dab-detection-of-biocytin-labeled-tissue-bg5yjy7w | Allen Institute for Brain Science | TITLE: DAB Detection of Biocytin Labeled Tissue
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the process for diaminobenzidine (DAB) detection of biocytin filled cells. This protocol is optimized for use with brain slices cut at 3... | [] |
90,449 | NEBNext Ultra II Library Prep for Illumina Low Volume Version (Naturalis) | 4 | null | https://www.protocols.io/view/nebnext-ultra-ii-library-prep-for-illumina-low-vol-c4jryum6 | Stacey Dubbeldam | TITLE: NEBNext Ultra II Library Prep for Illumina Low Volume Version (Naturalis)
AUTHORS: Stacey Dubbeldam
[DESCRIPTION]
Low volume version of NEBNext Ultra II DNA library protocol (Naturalis).
[STEPS]
SECTION: NEBNext Ultra II Library Prep for Illumina Low Volume Version (Naturalis)
1. Make sure that the DNA is elu... | ["[NEBNext Ultra II Library Prep for Illumina Low Volume Version (Naturalis)] Make sure that the DNA is eluted in . If this is not the case, samples can be diluted using 10nM Tris-HCl, pH 8.0 or 0.1X TE.", "[NEBNext Ultra II Library Prep for Illumina Low Volume Version (Naturalis)] Check the DNA concentration of your ... |
103,246 | Immunohistochemistry - uPAR in mouse lung tissue | 0 | dx.doi.org/10.17504/protocols.io.x54v923dql3e/v1 | https://www.protocols.io/view/immunohistochemistry-upar-in-mouse-lung-tissue-dg3n3yme | Sojin Kim | TITLE: Immunohistochemistry - uPAR in mouse lung tissue
AUTHORS: Sojin Kim
[DESCRIPTION]
Immunohistochemistry (IHC) is a method to detect specific target antigens (proteins) in tissue sections using antibodies. Immunocytochemistry (ICC) uses similar techniques to localize cellular proteins in cell preparations. Both I... | ["[Tissue Preparation] Cut and mount sections on slides (The thickness of sectioning: ))", "[Antigen Retrieval] Tris-based vs. Citrated-based antigen retrieval reagents\nAntibody/Epitope Sensitivity: Depending on the sensitivity of the specific antigen or antibody being targeted, one might be preferred over the other.... |
31,221 | GC-MS protocol for the manuscript, "Urinary chemical fingerprint left behind by repeated NSAID administration: Discovery of putative biomarkers using artificial intelligence". | null | dx.doi.org/10.17504/protocols.io.baqvidw6 | null | Liam Broughton, Nicolas F. Villarino | TITLE: GC-MS protocol for the manuscript, "Urinary chemical fingerprint left behind by repeated NSAID administration: Discovery of putative biomarkers using artificial intelligence".
AUTHORS: Liam Broughton, Nicolas F. Villarino
[STEPS] | [] |
44,675 | Growth curve for Chlamydomonas reinhardtii | 4 | null | https://www.protocols.io/view/growth-curve-for-chlamydomonas-reinhardtii-bpvbmn2n | Joao Vitor Molino | TITLE: Growth curve for Chlamydomonas reinhardtii
AUTHORS: Joao Vitor Molino
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocols describe the steps required for obtain a growth curve of </span><span style = "font-style:italic;">Chlamydomonas reinhardtii </span><span>and fluorescent ... | ["[Material ]\nTAP media or other (How to prepare TAP media here)Erlenmeyer flaskOrbital shakerLight source96 well plate, Black Frame, Clear bottom (Ex: )", "[Inocullum]\nInnoculate of the cells from a culture in stationary phase ( to )in an erlenmeyer flask containing of TAP media.Place the flask in a with of... |
62,776 | Synchronization of kinetic and kinematic hand tasks during awake craniotomy | 5 | dx.doi.org/10.17504/protocols.io.5jyl89638v2w/v2 | https://www.protocols.io/view/synchronization-of-kinetic-and-kinematic-hand-task-b9iyr4fw | ltaquet, bjconway, Timothy F Boerger, Sarah C Young, stschwartz, Brian Schmit, maxkrucoff | TITLE: Synchronization of kinetic and kinematic hand tasks during awake craniotomy
AUTHORS: ltaquet, bjconway, Timothy F Boerger, Sarah C Young, stschwartz, Brian Schmit, maxkrucoff
[DESCRIPTION]
Title: Synchronization of kinetic and kinematic hand tasks with electrocorticography and cortical stimulation during awake ... | ["[Constructing Synchronization Circuit] Obtaining Circuit Parts and Devices\n\nThe TekScan and CyberGlove system devices can be procured directly from the companies. Any clinical EEG device used for seizure monitoring during an awake craniotomy and cortical mapping can be used if it has at least two parallel DC channe... |
74,887 | Terrific broth (TB) medium | 4 | null | https://www.protocols.io/view/terrific-broth-tb-medium-cmdfu23n | Andreas Sagen | TITLE: Terrific broth (TB) medium
AUTHORS: Andreas Sagen
[DESCRIPTION]
IBI’s Terrific Broth is used with Glycerol in cultivating recombinant strains of E. coli. Terrific broth is a highly enriched medium for improving yield in plasmid bearing E. coli. Recombinant strains have an extended growth phase in the medium. Th... | ["[500 mL Terrific broth] Create a base solution consistent of Tryptone, Yeast extract, Potassium phosphate monobasic and Potassium phosphate dibasic in a 500 mL Reagent Bottle", "[500 mL Terrific broth] Fill the bottle with 300 mL double-distilled water", "[500 mL Terrific broth] Measure 11800 mg Yeast extract, 5900 m... |
45,904 | The effects of antibiotics for Helicobacter pylori eradication or dapsone on chronic spontaneous urticaria: A systematic review and meta-analysis (protocol) | 1 | dx.doi.org/10.17504/protocols.io.bq3qmymw | https://www.protocols.io/view/the-effects-of-antibiotics-for-helicobacter-pylori-bq3qmymw | Jun Watanabe, Junya Shimamoto, Kazuhiko Kotani | TITLE: The effects of antibiotics for Helicobacter pylori eradication or dapsone on chronic spontaneous urticaria: A systematic review and meta-analysis (protocol)
AUTHORS: Jun Watanabe, Junya Shimamoto, Kazuhiko Kotani
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;... | [] |
91,849 | Radiolabeled spermine uptake in cells | 4 | dx.doi.org/10.17504/protocols.io.j8nlkorm5v5r/v1 | https://www.protocols.io/view/radiolabeled-spermine-uptake-in-cells-c5xhy7j6 | Stephanie Vrijsen, Marine Houdou, Nathalie Jacobs, Peter Vangheluwe | TITLE: Radiolabeled spermine uptake in cells
AUTHORS: Stephanie Vrijsen, Marine Houdou, Nathalie Jacobs, Peter Vangheluwe
[DESCRIPTION]
This protocol provides a technique to determine radiolabeled spermine uptake in cells, via the acquisition of counts per minute (CPM) using a Liquid Scintillation Counter.
[GUIDELIN... | ["Cells are seeded in 12-well plates, such that 70-80% confluency is reached on the day of the assay. Seed out 2 'treatment' wells and 1 'background' well per cell line.", "Remove the culture medium from all wells.", "Incubate 37 °C 30 min", "Aspirate the medium.", "Wash wells 2x with 1 mL PBS (-/-).", "Remove the last... |
43,337 | Scalable high-molecular weight DNA extraction for long-read sequencing | 1 | dx.doi.org/10.17504/protocols.io.bnjhmcj6 | https://www.protocols.io/view/scalable-high-molecular-weight-dna-extraction-for-bnjhmcj6 | Ashley Jones, Cynthia Torkel, David Stanley, Jamila Nasim, Justin Borevitz, Benjamin Schwessinger | TITLE: Scalable high-molecular weight DNA extraction for long-read sequencing
AUTHORS: Ashley Jones, Cynthia Torkel, David Stanley, Jamila Nasim, Justin Borevitz, Benjamin Schwessinger
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>With rapid advances in long-read DNA sequencing technologies,... | ["[PREPARATION]\nSet a water bath (or equivalent alternative) to 55°C (temperature range 50-60°C)\nWill be used to dissolve lysis buffer and also used during lysis (30-90 min).", "[PREPARATION]\nPrepare fresh lysis buffer based on the prep size and heat at 55°C in water bath until ready to use. ABC1Prep sizeTissue inp... |
55,098 | Micropatterning EM grids for cryo-electron tomography of cells | 1 | dx.doi.org/10.17504/protocols.io.bz22p8ge | https://www.protocols.io/view/micropatterning-em-grids-for-cryo-electron-tomogra-bz22p8ge | Leeya Engel, Richard Held, Claudia G. Vasquez, William I. Weis, Alexander R. Dunn | TITLE: Micropatterning EM grids for cryo-electron tomography of cells
AUTHORS: Leeya Engel, Richard Held, Claudia G. Vasquez, William I. Weis, Alexander R. Dunn
[DESCRIPTION]
Micropatterning of electron microscopy (EM) grids facilitates cryo-focused ion beam and cryo-electron tomography pipelines by optimally p... | ["[Passivation] Cut out a rectangle (<24 x 60 mm) of silicone sheeting so that it can be mounted on a glass coverslip.", "[Passivation] Place grids gold mesh side down (holey Quantifoil or UltrAuFoil thin film-side up) on the silicone.", "[Passivation] Line the bottom of a 10 cm plastic petri dish with parafilm.", "[Pa... |
null | null | null | dx.doi.org/10.17504/protocols.io.jipckdn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
31,579 | Whole-body clearing of beetles by successive treatment of hydrogen peroxide and CUBIC reagents | null | dx.doi.org/10.17504/protocols.io.ba33igqn | null | Monto Kuroda, Shinya Kuroda | TITLE: Whole-body clearing of beetles by successive treatment of hydrogen peroxide and CUBIC reagents
AUTHORS: Monto Kuroda, Shinya Kuroda
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Internal tissues of multicellular organisms cannot directly be seen because they contain pigments. For this reaso... | [] |
28,421 | Propagation and attenuation of FAdV isolate in CEL cells | null | dx.doi.org/10.17504/protocols.io.7zdhp26 | null | Norfitriah Mohamed Sohaimi, Mohd Hair Bejo, Abdul Rahman Omar, Aini Ideris, Nurulfiza Mat Isa | TITLE: Propagation and attenuation of FAdV isolate in CEL cells
AUTHORS: Norfitriah Mohamed Sohaimi, Mohd Hair Bejo, Abdul Rahman Omar, Aini Ideris, Nurulfiza Mat Isa
[STEPS] | [] |
14,646 | Human Pancreas Biopsy Collection, ex vivo | null | dx.doi.org/10.17504/protocols.io.siwecfe | null | James Lyon, Patrick MacDonald, Jocelyn Manning Fox | TITLE: Human Pancreas Biopsy Collection, ex vivo
AUTHORS: James Lyon, Patrick MacDonald, Jocelyn Manning Fox
[STEPS]
?. This protocol is associated with Isolation of Human Pancreatic Islets of Langerhans for Research step 7.
?. Label a 15ml conical tube with the internal identifier number (Rxxx) and “biopsy”.
?. Follo... | ["This protocol is associated with Isolation of Human Pancreatic Islets of Langerhans for Research step 7.", "Label a 15ml conical tube with the internal identifier number (Rxxx) and “biopsy”.", "Following pancreas perfusion, use surgical scissors to excise a 5mm cubic piece of tissue from the tail of the pancreas.", "... |
30,639 | Protocol Griess Test | null | dx.doi.org/10.17504/protocols.io.96ph9dn | null | Tamiris Silva, Carolina de Oliveira Rodini, Sandra Kalil Bussadori, Kaline de Brito Sousa, Kristianne Porta Santos Fernandes | TITLE: Protocol Griess Test
AUTHORS: Tamiris Silva, Carolina de Oliveira Rodini, Sandra Kalil Bussadori, Kaline de Brito Sousa, Kristianne Porta Santos Fernandes
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">To assess nitrite levels in individuals with relapsing-remitting multiple sclerosis, the... | [] |
65,261 | Tyler Perry CBD Gummies Review: Steve Harvey CBD Gummies Fake Or Trusted? | 1 | dx.doi.org/10.17504/protocols.io.dm6gpb1zjlzp/v1 | https://www.protocols.io/view/tyler-perry-cbd-gummies-review-steve-harvey-cbd-gu-cbymspu6 | Uly CBD Gummies | TITLE: Tyler Perry CBD Gummies Review: Steve Harvey CBD Gummies Fake Or Trusted?
AUTHORS: Uly CBD Gummies
[DESCRIPTION]
Tyler Perry CBD Gummies Review: Steve Harvey CBD Gummies Fake Or Trusted?
[STEPS]
SECTION: Tyler Perry CBD Gummies Review: Steve Harvey CBD Gummies Fake Or Trusted? Kelly Clarkson CBD Gummies- The ... | ["[Tyler Perry CBD Gummies Review: Steve Harvey CBD Gummies Fake Or Trusted? Kelly Clarkson CBD Gummies- The Purely Concentrated CBD Product to Lose Pains! Kelly Clarkson CBD Gummies Reviews- The verity that the true wealth we've is our health is known to numerous, but many know the true meaning of it and realize... |
86,904 | Metabarcoding based gut content analysis of arachnids | 4 | dx.doi.org/10.17504/protocols.io.5jyl8ppyrg2w/v1 | https://www.protocols.io/view/metabarcoding-based-gut-content-analysis-of-arachn-cy4yxyxw | Yuval Zaltz, Evgenia Propistsova, Efrat Gavish-Regev, Jordan P Cuff | TITLE: Metabarcoding based gut content analysis of arachnids
AUTHORS: Yuval Zaltz, Evgenia Propistsova, Efrat Gavish-Regev, Jordan P Cuff
[DESCRIPTION]
This protocol describes the workflow used for the gut content analysis via DNA metabarcoding of scorpions and spiders for some work conducted in the Hebrew University ... | ["[Sample preparation] Collect arachnids from study sites, place them into 100 % volume ethanol and store them at -20 °C until ready to proceed with DNA extraction.", "[PCR amplification] Decide how samples will be distributed across plates (but don't distribute DNA yet). Consider including a negative control in each r... |
86,580 | Optical sensors 2-photon imaging | 4 | dx.doi.org/10.17504/protocols.io.kxygx33yog8j/v1 | https://www.protocols.io/view/optical-sensors-2-photon-imaging-cysuxwew | Beatriz E Nielsen, Andrew G Yee | TITLE: Optical sensors 2-photon imaging
AUTHORS: Beatriz E Nielsen, Andrew G Yee
[DESCRIPTION]
This protocol describes the steps to collect genetically encoded optical sensors fluorescence in mouse brain slices using 2-photon microscopy.
2-photon imaging was performed using a 2-photon laser scanning microscopy system,... | ["[Acute brain slice preparation] Steps are described in the protocol linked below.", "[Rig setup] Turn on required devices and software for acquisition (Toronado and Axograph).\n\nToronado: https://github.com/StrowbridgeLab/Toronado-Laser-Scanning \nAxograph X (Axograph Scientific).", "[Rig setup] Place the intake lin... |
40,880 | Isolation of Salmonella pathogens from oysters | 4 | dx.doi.org/10.17504/protocols.io.bj6qkrdw | https://www.protocols.io/view/isolation-of-salmonella-pathogens-from-oysters-bj6qkrdw | Sade Aisha Folashade John, Patrick E. Akpaka, Chandrashekhar Unakal, Arvind Kurhade, Angel Justiz-Vaillant | TITLE: Isolation of Salmonella pathogens from oysters
AUTHORS: Sade Aisha Folashade John, Patrick E. Akpaka, Chandrashekhar Unakal, Arvind Kurhade, Angel Justiz-Vaillant
[STEPS]
?. The filtered homogenate was streaked using standardized loops on Salmonella Shigella agar (selective and differential media for Salmonell... | ["The filtered homogenate was streaked using standardized loops on Salmonella Shigella agar (selective and differential media for Salmonella and Shigella); the loops were flamed periodically to ensure sterility. This was done in duplicate. The plates were then incubated at 34°C. After an overnight incubation at 34°C, t... |
70,391 | Synchronized C. elegans culture on NGM plates for FACS isolation of intestine cells | 4 | dx.doi.org/10.17504/protocols.io.8epv59zjng1b/v2 | https://www.protocols.io/view/synchronized-c-elegans-culture-on-ngm-plates-for-f-cgyxtxxn | Robert TP Williams, Erin Osborne Nishimura | TITLE: Synchronized C. elegans culture on NGM plates for FACS isolation of intestine cells
AUTHORS: Robert TP Williams, Erin Osborne Nishimura
[DESCRIPTION]
This protocol details the steps necessary to scale-up and synchronize C. elegans cultures for FACS isolation of intestine cells. We cultured worms with agar-based... | ["[Prepare OP50 seeded NGM plates] Using sterile technique, pick an OP50 colony and inoculate a 250 ml bottle of sterile LB.", "[Prepare OP50 seeded NGM plates] Incubate OP50 liquid culture at 37°C overnight", "[Prepare OP50 seeded NGM plates] Make 3 liters of Nematode Growth Media (NGM) with 150 mm petri dish (hereaft... |
31,032 | Peer Review Skills Development - Study Protocols | 1 | dx.doi.org/10.17504/protocols.io.baiyicfw | https://www.protocols.io/view/peer-review-skills-development-study-protocols-baiyicfw | Tiffani Conner, Miriam L.E. Steiner Davis | TITLE: Peer Review Skills Development - Study Protocols
AUTHORS: Tiffani Conner, Miriam L.E. Steiner Davis
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Development of interview protocol, the results of which informed a survey for university faculty members concerning grants peer reviewers.</div><... | [] |
25,935 | CULTURING i3NEURONS (Basic Protocol 6) | null | dx.doi.org/10.17504/protocols.io.5jpg4mn | null | Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward | TITLE: CULTURING i3NEURONS (Basic Protocol 6)
AUTHORS: Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Following Day 3 replating, i</span><span style = "vertical-align:super;">3</span><span>Neuron... | ["[Coating dishes]\nPrepare stock solutions of PLO or PEI (see Table 3).", "[Coating dishes]\nAdd one half culture volume of the coating solution prepared in step 1 to the tissue culture dishes to be used for plating the Day 3 partially differentiated i3Neurons. Gently tilt plate to ensure full coverage.", "[Coating di... |
55,732 | ATAC-STARR-seq | 1 | dx.doi.org/10.17504/protocols.io.b2nuqdew | https://www.protocols.io/view/atac-starr-seq-b2nuqdew | Tyler Hansen, Emily Hodges | TITLE: ATAC-STARR-seq
AUTHORS: Tyler Hansen, Emily Hodges
[DESCRIPTION]
Massively parallel reporter assays test the capacity of putative cis-regulatory elements (CREs) to drive transcription on a genome-wide scale. In nearly all cases, chromatin accessibility is necessary to drive activity, so most CREs are inactive ... | ["[Anneling Oligos] Dilute oligos to 100 µM in STE buffer.", "[Anneling Oligos] Make Adaptor Mixes in 200μL PCR tubes:\n\nMix (Adaptor A) [50µL]: \n 5µL Tn5MERV oligo (100µM)\n 5µL Tn5_1 Oligo (100µM)\n 40µL H2O\n\nMix (Adaptor B) [50µL]: \n 5µL Tn5MERV oligo (100µM)\n 5µL Tn5_2_ME_Comp Oligo (100µM)\n ... |
46,682 | PCR Prep from Glycerol Stock for IVT Reactions | 1 | dx.doi.org/10.17504/protocols.io.brt2m6qe | https://www.protocols.io/view/pcr-prep-from-glycerol-stock-for-ivt-reactions-brt2m6qe | Allen Institute for Brain Science | TITLE: PCR Prep from Glycerol Stock for IVT Reactions
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used for the PCR reaction from clone templates in glycerol stocks generating transcript templates ready for IVT reaction.</div><div class ... | [] |
28,487 | transformation of E.coli DH5α with plasmid DNA | null | dx.doi.org/10.17504/protocols.io.73fhqjn | null | iGEM Dusseldorf | TITLE: transformation of E.coli DH5α with plasmid DNA
AUTHORS: iGEM Dusseldorf
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">common transformation of E.coli DH5α with plasmid DNA</div></div>
[STEPS]
?. thaw competent cells on ice
?. add 1 µl plasmid DNA to cells
?. incubate cells on ice
?. cool o... | ["thaw competent cells on ice", "add 1 µl plasmid DNA to cells", "incubate cells on ice", "cool on ice", "add 700 µl LB without antibiotics to the cells", "incubate at 37°C (with shaking)", "plate 100 µl on antibiotic plates with Drigalski spatula", "incubate over night at 37°C", "heat shock cells at 42°C"] |
45,534 | HuBMAP | Formalin Fixation and Paraffin Embedding of Tissue Samples | 4 | dx.doi.org/10.17504/protocols.io.bqp6mvre | https://www.protocols.io/view/hubmap-formalin-fixation-and-paraffin-embedding-of-bqp6mvre | Kelley Knizner, Christopher Simmons | TITLE: HuBMAP | Formalin Fixation and Paraffin Embedding of Tissue Samples
AUTHORS: Kelley Knizner, Christopher Simmons
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This method details formalin fixation and paraffin embedding of the HuBMAP tissue specimens.</div><div class = "text-block"><sp... | ["[POST-PROCESSING]\nProcessed cassette should be placed in wax holding chamber of embedding center.", "[POST-PROCESSING]\nPre-heat embedding utensils in the forceps warming station; warming chambers are located on the side of the paraffin dispensing nozzle.", "[POST-PROCESSING]\nTurn on the station cold plate module."... |
49,752 | The methodological quality of physical therapy articles published in open access and subscription journals: A cross-sectional meta-epidemiological study | 1 | dx.doi.org/10.17504/protocols.io.butynwpw | https://www.protocols.io/view/the-methodological-quality-of-physical-therapy-art-butynwpw | Takashi Ariie, Yusuke Tsutsumi, Shunsuke Taito | TITLE: The methodological quality of physical therapy articles published in open access and subscription journals: A cross-sectional meta-epidemiological study
AUTHORS: Takashi Ariie, Yusuke Tsutsumi, Shunsuke Taito
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Objective:</div><div class = "text-b... | [] |
22,638 | Laboratory Measurements of MICA genetic variants and s-MICA | null | dx.doi.org/10.17504/protocols.io.2cngave | null | Guillaume Onyeaghala, John Lane, Nathan Pankratz, Heather H. Nelson, Bharat Thyagarajan, Bruce Walcheck, Kristin E. Anderson, Anna E. Prizment | TITLE: Laboratory Measurements of MICA genetic variants and s-MICA
AUTHORS: Guillaume Onyeaghala, John Lane, Nathan Pankratz, Heather H. Nelson, Bharat Thyagarajan, Bruce Walcheck, Kristin E. Anderson, Anna E. Prizment
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">1. Study design</div><div class =... | [] |
40,552 | SMRT-OTS | 4 | null | https://www.protocols.io/view/smrt-ots-bjugkntw | Ida Hoijer, Josefin Johansson, Sanna Gudmundsson, Chen-Shan Chin, Ignas Bunikis, Susana Häggqvist, Anastasia Emmanouilidou, Maria Wilbe, Marcel den Hoed, Marie-Louise Bondeson, Lars Feuk, Ulf Gyllensten, Adam Ameur | TITLE: SMRT-OTS
AUTHORS: Ida Hoijer, Josefin Johansson, Sanna Gudmundsson, Chen-Shan Chin, Ignas Bunikis, Susana Häggqvist, Anastasia Emmanouilidou, Maria Wilbe, Marcel den Hoed, Marie-Louise Bondeson, Lars Feuk, Ulf Gyllensten, Adam Ameur
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This i... | ["[Shearing of genomic DNA]\nShear 10-20 µg of HMW genomic DNA to 8 kb using Megaruptor 2.", "[Shearing of genomic DNA]\nAdd 0.45x AMPure PB beads to the sample and incubate at 2000 rpm using a vortex mixer for 10 min.", "[Shearing of genomic DNA]\nPlace the tube on a magnetic rack until the beads collect on the side o... |
95,353 | Multi-parameter confocal TCSPC spectroscopy analysis | 1 | null | https://www.protocols.io/view/multi-parameter-confocal-tcspc-spectroscopy-analys-c9czz2x6 | Amber Yanas | TITLE: Multi-parameter confocal TCSPC spectroscopy analysis
AUTHORS: Amber Yanas
[DESCRIPTION]
The following outlines the analysis of data generated by multi-parameter confocal time-correlated single photon counting (TCSPC) microscopy and spectroscopy (MicroTime-200; PicoQuant, GmbH).
[STEPS]
SECTION: Conversion of .... | ["[Conversion of .ptu to .hdf5]", "[Conversion of .ptu to .hdf5] Use program: PQ_To_hdf5_All.ipynb", "[Conversion of .ptu to .hdf5] Enter pathname and run all to convert files from .ptu to .hdf5", "[Conversion of .ptu to .hdf5] A new folder will be created with these hdf5 files \na. Hint – convert to hdf5 in bulk t... |
74,175 | Tissue perfusion parameter-guided initial resuscitation in adult patients with sepsis or septic shock: A systematic review and network meta-analysis | 1 | dx.doi.org/10.17504/protocols.io.14egn29oyg5d/v1 | https://www.protocols.io/view/tissue-perfusion-parameter-guided-initial-resuscit-ckn7uvhn | Tomoki Kuribara, Tetsuya Yumoto, Kohei Yamada, Takehito Sato, Shigeru Koba, Kenichi Tetsuhara, Masahiro Kashiura, Masaaki Sakuraya,MD, MPH | TITLE: Tissue perfusion parameter-guided initial resuscitation in adult patients with sepsis or septic shock: A systematic review and network meta-analysis
AUTHORS: Tomoki Kuribara, Tetsuya Yumoto, Kohei Yamada, Takehito Sato, Shigeru Koba, Kenichi Tetsuhara, Masahiro Kashiura, Masaaki Sakuraya,MD, MPH
[DESCRIPTION]
... | [] |
85,294 | Processing frozen human blood samples for population-scale SQK-LSK114 Oxford Nanopore long-read DNA sequencing SOP | 1 | dx.doi.org/10.17504/protocols.io.x54v9py8qg3e/v1 | https://www.protocols.io/view/processing-frozen-human-blood-samples-for-populati-cxinxkde | Abigail Miano-Burkhardt, Pilar Alvarez Jerez, Laksh Malik, Cornelis Blauwendraat, Kimberley J Billingsley, on behalf of the CARD Long-read Team | TITLE: Processing frozen human blood samples for population-scale SQK-LSK114 Oxford Nanopore long-read DNA sequencing SOP
AUTHORS: Abigail Miano-Burkhardt, Pilar Alvarez Jerez, Laksh Malik, Cornelis Blauwendraat, Kimberley J Billingsley, on behalf of the CARD Long-read Team
[DESCRIPTION]
Abstract:
As part of the GP2 ... | ["Part 1: Preparing Blood Samples (~30 min for 24 samples)", "Obtain blood samples from -80C freezer and thaw in water bath at 37 °C for 15 min\n\nNote: This is specifically for 6mL tubes, if starting with only 1mL thaw until warm (~ 5 min)", "Inversion mix blood 10x immediately before use. \n\nNote: The blood sample n... |
55,609 | NCBI submission protocol for SARS-CoV-2 wastewater data: SRA, BioSample, and BioProject | 1 | dx.doi.org/10.17504/protocols.io.b2izqcf6 | https://www.protocols.io/view/ncbi-submission-protocol-for-sars-cov-2-wastewater-b2izqcf6 | Ruth Timme, Maria Balkey | TITLE: NCBI submission protocol for SARS-CoV-2 wastewater data: SRA, BioSample, and BioProject
AUTHORS: Ruth Timme, Maria Balkey
[DESCRIPTION]
PURPOSE:
This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in ... | ["["Ingredients" to have in place before starting your submissions] Set up a new NCBI submission environment for your lab\n1.1: Create an NCBI user account\n1.2: Set up an NCBI submission user group for your lab\n1.4: Bookmark the link to your Submission Portal\n1.5. Identify or establish new BioProjects (det... |
83,026 | How to Measure the Illumination Overhead (IO) of a Fluorescence Microscope | 1 | dx.doi.org/10.17504/protocols.io.rm7vzxm35gx1/v1 | https://www.protocols.click/view/how-to-measure-the-illumination-overhead-io-of-a-f-cvbsw2ne | Claire M Brown, Cesar Leonardo Villa, Alexander Kiepas, kmichiel, Alexander Nowakowski | TITLE: How to Measure the Illumination Overhead (IO) of a Fluorescence Microscope
AUTHORS: Claire M Brown, Cesar Leonardo Villa, Alexander Kiepas, kmichiel, Alexander Nowakowski
[DESCRIPTION]
This protocol outlines in detail how to measure illumination overhead (IO) and collect raw illumination intensity data using th... | ["[Measuring IO Using the Rigol DS1054Z Oscilloscope.] Turn on the oscilloscope by plugging it into an outlet and pressing the power button at the bottom left.", "[Measuring IO Using the Rigol DS1054Z Oscilloscope.] Set up the oscilloscope light sensor over the objective lens such that the light falls onto the sensor w... |
97,497 | 616.1 URMC HTC BSL2+ Formalin-Inflated, Paraffin-Embedded Human Lung Tissue | 4 | dx.doi.org/10.17504/protocols.io.kxygxejwdv8j/v3 | https://www.protocols.io/view/616-1-urmc-htc-bsl2-formalin-inflated-paraffin-emb-dbfz2jp6 | Gloria S Pryhuber, Heidie Huyck, Lisa Rogers | TITLE: 616.1 URMC HTC BSL2+ Formalin-Inflated, Paraffin-Embedded Human Lung Tissue
AUTHORS: Gloria S Pryhuber, Heidie Huyck, Lisa Rogers
[DESCRIPTION]
Processing of Formalin Fixed Lung and Non-Lung Tissue for the LungMAP HTC and includes acquisition of limited Control tissue from Surgical Pathology.
[GUIDELINES]
Sci... | ["[Record Process] Record details of procedure in Worksheet or Directly in Inventory or ELN", "[Record Process] Keep photographic recording of inflation and all steps of sectioning and blocking of lung lobe and tissue", "[Inflation Fixed (Formalin) Lung Lobe] Inflation fixation procedure should be accomplished in a bio... |
75,762 | PSF measurements for ELYRA 7 | 1 | null | https://www.protocols.io/view/psf-measurements-for-elyra-7-cm8su9we | Rafael Camacho | TITLE: PSF measurements for ELYRA 7
AUTHORS: Rafael Camacho
[DESCRIPTION]
Protocol for measuring PSFs at the ELYRA 7. This protocol was developed to follow guidelines from ZEISS application specialists. It is therefore, based on the tools and software provided by ZEISS.
As sample you can use the fluorescent beads pro... | ["[Warming up the microscope] Turn on the ELYRA 7", "[Warming up the microscope] Turn on Main Switch", "[Warming up the microscope] Let the microscope warmup overnight.\nDuring this process make sure to leave the sample, and the immersion oil inside the chamber, so they also reach the desired temperature.", "[Warming u... |
92,399 | hsqc_metab.nan | 5 | dx.doi.org/10.17504/protocols.io.5jyl8pd2dg2w/v5 | https://www.protocols.io/view/hsqc-metab-nan-c6gpzbvn | NAN KB, John Glushka, Mario Uchimiya, Saraa Al Jawad, Christopher Esselman, Leandro I Ponce, Laura Morris, Arthur Edison | TITLE: hsqc_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 "hsqcetgpsisp2".
[BEFORE_START]
This protocol assumes:
Your sample is loaded, locked, tuned for ... | ["[Create a new dataset]", "[Create a new dataset] A new window opens. On the right top bar, select\nSource = /opt/NAN_METAB/par\n \nIn the list, select the one you want to use:\n\nFor serum and plasma samples:\nHSQC_br600_serum.par: Parameter set using an acquisition mode \"traditional planes\"\nHSQC_NUS_br600_serum.p... |
46,700 | Clearing-enhanced 3D (Ce3D) clearing method, immunohistochemistry and quantitation of rat gastric enteric ganglia | 1 | dx.doi.org/10.17504/protocols.io.bp2l6b845gqe/v1 | https://www.protocols.io/view/clearing-enhanced-3d-ce3d-clearing-method-immunohi-brukm6uw | Billie Hunne, John Furness, Martin Stebbing, Linda Fothergill | TITLE: Clearing-enhanced 3D (Ce3D) clearing method, immunohistochemistry and quantitation of rat gastric enteric ganglia
AUTHORS: Billie Hunne, John Furness, Martin Stebbing, Linda Fothergill
[DESCRIPTION]
The enteric nervous system is an important regulator of gastrointestinal, digestive and metabolic function. Here ... | ["Experiments were conducted on male and female Sprague-Dawley rats of 6.5-8 weeks (175-220 g female, 220-360 g male). Procedures were approved by the University of Melbourne Animal Ethics Committee. Rats were supplied with food and water ad libitum prior to the experiments.", "Rats were deeply anaesthetised with a mix... |
20,479 | Neural rosette banking | null | dx.doi.org/10.17504/protocols.io.x87frzn | null | Celeste Karch, Rita Martinez, Jacob Marsh | TITLE: Neural rosette banking
AUTHORS: Celeste Karch, Rita Martinez, Jacob Marsh
[STEPS]
?. Make 2x stock of serum-free neural freezing medium by adding of sterile DMSO to of sterile KOSR into a 50 ml conical tube. Mix by inverting 3-4 times. Store at for up to 4 weeks.
10 ml
40 ml
?. Aspirate supernatant from 15mL c... | ["Make 2x stock of serum-free neural freezing medium by adding of sterile DMSO to of sterile KOSR into a 50 ml conical tube. Mix by inverting 3-4 times. Store at for up to 4 weeks.\n10 ml\n40 ml", "Aspirate supernatant from 15mL conical tube containing 1 well of neural rosette clusters. See protocol below.", "Add of n... |
94,642 | Scoping Review: Analytical Approaches to Estimating Malaria Intervention Effectiveness and Impact | 1 | dx.doi.org/10.17504/protocols.io.36wgq38nolk5/v1 | https://www.protocols.io/view/scoping-review-analytical-approaches-to-estimating-c8nszvee | Jessica Craig, Donal Bisanzio, Richard Reithinger | TITLE: Scoping Review: Analytical Approaches to Estimating Malaria Intervention Effectiveness and Impact
AUTHORS: Jessica Craig, Donal Bisanzio, Richard Reithinger
[DESCRIPTION]
Context: Ministries of Health and National Malaria Control
Programs need simple approaches to be able to regularly estimate the
effectiveness... | ["[Rationale] Malaria is an acute febrile illness caused by a parasitic\ninfection transmitted by Anopheles mosquitoes. Human malaria is caused by five\ndifferent Plasmodium parasites, with P. falciparum being the predominant\nspecies in sub-Saharan Africa (SSA) [1]. In the past 15–20 years, the combined\nefforts of Mi... |
75,200 | Assembly: Chronic recoverable Neuropixels in mice | 1 | null | https://www.protocols.io/view/assembly-chronic-recoverable-neuropixels-in-mice-cmn8u5hw | Emily A Aery Jones | TITLE: Assembly: Chronic recoverable Neuropixels in mice
AUTHORS: Emily A Aery Jones
[DESCRIPTION]
This protocol collection explains how to build a low-cost, lightweight system to implant 1 Neuropixels 1.0 probe or 2 2.0 beta probes into mice, record during freely moving behavior, then recover the probe for future use... | ["[3D print components] Single 1.0 probe: Build a print file for the following pieces per mouse: 1 each of body piece, back and front flex cable holders, and dome, plus 2 wings. \n\nDual 2.0 probes: Build a print file for the following pieces per mouse: 1 each of left body, right body, dovetail, flex holder 1, flex hol... |
25,186 | A Monolayer Culture Method for Neural Induction of Human Pluripotent Stem Cells | null | dx.doi.org/10.17504/protocols.io.4uagwse | null | STEMCELL Technologies | TITLE: A Monolayer Culture Method for Neural Induction of Human Pluripotent Stem Cells
AUTHORS: STEMCELL Technologies
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Multipotent neural progenitor cells (NPCs) generate the major cell types of the central nervous system (CNS): neurons, astrocytes and ... | ["[Preparation of Materials]\nBefore beginning the experiment, prepare Poly-Ornithine/Laminin- or Matrigel®-coated plates or coverslips.", "[Procedure for Neural Induction]\nPre-warm STEMdiff™ Neural Induction Medium, Gentle Cell Dissociation Reagent, phosphate buffered saline (PBS) without Ca2+ and Mg2+, and DMEM/F-12... |
100,681 | Pre-Imaging Liquid Growth Medium - Yeast | 0 | dx.doi.org/10.17504/protocols.io.81wgbzxe1gpk/v1 | https://www.protocols.io/view/pre-imaging-liquid-growth-medium-yeast-dejh3cj6 | Mathias Hammer, Ammeret Rossouw, Azra Lari, Ben Montpetit, David Grunwald | TITLE: Pre-Imaging Liquid Growth Medium - Yeast
AUTHORS: Mathias Hammer, Ammeret Rossouw, Azra Lari, Ben Montpetit, David Grunwald
[DESCRIPTION]
This protocol describes the steps to prepare liquid culture medium for Saccharomyces cerevisiae. This liquid medium is used to optimize yeast cultures for fluorescence imagin... | ["[Preparation of 500ml liquid pre-imaging growth medium] Compound medium for autoclave", "[Preparation of 500ml liquid pre-imaging growth medium] Fill a 500 ml flask with 445 mLddH2O. \nAdd a magnetic stirring bar and place the flask on a stirring hot plate.", "[Preparation of 500ml liquid pre-imaging growth medium] A... |
28,380 | MojoSort™ Human CD14 Nanobeads Protocol | null | dx.doi.org/10.17504/protocols.io.7x4hpqw | null | Sam Li | TITLE: MojoSort™ Human CD14 Nanobeads Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Product description and procedure summary:</span></div><div class = "text-block">The cells targeted by the Nanobeads are either selected or depleted by inc... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes. Kits for human samples have been optimized for PBMCs, please prepare the cells using a suitable method.", "In the final wash of your sample preparation, resuspend the cells in MojoSort™ Buffer by adding up to 4 mL in a 5 mL (12 x 75 mm) ... |
null | null | null | dx.doi.org/10.17504/protocols.io.c3wypd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol describes the use of a sucrose cushion to purify viruses. It is the Matthew Sullivan Lab adaptation of the Shannon Williamson protocol.<br /><br />DNase I treatment, CsCl purification, and sucrose purification methods were compared using replicated viral ... | [] |
28,668 | GFP-RFP plate reader assay | null | dx.doi.org/10.17504/protocols.io.784hryw | null | Sebastiaan Kuiper | TITLE: GFP-RFP plate reader assay
AUTHORS: Sebastiaan Kuiper
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Fluorescence measurements of Green fluorescent protein (GFP) and/or Red fluorescent protein (RFP) in </span><span style = "font-style:italic;">Escherichia coli.</span></div></div>
[STE... | ["[media preparations:]\nPrepare the following media and autoclave them according to standard procedures. M9TG Media: ABC1 Reagent Amount to add for 1L Final concentration (1×)2 M9 salts 1x 1x 3 Tryptone 10 g 10 g/L 4 Glycerol 5 g 5 g/L PBS buffer: ABC1 Reagent Amount to add f... |
36,801 | EVALUATION OF TEST ITEMS EFFICACY IN PROMOTING STROKE REHABILITATION IN THE RAT STROKE MODEL (t-MCAO). | null | dx.doi.org/10.17504/protocols.io.bf69jrh6 | https://www.protocols.io/view/evaluation-of-test-items-efficacy-in-promoting-str-bf69jrh6 | , | TITLE: EVALUATION OF TEST ITEMS EFFICACY IN PROMOTING STROKE REHABILITATION IN THE RAT STROKE MODEL (t-MCAO).
AUTHORS: ,
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The objective of this protocol is to present the details of the procedures for evaluating test items’ (such as small molecules, ... | [] |
41,753 | Mask-Based Covid-10 testing system using Exhaled Breath Condensate | 4 | dx.doi.org/10.17504/protocols.io.bkzzkx76 | https://www.protocols.io/view/mask-based-covid-10-testing-system-using-exhaled-b-bkzzkx76 | John Daniels | TITLE: Mask-Based Covid-10 testing system using Exhaled Breath Condensate
AUTHORS: John Daniels
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The Kinaptic mask-based COVID-19 testing system uses a unique Exhaled Breath Condensate (EBC) collector that converts breath vapor to a liquid biosamp... | ["Remove release liner from double stick tape on electronics", "Remove release liner from double sided tape on mask", "Pull tab to Activate Battery and Adhere electonics to mask", "Put mask on and breath normally.", "Open APP on Smartphone", "Connect to Mask Electronics", "Continue to breath normaly", "Testing is Compl... |
20,226 | U Mass - Hyperglycemic clamp | null | dx.doi.org/10.17504/protocols.io.xzafp2e | null | Jason Kim | TITLE: U Mass - Hyperglycemic clamp
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">Hyperglycemic clamp measures insulin secretion and pancreatic -cell function in awake mice. Islet function is affec... | ["Survival surgery is performed to establish a chronic indwelling catheter at 5~6 days prior to experiment for intravenous infusion. (refer to M1023: Surgery-jugular vein cannulation)", "Mice are fasted overnight (~15 hours) or for 5 hours prior to the start of experiment.", "Place a mouse in a rat-size restrainer wit... |
28,287 | MojoSort™ Nanobeads Protocol - 2 | null | dx.doi.org/10.17504/protocols.io.7u7hnzn | null | Sam Li | TITLE: MojoSort™ Nanobeads Protocol - 2
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Product description and procedure summary:</span></div><div class = "text-block">The cells targeted by the Nanobeads are either selected or depleted by incubating... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes. Kits for human samples have been optimized for PBMCs, please prepare the cells using a suitable method.", "In the final wash of your sample preparation, resuspend the cells in MojoSort™ Buffer by adding up to 4 mL in a 5 mL (12 x 75 mm) ... |
17,662 | Holo-ZitRMG structure determination by x-ray crystallography | null | dx.doi.org/10.17504/protocols.io.vg6e3ze | null | PALOMA VARELA | TITLE: Holo-ZitRMG structure determination by x-ray crystallography
AUTHORS: PALOMA VARELA
[STEPS] | [] |
106,075 | Pan-microbial metagenomics protocol v1 | 0 | null | https://www.protocols.io/view/pan-microbial-metagenomics-protocol-v1-djt34nqn | Adela Alcolea-Medina, Luke Blagdon Snell, Chris Alder, Rahul Batra | TITLE: Pan-microbial metagenomics protocol v1
AUTHORS: Adela Alcolea-Medina, Luke Blagdon Snell, Chris Alder, Rahul Batra
[DESCRIPTION]
DOI: 10.1038/s43856-024-00554-3
[STEPS]
SECTION: Preparation of quality controls:
2. Mix 300μL of control 1 and 300μL of control 2 in an Eppendorf. Label with date and LOT number. ... | ["[Preparation of quality controls:] Mix 300μL of control 1 and 300μL of control 2 in an Eppendorf. Label with date and LOT number.", "[Preparation of quality controls:] Vortex for 1 minute and Centrifuge at 1,200xg for 5min immediately prior to each use.", "[Preparation of quality controls:] Aliquot the volume specifi... |
50,917 | ABI Sanger Sequencing of Avian Clock genes to elucidate markers for Migration Phenology | 4 | dx.doi.org/10.17504/protocols.io.3byl4k6zrvo5/v1 | https://www.protocols.io/view/abi-sanger-sequencing-of-avian-clock-genes-to-eluc-bvydn7s6 | Louis-Stéphane Le Clercq, Desiré Lee Dalton, Antoinette Kotzé, Paul Grobler | TITLE: ABI Sanger Sequencing of Avian Clock genes to elucidate markers for Migration Phenology
AUTHORS: Louis-Stéphane Le Clercq, Desiré Lee Dalton, Antoinette Kotzé, Paul Grobler
[DESCRIPTION]
This protocol follows up on "PCR Amplification of Clock genes with EmeraldAmp® GT PCR Master Mix in Avian species" and is int... | ["[Big Dye Master Mix setup] Prepare Master mix and Samples* for Sanger Sequencing.\n\n*Sample information has been deposited to BioSample and associated to the BioProject (PRJNA737185) which used this protocol.\n\n(An experiment template is included as an excel spreadsheet)", "[Cycle sequencing] Program and run the ... |
90,651 | Initial Installation of the Uavionix PingRID | 1 | dx.doi.org/10.17504/protocols.io.14egn3n4zl5d/v1 | https://www.protocols.io/view/initial-installation-of-the-uavionix-pingrid-c4r3yv8n | marshall.bennett | TITLE: Initial Installation of the Uavionix PingRID
AUTHORS: marshall.bennett
[DESCRIPTION]
Instructions for the initial installation and registration of the Uavionix PingRID device.
[STEPS]
1. Unbox the PingRID unit. Save the cardboard tag from the packaging with the PingRID serial number on it.
2. Record the Pin... | ["Unbox the PingRID unit. Save the cardboard tag from the packaging with the PingRID serial number on it.", "Record the PingRID, SSID, and Password information from the device (included in the packaged materials) with the drone's stored records and registration information.", "Charge the PingRID unit using the provided... |
63,818 | Qiagen All-Prep DNA/RNA Mini Kit | 1 | null | https://www.protocols.io/view/qiagen-all-prep-dna-rna-mini-kit-cajiscke | George Testo | TITLE: Qiagen All-Prep DNA/RNA Mini Kit
AUTHORS: George Testo
[DESCRIPTION]
The AllPrep DNA/RNA Mini Kit is designed to purify genomic DNA and total RNA simultaneously from a single biological sample. Lysate is first passed through an AllPrep DNA spin column to selectively isolate DNA and then through an RNeasy spin ... | ["[Homogenization] Add 600 µL of to Lysing Matrix E tubes.", "[Homogenization] Place the entire tissue or a portion into Lysing Matrix E tubes for homogenization.", "[Homogenization] For Swab(s): pick up with tweezers and cut with surgical scissors sterilized in a Germinator 500. Place the cut end of a single swab in... |
43,119 | 4 Optimizing AFM Imaging in PFT for High Resolution AFM Imaging on DNA | 1 | dx.doi.org/10.17504/protocols.io.bncpmavn | https://www.protocols.io/view/4-optimizing-afm-imaging-in-pft-for-high-resolutio-bncpmavn | Philip J. Haynes, Kavit H. S. Main, Alice Pyne | TITLE: 4 Optimizing AFM Imaging in PFT for High Resolution AFM Imaging on DNA
AUTHORS: Philip J. Haynes, Kavit H. S. Main, Alice Pyne
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is part 4 of the "Atomic Force Microscopy of DNA and DNA-Protein Interactions" collection of protocols.</div><div... | ["[Optimizing AFM Imaging in PFT for High Resolution AFM Imaging on DNA]\nOnce the tip has reached the surface, minimize the setpoint to the point at which the maximum force barely exceeds the force noise (~70 pN).", "[Optimizing AFM Imaging in PFT for High Resolution AFM Imaging on DNA]\nOptimise Sync Distance New suc... |
86,250 | Immunopeptidomic analyses of RAW 264.7 macrophages | 2 | dx.doi.org/10.17504/protocols.io.rm7vzxbergx1/v1 | https://www.protocols.io/view/immunopeptidomic-analyses-of-raw-264-7-macrophages-cygixtue | Joel Lanoix, Pierre Thibault | TITLE: Immunopeptidomic analyses of RAW 264.7 macrophages
AUTHORS: Joel Lanoix, Pierre Thibault
[DESCRIPTION]
Here, we describe protocols for a novel proteogenomic approach to identify MHC I–associated peptides from RAW 264.7 cells after LPS stimulation. These antigens are rare and are most effectively identified with... | [] |
96,371 | Investigation of the pain factors of rotator cuff tears: a protocol for a scoping review | 1 | dx.doi.org/10.17504/protocols.io.eq2lyjmwelx9/v1 | https://www.protocols.io/view/investigation-of-the-pain-factors-of-rotator-cuff-dact2awn | Tomohisa Yuda, Katsuya Sakai, Takashi Saito, Hayato Shigetoh, Masateru Hayashi, Takashi Kitagawa | TITLE: Investigation of the pain factors of rotator cuff tears: a protocol for a scoping review
AUTHORS: Tomohisa Yuda, Katsuya Sakai, Takashi Saito, Hayato Shigetoh, Masateru Hayashi, Takashi Kitagawa
[DESCRIPTION]
Objective：
The purpose of this scoping review is to investigate factors associated with rotator cuff te... | [] |
77,713 | COAST Biostic gDNA extraction using vacuum manifold | 4 | null | https://www.protocols.io/view/coast-biostic-gdna-extraction-using-vacuum-manifol-cp5rvq56 | holly.steininger | TITLE: COAST Biostic gDNA extraction using vacuum manifold
AUTHORS: holly.steininger
[DESCRIPTION]
COAST Extraction Protcol - HMS
[STEPS]
SECTION: DNA isolation
5. Secure the PowerBead Tube horizontally using the Vortex Adapter tube holder for the vortex (cat. no. 13000-V1-24). Vortex at maximum speed for 10 min.
due... | ["[DNA isolation] Secure the PowerBead Tube horizontally using the Vortex Adapter tube holder for the vortex (cat. no. 13000-V1-24). Vortex at maximum speed for 10 min.\ndue to limited vortex attachments you have to vortex in batches of 48", "[DNA isolation] Centrifuge the PowerBead Tube to pellet debris at 10.000 x g,... |
29,025 | Single Cell Seeding of BBB Stem Cell Model | null | dx.doi.org/10.17504/protocols.io.8j9hur6 | null | Ethan Lippmann, Hannah Wilson, Emma Neal | TITLE: Single Cell Seeding of BBB Stem Cell Model
AUTHORS: Ethan Lippmann, Hannah Wilson, Emma Neal
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Standardized single cell seeding protocol for Blood-Brain Barrier (BBB) differentiation.</div></div>
[STEPS]
?. [Reagent Preparation]
ROCK inhibitor:Ma... | ["[Reagent Preparation]\nROCK inhibitor:Make working stock solution by diluting into . Use at 1:1000 for final concentration. Aliquots can be stored long term at for up to 1 year and frozen/thawed as many times as necessary. E8 mediaMake working stock solution by diluting into . Use at 1:1000 for final ... |
null | null | null | dx.doi.org/10.17504/protocols.io.rr9d596 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Question: Determine if there are differences in localization of MRTF and SRF between wildtype and pirin KO fibroblasts. </p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
47,430 | Recan: R-based tool for detection of recombination in viral genomes | 5 | dx.doi.org/10.17504/protocols.io.bsjencje | https://www.protocols.io/view/recan-r-based-tool-for-detection-of-recombination-bsjencje | Vasily Pavelko | TITLE: Recan: R-based tool for detection of recombination in viral genomes
AUTHORS: Vasily Pavelko
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Recan is an R version of the Python library that allows the identification of recombination events through construction and exploration of similarity plo... | ["[Benchmarking of recan package in R]\nCalculating average execution time of code using Hepatitis C virus datasets.", "[Benchmarking of seqcombo package in R]\nCalculating average execution time of code using Lumpy Skin Disease Virus datasets.", "[Benchmarking of recan package in R]\nCalculating average execution time... |
92,775 | Environmental DNA (eDNA) extraction using Qiagen DNeasy 96 Blood and Tissue Kit | 1 | dx.doi.org/10.17504/protocols.io.kqdg3xbx1g25/v2 | https://www.protocols.io/view/environmental-dna-edna-extraction-using-qiagen-dne-c6ufzetn | Kathleen Pitz, Jacoby Baker, truelove | TITLE: Environmental DNA (eDNA) extraction using Qiagen DNeasy 96 Blood and Tissue Kit
AUTHORS: Kathleen Pitz, Jacoby Baker, truelove
[DESCRIPTION]
This protocol is a modified version of the Qiagen DNeasy 96-sample protocol: Purification of Total DNA from Animal Tissues.
[STEPS]
SECTION: MIOP: Minimum Information abo... | ["[MIOP: Minimum Information about an Omics Protocol] MIOP Term\nValue\n \nmethodology category\n\n \nproject\n\n \npurpose\n\n \nanalyses\n\n \ngeographic location\n\n \nbroad-scale environmental context\n\n \nlocal environmental context\n\n \nenvironmental medium\n\n \ntarget\n\n \ncreator\n\n \nmaterials required\... |
30,928 | Cryopreservation of marine diatoms | 1 | null | https://www.protocols.io/view/cryopreservation-of-marine-diatoms-bafqibmw | Jana Hinners, Sinead Collins | TITLE: Cryopreservation of marine diatoms
AUTHORS: Jana Hinners, Sinead Collins
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Cryopreservation and thawing protocol for </span><span style = "font-style:italic;">Thallasiosira </span><span>diatoms.</span></div></div>
[STEPS]
?. [Prepare diatom... | ["[Prepare diatom cultures]\nGrow 40mL diatom cultures in 50mL flasks until mid to end exponential phase.Do not invert samples for at least 24 hours before cryopreservation, so that diatoms are accumulated close to the bottom of the flask", "[1 day before cryopreservation]\nPrepare fresh culture media (e.g. f/2) with 2... |
68,927 | Wire Hang Test | 1 | dx.doi.org/10.17504/protocols.io.14egn7pypv5d/v1 | https://www.protocols.io/view/wire-hang-test-cfi7tkhn | Sabina Marciano, Tae-In Kam, Roberta Marongiu, Ted Dawson | TITLE: Wire Hang Test
AUTHORS: Sabina Marciano, Tae-In Kam, Roberta Marongiu, Ted Dawson
[DESCRIPTION]
This behavioral test is used to assess motor deficits in mouse models of Parkinson's disease.
[STEPS]
2. Hold the mouse by the tail and place it gently so that only its forepaws reaches and holds the wire. As soon ... | ["Hold the mouse by the tail and place it gently so that only its forepaws reaches and holds the wire. As soon as the animal is properly suspended, start the timer. After being released, most animals catch the wire with the four limbs. This is allowed.", "If the mouse reaches one of the ring stands, stop the timer.\nRe... |
36,022 | Preparation of 5M NaOH | null | dx.doi.org/10.17504/protocols.io.bfewjjfe | https://www.protocols.io/view/preparation-of-5m-naoh-bfewjjfe | Nicola O'Reilly | TITLE: Preparation of 5M NaOH
AUTHORS: Nicola O'Reilly
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Purpose of examination / Clinical relevance</span></div><div class = "text-block">At the end of 2019, several pneumonia cases were reported in Wuhan, China and the... | ["[Preparation of 300 ml 5M NaOH]\nWeigh out . Add to 500 mL beaker.\nWork in fume hood!\n[NaOH]", "[Preparation of 300 ml 5M NaOH]\nMeasure out and add to beaker.\n[milliQ water]", "[Preparation of 300 ml 5M NaOH]\nTransfer to a 500 ml graduated cylinder. Make up to 300 ml using milliQ water, if necessary.", "[Prepar... |
76,412 | Cost-effective targeted nanopore sequencing of P. falciparum malaria | 1 | null | https://www.protocols.io/view/cost-effective-targeted-nanopore-sequencing-of-p-f-cnu4veyw | Mariateresa de Cesare, Mulenga Mwenda, Anna E. Jeffreys, Daniel J Bridges, Jason A Hendry | TITLE: Cost-effective targeted nanopore sequencing of P. falciparum malaria
AUTHORS: Mariateresa de Cesare, Mulenga Mwenda, Anna E. Jeffreys, Daniel J Bridges, Jason A Hendry
[DESCRIPTION]
This protocol outlines a cost-effective approach for amplicon sequencing of P. falciparum malaria from dried blood spots (DBS). Th... | ["[Preparation of primer pools.] Prepare the sWGA primer pool (see Materials).", "[Reduced cost sWGA (modified from Samuel O. Oyola et al. (2016))] Prepare the sample DNA.", "[Preparation of primer pools.] If you have ordered the primers lyophilised, make them up to 1000uM in nuclease-free water.", "[Preparation of pri... |
88,154 | Optimized Macherey-Nagel NucleoSpin Tissue Protocol for Environmental DNA Extraction | 4 | dx.doi.org/10.17504/protocols.io.261gede6ov47/v1 | https://www.protocols.io/view/optimized-macherey-nagel-nucleospin-tissue-protoco-c2b2yaqe | Michaela Harris, Jade Larivière, Valérie Belliveau, Marion Chevrinais, Laury-Ann Dumoulin, Francis LeBlanc, Cloé Lepage, Nellie Gagné, Geneviève J. Parent | TITLE: Optimized Macherey-Nagel NucleoSpin Tissue Protocol for Environmental DNA Extraction
AUTHORS: Michaela Harris, Jade Larivière, Valérie Belliveau, Marion Chevrinais, Laury-Ann Dumoulin, Francis LeBlanc, Cloé Lepage, Nellie Gagné, Geneviève J. Parent
[DESCRIPTION]
This document aims at providing a transparent met... | ["[Filter preparation] Install all the material on the benchtop including 2 mL microtubes with Lyse&Spin baskets for extraction, pre-identified 2 mL Eppendorf Safe-Lock for back up, tweezers, scissors, weigh boats, waste beaker, microtube opener, and gloves.", "[DNA Extraction] Before use, clean bench with water, 0.5% ... |
46,720 | Haematoxylin-Eosin stain for cryosections | 4 | dx.doi.org/10.17504/protocols.io.bru8m6zw | https://www.protocols.io/view/haematoxylin-eosin-stain-for-cryosections-bru8m6zw | Simon Blanchoud | TITLE: Haematoxylin-Eosin stain for cryosections
AUTHORS: Simon Blanchoud
[STEPS]
?. [Groat's haematoxylin]
Mix: - of Ammonium iron(III) sulfate [Iron alum] (CAS 7783-83-7) - of dH2O - of sulfuric acid (CAS 7664-93-9)
1 g
50 mL
0.8 g
?. [Groat's haematoxylin]
Mix separately: - of hematoxylin (CAS 517-28-2) diss... | ["[Groat's haematoxylin]\nMix:\t- of Ammonium iron(III) sulfate [Iron alum] (CAS 7783-83-7)\t- of dH2O\t- of sulfuric acid (CAS 7664-93-9)\n1 g\n50 mL\n0.8 g", "[Groat's haematoxylin]\nMix separately:\t- of hematoxylin (CAS 517-28-2) dissolved in of EtOH (96%)\n0.5 g\n50 mL", "[Groat's haematoxylin]\nPour the w... |
null | null | null | dx.doi.org/10.17504/protocols.io.iyucfww | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong><em>Objectives</em></strong></p>
<p>The objectives of our studies were to determine:</p>
<p>a) the prevalence of chronic toxoplasmosis in population of Moscow city and Moscow region; b) to determine a probable role of the disease in the epidemiology of the RTA in Russ... | [] |
27,032 | Comments testing | null | dx.doi.org/10.17504/protocols.io.6myhc7w | null | Jenny Smith | TITLE: Comments testing
AUTHORS: Jenny Smith
[STEPS]
?. Rendered her for put improved concerns his. Ladies bed wisdom theirs mrs men months set. Everything so dispatched as it increasing pianoforte. Hearing now saw perhaps minutes herself his. Of instantly excellent therefore difficult he northward. Joy green but leas... | ["Rendered her for put improved concerns his. Ladies bed wisdom theirs mrs men months set. Everything so dispatched as it increasing pianoforte. Hearing now saw perhaps minutes herself his. Of instantly excellent therefore difficult he northward. Joy green but least marry rapid quiet but. Way devonshire introduced expr... |
45,856 | Predictors of Death Less Than versus More Than 90 days after Receiving a Modified Blalock-Taussig Shunt in Cyanotic Heart Children | 1 | dx.doi.org/10.17504/protocols.io.bqz8mx9w | https://www.protocols.io/view/predictors-of-death-less-than-versus-more-than-90-bqz8mx9w | oomaliwa | TITLE: Predictors of Death Less Than versus More Than 90 days after Receiving a Modified Blalock-Taussig Shunt in Cyanotic Heart Children
AUTHORS: oomaliwa
[STEPS]
?. [Objective]
To determine risk factors affecting time-to-death ≤90 and >90 days in children who underwent a modified Blalock-Taussig shunt (MBTS).
?. [M... | ["[Objective]\nTo determine risk factors affecting time-to-death ≤90 and >90 days in children who underwent a modified Blalock-Taussig shunt (MBTS).", "[Method]\nAfter the study was approved,all electronic records of consecutive patients aged 0-3 years admitted for MBTS between January 2005 and December 2016 were revie... |
94,359 | SOP for Immune cells isolation mouse adult brain with CD45 beads | 4 | dx.doi.org/10.17504/protocols.io.n92ldmxxnl5b/v1 | https://www.protocols.io/view/sop-for-immune-cells-isolation-mouse-adult-brain-w-c8dxzs7n | Malu G Tansey | TITLE: SOP for Immune cells isolation mouse adult brain with CD45 beads
AUTHORS: Malu G Tansey
[DESCRIPTION]
SOP for Immune cells isolation mouse adult brain with CD45 beads
[STEPS]
SECTION: A. Brain dissociation
7. Remove mice brains and put them in pre-prepared 15mL falcon tubes filled with 3mL cold D-PBS.
SECTION:... | ["[A. Brain dissociation] Remove mice brains and put them in pre-prepared 15mL falcon tubes filled with 3mL cold D-PBS.", "[A. Brain dissociation] Add 1900 ul of buffer Z in each C-tube.", "[A. Brain dissociation] Cut brain in ~8 equal pieces and add them in C-tubes (do not cut too much or viability will be affected)."... |
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