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 |
|---|---|---|---|---|---|---|---|
24,819 | Recovering Plasmid DNA from Bacterial Culture | null | dx.doi.org/10.17504/protocols.io.4gtgtwn | null | Addgene The Nonprofit Plasmid Repository | TITLE: Recovering Plasmid DNA from Bacterial Culture
AUTHORS: Addgene The Nonprofit Plasmid Repository
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is for recovering plasmid DNA from Bacterial Culture. To see the full abstract and other resources, visit </span><a href="https:/... | ["[Generalized DNA Purification]\nGrow an overnight culture of bacteria.\n*Pro-Tip*Refer to appropriate DNA prep protocol for volume of bacteria to grow (low copy plasmids require larger cultures).", "[Generalized DNA Purification]\nCentrifuge the culture to pellet the bacteria before proceeding with DNA preparation.\n... |
104,649 | USDA LTAR Common Experiment measurement: Irrigation water applied | 0 | dx.doi.org/10.17504/protocols.io.j8nlk86ydl5r/v1 | https://www.protocols.io/view/usda-ltar-common-experiment-measurement-irrigation-difh4bj6 | Rachel DuBose, Andrew M. O'Reilly, Lindsey Witthaus, Claire Baffaut | TITLE: USDA LTAR Common Experiment measurement: Irrigation water applied
AUTHORS: Rachel DuBose, Andrew M. O'Reilly, Lindsey Witthaus, Claire Baffaut
[DESCRIPTION]
Irrigation is the amount of water applied to a field or plot per unit area. Irrigation supplements rainfall to provide adequate soil moisture for successfu... | ["[Data collection - Equipment] A flowmeter with a totalizer that displays the cumulative flow volume is recommended. The totalizer tracks the cumulative volume of irrigation water and the duration of its application.", "[Data collection - Equipment] Flowmeters are available from various manufacturers (e.g., McCrometer... |
62,879 | Weight Crasher Keto Gummies Review Is It Worth For Buying? | 1 | dx.doi.org/10.17504/protocols.io.q26g74w8qgwz/v1 | https://www.protocols.io/view/weight-crasher-keto-gummies-review-is-it-worth-for-b9m7r49n | Acv keto Gummies | TITLE: Weight Crasher Keto Gummies Review Is It Worth For Buying?
AUTHORS: Acv keto Gummies
[DESCRIPTION]
Weight Crasher Keto Gummies Review Is It Worth For Buying?
[STEPS]
SECTION: weighasherketoreview@outlook.com
1. | ["[weighasherketoreview@outlook.com]"] |
38,705 | Capture and concentration of SARS-CoV-2 and other respiratory viruses from VTM / UTM samples using Magnetic Nanotrap® particles for direct RNA extraction | 1 | null | https://www.protocols.io/view/capture-and-concentration-of-sars-cov-2-and-other-bh2rj8d6 | Ben Lepene, Anurag Patnaik, Robert Barclay | TITLE: Capture and concentration of SARS-CoV-2 and other respiratory viruses from VTM / UTM samples using Magnetic Nanotrap® particles for direct RNA extraction
AUTHORS: Ben Lepene, Anurag Patnaik, Robert Barclay
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol provides a method for Mag... | ["[Virus Capture and RNA Extraction]\nAdd to the sample.\n[of Magnetic Nanotrap® particles]", "[Virus Capture and RNA Extraction]\nIncubate samples with Magnetic Nanotrap® particles at for .\n0 Room temperature", "[Virus Capture and RNA Extraction]\nResuspend particle pellet in .\n[of extraction buffer]", "[Virus Cap... |
null | null | null | dx.doi.org/10.17504/protocols.io.tp8emrw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
International and national studies on dating violence have concluded about the higher involvement of adolescents and youths in comparison to adult couples. At the same time, prevention programs have resulted more successful in adolescent population than in older ages, yielding p... | [] |
38,358 | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time RT-PCR N gene 2020 | 1 | dx.doi.org/10.17504/protocols.io.bhpwj5pe | https://www.protocols.io/view/severe-acute-respiratory-syndrome-coronavirus-2-sa-bhpwj5pe | Judy Northill, Ian Mackay | TITLE: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time RT-PCR N gene 2020
AUTHORS: Judy Northill, Ian Mackay
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><ul style = "list-style-type:disc;"><li style = "counter-reset:ol0;list-style-type:disc;">A real-time RT-PCR to designe... | ["[Mix]\nOligonucleotides ABC1Oligo NameSequence 5'-3'Location based on NC_045512.2*2Wuhan-TM2020ForTCGTGCTACAACTTCCTCAAG28743-287633Wuhan-TM2020Probe6FAM-CCGCCTCTGCTCCCTTCTGC-BHQ128809-287904SARS2-28875R-GCTGCCTGGAGTTGAATTTCTTG28875-288545SARS2-28875R-A CTGCCTGGAGTTGAATTTCTTA 28875-28854\nABC1Oligo NameSequence 5'-3'... |
58,947 | Overall protocol for top-down LC-MS/MS of human small intestine tissue | 1 | dx.doi.org/10.17504/protocols.io.b5tbq6in | https://www.protocols.io/view/overall-protocol-for-top-down-lc-ms-ms-of-human-sm-b5tbq6in | Jeannie Camarillo, Bryon Drown, Neil Kelleher | TITLE: Overall protocol for top-down LC-MS/MS of human small intestine tissue
AUTHORS: Jeannie Camarillo, Bryon Drown, Neil Kelleher
[DESCRIPTION]
Overview description of the process for acquiring top-down LC-MS/MS data on human small intestine tissue
[STEPS]
SECTION: Tissue Collection
1. Small intestine tissue wa... | ["[Tissue Collection] Small intestine tissue was provided by Stanford University TMC. Tissue was collected according to the following: \n\nhttps://dx.doi.org/10.17504/protocols.io.bin8kdhw", "[Sample Preparation] Perform LC based Proteomics on adjacent tissue sections:", "[Data Acquisition]", "[Sample Preparation]"] |
46,610 | CAN-ASC CONSENSUS PROTOCOL: Isolation, Cryopreservation and Thawing of Peripheral Blood Mononuclear Cells | 1 | dx.doi.org/10.17504/protocols.io.brrsm56e | https://www.protocols.io/view/can-asc-consensus-protocol-isolation-cryopreservat-brrsm56e | CAN-ASC Canadian Autoimmunity Standardization Core | TITLE: CAN-ASC CONSENSUS PROTOCOL: Isolation, Cryopreservation and Thawing of Peripheral Blood Mononuclear Cells
AUTHORS: CAN-ASC Canadian Autoimmunity Standardization Core
[STEPS]
?. [Isolation and Cryopreservation of PBMCs]
Draw blood using an appropriate anti-coagulant and ensure it is filled to the top and immedi... | ["[Isolation and Cryopreservation of PBMCs]\nDraw blood using an appropriate anti-coagulant and ensure it is filled to the top and immediately inverted 5 x to prevent clotting.\nChoice of anti-coagulant will depend on downstream application; heparin is better for processing delays but not for DNA isolation, EDTA may in... |
76,053 | RNA-Stable Isotope Probing | 1 | dx.doi.org/10.17504/protocols.io.kxygxm23kl8j/v9 | https://www.protocols.io/view/rna-stable-isotope-probing-cnhvvb66 | Roey Angel, Eva Petrova, Ana Lara | TITLE: RNA-Stable Isotope Probing
AUTHORS: Roey Angel, Eva Petrova, Ana Lara
[DESCRIPTION]
The following protocol describes how to perform an RNA-Stable Isotope Probing experiment. The scope of this protocol only covers the parts involving separating labelled RNA from unlabelled RNA using ultracentrifugation in a caes... | ["[Solutions for SIP] Prepare the following solutions:", "[Solutions for SIP] Gradient buffer (0.1 M Tris-HCl, 0.1 M KCl, 1 mM EDTA) pH 8.0 :\n15.76 g \n7.455 g \n0.37224 g \n\nDissolve the salts in RNase-free water and fill up to1000 ml. Filter sterilise (0.1-0.2 μm). Autoclave.\n \n\n \n\n \nStore atRoom temperature"... |
106,633 | Generation of preformed αS fibrils | 0 | dx.doi.org/10.17504/protocols.io.81wgbzo71gpk/v1 | https://www.protocols.io/view/generation-of-preformed-s-fibrils-dkdh4s36 | Isabel Lam, Alain Ndayisaba, Vikram Khurana | TITLE: Generation of preformed αS fibrils
AUTHORS: Isabel Lam, Alain Ndayisaba, Vikram Khurana
[DESCRIPTION]
Generation of preformed αS fibrils
[STEPS]
1. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.nqddds6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This work aims for modeling and simulating the metastasis of cancer, via the analogy between the cancer process and the board game Go. In the game of Go, black stones that play first could correspond to a metaphor of the birth, growth, and metastasis of cancer. Moreover, play... | [] |
55,147 | Detecting the acellular oxidative reactivity of nanoparticles | 4 | dx.doi.org/10.17504/protocols.io.bz4jp8un | https://www.protocols.io/view/detecting-the-acellular-oxidative-reactivity-of-na-bz4jp8un | Liza M M Roger, Nastassja Lewinski, Lynn Secondo, Jasmine Wang | TITLE: Detecting the acellular oxidative reactivity of nanoparticles
AUTHORS: Liza M M Roger, Nastassja Lewinski, Lynn Secondo, Jasmine Wang
[DESCRIPTION]
This protocol was designed to detect acellular oxidative reactivity of nanoparticles
[GUIDELINES]
Health and safety precautions
All work should be conducted in a ... | ["[Materials] - Hydrogen peroxide solution (30 wt% in water, Sigma Aldrich cat. no. 216763)\n- 2′,7′-Dichlorodihydrofluorescein diacetate (>97%, Sigma Aldrich cat. no. D6883)\n NOTE: Once opened, the solid DCFH-DA must be kept under argon at -20°C.\n- Methanol (HPLC grade)\n NOTE: Can substitute with pure Ethanol... |
null | null | null | dx.doi.org/10.17504/protocols.io.fyybpxw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 1">
<div class="layoutArea">
<div class="column">
<p>The SensiFAST™ Probe No-ROX One-Step Kit has been formulated for highly reproducible first-strand cDNA synthesis and subsequent real-time PCR in a single tube. The kit is formulated for use with p... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.jh8cj9w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Set up your Unix PATH so you can find important tools on the HPC for the class.</p>
[STEPS]
?.
?.
?.
?.
?. | [] |
71,278 | Preparation of tissue for transmission electron microscopy ultrastructural analysis | 4 | dx.doi.org/10.17504/protocols.io.j8nlk47ewg5r/v2 | https://www.protocols.io/view/preparation-of-tissue-for-transmission-electron-mi-chunt6ve | Jillian C Danne, Simon A Crawford, Rachel Templin, Joan Clark, Viola Oorschot, Georg Ramm | TITLE: Preparation of tissue for transmission electron microscopy ultrastructural analysis
AUTHORS: Jillian C Danne, Simon A Crawford, Rachel Templin, Joan Clark, Viola Oorschot, Georg Ramm
[DESCRIPTION]
A transmission electron microscope (TEM) enables the magnification and visualisation of cell and tissue ultrastru... | ["[Fixation] All fixation and processing steps must be performed in a fume hood wearing appropriate personal protective equipment (PPE). The Material Safety Data Sheet (MSDS) for each chemical must be read before commencing.\n\nDissect out the tissue of interest on a Teflon plate or dental wax sheet using fine forceps ... |
32,593 | A simple laboratory rearing method for chalcid wasps | 1 | dx.doi.org/10.17504/protocols.io.bb3riqm6 | https://www.protocols.io/view/a-simple-laboratory-rearing-method-for-chalcid-was-bb3riqm6 | Lilian Matallana Ramirez, Kelly Goode, Nicholas Moore, Robert Jetton, John Frampton | TITLE: A simple laboratory rearing method for chalcid wasps
AUTHORS: Lilian Matallana Ramirez, Kelly Goode, Nicholas Moore, Robert Jetton, John Frampton
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>For several years, studies on insect behavior, larval development, infestation patterns, para... | ["[Rearing protocol]\nHoles were punctured into 10 cm x 14 cm clear, plastic, sealable bags for air exchange using dissecting needles.Place approximately 80-100 Fraser fir seeds in each bag. This will be referred to as an experimental unit (EU).Soil media or substrate to the bags can be added to simulate natural condit... |
67,382 | Green Earth CBD Gummies | 1 | dx.doi.org/10.17504/protocols.io.6qpvr6512vmk/v1 | https://www.protocols.io/view/green-earth-cbd-gummies-cd2ws8fe | jehey | TITLE: Green Earth CBD Gummies
AUTHORS: jehey
[DESCRIPTION]
Your endocannabinoid framework, or ECS, controls everything from unwinding to resting, eating, and, surprisingly, mental capabilities.
[STEPS]
SECTION: Green Earth CBD Gummies
1. ➢ Product Name — Green Earth CBD Gummies
➢ Composition—Natural Organic Compou... | ["[Green Earth CBD Gummies] ➢ Product Name — Green Earth CBD Gummies\n➢ Composition—Natural Organic Compound\n➢ Side-Effects —NA\n➢ Price — ($0.1)\n➢ Availability—Online\n➢ Rating: —⭐⭐⭐⭐⭐\n➢Official Website– https://reviewbylogix.online/xhoq\n\n \n\n\nWhat are Green Earth CBD Gummies?\nGreen Earth CBD Gummies is one of... |
97,361 | Donor Case Selection | HuBMAP | JHU-TMC | 0 | dx.doi.org/10.17504/protocols.io.dm6gpz8e1lzp/v1 | https://www.protocols.io/view/donor-case-selection-hubmap-jhu-tmc-dbbr2im6 | Kyu Sang Han, peihsun.wu, Joel Sunshine, Sashank Reddy, Denis Wirtz | TITLE: Donor Case Selection | HuBMAP | JHU-TMC
AUTHORS: Kyu Sang Han, peihsun.wu, Joel Sunshine, Sashank Reddy, Denis Wirtz
[DESCRIPTION]
Donor case selection protocol for Johns Hopkins TMC describes criteria for human tissue biopsy collection.
[BEFORE_START]
Patient samples are obtained from skin that is to be disca... | ["[Inclusion] Age 18-35 or 50 and over\nEnglish Speaking\nAble to provide consent\nUndergoing reconstructive or aesthetic procedures necessitating skin excision at the scalp or abdomen", "[Exclusion] Known collagen disorder\nStrong personal history of keloid formation\nDeemed unfit for general anesthesia\nActive infect... |
69,029 | To test fork notification v.3 20220822 | 1 | dx.doi.org/10.17504/protocols.io.n92ldzjxxv5b/v3 | https://www.protocols.io/view/to-test-fork-notification-v-3-20220822-cfndtma6 | Gabriel Gasque | TITLE: To test fork notification v.3 20220822
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"] |
108,430 | The perfect slice - Cutting bread made easy | 0 | dx.doi.org/10.17504/protocols.io.14egn6qyzl5d/v3 | https://www.protocols.io/view/the-perfect-slice-cutting-bread-made-easy-dm5n485e | Bread Pitt, Rye-an Reynolds, Crumbelina Jolie, Elon Crust | TITLE: The perfect slice - Cutting bread made easy
AUTHORS: Bread Pitt, Rye-an Reynolds, Crumbelina Jolie, Elon Crust
[DESCRIPTION]
Bread cutting, while seemingly simple, is an art that embodies both precision and mindfulness. "Cutting bread is the simplest form of precision, where a steady hand meets the resistance ... | ["[Prepare to cut] Gather Your Tools: a serrated bread knife (aka \"Loaf Saber\"), a sturdy wooden cutting board, a nice loaf of bread, and a piece of cloth for crum control", "[Prepare to cut] Make sure your bread is at Room temperature . Warm bread will squish under pressure, like a marshmallow in a vice. If you’re d... |
98,665 | SOP for personalized directions in e-prescription | 0 | dx.doi.org/10.17504/protocols.io.3byl49k92go5/v1 | https://www.protocols.io/view/sop-for-personalized-directions-in-e-prescription-dckh2ut6 | Zilma Reis, Adriana Silvina Pagano, eura lage, Cristiane dos Santos Dias, Isaias José Ramos de Oliveira, Glaucia Miranda Varella Pereira, Ricardo João Cruz Correia, Vinicius Araujo Basilio | TITLE: SOP for personalized directions in e-prescription
AUTHORS: Zilma Reis, Adriana Silvina Pagano, eura lage, Cristiane dos Santos Dias, Isaias José Ramos de Oliveira, Glaucia Miranda Varella Pereira, Ricardo João Cruz Correia, Vinicius Araujo Basilio
[DESCRIPTION]
Purpose: This SOP outlines a set of patient-cente... | ["[Instruções personalizadas para o uso correto de medicamentos dentro de prescrições elaborada por profissionais de saúde habilitados, no contexto da atenção primária] Padrão geral para as orientações:", "[Instruções personalizadas para o uso correto de medicamentos dentro de prescrições elaborada por profissionais de... |
59,191 | Creating Gelvatol Solution | 6 | dx.doi.org/10.17504/protocols.io.4r3l2o2rqv1y/v1 | https://www.protocols.io/view/creating-gelvatol-solution-b52xq8fn | Daniela Boassa, Mark Ellisman | TITLE: Creating Gelvatol Solution
AUTHORS: Daniela Boassa, Mark Ellisman
[DESCRIPTION]
A gel-like mounting media (with an anti-fade ingredient) for fluorescence slides.
[BEFORE_START]
Add a small drop of Gelvatol to specimen.
Carefully place coverslip on the drop(s) avoiding bubbles.
The mounting media will set ove... | ["Add 2.4 g of Polyvinyl Alcohol (Mol. Wt. 30,000-70,000) to 6ml of glycerol.", "Stir well to mix.", "Add 6ml of double distilled water and leave for at least 2 hours at room temperature (rotate overnight)", "Add 12ml of 0.2M Tris (pH 8.5).\n\n2.4 ml Tris 1M\n9.6 ml H2O", "Heat to 50° C for 10 minutes with occasional m... |
28,328 | MojoSort™ Streptavidin Nanobeads Protocol - Positive Selection | null | dx.doi.org/10.17504/protocols.io.7wghpbw | null | Sam Li | TITLE: MojoSort™ Streptavidin Nanobeads Protocol - Positive Selection
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"><span style = "font-weight:bold;">If your target ce... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes.", "In the final wash of your sample preparation, resuspend the cells in MojoSort™ Buffer by adding up to 4 mL in a 5 mL (12 x 75 mm) polypropylene tube.Note: Keep MojoSort™ Buffer on ice throughout the procedure.", "Filter the cells with... |
28,894 | Advanced Marfey's | null | dx.doi.org/10.17504/protocols.io.8f6htre | null | Jaclyn Winter | TITLE: Advanced Marfey's
AUTHORS: Jaclyn Winter
[STEPS] | [] |
52,820 | NEBNext® ARTIC SARS-CoV-2 Companion Kit (Oxford Nanopore Technologies®) E7660 -- Express Protocol without PCR Bead Cleanup and Varskip Primers | 4 | dx.doi.org/10.17504/protocols.io.bxtupnnw | https://www.protocols.io/view/nebnext-artic-sars-cov-2-companion-kit-oxford-nano-bxtupnnw | New England Biolabs | TITLE: NEBNext® ARTIC SARS-CoV-2 Companion Kit (Oxford Nanopore Technologies®) E7660 -- Express Protocol without PCR Bead Cleanup and Varskip Primers
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details methods for the NEBNext® ARTIC SARS-CoV-2 Companio... | ["[cDNA Synthesis]\nGently mix 10 times by pipetting and spin down the LunaScript RT SuperMix reagent (contains primers). Prepare the cDNA synthesis reaction as described below:COMPONENTVOLUMERNA Sample8 µl\n(lilac) LunaScript RT SuperMix2 µlTotal Volume10 µl\nCOMPONENTVOLUMERNA Sample8 µl\n(lilac) LunaScript RT SuperM... |
90,812 | Electron microscopy (EM) and quantification | 1 | dx.doi.org/10.17504/protocols.io.yxmvm3zm6l3p/v1 | https://www.protocols.io/view/electron-microscopy-em-and-quantification-c4w4yxgw | Leonardo A Parra-Rivas | TITLE: Electron microscopy (EM) and quantification
AUTHORS: Leonardo A Parra-Rivas
[DESCRIPTION]
Electron microscopy (EM) and quantification
[STEPS]
SECTION: Electron microscopy (EM)
1.
Hippocampal neurons were plated at a density of
60,000 cells/cm2. DIV-3 neurons were infected with lentiviruses
carrying α-syn tagg... | ["[Electron microscopy (EM)] Hippocampal neurons were plated at a density of\n60,000 cells/cm2. DIV-3 neurons were infected with lentiviruses\ncarrying α-syn tagged at the C-terminus to mScarlet, or mScarlet alone\n(multiplicity of infection or MOI=2.5). The transduced neurons were cultured to\nmaturity (DIV17-DIV21) b... |
47,415 | Manual Gentra Puragene DNA Extraction | 4 | dx.doi.org/10.17504/protocols.io.n2bvjx2nblk5/v1 | https://www.protocols.io/view/manual-gentra-puragene-dna-extraction-bsixncfn | Clemens Scherzer, Bradley Hyman, Charles Jennings | TITLE: Manual Gentra Puragene DNA Extraction
AUTHORS: Clemens Scherzer, Bradley Hyman, Charles Jennings
[DESCRIPTION]
This protocol explains the Standard Operating Protocol for manually extracting DNA using Gentra Puragene.
[BEFORE_START]
DNA Q/C GOALS
1. Cary Concentration Assay
a. 260/280 = 1.8-2.0
... | ["[Manual Gentra Puregene DNA Extraction] Add 3 mL and mix by inverting 10 times.", "[Manual Gentra Puregene DNA Extraction] Incubate sample for 5 min at 65 Room temperature (15°C-25°C). Invert once during the incubation.", "[Manual Gentra Puregene DNA Extraction] Centrifuge at 2000 x g, 2 min, 25 °C.", "[Manual Gentra... |
42,840 | Collection of skin biopsies from cattle | 4 | dx.doi.org/10.17504/protocols.io.bm3yk8pw | https://www.protocols.io/view/collection-of-skin-biopsies-from-cattle-bm3yk8pw | Froylan Sosa, Peter Hansen | TITLE: Collection of skin biopsies from cattle
AUTHORS: Froylan Sosa, Peter Hansen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a simple protocol for collecting skin biopsies from cattle. The procedure described here was used to collect skin for histological analysis but it could also be ... | ["[Procedure]\nRestrain the animal in a head chute.", "[Procedure]\nLabel the cassettes - make sure to use a permanent marker for histology or pencil.", "[Procedure]\nClip the biopsy area with clippers and wipe down with ethanol-soaked gauze. We typically sample the thorax (middle of 5 or 6th rib) - or shoulder area", ... |
79,441 | Structural MRI Using the University of Washington 14T Vertical Bore Bruker MRI | 4 | dx.doi.org/10.17504/protocols.io.3byl4j8p2lo5/v1 | https://www.protocols.io/view/structural-mri-using-the-university-of-washington-crtrv6m6 | Yoni Browning, Galen Lynch, Josh Siegle | TITLE: Structural MRI Using the University of Washington 14T Vertical Bore Bruker MRI
AUTHORS: Yoni Browning, Galen Lynch, Josh Siegle
[DESCRIPTION]
This protocol describes the process of obtaining pre-insertion MRI images using the University of Washington 14T vertical bore Bruker MRI. These structural scans allow fo... | ["[Prepare MnCl2 solution for injection.] Mix 100 millimolar (mM) MnCl2 solution. (These steps are from section 3.1.1 of Massaad and Pautler (2011).)", "[Prepare MnCl2 solution for injection.] Create 100 mL of a 100 millimolar (mM) bicine buffer solution by mixing 1.63 g bicine into 100 mL MilliQ water in a beaker.", "... |
83,147 | Growth of Chitosan nano brushes using FMED as electropolymerization method | 6 | dx.doi.org/10.17504/protocols.io.eq2lyjz6elx9/v1 | https://www.protocols.io/view/growth-of-chitosan-nano-brushes-using-fmed-as-elec-cvfjw3kn | Maria J Torres, Eric S McLamore, Lidadi Agbomi | TITLE: Growth of Chitosan nano brushes using FMED as electropolymerization method
AUTHORS: Maria J Torres, Eric S McLamore, Lidadi Agbomi
[DESCRIPTION]
This protocol describes the electropolymerization of chitosan nanobrushes in the working electrode of a Laser-induced graphene (LIG) sensor. The process requires appro... | ["[SECTION 1) Preparation] Prepare a glass cell vial with lower molecular weight deacylated chitosan solution.\n\nPrevious microwave-assisted synthesis of lower molecular weight deacylated chitosan solution prepared is required following the next protocol (Link here):", "[SECTION 2) Electropolymerization using FMED met... |
86,419 | Detection of Equatorial Plasma Bubbles | 5 | dx.doi.org/10.17504/protocols.io.rm7vzbb12vx1/v2 | https://www.protocols.io/view/detection-of-equatorial-plasma-bubbles-cymtxu6n | Swapna Raghunath | TITLE: Detection of Equatorial Plasma Bubbles
AUTHORS: Swapna Raghunath
[DESCRIPTION]
Slant Total Electron Content values from Global Navigation Satellite System are used to detect the Equatorial Plasma Bubbles in the Ionosphere.
[STEPS]
1. Download GPS data from SOPAC website in RINEX format
2. Data is converted fro... | ["Download GPS data from SOPAC website in RINEX format", "Data is converted from RINEX to .cmn format using GPS TEC software", "Calculate ROT and ROTI", "Difference between Evening ROTI and Day time ROTI is calculated", "If the difference exceeds 0.05, then Equatorial Plasma Bubble is Detected"] |
95,808 | Выделение, пробоподготовка и секвенирование тотальной ДНК грибов на Nanopore MinION | 0 | dx.doi.org/10.17504/protocols.io.kxygx3jwkg8j/v1 | https://www.protocols.io/view/nanopore-minion-c9s8z6hw | Elena Zvyagina, Nina Filippova | TITLE: Выделение, пробоподготовка и секвенирование тотальной ДНК грибов на Nanopore MinION
AUTHORS: Elena Zvyagina, Nina Filippova
[DESCRIPTION]
[EN] Protocols for sampling, sample preparation, and sequencing on the Nanopore MinION platform. The target material is total fungal DNA (amplicons) from soil and other subst... | ["[Подготовка проб почвы для выделения тотальной ДНК] Выделение тотальной ДНК ведется из небольших объемов субстрата (в стандартных наборах для выделения 500 mg), что может препятствовать полноценному отбору всего сообщества и гомогенности его распределения. Альтернативным способом является вымывание внеклеточной тотал... |
null | null | null | dx.doi.org/10.17504/protocols.io.ib8carw | null | null | TITLE: No Title
AUTHORS:
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.dse6bd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
The diversity of ribonucleic acid (RNA) viruses in the ocean and the ongoing isolation and characterization of RNA viruses that infect important primary producers suggests that RNA viruses are active members of the marine microbial assemblage. At this point, little is known abou... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.e5mbg46 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a collection of protocols for the G-Biosciences CB-X™ Protein Assay.</p>
[STEPS]
?. | [] |
85,227 | Miniaturized and Automatized Whole-Genome Amplification of SARS-CoV 2 Virus using Illumina CovidSeq reagents for Next-Generation Sequencing V.1 | 4 | dx.doi.org/10.17504/protocols.io.14egn3zpzl5d/v1 | https://www.protocols.io/view/miniaturized-and-automatized-whole-genome-amplific-cxgjxjun | Quentin Semanas, christophe GINEVRA, Richard Chalvignac | TITLE: Miniaturized and Automatized Whole-Genome Amplification of SARS-CoV 2 Virus using Illumina CovidSeq reagents for Next-Generation Sequencing V.1
AUTHORS: Quentin Semanas, christophe GINEVRA, Richard Chalvignac
[DESCRIPTION]
Since December 2019, the rapid spread of severe acute respiratory syndrome coronavirus 2 ... | ["[Abstract] Since December 2019, the rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) worlwide has necessitated to drastically scale-up the viral genomic surveillance to track the emergence of variant of concern.\n\nThe limitations of NGS workflow for increasing the genomic surveillance in... |
47,566 | Hematoxylin and Eosin Stain of FFPE Tumor Tissue | 1 | null | https://www.protocols.io/view/hematoxylin-and-eosin-stain-of-ffpe-tumor-tissue-bspnndme | John Herndon, William Gillanders | TITLE: Hematoxylin and Eosin Stain of FFPE Tumor Tissue
AUTHORS: John Herndon, William Gillanders
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the steps for doing a manual Hematoxylin and Eosin (H&E) Stain of formalin fixed tissue. This stain is used to distinguish tumor t... | ["[Tissue Preparation]\nDe-Paraffization of slidesPlace slides in to oven at 60o C for one hour", "[Tissue Preparation]\nPlace slides in to Fresh Xylene for 2 minutes, repeat", "[Tissue Preparation]\nRehydration of sections100% Ethanol, 1 minute, repeat", "[Tissue Preparation]\n90% Ethanol, 1 minute, repeat", "[Tissue ... |
null | null | null | dx.doi.org/10.17504/protocols.io.n32dgqe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The ability to image RNA identity and location with nanoscale precision in intact tissues is of great interest for defining cell types and states in normal and pathological biological settings. Here, we present a strategy for expansion microscopy of RNA. We developed a small-... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.meqc3dw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Staining hundreds to thousands of RNA species each of which requires tens of unique encoding probes requires a very large number of unique oligonucleotide sequences. The sheer number of unique sequences makes traditional solid phase oligonucleotide synthesis prohibitively exp... | [] |
33,863 | nCoV-2019 sequencing protocol (single sample) | null | dx.doi.org/10.17504/protocols.io.bdbfi2jn | null | Josh Quick | TITLE: nCoV-2019 sequencing protocol (single sample)
AUTHORS: Josh Quick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">ARTIC amplicon sequencing protocol for MinION for nCoV-2019</div></div>
[STEPS]
?. [cDNA preparation]
Mix the following components in an 0.2mL 8-strip tube;Component ... | ["[cDNA preparation]\nMix the following components in an 0.2mL 8-strip tube;Component Volume50µM random hexamers 10mM dNTPs mix (10mM each) Template RNA Total\n1 µl\n1 µl\n11 µl\n13 µl\nViral RNA input from a clinical sample sho... |
36,323 | Preparing worms for the COPAS (wormsorter) | null | dx.doi.org/10.17504/protocols.io.bfqbjmsn | https://www.protocols.io/view/preparing-worms-for-the-copas-wormsorter-bfqbjmsn | Priota Islam | TITLE: Preparing worms for the COPAS (wormsorter)
AUTHORS: Priota Islam
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is a guide of how to prepare the worms to be used in the COPAS (wormsorter)</div></div>
[STEPS]
?. Wash the worms off the plates using few milliliters of M9 and coll... | ["Wash the worms off the plates using few milliliters of M9 and collect in a 15ml falcon tube and fill up till 15ml with M9", "Centrifuge the tube at 1500rpm for 2mins followed by removal of the supernatant using a pasteur pipette and addition of another 15ml of M9", "Repeat the steps 2 more times", "After the final wa... |
53,348 | Primer TE (10mM Tris, 0.1mM EDTA, pH8.0) | 4 | dx.doi.org/10.17504/protocols.io.byccpssw | https://www.protocols.io/view/primer-te-10mm-tris-0-1mm-edta-ph8-0-byccpssw | Jacquelina.Woods | TITLE: Primer TE (10mM Tris, 0.1mM EDTA, pH8.0)
AUTHORS: Jacquelina.Woods
[DESCRIPTION]
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 wastewater. Protocols developed for this project cover wastewate... | ["Mix components together.", "Store at Room temperature.", "100 µL ,, or equivalent.", "20 µL ,, or equivalent.", "9.88 mL , or equivalent."] |
null | null | null | dx.doi.org/10.17504/protocols.io.cjpumm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is the protocol for the Q5® Site-Directed Mutagenesis Kit (E0554)
[GUIDELINES]
<strong>DESCRIPTION</strong><br /><br />The Q5® Site-Directed Mutagenesis Kit enables rapid, site-specific mutagenesis of double-stranded plasmid DNA in less than 2 hours (Figure 1). The... | [] |
80,835 | Retrospective audit | 1 | dx.doi.org/10.17504/protocols.io.n92ldpdr9l5b/v1 | https://www.protocols.io/view/retrospective-audit-cs7bwhin | Kajiru Gad Kilonzo, Stefanie J. Krauth, Jo Halliday, Clive Kelly, Stefan Siebert, Gloria Temu, Christopher Bunn, Nateiya M Yongolo, Sally Wyke, Emma McIntosh, Blandina Mmbaga | TITLE: Retrospective audit
AUTHORS: Kajiru Gad Kilonzo, Stefanie J. Krauth, Jo Halliday, Clive Kelly, Stefan Siebert, Gloria Temu, Christopher Bunn, Nateiya M Yongolo, Sally Wyke, Emma McIntosh, Blandina Mmbaga
[DESCRIPTION]
This protocol details retrospective audit.
[STEPS]
SECTION: Retrospective audit
1. A retrospe... | ["[Retrospective audit] A retrospective audit of all adults aged 18 years or above of hospital medical records for signs & symptoms related to joint pain and arthritis-related diagnoses and relevant comorbidities will be undertaken. The audit will establish a retrospective frequency of joint pain among patients admitte... |
56,968 | Rapid, high throughput library preparation of SARS-CoV2 using Illumina’s DNA Prep Library Preparation Kit | 4 | dx.doi.org/10.17504/protocols.io.b3vgqn3w | https://www.protocols.click/view/rapid-high-throughput-library-preparation-of-sars-b3vgqn3w | Jason Nguyen, Rebecca Hickman, Tracy Lee, Natalie Prystajecky, John Tyson | TITLE: Rapid, high throughput library preparation of SARS-CoV2 using Illumina’s DNA Prep Library Preparation Kit
AUTHORS: Jason Nguyen, Rebecca Hickman, Tracy Lee, Natalie Prystajecky, John Tyson
[DESCRIPTION]
This procedure provides instructions on how to prepare DNA libraries for whole genome sequencing on an Illumi... | ["[Tagment Genomic DNA] Add 15 µL of DNA to each well of 96 well PCR plate. If the DNA volume is less than 15 µl, add nuclease-free water to the DNA samples to bring the total volume to 15 µl. \n\nNote: it is assumed that the samples from your PCR plate (labeled “ amplicon”) have at least 3.3ng/µl.", "[Tagment Genomic... |
99,639 | A large scale bacterial attraction assay: a new quantitative bacterial migration assay suitable for genetic screens | 0 | dx.doi.org/10.17504/protocols.io.n2bvjn65bgk5/v1 | https://www.protocols.io/view/a-large-scale-bacterial-attraction-assay-a-new-qua-ddix24fn | Thomas Quiroz Monnens, Alice Boulanger | TITLE: A large scale bacterial attraction assay: a new quantitative bacterial migration assay suitable for genetic screens
AUTHORS: Thomas Quiroz Monnens, Alice Boulanger
[DESCRIPTION]
Bacteria use various motility mechanisms to explore their environments. Chemotaxis is the ability of a motile bacterial cell to direct... | [] |
55,885 | DNA Extraction from Bacteriophages | 1 | null | https://www.protocols.io/view/dna-extraction-from-bacteriophages-b2tmqek6 | Frej Larsen | TITLE: DNA Extraction from Bacteriophages
AUTHORS: Frej Larsen
[DESCRIPTION]
DNA/RNA extraction is performed using the QIAamp® Viral RNA Mini kit from Qiagen without the addition of carrier RNA to the AVL buffer and an additional nuclease step prior to extraction. The nuclease step is introduced to degrade any DNA/R... | ["For each sample, pipet 1 µL 100x diluted Pierce Universal Nuclease (2.5units/uL) to an empty 1.5 mL tube.", "Transfer 140 µL of each sample from the outer chamber of the CentrisArt filter tube to the tube and mix by pipetting", "Incubate for at least 3 min at room temperature.", "Add 540 µL AVL buffer to inactivat... |
null | null | null | dx.doi.org/10.17504/protocols.io.g5rby56 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a slightly modified version of Thermo Fisher's gateway BP protocol which uses less enzyme and is therefore more economical.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
82,480 | Collecting needle and branch samples for terpenoid and expression analysis | 1 | dx.doi.org/10.17504/protocols.io.rm7vzbryrvx1/v2 | https://www.protocols.click/view/collecting-needle-and-branch-samples-for-terpenoid-cusqwwdw | Vidya S Vuruputoor, karlfetter, victoriaburton, Jill Wegrzyn | TITLE: Collecting needle and branch samples for terpenoid and expression analysis
AUTHORS: Vidya S Vuruputoor, karlfetter, victoriaburton, Jill Wegrzyn
[DESCRIPTION]
This protocol is used by the PCG group for sampling needle and branch tissue from hemlock conifers for terpenoid analysis, as well as RNA expression anal... | ["Open Treesnap (https://treesnap.org/), record the accession number on the tree and fill in notes for hemlock woolly adelgid infestation (HWA) levels (scale provided by the app).", "Use the comment field to enter: EHS present OR EHS absent to record the hemlock scale.", "Take at least 3 photos with TreeSnap. This incl... |
48,464 | nCoV-2019 sequencing protocol for illumina | 1 | null | https://www.protocols.io/view/ncov-2019-sequencing-protocol-for-illumina-btjqnkmw | Kentaro Itokawa, Tsuyoshi Sekizuka, Masanori Hashino, Rina Tanaka, Satsuki Eto, Risa Someno, Makoto Kuroda | TITLE: nCoV-2019 sequencing protocol for illumina
AUTHORS: Kentaro Itokawa, Tsuyoshi Sekizuka, Masanori Hashino, Rina Tanaka, Satsuki Eto, Risa Someno, Makoto Kuroda
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol was originally folked from "</span><a href="https://dx.doi.org/10.... | ["[cDNA preparation]\nMix the following components in an 0.2mL 8-strip tube or 96 well PCR plate;Component VolumeLunaScript RT SuperMix Template RNA (purified) Total\nThis protocol uses 5/8 reagents per sample compared to the original LunaScript... |
77,960 | Assessment of Knowledge, Attitude and Practice toward Hepatitis B virus infection among Healthcare Providers working at sixty Public and Private Hospitals in Khartoum State Sudan 2023 | 1 | dx.doi.org/10.17504/protocols.io.6qpvr4reogmk/v2 | https://www.protocols.io/view/assessment-of-knowledge-attitude-and-practice-towa-cqdgvs3w | essam.abuobaida | TITLE: Assessment of Knowledge, Attitude and Practice toward Hepatitis B virus infection among Healthcare Providers working at sixty Public and Private Hospitals in Khartoum State Sudan 2023
AUTHORS: essam.abuobaida
[DESCRIPTION]
Introduction: Hepatitis B infection is a major public health problem worldwide, accordin... | ["[Research Steps] Writing the study protocol", "[Research Steps] Data collection and analysis", "[Research Steps] Writing the manuscript", "[Research Steps] Publishing"] |
103,378 | Refractive index adjusted imaging medium: Iohexol (RI ~ 1.4) - Yeast | 0 | dx.doi.org/10.17504/protocols.io.261ge5xxwg47/v1 | https://www.protocols.io/view/refractive-index-adjusted-imaging-medium-iohexol-r-dg7s3zne | Mathias Hammer, Ammeret Rossouw, Azra Lari, Ben Montpetit, David Grunwald | TITLE: Refractive index adjusted imaging medium: Iohexol (RI ~ 1.4) - Yeast
AUTHORS: Mathias Hammer, Ammeret Rossouw, Azra Lari, Ben Montpetit, David Grunwald
[DESCRIPTION]
This protocol describes the steps to prepare imaging medium for Saccharomyces cerevisiae with adjusted refractive index. This medium is optimized ... | ["[Preparation of 30ml refractive index adjusted imaging medium with Iohexol] Compound medium for autoclave", "[Preparation of 30ml refractive index adjusted imaging medium with Iohexol] Fill a 50 ml flask with 21.9 mLddH2O\nAdd a magnetic stirring bar and place the flask on a stirring hot plate.", "[Preparation of 30m... |
62,305 | Infection of mice with Citrobacter rodentium ICC180 by natural transmission | 4 | dx.doi.org/10.17504/protocols.io.8epv59b96g1b/v1 | https://www.protocols.io/view/infection-of-mice-with-citrobacter-rodentium-icc18-b839ryr6 | Hannah Read, Priyali Patel (University of Auckland), Siouxsie Wiles | TITLE: Infection of mice with Citrobacter rodentium ICC180 by natural transmission
AUTHORS: Hannah Read, Priyali Patel (University of Auckland), Siouxsie Wiles
[DESCRIPTION]
Citrobacter rodentium is a Gram-negative bacterium which infects laboratory mice in a similar way to how enteropathogenic Escherichia coli (EPEC)... | ["[Preparation of Citrobacter rodentium ICC180] At least two days before needed, revive bacteria from frozen stocks stored at –70-80°C. Plate onto LB-Lennox media. At this stage, you can grow them with or without kanamycin 50 ug/mL . Incubate 1440 min at 37 °C", "[Preparation of Citrobacter rodentium ICC180] The day ... |
28,248 | MojoSort™ Human CD4 T Cell Selection Kit Column Protocol - CD4 Nanobeads | null | dx.doi.org/10.17504/protocols.io.7tyhnpw | null | Sam Li | TITLE: MojoSort™ Human CD4 T Cell Selection Kit Column Protocol - CD4 Nanobeads
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>BioLegend MojoSort™ nanobeads work in commonly used separation columns, based on our internal research as well as validation by external testing by ac... | ["After monocyte depletion using the CD14 selection protocol, centrifuge the pooled unlabeled CD4+T Cells at 300xg for 5 minutes, discard supernatant, and resuspend in an appropriate volume of MojoSort™ Buffer. Count and adjust the cell concentration to 1 x 108 cells/mL.Note: Keep MojoSort™ Buffer on ice throughout the... |
null | null | null | dx.doi.org/10.17504/protocols.io.e6jbhcn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p> </p>
<p> </p>
<p>The OmniPrep™ kit isolates high quality genomic DNA from many different species and tissue types including animal, plant, bacteria, yeast, fungi, whole blood, and cells in culture. DNA can be isolated from samples high in polysaccharides or other contaminant... | [] |
64,026 | UroMOCA and StimPod Implantation | 3 | dx.doi.org/10.17504/protocols.io.rm7vzyq3rlx1/v1 | https://www.protocols.io/view/uromoca-and-stimpod-implantation-car2sd8e | Dennis Bourbeau | TITLE: UroMOCA and StimPod Implantation
AUTHORS: Dennis Bourbeau
[DESCRIPTION]
This protocol gives an overview of the surgical procedure to implant the UroMOCA and StimPods.
[STEPS] | [] |
53,713 | DIVA Design instructions SOP (User's section) | 1 | null | https://www.protocols.io/view/diva-design-instructions-sop-user-39-s-section-byprpvm6 | Henrique De Paoli, Christopher J Petzold | TITLE: DIVA Design instructions SOP (User's section)
AUTHORS: Henrique De Paoli, Christopher J Petzold
[DESCRIPTION]
This is a "how to" step-by-step instruction for creating Projects and Designs in DIVA for automated design of oligos, plasmids and build instructions. User can either build plasmids on their own or ... | ["[DIVA access] Go to DIVA server at https://diva.agilebiofoundry.org/ and login by using your LBNL LDAP/affiliate username and password.", "[Define Project] Click the New Project button.", "[Define Project] Input a Project Name, Description and define the DIVA Team who will review your design.", "[Define Project] Add... |
55,767 | Acute Brain Slices | 4 | dx.doi.org/10.17504/protocols.io.4r3l2omjpv1y/v1 | https://www.protocols.io/view/acute-brain-slices-b2pxqdpn | Beatriz E Nielsen | TITLE: Acute Brain Slices
AUTHORS: Beatriz E Nielsen
[DESCRIPTION]
This protocol describes the steps for preparing acute brain slices.
[BEFORE_START]
Prepare stock solutions: 10X Stock solutions can be made ahead of time and are shelf stable at Room temperature for 1 month; 1X solutions must be made fresh
10X ACSF
... | ["[Acute Brain Slices] Set up vibratome and cutting station:", "[Acute Brain Slices] Set up vibratome\nCarefully clean blade with ethanol and water\nUsing a hex wrench, insert blade in blade holder assembly\nRun VibroCheck calibration\nPlace buffer tray in ice tray and fill ice tray with ice; load on to vibratome\nSupe... |
94,599 | Clusterin cellular uptake assay | 1 | dx.doi.org/10.17504/protocols.io.14egn3k2yl5d/v1 | https://www.protocols.io/view/clusterin-cellular-uptake-assay-c8mfzu3n | Patricia Yuste Checa, F Ulrich Hartl | TITLE: Clusterin cellular uptake assay
AUTHORS: Patricia Yuste Checa, F Ulrich Hartl
[DESCRIPTION]
This protocol details how to efficiently monitor Clusterin and Clusterin/Substrate uptake in different cell types, like HEK293T, iNeurons and iMicroglia.
[GUIDELINES]
To study Clusterin-A488 uptake in the presence of su... | ["[Clusterin cellular uptake assay - HEK293T cells] Plate 100,000 HEK293T cells per well in a 24-well plate.", "[Clusterin cellular uptake assay - HEK293T cells] On the next day, add 5 1527 of Clusterin-A488 together with 300 µL of fresh DMEM (without fetal bovine serum, 1.5 µg in 300 µL medium) to the cells and place ... |
44,992 | METATAC V.1 | 4 | dx.doi.org/10.17504/protocols.io.kqdg36x51g25/v1 | https://www.protocols.io/view/metatac-v-1-bp68mrhw | Honggui Wu, Xiang Li, Fanchong Jian, Ayijiang Yisimayi, X. Sunney Xie | TITLE: METATAC V.1
AUTHORS: Honggui Wu, Xiang Li, Fanchong Jian, Ayijiang Yisimayi, X. Sunney Xie
[DESCRIPTION]
Abstract
Here we describe a protocol for multiplexed end-tagging amplification of transposase accessible
chromatin (METATAC), a high-sensitivity single-cell ATAC-seq technique with the help of META chemis... | ["[Bulk Transposition] Harvest fresh culture in a conical centrifuge tube (15 ml or 50 ml) at room temperature, centrifuge at 500 x g for 5 min at room temperature, then wash twice with 1x PBS pH 7.4, count cell number, stain with Trypan blue, and ensure viability >90%. then aliquot 50, 000 cells to a 200 µL PCR tube."... |
78,228 | Impedance (xCELLigence) | 1 | dx.doi.org/10.17504/protocols.io.5jyl8jqz6g2w/v1 | https://www.protocols.io/view/impedance-xcelligence-cqmuvu6w | Amanda Russell, Philippa R Kennedy | TITLE: Impedance (xCELLigence)
AUTHORS: Amanda Russell, Philippa R Kennedy
[DESCRIPTION]
This assay is used as a readout of NK cell cytotoxicity of adherent tumor cell lines. Tumor cells are seeded onto a 96-well gold-coated plate. As tumor cells adhere to the plate and proliferate, the flow of electrons is impeded ac... | ["[Preparation - target cell titration] Target cell density should be titrated, so that the full assay can be run with logarithmic cell growth, with the greatest impedance and maximum sensitivity/reliability possible. \n \n\ne.g. If target cells reach confluence at 48h, this gives you 24h for target cell adherence and ... |
null | null | null | dx.doi.org/10.17504/protocols.io.er4bd8w | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
3-4 hour XZ-6E virus infected NC64A, pellets frozen at -80°C
[GUIDELINES]
<strong>MATERIALS AND ASSAY CONDITIONS:</strong><br /><br /> 1) 3-4 hour XZ-6E virus infected NC64A, pellets frozen at -80°C<br /> 2) Buffer A: <br />
<ul>
<li>10 mM Tris-HCl, pH 8.0</li>
<li>10 mM 2-ME<... | [] |
65,799 | NLDM: A Defined Medium for Cultivation and Exometabolite Profiling of Soil Bacteria | 4 | dx.doi.org/10.17504/protocols.io.14egn7o2yv5d/v1 | https://www.protocols.io/view/nldm-a-defined-medium-for-cultivation-and-exometab-cchfst3n | Markus De Raad, Yifan V. Li, Jennifer V. Kuehl, Peter F. Andeer, Suzanne M. Kosina, Andrew Hendrickson, Nicholas R. Saichek, Amber N. Golini, La Zhen Han, Ying Wang, Benjamin P. Bowen, Adam M. Deutschbauer, Adam Arkin, Romy Chakraborty, Trent R. Northen | TITLE: NLDM: A Defined Medium for Cultivation and Exometabolite Profiling of Soil Bacteria
AUTHORS: Markus De Raad, Yifan V. Li, Jennifer V. Kuehl, Peter F. Andeer, Suzanne M. Kosina, Andrew Hendrickson, Nicholas R. Saichek, Amber N. Golini, La Zhen Han, Ying Wang, Benjamin P. Bowen, Adam M. Deutschbauer, Adam Arkin, R... | ["[NLDM Components] NLDM stock solutions\nSee Materials section on how to prepare stock solutions\n\n Medium components NLDM Solution1 - 'Sugars' - 10X NLDM Solution 2 - 'Organic_Acids' - 10X NLDM Solution3 - 'Amino_Acid' - 10X NLDM Solution 4 - 'Nucleobase/Nucleoside' - 50X NLDM Solution... |
58,613 | Southern transect resurvey | 1 | null | https://www.protocols.io/view/southern-transect-resurvey-b5gvq3w6 | Lauren Ponisio | TITLE: Southern transect resurvey
AUTHORS: Lauren Ponisio
[DESCRIPTION]
This protocol details the Ponisio Lab's collecting protocol for the 2022 Moldenke re-survey of the southern transect. Each site consists of two 900m long transects, marked every 100m with flagging tape and a nail. Each transect has three 10m² vege... | ["[Field station prep] Prior to collection, it is important to make sure that the following preparations are made:\n\nShared sampling box:\nGPS x2\nspare batteries \nflagging tape\npin flags \nspare sharpies, microns etc \ntransect tapes \norange cones \n\nShared collection equipment/consumables:\nFreezeproof snap caps... |
22,001 | Disturbing the rhythm of thought: speech pausing patterns in schizophrenia, with and without formal thought disorder | null | dx.doi.org/10.17504/protocols.io.zqrf5v6 | null | Derya Cokal, Vitor Zimmerer, Douglas Turkington, Nicol Ferrier, Rosemary Varley, Stuart Watson, Wolfram Hinzen | TITLE: Disturbing the rhythm of thought: speech pausing patterns in schizophrenia, with and without formal thought disorder
AUTHORS: Derya Cokal, Vitor Zimmerer, Douglas Turkington, Nicol Ferrier, Rosemary Varley, Stuart Watson, Wolfram Hinzen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Ev... | [] |
68,367 | IPTG_induction | 4 | dx.doi.org/10.17504/protocols.io.4r3l2od1pv1y/v1 | https://www.protocols.io/view/iptg-induction-cezptf5n | Ana Belem García González, Georgina Diego, Jair Alexis Gardea Sáenz, Irán Alessandra Chaparro Rodríguez | TITLE: IPTG_induction
AUTHORS: Ana Belem García González, Georgina Diego, Jair Alexis Gardea Sáenz, Irán Alessandra Chaparro Rodríguez
[DESCRIPTION]
Protocol to induce protein expression using IPTG.
[STEPS]
SECTION: Protocol
1. From a relatively fresh plate, grab a colony and grow at 37 °C and in 10 mL of LB+CAM.
... | ["[Protocol] From a relatively fresh plate, grab a colony and grow at 37 °C and in 10 mL of LB+CAM.", "[Protocol] Inoculate 3 mL in 30 mL of LB+CAM and incubate at 37 °C and", "[Protocol] When the cells reach to a OD600 between 0.4 and 0.8, the protein expression must be induced (IPTG concentrations can vary from 0... |
20,956 | UC Davis - Intraperitoneal Glucose Tolerance Test | null | dx.doi.org/10.17504/protocols.io.yp4fvqw | null | Fawaz G. Haj | TITLE: UC Davis - Intraperitoneal Glucose Tolerance Test
AUTHORS: Fawaz G. Haj
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">
An intraperitoneal Glucose tolerance test or ipGTT is designed to determine clearance of an... | ["Fast mice for 16hours by taking away food the day before (3:00pm)", "The following day, Calibrate the glucose meter according to the manufacturer’s instructions.", "Deprive mice from water then remove approximately 5 μl of blood (one drop) from thetail via a tail tip cut and transfer directly onto a glucose indicator... |
23,089 | Extraction of Nuclei from Brain Tissue | null | dx.doi.org/10.17504/protocols.io.2srged6 | null | Laura Bortolin, Melissa Goldman, Steven McCarroll | TITLE: Extraction of Nuclei from Brain Tissue
AUTHORS: Laura Bortolin, Melissa Goldman, Steven McCarroll
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol enables rapid isolation of intact nuclei from brain tissue, including highly myelinated adult brain tissue. We have used it successf... | ["Retrieve dissection tray from -20°C, and the glass slide and razor blade from 4°C.", "Place the glass slide, razor blade, and ruler on the dissection tray and perform all cutting on slide to minimize damage to, and contamination of, the tray.\nIt is helpful to put the dissecting tray on ice to keep it cold and preven... |
null | null | null | dx.doi.org/10.17504/protocols.io.fkbbksn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
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?.
?.
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?. | [] |
97,717 | Evaluating Peanut Germ Plasm for Resistance to Pythium myriotylum using Sorghum Seeds | 0 | null | https://www.protocols.io/view/evaluating-peanut-germ-plasm-for-resistance-to-pyt-dbnv2me6 | Nimalka Weerasuriya | TITLE: Evaluating Peanut Germ Plasm for Resistance to Pythium myriotylum using Sorghum Seeds
AUTHORS: Nimalka Weerasuriya
[DESCRIPTION]
Using sorghum colonized by Pythium myriotylum to evaluate the peanut germ plasm resistance of peanut seedlings in a greenhouse.
[STEPS]
SECTION: Prep and Seed Planting
1. Make a 1:1 ... | ["[Prep and Seed Planting] Make a 1:1 sand-soil (v/v) potting mixture for the required number of pot replicates. Include 1-2 additional replicates for each treatment, in case seedling emergence is inconsistent.\nPlace pots in trays and water to soak medium. \nLet pots soak overnight.", "[Planting (Day 0)] Check that th... |
33,894 | RNA extraction from field-collected brain tissue samples from suspect rabid animals | null | dx.doi.org/10.17504/protocols.io.bdcei2te | null | Kirstyn Brunker | TITLE: RNA extraction from field-collected brain tissue samples from suspect rabid animals
AUTHORS: Kirstyn Brunker
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details the steps involved to perform RNA extraction on rabies virus brain tissue samples collected by the WHO recommended... | ["[Sample preparation]\nBrain tissue samples collected in the field may be stored in glycerol-saline, RNA Later or DNA/RNA shield according to the resources available to the sample collector. Instructions to process commonly received samples for use with the Zymo Research Quick-RNA miniprep kit are indicated below (for... |
null | null | null | dx.doi.org/10.17504/protocols.io.tutenwn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Moral licensing or, what is equivalently called, “self-licensing” is the use of a Good Act instrumentally: to cover up a Bad Act. This paper’s thesis is that moral licensing is inextricably the same as “instrumental apology,” i.e., bad-faith apology. For instance, a decision mak... | [] |
91,662 | Pole test | 1 | dx.doi.org/10.17504/protocols.io.e6nvwdq5dlmk/v1 | https://www.protocols.io/view/pole-test-c5rny55e | Pranay Srivastava | TITLE: Pole test
AUTHORS: Pranay Srivastava
[DESCRIPTION]
Pole test is a behavior test for assessing motor dysfunction in rodents.
[STEPS]
1. Set up a vertical pole (1 cm diameter, 50 cm height) in a controlled testing
environment.
2. Allow the animals to acclimate to the testing environment for one hour before start... | ["Set up a vertical pole (1 cm diameter, 50 cm height) in a controlled testing\nenvironment.", "Allow the animals to acclimate to the testing environment for one hour before starting the test.", "Mice were trained on the pole one day before the start of the experiment for 120s. Time taken by the mice to turn (T turn) a... |
59,848 | S2 File The Protocols of the laboratory practical lessons | 4 | dx.doi.org/10.17504/protocols.io.b6pgrdjw | https://www.protocols.io/view/s2-file-the-protocols-of-the-laboratory-practical-b6pgrdjw | Jessica Gasparello, Chiara Papi, Matteo Zurlo, Lucia Carmela Cosenza, Giulia Breveglieri, Cristina Zuccato, Roberto Gambari, Alessia Finotti | TITLE: S2 File The Protocols of the laboratory practical lessons
AUTHORS: Jessica Gasparello, Chiara Papi, Matteo Zurlo, Lucia Carmela Cosenza, Giulia Breveglieri, Cristina Zuccato, Roberto Gambari, Alessia Finotti
[DESCRIPTION]
The protocols here described are related to the sections presented in Figure 1B focusing ... | ["[Part 1: Quality control of (i) the pCMV3-Spike-GFPSpark plasmid (Spike plasmid) and (ii) RNA extracted from A549 and Spike-plasmid transfected A549 cells] In a graduated cylinder prepare 1 L of solution diluting stock solution; with deionized water: 20 mL of TAE 50x and 980 mL of deionized water are required"... |
43,870 | RT&Tag (Reverse Transcribe & Tagment) | 4 | dx.doi.org/10.17504/protocols.io.x54v9jyjqg3e/v1 | https://www.protocols.io/view/rt-amp-tag-reverse-transcribe-amp-tagment-bn36mgre | Nadiya Khyzha | TITLE: RT&Tag (Reverse Transcribe & Tagment)
AUTHORS: Nadiya Khyzha
[DESCRIPTION]
Reverse Transcribe & Tagment (RT&Tag) is a method that capitalizes on the ability of the Tn5 transposase to tagment RNA-cDNA hybrids. RT&Tag bypasses immunoprecipitation and instead uses antibodies to tether a protein A-Tn5 trans... | ["[Prepare Concanavalin A beads] Mix the Concanavalin A (conA) bead slurry. Transfer 5μl of beads per sample into a 1.5ml eppendorf tube.\nWash with 1ml of Binding Buffer.\nPlace on magnet and remove the Binding Buffer.\nPerform a second wash with 1ml of Binding Buffer.\nResupend in 5μl of Binding Buffer per sample.\nA... |
28,961 | Virus Concentration and Infection | null | dx.doi.org/10.17504/protocols.io.8h9ht96 | null | Aditya Mohan | TITLE: Virus Concentration and Infection
AUTHORS: Aditya Mohan
[STEPS]
?. [Lentivirus Concentration]
Harvest the lentivirus-containing supernatants. (Caution: supernatants contain live lentivirus.) Pool similar stocks, if desired. Filter through a 0.45 μm filter.
?. [RetroNectin Plate Preparation]
Prepare RetroNectin ... | ["[Lentivirus Concentration]\nHarvest the lentivirus-containing supernatants. (Caution: supernatants contain live lentivirus.) Pool similar stocks, if desired. Filter through a 0.45 μm filter.", "[RetroNectin Plate Preparation]\nPrepare RetroNectin solution (30 ug/mL) by diluting RetroNectin powder (0.5 mg) into 16.6 m... |
90,785 | Working with patient-derived intestinal/colonic fibroblasts | 4 | null | https://www.protocols.io/view/working-with-patient-derived-intestinal-colonic-fi-c4v9yw96 | Tatiana Karakasheva | TITLE: Working with patient-derived intestinal/colonic fibroblasts
AUTHORS: Tatiana Karakasheva
[DESCRIPTION]
This is a protocol for working with patient-derived fibroblasts isolated from intestinal or colonic biopsies.
[STEPS] | [] |
92,177 | Understanding the influence of altered lipid metabolism on TDP-43 pathology: a protocol for a systematic review and meta-analysis | 3 | dx.doi.org/10.17504/protocols.io.8epv5xk75g1b/v1 | https://www.protocols.io/view/understanding-the-influence-of-altered-lipid-metab-c59ry956 | Holly Spence, Fergal M Waldron, Jenna Gregory, Tatiana Langerova | TITLE: Understanding the influence of altered lipid metabolism on TDP-43 pathology: a protocol for a systematic review and meta-analysis
AUTHORS: Holly Spence, Fergal M Waldron, Jenna Gregory, Tatiana Langerova
[DESCRIPTION]
Background: TDP-43 aggregation is the hallmark pathology seen at post-mortem in the majority o... | [] |
61,462 | 3D-correlative FIB-milling and Cryo-ET of Autophagic structures in Yeast Cells | 1 | dx.doi.org/10.17504/protocols.io.b79wrr7e | https://www.protocols.io/view/3d-correlative-fib-milling-and-cryo-et-of-autophag-b79wrr7e | Cristina Capitanio, Anna Bieber, Philipp S Erdmann, Brenda A Schulman, Florian Wilfling, Wolfgang Baumeister | TITLE: 3D-correlative FIB-milling and Cryo-ET of Autophagic structures in Yeast Cells
AUTHORS: Cristina Capitanio, Anna Bieber, Philipp S Erdmann, Brenda A Schulman, Florian Wilfling, Wolfgang Baumeister
[DESCRIPTION]
This protocol describes how to plunge-freeze yeast on EM grids and how to target autophagic s... | ["[YEAST CELL CULTURE] Prepare and starve yeast cells before plunging:", "[CRYO-CONFOCAL FLUORESCENCE MICROSCOPY] Take fluorescence stacks of target cells on a cryo-confocal fluorescence microscope for correlative focused ion beam milling and cryo-ET:", "[3D-CORRELATIVE FIB-MILLING] 3D-CORRELATIVE FIB MILLING\n\nTarget... |
91,748 | pHluorin assays, analysis, and fluorescence microscopy | 1 | dx.doi.org/10.17504/protocols.io.bp2l6xyx5lqe/v1 | https://www.protocols.io/view/phluorin-assays-analysis-and-fluorescence-microsco-c5ucy6sw | Leonardo A Parra-Rivas | TITLE: pHluorin assays, analysis, and fluorescence microscopy
AUTHORS: Leonardo A Parra-Rivas
[DESCRIPTION]
pHluorin assays, analysis, and fluorescence microscopy
[STEPS]
SECTION: Vesicle recycling measurements
1. Neurons expressing sypHy were imaged at 12-14 DIV. Experiments were conducted in standard extracellular ... | ["[Vesicle recycling measurements] Neurons expressing sypHy were imaged at 12-14 DIV. Experiments were conducted in standard extracellular solution containing (in mM): NaCl 150, KCl 3,Glucose 20, HEPES 10, CaCl2 2, MgCl2 3, pH adjusted to 7.35. To block recurrent network activity, experiments were conducted in the pres... |
67,370 | Organ Biopsy Protocol (Mammals): Post-mortem Sampling | 1 | dx.doi.org/10.17504/protocols.io.x54v9yx9mg3e/v1 | https://www.protocols.io/view/organ-biopsy-protocol-mammals-post-mortem-sampling-cd2is8ce | sanaz.arenivas, comizzolip, mhouck, racheljohnston, Jacquelyn Mountcastle, Budhan Pukazhenthi, phil.purdy | TITLE: Organ Biopsy Protocol (Mammals): Post-mortem Sampling
AUTHORS: sanaz.arenivas, comizzolip, mhouck, racheljohnston, Jacquelyn Mountcastle, Budhan Pukazhenthi, phil.purdy
[DESCRIPTION]
Version date: January 2023
The following protocol illustrates how to collect and ship living tissue from a deceased wild or capt... | ["[Tissue Collection] Wet the entire sampling area of the carcass in rubbing alcohol and blot with sterile absorbent gauze.", "[Tissue Collection] Remove the biopsy containers from the kit and have them readily available.", "[Tissue Collection] With sterile scissors or scalpel, cut through the body wall and aseptically... |
21,345 | Yale - Tissue Glycogen | null | dx.doi.org/10.17504/protocols.io.y39fyr6 | null | John Stack, Gary Cline | TITLE: Yale - Tissue Glycogen
AUTHORS: John Stack, Gary Cline
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Procedure for determining the glycogen content within liver and muscle tissue.</div></div>
[STEPS]
?. Homog... | ["Homogenization 1) Obtain samples of around 25mg. Keep samples in liquid nitrogen until ready to weigh. 2) Record weight. 3) Multiply weight of tissue by 5, and add that amount of 0.6N perchloric acid (PCA) to labeled 12x75mm plastic shaker tubes. Keep these tubes on ice. 4) Once done with above, add tissue to plastic... |
96,734 | Preparation for OCT embedding Mouse Kidney Tissue (TDA-University of Washington) | 0 | dx.doi.org/10.17504/protocols.io.6qpvr31b2vmk/v1 | https://www.protocols.io/view/preparation-for-oct-embedding-mouse-kidney-tissue-dap62dre | kangsk, Runze Dong, Liangcai Gu | TITLE: Preparation for OCT embedding Mouse Kidney Tissue (TDA-University of Washington)
AUTHORS: kangsk, Runze Dong, Liangcai Gu
[DESCRIPTION]
Preparation for OCT embedding Mouse Kidney Tissue (TDA-University of Washington)
[STEPS]
SECTION: Kidney tissue collection
1. C57BL/6J male mice from the National Institute of... | ["[Kidney tissue collection] C57BL/6J male mice from the National Institute of Aging Rodent Resource were handled according to the guidelines of the Institutional Animal Care Committee at the University of Washington. Mice aged 5 and 26 months were selected for the study. Kidney tissue extraction was conducted immedia... |
89,157 | Single-cell Fixed RNA sequencing from Formalin-Fixed, Paraffin-Embedded (FFPE)-Lung Tissue by Chromium Fixed RNA Profiling for Multiplexed Samples | 1 | dx.doi.org/10.17504/protocols.io.81wgbx483lpk/v1 | https://www.protocols.io/view/single-cell-fixed-rna-sequencing-from-formalin-fix-c3bdyii6 | Natalia-Del Pilar Vanegas, Jose A. Ovando-Ricardez, Lorena Rosas, Ana L. Mora, Mauricio Rojas | TITLE: Single-cell Fixed RNA sequencing from Formalin-Fixed, Paraffin-Embedded (FFPE)-Lung Tissue by Chromium Fixed RNA Profiling for Multiplexed Samples
AUTHORS: Natalia-Del Pilar Vanegas, Jose A. Ovando-Ricardez, Lorena Rosas, Ana L. Mora, Mauricio Rojas
[DESCRIPTION]
Fixed RNA Profiling provides an approach to FFPE... | ["Isolation of Cells from FFPE Tissue Sections for Chromium Fixed RNA Profiling According to Demonstrated Protocol CG000632 by 10x genomics.", "[Protocol] Prepare two 50 μm sections from the rehydrated FFPE tissue block and transfer them into a gentleMACSTM C Tube while keeping the scrolls intact.", "[Protocol] Add 3 m... |
39,685 | Tail Immersion Test | 1 | dx.doi.org/10.17504/protocols.io.eq2ly3rzpgx9/v2 | https://www.protocols.io/view/tail-immersion-test-bizdkf26 | Lani Tieu, Brent Boomhower, Olivier George | TITLE: Tail Immersion Test
AUTHORS: Lani Tieu, Brent Boomhower, Olivier George
[DESCRIPTION]
The tail immersion test measures pain response (tail flick latency) to thermal stimuli, and can be used to evaluate the effectiveness of and tolerance to analgesics (e.g. oxycodone).
[BEFORE_START]
Set up water bath:
Fill ap... | ["[General Procedure] Pick up rat from its home cage and wrap it in a towel or pee pad to restrain it, leaving tail exposed.", "[General Procedure] The dipper will hold the restrained animal over the water bath and count down before dipping 1 cm of the distal tail into the water. As soon as the tip of the tail is subme... |
76,489 | SMRT-Tag - Direct transposition of native DNA for sensitive multimodal single-molecule sequencing | 4 | dx.doi.org/10.17504/protocols.io.e6nvwk3b9vmk/v2 | https://www.protocols.io/view/smrt-tag-direct-transposition-of-native-dna-for-se-cnxhvfj6 | Scott Nanda, Ke Wu, Iryna Irkliyenko, Siva Kasinathan, vijay.ramani | TITLE: SMRT-Tag - Direct transposition of native DNA for sensitive multimodal single-molecule sequencing
AUTHORS: Scott Nanda, Ke Wu, Iryna Irkliyenko, Siva Kasinathan, vijay.ramani
[DESCRIPTION]
Here we describe a protocol for SMRT-Tag: Single-Molecule Real-Time sequencing by Tagmentation - a transposase-mediatedstra... | ["[Annealing SMRT-Tag adaptors] Reconstitute HPLC-purified SMRT-Tag adaptors (IDT) to 100 µM in nuclease-free water.", "[Annealing SMRT-Tag adaptors] Dilute adaptors to 20 µM in 1x annealing buffer (10mM Tris-HCl pH 7.5 and 100mM NaCl) in PCR tubes.", "[Annealing SMRT-Tag adaptors] Place the tubes in a thermocycler at ... |
null | null | null | dx.doi.org/10.17504/protocols.io.etnbeme | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is based on the study done by two members of the Biological and Agricultural Engineering department at UC Davis which analyzes the ability of infrared spectroscopy to detect fungal infections in almonds. The methods section of this article was adapted to fit the... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.pa9dih6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes how to prepare bacteria for further storage at -80 °C.</p>
[GUIDELINES]
<p>Always work under sterile conditions to avoid contamination.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.fbebije | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.fs5bng6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?. | [] |
36,585 | Tris-HCl Buffer | null | dx.doi.org/10.17504/protocols.io.bfyhjpt6 | https://www.protocols.io/view/tris-hcl-buffer-bfyhjpt6 | Neilier Junior | TITLE: Tris-HCl Buffer
AUTHORS: Neilier Junior
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A buffer solution has the function of resisting changes in pH even when adding powerful acids or bases. However, in the physiological environment the buffered system also provides cofactors for enzymatic r... | ["[Tris-HCl Buffer]\nMix and indicated volume of hydrochloric acid. ABCDEFGH1mL of HCl44.241 .438.432.521 .912.25.02pH7.27.47.67.88.28.69.0\npH range: to \n(a) 0.1 M Tris(hydroxymethyl)aminomethane; 12.1 g L-1 (M.W.: 121.0 g mol-1)(b) 0.1 M Hydrochloric acid\n[Tris(hydroxymethyl)aminomethane]\nABCDEFGH1mL of HCl44... |
78,522 | Protein Concentration Determination using Qubit 4 Fluorometer | 4 | null | https://www.protocols.io/view/protein-concentration-determination-using-qubit-4-cqw2vxge | Steven J Burgess | TITLE: Protein Concentration Determination using Qubit 4 Fluorometer
AUTHORS: Steven J Burgess
[DESCRIPTION]
Procedure for quantification of protein concentration using a Qubit 4 Fluorometer. The procedure follows the manufacturer's instructions, this version is adapted for use with samples that have been extracted in... | ["[Create Working Solution for Analysis] Create a working solution of Qubit assay buffer by diluting the reagent 1:200 in the provided buffer.", "[Create Sample Dilution for Analysis] Dilute sample 1:50 (196 µL dH2O + 4 µL sample)", "[Create Sample Dilution for Analysis] Add 190 µL of Qubit working solution to a fresh ... |
29,534 | cFos DAB IHC Protocol | 1 | null | https://www.protocols.io/view/cfos-dab-ihc-protocol-836hyre | Yueyi Chen, Adam Kimbrough, Olivier George | TITLE: cFos DAB IHC Protocol
AUTHORS: Yueyi Chen, Adam Kimbrough, Olivier George
[STEPS]
?. Day 1
?. Rinse in PBS (if sections have been stored in PBS/Azide)
?. Quench endogenous peroxidase activity: Incubate sections for 20 minutes in 1% Hydrogen peroxide/ PBS (330µl 30% H2O2 in 10 ml PBS)
?. Rinse in PBS 3 times ... | ["Day 1", "Rinse in PBS (if sections have been stored in PBS/Azide)", "Quench endogenous peroxidase activity: Incubate sections for 20 minutes in 1% Hydrogen peroxide/ PBS (330µl 30% H2O2 in 10 ml PBS)", "Rinse in PBS 3 times x 10 minutes each", "Blocking: Incubate section at room temperature for a minimum of 60 ... |
41,878 | Accessible Health Sentinal Test Protocol | 4 | dx.doi.org/10.17504/protocols.io.bk5wky7e | https://www.protocols.io/view/accessible-health-sentinal-test-protocol-bk5wky7e | John Warner, Rebecca Silveston, Delphine Dean | TITLE: Accessible Health Sentinal Test Protocol
AUTHORS: John Warner, Rebecca Silveston, Delphine Dean
[STEPS]
?. [App Download]
Once the user receives their test kit, they will download the Accessible Health App to their phone through the Apple App Store or Google Play store.
?. [App Download]
The app can be found ... | ["[App Download]\nOnce the user receives their test kit, they will download the Accessible Health App to their phone through the Apple App Store or Google Play store.", "[App Download]\nThe app can be found on the store by searching manually or automatically downloaded by using a QR code on the test kit packaging.", "[... |
null | null | null | dx.doi.org/10.17504/protocols.io.kx5cxq6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol covers the inoculation, cultivation, IPTG-induction and plate reader measurement of <em>E. coli</em> BL21 strains carrying constructs with various toehold switch devices from Green <em>et al</em>., 2014.</p>
[BEFORE_START]
<p> </p>
<table style="height: 184px; ... | [] |
36,797 | TissueCyte Specimen Embedding Acrylamide Coembedding | null | dx.doi.org/10.17504/protocols.io.bf65jrg6 | https://www.protocols.io/view/tissuecyte-specimen-embedding-acrylamide-coembeddi-bf65jrg6 | Allen Institute for Brain Science | TITLE: TissueCyte Specimen Embedding Acrylamide Coembedding
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the preparation of a fixed mouse brain specimen bonded to an agarose block for blockface imaging and sectioning using the Tis... | [] |
10,999 | Salty sample derivatization protocol for GC-MS | null | dx.doi.org/10.17504/protocols.io.nyxdfxn | null | Emilia Sogin, Erik Pukus, Nicole Dubilier, Manuel Liebeke | TITLE: Salty sample derivatization protocol for GC-MS
AUTHORS: Emilia Sogin, Erik Pukus, Nicole Dubilier, Manuel Liebeke
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Metabolomic footprinting, or exometabolomics, seeks to describe the complex chemical space surrounding cells. However, metabo... | ["[Sample Drying]\nDry 0.5 to 1 ml of a salty sample for 6 hr using an eppendorf Concentrator plus SpeedVac at 45 °C in V-AQ mode. Critical step: the drying in the SpeedVac should take no longer than 6h, otherwise the samples could degrade. Samples can be kept in SpeedVac overnight after the run", "[Sample Drying]\nAft... |
29,063 | FFPE Tissue Sectioning for CODEX | null | dx.doi.org/10.17504/protocols.io.8mfhu3n | null | Marda Jorgensen, Franchesca Farris | TITLE: FFPE Tissue Sectioning for CODEX
AUTHORS: Marda Jorgensen, Franchesca Farris
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">FFPE tissues for CODEX® analysis must adhere directly onto Poly-lysine-coated coverslips. Preparation and storage of tissue slices are critical for sample integrity.</d... | ["Prepare a water bath at 40°C and place it next to the Microtome.", "Prepare a clean, dry surface for laying the coverslips next to the Microtome.", "Use an aerosol spray to clean coverslips from dust and lint prior to use.", "Insert a new blade for sectioning each block", "Section the tissue between 5-10 µm thick.", ... |
84,260 | Chronic Recoverable Neuropixels in Mice | 2 | dx.doi.org/10.17504/protocols.io.e6nvwjo87lmk/v2 | https://www.protocols.click/view/chronic-recoverable-neuropixels-in-mice-cwicxcaw | Emily A Aery Jones | TITLE: 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 Neuropixels 2.0 probes into mice, record during freely moving behavior, then recover the probes for future use. ... | [] |
47,817 | S.O.F protocol for nuclei isolation from fresh and frozen tissues using OptiPrep® discontinuous gradient | 1 | dx.doi.org/10.17504/protocols.io.bsxhnfj6 | https://www.protocols.io/view/s-o-f-protocol-for-nuclei-isolation-from-fresh-and-bsxhnfj6 | Luciano Martelotto | TITLE: S.O.F protocol for nuclei isolation from fresh and frozen tissues using OptiPrep® discontinuous gradient
AUTHORS: Luciano Martelotto
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is the result of the combination of various nuclei isolation protocols for single cell RNA-seq ex... | ["[Tissue Homogenization]\nMince/chop tissue with a razor blade to small pieces. The tissue may be as small as a grain of rice.\nFor mincing the tissue, you may take the tube out of ice, however, be quick and return to ice.", "[Tissue Homogenization]\nAdd of chilled Nuclei EZ Lysis Buffer (supplemented with RNAse Inhi... |
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