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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85,854 | Indirect Proximity Ligation Assay (PLA) - Fluoresence | 1 | dx.doi.org/10.17504/protocols.io.261ged36dv47/v1 | https://www.protocols.io/view/indirect-proximity-ligation-assay-pla-fluoresence-cx36xqre | Ayse Ulusoy, Rita Pinto-Costa, Angela Rollar, Donato Di Monte | TITLE: Indirect Proximity Ligation Assay (PLA) - Fluoresence
AUTHORS: Ayse Ulusoy, Rita Pinto-Costa, Angela Rollar, Donato Di Monte
[DESCRIPTION]
Indirect Proximity Ligation Assay (PLA) is a powerful molecular technique used to detect and visualize protein-protein interactions, protein modifications, and protein compl... | ["[Day 1] Pick 35um cut brain sections and transfer them to 1.5 mL Eppendorf tubes:\nNote: all incubation and wash steps are performed by shaking Eppendorf tubes at 250rpm (e.g., thermomixer)", "[Day 1] Wash 2x5 min with Tris-HCl", "[Day 1] Wash 3x5 min with wash buffer A (see materials)", "[Day 1] Antigen-retrieval wi... |
61,521 | Code_file_Laborde-et-al_Environmental-barriers_Functional-decline | 3 | dx.doi.org/10.17504/protocols.io.ewov1nzw2gr2/v1 | https://www.protocols.io/view/code-file-laborde-et-al-environmental-barriers-fun-b8brrsm6 | laborde_caroline | TITLE: Code_file_Laborde-et-al_Environmental-barriers_Functional-decline
AUTHORS: laborde_caroline
[DESCRIPTION]
Code file for "Environmental barriers matter from the early stages of functional decline among older adults in France" by: Caroline Laborde, Joël Ankri and Emmanuelle Cambois
[STEPS] | [] |
89,936 | A Condução do Experimento - Avaliando o Jogo de Fisica | 1 | dx.doi.org/10.17504/protocols.io.yxmvm35k9l3p/v1 | https://www.protocols.io/view/a-condu-o-do-experimento-avaliando-o-jogo-de-fisic-c33qyqmw | Geiser Chalco Challco | TITLE: A Condução do Experimento - Avaliando o Jogo de Fisica
AUTHORS: Geiser Chalco Challco
[DESCRIPTION]
O protocolo corresponde ao teste de duas versões de jogo de ensino de fisica , uma fundamentada na experiencia de fluxo e uma outra sem fundamentação da teoria da experiencia de fluxo
[STEPS]
SECTION: Pre-teste
... | ["[Pre-teste] Todos os participantes devem assinar TCLE (se for menor de idade) ou TALE(se for maior de idade)", "[Pos-Teste] Aplicar o FSS-2 (https://forms.gle/pjPyS168Rzv8FKQT6) e formulário de usabilidade (https://forms.gle/9s5fkfSX7LwGnyjh7) 10 min", "[Pos-Teste] Aplicar o FSS-2 (https://forms.gle/pjPyS168Rzv8FKQT6... |
89,376 | Real-time and programmable transcriptome sequencing with PROFIT-seq | 5 | dx.doi.org/10.17504/protocols.io.5jyl8p19rg2w/v1 | https://www.protocols.io/view/real-time-and-programmable-transcriptome-sequencin-c3h8yj9w | lingling hou, Jinyang Zhang | TITLE: Real-time and programmable transcriptome sequencing with PROFIT-seq
AUTHORS: lingling hou, Jinyang Zhang
[DESCRIPTION]
PROgrammable Full-length Isoform Transcriptome sequencing (PROFIT-seq) is a method that enriches target transcripts while maintaining unbiased quantification of the whole transcriptome. PROFIT-... | ["[Ribosomal RNA depletion] Remove ribosomal RNA from extracted RNA samples:", "[4. Nanopore sequencing] Install and configuration MinKNOW", "[Reverse transcription] Add 0.5 µLof 1.4 micromolar (µM)RT.N6.ds oligos to the mixture.", "[Reverse transcription] Prepare the following mix containing the components listed belo... |
62,058 | Cómo hacer un protocolo nuevo | 1 | dx.doi.org/10.17504/protocols.io.6qpvr6myzvmk/v1 | https://www.protocols.io/view/c-mo-hacer-un-protocolo-nuevo-b8uirwue | Anita Broellochs, Lenny Teytelman, Alexei Stoliartchouk, Gabriel Gasque | TITLE: Cómo hacer un protocolo nuevo
AUTHORS: Anita Broellochs, Lenny Teytelman, Alexei Stoliartchouk, Gabriel Gasque
[DESCRIPTION]
Este protocolo describe cómo crear un nuevo protocolo en protocols.io.
[BEFORE_START]
Todas los cambios que realice en el protocolo se guardarán automáticamente.
[GUIDELINES]
prot... | ["[Comenzando nuevo protocolo] Haga clic en el ícono + en la esquina superior derecha para abrir el menú principal y seleccione 'New protocol'.", "[Adición de descripción de protocolo] Añada un titulo. Este será el nombre de su protocolo.", "[Adicione instrucciones y advertencias] Vaya a la pestaña \"Guidelines & Warni... |
34,693 | Probe-based target enrichment of SARS-CoV-2 | null | dx.doi.org/10.17504/protocols.io.bd5di826 | null | Mariateresa De Cesare | TITLE: Probe-based target enrichment of SARS-CoV-2
AUTHORS: Mariateresa De Cesare
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><ul style = "list-style-type:disc;"><li style = "counter-reset:ol0;list-style-type:disc;"><span>Viral RNA library prep using </span><span style = "font-weight:bold;">SMAR... | ["[Preparations]\nBring the RNAClean XP (A63987) to .\n0 Room temperature", "[Preparations]\nEnsure a chilling block to accommodate 384-well plates is at .\n-20 °C", "[Preparations]\nDefrost reagents (SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian and SMART TSO Mix v2) .\non ice", "[Preparations]\nPrepare... |
79,422 | hissPCR: A simple, single-tube overlapping amplicon-targeted Illumina sequencing assay. | 4 | dx.doi.org/10.17504/protocols.io.q26g7yw79gwz/v1 | https://www.protocols.io/view/hisspcr-a-simple-single-tube-overlapping-amplicon-crs6v6he | Jason D Limberis, Alina Nalyvayko, Joel Ernst, john.metcalfe | TITLE: hissPCR: A simple, single-tube overlapping amplicon-targeted Illumina sequencing assay.
AUTHORS: Jason D Limberis, Alina Nalyvayko, Joel Ernst, john.metcalfe
[DESCRIPTION]
Targeted amplicon sequencing to identify pathogens, resistance-conferring mutations, and strain types is an important tool in diagnosing and... | ["[Stage 1 PCR] COMPONENT FINAL C. 50ul 5X Reaction Buffer 1X 10 5X GC Buffer 1X 10 10 mM dNTPs 200 µM 1 AtpE_stilPCRm1_F1 0.1µM 0.5 AtpE_stilPCRm1_R1 0.1µM 0.5 Rv0678_stilPCRm1_F1 0.1µM 0.5 Rv0678_stilPCRm1_R2 0.1µM 0.5 Template DNA – 2 Q5 High-Fidelity DNA Polymerase 0.... |
null | null | null | dx.doi.org/10.17504/protocols.io.eimbcc6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol outlines our alpha diversity analyses of the virome (from PHACCS) and whole metagenome (from MetaPhlan OTU table). We start by comparing the virome and whole metagenome alpha diversity values, and then look at the differences in virome and whole metagenome diversit... | [] |
102,584 | Optimized Protocol for RNA Extraction from Insect Samples Using TRIzol Reagent | 0 | dx.doi.org/10.17504/protocols.io.yxmvmepx9g3p/v1 | https://www.protocols.io/view/optimized-protocol-for-rna-extraction-from-insect-dgey3tfw | Monique da Silva Bonjour, Ian de Paula Alves Pinto, Angelo José Rinaldi | TITLE: Optimized Protocol for RNA Extraction from Insect Samples Using TRIzol Reagent
AUTHORS: Monique da Silva Bonjour, Ian de Paula Alves Pinto, Angelo José Rinaldi
[DESCRIPTION]
RNA extraction from insect samples is a crucial step in molecular biology studies aimed at understanding gene expression, functional genom... | ["[Steps] Cover the crucible with liquid nitrogen to keep the sample cold", "[Steps] Place the sample (about 50mg) and macerate, keeping it cold. Remove the wings and macerate insect samples as they have a strong exoskeleton and the presence of chitin", "[Steps] Add 1mL of Trizol and wait for it to thaw", "[Steps] Mix ... |
90,885 | Immunohistochemistry on free-floating and paraffin-embedded tissue sections | 4 | dx.doi.org/10.17504/protocols.io.dm6gp356pvzp/v1 | https://www.protocols.io/view/immunohistochemistry-on-free-floating-and-paraffin-c4zdyx26 | Ching-Chieh Chou, Judith Frydman | TITLE: Immunohistochemistry on free-floating and paraffin-embedded tissue sections
AUTHORS: Ching-Chieh Chou, Judith Frydman
[DESCRIPTION]
This protocol is used for free-floating frozen (30-50 microns) and paraffin-embedded (10 microns) tissue sections.
[STEPS]
SECTION: Materials
1. Free-floating
PBS
0.3% Triton-X-10... | ["[Materials] Free-floating\nPBS\n0.3% Triton-X-100 in PBS 1x, stored at 4°C\nNormal Donkey Serum (NDS), stored at -20°C\nBlocking Buffer: 10% NDS and 0.03% Triton-X-100 in PBS 1x. Diluted from 100% NDS (stored at -20°C) and 0.3% Triton-X-100. Filtered with 0.22 µM filter.\nPrimary Antibody\nSecondary Antibody\nHoechst... |
null | null | null | dx.doi.org/10.17504/protocols.io.qz2dx8e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The concentration and purification of giant DNA viruses from bacteria-containing cultures can present problems because the particle size of giant viruses overlaps with that of smaller bacteria, hence filtration as the only separation method is not possible.</p>
<p>In this pro... | [] |
86,215 | Preparing mitochondrial samples for immunoblot analysis | 4 | dx.doi.org/10.17504/protocols.io.n2bvj38enlk5/v1 | https://www.protocols.io/view/preparing-mitochondrial-samples-for-immunoblot-ana-cyffxtjn | Louise Uoselis | TITLE: Preparing mitochondrial samples for immunoblot analysis
AUTHORS: Louise Uoselis
[DESCRIPTION]
Protocol for preparation of mitochondrial samples for immunoblot analysis.
[STEPS]
1. Thaw mitochondrial stocks on ice, and aliquot out the desired amount of mitochondria.
2. Centrifuge each aliquot for 10 min 10000 ... | ["Thaw mitochondrial stocks on ice, and aliquot out the desired amount of mitochondria.", "Centrifuge each aliquot for 10 min 10000 x g, 4 °C", "Carefully aspirate the supernatant from each sample.", "Add a volume of 1x SDS sample buffer (5% w/v SDS, 10% v/v glycerol, 100 mM DTT, 50 mM Tris-Cl pH 6.8) equal to the amo... |
99,132 | DNA EXTRACTION Protocol Template | 1 | null | https://www.protocols.io/view/dna-extraction-protocol-template-dc242ygw | Andreas Novotny | TITLE: DNA EXTRACTION Protocol Template
AUTHORS: Andreas Novotny
[DESCRIPTION]
A protocol template created through the BeBOP project for DNA Extraction.
[BEFORE_START]
Read background information, MIOP and BePOP-OBON information under the "Guidelines" tab.
[GUIDELINES]
MIOP: Minimum Information about an Omics Proto... | ["[STANDARD OPERATING PROCEDURE] In the following SOP, please use the exact names of equipment as noted in the table above.\n\nProvide a step-by-step description of the protocol. The identification of difficult steps in the protocol and the provision of recommendations for the execution of those steps are encouraged.",... |
45,875 | C-SOP-202: Genomic DNA Purity Measurement using a Nanodrop Spectrophotometer | 4 | null | https://www.protocols.io/view/c-sop-202-genomic-dna-purity-measurement-using-a-n-bq2tmyen | Mihir Kekre | TITLE: C-SOP-202: Genomic DNA Purity Measurement using a Nanodrop Spectrophotometer
AUTHORS: Mihir Kekre
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A standard technique for performing purity measurements is UV absorbance with a spectrophotometer. Microvolume spectrophotometers are commonly used... | ["[Before Starting]\nAn initial cleaning of measurement surfaces with nuclease-free (NF) water is recommended prior to making the blank measurement. To clean the pedestal, pipette of NF water onto the pedestal and lower the arm. Leave to sit for and then wipe away with lint-free tissue. Fig. 1a and 1b illustrate the... |
102,851 | Antibody and TDP-43 RNA aptamer dual staining to detect patterns of co-pathology in FFPE-preserved human tissue, as described in Rifai et al., 2024 (Brain Pathology): A SOP and tick-sheet. | 0 | dx.doi.org/10.17504/protocols.io.14egn6wnml5d/v1 | https://www.protocols.io/view/antibody-and-tdp-43-rna-aptamer-dual-staining-to-d-dgpb3vin | Fergal M Waldron, Olivia Rifai, Jenna Gregory | TITLE: Antibody and TDP-43 RNA aptamer dual staining to detect patterns of co-pathology in FFPE-preserved human tissue, as described in Rifai et al., 2024 (Brain Pathology): A SOP and tick-sheet.
AUTHORS: Fergal M Waldron, Olivia Rifai, Jenna Gregory
[DESCRIPTION]
Here we provide a SOP to outline the correct procedur... | [] |
19,283 | Immunohistochemistry and high resolution microscopy of human gastric enteroendocrine cells | 1 | dx.doi.org/10.17504/protocols.io.w3tfgnn | https://www.protocols.io/view/immunohistochemistry-and-high-resolution-microscop-w3tfgnn | Josiane Fakhry, Martin Stebbing, Billie Hunne, John B. Furness | TITLE: Immunohistochemistry and high resolution microscopy of human gastric enteroendocrine cells
AUTHORS: Josiane Fakhry, Martin Stebbing, Billie Hunne, John B. Furness
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Enteroendocrine cells are important regulators of gastrointestinal, digestive and ... | ["Stomach regions were collected from six patients who were undergoing gastric sleeve surgery for obesity at the Renown Regional Medical Center, Reno, Nevada. Resections were of the full greater curvature (from the fundus to the antrum) from male and female patients between the ages of 48 and 60 who were non-diabetic. ... |
null | null | null | dx.doi.org/10.17504/protocols.io.mpvc5n6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>In vitro transcriptions assay for cyanobacterial RNA polymerase. This protocol can be used either to do an in vitro transcription with small DNA fragments with desired promoter region or to use it with a promoter region integrated in a plasmid.</p>
[BEFORE_START]
<p>Prepare ... | [] |
73,350 | RAPIDprep: A simple, fast protocol for RNA metagenomic sequencing of clinical samples | 1 | null | https://www.protocols.io/view/rapidprep-a-simple-fast-protocol-for-rna-metagenom-cjveun3e | Karan Kim, Racheltulloch, John-Sebastian Eden | TITLE: RAPIDprep: A simple, fast protocol for RNA metagenomic sequencing of clinical samples
AUTHORS: Karan Kim, Racheltulloch, John-Sebastian Eden
[DESCRIPTION]
The protocol allows rapid RNA metagenome sequencing of pathogens of clinical respiratory samples. The protocol has been designed to be simple and quick to en... | ["[RNA extraction] Extract RNA with , following manufacturer's instructions.", "[DNase treatment] Mix well by gently pipetting up and down, and briefly centrifuge.", "[DNA libarary preparation and sequencing]", "[DNA libarary preparation and sequencing] Run in Illumina iSeq.", "[DNase treatment] Setup the following re... |
32,560 | Quick Ligation Protocol (M2200) | 1 | dx.doi.org/10.17504/protocols.io.bb2qiqdw | https://www.protocols.io/view/quick-ligation-protocol-m2200-bb2qiqdw | New England Biolabs | TITLE: Quick Ligation Protocol (M2200)
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocols is to be performed with the Quick Ligation Reaction Buffer. Please see the NEB website for more information.</div></div>
[STEPS]
?. Set up the following reaction in a ... | ["Set up the following reaction in a microcentrifuge tube . AB1COMPONENT20 μl REACTION2Quick Ligase Reaction Buffer (2X)*10 µl3Vector DNA (3 kb)50 ng (0.020 pmol)4Insert DNA (1 kb)37.5 ng (0.060 pmol)5Nuclease-free Waterto 20 µl6Quick Ligase1 µl\non ice\nQuick Ligase should be added last. Note that the table shows a l... |
28,132 | Protein Purification strep-tag FPLC | null | dx.doi.org/10.17504/protocols.io.7qchmsw | null | Cleo B. | TITLE: Protein Purification strep-tag FPLC
AUTHORS: Cleo B.
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protein purification of proteins containing a strep-tag using FPLC. </div><div class = "text-block">Necessary: </div><div class = "text-block">Have performed Protein expression using E. coli ... | ["[Buffers]\n1 L Buffer W: 100 mM Tris-HCl (pH 8.0) 150 mM NaCl1 mM EDTAFilter this buffer with a 22 um filter \n100 mL Buffer E: 100 mM Tris-HCl (pH 8.0) 150 mM NaCl1 mM EDTA2.5 mM desthiobiotin Filter this buffer with a 22 um filter 100 mL Buffer E: 100 mM Tris-HCl (pH 8.0) 150 mM NaCl1 mM EDTA2.5 mM desthiobiotin 1L... |
null | null | null | dx.doi.org/10.17504/protocols.io.rikd4cw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The major ion concentration data of sodium (Na), potassium (K), calcium (Ca), magnesium (Mg), chloride (Cl), sulphate (SO<sub>4</sub>), bicarbonate (HCO<sub>3</sub>), carbonate (CO<sub>3</sub>) and pH (if it was coupled with ion data) were input into the database. The data we... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.e26bghe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Anti-Neu5Gc may be used for staining cells prior to analysis by Flow Cytometry. This kit contains all the essential components needed to identify Neu5Gc on the surface of cells by flow cytometry.</p>
<p> </p>
<p>Use of the blocking agent (Neu5Gc Assay Blocking Solution) provi... | [] |
71,156 | SDS-PAGE | 4 | dx.doi.org/10.17504/protocols.io.5jyl85o7dl2w/v2 | https://www.protocols.io/view/sds-page-chqut5ww | Anna Bird, Chiara Gandini | TITLE: SDS-PAGE
AUTHORS: Anna Bird, Chiara Gandini
[DESCRIPTION]
SDS-PAGE gels are used to visualize proteins. This protocol describes how to prepare all the buffers required for casting and running SDS-PAGE gels, as well as how to prepare whole cell samples.
[STEPS]
SECTION: Buffers
1. 4X Resolving Buffer (1.5 M Tri... | ["[Buffers] 4X Resolving Buffer (1.5 M Tris-HCl, pH 8.8)\nAdd 90.75 g to 400 mL DI water\nTitrate the solution with ~18% HCl to pH 8.8\nAdd water to a final volume of 500 mL \nStore at 4°C", "[Buffers] 4X Stacking Buffer (0.5 M Tris-HCl, pH 6.8)\nAdd 30.25 g to 400 mL DI water\nTitrate the solution with ~18% HCl ... |
95,582 | Lysosome analysis with confocal microscopy | 4 | null | https://www.protocols.io/view/lysosome-analysis-with-confocal-microscopy-c9j6z4re | Sjors Maassen | TITLE: Lysosome analysis with confocal microscopy
AUTHORS: Sjors Maassen
[DESCRIPTION]
This protocol provides an overview of lysosomal analysis using confocal microscopy and Fiji
[STEPS]
SECTION: Sterilize glass cover slips
1. Put the glass coverslips in a 24-well plate, submerge the coverslips in 70% ethanol, and th... | ["[Sterilize glass cover slips] Put the glass coverslips in a 24-well plate, submerge the coverslips in 70% ethanol, and then expose them to UV light in a tissue culture hood for between 20 and 30 minutes.", "[Sterilize glass cover slips] Remove the ethanol, wash the wells containing coverslips three times with sterile... |
null | null | null | dx.doi.org/10.17504/protocols.io.srfed3n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><em></em>The light/dark test is increasingly being adopted as one of the main behavioral assays in zebrafish neuroscience research. It is based on the innate preference of adult zebrafish for a black vs. a white compartment. Modifications and extensions of the protocol increa... | [] |
70,239 | MILLIPLEX® Human Cytokine/Chemokine/Growth Factor Panel A - Immunology Multiplex Assay | 1 | dx.doi.org/10.17504/protocols.io.n2bvj8rkbgk5/v1 | https://www.protocols.io/view/milliplex-human-cytokine-chemokine-growth-factor-p-cgt7twrn | Jen Frye | TITLE: MILLIPLEX® Human Cytokine/Chemokine/Growth Factor Panel A - Immunology Multiplex Assay
AUTHORS: Jen Frye
[DESCRIPTION]
This protocol describes lab processing as well as data processing for the MILLIPLEX‱ Human Cytokine/Chemokine/Growth Factor Panel A - Immunology Multiplex Assay
[STEPS]
SECTION: Sample prepara... | ["[Sample preparation] Thaw plasma samples completely on ice.15 min", "[Sample preparation] Centrifuge thawed samples at 5000 x g @ 4°C for 10 minutes to remove particulates.5000 x g, 10 min, 4 °C", "[Sample preparation] Mix well by vortexing.", "[Reagent preparation] Preparation of Quality Controls", "[Reagent prepara... |
79,155 | Organ Biopsy Protocol (Mammals): Post-mortem Sampling | 1 | dx.doi.org/10.17504/protocols.io.x54v9yx9mg3e/v2 | https://www.protocols.io/view/organ-biopsy-protocol-mammals-post-mortem-sampling-critv4en | sanaz.arenivas, comizzolip, mhouck, Rachel A Johnston, Jacquelyn Mountcastle, Budhan Pukazhenthi, phil.purdy | TITLE: Organ Biopsy Protocol (Mammals): Post-mortem Sampling
AUTHORS: sanaz.arenivas, comizzolip, mhouck, Rachel A Johnston, Jacquelyn Mountcastle, Budhan Pukazhenthi, phil.purdy
[DESCRIPTION]
Version date: April 2023
The following protocol illustrates how to collect and ship living tissue from a deceased wild or cap... | ["[Preparation] Pre-chill icepacks in the freezer the day before planning to collect and ship samples.", "[Preparation] Record all information indicated in the biopsy form, including a picture of the animal for identification and GPS location where the animal was found.", "[Preparation] Proper protective equipment must... |
null | null | null | dx.doi.org/10.17504/protocols.io.kcvcsw6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This method describes magnetic particle based DNA purification. </p>
<p> </p>
<p> </p>
<p> </p>
[BEFORE_START]
<p>Make 80% Ethanol. Do not use 80% Ethanol that is more than 3 days old. </p>
[GUIDELINES]
<p><strong>Materials:</strong></p>
<p> </p>
<p>80% Ethanol, made fres... | [] |
17,081 | Practical guide to characterize the source of pain in pet animals | null | dx.doi.org/10.17504/protocols.io.uwzexf6 | null | Eric Troncy, Beatriz P Monteiro, Maxim Moreau, Colombe Otis | TITLE: Practical guide to characterize the source of pain in pet animals
AUTHORS: Eric Troncy, Beatriz P Monteiro, Maxim Moreau, Colombe Otis
[STEPS]
?. [Practical guide to characterize the source of pain in pet animals] | ["[Practical guide to characterize the source of pain in pet animals]"] |
100,386 | Calculating the Cause of Death Association Indicator and the Contributing Cause of Death Association Indicator in Mortality Analysis | 0 | dx.doi.org/10.17504/protocols.io.e6nvw1dd7lmk/v1 | https://www.protocols.io/view/calculating-the-cause-of-death-association-indicat-deaa3aae | Agnieszka Fihel, Anna Janicka | TITLE: Calculating the Cause of Death Association Indicator and the Contributing Cause of Death Association Indicator in Mortality Analysis
AUTHORS: Agnieszka Fihel, Anna Janicka
[DESCRIPTION]
The protocol describes the input data and the method used to calculate the Cause of Death Association Indicators and the Contr... | ["[Input data] The input data consists of death counts aggregated by country, year, sex, age group (30-59 and 60+), the underlying cause of death u, and cause c reported in any section of the death certificate other than the underlying cause of death. In practice, causes u and c refer to groups of causes of death, agg... |
60,898 | Depletion of mtDNA with Ethidium Bromide | 4 | dx.doi.org/10.17504/protocols.io.rm7vzy6e5lx1/v1 | https://www.protocols.io/view/depletion-of-mtdna-with-ethidium-bromide-b7qarmse | William Hancock-Cerutti, Pietro De Camilli | TITLE: Depletion of mtDNA with Ethidium Bromide
AUTHORS: William Hancock-Cerutti, Pietro De Camilli
[DESCRIPTION]
This protocol describes the depletion of mitochondrial DNA (mtDNA) from HeLa cells using ethidium bromide (EtBr).
[STEPS] | [] |
98,576 | Cell culture of THP-1 monocytes and differentiation into macrophages with PMA | 0 | dx.doi.org/10.17504/protocols.io.5jyl8255dl2w/v1 | https://www.protocols.io/view/cell-culture-of-thp-1-monocytes-and-differentiatio-dchq2t5w | Sylvia Oghogho Omage, Maria Wallert, Stefan Lorkowski | TITLE: Cell culture of THP-1 monocytes and differentiation into macrophages with PMA
AUTHORS: Sylvia Oghogho Omage, Maria Wallert, Stefan Lorkowski
[DESCRIPTION]
THP-1 is a human monocytic cell line originally isolated from a 1-year old male subject with acute monocytic leukemia (Tsuchiya et al., 1980). The cells are ... | ["[Thawing of THP-1 cells] Transfer the cryotube containing THP-1 monocytes from the liquid nitrogen tank to the cell culture lab on ice.\n\nNote: Wear protective gloves, goggles and a lab coat when handling liquid nitrogen to prevent burns.", "[Thawing of THP-1 cells] Thaw the cells immediately in a 37 °C water bath u... |
75,095 | LEGACY01: STUDY DESIGN | 1 | null | https://www.protocols.io/view/legacy01-study-design-cmjxu4pn | Katrina M Pollock, Calliope Dendrou | TITLE: LEGACY01: STUDY DESIGN
AUTHORS: Katrina M Pollock, Calliope Dendrou
[DESCRIPTION]
This protocol details the study design in an experimental medicine study of seasonal influenza vaccination responses in Lymph nodE single-cell Genomics in AnCestrY (LEGACY01).
[GUIDELINES]
STUDY DESIGN
Interventional experimenta... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ivdce26 | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
<p>The protocol remains unmodified from original kit protocol, with the exception of steps 9, 10 and 11.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
20,137 | Bulk Calling Cards Library Preparation | null | dx.doi.org/10.17504/protocols.io.xwhfpb6 | null | Arnav Moudgil, Michael N. Wilkinson, Xuhua Chen, Robi D. Mitra | TITLE: Bulk Calling Cards Library Preparation
AUTHORS: Arnav Moudgil, Michael N. Wilkinson, Xuhua Chen, Robi D. Mitra
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes how to create calling card libraries from bulk RNA. This protocol assumes you have successfully transfor... | ["[RNA Extraction with QIAGEN's RNEasy Plus Mini Kit]\nHarvest cells. Process each replicate independently. Do not overload gDNA Eliminator columns. If you have more than 107 cells, split cells in half and process on two columns, then merge the RNA pools. Adherent cells may have to be dissociated using trypsin or a cel... |
54,041 | Virome Extraction | 4 | dx.doi.org/10.17504/protocols.io.byzzpx76 | https://www.protocols.io/view/virome-extraction-byzzpx76 | Frej Larsen | TITLE: Virome Extraction
AUTHORS: Frej Larsen
[DESCRIPTION]
This protocol is for isolation of bacteriophages from fecal matter. It is based on the protocol used for the COPSAC10 cohort and was originally described by Ling Deng in doi:10.3390/v11070667. Extraction is performed using centrifugation and ultrafiltration... | ["Thaw frozen sample in ice bucket", "Transfer up to 500 mg of sample to centrifuge tube and add SM buffer to reach a final volume of 5 mL. Place centrifuge tube back in ice box", "Homogenize samples by placing ice box on shaking board at", "Centrifuge samples at5000 rcf, 30 min, 4 °C", "Filter the supernatant throug... |
58,483 | Gene knockout strategy | 4 | dx.doi.org/10.17504/protocols.io.n92ldzp2xv5b/v1 | https://www.protocols.io/view/gene-knockout-strategy-b5ctq2wn | Carolyn N Bayer, Ana Gabriela Veiga Sepulchro, Maja Rennig, Morten Norholm | TITLE: Gene knockout strategy
AUTHORS: Carolyn N Bayer, Ana Gabriela Veiga Sepulchro, Maja Rennig, Morten Norholm
[DESCRIPTION]
This protocol collection describes how to use our optimised tetAOPT dual selection marker in E. coli K12 and Nissle. This dual selection marker can be used for positive selection based on tet... | ["[Ordering of oligonucleotides] order the following oligonucleotides:", "[Ordering of oligonucleotides] 2 primers annealing in the tetA cassette including 50 bp overhangs that correspond to the regions up-and downstream of the locus that will be removed.", "[Ordering of oligonucleotides] 1 oligonucleotide (100bp) with... |
16,731 | S1File_FullQuestionnaire | null | dx.doi.org/10.17504/protocols.io.uj3euqn | null | Chris Englert, Dennis Koroma, Alex Bertrams, Corinna Martarelli | TITLE: S1File_FullQuestionnaire
AUTHORS: Chris Englert, Dennis Koroma, Alex Bertrams, Corinna Martarelli
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The attention control video has been frequently applied to test the ego depletion effect. However, its validity has never been tested, a shor... | [] |
19,859 | U Cinn - Non-invasive Measurement of Intestinal Fat Absorption | null | dx.doi.org/10.17504/protocols.io.xmtfk6n | null | Patrick Tso, Dana Lee | TITLE: U Cinn - Non-invasive Measurement of Intestinal Fat Absorption
AUTHORS: Patrick Tso, Dana Lee
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Dietary fat containing 5% sucrose polybehenate, a non-absorbable foo... | ["Animal Feeding and Fecal Collection: MONDAY: REPLACE CHOW WITH TEST DIET TUESDAY: CONTINUE TEST DIET, NEW CAGE BEDDING BEFORE FEEDING PERIOD WEDNESDAY: CONTINUE TEST DIET(DAY 3 – RETURN) ... |
null | null | null | dx.doi.org/10.17504/protocols.io.rw7d7hn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
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?. | ["Both mitotypes were raised on the 1:16 P:C diet", "Dye labeled food was produced by combining 72 ml of food with 8 ml FD&C blue 1 dye (0.5% w/v) while the food was at 60° C", "50 second instar larvae from each mitotype were placed on the dye labelled food", "Larvae were allowed to feed for 60 min", "Larvae with dye v... |
78,940 | CARD COUNT PROTOCOL | 4 | dx.doi.org/10.17504/protocols.io.5qpvor1nbv4o/v1 | https://www.protocols.io/view/card-count-protocol-crb4v2qw | Grace Sandel | TITLE: CARD COUNT PROTOCOL
AUTHORS: Grace Sandel
[DESCRIPTION]
Procedure to conduct the card count portion of "Crazy Yellow Ant Sampling on Tetiaroa"
The point of this protocol is to quantify the prevalence of yellow crazy ants in given transects around Tetiaroa.
[BEFORE_START]
Follow this protocol after arriving at... | ["[Card Count Protocol] If needed, scrape the ground (at least a 10x10cm area) at the site so the card sits flat on the ground (i.e. if there are branches or leaf litter, scrape them away).", "[Card Count Protocol] Place the card down on the ground.", "[Card Count Protocol] For 30 seconds, count the number of yellow cr... |
55,176 | Test protocol II | 1 | null | https://www.protocols.io/view/test-protocol-ii-bz5gp83w | Abby Moore | TITLE: Test protocol II
AUTHORS: Abby Moore
[DESCRIPTION]
This is a test protocol
Here's an protocol reference:
Here's a citation:
[BEFORE_START]
This is what you should know before you start
[GUIDELINES]
Responsibilities....
[STEPS]
1. Use 80:20 MeOH:H2O for this step. This is not easy to access... | ["Use 80:20 MeOH:H2O for this step. This is not easy to access by machine.", "If you haven't already, make a solution with the following components:\n\n80 % volume \n20 % volume", "If you haven't already, make a solution with the following components:\n\n80 % volume \n20 % volume", "Use this piece of equipment:"] |
28,598 | Gamma radiation of Drosophila suzukii under hypoxia and normoxia atmosphere conditions. | null | dx.doi.org/10.17504/protocols.io.76whrfe | null | Fabiana Sassu, Katerina Nikolouli, Rui Pereira, Marc Vreysen, Christian Stauffer, Carlos Cáceres | TITLE: Gamma radiation of Drosophila suzukii under hypoxia and normoxia atmosphere conditions.
AUTHORS: Fabiana Sassu, Katerina Nikolouli, Rui Pereira, Marc Vreysen, Christian Stauffer, Carlos Cáceres
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify"... | ["[Pupae collection]\nTwo days before adult emergence, D. suzukii pupae were carefully separated from the larva medium and placed on a moist paper ensuring that the pupae will not dry while completing their maturation.\n[ 65% ± 5% RH and 14:10 (L: D) ]\nDepending on the design of the experiment the number of pupae used... |
86,092 | DNA extraction from recently fertilised Atlantic salmon embryos for use in microsatellite validation of triploidy | 4 | dx.doi.org/10.17504/protocols.io.kqdg3x93pg25/v1 | https://www.protocols.io/view/dna-extraction-from-recently-fertilised-atlantic-s-cybkxskw | Callum Howard, John B. Taggart, Caroline R. Bradley, Alejandro P. Gutierrez, John F. Taylor, Paulo A. Prodöhl, Herve Migaud, Michaël Bekaert | TITLE: DNA extraction from recently fertilised Atlantic salmon embryos for use in microsatellite validation of triploidy
AUTHORS: Callum Howard, John B. Taggart, Caroline R. Bradley, Alejandro P. Gutierrez, John F. Taylor, Paulo A. Prodöhl, Herve Migaud, Michaël Bekaert
[DESCRIPTION]
The current methods used for produ... | ["[DNA extraction] If eggs stored in ethanol, remove using forceps and place on clean tissue to remove excess ethanol.", "[DNA extraction] Place embryos in a beaker of Tris-HCl (5 millimolar (mM), pH 8) for 15 min.", "[DNA extraction] Remove the eggs and remove excess liquid with clean tissue.", "[DNA extraction] For l... |
52,595 | WIPI2d construct cloning | 4 | dx.doi.org/10.17504/protocols.io.bxktpkwn | https://www.protocols.io/view/wipi2d-construct-cloning-bxktpkwn | lmstrong | TITLE: WIPI2d construct cloning
AUTHORS: lmstrong
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">WIPI2d cloning </div></div>
[STEPS]
?. Amplify gene using PCR with Q5 polymerase. Design primers to be cut with ClaI and XmaI. For mutants, design overlapping primers in opposing direction as if using... | ["Amplify gene using PCR with Q5 polymerase. Design primers to be cut with ClaI and XmaI. For mutants, design overlapping primers in opposing direction as if using around the horn. Use these to perform 2-step PCR, verifying each step via gel.", "Gel extract correct size band and measure concentration", "Digest insert w... |
77,573 | MAPDH Patterning Protocol | 1 | dx.doi.org/10.17504/protocols.io.j8nlkw2ywl5r/v1 | https://www.protocols.io/view/mapdh-patterning-protocol-cpzdvp26 | Misha Rubanov, jcole, hlee, Rebecca Schulman | TITLE: MAPDH Patterning Protocol
AUTHORS: Misha Rubanov, jcole, hlee, Rebecca Schulman
[DESCRIPTION]
DNA-functionalized hydrogels are capable of sensing oligonucleotides, proteins, and small molecules, and specific DNA sequences sensed in the hydrogels’ environment can induce changes in these hydrogels’ shape and fluo... | ["Turn on all MAPDH hardware, connect to Micromanager and Pycromanager.", "Insert the waste tube, 24-inch length of Tygon tubing (0.02”x0.06”), into the outlet of the 5-inlet 100µm-height empty (air-filled) microfluidic chamber.", "Make four 200 µL ink solutions in four vials in 1x TAEM buffer.\n 10 % (v/v) 1 Mass Per... |
89,833 | Model building and refinement of RCKW and FL-LRRK2 bound to inhibitors | 5 | dx.doi.org/10.17504/protocols.io.81wgbx5m1lpk/v1 | https://www.protocols.io/view/model-building-and-refinement-of-rckw-and-fl-lrrk2-c3yhypt6 | Marta Sanz Murillo | TITLE: Model building and refinement of RCKW and FL-LRRK2 bound to inhibitors
AUTHORS: Marta Sanz Murillo
[DESCRIPTION]
Protocol to model and refine a PDB against a cryo-EM map.
[BEFORE_START]
Install the needed software (Chimera, COOT) and Phenix or Rosetta.
[STEPS]
1. Split into domains protein models using Chime... | ["Split into domains protein models using Chimera that will be used as a starting point (PDBs 6VP7 and 7LHW for RCKW and FL LRRK2, respectively). Save each domain in a PDB file separately.", "Open maps with the best resolution in Chimera and fit every domain PDB into the map. Save the new position for each PDB domain f... |
56,531 | NEBNext® Immune Sequencing Kit (Human) (E6320) | 1 | dx.doi.org/10.17504/protocols.io.q26g74b83gwz/v1 | https://www.protocols.io/view/nebnext-immune-sequencing-kit-human-e6320-b3ftqjnn | maria.matos , New England Biolabs | TITLE: NEBNext® Immune Sequencing Kit (Human) (E6320)
AUTHORS: maria.matos , New England Biolabs
[DESCRIPTION]
This protocol details NEBNext® Immune Sequencing Kit (Human).
https://www.neb.com/-/media/nebus/files/manuals/manuale6320.pdf?rev=1dca310ed12a4e89b322063d31db030d&hash=D4D7E9FBED23CC7448447137DBFF8C0B
[... | ["[NEBNext Immune Sequencing Reverse Transcription and cDNA Synthesis] Mix the following components in a sterile nuclease-free tube:", "[NEBNext Immune Sequencing Reverse Transcription and cDNA Synthesis] Set a 100 µl or 20 µl pipette to 15 µl and then pipette the entire volume up and down at least 10 times to mix thor... |
89,823 | Section 2: NGS library preparation for sequencing | 1 | dx.doi.org/10.17504/protocols.io.eq2lyjeoqlx9/v1 | https://www.protocols.io/view/section-2-ngs-library-preparation-for-sequencing-c3x7yprn | Ester Kalef-Ezra, Ben Harvey, Katherine Roper, Christos Proukakis | TITLE: Section 2: NGS library preparation for sequencing
AUTHORS: Ester Kalef-Ezra, Ben Harvey, Katherine Roper, Christos Proukakis
[DESCRIPTION]
This protocol details NGS library preparation for sequencing and should be performed after Section 1: Enzymatic DNA Fragmentation (Manually).
[STEPS]
SECTION: Section 2: NG... | ["[Section 2: NGS library preparation for sequencing] NGS library preparation for sequencing can be done in two ways.", "[Prepare the ligation master mix] Remove the AMPure XP beads from cold storage and equilibrate to Room temperature for at least 30 min prior use.", "[Prepare the ligation master mix] Thaw on ice End ... |
34,439 | Assessing sequence quality in GalaxyTrakr | null | dx.doi.org/10.17504/protocols.io.bdvfi63n | null | Ruth Timme, Sai Laxmi Gubbala Venkata, Maria Balkey, Robyn Randolph, William Wolfgang, Errol Strain | TITLE: Assessing sequence quality in GalaxyTrakr
AUTHORS: Ruth Timme, Sai Laxmi Gubbala Venkata, Maria Balkey, Robyn Randolph, William Wolfgang, Errol Strain
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">PURPOSE: </span><span>Step-by-step instructions for checking... | ["[Account set up]\nCreate a GalaxyTrakr account here: https://account.galaxytrakr.org/Account/Register", "[Account set up]\nLog into your GalaxyTrakr account: https://galaxytrakr.org", "[Create a new history]\nCreate a new history. We recommend creating a new history for each new MiSeq Run and including the flow-cell ... |
73,744 | Total Starch Enzymatic Digestion | 1 | null | https://www.protocols.io/view/total-starch-enzymatic-digestion-cj9qur5w | Lynn Doran, Amanda P. De Souza | TITLE: Total Starch Enzymatic Digestion
AUTHORS: Lynn Doran, Amanda P. De Souza
[DESCRIPTION]
Enzymatic digestion of total soluble starch to glucose in plant tissue extracts for preparation for quantification via the GOD-POD Method (NZYtech).
[BEFORE_START]
Extract and dry total starch pellet from plant tissue per... | ["Prepare fresh daily 120 U/mL α-amylase in MOPS buffer. 1 mL per sample will be needed. Initial concentration of α-amylase is 1000 U/mL. Use C1V1 = C2V2 to calculate the volume of α-amylase and MOPS buffer to use.", "Prepare fresh daily 30 U/mL amyloglucosidase in acetate buffer. 1 mL per sample will be needed. Initi... |
35,900 | NEBExpress Ni Resin Pressurized Column Typical Protocol (NEB #S1428) | null | dx.doi.org/10.17504/protocols.io.bfa4jigw | https://www.protocols.io/view/nebexpress-ni-resin-pressurized-column-typical-pro-bfa4jigw | New England Biolabs | TITLE: NEBExpress Ni Resin Pressurized Column Typical Protocol (NEB #S1428)
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>NEBExpress® Ni Resin is an affinity matrix for the isolation and purification of polyhistidine-tagged (His-ta</span><span style = "font-styl... | ["[Preparation of Buffers under Denaturing Conditions]\nIf continuing with Denaturing conditions: Bring all three buffers (Lysis/Binding, Wash and Elution Buffers) to a final concentration of 8M Urea or 6M Guanidine.\nNotes:1. Crude lysate should be prepared with a lysis buffer without imidazole. To further minimize co... |
43,546 | Laboratory protocol | 3 | dx.doi.org/10.17504/protocols.io.bnr2md8e | https://www.protocols.io/view/laboratory-protocol-bnr2md8e | thananda | TITLE: Laboratory protocol
AUTHORS: thananda
[STEPS] | [] |
58,133 | Taxon group: Non-larval Arthropods (TSS1) | 1 | dx.doi.org/10.17504/protocols.io.81wgb66jylpk/v1 | https://www.protocols.io/view/taxon-group-non-larval-arthropods-tss1-b4zvqx66 | Lyndall Pereira da Conceicoa, Olga Sivell, Laura Sivess, Chris Fletcher, Gavin R. Broad, Liam Crowley, Inez Januszczak | TITLE: Taxon group: Non-larval Arthropods (TSS1)
AUTHORS: Lyndall Pereira da Conceicoa, Olga Sivell, Laura Sivess, Chris Fletcher, Gavin R. Broad, Liam Crowley, Inez Januszczak
[DESCRIPTION]
This is part of the collection "DToL Taxon-specific Standard Operating Procedure (SOP) for the Terrestrial and Freshwater Arthr... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.nibdcan | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a handout that was created by Code Ocean, Addgene, and protocols.io for the Caltech workshop on reproducibility. For more information and slides from the workshop, please see: <a href="https://codeocean.com/workshop/caltech" target="_blank">https://codeocean.com/works... | [] |
89,111 | The Parkinson’s Progression Markers Initiative (PPMI) Clinical - Establishing a Deeply Phenotyped PD Cohort | 1 | dx.doi.org/10.17504/protocols.io.n92ldmw6ol5b/v1 | https://www.protocols.io/view/the-parkinson-s-progression-markers-initiative-ppm-c29xyh7n | Kenneth Marek | TITLE: The Parkinson’s Progression Markers Initiative (PPMI) Clinical - Establishing a Deeply Phenotyped PD Cohort
AUTHORS: Kenneth Marek
[DESCRIPTION]
This protocol details the Parkinson’s Progression Markers Initiative (PPMI) Clinical - establishing a deeply phenotyped PD cohort.
[GUIDELINES]
APPENDIX 1 – Healthy C... | ["[PURPOSE OF STUDY] Primary Objectives of PPMI Clinical:\nThe primary objectives include to:", "[PURPOSE OF STUDY] Establish standardized protocols for acquisition, transfer and analysis of clinical, digital, imaging, biologic and genetic data that can be used by the PD research community. This protocol will build on ... |
null | null | null | dx.doi.org/10.17504/protocols.io.mamc2c6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.p6adrae | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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91,484 | Wide-field imaging of voltage sensors expressed in ex vivo mouse brain slices | 1 | dx.doi.org/10.17504/protocols.io.yxmvm3q46l3p/v1 | https://www.protocols.io/view/wide-field-imaging-of-voltage-sensors-expressed-in-c5j4y4qw | Yan-Feng Zhang, Stephanie J Cragg | TITLE: Wide-field imaging of voltage sensors expressed in ex vivo mouse brain slices
AUTHORS: Yan-Feng Zhang, Stephanie J Cragg
[DESCRIPTION]
This protocol describes how to perform wide-field imaging of voltage sensors using high frame rates (660 Hz minimum every 2.5 minutes) in mouse midbrain using ex vivo brain slic... | ["[Image Acquisition] Using a x40/0.8 NA water-objective (Olympus UK), position the stimulating electrode on the surface of the brain slice and centre it in the field of view.", "[Image Analysis] The following steps were performed in MATLAB vR2019b and Fiji v1.5.\n\nExtract fluorescence intensity from the region of inte... |
16,424 | Swarming assay (high number) | 1 | dx.doi.org/10.17504/protocols.io.uagesbw | https://www.protocols.io/view/swarming-assay-high-number-uagesbw | Serena Ding | TITLE: Swarming assay (high number)
AUTHORS: Serena Ding
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">For imaging swarming behaviour of a very high number (thousands+) of young adult C. elegans on agar using the Cyclops single worm tracker. Worms are synchronised by bleaching and refeeding for 72... | ["[Bleach synchronising worms (-7 to -4 day)]\nBleach synchronise 3 large plates (90mm) worth of animals, making sure lots of gravid hermaphrodites are present. Leave on rotator at 20 °C until use.", "[Imaging (Day 0 PM)]\nPlace the plate inside the tracker with an appropriate field of view (i.e. worm front at the edge... |
79,804 | Nanopore amplicon sequencing with DIY adapter | 4 | dx.doi.org/10.17504/protocols.io.5jyl8jow9g2w/v1 | https://www.protocols.click/view/nanopore-amplicon-sequencing-with-diy-adapter-cr64v9gw | Jie Hao Ou, Yin-Tse Huang | TITLE: Nanopore amplicon sequencing with DIY adapter
AUTHORS: Jie Hao Ou, Yin-Tse Huang
[DESCRIPTION]
Nanopore amplicon sequencing with DIY adapter
[STEPS]
SECTION: Workflow
1.
SECTION: Preparation of amplicons
2. Use a primer with a HEAD to make amplicons, as in a regular procedure.
Enzymes with or without pro... | ["[Workflow]", "[Preparation of amplicons] Use a primer with a HEAD to make amplicons, as in a regular procedure. \nEnzymes with or without proofreading can be used, and purification is not necessary.", "[Pooling & 5' Phosphorylation] Mix the following materials in order:\n(10 samples as an example)\n \n#Mater... |
66,024 | Automated DNA/RNA Extractions from a stony coral (Acropora palmata) using ZymoBIOMICS DNA/RNA Magbead Kit and the Kingfisher Flex | 4 | dx.doi.org/10.17504/protocols.io.bp2l61wykvqe/v1 | https://www.protocols.io/view/automated-dna-rna-extractions-from-a-stony-coral-a-ccqgsvtw | Benjamin Young | TITLE: Automated DNA/RNA Extractions from a stony coral (Acropora palmata) using ZymoBIOMICS DNA/RNA Magbead Kit and the Kingfisher Flex
AUTHORS: Benjamin Young
[DESCRIPTION]
This is the protocol used to extract DNA and RNA from the same piece of coral tissue and skeleton using the Zymo DNA/RNA MagBead and ZymoBIOM... | ["[Coral Tissue Sampling and Storage] For each sample, bonecutters and tweezers were cleaned with 80% bleach and then flame sterilized with 70% ethanol. The bench space was also cleaned between each sample with 80% bleach and 70% ethanol.", "[Tissue Homogenization and Prep for Kingfisher Flex] Thaw stored coral samples... |
null | null | null | dx.doi.org/10.17504/protocols.io.n2ydgfw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is aimed at amplifying the 16S rRNA hypervariable region 4 (16S V4) in prokaryotes. The primers (515fB and 806rB, <span style="font-weight: 400;">926R</span>) used in this protocol are based on the primer utilized in Apprill et al 2015 and the Earth Microbiome P... | [] |
63,603 | Sight Care *CRITICAL RESEARCH* Relief Anxiety and Stress Sight Care Reviews! | 3 | dx.doi.org/10.17504/protocols.io.14egn7jwzv5d/v1 | https://www.protocols.io/view/sight-care-critical-research-relief-anxiety-and-st-cactsawn | R H | TITLE: Sight Care *CRITICAL RESEARCH* Relief Anxiety and Stress Sight Care Reviews!
AUTHORS: R H
[DESCRIPTION]
If you just treat the symptoms then there is a very good chance that your Thrush will continually come back.
[STEPS] | [] |
85,690 | Isolation of intestinal organoids from matrigel for protein or RNA extraction | 4 | dx.doi.org/10.17504/protocols.io.36wgq37kolk5/v1 | https://www.protocols.io/view/isolation-of-intestinal-organoids-from-matrigel-fo-cxw2xpge | rachel.bates | TITLE: Isolation of intestinal organoids from matrigel for protein or RNA extraction
AUTHORS: rachel.bates
[DESCRIPTION]
Isolation of intestinal organoids from matrigel or cultrex growth domes ready for protein or RNA isolation.
[STEPS]
1. Intestinal organoids are grown in 30 µL domes for 14400 min
2. Once org... | ["Intestinal organoids are grown in 30 µL domes for 14400 min", "Once organoids are large enough for harvest domes are washed three times with ice cold .", "Add 1 mL per well. incubate on ice for 60 min with orbital shaking at .", "Harvest well contents into centrifuge tube. Centrifuge 6000 rpm, 1 min . Carefu... |
null | null | null | dx.doi.org/10.17504/protocols.io.ecvbaw6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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73,799 | Qubit | 1 | dx.doi.org/10.17504/protocols.io.14egn298pg5d/v1 | https://www.protocols.io/view/qubit-ckbfusjn | Dakota Betz | TITLE: Qubit
AUTHORS: Dakota Betz
[DESCRIPTION]
Our protocols are constantly evolving and old versions will be deleted.
The documents here are not intended to be cited in publications
[STEPS]
SECTION: Setup
2. Take out standards (1 and 2) and Qubit buffer from cabinet above NGS bench. Also get the Qubit reagent from ... | ["[Setup] Take out standards (1 and 2) and Qubit buffer from cabinet above NGS bench. Also get the Qubit reagent from the labled blue box in the drawer under the NGS bench. Retrieve DNA extractions and defrost (if they were frozen previously). Be sure to vortex and centrifuge samples.", "[Setup] Clean the NGS area well... |
38,453 | Covalent Coupling Protein to Carboxylated Microparticles via EDAC | 6 | dx.doi.org/10.17504/protocols.io.bhsvj6e6 | https://www.protocols.io/view/covalent-coupling-protein-to-carboxylated-micropar-bhsvj6e6 | Kenneth Schackart, Kattika Kaarj | TITLE: Covalent Coupling Protein to Carboxylated Microparticles via EDAC
AUTHORS: Kenneth Schackart, Kattika Kaarj
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol details how to covalently couple proteins to carboxylated polystyrene particles (microspheres) via EDAC. In this rea... | ["[Wash Particles]\nVortex particle mixture.Centrifuge at Remove supernatant.Resuspend in Activation buffer.Repeat for a total of two washes; Do not resuspend in Activation Buffer the second time.\nCentrifuge: 9900 34, 10 min\n500 µl\nAll centrifugation times and speeds will depend on particle size. They will need to ... |
65,947 | Study_Protocol_English_Wintermann_V2 | 3 | dx.doi.org/10.17504/protocols.io.ccm3su8n | https://www.protocols.io/view/study-protocol-english-wintermann-v2-ccm3su8n | gloria.wintermann | TITLE: Study_Protocol_English_Wintermann_V2
AUTHORS: gloria.wintermann
[DESCRIPTION]
Objectives: Patients with Panic Disorder (PD) show an abnormal stress-induced functioning of the Hypothalamic-Pituitary-adrenal (HPA)-axis. Different protocols for stress induction are of rather low relevance for the psychotherapeutic... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.gypbxvn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p style="text-align: center;"><img style="display: block; margin-left: auto; margin-right: auto;" src="https://s3.amazonaws.com/pr-journal/hnnfjtn.png" width="100" height="90" data-src="https://s3.amazonaws.com/pr-journal/hnnfjtn.png" data-ofn="nehirarma-üst-Tr.png" /> </p>
<p... | [] |
49,955 | Pharmacological management and potentially inappropriate prescriptions for patients with acne | 1 | dx.doi.org/10.17504/protocols.io.bu2bnyan | https://www.protocols.io/view/pharmacological-management-and-potentially-inappro-bu2bnyan | Jorge Machado Alba | TITLE: Pharmacological management and potentially inappropriate prescriptions for patients with acne
AUTHORS: Jorge Machado Alba
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-style:italic;">Introduction</span><span>. Acne is a chronic inflammatory disease that involves the pil... | [] |
45,384 | Ney's Spring Media Preparation | 4 | dx.doi.org/10.17504/protocols.io.bqjgmujw | https://www.protocols.io/view/ney-39-s-spring-media-preparation-bqjgmujw | Annette Rowe, Leah Trutschel | TITLE: Ney's Spring Media Preparation
AUTHORS: Annette Rowe, Leah Trutschel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is for protocol for making Ney's Spring high pH media and plates. These consist of a basal minimal media with differing electron donors and acceptors depending on wh... | ["[Ney's Spring Basal Salts]\nThese are the basal salts used in all medias. If making liquid media, add salts to 700mL milli Q water. If making plates, then start with 400 mL Milli Q (additional components will then be added to bring up to 1L later)ComponentMW (g/mol)Amount added (g)Concentration (mM)NaCl58.4411.7200N... |
55,398 | Preparation of Competent Cells of M. bovis BCG | 4 | dx.doi.org/10.17504/protocols.io.b2ceqate | https://www.protocols.io/view/preparation-of-competent-cells-of-m-bovis-bcg-b2ceqate | Jonathan Rey A Ibale | TITLE: Preparation of Competent Cells of M. bovis BCG
AUTHORS: Jonathan Rey A Ibale
[DESCRIPTION]
This protocol is a standardized protocol obtained from the Polytechnic University of Hong Kong and is in current use in SC 193 Laboratory under Prof. Au Wing Ngor for M. bovis BCG experimentation. The cells produced there... | ["Inoculate a starter bacterial stock to 100 mL 7H9 broth (0.1g casitone, 0.44 g sodium pyruvate) incubate in 37 °C for 7-8 days without shaking. (Prolonged incubation causes dehydration so seal the flask/tube during incubation.)", "Aliqout 1 mL from the primary culture into a fresh, pre-warmed 100 mL 7H9 broth and in... |
65,862 | Impact of CBR | 4 | dx.doi.org/10.17504/protocols.io.e6nvwk7bdvmk/v1 | https://www.protocols.io/view/impact-of-cbr-ccjesuje | Dr. Md. Zahid Hossain, Dr. Kazi Md. Amran Hossain, Dr. Md. Feroz Kabir | TITLE: Impact of CBR
AUTHORS: Dr. Md. Zahid Hossain, Dr. Kazi Md. Amran Hossain, Dr. Md. Feroz Kabir
[DESCRIPTION]
Background
Community-Based Rehabilitation (CBR) is reaching the rehabilitation services to the doorstep of the stakeholders. The stakeholders include the persons with disabilities, their family members ... | ["[Screening Camps] Screening Camps", "[Screening Camps] Inclusion according to eligibility", "[Pretest Measures] Pretest Measures through Baseline measures", "[Pretest Measures] Primary Intervention", "[Pretest Measures] Immediate Posttest (if required)", "[Intervention] Customized intervention for 12 sessions in 4 we... |
38,605 | Dye-terminator DNA sequencing | 1 | dx.doi.org/10.17504/protocols.io.bhxmj7k6 | https://www.protocols.io/view/dye-terminator-dna-sequencing-bhxmj7k6 | Diep Ganguly | TITLE: Dye-terminator DNA sequencing
AUTHORS: Diep Ganguly
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol (based on the BigDye® Terminator v3.1 Cycle Sequencing Kit) is for performing terminator cycling sequencing reactions for Sanger sequencing of amplified PCR products or plasmid DN... | ["[Enzymatic PCR clean-up]\nIf sequencing a PCR amplified DNA fragment, gel purify target DNA band based on expected fragment size (if multiple bands present). Perform gel purification with Wizard SV Gel and PCR Clean-Up System (Promega, as per attached Manufacterer's instructions) followed by enzymatic clean-up (hydro... |
93,708 | CompDuplex: Accurate detection of somatic mutations by duplex-seq with comprehensive genome coverage | 4 | dx.doi.org/10.17504/protocols.io.kxygx3x4og8j/v1 | https://www.protocols.io/view/compduplex-accurate-detection-of-somatic-mutations-c7rkzm4w | Muchun Niu, Chenghang Chuck Zong | TITLE: CompDuplex: Accurate detection of somatic mutations by duplex-seq with comprehensive genome coverage
AUTHORS: Muchun Niu, Chenghang Chuck Zong
[DESCRIPTION]
Somatic mutations continuously accumulate in the human genome, posing vulnerabilities towards aging and increased risk of various diseases. However, accura... | ["[Custom Tn5 transposase assembly] Prepare 500 µL of 2X Annealing Buffer.\n40 µL \n10 µL \n450 µL", "[Custom Tn5 transposase assembly] Transposon annealing.\nPrepare the following mix in a PCR tube.\n\n20 µL 2X Annealing Buffer\n10 µL 200 micromolar (µM) \n10 µL 200 micromolar (µM) \n\nOligonucleotides sequence... |
101,003 | Differentiation between different soft hammers stigmats, quantitative and traceological approach | 0 | dx.doi.org/10.17504/protocols.io.eq2lyw3mmvx9/v2 | https://www.protocols.io/view/differentiation-between-different-soft-hammers-sti-devj3e4n | Jean-Thomas Vie, Zixuan Shen | TITLE: Differentiation between different soft hammers stigmats, quantitative and traceological approach
AUTHORS: Jean-Thomas Vie, Zixuan Shen
[DESCRIPTION]
Many studies in archaeology focus on the traces associated with stone knapping during prehistory, debating their correlation with the techniques used (Clément, 202... | ["[Selection of a specific raw material] Select Raw material : Sandstone quartzite, Quartzite, Flint, Quartz", "[Knapping with different hammers in order to produce flakes] Use hammer from low to high hardness to produce flakes : \nSoft rock percussor, volcanic rock percussor.\nWe plan to knap in the order of Sandstone... |
69,865 | Nano3P-seq Protocol | 4 | null | https://www.protocols.io/view/nano3p-seq-protocol-cgghttt6 | Oguzhan Begik | TITLE: Nano3P-seq Protocol
AUTHORS: Oguzhan Begik
[DESCRIPTION]
Here, we develop Nanopore 3’ end-capture sequencing (Nano3P-seq), a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance, tail composition and tail length dynamics at per-read resolution. By employing a template sw... | ["[Without Barcoding] Materials and consumables required\n\n●Direct cDNA Sequencing Kit (ONT, SQK-DCS109)\n●Flow Cell Priming Kit (ONT, EXP-FLP001)\n●AMPure XP Reagent (Agencourt , A63881)\n●Blunt/TA Ligase Master Mix (NEB, M0367)\n●TGIRT™-III Enzyme (InGex)\n●RNase Inhibitor, Murine (NEB,M0314L)\n●RNase Cocktail Enzy... |
33,925 | Gibson Assembly® Protocol (E5510) | 1 | dx.doi.org/10.17504/protocols.io.bdddi226 | https://www.protocols.io/view/gibson-assembly-protocol-e5510-bdddi226 | New England Biolabs | TITLE: Gibson Assembly® Protocol (E5510)
AUTHORS: New England Biolabs
[DESCRIPTION]
This protocol explains methods for the Gibson Assembly using the Gibson Assembly® Cloning Kit (E5510).
[GUIDELINES]
Optimal Quantities
NEB recommends a total of 0.02–0.5 pmols of DNA fragments when 1 or 2 fragments are being assem... | ["Set up the following reaction on ice:\n 2-3 Fragment", "Move further with the protocol, based on whether you are assembling 2-3 fragments or 4-6 fragments:", "Store samples on ice or at 20 °C for subsequent transformation.", "Transform NEB 5-alpha Competent E. coli cells (provided with the kit) with 2 µL, followi... |
62,847 | Mosquito vector surveillance, processing and storage | 1 | null | https://www.protocols.io/view/mosquito-vector-surveillance-processing-and-storag-b9k7r4zn | Tanya L Russell, Kyran Staunton, Thomas Burkot, Amanda Murphy | TITLE: Mosquito vector surveillance, processing and storage
AUTHORS: Tanya L Russell, Kyran Staunton, Thomas Burkot, Amanda Murphy
[DESCRIPTION]
The purpose of this Standard Operating Procedure (SOP) is to outline processes for the surveillance, processing and storage of mosquito samples in the field.
A detailed... | ["[Overview of surveillance procedures] Preparation for vector surveillance activities\n· Develop vector surveillance work plan, with required standard operating protocols.\n· Secure the require funding.\n· Gain required research or ethical approvals.\n· Perform a stock-take and then order required equipment and consum... |
34,535 | Basic Protocol 3: Testing auxin-mediated degradation of the AID-tagged protein | null | dx.doi.org/10.17504/protocols.io.bdyfi7tn | null | Kizhakke Mattada Sathyan, Thomas G. Scott, Michael J. Guertin | TITLE: Basic Protocol 3: Testing auxin-mediated degradation of the AID-tagged protein
AUTHORS: Kizhakke Mattada Sathyan, Thomas G. Scott, Michael J. Guertin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Please refer to the description section of the protocol collection.</div></div>
[STEPS]
?. Mak... | ["Make auxin in water, aliquot and store at . The auxin is stable at for several months. Use a fresh aliquot each time and do not refreeze.\n-20 °C\n-20 °C", "Seed 6-well plates with AID-tagged cells to achieve ~75% confluent cells the following day (plate approximately 7-8x105 HEK293T cells).", "Add a final concentr... |
95,559 | BAF_Protocol_006 On-Bead Peptide Cleanup (Digested by Other Method) | 1 | dx.doi.org/10.17504/protocols.io.n92ldmkknl5b/v1 | https://www.protocols.io/view/baf-protocol-006-on-bead-peptide-cleanup-digested-c9jfz4jn | nesf | TITLE: BAF_Protocol_006 On-Bead Peptide Cleanup (Digested by Other Method)
AUTHORS: nesf
[DESCRIPTION]
This protocol is for using beads as a cleanup step after protein is digested using a different method (not directly on Sera-Mag beads), for example solution digest. The peptides are precipitated onto the beads to a... | ["[On-Bead Clean-up] Stock Solution of magnetic Sera-Mag beads is made in section 1 of BAF_Protocol_004 and can be stored at 4C indefinitely and used as needed (never freeze).", "[On-Bead Clean-up] Peptide digest (for example from a solution or in-gel digest) should be reduced in volume so that a 95% ACN (acetonitrile)... |
88,006 | Acetylation of lysines on affinity-purification matrices to reduce co-digestion of bead-bound ligands | 4 | dx.doi.org/10.17504/protocols.io.kxygxzexkv8j/v3 | https://www.protocols.io/view/acetylation-of-lysines-on-affinity-purification-ma-cz7ex9je | David M. Hollenstein, Margarita Maurer-Granofszky, Dorothea Anrather, Thomas Gossenreiter, Natascha Hartl, Markus Hartl | TITLE: Acetylation of lysines on affinity-purification matrices to reduce co-digestion of bead-bound ligands
AUTHORS: David M. Hollenstein, Margarita Maurer-Granofszky, Dorothea Anrather, Thomas Gossenreiter, Natascha Hartl, Markus Hartl
[DESCRIPTION]
In mass-spectrometry-based interaction proteomics on-bead digestion... | ["[Acetylation protocol] Wash beads 3x with 100µl Reaction buffer, using the magnetic rack. \nRemove supernatant after the final wash.", "[Acetylation protocol] Add 19 µl Reaction buffer and 1 µl Sulfo-NHS-Acetate (100 mM) to obtain a final concentration of 5 mM Sulfo-NHS-Acetate. \nIncubate 1h at room temperature with... |
54,155 | Background control of Gotcha RCA | 4 | null | https://www.protocols.io/view/background-control-of-gotcha-rca-by5jpy4n | Chia-Hsien Shih | TITLE: Background control of Gotcha RCA
AUTHORS: Chia-Hsien Shih
[DESCRIPTION]
This protocol aims to verify that GotCha design works as expected.
[STEPS]
SECTION: Preparation
1. Add 5 µL of functional beads(Gotcha) into eppendorf
SECTION: Preparation
2. Centrifuge for 15000 rpm, 5 min and remove supernatant. Make s... | ["[Preparation] Add 5 µL of functional beads(Gotcha) into eppendorf", "[Preparation] Centrifuge for 15000 rpm, 5 min and remove supernatant. Make sure that eppendorf should put on DynaMag when removing supernatant.", "[Protocol of Control group without miRNA] Add 3 µL of 10X phi29 polymerase reaction buffer into eppend... |
97,721 | Loss of Function Mutagenesis Protocol | 0 | dx.doi.org/10.17504/protocols.io.ewov19ymklr2/v1 | https://www.protocols.io/view/loss-of-function-mutagenesis-protocol-dbnz2mf6 | Lilia Peyton, Ada McCarroll, Hanwen Zhang | TITLE: Loss of Function Mutagenesis Protocol
AUTHORS: Lilia Peyton, Ada McCarroll, Hanwen Zhang
[DESCRIPTION]
This protocols offers a description of the loss of function mutagenesis procedure for induced pluripotent stem cells.
[STEPS]
SECTION: iPSC Maintenance
1. Change media every other day – mTeSR Plus with 1ml pr... | ["[iPSC Maintenance] Change media every other day – mTeSR Plus with 1ml primocin", "[iPSC Maintenance] Always warm media to room temperature before use", "[iPSC Maintenance] Aspirate using glass pipette attached to vacuum and replenish with mTeSR plus", "[Passaging] Passage every 4-6 days (whenever colonies are 70-80% ... |
73,516 | 615.1 URMC HTC Non-Inflated Fresh-Frozen Embedded Lung and Associated Tissue | 4 | dx.doi.org/10.17504/protocols.io.rm7vz84k2vx1/v2 | https://www.protocols.io/view/615-1-urmc-htc-non-inflated-fresh-frozen-embedded-cj2kuqcw | Gloria S Pryhuber, Heidie Huyck, Lisa Rogers, Cory Poole | TITLE: 615.1 URMC HTC Non-Inflated Fresh-Frozen Embedded Lung and Associated Tissue
AUTHORS: Gloria S Pryhuber, Heidie Huyck, Lisa Rogers, Cory Poole
[DESCRIPTION]
Purpose and Scope of the Procedure
- Rapid blocking, embedding and freezing of human lung tissue in no freezing media, 100% OCT or 5% CMC
- Rapid fre... | ["[Fresh Tissue Frozen in Cryomolds] Slicing and blocking procedure should be accomplished in a grossing station or fume hood with the operator taking appropriate blood and body fluid precautions", "[Fresh Tissue Frozen in Cryomolds] Prepare dry ice-ethanol (or isobutane) bath by covering bottom of flat ice bucket or s... |
57,620 | Quantification of Isolated Circulating MicroRNAs using Qiagen LNA Panels | 4 | null | https://www.protocols.io/view/quantification-of-isolated-circulating-micrornas-u-b4huqt6w | Dakota Gustafson | TITLE: Quantification of Isolated Circulating MicroRNAs using Qiagen LNA Panels
AUTHORS: Dakota Gustafson
[DESCRIPTION]
A protocol for quantification of circulating microRNA using the Qiagen LNA Low Density Array MicroRNAs isolated from platelet-poor plasma. During the purification step samples are spiked with cel-mi... | ["[Reverse Transcription] Dilute each template RNA sample to 5 ng/µl using nuclease-free water.", "[Reverse Transcription] Prepare the reverse transcription master mix using: .", "[Reverse Transcription]", "[Reverse Transcription] Incubate for 60 min at 42 °C , then 5 min at 95 °C , and immediately cool to 4 °C... |
null | null | null | dx.doi.org/10.17504/protocols.io.kdkcs4w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Evaluación de la capacidad de neutralización del efecto del Lipopolisacarido (LPS) de inducir la producción de Factor de Necrosis Tumoral (TNFalfa) en Células Mononucleares de Sangre Periférica (PBMCs) tratadas con peptidos cationicos. </p>
<p> </p>
<p>La realizacion de este... | [] |
37,075 | Body mass index, healthy diet and mortality | 3 | dx.doi.org/10.17504/protocols.io.bgftjtnn | https://www.protocols.io/view/body-mass-index-healthy-diet-and-mortality-bgftjtnn | Karl Michaëlsson | TITLE: Body mass index, healthy diet and mortality
AUTHORS: Karl Michaëlsson
[STEPS] | [] |
40,166 | nCoV-2019 McGill RT Protocol, Lunascript | 1 | dx.doi.org/10.17504/protocols.io.bjgekjte | https://www.protocols.io/view/ncov-2019-mcgill-rt-protocol-lunascript-bjgekjte | Shu-Huang Chen, Sarah Reiling, Josh Quick | TITLE: nCoV-2019 McGill RT Protocol, Lunascript
AUTHORS: Shu-Huang Chen, Sarah Reiling, Josh Quick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Artic nCoV-2019 McGill modified Lunascript Reverse Transcriptase sequencing protocol.</div></div>
[STEPS]
?. [cDNA preparation]
Mix the following compon... | ["[cDNA preparation]\nMix the following components in a 0.2 mL 8-strip tube; Component VolumeLunaScript RT SuperMix (5x) Nuclease-free water Template RNA Total\n4 µl\n5 µl\n11 µl\n20 µl\nViral RNA input from a clin... |
83,100 | 2-step PCR mixture and conditions (Barcoded-head primers for seqs pooling) | 4 | dx.doi.org/10.17504/protocols.io.yxmvm263og3p/v2 | https://www.protocols.click/view/2-step-pcr-mixture-and-conditions-barcoded-head-pr-cvd4w28w | Yin-Tse Huang, Tsu-Chun Hung | TITLE: 2-step PCR mixture and conditions (Barcoded-head primers for seqs pooling)
AUTHORS: Yin-Tse Huang, Tsu-Chun Hung
[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 m... | ["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... |
null | null | null | dx.doi.org/10.17504/protocols.io.qhtdt6n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Protocol obtained from the Alsford Lab at the London School of Hygiene & Tropical Medicine</strong></p>
<p>(https://blogs.lshtm.ac.uk/alsfordlab/protocols/bloodstream-form-culture/)</p>
[STEPS]
?.
?.
?.
?. | [] |
45,650 | Phantom Preparation and Acquisition | 1 | dx.doi.org/10.17504/protocols.io.bqtsmwne | https://www.protocols.io/view/phantom-preparation-and-acquisition-bqtsmwne | Cláudia Régio Brambilla, Jürgen Scheins, Ahlam Issa, Lutz Tellmann, Hans Herzog, Elena Rota Kops, N. Jon Shah, Irene Neuner, Christoph W. Lerche | TITLE: Phantom Preparation and Acquisition
AUTHORS: Cláudia Régio Brambilla, Jürgen Scheins, Ahlam Issa, Lutz Tellmann, Hans Herzog, Elena Rota Kops, N. Jon Shah, Irene Neuner, Christoph W. Lerche
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The PET data were acquired using a 3T hybrid MR-BrainPE... | ["[Positioning and Acquisition:]\nThe phantom was positioned in the same conditions to represent an [11C]ABP688 acquisition protocol of the human brain study in the PET scanner FOV. Schematic positioning can be observed below comparing human head and phantom:Phantom acquisition was performed during 8T1/2 of 11C (tabl... |
16,622 | Preparation of dsRNA viruses for next-generation sequencing | null | dx.doi.org/10.17504/protocols.io.ugnetve | null | Alexander H Wilcox, Erik Delwart, Samuel L Díaz Muñoz | TITLE: Preparation of dsRNA viruses for next-generation sequencing
AUTHORS: Alexander H Wilcox, Erik Delwart, Samuel L Díaz Muñoz
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Viral lysates should be passed through a 0.22μm filter to remove host debris, then treated with nucleases to degrade extracapsula... | ["Viral lysates should be passed through a 0.22μm filter to remove host debris, then treated with nucleases to degrade extracapsular nucleic acids. We added 25μl DNAse I, 50μl RNAse A/T1 and 1X DNAse I Buffer to 1ml filtrate, and incubated for 1 hour 30 minutes at 37ºC.", "RNA should be extracted using a commercially ... |
null | null | null | dx.doi.org/10.17504/protocols.io.f5cbq2w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 12">
<div class="layoutArea">
<div class="column">
<div class="column">The steps for preparing the lysate are different depending on the starting material. Please ensure you follow the correct procedure for your starting material (see the section <a... | [] |
42,266 | Fluorescence-activated nuclei sorting (FANS) on human post-mortem cortex tissue enabling the isolation of distinct neural cell populations for multiple omic profiling | 4 | dx.doi.org/10.17504/protocols.io.bmh2k38e | https://www.protocols.io/view/fluorescence-activated-nuclei-sorting-fans-on-huma-bmh2k38e | Stefania Policicchio, Jonathan P Davies, Barry Chioza, Joe Burrage, Jonathan Mill, Emma Dempster | TITLE: Fluorescence-activated nuclei sorting (FANS) on human post-mortem cortex tissue enabling the isolation of distinct neural cell populations for multiple omic profiling
AUTHORS: Stefania Policicchio, Jonathan P Davies, Barry Chioza, Joe Burrage, Jonathan Mill, Emma Dempster
[DESCRIPTION]
<div class = "text-blo... | ["[Nuclear prep for FACS separation (using SOX10, IRF8, NeuN and Hoechst)]\nThe protocol below yields at least 1,000,000 NeuN +ve, 1,000,000 SOX10 +ve, 400,000 IRF8 +ve (when the population is present) and 200,000 triple negative (NeuN-ve/SOX10-ve/IRF8-ve) nuclei per of frozen human post-mortem cortex tissue. Recovery... |
27,474 | Restriction Digest of Plasmid DNA | null | dx.doi.org/10.17504/protocols.io.63shgne | null | Addgene the Nonprofit Plasmid Repository | TITLE: Restriction Digest of Plasmid DNA
AUTHORS: Addgene the Nonprofit Plasmid Repository
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is for restriction digest of plasmid DNA. To see the full abstract and additional resources, please visit </span><a href="http://www.addgene.... | ["Select restriction enzymes to digest your plasmid.\nNotes:For a list of many commonly used restriction enzymes, visit NEB.To determine which restriction enzymes will cut your DNA sequence (and where they will cut), use a sequence analysis program such as Addgene's Sequence Analyzer.", "Determine an appropriate reacti... |
75,185 | Liposome Synthesis Protocol : Synthesis of anionic and cationic unilamellar liposome nanoparticles using a thin film dispersed hydration and extrusion method. | 6 | dx.doi.org/10.17504/protocols.io.dm6gpjyx1gzp/v1 | https://www.protocols.io/view/liposome-synthesis-protocol-synthesis-of-anionic-a-cmnru5d6 | Joanna Carroll, Noah Daly, Julie Rose Mae Mondala, Alancasey, Brijeshtiwari, James F Curtin, Alessandro Cazzolla | TITLE: Liposome Synthesis Protocol : Synthesis of anionic and cationic unilamellar liposome nanoparticles using a thin film dispersed hydration and extrusion method.
AUTHORS: Joanna Carroll, Noah Daly, Julie Rose Mae Mondala, Alancasey, Brijeshtiwari, James F Curtin, Alessandro Cazzolla
[DESCRIPTION]
Nanoparticles ar... | ["[Synthesis of liposomes via thin film dispersed hydration] The thin-film dispersed hydration method can be used to prepare anionic and cationic liposomes and encapsulated liposomes with (fluorescent dyes, bio compounds or drugs). \n\nIn a round bottom pyrex flask (50 ml), add 7 mM of the chosen lipid and 3 mmol of ch... |
69,739 | Hybridization of Soybean Via Cross-Pollination | 1 | null | https://www.protocols.io/view/hybridization-of-soybean-via-cross-pollination-cgcjtsun | Lynn Doran | TITLE: Hybridization of Soybean Via Cross-Pollination
AUTHORS: Lynn Doran
[DESCRIPTION]
Cross-pollination of soybean to hybridize two lines, introgress alleles, or transfer a transgenic event to a new genetic background.
https://www.youtube.com/watch?v=-iJXSPzKZO0
https://www.youtube.com/watch?v=VnjGijF4KQI
https:/... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.huub6ww | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes the tracing of newly deposited silica using PDMPO (2-(4-pyridyl)-5-((4-(2-dimethylaminoethylaminocarbamoyl)methoxy)phenyl)oxazole) in reproductive studies of diatoms.</p>
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
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