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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45,751 | Protocol for the field detection of the European filovirus (Lloviu cuevavirus) | 4 | null | https://www.protocols.io/view/protocol-for-the-field-detection-of-the-european-f-bqwxmxfn | Gábor Tóth, Sándor Boldogh, Ágnes Balázs-Nagy, Tamás Görföl, Gabor Kemenesi | TITLE: Protocol for the field detection of the European filovirus (Lloviu cuevavirus)
AUTHORS: Gábor Tóth, Sándor Boldogh, Ágnes Balázs-Nagy, Tamás Görföl, Gabor Kemenesi
[DESCRIPTION]
Lloviu cuevavirus (LLOV) is the only filovirus endemic in Europe and the only known host for this virus is the Miniopterus schreirbers... | ["[Bat sampling] 1, The bat handler should hold the animal by the abdominal side faced upwards. Pressing the chest too hard must be avoided as this can cause injuries for the bat. The handler should place the index finger under the interfemoral vein (hand protection is necessary to avoid the puncture of the human fing... |
49,370 | A novel RT-qPCR assay for detection of SARS-CoV-2 variants based on RhAmp technology (IDT technologies) | 4 | dx.doi.org/10.17504/protocols.io.buf2ntqe | https://www.protocols.io/view/a-novel-rt-qpcr-assay-for-detection-of-sars-cov-2-buf2ntqe | Victor Emmanuel Viana Geddes, Filipe Moreira, Diego Menezes Bonfim, Hugo José Alves, João Locke Ferreira de Araújo, Daniel Costa Queiroz, Rafael Marques de Souza, Rennan Garcias Moreira, Camila Zolini de Sá, Danielle Alves Gomes Zauli, Joice do Prado Silva, Aline Brito de Lima, Frederico Scott Varella Malta, Alessandro... | TITLE: A novel RT-qPCR assay for detection of SARS-CoV-2 variants based on RhAmp technology (IDT technologies)
AUTHORS: Victor Emmanuel Viana Geddes, Filipe Moreira, Diego Menezes Bonfim, Hugo José Alves, João Locke Ferreira de Araújo, Daniel Costa Queiroz, Rafael Marques de Souza, Rennan Garcias Moreira, Camila Zolini... | ["Prepare the genotyping reaction mix as follows:Reagent1 reaction (µl)100 reactions (µl)Combined Master Mix5.3530SNP assay 20X (for K417T or N501Y assays)0.550Sample cDNA4.2-Total volume101000\nReagent1 reaction (µl)100 reactions (µl)Combined Master Mix5.3530SNP assay 20X (for K417T or N501Y assays)0.550Sample cDNA4.2... |
43,711 | Keio Screen | 4 | null | https://www.protocols.io/view/keio-screen-bnw7mfhn | Saul Moore | TITLE: Keio Screen
AUTHORS: Saul Moore
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Protocol for screening </span><span style = "font-style:italic;">Caenorhabditis elegans</span><span> behavioural response to bacterial gene-deletion mutants from the 'Keio Collection', to identify behaviour-... | ["[Seeding bacterial lawns (96WP)]\nEnsure that the imaging plates have lost approximately 3-5% of their original weight. Place under a hood (or drying cabinet) until this is the case. (Friday, -4 days)", "[Seeding bacterial lawns (96WP)]\nRemove overnight cultures for 'Old Lawn' plates that were prepared in Step 24, a... |
41,412 | Chlamydomonas reinhardtii cell wall extraction with perchlorate | 4 | null | https://www.protocols.io/view/chlamydomonas-reinhardtii-cell-wall-extraction-wit-bkpckviw | Joao Vitor Molino | TITLE: Chlamydomonas reinhardtii cell wall extraction with perchlorate
AUTHORS: Joao Vitor Molino
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocols describe the steps required for the perchlorate extraction of cell wall proteins from Chlamydomonas reinhardtii. </div><div class = "text-b... | ["[Material]\nSodium PerchlorateCentrifuge tubesPipettes and tipsCentrifuge", "[Perchlorate solution]\nSodium perchlorate has the following safety concerns.", "[Cell preparation]\nGrow cells until the beginning of the stationary phase. (Until obtained the highest amount of cells)Count the cells concentration, and harve... |
82,964 | Complete Hepatitis B Virus Sequencing using an ONT-Based Next-Generation Sequencing Protocol | 4 | dx.doi.org/10.17504/protocols.io.5qpvo3xxzv4o/v1 | https://www.protocols.io/view/complete-hepatitis-b-virus-sequencing-using-an-ont-cu9uwz6w | Wonderful T. CHOGA, yeshnee.m, Lucious B. Chabuka, Tongai Maponga, Derek Tshiabuila, James Emmanuel San, Houriiyah Tegally, Monika Moir, Sureshnee Pillay, Richard Lessells, Cheryl Baxter, Jennifer Giandhari, Eduan Wilkinson, Tulio De Oliveira | TITLE: Complete Hepatitis B Virus Sequencing using an ONT-Based Next-Generation Sequencing Protocol
AUTHORS: Wonderful T. CHOGA, yeshnee.m, Lucious B. Chabuka, Tongai Maponga, Derek Tshiabuila, James Emmanuel San, Houriiyah Tegally, Monika Moir, Sureshnee Pillay, Richard Lessells, Cheryl Baxter, Jennifer Giandhari, Edu... | ["[Quantification of DNA using Qubit] Prepare the two standards calibrate the Qubit Fluorometer using Qubit dsDNA HS Assay kit Thermo Fisher Scientific (Qubit® dsDNA HS Reagent).", "[Quantification of DNA using Qubit] For standards [STD]: Aliquot 190 µL of Qubit® dsDNA HS Reagent working solution to each 500 µL thin-w... |
null | null | null | dx.doi.org/10.17504/protocols.io.cpivkd | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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76,420 | HEPES transformation buffer | 4 | null | https://www.protocols.io/view/hepes-transformation-buffer-cnvcve2w | Andreas Sagen | TITLE: HEPES transformation buffer
AUTHORS: Andreas Sagen
[DESCRIPTION]
HEPES buffer is commonly used to prepare prokaryotic (bacterial) cells for electroporation.
[STEPS]
SECTION: 1 M HEPES buffer
1. Add 40 mL distilled water to a 50 mL tube
SECTION: 1 M HEPES buffer
2. Measure and add 11.915 g HEPES
Materials:
S... | ["[1 M HEPES buffer] Add 40 mL distilled water to a 50 mL tube", "[1 M HEPES buffer] Measure and add 11.915 g HEPES\n\nMaterials:", "[1 M HEPES buffer] Adjust pH to pH 7.4 with concentrated sodium hydroxide or hydrogen chloride", "[1 M HEPES buffer] Add distilled water to 50 mL", "[1 M HEPES buffer] Filter sterilize wi... |
27,446 | X2Go Client Set-Up | null | dx.doi.org/10.17504/protocols.io.62whgfe | null | Laurel Dieckhaus | TITLE: X2Go Client Set-Up
AUTHORS: Laurel Dieckhaus
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">X2Go Client set-up to run Linux from Windows computer (on and off campus). </div><div class = "text-block">Use the following link for more information or help on setting up X2Go Client:</div><div clas... | ["[Install X2Go Client]\nInstall X2Go Client from the following site in the section labeled Get X2Go: https://wiki.x2go.org/doku.php. Choose the correct client install based on your type of computer you have (for example, for Windows, you will choose the Windows Installer).", "[Define X2Go Client Session]\nOpen X2Go Cl... |
null | null | null | dx.doi.org/10.17504/protocols.io.egybbxw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol provides a method to study phage-bacteria interactions by generating a Network in Cytoscape using the application CoNet. To <a href="http://psbweb05.psb.ugent.be/conet/tutorial5.php" target="_blank">CoNet tutorial</a> can help with analysis. Based on the methods fr... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.d659g5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Taken directly from NEB's website, this is the protocol for using their optimized sticky-end ligation and transformation. For more information, see <a href="https://www.neb.com/products/m0370-instant-sticky-end-ligase-master-mix" target="_blank">https://www.neb.com/products/m037... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ijxccpn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The protocol describes a molecular cloning method in our laboratory. </p>
[STEPS]
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43,756 | Transformation | 1 | dx.doi.org/10.17504/protocols.io.bnykmfuw | https://www.protocols.io/view/transformation-bnykmfuw | Zhujun Wei | TITLE: Transformation
AUTHORS: Zhujun Wei
[STEPS]
?. Put DH5α chemically competent bacterium on ice for melting about 5 min.
?. Add 50 μl DH5α chemically competent bacterium into 1.5 ml tubes, mix with ligation product or digested product thoroughly, incubate the bacterium on ice for 30 min.
?. Heat shock the bacteriu... | ["Put DH5α chemically competent bacterium on ice for melting about 5 min.", "Add 50 μl DH5α chemically competent bacterium into 1.5 ml tubes, mix with ligation product or digested product thoroughly, incubate the bacterium on ice for 30 min.", "Heat shock the bacterium for exactly 45 s at 42 ℃ water bath.", "Place back... |
79,001 | Moorea Transect Protocol | 1 | null | https://www.protocols.io/view/moorea-transect-protocol-crdzv276 | Ellis Gelt, Kiran Bengard, jparadise, slicata, Ellinor Arzbaecher, Juliet Capriola, Laura Barragan, Grace Sandel | TITLE: Moorea Transect Protocol
AUTHORS: Ellis Gelt, Kiran Bengard, jparadise, slicata, Ellinor Arzbaecher, Juliet Capriola, Laura Barragan, Grace Sandel
[DESCRIPTION]
This procedure is used for costal monitoring and has been tested along the majority of the coast of Mo'orea, French Polynesia; completed by UC Berkeley... | ["When done tracking, don’t forget to save and export track as .gpx file.", "[Coastal Armoring] Start time-stamp as soon as coastal profile changes or as soon as you are no longer able to monitor.", "[Boats] Walking along the shore, take a time stamp of any boats, canoes, jetskis, or other vessels on the water that are... |
28,378 | MojoSort™ Human anti-APC Nanobeads Protocol | null | dx.doi.org/10.17504/protocols.io.7x2hpqe | null | Sam Li | TITLE: MojoSort™ Human anti-APC Nanobeads Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Product description and procedure summary:</span></div><div class = "text-block">Target cells are positively selected or depleted by incubating the sam... | ["Prepare cells from your tissue of interest. Kits for human samples have been optimized for PBMCs, please prepare the cells using a suitable method.", "In the final wash of your sample preparation, resuspend the cells in MojoSort™ Buffer by adding up to 4 mL in a 5 mL (12 x 75 mm) polypropylene tube.Note: Keep MojoSor... |
94,983 | Recombinant retroviral vectors that express EGF, TGF alpha, NRG2 beta, and the NRG2 beta Q43L mutant | 1 | dx.doi.org/10.17504/protocols.io.kxygx3d6og8j/v1 | https://www.protocols.io/view/recombinant-retroviral-vectors-that-express-egf-tg-c8zfzx3n | Ella Wilson, Markelle Scott, Vipasha Dwivedi, Madison Zelan, David J Riese II | TITLE: Recombinant retroviral vectors that express EGF, TGF alpha, NRG2 beta, and the NRG2 beta Q43L mutant
AUTHORS: Ella Wilson, Markelle Scott, Vipasha Dwivedi, Madison Zelan, David J Riese II
[DESCRIPTION]
Here we describe the construction of recombinant retroviral expression vectors based on pLXSN-HygR that drive ... | ["[Introduction] Elevated signaling by members of the epidermal growth factor receptor (EGFR/ErbB) family of receptor tyrosine kinases contributes to numerous human malignancies. This elevated signaling may be due to gain-of-function mutations in the receptor genes, increased receptor gene transcription, or elevated l... |
null | null | null | dx.doi.org/10.17504/protocols.io.h8yb9xw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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99,445 | BrainSaw agar stock solution | 0 | null | https://www.protocols.io/view/brainsaw-agar-stock-solution-ddcv22w6 | Rob Campbell | TITLE: BrainSaw agar stock solution
AUTHORS: Rob Campbell
[DESCRIPTION]
Making agar stock solution for serial sectioning imaging.
[STEPS]
SECTION: Before you start
1. You will need at least 100 mL of 50 mM PB.
SECTION: Make the stock
2. Rinse out the 100 ml bottle in which the stock is kept.
SECTION: Make t... | ["[Before you start] You will need at least 100 mL of 50 mM PB.", "[Make the stock] Rinse out the 100 ml bottle in which the stock is kept.", "[Make the stock] Fill the bottle with 100 mL of 50 mM PB to the notched fill line.", "[Make the stock] Weigh out 5 g of and pour into the bottle. Cap the bottle and shake it.... |
93,386 | Dispensing agar into multiwell plates | 1 | dx.doi.org/10.17504/protocols.io.e6nvwd759lmk/v1 | https://www.protocols.io/view/dispensing-agar-into-multiwell-plates-c7fizjke | Bonnie Evans | TITLE: Dispensing agar into multiwell plates
AUTHORS: Bonnie Evans
[DESCRIPTION]
Updated protocol for pouring agar into multiwell plates using Integra VIAFILL dispenser. Agar should be prepared in advance, and kept in 60oC waterbath until ready to dispense, and whilst dispensing. The X, Y, Z positions for dispensing c... | ["[Configure Integra VIAFILL] Insert large cassette into the machine", "[Configure Integra VIAFILL] Configure X, Y, and Z settings for the multiwell plate by clicking on tool symbol -> stage alignment.", "[Configure Integra VIAFILL] Exit settings by pressing the back button", "[Dispensing Agar] Press on the program you... |
108,045 | snASE - MAS-Seq protocol | 0 | dx.doi.org/10.17504/protocols.io.ewov19w7plr2/v1 | https://www.protocols.io/view/snase-mas-seq-protocol-dmrm4546 | Asa Shin, Aziz Al'Khafaji | TITLE: snASE - MAS-Seq protocol
AUTHORS: Asa Shin, Aziz Al'Khafaji
[DESCRIPTION]
Modified version of PacBio's MAS-seq protocol for snASE samples.
[STEPS]
SECTION: Quality Control
1. 1 Bring the Qubit 1X dsDNA HS working solution and standards to room temperature.
SECTION: Quality Control
2. 2 Pulse vortex or pipette... | ["[Quality Control] 1 Bring the Qubit 1X dsDNA HS working solution and standards to room temperature.", "[Quality Control] 2 Pulse vortex or pipette mix each sample to homogenize the DNA in solution.", "[Quality Control] 3 Quick spin each sample to collect liquid.", "[Quality Control] 4 Take a 1 μL aliquot from each sa... |
72,245 | Extraction-Protocol-miRNA-SCALONMC | 6 | null | https://www.protocols.io/view/extraction-protocol-mirna-scalonmc-cisvuee6 | Marcela Scalon, Giane Regina Paludo, Christine Souza Martins, Ricardo Titze de Almeida, Gabriel Ginani Ferreira, Franciele Schlemmer | TITLE: Extraction-Protocol-miRNA-SCALONMC
AUTHORS: Marcela Scalon, Giane Regina Paludo, Christine Souza Martins, Ricardo Titze de Almeida, Gabriel Ginani Ferreira, Franciele Schlemmer
[DESCRIPTION]
This protocol is intended as a guideline for the purification of total miRNAs, from serum and plasma, using the miRNeasy ... | ["Prepare serum or plasma or thaw frozen samples:\n- Aliquots has to have 100µl of plasma or serum.", "Add 500µl of QIAzol Lysis Reagent. Mix by vortexing or pipetting up and down.\nNote: After addition of QIAzol Lysis Reagent, lysates can be stored at -70ºC for severa months.", "Place the tube containing the homogenat... |
80,322 | gDNA RNA Clean Up Protocol | 4 | dx.doi.org/10.17504/protocols.io.x54v9dn14g3e/v1 | https://www.protocols.io/view/gdna-rna-clean-up-protocol-cspawdie | Wesley Elias Bhering Barrios, Débora Gonçalves Gouveia | TITLE: gDNA RNA Clean Up Protocol
AUTHORS: Wesley Elias Bhering Barrios, Débora Gonçalves Gouveia
[DESCRIPTION]
Protocol used to eliminate DNA fragments and gDNA from purified RNA and to remove impurities from the sample.
[BEFORE_START]
*** Use only sterile RNAse-Free tubes - AM12425 - or sterile Axygen RNAse Free m... | ["[Procedure] Starting with the 27 uL left over from each sample, add another 62 uL of RNAse-Free H2O at room temperature to all samples;", "[Procedure] Prepare DNAse Mix I and add 11 uL of the Mix per sample;\n 10 uL of 10X DNAse I Buffer * No. of samples;\n 1 uL of DNAse I * No. of samples;\n __\n 11 uL *... |
50,358 | DNA Short-insert Library Construction Protocol for Illumina HiSeq 2500/4000/X Ten or NovaSeq | 4 | dx.doi.org/10.17504/protocols.io.bvewn3fe | https://www.protocols.io/view/dna-short-insert-library-construction-protocol-for-bvewn3fe | Hongfang Zhang | TITLE: DNA Short-insert Library Construction Protocol for Illumina HiSeq 2500/4000/X Ten or NovaSeq
AUTHORS: Hongfang Zhang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">HiSeq DNA pair-end library construction is used for DNA sequencing on Illumina HiSeq 2500/HiSeq 4000/HiSeq X Ten/ and NovaSeq se... | ["Fragment Genomic DNA genomic DNA was randomly fragmented using a Covaris ultrasonicator. The fragmented DNAs were tested by Gel-electrophoresis, then purified using an paramagnetic bead based AxyPrep Mag PCR clean up Kit.\n1 µl", "End RepairThe fragmented DNAs were combined with the End Repair Mix, incubated at for ... |
100,996 | Recovery and preparation for transplantation of cryopreserved vmDA progenitors for transplantation. | 0 | dx.doi.org/10.17504/protocols.io.bp2l622d1gqe/v1 | https://www.protocols.io/view/recovery-and-preparation-for-transplantation-of-cr-devc3e2w | Tyra Fraser, Lachlan Thompson | TITLE: Recovery and preparation for transplantation of cryopreserved vmDA progenitors for transplantation.
AUTHORS: Tyra Fraser, Lachlan Thompson
[DESCRIPTION]
This protocol outlines the recovery of cryopreserved vmDA progenitors. After recovery, this outlines the process to prepare these cells for xenotransplantation... | ["[Recovery of cells] Prepare NBB27 base media according to the materials table.", "Aspirate supernatant. Flick pellet twice.\n Resuspend in 1 mLof NBB27 + All + Ri 1:1000.\nPipette 10 µL into a small Eppendorf tube for cell counting. Repeat for a second Eppendorf tube.\nTake the 2 tubes and add 10 µL trypan blue to ce... |
39,858 | Extraction of RNA from Wastewater Primary Solids Using a Direct Extraction Method for Downstream SARS-CoV-2 RNA Quantification | 1 | dx.doi.org/10.17504/protocols.io.bi6skhee | https://www.protocols.io/view/extraction-of-rna-from-wastewater-primary-solids-u-bi6skhee | Stephanie Loeb, Katy Graham, Marlene Wolfe, Krista Wigginton, Alexandria Boehm | TITLE: Extraction of RNA from Wastewater Primary Solids Using a Direct Extraction Method for Downstream SARS-CoV-2 RNA Quantification
AUTHORS: Stephanie Loeb, Katy Graham, Marlene Wolfe, Krista Wigginton, Alexandria Boehm
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><h1>Overview</h1></div><div cl... | ["[Separate Solids and Spike BCoV]\nCentrifuge at .\nCentrifuge: 14500 33, 30 min, 4 10\nBring the centrifuge rotor to the BSC before loading or opening.", "[Separate Solids and Spike BCoV]\nDecant the supernatant into an empty 50 mL falcon tube or larger container. Record the weight and volume of the remaining solids.... |
null | null | null | dx.doi.org/10.17504/protocols.io.kw8cxhw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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95,619 | hmbc_metab.nan | 5 | dx.doi.org/10.17504/protocols.io.4r3l22dm4l1y/v1 | https://www.protocols.io/view/hmbc-metab-nan-c9mbz42n | NAN KB, John Glushka, Mario Uchimiya, Christopher Esselman, Saraa Al Jawad, Leandro I Ponce, Laura Morris, Arthur Edison | TITLE: hmbc_metab.nan
AUTHORS: NAN KB, John Glushka, Mario Uchimiya, Christopher Esselman, Saraa Al Jawad, Leandro I Ponce, Laura Morris, Arthur Edison
[DESCRIPTION]
This is a protocol for running the Bruker pulse program "hmbcetgpl3nd" for metabolomics samples.
[BEFORE_START]
This protocol assumes:
Your sample is lo... | ["[Create a new dataset]", "[Create a new dataset] On the menu bar on TopSpin, click on\nStart → Create Dataset", "[Create noesypr1d experiment file] When Lock, Tune, Shim are complete proceed to the specific protocol for your desired pulseprogram(s).", "[Create a new dataset] Enter\nNAME: Name of a set of datasets (e.... |
106,734 | ImageJ Analyses of Mitochondria (HSP60) in TH+ cells | 0 | dx.doi.org/10.17504/protocols.io.6qpvr8y83lmk/v1 | https://www.protocols.io/view/imagej-analyses-of-mitochondria-hsp60-in-th-cells-dkgn4tve | Chiara Pavan, Clare Parish | TITLE: ImageJ Analyses of Mitochondria (HSP60) in TH+ cells
AUTHORS: Chiara Pavan, Clare Parish
[DESCRIPTION]
This protocol explains how to use Fiji to analyse mitochondria in iPSC derived dopaminergic neurons in culture for parameters such as network branching, sphericity and mean total branch length.
[BEFORE_START]... | ["[Image acquisition] Images analysed with this protocol were taken with Leica Stellaris 8 confocal (for mitochondrial morphology and ATG13-HSP60 co-localization, with FLIM 40x/1.30 oil immersion objective, HC PL\nAPO, CS2, using Leica Power HyD detector S and HyD detector X).\n\nAll mitochondria morphology images were... |
61,183 | Mouse Whole Cell Tissue Processing for 10x Genomics Platform | 1 | dx.doi.org/10.17504/protocols.io.q26g7b52klwz/v9 | https://www.protocols.io/view/mouse-whole-cell-tissue-processing-for-10x-genomic-b7y7rpzn | Allen Institute for Brain Science | TITLE: Mouse Whole Cell Tissue Processing for 10x Genomics Platform
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
This protocol describes how to isolate tissue from various ROI’s of the mouse brain followed by preparation of a highly concentrated single cell suspension for transcriptomic profiling on 10x Ge... | [] |
51,270 | Conexão do actígrafo no computador - ActTrust - V.1 | 5 | dx.doi.org/10.17504/protocols.io.bwbepaje | https://www.protocols.io/view/conex-o-do-act-grafo-no-computador-acttrust-v-1-bwbepaje | Daniel Vartanian | TITLE: Conexão do actígrafo no computador - ActTrust - V.1
AUTHORS: Daniel Vartanian
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Este protocolo faz parte do processo de coleta de dados actigráficos do Grupo Interdisciplinar de Pesquisa em Sono (GIPSO). Ele foi desenhado para os actígrafos ... | ["Abra o software ActStudio\nCaso apareça algum pop-up solicitando a configuração da latitude e longitude, clique em Não. Para este procedimento essa configuração não é necessária.", "Acesse a tela Controle\nNa parte superior do ActStudio você verá um botão chamado Controle. Clique sobre ele e depois selecione a aba CO... |
62,319 | Creating iPSC lines with Ribonucleoprotein (RNP): Nucleofection, Single-cell Sorting, Genotyping, and Line Maintenance Protocol | 1 | dx.doi.org/10.17504/protocols.io.4r3l2oeopv1y/v1 | https://www.protocols.io/view/creating-ipsc-lines-with-ribonucleoprotein-rnp-nuc-b84pryvn | Kamaljot Gill, Aradhana Sachdev, Bruce Conklin, Claire D Clelland | TITLE: Creating iPSC lines with Ribonucleoprotein (RNP): Nucleofection, Single-cell Sorting, Genotyping, and Line Maintenance Protocol
AUTHORS: Kamaljot Gill, Aradhana Sachdev, Bruce Conklin, Claire D Clelland
[DESCRIPTION]
This protocol describes how to perform gene editing on human induced pluripotent stem cells (i... | ["[Nucleofecting] Cell Culture", "[Nucleofecting] Grow iPSCs in 1 well of a 6 well-plate until ~70-80% confluency.", "[Nucleofecting] Coating plates", "[Nucleofecting] Coat 1 x 6 well-plate with Matrigel.\n\nMatrigel is diluted in KO DMEM to make a working concentration of 80 μl/ml (keep the Matrigel ice-cold) \nMatrig... |
86,276 | L-1 LEECH FIELD SAMPLING | 4 | dx.doi.org/10.17504/protocols.io.kxygx3peog8j/v1 | https://www.protocols.io/view/l-1-leech-field-sampling-cyhcxt2w | REDI-NET Consortium | TITLE: L-1 LEECH FIELD SAMPLING
AUTHORS: REDI-NET Consortium
[DESCRIPTION]
This protocol describes leech field sampling.
[GUIDELINES]
OBJECTIVE
To document the field processes for collecting hematophagous leeches (Family Hirudinea).
SUMMARY/SCOPE
The overarching aim of the REDI-NET is to develop a collaborative la... | ["[SAMPLING TEAMS] Field sampling of iDNA (leech) samples involves two people. One person serves as the ‘sampler’ and the other person serves as a ‘helper’. The helper can look up details in these instructions when needed, keep track of samples, handle objects that are contamination risks, serve as a second set of eyes... |
27,715 | 10 simple rules for writing Selenium automated tests | null | dx.doi.org/10.17504/protocols.io.7bbhiin | null | Sebastian Bassi | TITLE: 10 simple rules for writing Selenium automated tests
AUTHORS: Sebastian Bassi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Some advices regarding writing Selenium tests. The examples are in Python but the rules are language agnostic, so it can be implemented in any supported language.</div... | [] |
45,910 | Ribosomal RNA Depletion and cDNA Synthesis | 4 | null | https://www.protocols.io/view/ribosomal-rna-depletion-and-cdna-synthesis-bq3wmype | Alicia Rich | TITLE: Ribosomal RNA Depletion and cDNA Synthesis
AUTHORS: Alicia Rich
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Ribosomal RNA depletion and cDNA synthesis using the Zymo-Seq RiboFree Universal cDNA Kit. This protocol should follow RNA isolation and purification using the Direct-zol™ RNA Micro... | ["[0.0 Estimate Starting RNA concentration]\nEstimate the starting RNA concentration of each extract using the Nanodrop.", "[0.0 Estimate Starting RNA concentration]\nBring RNA extracts and RNase-free water on a cold block to the spectrophotometer downstairs.\non ice", "[0.0 Estimate Starting RNA concentration]\nWash t... |
24,608 | Fabrication and Deployment of the In Situ Chemotaxis Assay (ISCA) | null | dx.doi.org/10.17504/protocols.io.398gr9w | null | Bennett Lambert, Jean-Baptiste Raina | TITLE: Fabrication and Deployment of the In Situ Chemotaxis Assay (ISCA)
AUTHORS: Bennett Lambert, Jean-Baptiste Raina
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Here we outline the process of fabricating and deploying the </span><span style = "font-style:italic;">In Situ</span><span> Che... | ["[Assembling the ISCA]\nCast 26g of 1:10 (curing agent:base) polydimethylsiloxane (PDMS aka. Sylgard 184) onto the 3D printed moulds. Here, it is of critical importance that the PDMS is degassed under vacuum and that there are no bubbles left within the mould.We use a process similar to that described here in order t... |
null | null | null | dx.doi.org/10.17504/protocols.io.dej3cm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in "<a href="http://protocols.io/view/FASP-Kit-Protocol-ORNL-Developed-for-Bacteriophage-ddn25d" target="_blank">FASP Kit Protocol-ORNL Developed for Bacteriophage</a>"
[STEPS]
?. | [] |
35,675 | Protocol for publishing 2 | null | dx.doi.org/10.17504/protocols.io.be33jgqn | https://www.protocols.io/view/protocol-for-publishing-2-be33jgqn | Andrew Khramchenkov | TITLE: Protocol for publishing 2
AUTHORS: Andrew Khramchenkov
[STEPS]
?. [Section 1]
?. [Section 1]
?. [Section 2] | ["[Section 1]", "[Section 1]", "[Section 2]"] |
70,200 | Drosophila genomic DNA isolation using NEB Monarch kit | 4 | dx.doi.org/10.17504/protocols.io.bp2l694qklqe/v1 | https://www.protocols.io/view/drosophila-genomic-dna-isolation-using-neb-monarch-cgsytwfw | David Loehlin | TITLE: Drosophila genomic DNA isolation using NEB Monarch kit
AUTHORS: David Loehlin
[DESCRIPTION]
Genomic DNA extraction protocol for Drosophila flies, using the Monarch® Genomic DNA Purification Kit from New England Biolabs. The protocol has been adapted from the manufacturer's protocol "Genomic DNA Purification fr... | ["Pre-heat a heat block or shaking heat block to 56˚C before starting. Prewarm a tube of gDNA Elution Buffer in the heat block.", "For each sample, pipet 20 µL EDTA (0.5M) into the bottom of a 1.5mL tube. Label tubes and place on ice.", "Anaesthetize flies (e.g., with CO2), then sweep flies into the tube. Incubate on... |
58,872 | Total High Molecular Weight DNA Extraction from plant tissues for Long Read Sequencing | 4 | dx.doi.org/10.17504/protocols.io.b5qyq5xw | https://www.protocols.io/view/total-high-molecular-weight-dna-extraction-from-pl-b5qyq5xw | Subash Rai | TITLE: Total High Molecular Weight DNA Extraction from plant tissues for Long Read Sequencing
AUTHORS: Subash Rai
[DESCRIPTION]
This protocol is a combination of two published protocols (10.1186/1746-4811-8-26 and 10.2144/000114460) with modifications and was developed as a research within GIH collaborative projects.... | ["[Tissues preparation and lysis] Take 10 mL lysis buffer and warm it at 60 °C for 15-20 min.", "[Tissues preparation and lysis] Take ~1 L of liquid nitrogen (LN2) in Dewar Flask that requires for chilling mortar and pestle and grinding the tissues.", "[Tissues preparation and lysis] Take dry ice in an esky/insulated c... |
56,681 | Dynamic Contrast Enhanced MRI of mouse Abdomen | 1 | dx.doi.org/10.17504/protocols.io.81wgb6pnolpk/v1 | https://www.protocols.io/view/dynamic-contrast-enhanced-mri-of-mouse-abdomen-b3khqkt6 | Mamtaaryagupta | TITLE: Dynamic Contrast Enhanced MRI of mouse Abdomen
AUTHORS: Mamtaaryagupta
[DESCRIPTION]
Dynamic Contrast Enhanced MRI of mouse Abdomen
[STEPS]
SECTION: Animal Preparation
1. This SOP includes a brief DCE protocol that consists of following major steps:
1. Animal Preparation for tail vein catheterization
2. MR... | ["[Animal Preparation] This SOP includes a brief DCE protocol that consists of following major steps:\n\n1. Animal Preparation for tail vein catheterization\n\n2. MRI calibration, acquisition of B1, T1 and DCE perfusion MRI\n\n3. Animal recovery\n\nNote: The technical details for the acquisition of B1, T1 and DCE perfu... |
28,021 | Chloroform Phenol Phage genome isolation | null | dx.doi.org/10.17504/protocols.io.7kvhkw6 | null | Marijn Ceelen | TITLE: Chloroform Phenol Phage genome isolation
AUTHORS: Marijn Ceelen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol of the isolation of genomic DNA from phage lambda and phage T7. </div></div>
[STEPS]
?. Use cleaned phage stock from the phage stock protocol. Add DNase I 10x buffer, DNa... | ["Use cleaned phage stock from the phage stock protocol. Add DNase I 10x buffer, DNase I (1 U/µL), and RNase A (10 mg/mL) for at without shaking to remove E. coli DNA and RNA.\n50 µl\n1 µl\n1 µl\n37 °C", "Add of EDTA (final concentration ) and incubate for at to deactivate DNase I and RNase A\n20 µl\n75 °C", "Ad... |
78,790 | Immunohistochemistry of liver tissue sections | 4 | dx.doi.org/10.17504/protocols.io.36wgqjpkxvk5/v1 | https://www.protocols.io/view/immunohistochemistry-of-liver-tissue-sections-cq7evzje | Presha Rajbhandari, Taruna Neelakantan, Brent R. Stockwell | TITLE: Immunohistochemistry of liver tissue sections
AUTHORS: Presha Rajbhandari, Taruna Neelakantan, Brent R. Stockwell
[DESCRIPTION]
This protocol outlines the steps used to perform standard immunohistochemistry for antibody validation in frozen human liver tissue samples, performed at Molecular Pathology Core faci... | ["Cryosection the frozen liver tissue at 5µm thickness and place it on charged slide", "Air dry the sections for 3 minutes 180 min", "Fix the tissue sections in cold acetone for 15 minutes 15 min . Alternatively, fix with 1% paraformaldehyde at 4C for 15min followed by ice-cold methanol at -20C for 5min.", "Air dry the... |
38,365 | QUESTIONNAIRE ABOUT ECO METHOD IMPLEMENTATION IN THE UNIVERSITY | 3 | dx.doi.org/10.17504/protocols.io.bhp5j5q6 | https://www.protocols.io/view/questionnaire-about-eco-method-implementation-in-t-bhp5j5q6 | Juan Jesus Torres-Gordillo | TITLE: QUESTIONNAIRE ABOUT ECO METHOD IMPLEMENTATION IN THE UNIVERSITY
AUTHORS: Juan Jesus Torres-Gordillo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The purpose of this questionnaire is to know the impact of the implementation of the ECO method in the University. It is part of an innovat... | [] |
28,902 | Acetone precipitation of proteins | null | dx.doi.org/10.17504/protocols.io.8gehtte | null | iGEM Dusseldorf | TITLE: Acetone precipitation of proteins
AUTHORS: iGEM Dusseldorf
[STEPS]
?. Add 4 times the volume -20°C acetone to the extract and vortexed
?. Incubate sample at -20°C for 2 hours
?. Centrifuge at 14000 x g for 4 min at 4°C and discard the supernatant
?. Wash pellet twice with a 4:1 acetone/water mixture at -20°C un... | ["Add 4 times the volume -20°C acetone to the extract and vortexed", "Incubate sample at -20°C for 2 hours", "Centrifuge at 14000 x g for 4 min at 4°C and discard the supernatant", "Wash pellet twice with a 4:1 acetone/water mixture at -20°C until the pellet is well broken up", "Centrifuge at 14000 x g at 4°C for 10 mi... |
34,208 | Experiences of oldest-old caregivers whose partner is approaching end-of-life: a mixed-method systematic review and narrative synthesis | 1 | dx.doi.org/10.17504/protocols.io.bdm8i49w | https://www.protocols.io/view/experiences-of-oldest-old-caregivers-whose-partner-bdm8i49w | Tessa Morgan, Aamena Bharmal, Robbie Duschinsky, Stephen Barclay | TITLE: Experiences of oldest-old caregivers whose partner is approaching end-of-life: a mixed-method systematic review and narrative synthesis
AUTHORS: Tessa Morgan, Aamena Bharmal, Robbie Duschinsky, Stephen Barclay
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">B... | [] |
90,415 | Liquid biopsy in sentinel mussels | 4 | dx.doi.org/10.17504/protocols.io.81wgb6z9olpk/v2 | https://www.protocols.io/view/liquid-biopsy-in-sentinel-mussels-c4ipyudn | Sophia Ferchiou, France Caza, Yves St-Pierre | TITLE: Liquid biopsy in sentinel mussels
AUTHORS: Sophia Ferchiou, France Caza, Yves St-Pierre
[DESCRIPTION]
This protocol has been optimized for sampling hemolymph in sentinel mussels in remote areas, such as polar regions. A detailed protocol can be found in Caza et al. (2019).
[BEFORE_START]
A. Sampling Section (... | ["[Sampling] Collect mussels (Mytilus spp.) with a shell length range between 50 to 70 mm.", "[Sampling] Remove intervalvar liquid by opening gently the valves with the tip of a knife.", "[Sampling] Transfer immediately the hemolymph to a sterile 1.5 mL Eppendorf tube (Optional: You can pool 3 or 4 hemolymph samples to... |
108,185 | Study of prescription-indication of antivirals for herpesviruses in a Colombian population. A cross-sectional study | 0 | dx.doi.org/10.17504/protocols.io.dm6gpzkk1lzp/v1 | https://www.protocols.io/view/study-of-prescription-indication-of-antivirals-for-dmvz4676 | Jorge Machado Alba | TITLE: Study of prescription-indication of antivirals for herpesviruses in a Colombian population. A cross-sectional study
AUTHORS: Jorge Machado Alba
[DESCRIPTION]
Introduction:
Herpesviruses are among the most common pathogens worldwide.
Objective: To
determine the prescription patterns and indications for the use... | [] |
47,414 | Manual QIAgen DNA Extraction | 4 | dx.doi.org/10.17504/protocols.io.e6nvw5z12vmk/v1 | https://www.protocols.io/view/manual-qiagen-dna-extraction-bsiwncfe | Clemens Scherzer, Bradley Hyman, Charles Jennings | TITLE: Manual QIAgen DNA Extraction
AUTHORS: Clemens Scherzer, Bradley Hyman, Charles Jennings
[DESCRIPTION]
This protocol explains the Standard Operating Protocol for manually extracting DNA using Qiagen.
[BEFORE_START]
DNA Q/C GOALS
1. Cary Concentration Assay
a. 260/280 = 1.8-2.0
b. Manual Pur... | ["[Manual Qiagen DNA Extraction] Thaw buffy coats or whole bloods by equilibrating to Room temperature.", "[Manual Qiagen DNA Extraction] Heat a heating block to 56 °C.", "[Manual Qiagen DNA Extraction] Gather all the necessary reagents/buffers (Buffer AE, Buffer AW1, Buffer AW2, Buffer AL, 100% ethanol, Qiagen Proteas... |
96,896 | The knowledge and perception of the general public and young adults of Palliative Care - A systematic Review | 0 | dx.doi.org/10.17504/protocols.io.261gedymwv47/v2 | https://www.protocols.io/view/the-knowledge-and-perception-of-the-general-public-dau82ezw | Yann-Nicolas Batzler | TITLE: The knowledge and perception of the general public and young adults of Palliative Care - A systematic Review
AUTHORS: Yann-Nicolas Batzler
[DESCRIPTION]
Background: As a result of demographic change, chronic and oncological diseases gain importance in the context of public health. Palliative care plays a crucia... | ["[Preparation] General screening of literature", "[Development of the search algorithm] Develop search string", "[Identification of inclusion and exclusion criteria] Using PICOS process", "[Preparation] Screening for suitable databases", "[Preparation] Identify lack of knowledge", "[Development of the search algorithm... |
91,222 | Protocol for breeding Hymenochirus boettgeri in captivity | 1 | dx.doi.org/10.17504/protocols.io.x54v9pzrqg3e/v1 | https://www.protocols.io/view/protocol-for-breeding-hymenochirus-boettgeri-in-ca-c5bwy2pe | Tamilie Carvalho, Timothy Y. James | TITLE: Protocol for breeding Hymenochirus boettgeri in captivity
AUTHORS: Tamilie Carvalho, Timothy Y. James
[DESCRIPTION]
Hymenochirus boettgeri is a sexually dimorphic species, with females ty pically exhibiting a larger oval-shaped body (up to 35 mm in snout-vent length (SVL)), while males possess a large obiculate... | ["[Sexual selection] Select male H. boettgeri specimens with heavily vascularized glands and the largest females for breeding.", "[Sexual selection] Keep males and females in separate 38 L glass tanks by sex at 25 °C with conditioned water as described in the “Housing and Care for Hymenochirus boettgeri” protocol and 1... |
63,624 | 2-step PCR mixture and conditions (Barcoded-head primers for seqs pooling) | 4 | null | https://www.protocols.io/view/2-step-pcr-mixture-and-conditions-barcoded-head-pr-cadgsa3w | Yin-Tse Huang | TITLE: 2-step PCR mixture and conditions (Barcoded-head primers for seqs pooling)
AUTHORS: Yin-Tse Huang
[DESCRIPTION]
PCR mixture and condition (2X SUPERGREEN PCR MASTER MIX)
[STEPS]
1. Wear glove, clean up the working bench w. 1% bleach
SECTION: For 1' PCR head-primers
2. Prepare 1' PCR master mixutre for hea... | ["Wear glove, clean up the working bench w. 1% bleach", "[For 1' PCR head-primers] Prepare 1' PCR master mixutre for head-primers (prepare 1.2X of solutions for pipetting error if needed)\n \nPCR mixture for head-primers for each reaction", "[For 1' PCR head-primers] Mix the 1' PCR master mixture gently by pi... |
null | null | null | dx.doi.org/10.17504/protocols.io.nusdewe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The RCC Team, Station Biologique de Roscoff, CNRS/Université P. & M. Curie, Place G. Teissier, 29680 Roscoff, France</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.hgcb3sw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes the RT-PCR from 'Flower Ca<sup>2+</sup> channel in CME and ADBE' of Yao CK et al.</p>
<p> </p>
<p>Please see the manuscript for the full method details.</p>
[STEPS]
?.
?.
?.
?.
?. | [] |
47,350 | How many systematic reviews include outcomes in their search strategy and acknowledge the limitation? A meta-epidemiological review | 1 | dx.doi.org/10.17504/protocols.io.bsgwnbxe | https://www.protocols.io/view/how-many-systematic-reviews-include-outcomes-in-th-bsgwnbxe | Yasushi Tsujimoto, Yusuke Tsutsumi, Yuki Kataoka, Masahiro Banno, Toshi A Furukawa | TITLE: How many systematic reviews include outcomes in their search strategy and acknowledge the limitation? A meta-epidemiological review
AUTHORS: Yasushi Tsujimoto, Yusuke Tsutsumi, Yuki Kataoka, Masahiro Banno, Toshi A Furukawa
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">MAIN PROTOCOL</div></... | ["How many systematic reviews include outcomes in their search strategy and acknowledge the limitation? A meta-epidemiological review\n\t\t\t\t\t\t\t .justify:after {\n\t\t\t\t\t\t\t content: \"\";\n\t\t\t\t\t\t\t display:inline-block;\n\t\t\t\t\t\t\t width: 100%;\n\t\t\t\t\t\t\t }\n\t\t\t\t\t\t\tYasushi Tsu... |
15,930 | 20/9 doc | null | dx.doi.org/10.17504/protocols.io.ts2enge | https://www.protocols.io/view/20-9-doc-ts2enge | null | TITLE: 20/9 doc
AUTHORS:
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. dfsf | ["dfsf"] |
57,639 | pasefRiQ_V1 | 1 | dx.doi.org/10.17504/protocols.io.b4ifqubn | https://www.protocols.io/view/pasefriq-v1-b4ifqubn | lcmsmethods , Yuting Yuan, Namandje' N Bumpus | TITLE: pasefRiQ_V1
AUTHORS: lcmsmethods , Yuting Yuan, Namandje' N Bumpus
[DESCRIPTION]
We have developed optimized methods for reporter ion quantification on a TIMSTOF Flex (TIMS B configuration) by iterative analysis of the TMT triple knock out yeast standard and an in-house developed two-proteome standard. For th... | [] |
85,764 | Agarose gel for RNA and DNA | 4 | dx.doi.org/10.17504/protocols.io.5qpvo3bm7v4o/v1 | https://www.protocols.io/view/agarose-gel-for-rna-and-dna-cxzcxp2w | kaylee Beine | TITLE: Agarose gel for RNA and DNA
AUTHORS: kaylee Beine
[DESCRIPTION]
General method for running agarose gels for RNA and DNA samples
[STEPS]
SECTION: Preparing the agarose gel and plate
1. 1 g agarose in 100 mL of
SECTION: Preparing the agarose gel and plate
2. Microwave solution in a flask for 3 min until the... | ["[Preparing the agarose gel and plate] 1 g agarose in 100 mL of", "[Preparing the agarose gel and plate] Microwave solution in a flask for 3 min until the agarose is dissolved. Microwave for 1 min thereafter 30 s", "[Preparing the agarose gel and plate] Allow to cool before adding 1 µL in the gel medium before comp... |
44,627 | 3.4 Assay Runtime | 4 | dx.doi.org/10.17504/protocols.io.bpttmnnn | https://www.protocols.io/view/3-4-assay-runtime-bpttmnnn | Peter Simons, Virginie Bondu, Angela Wandinger-Ness, Tione Buranda | TITLE: 3.4 Assay Runtime
AUTHORS: Peter Simons, Virginie Bondu, Angela Wandinger-Ness, Tione Buranda
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Small, monomeric guanine triphosphate hydrolases (GTPases) are ubiquitous cellular integrators of signaling. A signal activates the GTPase, which... | ["[3.4 Assay Runtime]\nJust before the addition of lysates, mix the five different effector beads, centrifuge at , and reduce the supernatant to about 5 μL. Resuspend the beads in , giving approximately . Add to twelve 0.65 mL microcentrifuge tubes for 12 multiplex assays. Leftover beads can be used later to set up th... |
22,680 | Gravimetric Soil Moisture X-CZO, Modified from KBS-LTER, as per Robertson et al. 1999 | null | dx.doi.org/10.17504/protocols.io.2dyga7w | null | Mia Maltz, Emma Aronson, Keshav Arogyaswamy, Natalie Rodriguez | TITLE: Gravimetric Soil Moisture X-CZO, Modified from KBS-LTER, as per Robertson et al. 1999
AUTHORS: Mia Maltz, Emma Aronson, Keshav Arogyaswamy, Natalie Rodriguez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Samples were collected from a network of ten Critical Zone Observatories (CZOs) a... | ["On the soil moisture spreadsheet record the sampling date, treatment, replicate, etc.", "[Weighing Out Soils]\nFor sieved composite soil samples:Place the soil moisture tin on the balance and tare the weight by zeroing the scale.Use a plastic spoon to add about 40-50 g of the soil into the tared soil moisture tin. Re... |
null | null | null | dx.doi.org/10.17504/protocols.io.c87zzm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in <a href="https://www.protocols.io/view/Wet-mount-Method-for-Enumeration-of-Aquatic-Viruse-c8pzvm" target="_blank">Wet-mount Method for Enumeration of Aquatic Viruses.</a>
[GUIDELINES]
This solution is needed only if analyzing unconcentrated samples.
[STEPS]
?.... | [] |
99,538 | USDA LTAR Common Experiment measurement: Rainfall | 0 | dx.doi.org/10.17504/protocols.io.e6nvw1kyzlmk/v1 | https://www.protocols.io/view/usda-ltar-common-experiment-measurement-rainfall-ddfs23ne | Rachel DuBose, Andrew M O'Reilly, Lindsey Witthaus, Claire Baffaut | TITLE: USDA LTAR Common Experiment measurement: Rainfall
AUTHORS: Rachel DuBose, Andrew M O'Reilly, Lindsey Witthaus, Claire Baffaut
[DESCRIPTION]
Rainfall includes any moisture falling from the atmosphere in liquid form. Rainfall is often called precipitation, but precipitation includes liquid water as well as a soli... | ["[1.\tData collection] Equipment\n\nMeasure precipitation and record rainfall timing with an electronic weighing rain gauge because of reduced error (Hansen et al. 2001, Keefer et al. 2008). These instruments are available from several manufacturers (e.g., OTT Hydromet, Kemptem, Germany; Texas Electronics, Dallas, TX,... |
null | null | null | dx.doi.org/10.17504/protocols.io.dnb5am | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Final concentration <br />2 µl 10x Buffer 1x <br />2 µl ATP (100 mM) 10 mM <br />2µl GTP (100 mM) 10 mM <br />2 µl CTP (100 mM) 10 mM <br />2 µl UTP (100 mM) 10 mM <br />8 µl DNA template (85 ng/µl) ←PCR PDTS 25 ng/µl <br />2 ... | [] |
95,699 | Nuclei Preparation from Frozen Tissue for 10X Multiome using gentleMACS Homogenization and FANS, v1.2 Feb 2024 | 0 | dx.doi.org/10.17504/protocols.io.14egn35zml5d/v1 | https://www.protocols.io/view/nuclei-preparation-from-frozen-tissue-for-10x-mult-c9ptz5nn | ereisner | TITLE: Nuclei Preparation from Frozen Tissue for 10X Multiome using gentleMACS Homogenization and FANS, v1.2 Feb 2024
AUTHORS: ereisner
[DESCRIPTION]
This protocol describes isolation of nuclei from frozen tissue using gentleMACS homogenization and FANS. Nuclei are permeabilized, washed, and counted; single-nucleus su... | ["[Reagent preparation:] Prepare buffers fresh and leave on ice.", "[Reagent preparation:] The volume of MACS Buffer prepared depends on the input mass of each sample. An additional 1 mL should be prepared for rinsing in addition to the homogenization volume. Refer to the chart below:", "[Nuclei Preparation] Pre-chill ... |
86,202 | Mitophagy induction using Difereprone | 1 | dx.doi.org/10.17504/protocols.io.rm7vzxbqrgx1/v1 | https://www.protocols.io/view/mitophagy-induction-using-difereprone-cye2xtge | Louise Uoselis | TITLE: Mitophagy induction using Difereprone
AUTHORS: Louise Uoselis
[DESCRIPTION]
Mitophagy induction in HeLa cells using Difereprone (DFP).
[STEPS]
SECTION: Day 1
1. Seed cells, aiming for a confluency of 80-90% at the time of treatment the next day.
SECTION: Day 2
2. Feed cells for 60 min in an appropriate volume... | ["[Day 1] Seed cells, aiming for a confluency of 80-90% at the time of treatment the next day.", "[Day 2] Feed cells for 60 min in an appropriate volume of standard growth media.", "[Day 2] During the feed, warm up the difereprone (DFP) stock aliquot in a 37 °C waterbath. Centrifuge the stock tube after thawing to ensu... |
92,954 | Norovirus genotyping and phylogeny analysis_ViroTrakr workflow 1_v.1 | 1 | dx.doi.org/10.17504/protocols.io.261ged1eov47/v1 | https://www.protocols.io/view/norovirus-genotyping-and-phylogeny-analysis-virotr-c6z2zf8e | Jayanthi Gangiredla, Mark Mammel, Zhihui Yang | TITLE: Norovirus genotyping and phylogeny analysis_ViroTrakr workflow 1_v.1
AUTHORS: Jayanthi Gangiredla, Mark Mammel, Zhihui Yang
[DESCRIPTION]
This workflow provides step-by-step instructions for norovirus analysis within the GalaxyTrakr platform. It includes the quality assessment for raw sequencing data (from most... | ["Log into your GalaxyTrakr account.", "Create a GalaxyTrakr account if you are the first-time user:\nUser Registration Form - Galaxy Genome Trakr (galaxytrakr.org)", "Log into your GalaxyTrakr account if you already have one:\nGalaxy (galaxytrakr.org)", "Get familiar with Galaxy components: Tools, Menu and History.", ... |
93,721 | Protocol 1 | 5 | dx.doi.org/10.17504/protocols.io.ewov1qbkygr2/v1 | https://www.protocols.io/view/protocol-1-c7rzzm76 | Mitt Coats | TITLE: Protocol 1
AUTHORS: Mitt Coats
[DESCRIPTION]
A short abstract
[STEPS]
3.
SECTION: S2
4.
SECTION: S2
5.
SECTION: S2
6.
SECTION: S0
1.
SECTION: S1
2. | ["[S2]", "[S2]", "[S2]", "[S0]", "[S1]"] |
35,855 | HuBMAP TMC-Florida/Zurich CODEX Modality Overview | null | dx.doi.org/10.17504/protocols.io.be9pjh5n | https://www.protocols.io/view/hubmap-tmc-florida-zurich-codex-modality-overview-be9pjh5n | Marda Jorgensen, Jerelyn Nick, Franchesca Farris, Jesus Penaloza | TITLE: HuBMAP TMC-Florida/Zurich CODEX Modality Overview
AUTHORS: Marda Jorgensen, Jerelyn Nick, Franchesca Farris, Jesus Penaloza
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is an overview of all of the protocols currently in use for the CODEX modality at HubMAP Tissue Mapping ... | ["Process donor organs into samples for analysis. Lymph Node: dx.doi.org/10.17504/protocols.io.bbgnijveThymus: dx.doi.org/10.17504/protocols.io.bbgmiju6Spleen: dx.doi.org/10.17504/protocols.io.bc3kiykw", "Register organ donor, organs received and common coordinate region information in the HuBMAP UUID generator at http... |
76,432 | Wheat disease symptoms observation, capture, description, and evaluation | 4 | null | https://www.protocols.io/view/wheat-disease-symptoms-observation-capture-descrip-cnvqve5w | Erin H Hill, Benjamin Schwessinger | TITLE: Wheat disease symptoms observation, capture, description, and evaluation
AUTHORS: Erin H Hill, Benjamin Schwessinger
[DESCRIPTION]
This protocols is part of the ANU Biosecurity mini-research project #1 "Plant Pathogen Diagnostics: Visuals, subcultures, and genomics".
You will be provided four pots of 3-4 week... | ["[Disease symptom capture] You will receive five pots with wheat plants as detailed in the \"Description\" section. Please label each pot with your research group name, the date, and the treatment group.", "[Disease symptom capture] Carefully, study the plants in each pot. Select four to five leaves for each treatment... |
93,907 | BG-11 media | 4 | dx.doi.org/10.17504/protocols.io.q26g7pkzkgwz/v1 | https://www.protocols.io/view/bg-11-media-c7xtzpnn | is Sparrow | TITLE: BG-11 media
AUTHORS: is Sparrow
[DESCRIPTION]
From McCormick lab, University of Edinburgh
(written by Anja Nenninger, Grant Gale, Alejandra Schiavon and Anton Puzorjov), introduced to protocols.io by myself
[STEPS]
SECTION: Stock solutions
1. BG11 media
100XBG11:
Trace elements
Iron stock
... | ["[Stock solutions] BG11 media\n \n100XBG11:\n\n \n\n \n \nTrace elements\n \n\n \n\n \nIron stock\n \n\n \n\n \nPhosphate stock\n \n \n\n \n\nGlucose stock\n \n \n\n \n\nSoidum carbonate stock\n \n \n\n \n\n \nAutoclave all above solutions\n \n \n \nFilter sterilize all below solutions\nHEPES buffer\n \n \n\n \n\nAdju... |
null | null | null | dx.doi.org/10.17504/protocols.io.imecc3e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>We developed a mini-barcode based on the 12S rRNA gene to identify predator from scats in Tasmania. </p>
<p>To test the sensitivity of our primers to detect low template DNA samples, we set up serial dilutions of six DNA extracts originating from museum samples, representing ... | [] |
26,972 | In vitro pmel-1 T cell-mediated cytotoxicity assay with CytoTox-ONE Homogenous Membrane Integrity Assay (Promega) | null | dx.doi.org/10.17504/protocols.io.6j4hcqw | null | Elinor Gottschalk, Bulent Arman Aksoy, Pinar Aksoy, Jeff Hammerbacher | TITLE: In vitro pmel-1 T cell-mediated cytotoxicity assay with CytoTox-ONE Homogenous Membrane Integrity Assay (Promega)
AUTHORS: Elinor Gottschalk, Bulent Arman Aksoy, Pinar Aksoy, Jeff Hammerbacher
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left"><s... | ["The day before adding T cells to co-culture with the target cancer cells, plate the target cells in a 96 well plate at 25,000 cells per well in DMEM with 10 % FBS.An example plate layout is below:Plate the target cells in columns 2-7. Leave the rest of the wells empty.Each column has 6 replicates (we do not recommend... |
66,896 | Burn Boost Reviews 2022 | 1 | dx.doi.org/10.17504/protocols.io.bp2l615bdvqe/v1 | https://www.protocols.io/view/burn-boost-reviews-2022-cdjqs4mw | condorcbdfly | TITLE: Burn Boost Reviews 2022
AUTHORS: condorcbdfly
[DESCRIPTION]
We live in a furious world, where we lack the opportunity to appreciate things. Subsequently, the corpulence issue is deteriorating continuously. It is the most significant general medical condition on the planet. Weight is generally exacerbated by a... | [] |
45,552 | 1.2 Bradford assay | 4 | null | https://www.protocols.io/view/1-2-bradford-assay-bqqqmvvw | Elizabeth Fozo | TITLE: 1.2 Bradford assay
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protein concentration estimation using Bradford assay</div></div>
[STEPS]
?. [Protein concentration estimation using Bradford assay]
Prepare working reagent by diluting 1part Dye Reagent Concentrate wi... | ["[Protein concentration estimation using Bradford assay]\nPrepare working reagent by diluting 1part Dye Reagent Concentrate with 4 parts distilled, deionized water. This diluted reagent may be used for approximately 2 weeks when kept at room temperature.", "[Protein concentration estimation using Bradford assay]\nPrep... |
25,318 | RNA Isolation from Plant Tissue Protocol 9: CTAB/Acid Phenol/Silica Membrane Method | null | dx.doi.org/10.17504/protocols.io.4yegxte | null | null | TITLE: RNA Isolation from Plant Tissue Protocol 9: CTAB/Acid Phenol/Silica Membrane Method
AUTHORS:
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Implemented by: Henrietta Myburg and Marc Johnson</div><div class = "text-block"><span>This protocol is a modification of protocol 8. It was developed ... | ["Chill mortar and pestle with liquid nitrogen (fill the mortar carefully with liquid nitrogen, let it evaporate, repeat one more time. Keep the pestle in the mortar when doing this).", "Fill the mortar again.", "Carefully grind tissue to a powder in liquid Nitrogen.\nAdd more nitrogen if needed, but it is important to... |
88,302 | SEQUENCING Protocol Template | 1 | null | https://www.protocols.io/view/sequencing-protocol-template-c2gnybve | Kathleen Pitz, Raissa.meyer | TITLE: SEQUENCING Protocol Template
AUTHORS: Kathleen Pitz, Raissa.meyer
[DESCRIPTION]
A protocol template created through the BeBOP project for sequencing.
[STEPS]
SECTION: Protocol Template
1. Minimum Information about an Omics Protocol (MIOP)
See https://github.com/BeBOP-OBON/miop/blob/main/model/schema/terms.y... | ["[Protocol Template] Minimum Information about an Omics Protocol (MIOP)\n\nSee https://github.com/BeBOP-OBON/miop/blob/main/model/schema/terms.yaml for list and definitions.\n\n\n\n \nMIOP Term\nValue\n \nmethodology category\n\n \nproject\n\n \npurpose\n\n \nanalyses\n\n \ngeographic location\n\n \nbroad-scale env... |
null | null | null | dx.doi.org/10.17504/protocols.io.fjbbkin | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Commands for hands-on component of QIIME, which should be run from a local installation. Details can be found online at http://qiime.org/install/index.html.</p>
<p> </p>
<p>The files used in this hands-on component are also available the virtual machine (details in 'Start Ins... | [] |
35,095 | Anthropometric knee study in patients with Osteoarthritis: Evaluation of possible differences between genders | null | dx.doi.org/10.17504/protocols.io.behxjb7n | https://www.protocols.io/view/anthropometric-knee-study-in-patients-with-osteoar-behxjb7n | Fabrício Bolpato Loures, Rogério Franco de Araújo Góes, Eduardo Branco de Sousa, Naasson Cavanellas, João Maurício Barretto, Marcel Jun Sugawara Tamaoki, Rodrigo Sattaminni Pires e Albuquerque, Pedro José Labronici | TITLE: Anthropometric knee study in patients with Osteoarthritis: Evaluation of possible differences between genders
AUTHORS: Fabrício Bolpato Loures, Rogério Franco de Araújo Góes, Eduardo Branco de Sousa, Naasson Cavanellas, João Maurício Barretto, Marcel Jun Sugawara Tamaoki, Rodrigo Sattaminni Pires e Albuquerque, ... | [] |
42,739 | Lab 5--Cloning a PCR Fragment into a Plasmid (Paper Activity) | 1 | dx.doi.org/10.17504/protocols.io.bmytk7wn | https://www.protocols.io/view/lab-5-cloning-a-pcr-fragment-into-a-plasmid-paper-bmytk7wn | Harley King | TITLE: Lab 5--Cloning a PCR Fragment into a Plasmid (Paper Activity)
AUTHORS: Harley King
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This activity includes a pdf containing instructions for creating a paper plasmid and PCR fragment (gene of interest). I remember doing this with undergraduates w... | ["[Download and Print Activity]\nDownload and print the \"", "[Create PCR Insert]\nUse scissors to cut out the three lines of “PCR Insert.\" Overlap the lines and secure them with tape. Keep the PCR Insert in a line. Do not loop.", "[Create the Plasmid]\nUse scissors to cut out the seven lines of “Vector Backbone.\" Ov... |
51,410 | Mobile Phone Spectrophotometer Setup [Chlorophyll experiment version] | 1 | dx.doi.org/10.17504/protocols.io.bwfspbne | https://www.protocols.io/view/mobile-phone-spectrophotometer-setup-chlorophyll-e-bwfspbne | Katharine Hubbard | TITLE: Mobile Phone Spectrophotometer Setup [Chlorophyll experiment version]
AUTHORS: Katharine Hubbard
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol allows you to turn a mobile phone (smart phone) into a colorimeter/spectrophotometer. It goes through how to set up your phone and wor... | ["[Setting up your phone]\nYou first need to set up your phone to act as a colorimeter - video Instructions for this section are availabile: Setting up Your Mobile Phone as a Colorimeter", "[Setting up your phone]\nChoose a well lit space to work in. This protocol works better during the day under natural light. If you... |
null | null | null | dx.doi.org/10.17504/protocols.io.dsj6cm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is the injection mixture for one locus editing using home<strong>‐</strong>made Cas9
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
34,060 | Crosslinking Immunoprecipitation Beads | 1 | dx.doi.org/10.17504/protocols.io.bdhki34w | https://www.protocols.io/view/crosslinking-immunoprecipitation-beads-bdhki34w | Bryon Drown, Caroline DeHart, Kelleher Research Group | TITLE: Crosslinking Immunoprecipitation Beads
AUTHORS: Bryon Drown, Caroline DeHart, Kelleher Research Group
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Immunoprecipitation with non-covalent capture of antibodies is a rapid and effective method for enriching samples with desired antigens. Interf... | ["[Complex Formation]\nForm complex with beads and antibody", "[Complex Formation]\nAdd 900 uL Binding Buffer and 100 uL magnetic beads to 1.5 mL LoBind tube.", "[Complex Formation]\nCollect beads with magnet and resuspend with 900 uL Binding Buffer.", "[Complex Formation]\nAdd 50 ug IgG antibody.", "[Complex Formation... |
78,532 | INSTRUCTIONS FOR STOOL COLLECTION | 1 | dx.doi.org/10.17504/protocols.io.kxygx94wzg8j/v1 | https://www.protocols.io/view/instructions-for-stool-collection-cqxcvxiw | null | TITLE: INSTRUCTIONS FOR STOOL COLLECTION
AUTHORS:
[DESCRIPTION]
The protocol details the instructions for stool collection self administered by subjects.
[STEPS] | [] |
94,972 | Bioinformatic procedure for shotgun metagenomic analysis of human saliva microbiota | 1 | dx.doi.org/10.17504/protocols.io.bp2l6x5q1lqe/v1 | https://www.protocols.io/view/bioinformatic-procedure-for-shotgun-metagenomic-an-c8y4zxyw | Victoria Meslier, Florence Thirion , Florian Plaza-Onate , Emmanuelle Le Chatelier , mathieu.almeida | TITLE: Bioinformatic procedure for shotgun metagenomic analysis of human saliva microbiota
AUTHORS: Victoria Meslier, Florence Thirion , Florian Plaza-Onate , Emmanuelle Le Chatelier , mathieu.almeida
[DESCRIPTION]
This protocol describes the bioinformatical procedure for the study of human saliva microbiota.
[BEFORE... | ["[General description] Read Quality check", "[General description] Mapping and microbial gene count procedure", "[General description] Metagenomic Pangenome Species MSP profiles"] |
37,108 | Protocol for obtaining rodent brain slices for electrophysiological recordings or neuroanatomical studies | null | dx.doi.org/10.17504/protocols.io.bggujtww | https://www.protocols.io/view/protocol-for-obtaining-rodent-brain-slices-for-ele-bggujtww | Verónica Alejandra Cáceres-Chávez, J. Alejandra Parra-Reyes, Marco A.Herrera-Valdez, Erin Mckiernan | TITLE: Protocol for obtaining rodent brain slices for electrophysiological recordings or neuroanatomical studies
AUTHORS: Verónica Alejandra Cáceres-Chávez, J. Alejandra Parra-Reyes, Marco A.Herrera-Valdez, Erin Mckiernan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Patch clamp recording pe... | ["[Preparation for anesthesia and dissection]\nPrepare and check all materials and equipment: Before beginning the anesthesia and dissection protocol, verify that all the necessary materials are available and in good condition (Fig. 1). The perfusion and Krebs solutions should have been prepared previously and must not... |
58,790 | Filming Daphnia Swimming in 2D Protocol | 3 | null | https://www.protocols.io/view/filming-daphnia-swimming-in-2d-protocol-b5neq5be | Laura Lopez, Meghan Duffy | TITLE: Filming Daphnia Swimming in 2D Protocol
AUTHORS: Laura Lopez, Meghan Duffy
[DESCRIPTION]
This is a protocol used to record Daphnia individuals swimming (swimming speed, acceleration, time spent moving).
[STEPS] | [] |
55,328 | Rnase A treatment | 1 | null | https://www.protocols.io/view/rnase-a-treatment-bz98p99w | Rita Kuo | TITLE: Rnase A treatment
AUTHORS: Rita Kuo
[DESCRIPTION]
This protocol is used to remove RNA from genomic DNA. RNase A is an endoribonuclease that specifically degrades single-stranded RNA at C and U residues. It cleaves the phosphodiester bond between the 5'-ribose of a nucleotide and the phosphate group attached ... | ["[Rnase A treatment] Bring up the sample volume to 200 ul using TE buffer (pH 8.0)", "[Rnase A treatment] Add 10 ul of RNase A", "[Rnase A treatment] Incubate 37°C for 1 hour.", "[Sample QC] Run gel 10-15 minutes. If RNA is visible on the gel, add another 10 ul of RNase A and repeat the incubation step, otherwise proc... |
62,546 | Shipping wastewater samples to FDA-CFSAN | 1 | dx.doi.org/10.17504/protocols.io.14egn797zv5d/v4 | https://www.protocols.io/view/shipping-wastewater-samples-to-fda-cfsan-b9bsr2ne | Maria Balkey, Tina.Pfefer | TITLE: Shipping wastewater samples to FDA-CFSAN
AUTHORS: Maria Balkey, Tina.Pfefer
[DESCRIPTION]
This SOP provides guidance for shipping wastewater samples to the US FDA Center for Food Safety and Applied Nutrition (CFSAN), covering specific steps for registering samples with CFSAN and for the preparation of shipm... | ["[Submission of metadata] Fill out the BioSample custom wastewater template (extension of NCBI's Generic SARS-CoV-2: wastewater surveillance, v1.0 ) according to the NCBI submission protocol for SARS-Cov-2 protocol, once completed, send it to covidtrakr@fda.hhs.gov for registration. Successful registrations will rece... |
null | null | null | dx.doi.org/10.17504/protocols.io.dzu76v | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<strong>Note:</strong> It is recommended that rates of bacterial production be measured simultaneous to all time points for virus measurements. There are two reasons for this: (1) if measured simultaneously, the researcher can estimate virus production throughout the experiment, ... | [] |
21,181 | UC Davis - Uninary Albumin Excretion (UAE) Protocol | null | dx.doi.org/10.17504/protocols.io.yw5fxg6 | null | Peter Havel | TITLE: UC Davis - Uninary Albumin Excretion (UAE) Protocol
AUTHORS: Peter Havel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">
Albumin blue dye is a stain for the specific and sensitive spectrofluorometric determinati... | ["Prepare working reagent.", "Prepare standards by serially diluting 200 mg/l standard 1:1 to make 100, 50, 25, 12.5, 6.25 standards.", "Add 25 μl of standard and sample to each well.", "Add 125 μl of working reagent. Read in fluorimeter using 590 nm excitation and 616 nm emission.IMPORTANT: Make sure not to add any bu... |
47,888 | U-251MG Spheroid generation using a scaffold based method protocol | 1 | dx.doi.org/10.17504/protocols.io.bszqnf5w | https://www.protocols.io/view/u-251mg-spheroid-generation-using-a-scaffold-based-bszqnf5w | Lara Carroll, Brijesh Tiwari, James Curtin, Janith Wanigasekara | TITLE: U-251MG Spheroid generation using a scaffold based method protocol
AUTHORS: Lara Carroll, Brijesh Tiwari, James Curtin, Janith Wanigasekara
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">3D cell culture is a technique that is used to grow cells in vitro that will mimic an in vivo environment... | ["[Spheroid Generation]\nOnce U-251MG cell flasks are 70-80% confluent, medium from the flask is aspirated and U-251MG tumor cell monolayers re washed with 1X phosphate buffered saline (PBS; 5ml for a 25cm2 or 4ml for a 75cm2 flask), add 0.25 X Trypsin-EDTA cell dissociation enzyme (2ml for a 25cm2 or 4ml for a 75cm2 f... |
59,283 | HMW gDNA purification and ONT ultra-long-read data generation | 1 | dx.doi.org/10.17504/protocols.io.b55tq86n | https://www.protocols.io/view/hmw-gdna-purification-and-ont-ultra-long-read-data-b55tq86n | Glennis Logsdon | TITLE: HMW gDNA purification and ONT ultra-long-read data generation
AUTHORS: Glennis Logsdon
[DESCRIPTION]
This protocol describes the purification of high-molecular-weight genomic DNA from mammalian cells and the generation of ultra-long (N50 >100 kbp) Oxford Nanopore data using the PromethION. It is based on the S... | ["[Cell collection and lysis] Freeze down 2-7 x 10^7 cells as a cell pellet, and store at -80°C.", "[Cell collection and lysis] When you are ready to purify the DNA, thaw the cell pellet on ice (usually takes ~30 mins).", "[Cell collection and lysis] While the cells are thawing, add RNase A to the lysis buffer at a fin... |
89,749 | General western blot protocol | 1 | dx.doi.org/10.17504/protocols.io.j8nlkomj6v5r/v1 | https://www.protocols.io/view/general-western-blot-protocol-c3vvyn66 | Jailyn Izu | TITLE: General western blot protocol
AUTHORS: Jailyn Izu
[DESCRIPTION]
General western blot protocol
[STEPS]
SECTION: Sample preparation
1. Prepare appropriate cellular extract for analysis (for example, see Transfecting using FuGENE® 4K Transfection Reagent and cell lysis (M-PER) in a 6-well plate protocol).
SECTION... | ["[Sample preparation] Prepare appropriate cellular extract for analysis (for example, see Transfecting using FuGENE® 4K Transfection Reagent and cell lysis (M-PER) in a 6-well plate protocol).", "[Sample preparation] Measure the protein content of each sample (for example, see Bradford Assay protocol).", "[Run gel] Ad... |
15,163 | Bold SW 1 NV modified medium | null | dx.doi.org/10.17504/protocols.io.s23eggn | null | Roscoff Culture Collection | TITLE: Bold SW 1 NV modified medium
AUTHORS: Roscoff Culture Collection
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Medium used for some eukaryotes</div><div class = "text-block">Adapted from CCAP web site : https://www.ccap.ac.uk/media/documents/BB.pdf</div><div class = "text-block">See also :... | ["Change from standard Bold medium ABCDE1Volume\nfor 500 ml\nComponent\nConcentration Stock Solutions\n25 ml\nCaCl2\nCaCl2.2H2O\n0.5 gr\n200 ml\n35 ml\nNaNO3\nNaNO3\n16 gr\n200 ml\n45 ml\nMgSO4\nMgSO4.7H2O\n10 gr\n200 ml\n510 ml\nPO4\nFrom PCRS11 media\n65 ml\nNH4Cl (K)\nFrom K media\n \n \n73 ml\nK trace me... |
58,579 | SARS-CoV-2 Amplicon-based Illumina Sequencing Protocol | 1 | dx.doi.org/10.17504/protocols.io.b5ftq3nn | https://www.protocols.io/view/sars-cov-2-amplicon-based-illumina-sequencing-prot-b5ftq3nn | wgscov | TITLE: SARS-CoV-2 Amplicon-based Illumina Sequencing Protocol
AUTHORS: wgscov
[DESCRIPTION]
ARTIC amplicon sequencing protocol adapted from Josh Quick's https://www.protocols.io/view/ncov-2019-sequencing-protocol-v2-bdp7i5rn for Illumina sequencing of SARS-CoV-2
[STEPS]
SECTION: Preamble to cDNA Synthesis
1. Use ei... | ["[Preamble to cDNA Synthesis] Use either a SuperScript (step 2) or LunaScript kit (step 3) for cDNA synthesis", "[cDNA Synthesis] Option 1: SuperScipt mastermix", "[cDNA Synthesis] In a clean room, mix 1:1 dNTP and random hexamers. Aliquot 2 µL per reaction, and add 11 µL RNA, as per the table below. Seal plate and... |
63,368 | Phylogenetic Analysis of Complete Bovine Coronavirus Genome Sequences | 5 | dx.doi.org/10.17504/protocols.io.kqdg3pyeql25/v1 | https://www.protocols.io/view/phylogenetic-analysis-of-complete-bovine-coronavir-b95gr83w | Aspen M Workman, Tara G. McDaneld, Gregory P P Harhay, Subha Das, John Dustin Loy, Benjamin M. Hause | TITLE: Phylogenetic Analysis of Complete Bovine Coronavirus Genome Sequences
AUTHORS: Aspen M Workman, Tara G. McDaneld, Gregory P P Harhay, Subha Das, John Dustin Loy, Benjamin M. Hause
[DESCRIPTION]
Bovine coronavirus (BCoV) has spilled over to many species, including humans, where the host range variant coron... | ["[MAFFT Alignment] Align using MAFFT v7.450\n\nThe sequences were aligned using the MAFFT accuracy methods ---globalpair as defined in the mafft manual page below \n\n \n\n\nKeep in mind ...\n\nThe commands below generate files that contain both STDOUT (mafft output to the \"terminal\") as well as the multifasta ... |
25,211 | RNA Isolation from Plant Tissue Protocol 15: Hot Acid Phenol Method for Algae | null | dx.doi.org/10.17504/protocols.io.4u3gwyn | null | null | TITLE: RNA Isolation from Plant Tissue Protocol 15: Hot Acid Phenol Method for Algae
AUTHORS:
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Implemented by: Falicia Goh and Neil Clarke</div><div class = "text-block"><span>This RNA isolation method is modified from that described by Köhrer and Domd... | ["Preheat phenol and phenol:chloroform to . Heated phenol should not be re-used.\n65 °C", "Collect algae cells via centrifugation for at at .\n0 Room temperature", "Re-suspend frozen pellet in of preheated extraction buffer.\n800 µl", "Immediately add of hot acid phenol.\n800 µl", "Incubate at for . Vortex every 1... |
23,144 | BORG Protocols | null | dx.doi.org/10.17504/protocols.io.2uggetw | null | Bristow MR, Altman NL, Minobe WA, Lowes BD, Kao DP | TITLE: BORG Protocols
AUTHORS: Bristow MR, Altman NL, Minobe WA, Lowes BD, Kao DP
[STEPS] | [] |
76,181 | OMS Atlas FFPE Spatial Mapping | 1 | dx.doi.org/10.17504/protocols.io.8epv56ppjg1b/v6 | https://www.protocols.io/view/oms-atlas-ffpe-spatial-mapping-cnmvvc66 | Brett Johnson, Danielle Galipeau, George Thomas | TITLE: OMS Atlas FFPE Spatial Mapping
AUTHORS: Brett Johnson, Danielle Galipeau, George Thomas
[DESCRIPTION]
This protocol describes the procedure by which the OMS Atlas serially sections a FFPE block, prepares the resulting slides, and then distributes the specimens for downstream analysis.
[BEFORE_START]
Transfer... | ["[Preparation] Verify the identity of the FFPE block to be cut against written request for sectioning.", "[Preparation] Label all slides with a unique BEMS ID and slide number, corresponding to the written request and FFPE spatial map (below).", "[Sectioning] Align block on microtome to minimize tissue loss.", "[Secti... |
98,935 | Comparing Implementations of Explainable Artificial Intelligence using End-User Evaluations: Protocol for a Systematic Review | 0 | dx.doi.org/10.17504/protocols.io.n92ld89e8v5b/v1 | https://www.protocols.io/view/comparing-implementations-of-explainable-artificia-dcux2wxn | Mieke Ronckers, Rianne Conijn, Chris Snijders | TITLE: Comparing Implementations of Explainable Artificial Intelligence using End-User Evaluations: Protocol for a Systematic Review
AUTHORS: Mieke Ronckers, Rianne Conijn, Chris Snijders
[DESCRIPTION]
In this protocol, we outline the steps for a systematic review on different implementations of Explainable Artificia... | ["[Introduction] Objectives\nResearch question:\nWith this systematic review, we aim to answer the following research question: How do different implementations of explainable Artificial Intelligence (XAI) influence human-AI interaction, both subjectively (perceptions of humans on AI advice) and objectively (performanc... |
32,903 | Hematologic alterations and early mortality in a cohort of HIV positive African patients | null | dx.doi.org/10.17504/protocols.io.bcdfis3n | null | Fausto Ciccacci, Francesca Lucaroni, Roberto Latagliata, Laura Morciano, Elisa Mondlane, Moises Balama, Dyna Tembo, Jane Gondwe, Stefano Orlando, Leonardo Palombi, Maria Cristina Marazzi | TITLE: Hematologic alterations and early mortality in a cohort of HIV positive African patients
AUTHORS: Fausto Ciccacci, Francesca Lucaroni, Roberto Latagliata, Laura Morciano, Elisa Mondlane, Moises Balama, Dyna Tembo, Jane Gondwe, Stefano Orlando, Leonardo Palombi, Maria Cristina Marazzi
[DESCRIPTION]
<div class = ... | [] |
17,919 | Electronic Record for Continuity of Patient Care: A use case for Doctor's handovers, in a tertiary maternity | null | dx.doi.org/10.17504/protocols.io.vq7e5zn | null | José Carlos Serufo Filho, Denise Utsch Gonçalves, Zilma Reis | TITLE: Electronic Record for Continuity of Patient Care: A use case for Doctor's handovers, in a tertiary maternity
AUTHORS: José Carlos Serufo Filho, Denise Utsch Gonçalves, Zilma Reis
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><h2></h2></div><div class = "text-block"><div class = "justify" st... | ["[Timing of the duration of the shift session]\n1. Start the timer as soon as the session coordination begins to speak of a clinical case that wishes to transfer care to the next team.2. End the timer when the session coordination finishes reporting the last clinical case you wish to transfer care to the next team.", ... |
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