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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67,190 | Using the Thermo SPD1010 speedvac concentrator centrifuge for drying down peptides for LC-MS analysis | 1 | dx.doi.org/10.17504/protocols.io.36wgq78qyvk5/v1 | https://www.protocols.io/view/using-the-thermo-spd1010-speedvac-concentrator-cen-cduws6xe | ronan.ocualain | TITLE: Using the Thermo SPD1010 speedvac concentrator centrifuge for drying down peptides for LC-MS analysis
AUTHORS: ronan.ocualain
[DESCRIPTION]
This protocol details the procedure of using the Thermo SPD1010 speed vacuum concentrator centrifuge to dry peptide samples for storage and submission for LC-MS analysis. P... | ["[Speedvac drying:] Turn the power switch located on the rear right hand side of the unit to the ON position. Wait 45 min before starting drying.", "[Speedvac drying:] After waiting for the system to come to temperature, add the vials to the centrifuge by placing the neck of the vial in and under the hole, and secure... |
52,842 | Day 3: Morphological Taxonomy | 3 | dx.doi.org/10.17504/protocols.io.bxuipnue | https://www.protocols.io/view/day-3-morphological-taxonomy-bxuipnue | Tom Little | TITLE: Day 3: Morphological Taxonomy
AUTHORS: Tom Little
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Day 3: ADE practical instructions for morphological identifications</div></div>
[STEPS] | [] |
97,731 | Paraffin embedding of tissue specimen | HuBMAP | JHU-TMC | 0 | dx.doi.org/10.17504/protocols.io.q26g71rn8gwz/v1 | https://www.protocols.io/view/paraffin-embedding-of-tissue-specimen-hubmap-jhu-t-dbpb2min | Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Miklhail James, Sashank Reddy, Denis Wirtz | TITLE: Paraffin embedding of tissue specimen | HuBMAP | JHU-TMC
AUTHORS: Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Miklhail James, Sashank Reddy, Denis Wirtz
[DESCRIPTION]
The standard for tissue embedding is to ensure tissue samples are appropriately oriented and embedded on the “cut edge” or flattest... | ["[Orientation] The standard for tissue embedding is to ensure tissue samples are appropriately oriented and embedded on the “cut edge” or flattest edge available", "[Type of paraffin] the type of paraffin used in your laboratory should be optimal for your needs. Paraffin comes in many types. These types are differenti... |
null | null | null | dx.doi.org/10.17504/protocols.io.fukbnuw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><span class="TextRun SCX24498567" lang="EN-US" style="font-size: 14pt; font-family: Times New Roman,serif; line-height: 23px;" xml:lang="EN-US"><span class="NormalTextRun SCX24498567" style="background-color: inherit;">This protocol is designed to allow you to clean large</sp... | [] |
73,113 | Luciferase Activity Assay | 4 | dx.doi.org/10.17504/protocols.io.dm6gpj37dgzp/v1 | https://www.protocols.io/view/luciferase-activity-assay-cjmzuk76 | Electra Brunialti, Alessandro Maria Villa, Paolo Ciana | TITLE: Luciferase Activity Assay
AUTHORS: Electra Brunialti, Alessandro Maria Villa, Paolo Ciana
[DESCRIPTION]
Luciferase activity assay on cell extracts using Veritas (Turner) luminometer.
[STEPS]
1. Lysate the cell using 1X Luciferase Cell Culture LysisReagent (Cat. E1531, Promega) following manufacturer instructio... | ["Lysate the cell using 1X Luciferase Cell Culture LysisReagent (Cat. E1531, Promega) following manufacturer instruction;", "put 20 µl/well of cell lysate into the white plate (Cat 3912, Corning);", "prepare Reaction Buffer (100µl for each sample): 500 µM luciferin (Cat E160E, Promega), 20 mM Tricine, 0.1 mM EDTA, 1.07... |
107,457 | LRRK2 PhosphoSens Assay | 0 | dx.doi.org/10.17504/protocols.io.81wgbz8qngpk/v1 | https://www.protocols.io/view/lrrk2-phosphosens-assay-dk694zh6 | Nicolai D. Raig, Stefan Knapp | TITLE: LRRK2 PhosphoSens Assay
AUTHORS: Nicolai D. Raig, Stefan Knapp
[DESCRIPTION]
With this enzymatic activity assay we were able to determine IC50 values of published inhibitors aswell as newly synthesized compounds that inhibit LRRK2. The assay is based on the in vitro phosphorylation reaction between the enzymati... | ["Pipett a dilution series of eleven concentrations between 15µM and 0.4nM (calculated with an assay volume of 10µL) of the compounds into white 384-well plates (Greiner 781207) as duplicates with an ECHO acoustic dispenser (Labcyte). Pipett a equivalent of DMSO in two wells per compound as 0% (without protein and comp... |
79,800 | Tissue and blood collection | 1 | dx.doi.org/10.17504/protocols.io.bp2l69wmklqe/v1 | https://www.protocols.click/view/tissue-and-blood-collection-cr6yv9fw | michela.deleidi, Bianca Marchetti, Federico Bertoli, Carmela Giachino | TITLE: Tissue and blood collection
AUTHORS: michela.deleidi, Bianca Marchetti, Federico Bertoli, Carmela Giachino
[DESCRIPTION]
This protocol details tissue collection from mice.
[STEPS]
SECTION: Tissue and blood collection
1. For immunohistochemistry, mice (5-6 mice/genotype/age-group/treatment) were anesthetized an... | ["[Tissue and blood collection] For immunohistochemistry, mice (5-6 mice/genotype/age-group/treatment) were anesthetized and transcardially perfused with 0.9% NaCl, followed by 4 % paraformaldehyde in phosphate buffer (pH 7.2 at 4°C), the brains and peripheral tissues carefully removed and post-fixed for 2-4 hrs, in 4%... |
99,412 | Food grade colorimetry of anthocyanins (A Youth Summer Camp Activity) | 0 | dx.doi.org/10.17504/protocols.io.yxmvmenqng3p/v1 | https://www.protocols.io/view/food-grade-colorimetry-of-anthocyanins-a-youth-sum-ddbu22nw | Eric S McLamore, Geisianny AM Moreira, Diana Vanegas, dbahamo, Lisseth Casso-Hartmann, Lidadi Agbomi, Maria J Torres | TITLE: Food grade colorimetry of anthocyanins (A Youth Summer Camp Activity)
AUTHORS: Eric S McLamore, Geisianny AM Moreira, Diana Vanegas, dbahamo, Lisseth Casso-Hartmann, Lidadi Agbomi, Maria J Torres
[DESCRIPTION]
This protocol describes activities used in summer education camps for youth (14 years and older). The ... | ["[Anthocyanin activities for camp] Step 1) Gather and prepare materials\nGroup participants into teams of 2-4 people (Fig 1).\n\n \nTable 1 presents a planning table for a typical summer camp supporting 40 youth (ten teams of 4). For a camp of this size, 3-5 leaders are typically engaged to guide youth through activit... |
null | null | null | dx.doi.org/10.17504/protocols.io.cp9vr5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Radioactive Labeling with T4 Polynucleotide Kinase 3' phosphatase minus
[STEPS]
?.
?.
?. | [] |
63,618 | Measuring tension, pellet transit, and calcium imaging within cell subtypes in response to direct electrical field stimulation of colon | 4 | dx.doi.org/10.17504/protocols.io.36wgq7yokvk5/v1 | https://www.protocols.io/view/measuring-tension-pellet-transit-and-calcium-imag-cadasa2e | Dante Heredia, Thomas Gould | TITLE: Measuring tension, pellet transit, and calcium imaging within cell subtypes in response to direct electrical field stimulation of colon
AUTHORS: Dante Heredia, Thomas Gould
[DESCRIPTION]
Measurement of the effects of direct electrical stimulation of the mouse colon
[BEFORE_START]
Make sure there is enough g... | ["A ventral midline incision is made and the entire colon is excised and placed into a sylguard-lined dissection dish filled with oxygenated Krebs-Ringers solution. The colon is then gently flushed of its contents. For all experiments, the colon is perfused with 35-degree, oxygenated Krebs-Ringers for the duration of ... |
81,447 | GFP Immunoprecipitation and Sample Preparation for Tandem Mass Tag (TMT) Mass Spectrometry Analysis | 4 | dx.doi.org/10.17504/protocols.io.eq2ly7kxqlx9/v1 | https://www.protocols.io/view/gfp-immunoprecipitation-and-sample-preparation-for-ctsfwnbn | Prosenjit Pal, Raja S. Nirujogi, Francesca Tonelli, Dario R Alessi | TITLE: GFP Immunoprecipitation and Sample Preparation for Tandem Mass Tag (TMT) Mass Spectrometry Analysis
AUTHORS: Prosenjit Pal, Raja S. Nirujogi, Francesca Tonelli, Dario R Alessi
[DESCRIPTION]
We describe a method to identify potential interactors of any Green Fluorescent Protein (GFP) tagged protein expressed in ... | ["[Transient transfection of HEK293 cells] Plate cells in 10 cm dishes (one dish for each experimental condition) to give a 60-70% confluency the following day (around 2.2 x 106 cells seeded per 10 cm dish).", "[Transient transfection of HEK293 cells] Prepare a transfection mix in a sterile 1.5ml Eppendorf tube, contai... |
86,474 | Eastern Hemlock Tissue Collection for DNA | 4 | null | https://www.protocols.io/view/eastern-hemlock-tissue-collection-for-dna-cypixvke | Karl Fetter | TITLE: Eastern Hemlock Tissue Collection for DNA
AUTHORS: Karl Fetter
[DESCRIPTION]
Steps for collecting tissue from Eastern Hemlocks for DNA analysis. The Plant Computational Genomics lab is conducting a landscape genomics study of climate adaptation in the Eastern Hemlock. This protocol is a step-by-step guide to co... | ["[Introduction] This protocol is intended for field collection of leaf tissue for the Eastern Hemlock conservation genomics project sponsored by the Plant Computation Genomics lab at the University of Connecticut. The goal of the project is to identify climate adapted genomic variation for seed banking and potential u... |
99,205 | Lysosomal GCase (glucocerebrosidase) activity assay | 0 | dx.doi.org/10.17504/protocols.io.8epv5r9jdg1b/v1 | https://www.protocols.io/view/lysosomal-gcase-glucocerebrosidase-activity-assay-dc5d2y26 | Sara Gomes, Esther Sammler | TITLE: Lysosomal GCase (glucocerebrosidase) activity assay
AUTHORS: Sara Gomes, Esther Sammler
[DESCRIPTION]
Here we report a method to measure enzyme activity of lysosomal glucocerebrosidase (GBA1, GCase) by monitoring the hydrolysis of the fluorescent substrate 4-methylumbelliferyl-β-D-glucopyranoside. The assay is ... | ["[Buffer preparation] 0.1M citric acid: dissolve 19.2 g in 1 L", "[Buffer preparation] 0.2M sodium phosphate: dissolve 28.4 g in1 L.", "[Buffer preparation] Citrate-phosphate buffer, pH 5.4: mix 44.2 mLwith 56.8 mL to make 100mL citrate-phosphate buffer, pH 5.4.", "[Buffer preparation] 0.5M EDTA: dissolve 20.8 g in 8... |
43,614 | test 2 | 1 | null | https://www.protocols.io/view/test-2-bnt6mere | Maria Guliakina | TITLE: test 2
AUTHORS: Maria Guliakina
[STEPS]
?. test
?.
?. | ["test"] |
86,050 | Unconventional secretion of alpha-synucein mediated by palmitoylated DNAJC5 oligomers | 4 | dx.doi.org/10.17504/protocols.io.rm7vzxb65gx1/v1 | https://www.protocols.io/view/unconventional-secretion-of-alpha-synucein-mediate-cyaaxsae | iona.thomas-wright, Richard Wade-Martins | TITLE: Unconventional secretion of alpha-synucein mediated by palmitoylated DNAJC5 oligomers
AUTHORS: iona.thomas-wright, Richard Wade-Martins
[DESCRIPTION]
This protocol, carried out according to manufacturer’s instructions uses a classical ELISA experimental design with sensitive electrochemical detection to provide... | ["[Harvesting media and cell lysates] Harvest conditioned media from cells grown in a full-area 96 well plate, being careful not to disturb the cell monolayer. Add 30 uL RIPA lysis buffer (0.5% Triton X-100, 10 mM Tris/HCl, pH 8.0, 1 mM EDTA, 0.5 mM EDTA,0.1% sodium dodecyl sulfate, 0.02% sodium deoxycholate, and (140 ... |
44,584 | Drug Sensitivity Assays of Human Cancer Organoid Cultures | 4 | dx.doi.org/10.17504/protocols.io.bpsgmnbw | https://www.protocols.io/view/drug-sensitivity-assays-of-human-cancer-organoid-c-bpsgmnbw | Hayley E. Francies, Andrew Barthorpe, Anne McLaren-Douglas, William J. Barendt, Mathew J. Garnett | TITLE: Drug Sensitivity Assays of Human Cancer Organoid Cultures
AUTHORS: Hayley E. Francies, Andrew Barthorpe, Anne McLaren-Douglas, William J. Barendt, Mathew J. Garnett
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Drug sensitivity testing utilizing preclinical disease models such as cancer cel... | ["[3.1 Preparation of Drug Stocks and Drug Plates]\nDesign the layout of your drug plate (see Note 4 and Fig. 2).", "[3.1 Preparation of Drug Stocks and Drug Plates]\nDrugs are reconstituted in and stored frozen at or ideally in StoragePods® (Roylan Developments) kept at , providing a moisture-free, low-oxygen enviro... |
43,649 | DNA Extraction for Beetle DNA with Qiagen DNeasy | 3 | dx.doi.org/10.17504/protocols.io.bnu9mez6 | https://www.protocols.io/view/dna-extraction-for-beetle-dna-with-qiagen-dneasy-bnu9mez6 | Demian F Gomez, Caroline Storer | TITLE: DNA Extraction for Beetle DNA with Qiagen DNeasy
AUTHORS: Demian F Gomez, Caroline Storer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpose of this protocol is to extract DNA from beetles using the DNeasy protocol with additional notes to the manufacturer guidelines.</div><div class... | [] |
28,864 | Frequently sampled Insulin glucose tolerance test | null | dx.doi.org/10.17504/protocols.io.8e8hthw | null | Timothy Nichols, David Clemmons | TITLE: Frequently sampled Insulin glucose tolerance test
AUTHORS: Timothy Nichols, David Clemmons
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This assay is used by the DiaComp to measure glucose tolerance and insul... | ["FSIGT or Bergman analysis Pigs are studied after an overnight fast. The food intake of the animals is monitored for 3 days prior to the fast to ensure adequate carbohydrate intake. Two intravenous catheters are placed, one for sampling and one for infusing glucose and insulin. A bolus of glucose (0.3 gm/kg) is admini... |
78,725 | 3D Mesh Cleanup Tutorial: Fossil Plant Cupule (Beginner) | 1 | dx.doi.org/10.17504/protocols.io.j8nlkwyywl5r/v1 | https://www.protocols.io/view/3d-mesh-cleanup-tutorial-fossil-plant-cupule-begin-cq5dvy26 | Elizabeth G. Clark, Kelsey M Jenkins, Craig R Brodersen | TITLE: 3D Mesh Cleanup Tutorial: Fossil Plant Cupule (Beginner)
AUTHORS: Elizabeth G. Clark, Kelsey M Jenkins, Craig R Brodersen
[DESCRIPTION]
This protocol details 3D mesh cleanup tutorial of fossil plant cupule (Beginner).
[GUIDELINES]
Skills developed: Basic mesh editing
3D meshes of fossil specimens extracted d... | ["[Part 1: The Meshlab Interface] Open Meshlab and import “Cupule before.obj” into Meshlab via File > Import Mesh. Alternatively, drag the file into the project window (the large purple box with the crosshairs) if using Mac.", "[Part 1: The Meshlab Interface] The mesh now appears in the project window. You can rotate i... |
null | null | null | dx.doi.org/10.17504/protocols.io.fjrbkm6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?. | [] |
83,660 | Baiting Pythium myriotylum from Infested Soil | 4 | null | https://www.protocols.click/view/baiting-pythium-myriotylum-from-infested-soil-cvxkw7kw | Nimalka M Weerasuriya | TITLE: Baiting Pythium myriotylum from Infested Soil
AUTHORS: Nimalka M Weerasuriya
[DESCRIPTION]
Baiting Pythium from Ft. Cobb or other infested soil.
[STEPS]
SECTION: Preparation
1. Prep P5ARP Plates 1-2 days before plating.
Prepare working culture plates (CMA, PDA + amp) up to 1 week before plating.
SECTION: Tr... | ["[Preparation] Prep P5ARP Plates 1-2 days before plating.\nPrepare working culture plates (CMA, PDA + amp) up to 1 week before plating.", "[Transfer Culture] Check plates after 24-48 h.", "[Oospore Check] Check for \"gold coin\" oospores at plate edges to indicate Pythium myriotylum. \nUse CMA for oospore production\n... |
15,223 | Nodule cleaning | null | dx.doi.org/10.17504/protocols.io.s4xegxn | null | null | TITLE: Nodule cleaning
AUTHORS:
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Adapted for high throughput of small samples for sequencing.</div><div class = "text-block">Based on doi:10.1371/journal.pone.0047677</div></div>
[STEPS]
?. Cleanly cut nodules from plant roots and drop into a 2ml Eppe... | ["Cleanly cut nodules from plant roots and drop into a 2ml Eppendorf tube per plant.", "Add 1ml 100% EtOH to each tube", "Incubate for 5 seconds", "Remove as much liquid as possible without removing loose nodules", "Add 1ml 6% sodium hypochlorite", "Remove as much liquid as possible", "Add 2ml sterile water", "Remove a... |
92,909 | Single particle analysis of α-Synuclein fibrils | 1 | dx.doi.org/10.17504/protocols.io.81wgbxozylpk/v1 | https://www.protocols.io/view/single-particle-analysis-of-synuclein-fibrils-c6ymzfu6 | Kevin Sicking, Rubén Fernández-Busnadiego | TITLE: Single particle analysis of α-Synuclein fibrils
AUTHORS: Kevin Sicking, Rubén Fernández-Busnadiego
[DESCRIPTION]
Aggregates of α-Synuclein (α-Syn) have been implicated in the pathogenesis of a spectrum of disorders, including Parkinson’s disease, multiple system atrophy, and dementia with Lewy bodies. These agg... | ["[Preparation of α-Syn Pre-Formed Fibrils from α-Syn monomers] To produce pre-formed fibrils for structural analysis, adhere to the standardized protocol outlined here: [Protocol for Generation of Pre-formed Fibrils](https://www.protocols.io/view/protocol-forgeneration-of-pre-formed-fibrils-from-rm7vz3ezxgx1/v1).", "[... |
62,441 | Next Optimal Male Enhancement - (Consumers Warning!) Don’t Buy Until Read! | 3 | dx.doi.org/10.17504/protocols.io.3byl4bxz8vo5/v1 | https://www.protocols.io/view/next-optimal-male-enhancement-consumers-warning-do-b88hrzt6 | H Douglas Morris | TITLE: Next Optimal Male Enhancement - (Consumers Warning!) Don’t Buy Until Read!
AUTHORS: H Douglas Morris
[DESCRIPTION]
Plans with high deductibles will only cost you a lot if you actually use medical services.
[STEPS] | [] |
107,204 | Indirect Co-Culture Assay using Boyden Chambers | 0 | dx.doi.org/10.17504/protocols.io.5jyl82om7l2w/v1 | https://www.protocols.io/view/indirect-co-culture-assay-using-boyden-chambers-dkxc4xiw | Bianca Cruz Pachane, Heloisa Sobreiro Selistre de Araujo | TITLE: Indirect Co-Culture Assay using Boyden Chambers
AUTHORS: Bianca Cruz Pachane, Heloisa Sobreiro Selistre de Araujo
[DESCRIPTION]
Here, we describe a transwell assay using Boyden chambers as an indirect co-culture method, where two cell lines are grown together but separated by a porous membrane. This assay was u... | ["[Preparation of Gelatin-Coated Coverslips] In preparation: \nClean round glass coverslips (13 mm ø) with 70% ethanol wipes before use. Maintain slips in a clean container.\nPrepare a 0.5 % (v/v)and keep at 4 °C protected from light.", "[Preparation of Gelatin-Coated Coverslips] Drop coverslips atop the droplets and i... |
63,359 | Polychromatic UV Dose Determination | 1 | null | https://www.protocols.io/view/polychromatic-uv-dose-determination-b947r8zn | Daniel Ma, NATALIE HULL | TITLE: Polychromatic UV Dose Determination
AUTHORS: Daniel Ma, NATALIE HULL
[DESCRIPTION]
For polychromatic UV light sources, UV irradiance throughout the sample depth can be calculated by changing variables the “Germicidal Fluence (UV Dose) Calculations for a Low Pressure UV Lamp” obtained from Bolton Photoscience... | ["[Introduction] The purpose of this protocol is to document the steps used for determination of UV doses for polychromatic UV sources such as UV LEDs and medium pressure mercury lamps. The method is modified from Bolton and Linden (2003). Gather equipment and materials. Sterilize materials and prepare agar for enumera... |
86,705 | Levodopa-induced dyskinesia mouse model | 4 | dx.doi.org/10.17504/protocols.io.8epv5xxb5g1b/v1 | https://www.protocols.io/view/levodopa-induced-dyskinesia-mouse-model-cywrxxd6 | Beatriz E Nielsen | TITLE: Levodopa-induced dyskinesia mouse model
AUTHORS: Beatriz E Nielsen
[DESCRIPTION]
This protocol describes a mouse model of levodopa-induced dyskinesia (LID) and the behavioral assessment of its motor deficits. It includes open field locomotor activity and scoring of abnormal involuntary movements (AIMs).
[STEP... | ["[Levodopa-induced dyskinesia mouse model development] Generate unilaterally high dose 6-OHDA-lesioned mice (protocol linked below):", "[Levodopa-induced dyskinesia mouse model development] 3 weeks after 6-OHDA injections, verify unilateral dopamine depletion by assessing forelimb use assymetry in the cylinder test (p... |
85,814 | WU sn-prep Protocol for solid tumors- ATAC v2.7 | 1 | dx.doi.org/10.17504/protocols.io.e6nvwdkx2lmk/v1 | https://www.protocols.io/view/wu-sn-prep-protocol-for-solid-tumors-atac-v2-7-cx2wxqfe | Wagma Caravan, Reyka Jayasinghe, Nataly Naser Al Deen | TITLE: WU sn-prep Protocol for solid tumors- ATAC v2.7
AUTHORS: Wagma Caravan, Reyka Jayasinghe, Nataly Naser Al Deen
[DESCRIPTION]
Single nuclei dissociation protocol for snATAC-seq
[STEPS]
SECTION: Reagents and Tools
1. 1x Lysis buffer (2mL):
10mM Tris-HCl (pH 7.4) (Thermo; 15567027), 20μL
10mM NaCl (Thermo; AM9759... | ["[Reagents and Tools] 1x Lysis buffer (2mL):\n10mM Tris-HCl (pH 7.4) (Thermo; 15567027), 20μL\n10mM NaCl (Thermo; AM9759), 4μL\n3 mM MgCl2 (Thermo; AM9530G), 6μL\nNP-40 substitute (Sigma, 74385-1L), 2μL\n1 M DTT (Sigma, 646563), 2μL\nNuclease Free Water (Invitrogen, AM9937), 1.966mL", "[Reagents and Tools] Lysis Dilut... |
null | null | null | dx.doi.org/10.17504/protocols.io.gs4bwgw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol summarizes the process of primer design for assembly-based cloning methods, such as Gibson or AQUA-cloning. </p>
<p>Well-designed primers are necessary for efficient cloning of any kind.<strong> </strong></p>
<p>This protocol can also be used to design primers f... | [] |
48,064 | Multiplex Immunofluorescence on Fresh Frozen Tissue-V2 | 1 | dx.doi.org/10.17504/protocols.io.bs68nhhw | https://www.protocols.io/view/multiplex-immunofluorescence-on-fresh-frozen-tissu-bs68nhhw | Maya Brewer, Liz McDonough, Yuantee Zhu, Elizabeth Neumann, Mark De Caestecker, Danielle Gutierrez, Jeff Spraggins | TITLE: Multiplex Immunofluorescence on Fresh Frozen Tissue-V2
AUTHORS: Maya Brewer, Liz McDonough, Yuantee Zhu, Elizabeth Neumann, Mark De Caestecker, Danielle Gutierrez, Jeff Spraggins
[DESCRIPTION]
Scope:
To describe the procedure for multiple cycles of immunofluorescence on human kidney tissue embedded in c... | ["[Immunofluorescence] Place frozen slides from the -80˚C freezer directly into the formalin, and post-fix for 5 minutes.", "[Immunofluorescence] Pour used formalin into the appropriate waste container, then fill jar with 1X PBS and wash sections for 5 minutes four times.", "[Immunofluorescence] Using a hydrophobic pen... |
null | null | null | dx.doi.org/10.17504/protocols.io.fz4bp8w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Now includes media used for phosphate limitation experiments.</p>
[GUIDELINES]
<p>All media should be autoclaved unless otherwise noted</p>
<p> </p>
<p><u>Zobell plates, 100% nutrient (1 L) – for growing host; ~15 mL/plate</u></p>
<p>26 g sea salts</p>
<p>1 g yeast extract</... | [] |
69,611 | Passage cells | 4 | dx.doi.org/10.17504/protocols.io.n92ldpbd7l5b/v1 | https://www.protocols.io/view/passage-cells-cf8jtrun | Adita Ayu Permanasari | TITLE: Passage cells
AUTHORS: Adita Ayu Permanasari
[DESCRIPTION]
Passage Cells
[STEPS]
1. Observe cells under microscope
2. Wipe outside surface of cell culture dish with ethanol cotton and bring it inside Biosafety Cabinet (BSC)
3. Bring medium, PBS, Trypsin-EDTA 2x to BSC
4. Bring autopipetter, disposable pipet (1... | ["Observe cells under microscope", "Wipe outside surface of cell culture dish with ethanol cotton and bring it inside Biosafety Cabinet (BSC)", "Bring medium, PBS, Trypsin-EDTA 2x to BSC", "Bring autopipetter, disposable pipet (10ml, 2ml), one 15ml tube to BSC", "Discard old medium", "Rinse the bottom of dish with 10ml... |
53,631 | Genomic DNA extraction from the diatom Pseudo-nitzschia multistriata for Illumina sequencing | 1 | dx.doi.org/10.17504/protocols.io.byk7puzn | https://www.protocols.io/view/genomic-dna-extraction-from-the-diatom-pseudo-nitz-byk7puzn | Francesco Manfellotto, Monia Teresa Russo, Pina Marotta, Rossella Annunziata, Anna Santin, Antonella Ruggiero, Mariella Ferrante | TITLE: Genomic DNA extraction from the diatom Pseudo-nitzschia multistriata for Illumina sequencing
AUTHORS: Francesco Manfellotto, Monia Teresa Russo, Pina Marotta, Rossella Annunziata, Anna Santin, Antonella Ruggiero, Mariella Ferrante
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Genomic... | ["Detect the presence/absence of bacteria and collect the cultures as described in: dx.doi.org/10.17504/protocols.io.btt5nnq6", "Resuspend cells with 500 μL of TE buffer (10 mM TrisHCl pH 7.6 and 1 mM EDTA pH 8.0)", "Add: 400 mg of 0.2-0.3 mm diameter zirconia/silica beads 500 μL phenol (pH 7.8).", "Mix with vortex 3 t... |
24,336 | BiomekFXp Robot Minipreps (RoboPreps) | null | dx.doi.org/10.17504/protocols.io.3zqgp5w | null | James Angstman | TITLE: BiomekFXp Robot Minipreps (RoboPreps)
AUTHORS: James Angstman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">RoboPreps are great for high-throughput cloning and subcloning, especially if you’re going to be doing Maxipreps afterward anyway. RoboPreps must be done in 96 well format as of now, ... | ["[Cell Prep]\nPick colonies into into a 96-well assay block and grow at overnight with shaking.\n[LB cultures]\n37 °C", "[Cell Prep]\nPellet the cells by spinning at for 5-15 minutes .", "[Cell Prep]\nRemove the media by quickly inverting the block over a waste container.\nIf intended for later use, you can freeze... |
60,103 | Human Knee Cartilage Collection Protocol for Single Cell RNAseq | 4 | dx.doi.org/10.17504/protocols.io.14egn7996v5d/v1 | https://www.protocols.io/view/human-knee-cartilage-collection-protocol-for-singl-b6xfrfjn | molmer , Martin Lotz | TITLE: Human Knee Cartilage Collection Protocol for Single Cell RNAseq
AUTHORS: molmer , Martin Lotz
[DESCRIPTION]
Cartilage from the medial femoral condyle is shaved for Single Cell RNAseq processing. The attached image indicates where the cartilage shavings are collected from.
[BEFORE_START]
Knee blocks are shipp... | ["Prepare harvesting area with sterile drapes, tools and gauze. All harvesting is completed within an aseptic environment.", "Wipe down the knee blocks with 95% ethanol prior to opening the joint capsule.", "Once the joint capsule is opened, the femur and tibia are disarticulated. Wet a sterile gauze with DPBS+1% Anti-... |
18,603 | Analysis of the time evolution of auditory steady-state responses (ASSR) recorded in rats | null | dx.doi.org/10.17504/protocols.io.wejfbcn | null | Pavel Prado, Eduardo Martínez-Montes, Matías Zañartu | TITLE: Analysis of the time evolution of auditory steady-state responses (ASSR) recorded in rats
AUTHORS: Pavel Prado, Eduardo Martínez-Montes, Matías Zañartu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">Auditory steady-state responses (ASSRs) are ... | ["[Preparation]\nAnimals are anesthetized with ketamine (75.0 mg/kg, ip) and diazepam (5.0 mg/kg, ip).", "[Preparation]\nSupplemental doses of anesthesia are administered during the experiment at a level sufficient to maintain the animal in an areflexic state.", "[Preparation]\nAtropine sulfate (0.06 mg/kg; im) are adm... |
57,672 | Introductory Hydra Activities | 1 | null | https://www.protocols.io/view/introductory-hydra-activities-b4jgqujw | Callen Hyland | TITLE: Introductory Hydra Activities
AUTHORS: Callen Hyland
[DESCRIPTION]
This is a series of introductory lab activities for BIOL309-03: Research Methods. The purpose is to master vocabulary related to Hydra anatomy, become familiar with compound microscopes and dissecting microscopes, and practice microdissections ... | ["[Observation Activities] In this activity you will become familiar with the anatomy of Hydra including areas of the body, cell layers, and nematocysts, while practicing the new vocabulary we learned in lecture.\n\nLearning objectives:\nUse a compound microscope to examine prepared slides\nMaster vocabulary related to... |
null | null | null | dx.doi.org/10.17504/protocols.io.es4begw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
78,358 | Study Population (Part 4 of "Effects of Online Exercise Intervention on Physical and Mental Conditions in Young Adults with Chronic Neck Pain") | 1 | dx.doi.org/10.17504/protocols.io.6qpvr4wxbgmk/v1 | https://www.protocols.io/view/study-population-part-4-of-34-effects-of-online-ex-cqrwvv7e | Yiting Lin | TITLE: Study Population (Part 4 of "Effects of Online Exercise Intervention on Physical and Mental Conditions in Young Adults with Chronic Neck Pain")
AUTHORS: Yiting Lin
[DESCRIPTION]
This is a Part 4 of "Effects of Online Exercise Intervention on Physical and Mental Conditions in Young Adults with Chronic Ne... | ["[Inclusion Criteria] Adults between 18 and 50 years of age with neck pain (from occiput to 7thcervical vertebra) for at least 3 months.", "[Inclusion Criteria] A score of >= 4/50 on the NDI.", "[Exclusion Criteria] Adults with a history of previous neck surgery, cervical radiculopathy, acute neck injury or fracture."... |
67,422 | Alpha Extracts Pure Hemp Oil Reviews Canada: Free Trial and Price of Alpha Extracts CBD Oil | 3 | dx.doi.org/10.17504/protocols.io.x54v9y68pg3e/v1 | https://www.protocols.io/view/alpha-extracts-pure-hemp-oil-reviews-canada-free-t-cd36s8re | pure | TITLE: Alpha Extracts Pure Hemp Oil Reviews Canada: Free Trial and Price of Alpha Extracts CBD Oil
AUTHORS: pure
[DESCRIPTION]
Alpha Extracts Pure Hemp Oil
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.hg3b3yn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="bibliography-item-copy-text content col-md-12" data-clipboard-target="copy-target-228943496" data-redirect-target="/items/228943496/copy">Van Etten, J. (n.d.). Formulation of Modified Bold's Basal Medium (MBBM). Retrieved from http://ncv.unl.edu/vanettenlab/</div>
<d... | [] |
90,702 | General genotyping of Myzus persicae using PCR with microsatellite markers and gel electrophoresis | 4 | dx.doi.org/10.17504/protocols.io.bp2l6x29klqe/v2 | https://www.protocols.io/view/general-genotyping-of-myzus-persicae-using-pcr-wit-c4tnywme | Mariska M. Beekman, Marcel Dicke, Bas J. Zwaan, Eveline Verhulst, Bart Pannebakker | TITLE: General genotyping of Myzus persicae using PCR with microsatellite markers and gel electrophoresis
AUTHORS: Mariska M. Beekman, Marcel Dicke, Bas J. Zwaan, Eveline Verhulst, Bart Pannebakker
[DESCRIPTION]
This protocol can be used to 'roughly' genotype green peach aphids, Myzus persicae (Sulzer), based on micr... | ["[Materials] Chelex and proteinase K based DNA extraction\nPipettes and pipette tips\nEppendorf tubes \nCentrifuge \nHeat block or water bath \nUltrapure water \nChelex 100 resin (Bio-Rad, Hercules, CA, USA)\nProteinase K (20 mg/mL; Promega, Southampton, UK)\n\nPCR\nPipettes and pipette tips \nPCR machine \nPCR tubes ... |
55,463 | Scaffold Mapping Protocol - Version 1.0 | 1 | dx.doi.org/10.17504/protocols.io.b2efqbbn | https://www.protocols.io/view/scaffold-mapping-protocol-version-1-0-b2efqbbn | Mabelle Lin, Sonia Sharma | TITLE: Scaffold Mapping Protocol - Version 1.0
AUTHORS: Mabelle Lin, Sonia Sharma
[DESCRIPTION]
The scope of this protocol covers the steps involved in the mapping of image data to organ scaffolds.
[STEPS]
1. Check for the availability of segmentation files for image data.
Ensure the image data has already been ... | ["Check for the availability of segmentation files for image data.\n\nEnsure the image data has already been segmented with MBF software and the MBF XML file is available. If the MBF XML file has not already been uploaded to Pennsieve, advise the investigators to do so. Check the segmentation file to make sure the data... |
98,921 | MHV Tissue Titering Protocol | 0 | null | https://www.protocols.io/view/mhv-tissue-titering-protocol-dcuh2wt6 | Siddharth Krishnamurthy | TITLE: MHV Tissue Titering Protocol
AUTHORS: Siddharth Krishnamurthy
[DESCRIPTION]
This protocol is for isolating total nucleic acid from soft tissues in mice, for subsequent analysis of Viral RNA levels
[STEPS]
SECTION: Day -1: Prepare tissue collection tubes and plate
5. Add 650 µLto each bead containing tube
SE... | ["[Day -1: Prepare tissue collection tubes and plate] Add 650 µLto each bead containing tube", "[Day -1: Prepare tissue collection tubes and plate] Label a sufficient number of 1.1 mL 12-well cluster tubes, and then place them in a new rack.", "[Day -1: Prepare tissue collection tubes and plate] Add 5-10 2.0 mm Zirconi... |
108,368 | Meat identification protocol | 0 | null | https://www.protocols.io/view/meat-identification-protocol-dm3q48mw | openbioscience Adrian | TITLE: Meat identification protocol
AUTHORS: openbioscience Adrian
[DESCRIPTION]
Identifying species by identifying unique DNA sequences is common practice.
In this case we will identify the presence or absence of pork DNA in a meat sample.
We will use the alkaline method for DNA extraction and LAMP method for DNA am... | ["[Meat Preparation] Measure 500 mg pork meat without fat. This is our sample (aliquot.", "Measure 1 ml of the liquid meat and add it to a sterile centrifuge tube labeled \"raw sample\". This is done with a 100- 1000 μl micropipette.", "Prepare 5 ml of NaOH 0.2 mol/L (sodium hydroxide or caustic soda). This will be us... |
61,415 | Stranded Transcript Count Table Generation from Long Reads | 1 | dx.doi.org/10.17504/protocols.io.5qpvonn2bl4o/v15 | https://www.protocols.io/view/stranded-transcript-count-table-generation-from-lo-b78frrtn | David A Eccles | TITLE: Stranded Transcript Count Table Generation from Long Reads
AUTHORS: David A Eccles
[DESCRIPTION]
This protocol is for comparing different samples at the transcript level, using long reads that are mapped to transcripts.
Input(s): demultiplexed and oriented fastq files (see protocol Preparing Reads for Strande... | ["[Demultiplex Reads] Demultiplex and orient reads as per the protocol Preparing Reads for Stranded Mapping. It is expected that these demultiplexed reads will be split up in the current directory, and coupled with a 'barcode_counts.txt' file. If that's the case, the following should work:\n \nExample expected output:\... |
24,197 | Simple subtidal rocky reef environmental parameter station | 1 | null | https://www.protocols.io/view/simple-subtidal-rocky-reef-environmental-parameter-3vdgn26 | Gonzalo Bravo, Gregorio Bigatti, Juan Livore | TITLE: Simple subtidal rocky reef environmental parameter station
AUTHORS: Gonzalo Bravo, Gregorio Bigatti, Juan Livore
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">This is a simple system that can be deployed on rocky reefs to measure environmenta... | ["[PREPARATION OF SEDIMENT TRAPS]\nPVC tubes of 50 mm diameter were cut into 200 mm long pieces. One of the extremes of the tube was covered by fixing a PVC cup in order to perfectly close that end.Each trap was identified with ID number (Figure 1A). n=3 traps in each reef .130 cm Iron bars (8 mm diameter) were prepare... |
48,837 | Untargeted Top-down Proteomics by CZE-MS/MS on Eclipse | 1 | dx.doi.org/10.17504/protocols.io.btxdnpi6 | https://www.protocols.io/view/untargeted-top-down-proteomics-by-cze-ms-ms-on-ecl-btxdnpi6 | Kevin Jooß, Bryon Drown, Rafael Melani, Kelleher Research Group | TITLE: Untargeted Top-down Proteomics by CZE-MS/MS on Eclipse
AUTHORS: Kevin Jooß, Bryon Drown, Rafael Melani, Kelleher Research Group
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Describes the CZE-MS/MS data acquisition procedure for top-down proteomics samples using the Thermo Scientific Orbit... | ["Samples were analyzed on a Thermo Scientific Orbitrap Eclipse Tribrid mass spectrometer in line with a Sciex CESI 8000 Plus", "Samples were prepared in ( ) 0.3% acetic acid and transferred to sample vials.\n10 µl", "Prior each sample injection, the capillary is flushed with 0.1 M HCl, filled with new background elect... |
40,315 | Preparation of a protein-LG conjugated to horseradish peroxidase by the periodate method. | 6 | dx.doi.org/10.17504/protocols.io.bjk3kkyn | https://www.protocols.io/view/preparation-of-a-protein-lg-conjugated-to-horsera-bjk3kkyn | Angel Justiz-Vaillant | TITLE: Preparation of a protein-LG conjugated to horseradish peroxidase by the periodate method.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">SpLG comprises of 4 Ig-binding domains of SpL and 2 IgG Fc-binding SpG domains [1]. This hybrid molecule was found to bind... | ["Horseradish peroxidase (500 µg in 50 µl NaCO3 , pH 9.6) is mixed with freshly made sodium periodate solution (1.71 mg/ml) followed by incubation in the dark for 2 h.", "Mix 500 µg of staphylococcal protein-A (SpL) with an equal amount (500 micrograms) of a mix of horseradish peroxidase-sodium periodate. On the other ... |
63,623 | 2-step PCR mixture and conditions (Barcoded-head primers for seqs pooling) | 4 | null | https://www.protocols.io/view/2-step-pcr-mixture-and-conditions-barcoded-head-pr-cadfsa3n | Yin-Tse Huang | TITLE: 2-step PCR mixture and conditions (Barcoded-head primers for seqs pooling)
AUTHORS: Yin-Tse Huang
[DESCRIPTION]
PCR mixture and condition (2X SUPERGREEN PCR MASTER MIX)
[STEPS]
1. Wear glove, clean up the working bench w. 1% bleach
SECTION: For 1' PCR head-primers
2. Prepare 1' PCR master mixutre for hea... | ["Wear glove, clean up the working bench w. 1% bleach", "[For 1' PCR head-primers] Prepare 1' PCR master mixutre for head-primers (prepare 1.2X of solutions for pipetting error if needed)\n \nPCR mixture for head-primers for each reaction", "[For 1' PCR head-primers] Mix the 1' PCR master mixture gently by pi... |
84,651 | Microscopy-based bead assay | 4 | dx.doi.org/10.17504/protocols.io.14egn38pzl5d/v1 | https://www.protocols.io/view/microscopy-based-bead-assay-cwwjxfcn | Elias Adriaenssens | TITLE: Microscopy-based bead assay
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol describes the microscopy-based bead assay.
[STEPS]
SECTION: Microscopy-based bead assay
1. We use Glutathione Sepharose 4B beads (GE Healthcare) to bind GST-tagged bait proteins.
SECTION: Microscopy-based bead assay
2. To this ... | ["[Microscopy-based bead assay] We use Glutathione Sepharose 4B beads (GE Healthcare) to bind GST-tagged bait proteins.", "[Microscopy-based bead assay] To this end, wash 20 µL of beads twice with dH2O and equilibrate with bead assay\nbuffer.", "[Microscopy-based bead assay] Then, resuspend beads in 40 µL bead assay bu... |
95,560 | Sleep Data Analysis | 4 | null | https://www.protocols.io/view/sleep-data-analysis-c9jgz4jw | daniel.dautan, Per Svenningsson | TITLE: Sleep Data Analysis
AUTHORS: daniel.dautan, Per Svenningsson
[DESCRIPTION]
Sleep data analysis using Neuroscore V3.0 software.
[STEPS]
SECTION: Visual inspection and stage definitions
1. Import sleep data files into Neuroscore V3.0 software and visually inspect data.
Exclude data with interruptions, noise, or... | ["[Visual inspection and stage definitions] Import sleep data files into Neuroscore V3.0 software and visually inspect data.\n\nExclude data with interruptions, noise, or issues related to battery status from further analyses.\n\nUse the DSI-provided \"sleep scoring 2\" script for analysis, incorporating EEG, EMG, and ... |
59,233 | PBMC isolation | 4 | dx.doi.org/10.17504/protocols.io.b539q8r6 | https://www.protocols.io/view/pbmc-isolation-b539q8r6 | Michael Morgan | TITLE: PBMC isolation
AUTHORS: Michael Morgan
[DESCRIPTION]
Isolation of PBMCs from fresh whole human blood in Lithium Heparin blood tubes.
[STEPS]
SECTION: Lymphocyte separation
1. - Start with everything at room temperature:
SECTION: Lymphocyte separation
2. - Add 15 mL Ficoll-Paque Plus to each SepM... | ["[Lymphocyte separation] - Start with everything at room temperature:", "[Lymphocyte separation] - Add 15 mL Ficoll-Paque Plus to each SepMate tube by pipetting directly into centre of plastic separator (try not to introduce a lot of air beneath the separator)", "[Lymphocyte separation] - Pool anti-c... |
null | null | null | dx.doi.org/10.17504/protocols.io.cutwwm | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
The following is a list of antibody concentrations for use with the protocol 'Immunohistochemistry - Drosophila Embryo'<br />Custom antibodies were provided by the published authors.<br /><br />DSHB Antibodies<br /><table style='border-collapse: collapse; width: 853pt;' border='0... | [] |
53,701 | ADE 2022 Day 1: Background and Fieldwork | 3 | dx.doi.org/10.17504/protocols.io.bp2l6b67zgqe/v2 | https://www.protocols.io/view/ade-2022-day-1-background-and-fieldwork-bypdpvi6 | Tom Little | TITLE: ADE 2022 Day 1: Background and Fieldwork
AUTHORS: Tom Little
[DESCRIPTION]
ADE 2022 description of work to be done on Day 1 of the practical work
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.h5eb83e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes methods for a mouse xenograft study designed to measure in vivo BiTE® efficacy against antigen-expressing human tumor cells. In a modified version, the protocol is used to measure BiTE®-mediated bystander killing. Mixtures of human EGFR-positive (unlab... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.srred56 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol describes how to deliver ribonucleoprotein (RNP) complexes that consist of purified Cas9 nuclease duplexed with chemically modified synthetic single guide RNA (sgRNA) to induced pluripotent stem (iPS) cells derived from human fibroblasts. RNP delivery is accomplish... | ["[Pre-Nucleofection - Seed Cells] Culture iPS cells on Matrigel® Matrix-coated plates until they are semiconfluent.", "[Setup & Nucleofection - Prepare Destination Plate] Coat a new 6-well plate with Matrigel® Matrix and incubate according to the manufacturer’s instructions.", "[Setup & Nucleofection - Prepare Destina... |
70,931 | Luciferase Activity Assay for Neurospora crassa | 3 | dx.doi.org/10.17504/protocols.io.q26g7y883gwz/v1 | https://www.protocols.io/view/luciferase-activity-assay-for-neurospora-crassa-chhtt36n | kdcastillo | TITLE: Luciferase Activity Assay for Neurospora crassa
AUTHORS: kdcastillo
[DESCRIPTION]
Here, we describe an assay for screening for luciferase activity and performing a circadian luciferase rhythm assay in the filamentous fungus Neurospora crassa.
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.s5meg46 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This plasmid is designed to integrate within the small subunit ribosomal RNA gene region of <em>B. saltans</em>. It carries 1 kb of the <em>B. saltans</em> small subunit ribosomal RNA gene. To construct this cassette, we first sequenced the complete ribosomal operon of <em>B.... | [] |
52,747 | Plasmid construction | 4 | dx.doi.org/10.17504/protocols.io.bxrjpm4n | https://www.protocols.io/view/plasmid-construction-bxrjpm4n | Chunmei Chang | TITLE: Plasmid construction
AUTHORS: Chunmei Chang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">plasmid construction</div></div>
[STEPS]
?. Purify the DNA from gel using a Gel extraction kit (Bio Basic).
?. Linearize the backbone with restriction enzymes (NEB).
?. Amplify the insert gene fragme... | ["Purify the DNA from gel using a Gel extraction kit (Bio Basic).", "Linearize the backbone with restriction enzymes (NEB).", "Amplify the insert gene fragment by PCR with primers including 21 nt of overlapping sequence with the target gene.", "Run PCR products and linearized backbone in an agarose gel to confirm the ... |
91,038 | Preparation of ex-vivo brain slices for physiology experiments | 4 | dx.doi.org/10.17504/protocols.io.dm6gp328jvzp/v2 | https://www.protocols.io/view/preparation-of-ex-vivo-brain-slices-for-physiology-c456yy9e | enrico.zampese | TITLE: Preparation of ex-vivo brain slices for physiology experiments
AUTHORS: enrico.zampese
[DESCRIPTION]
This protocols describes the procedure to obtain ex-vivo mouse brain slices with a vibratome.
This protocol is originally meant to collect mibrain coronal slices or coronal/parasagittal striatal slices, but can ... | ["[Before the procedure:] A few hours/day before the procedure it is recommended to prepare some slicing solution and freeze it (~200ml).", "[Before the procedure:] Break the pre-frozen slicing solution into a large beaker and add freshly-made slicing solution. With the help of the immersion blender transform the froze... |
92,468 | Quantitative real-time PCR | 4 | dx.doi.org/10.17504/protocols.io.e6nvwd4o2lmk/v1 | https://www.protocols.io/view/quantitative-real-time-pcr-c6iuzcew | Tatiana Tkatch | TITLE: Quantitative real-time PCR
AUTHORS: Tatiana Tkatch
[DESCRIPTION]
Quantitative real-time PCR protocol used for Day et al.
[STEPS]
SECTION: gDNA digestion
1. -For each sample prepare 10ul gDNA digestion reaction mix according to SuperScript IV VILO Master Mix protocol (see pdf attached or substeps below).
SECT... | ["[gDNA digestion] -For each sample prepare 10ul gDNA digestion reaction mix according to SuperScript IV VILO Master Mix protocol (see pdf attached or substeps below).", "[gDNA digestion] Digest gDNA for 2 min min at 37 °C .", "[gDNA digestion] Place the tubes on ice.", "[gDNA digestion] Add SuperScript IV VILO Master ... |
null | null | null | dx.doi.org/10.17504/protocols.io.jwacpae | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
<p>Prepare primary stock solutions (in dH<sub>2</sub>O) of the following:</p>
<ul>
<li>NaNO<sub>3</sub>: 75.00 g/L</li>
<li>NaH<sub>2</sub>PO<sub>4</sub>·H<sub>2</sub>O: 5.00 g/L</li>
<li>Na<sub>2</sub>SiO<sub>3</sub>·9HO: 30.00 g/L (Note: this will only be used if phytoplankto... | [] |
88,174 | DNA barcoding on Oxford Nanopore: multiplexing up to 24 x 96-well plates | 4 | dx.doi.org/10.17504/protocols.io.rm7vzx6n4gx1/v1 | https://www.protocols.io/view/dna-barcoding-on-oxford-nanopore-multiplexing-up-t-c2cnyave | Robin Floyd, Sean Prosser, Saeideh Jafarpour | TITLE: DNA barcoding on Oxford Nanopore: multiplexing up to 24 x 96-well plates
AUTHORS: Robin Floyd, Sean Prosser, Saeideh Jafarpour
[DESCRIPTION]
This protocol describes laboratory methods for sequencing a standard COI marker (i.e. DNA barcoding), multiplexing up to 2,280 specimens (24 x 96 well plates, with one ne... | ["[1. Prepare Indexed PCR Plates] To prepare the partial mastermix (no primers), combine the following components in a sterile bottle of at least 250 mL volume: \n \n\nThis volume is calculated to make a slight excess of partial PCR mix, more than sufficient for 8 reactions x 96 wells x 24 plates.", "[1. Prepare Indexe... |
81,094 | The derived positive meaning of physical activity for people with a diabetic foot ulcer; a scoping review protocol | 1 | dx.doi.org/10.17504/protocols.io.x54v9dx4qg3e/v1 | https://www.protocols.click/view/the-derived-positive-meaning-of-physical-activity-ctfewjje | Birgit Rasmussen, Lisbeth Uhrenfeldt | TITLE: The derived positive meaning of physical activity for people with a diabetic foot ulcer; a scoping review protocol
AUTHORS: Birgit Rasmussen, Lisbeth Uhrenfeldt
[DESCRIPTION]
Objectives This scoping review aims to explore the derived positive meaning of physical activity in persons with diabetes who have been i... | ["[General Information] The derived positive meaning of physical activity for people with a diabetic foot ulcer; a scoping review protocol", "[General Information] Authors: Rasmussen B, Uhrenfeldt L", "[Background] For a person with diabetes mellitus the treatment of a diabetic foot ulcer entails off-loading treatment ... |
40,902 | ELISA for measurement of serum macrophage migration inhibitory factor (MIF). | 6 | dx.doi.org/10.17504/protocols.io.bj7ekrje | https://www.protocols.io/view/elisa-for-measurement-of-serum-macrophage-migrati-bj7ekrje | Angel Justiz-Vaillant, Belkis Ferrer-Cosme | TITLE: ELISA for measurement of serum macrophage migration inhibitory factor (MIF).
AUTHORS: Angel Justiz-Vaillant, Belkis Ferrer-Cosme
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. An anti-human MIF coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate... | ["An anti-human MIF 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 MIF present in the serum or plasma binds to antibodies adsorbed into the microwells.", "The microplate is blocked with 3% non-fat milk-PBS b... |
null | null | null | dx.doi.org/10.17504/protocols.io.fp3bmqn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a collection of Non-Interfering™ (NI) Protein Assay protocols from G-Biosciences.</p>
[STEPS]
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.prrdm56 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>A-2. <u>ISCO Sampling Protocol</u></strong></p>
<p>River and estuary samples will be collected using an automated ISCO sampler using the following protocol:</p>
<p> </p>
<ul>
<li>Sampler Description:</li>
</ul>
<ul>
<li>A Teledyne ISCO 3700 full size portable sequenti... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.gzsbx6e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol to prep plasmid DNA from yeast cells. Preps both plasmid and genomic DNA. Protocol for prepping an entire plate; for selection of correctly assembled plasmids, the prepped DNA is transformed into <em>E. coli</em>, and transformation can be followed by colony PCR to s... | [] |
28,895 | Qualitative paper ELONA test | null | dx.doi.org/10.17504/protocols.io.8f7htrn | null | Manuela de las Casas | TITLE: Qualitative paper ELONA test
AUTHORS: Manuela de las Casas
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The aim of this protocol is to test the best method that identifies the efficiency of the detection system that will be present in the strips. 3 methods are tested and compared.</div><di... | ["[Preparing the nitrocellulose strip]\nSet the hot plate to 100ºC or at least warm enough to melt the wax. Cut a small amount from one of the wax pencils and place it on a Petri dish. Set the Petri dish on the hot plate and wait for the wax to melt. Cut a strip from the nitrocellulose sheet with the desired size.Once... |
null | null | null | dx.doi.org/10.17504/protocols.io.qyndxve | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>e</p>
<p>qe</p>
<p> </p>
<p>wqeewq</p>
<p> </p>
<p>we</p>
<p>wq</p>
<p> </p>
<p> </p>
<p>e</p>
<p>wq</p>
<p>ew</p>
<p> </p>
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<p>wq</p>
<p>e</p>
<p>wqe</p>
<p>wqe</p>
<p>q</p>
<p>ewqe</p>
<p>wqe</p>
[BEFORE_START]
<p>qwd</p>
<p>qd... | [] |
46,887 | Mass Spectrometry analysis and Molecular MS/MS network | 4 | dx.doi.org/10.17504/protocols.io.br2fm8bn | https://www.protocols.io/view/mass-spectrometry-analysis-and-molecular-ms-ms-net-br2fm8bn | Rene Flores Clavo, Cristian Daniel Asmat Ortega, Nataly Ruiz Quinones | TITLE: Mass Spectrometry analysis and Molecular MS/MS network
AUTHORS: Rene Flores Clavo, Cristian Daniel Asmat Ortega, Nataly Ruiz Quinones
[STEPS]
?. [UHPLC ]
Resuspend the dry extract in 1 mL of methanol (HPLC grade) and dilute 100 µL in 900 µL of methanol (HPLC grade).
?. [UHPLC ]
Filter the final solution using a... | ["[UHPLC ]\nResuspend the dry extract in 1 mL of methanol (HPLC grade) and dilute 100 µL in 900 µL of methanol (HPLC grade).", "[UHPLC ]\nFilter the final solution using a syringe-filter into vials", "[UHPLC ]\nPerform Ultra-high pressure liquid chromatography-mass spectrometry (UHPLC-MS) analyses in a Thermo Scientifi... |
58,620 | Phytophthora pluvialis culture cultivation, maintenance, and detached needle assay protocol | 4 | dx.doi.org/10.17504/protocols.io.kqdg3p9d7l25/v1 | https://www.protocols.io/view/phytophthora-pluvialis-culture-cultivation-mainten-b5g4q3yw | Sophie Eccersall, Leann Seesom Vinson, Rebecca McDougal, Claudia-Nicole Meisrimler | TITLE: Phytophthora pluvialis culture cultivation, maintenance, and detached needle assay protocol
AUTHORS: Sophie Eccersall, Leann Seesom Vinson, Rebecca McDougal, Claudia-Nicole Meisrimler
[DESCRIPTION]
Phytophthora pluvialis is an oomycete that primarily infects Pinus radiata and Pseudotsuga menziesii causing the d... | ["[A. Growth of P. pluvialis from existing culture plates] Grow P. pluvialis isolate on 20% cV8 agar (modified from Jeffers, 2006) at ~18 ˚C.", "[A. Growth of P. pluvialis from existing culture plates] Seal plates with parafilm, and store upside down in an incubator at 17-21 ˚C in the dark. For zoospore production, all... |
79,363 | Aqueous (SBiP) Delipidation of a Whole Mouse Brain | 1 | dx.doi.org/10.17504/protocols.io.n2bvj81mwgk5/v1 | https://www.protocols.click/view/aqueous-sbip-delipidation-of-a-whole-mouse-brain-crrbv52n | Andrew Recknagel, Kevin Cao, Naveen Ouellette, Molly Logsdon, Judith Baka, Jayaram Chandrashekar | TITLE: Aqueous (SBiP) Delipidation of a Whole Mouse Brain
AUTHORS: Andrew Recknagel, Kevin Cao, Naveen Ouellette, Molly Logsdon, Judith Baka, Jayaram Chandrashekar
[DESCRIPTION]
Aqueous strategies for whole-brain delipidation involve lipid removal via phase separation and detergent washes. SBiP is an aqueous biphasic ... | ["[SBiP Delipidation] Use a 20 mL vial for processing an adult mouse brain. All steps in this section are carried out on a carousel rotator . \nReplace solution in vial with 20 mL SBiP for each of the following steps:\nSBiP for 180 min \nSBiP for 360 min \nSBiP \nSBiP for 1440 min \nSBiP for 1440 min\nSBiP for 1440 ... |
106,989 | Optimized Stereotactic Injection Protocol for Targeting the Locus Coeruleus with Minimal Neurotoxicity | 0 | dx.doi.org/10.17504/protocols.io.3byl4988ogo5/v1 | https://www.protocols.io/view/optimized-stereotactic-injection-protocol-for-targ-dkqm4vu6 | Csilla Novák, Rukhshona Kayomova, Matthias Prigge | TITLE: Optimized Stereotactic Injection Protocol for Targeting the Locus Coeruleus with Minimal Neurotoxicity
AUTHORS: Csilla Novák, Rukhshona Kayomova, Matthias Prigge
[DESCRIPTION]
The Locus Coeruleus is a critical brain region known for its vulnerability to mechanical perturbations, neuroinflammation, and axonal di... | ["[Animal Preparation] Weigh the mouse to calculate the precise dosage of anesthetic required. Administer ketamine at a dosage of 10 mg/kg and xylazine at a dosage of 20 mg/kg. Alternatively, use isoflurane as approved by your institutional animal care and use protocols. Ensure adherence to all relevant guidelines and ... |
38,703 | Isolation, Culture, and Maintenance of Patient-Derived Tumor Biopsy | 4 | null | https://www.protocols.io/view/isolation-culture-and-maintenance-of-patient-deriv-bh2pj8dn | Xiling Shen, Marcos Negrete, Kun Xiang | TITLE: Isolation, Culture, and Maintenance of Patient-Derived Tumor Biopsy
AUTHORS: Xiling Shen, Marcos Negrete, Kun Xiang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is split into 3 sections: collecting tumor cells, passaging, and cryopreserving organoids. </div><div class = "text... | ["[Disassociation of Tumor Cells]\nStore tissue samples in cold transport media (). Keep samples on ice at all time and process within\n10 mL", "[Disassociation of Tumor Cells]\nTransfer the tumor biopsy sample (1-2 cm3) and transport media into a petri dish and remove remnant non-tumor tissue with sterile tweezers.\nT... |
69,880 | Immunochemistry on paraffin sections | 4 | dx.doi.org/10.17504/protocols.io.kxygx9my4g8j/v1 | https://www.protocols.io/view/immunochemistry-on-paraffin-sections-cggyttxw | miquel.vila | TITLE: Immunochemistry on paraffin sections
AUTHORS: miquel.vila
[DESCRIPTION]
Immunochemistry protocol on paraffin-embedded rat brain sections
[STEPS]
SECTION: 1. Deparaffinization and hydratation :
1. Put the slides 30 min in the incubator at 60ºC.
SECTION: 1. Deparaffinization and hydratation :
2. Wash 3x3 min in... | ["[1. Deparaffinization and hydratation :] Put the slides 30 min in the incubator at 60ºC.", "[1. Deparaffinization and hydratation :] Wash 3x3 min in Xilen.", "[1. Deparaffinization and hydratation :] Wash 1x10 min in ethanol 100%.", "[1. Deparaffinization and hydratation :] Wash 1x10 min in ethanol 95%.", "[1. Depara... |
81,822 | NCEM Drop - Paramyxo confirmation, generation of RNP (TM-014) | 4 | dx.doi.org/10.17504/protocols.io.x54v9dq8pg3e/v1 | https://www.protocols.io/view/ncem-drop-paramyxo-confirmation-generation-of-rnp-ct56wq9e | sandra.crameri | TITLE: NCEM Drop - Paramyxo confirmation, generation of RNP (TM-014)
AUTHORS: sandra.crameri
[DESCRIPTION]
Generate RNP to confirm Paramyxoviurs
[STEPS]
SECTION: HEADER
1. SAN:
SPEC No:
OPERATOR:
SECTION: Conventional
4. Adsorb 10 µL sample to grid 10 min , inspect to ensure sample does not dry out.
SECTI... | ["[HEADER] SAN:\n\n\n\n\nSPEC No:\n\n\n\n\nOPERATOR:", "[Conventional] Adsorb 10 µL sample to grid 10 min , inspect to ensure sample does not dry out.", "[Conventional] Drain excess sample from grid using filter paper, leave wet.", "[Conventional] Stain 1 min", "Drain & dry using filter paper", "[Generation of RNP] Pr... |
63,838 | To test fork notification | 1 | dx.doi.org/10.17504/protocols.io.n92ldzjxxv5b/v2 | https://www.protocols.io/view/to-test-fork-notification-caj6scre | Gabriel Gasque | TITLE: To test fork notification
AUTHORS: Gabriel Gasque
[DESCRIPTION]
Test for Fork notifications
[STEPS]
1. Step 1
2. Step 2
3. Step 3
4. Step 4 | ["Step 1", "Step 2", "Step 3", "Step 4"] |
101,746 | The Impact of World Pandemics on Health Services Management: The Covid 19 Experience in Nigeria and Australia | 0 | dx.doi.org/10.17504/protocols.io.x54v92ro1l3e/v1 | https://www.protocols.io/view/the-impact-of-world-pandemics-on-health-services-m-dfks3kwe | Charles C Okonkwo, Rasheda Khanam, Gavin Beccaria, Ezekiel Uba Nwose | TITLE: The Impact of World Pandemics on Health Services Management: The Covid 19 Experience in Nigeria and Australia
AUTHORS: Charles C Okonkwo, Rasheda Khanam, Gavin Beccaria, Ezekiel Uba Nwose
[DESCRIPTION]
This research aims to evaluate the impact of COVID-19 pandemic on health services management using the COVID-1... | ["[Abstract] This research aims to evaluate the impact of COVID-19 pandemic on health services management using the COVID-19 experiences as the major means of measure. Secondary data would be used to compare the Low and Medium-Income Countries (LMIC) and the High-Income Countries (HIC), focusing on health systems in Ni... |
33,631 | Protocols for the draft genome assembly of the eastern banjo frog Limnodynastes dumerilii dumerilii | 2 | dx.doi.org/10.17504/protocols.io.bc37iyrn | https://www.protocols.io/view/protocols-for-the-draft-genome-assembly-of-the-eas-bc37iyrn | Qiye Li, Qunfei Guo, Yang Zhou, Huishuang Tan, Terry Bertozzi, Yuanzhen Zhu, Ji Li, Stephen Donnellan, Guojie Zhang | TITLE: Protocols for the draft genome assembly of the eastern banjo frog Limnodynastes dumerilii dumerilii
AUTHORS: Qiye Li, Qunfei Guo, Yang Zhou, Huishuang Tan, Terry Bertozzi, Yuanzhen Zhu, Ji Li, Stephen Donnellan, Guojie Zhang
[DESCRIPTION]
Background: Amphibian genomes are usually challenging to assemble due to ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ud9es96 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol is aimed at amplifying the 18S rRNA hypervariable region 9 (18S V9) in eukaryotes with a focus on microbial eukaryotes. Amplicons generated using this protocol can then be sequenced using the Illumina platform. The primers (1391F, EukBr) utilized in this protocol a... | ["[PCR] {\"blocks\":[{\"key\":\"9pc18\",\"text\":\"PCR reactions were run in triplicate 25-\\u03bcl reactions for each sample using 12-basepair Golay barcoded reverse primers (Amaral-Zettler et al., 2009).\\u00a0\\n\\nAmaral-Zettler LA, McCliment EA, Ducklow HW, Huse SM (2009) A Method for Studying Protistan Diversity ... |
36,569 | Perinatal 2016 Rio Grande - Urinary Incontinence | 3 | dx.doi.org/10.17504/protocols.io.bfxzjpp6 | https://www.protocols.io/view/perinatal-2016-rio-grande-urinary-incontinence-bfxzjpp6 | Yuan Hsu, Juraci A Cesar | TITLE: Perinatal 2016 Rio Grande - Urinary Incontinence
AUTHORS: Yuan Hsu, Juraci A Cesar
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.pmvdk66 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
85,115 | “Skeeter Pheeder”: inexpensive 3D printed, battery-powered blood feeder for mosquitoes and other haematophagous arthropods | 1 | null | https://www.protocols.click/view/skeeter-pheeder-inexpensive-3d-printed-battery-po-cxc3xiyn | Philip K Stoddard | TITLE: “Skeeter Pheeder”: inexpensive 3D printed, battery-powered blood feeder for mosquitoes and other haematophagous arthropods
AUTHORS: Philip K Stoddard
[DESCRIPTION]
A portable heated feeder for blood-feeding arthropods, the Skeeter Pheeder, has been designed to be constructed in the laboratory using conventional... | ["[Materials Needed] See Materials section \nA table is include with details, approximate costs, and possible suppliers.\n\nNote: One can purchase blunt #20 hypodermic needles at a premium price or make them by grinding the tips off sharp hypodermic needles (I used a Dremel hand grinder). The needle shaft should be ab... |
86,610 | U54 SCENT Pediatric Colonoscopy Tissue Collection Procedure | 1 | dx.doi.org/10.17504/protocols.io.yxmvm3oznl3p/v2 | https://www.protocols.io/view/u54-scent-pediatric-colonoscopy-tissue-collection-cytsxwne | Mary Jordan* | TITLE: U54 SCENT Pediatric Colonoscopy Tissue Collection Procedure
AUTHORS: Mary Jordan*
[DESCRIPTION]
This document outlines the required criteria and acquisition for pediatric colonoscopy colon specimens collected at Duke University Hospital through the Biorepository and Precision Pathology Center (BRPC) in the Depa... | ["[Inclusion and Exclusion Criteria] Inclusion Criteria:\n • Healthy patients age 5-18 years of age presenting for outpatient colonoscopy. \n • Screening may wish to focus on the following indications: abdominal pain, constipation, diarrhea, \n bloating/gas, patients with normal labs and/or imaging.... |
null | null | null | dx.doi.org/10.17504/protocols.io.imucc6w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>March, 2012; based on sample preparation guide v2, catalog # RS-930-1021, part # 15026495 Rev. A, August 2011</p>
<p> </p>
<p>Modifications: samples in PCR tubes (because a plate/seal will not be used, some numbered steps are skipped); include two rounds of poly-A selection (... | [] |
58,840 | Nested VP1 PCR and Nanopore Sequencing from Stool and ES Samples v1.11 | 1 | dx.doi.org/10.17504/protocols.io.b5pyq5pw | https://www.protocols.io/view/nested-vp1-pcr-and-nanopore-sequencing-from-stool-b5pyq5pw | Alex Shaw, Manasi Majumdar, Catherine Troman, Joyce Akello, Javier Martin, Nick Grassly | TITLE: Nested VP1 PCR and Nanopore Sequencing from Stool and ES Samples v1.11
AUTHORS: Alex Shaw, Manasi Majumdar, Catherine Troman, Joyce Akello, Javier Martin, Nick Grassly
[DESCRIPTION]
This protocol is updated from the protocol described in the paper "Rapid and sensitive direct detection and identification o... | ["[Nested PCR First Round (PanEV)] Nested PCR First Round (panEV primers):\nPrepare a Master mix using reaction volumes as detailed below, excluding forward primer and the RNA:\n\nForward Primer (5'NTR): [TGGCGGAACCGACTACTTTGGGTG] (Arita et al. 2015)\nReverse Primer (Cre): [TCAATACGGTGTTTGCTCTTGAACTG] (Arita et al.... |
64,025 | Pooling | 4 | null | https://www.protocols.io/view/pooling-carzsd76 | Allyson Hirsch, George Testo | TITLE: Pooling
AUTHORS: Allyson Hirsch, George Testo
[DESCRIPTION]
The throughput of modern sequencers grows higher and higher, allowing hundreds of millions of reads in a single microfluidic chamber. For many purposes this is actually far more than a single library requires. To keep sequencing cost-effective, resear... | ["[Preparations] DNA Away and Ethanol the workstation.", "[Preparations] Remove PCR plate(s) from the-20 °C freezer and thaw plates to be pooled while finishing workstation prep.", "[Preparations] Print plate table with volume of each amplicon to be pooled together (equal molar).", "[Preparations] Spin thawed plates do... |
55,691 | High Throughput SARS-COV-2, PMMOV, and BCoV quantification in settled solids using digital RT-PCR | 1 | dx.doi.org/10.17504/protocols.io.b2mjqc4n | https://www.protocols.io/view/high-throughput-sars-cov-2-pmmov-and-bcov-quantifi-b2mjqc4n | Aaron Topol (Verily Life Sciences), marlene.wolfe , Brad White (Verily Life Sciences), Krista Wigginton, Alexandria B B Boehm | TITLE: High Throughput SARS-COV-2, PMMOV, and BCoV quantification in settled solids using digital RT-PCR
AUTHORS: Aaron Topol (Verily Life Sciences), marlene.wolfe , Brad White (Verily Life Sciences), Krista Wigginton, Alexandria B B Boehm
[DESCRIPTION]
This process instruction describes the steps for quantitative a... | ["[Preparation (both assays)] Retrieve all kit components from the One-Step RT-ddPCR advanced kit for probes from the -20 °C freezer and thaw the components on ice.", "[Preparation (both assays)] Retrieve ddPCR positive control aliquots (50 copies per uL gRNA and 100 copies per µL BCoV and PMMoV gene blocks) from the -... |
105,358 | Fixation and Immunostaining | 0 | dx.doi.org/10.17504/protocols.io.rm7vzj2d2lx1/v2 | https://www.protocols.io/view/fixation-and-immunostaining-di5n4g5e | Gist Croft, Marta Skowronska | TITLE: Fixation and Immunostaining
AUTHORS: Gist Croft, Marta Skowronska
[DESCRIPTION]
This protocol is based on standard methods for formaldehyde fixation and immunostaining for fluorescence microscopy. However, it contains tested working reagents, advice, and tips.
[GUIDELINES]
Read all reagent SDS and follow all s... | ["[BUFFER PREPARATION] 2 x Fixation Buffer (8% Paraformaldehyde in 2x PBS): Use a 32% paraformaldehyde (PFA) in sealed EMS ampule + 30 mL PBS (+/+), pH 7.4 + 8 mL 10x PBS + 22 mL ddH2O\nOBS: You can use either PBS (+/+) (with Ca+2 and Mg+2) or (-/-). Some might prefer HBSS instead.", "[BUFFER PREPARATION] 1 x Fixation ... |
99,670 | Podocoryna ACME cell dissociations - draft v1.0, May 13 2024 | 0 | null | https://www.protocols.io/view/podocoryna-acme-cell-dissociations-draft-v1-0-may-ddjw24pe | Michael Connelly | TITLE: Podocoryna ACME cell dissociations - draft v1.0, May 13 2024
AUTHORS: Michael Connelly
[DESCRIPTION]
This protocol is intended to dissociate and fix cells of the hydrozoan Podocoryna carnea for single-cell RNA sequencing on the 10X Chromium platform following a FACS sorting step. ACME-fixed Podocoryna cells mai... | ["[Polyp ACME dissociation] Prepare for polyp dissection by placing a microscope slide with a Podocoryna colony in a glass dish with ~200 mL 0.2 um filtered seawater. Add menthol crystals at a concentration of ~1 g/L to relax the polyps for ~10 minutes.", "[Medusa ACME dissociation] Collect as many medusae as possible ... |
86,829 | High-Throughput Generation of Single Cell Libraries using SmartSeq2 Plate Assay | 1 | dx.doi.org/10.17504/protocols.io.8epv5xx54g1b/v1 | https://www.protocols.io/view/high-throughput-generation-of-single-cell-librarie-cy2mxyc6 | Michael Borja, Tabula Muris Consortium, Shayan Hosseinzadeh | TITLE: High-Throughput Generation of Single Cell Libraries using SmartSeq2 Plate Assay
AUTHORS: Michael Borja, Tabula Muris Consortium, Shayan Hosseinzadeh
[DESCRIPTION]
As part of the larger efforts of Quantitative Cell Science at the Chan Zuckerberg Biohub, single cell plate-based protocols such as the SmartSeq 2 as... | ["[Lysis Plate Preparation] Lysis plates were created by dispensing 0.4 μl lysis buffer master mix into 384-well hard-shell PCR plates (Bio- Rad HSP3901) using the SPT LabTech DragonFly. 96-well lysis plates were also prepared with 4 μl lysis buffer. All plates were sealed with Microseal Seal F foil seal and spun down ... |
81,996 | Protocol of Spotted Fever Rickettsia IgG | 4 | dx.doi.org/10.17504/protocols.io.bp2l69jdrlqe/v1 | https://www.protocols.io/view/protocol-of-spotted-fever-rickettsia-igg-cubkwskw | narankhajid | TITLE: Protocol of Spotted Fever Rickettsia IgG
AUTHORS: narankhajid
[DESCRIPTION]
All serum samples were tested for Rickettsia IgG using a commercial ELISA kit (NovaTec Immunodiagnostica GmbH, Dietzenbach, Germany) according to the manufacturer’s instructions(S9).
[STEPS]
SECTION: Protocol of Spotted Fever Rickettsi... | ["[Protocol of Spotted Fever Rickettsia IgG]", "[Protocol of Spotted Fever Rickettsia IgG] Dispense 100µl controls and diluted samples into their respective wells. Leave well A1 for substrate blank.", "[Protocol of Spotted Fever Rickettsia IgG] Cover wells with the foil supplied in the kit.", "[Protocol of Spotted Feve... |
39,565 | OptoPlate Calibration protocol | 1 | dx.doi.org/10.17504/protocols.io.bivmke46 | https://www.protocols.io/view/optoplate-calibration-protocol-bivmke46 | Edvard Grødem, Kieran Sweeney, Megan N. McClean | TITLE: OptoPlate Calibration protocol
AUTHORS: Edvard Grødem, Kieran Sweeney, Megan N. McClean
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Optogenetic systems use light to precisely control and investigate cellular processes. Until recently, there had been few instruments available for applying ... | ["[Configuring the optoPlate hardware]\nSection overviewWe assemble the optoPlate as published by Bugaj and Lim, but with two changes to suit the needs of our lab and allow calibration. First, we adapt the optoPlate to accommodate our 96 well optical-bottom plates (Nunc, #265300) via 3D printed adaptors, which can be f... |
71,406 | Human Liver Tissue Storage Methods For Multiomic Applications | 4 | dx.doi.org/10.17504/protocols.io.261ge34qdl47/v1 | https://www.protocols.io/view/human-liver-tissue-storage-methods-for-multiomic-a-chynt7ve | Diana Nakib, Catia Perciani, Sai Chung, Xue-Zhong Ma, Justin Manuel, Ian McGilvray, Sonya Macparland | TITLE: Human Liver Tissue Storage Methods For Multiomic Applications
AUTHORS: Diana Nakib, Catia Perciani, Sai Chung, Xue-Zhong Ma, Justin Manuel, Ian McGilvray, Sonya Macparland
[DESCRIPTION]
Sampling different areas of the diseased or healthy liver and storing the tissue in a variety of mediums to allow for an in-de... | ["[Sample Collection] Collect explanted tissue section in 30mL of HBSS 1x with Ca2+ and Mg2+ in a 50mL conical tube and keep on ice, ideally to process within 30 minutes of removal from patient or removal from the flushed donor organ in preservation solution.", "[Optimal Cutting Temperature (OCT)-Embedding Tissue Secti... |
68,850 | Modified Arabidopsis Root smRNA FISH Protocol | 4 | dx.doi.org/10.17504/protocols.io.rm7vzyworlx1/v1 | https://www.protocols.io/view/modified-arabidopsis-root-smrna-fish-protocol-cfgstjwe | Susan Duncan, Hans Johansson | TITLE: Modified Arabidopsis Root smRNA FISH Protocol
AUTHORS: Susan Duncan, Hans Johansson
[DESCRIPTION]
Single molecule RNA FISH (smRNA FISH) is an imaging method that labels individual mRNA molecules in cells to facilitate localization and quantitative studies. Here we present a modified protocol for mRNA labelling ... | ["[Plant Growth] Sterilize then sow a row of Col-0 Arabidopsis seeds onto half strength Murashige and Skoog Medium (1/2 MS) near the top of a 10 cm square petri plate.", "[Plant Growth] Stratify the seeds at 4 °Cfor two days.", "[Plant Growth] Take the plate out of the cold and place it vertically in a growth cabinet s... |
34,783 | 3D Printing Of Personal Protective Equipment And Repurposing Of Common Household Air Filters | null | dx.doi.org/10.17504/protocols.io.bd77i9rn | null | Giana Schena, Emma Murray | TITLE: 3D Printing Of Personal Protective Equipment And Repurposing Of Common Household Air Filters
AUTHORS: Giana Schena, Emma Murray
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>During the height of the COVID-19 outbreak, personal protective </span><a href="Https://time.com/5785223/medic... | ["[Two Piece Face Mask Printing and Assembly]\nOpen the facemask_filter_guard.stl file (currently on scale with the face unit, would also need to be scaled up). a. Support is not necessary b. Guard is in shape of a trapezoid: the face of the guard is 2.5 inches tall with 2.75 inch base length and 1.6 ... |
64,178 | Wedge sampling of pars petrosa (os temporale) for ancient DNA extraction | 1 | dx.doi.org/10.17504/protocols.io.261gen8wog47/v1 | https://www.protocols.io/view/wedge-sampling-of-pars-petrosa-os-temporale-for-an-cawssfee | Raphaela Stahl, Lena Semerau, Eleftheria Orfanou, Marie Himmel, Franziska Aron, Wolfgang Haak | TITLE: Wedge sampling of pars petrosa (os temporale) for ancient DNA extraction
AUTHORS: Raphaela Stahl, Lena Semerau, Eleftheria Orfanou, Marie Himmel, Franziska Aron, Wolfgang Haak
[DESCRIPTION]
This protocol describes how to obtain bone powder from the pars petrosa of disarticulated ossis temporalis, specifically f... | ["[Workstation preparation] Place a sheet of aluminium foil under the hood.\n\nPlace weighing paper, drill bits, and a pair of tooth pliers or forceps on a second sheet of aluminium foil on an easily accessible clean surface outside of the hood. Alternatively, you may place them within the hood but be sure to cover the... |
69,549 | Integration of malaria and schistosomiasis prevention and control programs: protocol for scoping review | 1 | dx.doi.org/10.17504/protocols.io.j8nlkwb1xl5r/v1 | https://www.protocols.io/view/integration-of-malaria-and-schistosomiasis-prevent-cf6mtrc6 | Claudia Duguay, Sydney Raduy, Natacha Protopopoff, Cindy Feng, Alison Krentel, Manisha Kulkarni | TITLE: Integration of malaria and schistosomiasis prevention and control programs: protocol for scoping review
AUTHORS: Claudia Duguay, Sydney Raduy, Natacha Protopopoff, Cindy Feng, Alison Krentel, Manisha Kulkarni
[DESCRIPTION]
Context: It is imperative to build resilient, and sustainable programs to maintain effo... | ["[Title and author identification] Integration of malaria and schistosomiasis prevention and control programs: protocol for scoping review\n\nClaudia Duguay1, Sydney Raduy1, Natacha Protopopoff2, Cindy Feng3, Alison Krentel1,4, Manisha A. Kulkarni1\n\n1 School of Epidemiology and Public Health, University of Ottawa, O... |
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