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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33,449 | SOP Appendix for Spleen | null | dx.doi.org/10.17504/protocols.io.bcwhixb6 | null | Franchesca Farris | TITLE: SOP Appendix for Spleen
AUTHORS: Franchesca Farris
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is an appendix for spleen SOP. </div></div>
[STEPS]
?. | [] |
36,621 | 10% Tween 20 | null | dx.doi.org/10.17504/protocols.io.bfzmjp46 | https://www.protocols.io/view/10-tween-20-bfzmjp46 | Allen Institute for Brain Science | TITLE: 10% Tween 20
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to prepare 10% Tween 20. Tween 20, when added to aqueous solutions acts as a surfactant, decreasing the surface tension of the solution. It also punches holes in membr... | [] |
50,828 | Clusterin purification from HEK293E cells | 1 | dx.doi.org/10.17504/protocols.io.bvvkn64w | https://www.protocols.io/view/clusterin-purification-from-hek293e-cells-bvvkn64w | Dr Patricia Yuste-Checa | TITLE: Clusterin purification from HEK293E cells
AUTHORS: Dr Patricia Yuste-Checa
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details the preocedure of clusterin purification from HEK293E cells.</div></div>
[STEPS]
?. [Clusterin expression]
Express Clusterin (Clu) in HEK293E cells... | ["[Clusterin expression]\nExpress Clusterin (Clu) in HEK293E cells cultured in FreeStyle 293 Expression Medium (Thermo Fisher Scientific, 12338018) for .\nNote: This protocol was optimized using HEK293E cells stably expressing Clu-Strep tag (pB-TPAF-CluStrep), however Clu without any affinity tag can be purified follow... |
null | null | null | dx.doi.org/10.17504/protocols.io.kr3cv8n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for TBS and sham stimulation, over the dorsolateral prefrontal cortex.</p>
[STEPS]
?.
?.
?. | [] |
57,203 | SHIMS 3.0: Highly efficient single-haplotype iterative mapping and sequencing using ultra-long nanopore reads | 4 | dx.doi.org/10.17504/protocols.io.b34tqqwn | https://www.protocols.io/view/shims-3-0-highly-efficient-single-haplotype-iterat-b34tqqwn | Daniel W Bellott, Ting-Jan Cho, Emily K Jackson, Helen Skaletsky, Jennifer F. Hughes, David C Page | TITLE: SHIMS 3.0: Highly efficient single-haplotype iterative mapping and sequencing using ultra-long nanopore reads
AUTHORS: Daniel W Bellott, Ting-Jan Cho, Emily K Jackson, Helen Skaletsky, Jennifer F. Hughes, David C Page
[DESCRIPTION]
The reference sequence of structurally complex regions can o... | ["[Pick Clones and Grow Cultures] Fill each well of a Nunc 96 DeepWell plate with 1.9 mLof 2X LB containing 34 µg/ml chloramphenicol.", "[Pick Clones and Grow Cultures] Use a clean pipette tip to scrape the surface of a frozen glycerol stock and drop the tip directly into the DeepWell plate to inoculate a well. Inocul... |
67,007 | Mito-Keima assay to assess mitophagy | 1 | dx.doi.org/10.17504/protocols.io.q26g74e1qgwz/v1 | https://www.protocols.io/view/mito-keima-assay-to-assess-mitophagy-cdn7s5hn | Thanh Ngoc Nguyen | TITLE: Mito-Keima assay to assess mitophagy
AUTHORS: Thanh Ngoc Nguyen
[DESCRIPTION]
This protocol details the procedure of mito-keima assay to assess mitophagy.
[STEPS]
SECTION: Procedure
1. Seed the HeLa cells the day before the treatment day in 24 well plates.
SECTION: Procedure
2. The next day, make sure the s... | ["[Procedure] Seed the HeLa cells the day before the treatment day in 24 well plates.", "[Procedure] The next day, make sure the seeded cells are spreading out.", "[Procedure] Aspirate off the old media and treat each well with 0.5 mL of growth media containing 4 micromolar (µM) Antimycin A, 10 micromolar (µM) Oligomyc... |
50,697 | Thymectomy procedure to remove native thymus of NSG mice | 4 | dx.doi.org/10.17504/protocols.io.bvrhn536 | https://www.protocols.io/view/thymectomy-procedure-to-remove-native-thymus-of-ns-bvrhn536 | Mohsen Khosravi-Maharlooei, Markus Holzl, Austin Chen, Megan Sykes | TITLE: Thymectomy procedure to remove native thymus of NSG mice
AUTHORS: Mohsen Khosravi-Maharlooei, Markus Holzl, Austin Chen, Megan Sykes
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details our approach to removing the native thymus from an NSG mouse. The NSG mouse thymus is atro... | ["The anterior neck is shaved and disinfected with betadine and 70% alcohol consisting of three alternate swabs followed by a final application of betadine solution. Limbs are gently restrained using rubber bands.", "Using a pair of forceps, the skin at the junction of the neck and chest is grasped and a vertical midli... |
29,174 | Determining Lipid Content in Embryos using Nile Red Fluorescence | null | dx.doi.org/10.17504/protocols.io.8qwhvxe | null | Luciano Bonilla, Peter J. Hansen | TITLE: Determining Lipid Content in Embryos using Nile Red Fluorescence
AUTHORS: Luciano Bonilla, Peter J. Hansen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The following protocol is derived from the protocol described by Genicot et al. (Theriogenology 63: 1181- 1194, 2005) and is based on the ... | [] |
94,981 | Propagating Serratia phage 92A1 and host | 4 | dx.doi.org/10.17504/protocols.io.81wgbxb3qlpk/v1 | https://www.protocols.io/view/propagating-serratia-phage-92a1-and-host-c8zdzx26 | Adair Borges | TITLE: Propagating Serratia phage 92A1 and host
AUTHORS: Adair Borges
[DESCRIPTION]
This is a protocol for propagating Serratia phage 92A1 and its host, Serratia strain 92. Serratia phage 92A1 (Genbank OR088902.1) is a 174 kb, T4-like phage with a probable arabinose-based modification of its genome. You can use this p... | ["[Propagating Serratia strain 92] Streak culture out on an LB agar plate and incubate at room temperature (25 °C) for two days. You should see the formation of light tan colonies that have a slightly gooey appearance.", "[Propagating Serratia strain 92] Set up a liquid culture of the host by inoculating 1 mL of LB bro... |
null | null | null | dx.doi.org/10.17504/protocols.io.jfscjne | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Background </strong>Elderly patients undergoing hip fracture surgery (HFS) are at increased risk of postoperative venous thromboembolism (VTE). Therefore, combined postoperative mechanical and chemical thromboprophylaxis has been routinely performed after HFS in these... | [] |
40,861 | Statistical Considerations (Part 9 of Phase 3 study of Vaccine Candidate for COVID-19) | 1 | dx.doi.org/10.17504/protocols.io.bj55kq86 | https://www.protocols.io/view/statistical-considerations-part-9-of-phase-3-study-bj55kq86 | Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores | TITLE: Statistical Considerations (Part 9 of Phase 3 study of Vaccine Candidate for COVID-19)
AUTHORS: Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is Part 9 of "Phase 3 randomized, double-blinded, placebo-controlled trial to evalu... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.sydefs6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This staining was employed to detect Fetuin-A in paraffin sections (1 μm thickness) of formalin-fixed human brain tissue. For fetuin-A staining, we used a monoclonal IgG2a mouse-anti-human antibody (clone MAHS-1, dilution 0.1-0.5 µg/mL), raised against purified human fetuin-... | ["[Clear slides] Place slides in hybridization oven: 37°C overnight, then 1 hour at 65°C", "Deparaffination in xylene 3x20 minutes (3 different containers) on a shaker", "Rehydration in graded ethanol: 3x2 minutes in 100% ethanol, followed by 2x2 minutes in 96% ethanol and at last 2 minutes in 70% ethanol", "Wash in ph... |
null | null | null | dx.doi.org/10.17504/protocols.io.rncd5aw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The isolation of nuclear genomic DNA of high molecular weight is becoming a crucial step for obtaining long read sequencing data produced by the PacBio and Oxford Nanopore platforms. Although it involves a few more steps than a standard total genomic DNA preparations, it is w... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.p4kdquw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A real-time PCR for Parapoxvirus targeting the DNA polymerase. It is used to screen human samples where Parapoxvirus is suspected.</p>
<p>This protocol is based on the published RVSS assay by Das et al 2017. Oligonucleotides have been modified and a different PCR kit is used.... | [] |
43,565 | LymphocyteCollection | 4 | dx.doi.org/10.17504/protocols.io.bnsmmec6 | https://www.protocols.io/view/lymphocytecollection-bnsmmec6 | Michaela McCown, Josie A Tueller, Scott Weber, Samuel H Payne | TITLE: LymphocyteCollection
AUTHORS: Michaela McCown, Josie A Tueller, Scott Weber, Samuel H Payne
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Purpose: To isolate in separate wells of B lymphocytes and wells of T lymphocytes from fresh whole blood. </div><div class = "text-block">Generally, lyse... | ["[Setup]\nClean biosafety cabinent by UV for 15 minutes, then wipe with Ethanol.Gather pipettes, tubes, racks, and waste container into the cabinent. One person can set up while another is bringing the blood over on ice if two people are available for prep, otherwise leave blood on ice during initial setup.Old blood (... |
29,981 | Synthesis of fluorinated neonicotinoids | null | dx.doi.org/10.17504/protocols.io.9h5h386 | null | Andrii Kyrylchuk, Andriy Bezdudnyy, Denys Klukovskyi | TITLE: Synthesis of fluorinated neonicotinoids
AUTHORS: Andrii Kyrylchuk, Andriy Bezdudnyy, Denys Klukovskyi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a general protocol for synthesis of fluorinated neonicotinoid analogues by interaction of amines with 2-chloro-5-(chloromethyl)pyridine... | ["Dissolve of corresponding substituted aniline in of anhydrous acetonitrile in round-bottom flask, add () of 2-chloro-5-(chloromethyl)pyridine and () of anhydrous potassium carbonate.\n2\n5 ml\n0.324 g\n1.9\n0.828 g\n6", "Put a water-cooled backflow condenser on top of the flask and heat the flask under vigorous... |
68,609 | OCT-Embedded Tissue Preparation | 4 | dx.doi.org/10.17504/protocols.io.81wgb6mpolpk/v1 | https://www.protocols.io/view/oct-embedded-tissue-preparation-ce89thz6 | Stephen Fisher, Marielena Grijalva, Rong Guo, sarahjoh, Hieu Nguyen, John Renz, Jean G Rosario, Steven Rudich, Brian Gregory, Junhyong Kim, Kate O'Neill | TITLE: OCT-Embedded Tissue Preparation
AUTHORS: Stephen Fisher, Marielena Grijalva, Rong Guo, sarahjoh, Hieu Nguyen, John Renz, Jean G Rosario, Steven Rudich, Brian Gregory, Junhyong Kim, Kate O'Neill
[DESCRIPTION]
This protocol describes embedding of tissue samples in optimal cutting temperature (OCT) compound (Lin &... | ["Label biopsy molds appropriately.", "Add a small amount of OCT to the bottom of each mold, ensuring no bubbles are present.", "Place tissue piece in the center of the mold on top of the OCT layer.", "Pour OCT slowly into the mold, ensuring the tissue piece is completely covered.", "Using a small piece of aluminum foi... |
null | null | null | dx.doi.org/10.17504/protocols.io.mdzc276 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Background</strong>: VEGF is elevated in plasma of colon cancer patients and increases after surgery. This study's purpose was to determine plasma VEGF levels before, during, and after open and laparoscopic colorectal surgery performed for left colon cancer (CD).</p>
... | [] |
100,760 | pGEM-T Cloning | 0 | dx.doi.org/10.17504/protocols.io.yxmvme389g3p/v1 | https://www.protocols.io/view/pgem-t-cloning-demy3c7w | Carolina Lopez | TITLE: pGEM-T Cloning
AUTHORS: Carolina Lopez
[DESCRIPTION]
Protocol for cloning in pGEM-T vector
[BEFORE_START]
PRINCIPLES BEHIND THE PROCEDURE MUST BE UNDERSTOOD. PLEASE CONSULT WITH EXPERIENCED LAB MEMBER THE FIRST TIME YOU USE THIS PROCEDURE. UPDATE AS A GENERAL PROCEDURE AS NECESSARY BUT DO NOT MODIFY WITH SPECI... | ["[Insert Generation] 1. Perform PCR to generate bands of interest in total volume of 50 µL. \n \n \n \n2. Make 1% low melt-agarose gel. \n a) Mix 1 g of Agar with 100 mL of TAE Buffer. \n b) Microwave to boil agarose and let cool until you can touch bottle, but gel is not solid.\n c) Add 1.5 µL of... |
106,614 | Induced Cortical Neuron Differentiation | 0 | dx.doi.org/10.17504/protocols.io.e6nvw1n9dlmk/v1 | https://www.protocols.io/view/induced-cortical-neuron-differentiation-dkcw4sxe | Isabel Lam, Alain Ndayisaba, Vikram Khurana | TITLE: Induced Cortical Neuron Differentiation
AUTHORS: Isabel Lam, Alain Ndayisaba, Vikram Khurana
[DESCRIPTION]
Induced Cortical Neuron Differentiation
[STEPS] | [] |
71,191 | Microscopy-based mitochondrial morphology measurements in iNeurons | 4 | dx.doi.org/10.17504/protocols.io.4r3l274bqg1y/v1 | https://www.protocols.io/view/microscopy-based-mitochondrial-morphology-measurem-chrxt57n | Felix Kraus | TITLE: Microscopy-based mitochondrial morphology measurements in iNeurons
AUTHORS: Felix Kraus
[DESCRIPTION]
Protocol for microscopy-based mitochondrial morphology measurements in iNeurons
[STEPS]
SECTION: Differentiation of iNeurons
1. Day 0: Treat AAVS1-TRE3G-NGN2 cells with Accutase and plate the dissociated cells... | ["[Differentiation of iNeurons] Day 0: Treat AAVS1-TRE3G-NGN2 cells with Accutase and plate the dissociated cells in matrigel-coated 6-well plates (2x105 cells/well) in ND1 Medium supplemented with Y27632 (10 μM). \nND1 Medium: \nDMEM/F12 \nN2 (100x) 1x \nBDNF 10 ng/ml \nNT3 10 n... |
70,392 | LAMP-QUASR Primer Design | 5 | null | https://www.protocols.io/view/lamp-quasr-primer-design-cgyytxxw | Felipe Navarro Martínez, Fernan Federici | TITLE: LAMP-QUASR Primer Design
AUTHORS: Felipe Navarro Martínez, Fernan Federici
[DESCRIPTION]
This protocol is designed for the design and adaptation of a LAMP primer set in order for it to be used with the QUASR technique. In order to do this, it requires an already designed (and hopefully experimentally validated)... | ["[Analyze existing primer set] In order to choose a primer for QUASR probe design, is important to understand the parameters present in a LAMP primer set. \n\nOne way to do this, is by checking the complete set of primers (including full-length FIP and BIP) for self-dimerization and/or cross-dimerization using the Mul... |
49,008 | Cost-effectiveness evaluation of the individual vs. group transdiagnostic psychological treatment for emotional disorders in Primary Care (PsicAP-COSTS) | 1 | null | https://www.protocols.io/view/cost-effectiveness-evaluation-of-the-individual-vs-bt4qnqvw | Angel Aguilera-Martin, Mario Gálvez-Lara, Fátima Cuadrado, Eliana Moreno, Francisco García-Torres, Carolina Pérez-Dueñas, Araceli Sánchez-Raya, José F. Venceslá, Jorge Corpas, Francisco Jurado, Juan A. Moriana | TITLE: Cost-effectiveness evaluation of the individual vs. group transdiagnostic psychological treatment for emotional disorders in Primary Care (PsicAP-COSTS)
AUTHORS: Angel Aguilera-Martin, Mario Gálvez-Lara, Fátima Cuadrado, Eliana Moreno, Francisco García-Torres, Carolina Pérez-Dueñas, Araceli Sánchez-Raya, José F.... | ["[RECRUITMENT AND FIRST ASSESSMENT]\nThe recruitment will be accomplished in three different primary care settings of the province of Cordoba: the \"Carlos Castilla del Pino\" Health Centre, the \"Levante Sur Dr. Manuel Barragán Solís\" Health Centre, and the Community Mental Health Unit of Montilla. General practitio... |
49,730 | DNA extraction and genomic sequencing library preparation for individual root-knot nematodes | 4 | dx.doi.org/10.17504/protocols.io.butanwie | https://www.protocols.io/view/dna-extraction-and-genomic-sequencing-library-prep-butanwie | Graham S Sellers, Dave Lunt | TITLE: DNA extraction and genomic sequencing library preparation for individual root-knot nematodes
AUTHORS: Graham S Sellers, Dave Lunt
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A simple, high molecular weight DNA extraction and long read genomic sequencing library preparation from individual... | ["[DNA extraction]\nSPRI based DNA extractionLysisAdd 200 μl Lysis Master Mix to 1.5 ml LoBind tube containing nematode sample. Vortex briefly to mix and centrifuge tube for 1 secPlace in Thermomixer at 55°C for 90 mins at 550 rpm.Centrifuge tube for 1 secInhibitor removalAdd 70 μl (0.3 X volume) of Flocculant Solution... |
null | null | null | dx.doi.org/10.17504/protocols.io.n7kdhkw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div>
<div>
<p>This protocol was designed and developed at this laboratory.</p>
<p>The assay specifically targets the 3' UTR region of DENV-2 strains and is designed as a qualitative screening test for human cases of DENV-2 infection, but not for infection due to other known DEN... | [] |
19,203 | DNA extraction: Campylobacter | null | dx.doi.org/10.17504/protocols.io.wzbff2n | null | Ben Pascoe | TITLE: DNA extraction: Campylobacter
AUTHORS: Ben Pascoe
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Protocol for DNA extraction from </span><span style = "font-style:italic;">Campylobacter </span><span>isolates using the QIAGEN QIAamp DNA Mini Kit (QIAGEN, Crawley, UK). </span></div></div... | [] |
59,970 | Human Brain Nuclei Isolation Using Sucrose Gradient Ultracentrifugation | 4 | dx.doi.org/10.17504/protocols.io.x54v9yrm4g3e/v1 | https://www.protocols.io/view/human-brain-nuclei-isolation-using-sucrose-gradien-b6tareie | Zhang Lab | TITLE: Human Brain Nuclei Isolation Using Sucrose Gradient Ultracentrifugation
AUTHORS: Zhang Lab
[DESCRIPTION]
This protocol describes about isolation of human brain nuclei by sucrose gradient ultracentrifugation.
[STEPS]
SECTION: Isolation of Human Brain Nuclei
1. Take brain tissue sample out of -80 °C freezer and ... | ["[Isolation of Human Brain Nuclei] Take brain tissue sample out of -80 °C freezer and put on dry ice. Transfer the sample from the bag or tube to a petri dish and carefully cut a small piece off with a surgical blade, keeping it on dry ice. Replace the remaining piece in the bag and put the small piece in a labeled Ep... |
null | null | null | dx.doi.org/10.17504/protocols.io.hukb6uw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is part of BioLegend's, "<a href="http://www.biolegend.com/media_assets/support_protocol/Intracellular_Staining_Protocol_082615.pdf" target="_blank">Intracellular Flow Cytometry Staining Protocol: For the Detection of Intracellular Cytokines and Other Intracellular Targe... | [] |
21,281 | Yale - Aspartate Amino Transferase | null | dx.doi.org/10.17504/protocols.io.yz9fx96 | null | Gary Cline, John Stack | TITLE: Yale - Aspartate Amino Transferase
AUTHORS: Gary Cline, John Stack
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Procedure used to measure the activity of Aspartate Amino Transferase (AST). AST activity is mea... | ["Calibrate Cobas for Aspartate Amine Transferase Activity analysis by running twoassayed control serum.", "Sample handling as performed by the Cobas Mira Plus. a) Pipette 16 µL of sample into a cuvette slot. b) Add 145 µL of Aspartate Amino Transferase Reagent. c) Mixture is incubated at 37˚C and spun for 10 ... |
87,782 | Complete WGS data processing in HPC environment | 5 | null | https://www.protocols.io/view/complete-wgs-data-processing-in-hpc-environment-czyex7te | Ireneusz Stolarek, Michał Zeńczak, Małgorzata Marcinkowska-Swojak, Magdalena Rakoczy, Luiza Handschuh, Natalia Koralewska, Marek Figlerowicz | TITLE: Complete WGS data processing in HPC environment
AUTHORS: Ireneusz Stolarek, Michał Zeńczak, Małgorzata Marcinkowska-Swojak, Magdalena Rakoczy, Luiza Handschuh, Natalia Koralewska, Marek Figlerowicz
[DESCRIPTION]
In the rapidly evolving landscape of genomics research, the advent of whole genome sequencing (WGS) ... | ["[Data Demultiplexing] In processing NGS data, data demultiplexing is often a first computational step. \nThe demultiplexing of illumina based data can be conducted using bcl2fastq software.", "[Pre-Alignment QC] QC of the NGS data can be performed with a variety of tools. Here we present a typical output of an intera... |
71,102 | Colony PCR for 2022 iGEM | 1 | dx.doi.org/10.17504/protocols.io.rm7vzb352vx1/v1 | https://www.protocols.io/view/colony-pcr-for-2022-igem-chn6t5he | Team Fudan iGEM | TITLE: Colony PCR for 2022 iGEM
AUTHORS: Team Fudan iGEM
[DESCRIPTION]
Based on manual included in Vazyme Taq product
[STEPS]
1. Select colonies on the agar plate to pick. Culture portion of the colony in LB media with antibiotic and grow in 37 degree. Put the remainder of the colony into a correspondingly numbered P... | ["Select colonies on the agar plate to pick. Culture portion of the colony in LB media with antibiotic and grow in 37 degree. Put the remainder of the colony into a correspondingly numbered PCR tube with 20 µL of reaction mix (as below), and pipetting to complete resuspend the bacteria.", "ComponentVolume/ulFinal Conce... |
100,915 | An affordable solution for investigating zebra finch intracranial EEG signals | 1 | dx.doi.org/10.17504/protocols.io.q26g7y2w8gwz/v2 | https://www.protocols.io/view/an-affordable-solution-for-investigating-zebra-fin-dest3een | Mohammad-Mahdi Abolghasemi, Shahrar Rezghi Shirsavar, Milad Yekani | TITLE: An affordable solution for investigating zebra finch intracranial EEG signals
AUTHORS: Mohammad-Mahdi Abolghasemi, Shahrar Rezghi Shirsavar, Milad Yekani
[DESCRIPTION]
The Zebra finch is a well-studied model animal to study neural mechanisms of speech, and electrophysiology is the primary technique for underst... | ["[Hardware preparation] Electrode preparation:\nFor recording electrodes, we used 2.5 cm of stainless steel wire and uncoat two ends of it with a scalpel blade. \nmake a loop in one end about 1 or 2mm in diameter. use a surgical clamp to bend it. \nDo not make a bigger loop, it may not fit into the hole in the sk... |
null | null | null | dx.doi.org/10.17504/protocols.io.s38egrw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Separates molecules based on size.
[BEFORE_START]
Have a DNA Sample ready, typically either from PCR or a recently performed Restriction Digest. Dilute down the 50X TAE Buffer to 1X.
[STEPS]
SECTION: Prep Work
?.
SECTION: Prep Work
?.
SECTION: Prep Work
?.
SECTION: Prep Wor... | ["[Prep Work] {\"blocks\":[{\"key\":\"5ahrl\",\"text\":\"Pour 150 mL of 0.5X TBE Buffer into a 250 ml Duran Bottle.\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"77ofa\",\"text\":\" \",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":... |
null | null | null | dx.doi.org/10.17504/protocols.io.ciuuev | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
The RT and amplification steps for SMARTseq2, as modified for previously extracted RNA slices.
[BEFORE_START]
Thaw RNA samples on ice, as well as:<br /><br />* First Strand Buffer (-20º)<br />* DTT (-20º)<br />* dNTPs (-20º)<br />* oligo dT30VN primer (-20º)... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.c36yrd | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
87,442 | Chocolate Chip Cookies (CCCOOCI) | 1 | dx.doi.org/10.17504/protocols.io.n92ldmy9nl5b/v2 | https://www.protocols.io/view/chocolate-chip-cookies-cccooci-czmsx46e | Richard J Acton | TITLE: Chocolate Chip Cookies (CCCOOCI)
AUTHORS: Richard J Acton
[DESCRIPTION]
A recipe for chocolate cookies
By running this protocol and supplying your results you will be particpating in CCCOOCI (chocolate chip cookie optimisation open colaborative initiative) to learn more visit the project page: https://renkulab... | ["[Ingredients] 175 2666 Plain Flour \n3 g bicabonate of soda \n1 g Salt \n113 g Butter\n\nThree Sugar Variant:\n58 g Caster sugar\n58 g Soft light brown sugar\n58 g Soft Dark Brown Sugar (Muscovado)\n\nTwo Sugar Variant:\n88 g Caster sugar\n88 g Soft brown sugar\n\n5 g Vanilla extract\n1 eggs\n200 g Dark chocola... |
61,439 | ASt Test Method | 6 | dx.doi.org/10.17504/protocols.io.n2bvj62b5lk5/v1 | https://www.protocols.io/view/ast-test-method-b787rrzn | AStracke.Privat | TITLE: ASt Test Method
AUTHORS: AStracke.Privat
[DESCRIPTION]
Sample preparation
[STEPS]
1. Heat sample to 35°C
2. Evaporate Acetone solvens
3. Cool down sample to 4°C
4. | ["Heat sample to 35°C", "Evaporate Acetone solvens", "Cool down sample to 4°C"] |
45,894 | RNA Extraction | 4 | null | https://www.protocols.io/view/rna-extraction-bq3emyje | Alicia Rich | TITLE: RNA Extraction
AUTHORS: Alicia Rich
[STEPS]
?. [Lyse and Homogenize]
Do not allow samples to thaw before adding the . If a sample needs to be thawed for measuring, do so on ice.
?. [Lyse and Homogenize]
Use sterilized forceps to transfer swab or ~90 mg of feces into a 2 ml microcentrifuge tube held on ice or in... | ["[Lyse and Homogenize]\nDo not allow samples to thaw before adding the . If a sample needs to be thawed for measuring, do so on ice.", "[Lyse and Homogenize]\nUse sterilized forceps to transfer swab or ~90 mg of feces into a 2 ml microcentrifuge tube held on ice or in a cooling block.\nWhen processing samples containi... |
28,705 | Creating Differential Transcript Expression Results with DESeq2 | null | dx.doi.org/10.17504/protocols.io.799hr96 | null | David A. Eccles | TITLE: Creating Differential Transcript Expression Results with DESeq2
AUTHORS: David A. Eccles
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Differential expression analysis of transcript count tables using DESeq2</div></div>
[STEPS]
?. [Collating count data]
Combine the transcript count data in... | ["[Collating count data]\nCombine the transcript count data into a single data structure. To reduce confusion when this protocol is run multiple times, we declare an analysisDate variable to be used for output file names:countDate We also load libraries that will be used in the protocol:## steps 1-2library(dplyr); #... |
45,205 | AMPHABIO HT-HiThroughput PCR COVID-19 Kit Protocol | 4 | dx.doi.org/10.17504/protocols.io.bqdvms66 | https://www.protocols.io/view/amphabio-ht-hithroughput-pcr-covid-19-kit-protocol-bqdvms66 | hohuutho | TITLE: AMPHABIO HT-HiThroughput PCR COVID-19 Kit Protocol
AUTHORS: hohuutho
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol shows procedure for sample handling and detection of SARS-CoV-2 using the AMPHABIO HT-HiThroughput PCR COVID-19 Kit.</div></div>
[STEPS]
?. [Amplification]
Pre-... | ["[Amplification]\nPre-amplification", "[Amplification]\nMaster mix preparation- Thaw all reagents to obtain homogeneous solutions. Mix all the tubes gently with the vortex mixer and briefly spin down. Do not leave the reagents at room temperature for more than 30 minutes.- Keep all the tubes on ice.- Prepare the pre-a... |
92,779 | In-vivo MRI and CT scanning protocol for non-human primates using a 3D printed MR-compatible stereotaxic frame | 1 | dx.doi.org/10.17504/protocols.io.q26g7p7rkgwz/v1 | https://www.protocols.io/view/in-vivo-mri-and-ct-scanning-protocol-for-non-human-c6ujzeun | Lucy Liang, dschaeff | TITLE: In-vivo MRI and CT scanning protocol for non-human primates using a 3D printed MR-compatible stereotaxic frame
AUTHORS: Lucy Liang, dschaeff
[DESCRIPTION]
This protocol describes the methods of using a custom 3D printed stereotaxic frame to acquire MRI and CT scans for nonhuman primates in detailed steps.
High... | ["[Preparation of the animal] Anesthetize the monkey with ketamine (10 mg/kg) in the home cage. Transfer the animal to the prep table.", "[Preparation of the animal] Transfer the animal to the prep/procedure room close to the imaging room, awake, with cage covered.", "[Preparation of the animal] Shave one calve of the ... |
19,964 | U Mass - Amylase | null | dx.doi.org/10.17504/protocols.io.xq4fmyw | null | Jason Kim | TITLE: U Mass - Amylase
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This experiment involves a spectrophotometric measurement using Roche Cobas Clinical Chemistry Analyzer.</div></div>
[STEPS]
?... | ["Perform daily quality control assessment of instrumentation before analysis.", "Load each sample into a specialized micro-sample cup for the clinical chemistry analyzer.", "Select Amylase test on display and run the analysis.", "Collect and analyze the data."] |
29,663 | Canine/feline serum or plasma deproteinization for amino acid analysis on Biochrom | 1 | dx.doi.org/10.17504/protocols.io.877hzrn | https://www.protocols.io/view/canine-feline-serum-or-plasma-deproteinization-for-877hzrn | Amanda Blake, Jan Suchodolski | TITLE: Canine/feline serum or plasma deproteinization for amino acid analysis on Biochrom
AUTHORS: Amanda Blake, Jan Suchodolski
[DESCRIPTION]
This protocol describes the deproteinization process that all canine and feline serum and plasma research samples undergo prior to amino acid analysis with a Biochrom 30+ Ami... | ["Aliquot 250 μl serum or plasma into 1.5 ml microcentrifuge tube.", "Add 250 μl [5% Sulfosalicylic acid (w/v), 500 μM L-Norleucine] to 1.5 ml microcentrifuge tube. Note: if less than 250 μl serum or plasma is available, can use as little as 100 μl and add reagent in 1:1 (v/v) ratio. i.e., if using 150 μl serum, would ... |
null | null | null | dx.doi.org/10.17504/protocols.io.pwxdpfn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Analytical methodology for the detection of sulfachloropyridazine (SCP) in samples of feathers via LC-MS/MS was implemented based on techniques previously published by other authors: </p>
<p><span lang="EN-US">1- Hindle R. A validated atmospheric pressure chemical ionization ... | [] |
92,879 | RNA Extraction from Frozen Brain Tissue Using a Bullet Blender | 4 | dx.doi.org/10.17504/protocols.io.q26g7p7yqgwz/v1 | https://www.protocols.io/view/rna-extraction-from-frozen-brain-tissue-using-a-bu-c6xpzfmn | Ashley V Kumar, Francesca Telese | TITLE: RNA Extraction from Frozen Brain Tissue Using a Bullet Blender
AUTHORS: Ashley V Kumar, Francesca Telese
[DESCRIPTION]
This protocol details a streamlined method for extracting high-quality RNA from small tissue samples using a bullet blender. By following this approach, researchers can efficiently isolate RNA ... | ["[Tissue homogenization and RNA extraction] Begin by resuspending the tissue sample in 500 µL of chilled TRIzol‱ Reagent. Transfer the mixture to a Safe-Lock tube, ensuring that the sample remains cold throughout handling. Add 10 µL of RNase-free Zirconium Beads (0.5 mm; Cat. no. ZrOB05-RNA) to the tube. Perform all s... |
63,569 | Systematic review and meta-analysis of incidence and outcomes of hip and vertebral fractures hip fracture in patients with end-stage kidney disease | 1 | dx.doi.org/10.17504/protocols.io.3byl4brjrvo5/v2 | https://www.protocols.io/view/systematic-review-and-meta-analysis-of-incidence-a-cabrsam6 | Yoshinosuke Shimamura, Yasutaka Kuniyoshi, Yasushi Tsujimoto | TITLE: Systematic review and meta-analysis of incidence and outcomes of hip and vertebral fractures hip fracture in patients with end-stage kidney disease
AUTHORS: Yoshinosuke Shimamura, Yasutaka Kuniyoshi, Yasushi Tsujimoto
[DESCRIPTION]
This is the protocol for a systematic review and meta-analysis to systematic... | ["[Authors' Information] Last update: May 31, 2022.\n\nAuthors: Yoshinosuke Shimamura MD, MPH1, 2; Yasutaka Kuniyoshi MD, PhD2,3; Yasushi Tsujimoto MD, MPH2, 4.\n\n1 Department of Nephrology, Teine Keijinkai Medical Center, Sapporo, Hokkaido, Japan.\n2 Scientific Review WorkshopS Peer Support Group (SRWS-PSG), Osa... |
null | null | null | dx.doi.org/10.17504/protocols.io.d2v8e5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Lawrence, J. E., and G. F. Steward. 2010. Purification of viruses by centrifugation, p. 166–181. In S. W. Wilhelm, M. G. Weinbauer, and C. A. Suttle [eds.], Manual of Aquatic Viral Ecology. ASLO.<br /><br />Please see the <a href="http://www.aslo.org/books/mave/MAVE_166.pdf" tar... | [] |
46,734 | HTAPP_Dissociation of primary neuroblastoma resection to a single-cell suspension for single-cell RNA-seq (using papain, density gradient, and optionally ACK) | 1 | dx.doi.org/10.17504/protocols.io.brvnm65e | https://www.protocols.io/view/htapp-dissociation-of-primary-neuroblastoma-resect-brvnm65e | Sara Napolitano, Jingyi Wu, Michal Slyper, Sébastien Vigneau, Asaf Rotem, Bruce Johnson, Orit Rozenblatt-Rosen, Aviv Regev | TITLE: HTAPP_Dissociation of primary neuroblastoma resection to a single-cell suspension for single-cell RNA-seq (using papain, density gradient, and optionally ACK)
AUTHORS: Sara Napolitano, Jingyi Wu, Michal Slyper, Sébastien Vigneau, Asaf Rotem, Bruce Johnson, Orit Rozenblatt-Rosen, Aviv Regev
[DESCRIPTION]
<div cl... | ["[Tissue Description]\nReport sample processing information.\nSample ID:Date:Time Received:Media Used for Transportation:Person Processing:", "[Tissue Description]\nTransfer sample to a Petri dish with cold PBS kept on ice to better visualize its composition. Take a picture of the resection alongside a ruler and annot... |
19,606 | Urea-mediated dissociation alleviate the false-positive Treponema pallidum-specific antibodies detected by ELISA | null | dx.doi.org/10.17504/protocols.io.xdwfi7e | null | qiang wang, Yan Lei, Xiaolan Lu, Guangrong Wang, Qin Du, Xiaolan Guo, Quming Fan, Guoyuan Zhang, Dongsheng Wang | TITLE: Urea-mediated dissociation alleviate the false-positive Treponema pallidum-specific antibodies detected by ELISA
AUTHORS: qiang wang, Yan Lei, Xiaolan Lu, Guangrong Wang, Qin Du, Xiaolan Guo, Quming Fan, Guoyuan Zhang, Dongsheng Wang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The s... | ["Design the experimental steps.", "Collect clinical samples to meet the needs of the experiment, especially false positive samples detected by ELISA.", "Using different methods to detect TP antibodies, and to understand the characteristics of different samples, so as to facilitate grouping.", "Pre-experiment to explo... |
20,356 | U Mass - Surgery – jugular vein cannulation | null | dx.doi.org/10.17504/protocols.io.x5cfq2w | null | Jason Kim | TITLE: U Mass - Surgery – jugular vein cannulation
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">Chronic indwelling catheter is placed in the jugular vein for intravenous infusion and injection of d... | ["Anesthetize mice with an intraperitoneal injection of ketamine (100 mg/kg body weight) and xylazine (10 mg/kg body weight).", "Check the level of general anesthesia using a pinch stimulus of animal's tail and/or foot.", "Make a transverse incision (~0.5 cm) over the trachea, and isolate the right jugular vein.", "Car... |
3,801 | Seagrass Microbiome Sample Collection and Preservation | null | dx.doi.org/10.17504/protocols.io.fxzbpp6 | null | Jonathan JA. Eisen, Jonathan Eisen Lab | TITLE: Seagrass Microbiome Sample Collection and Preservation
AUTHORS: Jonathan JA. Eisen, Jonathan Eisen Lab
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This collection protocol was developed as part of the Seagrass Microbiome Project. This was originally a collaboration among </span><a h... | ["[Collection: Seagrass Microbiome Tissue Samples]\nCollection: If possible, wear gloves whenever you handle the plants. Pull up one plant including the roots. Gently swish the plant in the water to remove loose sediment from the roots. Process these samples in the field according to steps 2 and 3.\nIf you cannot proce... |
61,688 | Phycopick protocol for isolating single phytoplankton cells | 1 | dx.doi.org/10.17504/protocols.io.5qpvobq59l4o/v1 | https://www.protocols.io/view/phycopick-protocol-for-isolating-single-phytoplank-b8gyrtxw | Carly M Moreno, Shady Amin | TITLE: Phycopick protocol for isolating single phytoplankton cells
AUTHORS: Carly M Moreno, Shady Amin
[DESCRIPTION]
Interactions between bacteria and eukaryotic phytoplankton have major influences on marine ecosystems and the global carbon cycle. Metabolite exchanges between specific bacteria and phytoplankton specie... | ["[Instrument set up] Flush the glass micropipette tip by removing the PicoPipet reservoir cap, attaching a small syringe filled with ultrapure MilliQ water, and pushing enough water through the PicoPipet head and glass micropipette tip to ensure there are no air bubbles in the system. Remove the syringe and reattach t... |
91,173 | Bacterial genome annotation script using BLASTN | 5 | dx.doi.org/10.17504/protocols.io.dm6gpjrb1gzp/v2 | https://www.protocols.io/view/bacterial-genome-annotation-script-using-blastn-c5ady2a6 | Ana Mariya Anhel, Lorea Alejaldre, Ángel Goñi-Moreno | TITLE: Bacterial genome annotation script using BLASTN
AUTHORS: Ana Mariya Anhel, Lorea Alejaldre, Ángel Goñi-Moreno
[DESCRIPTION]
This protocol uses a python based script and command-line BLASTn to annotate in a final table single-read sequencing results from genome amplifications, within other output files.
Its mai... | ["[Adquisition of files] Download reference genome file\n\nYou can download the genome of the organism that you want to compare to the reading sequences from different sources such as NCBI, GSA or even pages dedicated to the organism (i.e pseudomonas.com).\n\nFor this script to work, genome files need to be in FASTA fo... |
79,938 | SEWRL RS & GIS Team GPS Data Collection Storage Procedures | 5 | dx.doi.org/10.17504/protocols.io.e6nvwj777lmk/v1 | https://www.protocols.io/view/sewrl-rs-amp-gis-team-gps-data-collection-storage-csbawaie | marshall.bennett | TITLE: SEWRL RS & GIS Team GPS Data Collection Storage Procedures
AUTHORS: marshall.bennett
[DESCRIPTION]
Process for downloading and managing GPS data collection projects to centralize GPS Data for analysis
[STEPS]
1. Collect data in the field.
2. Download GPS Data to T:\sandbox\GPS_Data_Dump in an appropriate... | ["Collect data in the field.", "Download GPS Data to T:\\sandbox\\GPS_Data_Dump in an appropriate folder location for each project or data collection.", "Fill out record in \"Read Me\" Document"] |
null | null | null | dx.doi.org/10.17504/protocols.io.rq2d5ye | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?. | ["Female fecundity was assayed using flies that had been transferred from instant food to each experimental diet for one generation.", "Briefly, 47 female flies of each genotype and diet, ranging from 3-5 days old were randomly transferred into separate 6 mL glass vials (Sigma-Aldrich) and allowed to oviposit for 24 ho... |
60,856 | Soil Viromics Protocol - Emerson Lab v1 | 4 | null | https://www.protocols.io/view/soil-viromics-protocol-emerson-lab-v1-b7nyrmfw | Joanne Emerson, Sara Geonczy, Christian Santos Medellin, Anneliek Ter Horst, Jane Fudyma | TITLE: Soil Viromics Protocol - Emerson Lab v1
AUTHORS: Joanne Emerson, Sara Geonczy, Christian Santos Medellin, Anneliek Ter Horst, Jane Fudyma
[DESCRIPTION]
As of April 28, 2022, this is the soil viromics laboratory protocol used in the Emerson group at UC Davis to generate viral DNA from a soil sample for sho... | ["[Preparation] Prepare PPBS buffer (https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-020-0795-2) (2% BSA, 10% PBS, 1% K-citrate, 150 mM MgSO4)", "[Preparation] Clean ultracentrifuge tubes - scrub, fill with NaOH for at least 1 hour (also soak black caps, but NOT metal red caps), \nrinse 3x with Mill... |
79,099 | Differentiation NPCs to Dopaminergic/Midbrain Neurons | 4 | dx.doi.org/10.17504/protocols.io.14egn216qg5d/v1 | https://www.protocols.io/view/differentiation-npcs-to-dopaminergic-midbrain-neur-crg3v3yn | michela.deleidi | TITLE: Differentiation NPCs to Dopaminergic/Midbrain Neurons
AUTHORS: michela.deleidi
[DESCRIPTION]
This protocol details methods for differentiation of NPCs to Dopaminergic/Midbrain Neurons.
[STEPS]
SECTION: Day -2: split NPCs
1. Coat numbers of wells you need on a well-plate with Matrigel:
SECTION: Day -2: spl... | ["[Day\t-2: split NPCs] Coat numbers of wells you need on\ta well-plate with Matrigel:", "[Day\t-2: split NPCs] Dilute thawed Matrigel out of 4 °C 1/10 in DMEM/F12 without HEPES.", "[Day\t-2: split NPCs] Incubate 30 min 37 °C in incubator.", "[Day\t-2: split NPCs] Remove\told medium and add 500 µL (Sigma Aldrich, #A696... |
23,523 | Nuclear DNA purification from recalcitrant plant species for long-read sequencing | null | dx.doi.org/10.17504/protocols.io.28bghsn | null | Ashley Jones, Justin Borevitz | TITLE: Nuclear DNA purification from recalcitrant plant species for long-read sequencing
AUTHORS: Ashley Jones, Justin Borevitz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Evolution has driven genetic diversity of life on Earth, but also created highly complex genomes that are difficult to seque... | ["[NUCLEI ISOLATION]\nAdd 2.5 mL of 100% Triton X-100, or 25 mL of 10% (final concentration 0.5%).", "[NUCLEI ISOLATION]\nIncubate mixture on an ice bath with gentle rocking for 30 min.\nUse this time to clean the blender and space used for filtering. Cool the the centrifuge to 4°C.", "[NUCLEI ISOLATION]\nCentrifuge at... |
35,100 | Image J Nerve Density Percentage Analysis | null | dx.doi.org/10.17504/protocols.io.beh4jb8w | null | Elizabeth Smith, Jacqui Potter | TITLE: Image J Nerve Density Percentage Analysis
AUTHORS: Elizabeth Smith, Jacqui Potter
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">ImageJ Software can be used to find the percentage of nerve density in regions of interest. These regions of interest are imaged, and the nerve percentage is found... | ["Open Image", "Dowload ImageJ Software", "File>Open>Locate desired image file>Click desired individual image (JPEG or TIFF)", "Prepare Image for Analysis", "Image>Type>8-bit", "Remove over exposed areas, scale bar etc. by clicking on desired shape in Shape Tool Bar under File Tool Bar.", "Analyze Image", "Image>Adjust... |
94,578 | STC-1 Passaging and PD Associated Microbe Stimulation Protocol | 4 | dx.doi.org/10.17504/protocols.io.261gedmn7v47/v1 | https://www.protocols.io/view/stc-1-passaging-and-pd-associated-microbe-stimulat-c8kszuwe | Malu G Tansey | TITLE: STC-1 Passaging and PD Associated Microbe Stimulation Protocol
AUTHORS: Malu G Tansey
[DESCRIPTION]
STC-1 Passaging and PD Associated Microbe Stimulation Protocol
[STEPS]
SECTION: Passaging & Plating Protocol
1. Cells are passaged when they reach approximately 70% confluence
Warm trypsin, 1XPBS, and compl... | ["[Passaging & Plating Protocol] Cells are passaged when they reach approximately 70% confluence\n\nWarm trypsin, 1XPBS, and complete medium in water bath for 15 min.", "[Passaging & Plating Protocol] Aspirate off culture medium", "[Passaging & Plating Protocol] Rinse cells with 10mL D-PBS", "[Passaging &am... |
41,739 | XPRIZE SANATA Protocol for Swab LFIA Test | 4 | dx.doi.org/10.17504/protocols.io.bkzjkx4n | https://www.protocols.io/view/xprize-sanata-protocol-for-swab-lfia-test-bkzjkx4n | Mario Thomas, Jasmine Sollen, Natalia Ivanova, Heidi Abdilla, Reda Fayek, Michelle Feng, Stephanie Lim, Amanda Naaum | TITLE: XPRIZE SANATA Protocol for Swab LFIA Test
AUTHORS: Mario Thomas, Jasmine Sollen, Natalia Ivanova, Heidi Abdilla, Reda Fayek, Michelle Feng, Stephanie Lim, Amanda Naaum
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This procedure outlines the protocol using any swab suitable for a SARS-CoV-2... | ["[Collecting and Preparing Sample]\nCollect sample using any swab suitable for SARS-CoV-2 sample collection. For example:", "[Collecting and Preparing Sample]\nRinse the used swab inby submerging the swab in the lysis buffer and rotating 5-7 times against the tube walls. Discard the swab in a biohazardous waste contai... |
82,163 | 7.3: Taxon Group: Crustacea - Cirripedia | 1 | dx.doi.org/10.17504/protocols.io.n2bvj8kbpgk5/v1 | https://www.protocols.io/view/7-3-taxon-group-crustacea-cirripedia-cugtwtwn | Chris Fletcher, Paul Clark, Miranda Lowe, Lauren Hughes, Inez Januszczak | TITLE: 7.3: Taxon Group: Crustacea - Cirripedia
AUTHORS: Chris Fletcher, Paul Clark, Miranda Lowe, Lauren Hughes, Inez Januszczak
[DESCRIPTION]
This is part of the collection "DToL Taxon-specific Standard Operating Procedures (SOPs) for Marine Metazoa", lead by the Other Metazoa Working Group. The SOP collection conta... | [] |
44,554 | High GC-content PCR | 4 | null | https://www.protocols.io/view/high-gc-content-pcr-bprimm4e | Joao Vitor Molino | TITLE: High GC-content PCR
AUTHORS: Joao Vitor Molino
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">X7 is a a Pfu-sso7d fusion DNA polymerase that is compatible with uracil-excision cloning and has been used with sucess to amplify our high GC-content sequences and it is a valuable tool for USER cl... | ["[Reaction preparation]\nSet up the reaction using the following table on ice: AB1ReagentVolume (uL)2Phusion® GC Buffer (NEB) 5X103Betaine 5M104dNTPs 10 uM1510 µM Forward Primer2.5610 µM Forward Primer2.57Template DNAVariable (~0.5-1)8X70.59Nuclease-Free Water2310Final Volume50Mix the reaction gently and spin it dow... |
68,680 | Immunological detection of autophagy and mTORC1-related proteins | 4 | dx.doi.org/10.17504/protocols.io.kxygxzr94v8j/v1 | https://www.protocols.io/view/immunological-detection-of-autophagy-and-mtorc1-re-cfbgtijw | Harper JW, Sharan Sharan Swarup | TITLE: Immunological detection of autophagy and mTORC1-related proteins
AUTHORS: Harper JW, Sharan Sharan Swarup
[DESCRIPTION]
Here we present a general protocol for immunological detection by Western blotting MTOR, MTOR (pS2448), ULK1, ULK1 (pS757), p70S6K, p70S6K (pT389), SQSTM1, CALCOCO2, MAP1LC3B, GABARAP, TFEB... | ["[Western blotting] Lyse cell pellets by homogenization in KPBS buffer, urea buffer, or RIPA buffer with protease and phosphatase inhibitors. FOr some experiments, we employ 293 cells or alternatively HeLa cells with or without the GRN gene, created by CRISPR-based gene editing (DOI: dx.doi.org/10.17504/protocols.io.4... |
67,432 | Growth Matrix Male Enhancement Instant Girth And Length Increase! | 3 | dx.doi.org/10.17504/protocols.io.kxygxz6m4v8j/v1 | https://www.protocols.io/view/growth-matrix-male-enhancement-instant-girth-and-l-cd4gs8tw | alevinerames | TITLE: Growth Matrix Male Enhancement Instant Girth And Length Increase!
AUTHORS: alevinerames
[DESCRIPTION]
https://www.healthsupplement24x7.com/get-growth-matrix
[STEPS] | [] |
103,021 | Genetic expression suppressor screen | 0 | dx.doi.org/10.17504/protocols.io.ewov19z67lr2/v1 | https://www.protocols.io/view/genetic-expression-suppressor-screen-dgum3wu6 | Alexandros C Kokotos, Tim Ryan | TITLE: Genetic expression suppressor screen
AUTHORS: Alexandros C Kokotos, Tim Ryan
[DESCRIPTION]
This protocol describes a low-throughput genetic screen to identify glycolytic enzymes that improve neuronal function under hypometabolic conditions.
[STEPS]
SECTION: Neuronal culture and transfection
1. Use cultured rod... | ["[Neuronal culture and transfection] Use cultured rodent primary hippocampal neurons, transfected with vGlutI-pH, mTagBFP2 and a construct expressing a single glycolytic enzyme, as explained in dx.doi.org/10.17504/protocols.io.ewov1qxr2gr2/v1.", "[Live-cell imaging] Mount the coverslips with the cells on the imaging c... |
29,614 | RNA Extraction for RIN and DV 200 Analysis | null | dx.doi.org/10.17504/protocols.io.86nhzde | null | Jamie Allen, Elizabeth Neumann, Maya Brewer, Jeff Spraggins, Danielle Gutierrez, Mark de Caestecker | TITLE: RNA Extraction for RIN and DV 200 Analysis
AUTHORS: Jamie Allen, Elizabeth Neumann, Maya Brewer, Jeff Spraggins, Danielle Gutierrez, Mark de Caestecker
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Scope: Extract RNA for RIN and DV 200 Assessment.</div><div class = "text-block">Expected Out... | ["[Homogenize Tissue]\nPlace tissue section in 750 μL of TRIzoILS.", "[Homogenize Tissue]\nHomogenize the sample:Use a homogenizer or pass sample through a 23G then a 27G needle syringe.", "[Homogenize Tissue]\nFreeze samples on dry ice and re-thaw once. Mix well by vortexing.", "[Homogenize Tissue]\nAdd RNase free w... |
41,356 | Ultracentrifuge clean-up of phage lysate for TEM | 4 | null | https://www.protocols.io/view/ultracentrifuge-clean-up-of-phage-lysate-for-tem-bkmkku4w | Kathy Lam | TITLE: Ultracentrifuge clean-up of phage lysate for TEM
AUTHORS: Kathy Lam
[STEPS]
?. Take 1.1 ml of existing plate lysate
?. Take 1 ml to clean up; save remainder to titer pre- versus post-clean up
?. Transfer 1 ml to ultracentrifuge tube
?. Centrifuge 25,000 rpm (~25,000g) 60 min 4C
?. Pour off supernatant away from... | ["Take 1.1 ml of existing plate lysate", "Take 1 ml to clean up; save remainder to titer pre- versus post-clean up", "Transfer 1 ml to ultracentrifuge tube", "Centrifuge 25,000 rpm (~25,000g) 60 min 4C", "Pour off supernatant away from pellet; pipette off residual", "Wash with 0.1 M ammonium acetate", "Centrifuge 25,00... |
11,435 | PI staining of Arabidopsis seedling | null | dx.doi.org/10.17504/protocols.io.pejdjcn | null | Magdalena Julkowska | TITLE: PI staining of Arabidopsis seedling
AUTHORS: Magdalena Julkowska
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [transfer the seedlings from agar plate into a solution containing the nutrients as well as 5-10 µg/mL of propidium iodide. Incubate for 20 to 30 min.]
?. [Examine the red staining under ... | ["[transfer the seedlings from agar plate into a solution containing the nutrients as well as 5-10 µg/mL of propidium iodide. Incubate for 20 to 30 min.]", "[Examine the red staining under (confocal) microscope]", "[Examine the red staining under (confocal) microscope]"] |
98,429 | Mouse Organ Collection (Brain, Bone, Colon, Liver, and Mammary) | 4 | dx.doi.org/10.17504/protocols.io.j8nlkwx7wl5r/v2 | https://www.protocols.io/view/mouse-organ-collection-brain-bone-colon-liver-and-dcc52sy6 | Andrew Davis, Aaron Havas, Sha Li, Laurence Haddadin, Diana Jurk, Kenneth Kim, Peter Adams | TITLE: Mouse Organ Collection (Brain, Bone, Colon, Liver, and Mammary)
AUTHORS: Andrew Davis, Aaron Havas, Sha Li, Laurence Haddadin, Diana Jurk, Kenneth Kim, Peter Adams
[DESCRIPTION]
This is a mouse dissection protocol intended to collect the 5 organs outlined in the SBPMDI TMC: Brain, Bone Marrow, Colon, Liver, and... | ["[Pre-collection (at least 1 day before)] Re-melt and cool wax pad to ensure stable surface for pinning", "[Pre-collection (at least 1 day before)] Prepare labeled plastic cassettes for each PFA tissue and a larger container (250ml+) for depositing the closed cassettes once they have tissues in them. Prepare enough P... |
40,945 | Denaturing PAGE for resolving RNA | 1 | dx.doi.org/10.17504/protocols.io.bj8rkrv6 | https://www.protocols.io/view/denaturing-page-for-resolving-rna-bj8rkrv6 | Diep Ganguly, Anna Behle | TITLE: Denaturing PAGE for resolving RNA
AUTHORS: Diep Ganguly, Anna Behle
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Protocol denaturing PAGE separation and identification of total RNA extracts using Urea-PAGE with the BioRad Mini-PROTEAN II / Tetra Cell electrophoresis system. Modified ... | ["[Gel preparation]\nUse the following table to prepare the required gel recipe using either 30 % or 40 % PAA (~4 mL=1x0.75 mm gel). ABCDE1PAA percentage\n8 %\n10 %\n12 %\n15 %\n230 % / 40 % PAA2 / 2.67 mL2.5 / 3.33 mL3 / 4 mL3.75 / 5 mL38 M Urea5 g5 g5 g5 g410x TBE\n1 mL\n1 mL\n1 mL\n1 mL\n510 % APS80 µL\n80 µL\n80 ... |
57,493 | In vitro GCase activity assay (total cell lysate) | 1 | dx.doi.org/10.17504/protocols.io.b4dvqs66 | https://www.protocols.io/view/in-vitro-gcase-activity-assay-total-cell-lysate-b4dvqs66 | Federico Bertoli, Michela Deleidi | TITLE: In vitro GCase activity assay (total cell lysate)
AUTHORS: Federico Bertoli, Michela Deleidi
[DESCRIPTION]
Glucocerebrosidase is a lysosomal enzyme that catalyzes the hydrolysis of glucosylceramide (GlcCer), a membrane glyco-sphingolipid, to ceramide and glucose. This assay detects GBA activity by using a flu... | ["[Sample Lysis] Suspend samples in 50 µL of 1% Triton extraction buffer.", "[Sample Lysis] Homogenize with a Dounce homogenizer for 25 strokes.", "[Sample Lysis] Rotate samples for 30 min at 4 °C.", "[Sample Lysis] Centrifuge at 13500 x g, 4 °C for 15 min.", "[Sample Lysis] Collect supernatants.", "[Substrate prepara... |
89,096 | Protein Digestion with S-trap Spin Columns | 4 | dx.doi.org/10.17504/protocols.io.bp2l6x7zdlqe/v1 | https://www.protocols.io/view/protein-digestion-with-s-trap-spin-columns-c29gyh3w | J Bons, J P Rose, M A Watson, B Schilling | TITLE: Protein Digestion with S-trap Spin Columns
AUTHORS: J Bons, J P Rose, M A Watson, B Schilling
[DESCRIPTION]
Trypsin digestion of isolated proteins using S-trap Spin columns in preparation for downstream proteomic profiling.
[STEPS]
1. In a 2-mL microcentrifuge tube add up to 300 μg of the protein lysate, 10% ... | ["In a 2-mL microcentrifuge tube add up to 300 μg of the protein lysate, 10% SDS for a final concentration of 4% SDS, 1M TEAB pH 8 solution for a final concentration of 50 mM TEAB, and HPLC-grade water if necessary to bring the volume up to a minimum of 50 µL.", "Add 250 mM DTT for a final concentration of 20 mM and in... |
78,458 | protocols.io academic and non-profit contract | 1 | dx.doi.org/10.17504/protocols.io.e6nvwk5j7vmk/v4 | https://www.protocols.io/view/protocols-io-academic-and-non-profit-contract-cqu2vwye | protocols.io team | TITLE: protocols.io academic and non-profit contract
AUTHORS: protocols.io team
[DESCRIPTION]
Template Contract
This contract is hereby made between the UNIVERSITY/ORGANIZATION (Univ) and ZappyLab, Inc. (DBA “protocols.io”).
DATE:December 13, 2021START DATE:December 27, 2021END DATE:December 26, 2022DESCRIPTION OF S... | ["[Activation] Within thirty (30) days from the Start Date, Univ will provide to protocols.io a list of IP addresses for on-campus user notification about free Premium workspaces.", "[Activation] Within two (2) weeks from the Start Date, protocols.io will enable free Premium workspaces accounts to be created by any Uni... |
84,048 | Formalin Fixed Paraffin Embedded (FFPE) Tissue Preparation for Digital Pathology Quantification Using QuPath | 1 | dx.doi.org/10.17504/protocols.io.bp2l6x4jklqe/v1 | https://www.protocols.io/view/formalin-fixed-paraffin-embedded-ffpe-tissue-prepa-cwbqxamw | Toby J Curless, Yau Lim, Zane Jaunmuktane | TITLE: Formalin Fixed Paraffin Embedded (FFPE) Tissue Preparation for Digital Pathology Quantification Using QuPath
AUTHORS: Toby J Curless, Yau Lim, Zane Jaunmuktane
[DESCRIPTION]
QuPath is an open-source digital pathology analysis software. Here, it is used to quantify various misfolded proteins across anatomical re... | ["[Tissue Preparation] Generate tissue sections using standard microtome sectioning protocols.", "[Tissue Preparation] Perform immunohistochemistry staining as per standard protocols.", "[Tissue Preparation] Coverslip stained slides as per standard protocols.", "[Digitisation and Segmentation of Tissue Sections, and Im... |
71,140 | Mobility, well-being, and community participation among people with depression: an observation study using geographically-explicit ecological momentary assessment (GEMA) | 2 | dx.doi.org/10.17504/protocols.io.5qpvory7bv4o/v1 | https://www.protocols.io/view/mobility-well-being-and-community-participation-am-chqct5sw | Maritta A Välimäki, Man Sing Wong, Thomas Choi, Paul Lee, Lin Yang, Rick Kwan, Oscar Chung, Xinyu Yu, Rui Zhu, Sau-fong Leung | TITLE: Mobility, well-being, and community participation among people with depression: an observation study using geographically-explicit ecological momentary assessment (GEMA)
AUTHORS: Maritta A Välimäki, Man Sing Wong, Thomas Choi, Paul Lee, Lin Yang, Rick Kwan, Oscar Chung, Xinyu Yu, Rui Zhu, Sau-fong Leung
[DESCRI... | [] |
89,151 | DNA Barcoding Standard Operating Protocol Lichens at RBGE, Lab methods: DNA extraction | 1 | dx.doi.org/10.17504/protocols.io.14egn3woyl5d/v1 | https://www.protocols.io/view/dna-barcoding-standard-operating-protocol-lichens-c3a7yihn | Amanda L Jones, Laura L. Forrest, Michelle Hart, Rebecca Yahr | TITLE: DNA Barcoding Standard Operating Protocol Lichens at RBGE, Lab methods: DNA extraction
AUTHORS: Amanda L Jones, Laura L. Forrest, Michelle Hart, Rebecca Yahr
[DESCRIPTION]
This is part of the collection DToL Taxon-specific Standard Operating Procedures for the Plant Working Group (protocols.io). The SOP collect... | ["[DNA extraction (Qiagen DNeasy plant mini kits)] Sampling. \n\nLichen barcoding for the Darwin Tree of Life (DToL) project involves extraction of DNA from lichen material that has been flash-frozen or dried and then frozen, along with the required metadata, following the collecting and submission SOPs available in t... |
88,300 | SAMPLING Protocol Template | 1 | null | https://www.protocols.io/view/sampling-protocol-template-c2gkybuw | Kathleen Pitz, Raissa.meyer | TITLE: SAMPLING Protocol Template
AUTHORS: Kathleen Pitz, Raissa.meyer
[DESCRIPTION]
A protocol template created through the BeBOP project for sampling.
[STEPS]
SECTION: Protocol Template
1. Minimum Information about an Omics Protocol (MIOP)
See https://github.com/BeBOP-OBON/miop/blob/main/model/schema/terms.yaml... | ["[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.egmbbu6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
See upcoming paper by Watts, Hurwitz, Youens-Clark.<br /><br />Code is freely available at <a href="https://github.com/hurwitzlab/16sblaster" target="_blank">Github</a>.
[STEPS]
?.
?.
?. | [] |
63,899 | martha maccallum cbd gummies Review | 3 | dx.doi.org/10.17504/protocols.io.14egn7j5mv5d/v1 | https://www.protocols.io/view/martha-maccallum-cbd-gummies-review-cam3sc8n | EricRaiey | TITLE: martha maccallum cbd gummies Review
AUTHORS: EricRaiey
[DESCRIPTION]
Martha MacCallum CBD Gummies Are Scientifically Tested And Approved {Fake Or Trusted}
[STEPS] | [] |
35,288 | Patch-Seq Recording and Extraction | null | dx.doi.org/10.17504/protocols.io.bepyjdpw | null | Allen Institute for Brain Science | TITLE: Patch-Seq Recording and Extraction
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the process to obtain electrophysiological recordings and cellular contents from neurons in postnatal mouse and/or human brain slices.</div><di... | [] |
30,636 | Phonological Awareness tasks for Italian-English comparison | null | dx.doi.org/10.17504/protocols.io.96kh9cw | null | Valeria Marinelli, Pierluigi Zoccolotti, Cristina Romani | TITLE: Phonological Awareness tasks for Italian-English comparison
AUTHORS: Valeria Marinelli, Pierluigi Zoccolotti, Cristina Romani
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:center"><span style = "font-weight:bold;">Phonological Awareness tasks</span... | [] |
45,953 | Growth curves | 4 | null | https://www.protocols.io/view/growth-curves-bq49myz6 | Elizabeth Fozo | TITLE: Growth curves
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Rules of thumb and directions for making growth curves</div></div>
[STEPS]
?. [Rules of thumb]
Never remove > 1/3 of a culture for a growth curve
?. [Rules of thumb]
Read OD600 (optical density at 600 nm) o... | ["[Rules of thumb]\nNever remove > 1/3 of a culture for a growth curve", "[Rules of thumb]\nRead OD600 (optical density at 600 nm) of 200 microliters of culture added to 800 microliters of fresh media → 1,000 microliters of fluid in cuvette; = 1:5 dilution", "[Rules of thumb]\nEasier to measure 800 microliters of fresh... |
54,471 | Left atrial function by speckle tracking echocardography in HFpEF | 1 | dx.doi.org/10.17504/protocols.io.bzffp3jn | https://www.protocols.io/view/left-atrial-function-by-speckle-tracking-echocardo-bzffp3jn | RC Rimbas, SL Magda, S Mihaila-Baldea, ML Luchian, AM Chitroceanu, M Hayat, DJ Mihalcea, R Dragoi-Galrinho-Antunes-Guerra, M Stefan, A Velcea, A Andronic, L Lungeanu-Juravle, AI Nicula, D Vinereanu | TITLE: Left atrial function by speckle tracking echocardography in HFpEF
AUTHORS: RC Rimbas, SL Magda, S Mihaila-Baldea, ML Luchian, AM Chitroceanu, M Hayat, DJ Mihalcea, R Dragoi-Galrinho-Antunes-Guerra, M Stefan, A Velcea, A Andronic, L Lungeanu-Juravle, AI Nicula, D Vinereanu
[DESCRIPTION]
AIMS. None of the convent... | ["[LA function in FpEF]"] |
26,798 | DNA extraction from sputum | null | dx.doi.org/10.17504/protocols.io.6enhbde | null | Laszlo Irinyi, Lana Pasic, Wieland Meyer | TITLE: DNA extraction from sputum
AUTHORS: Laszlo Irinyi, Lana Pasic, Wieland Meyer
[STEPS]
?. [Breaking the cells with liquid nitrogen]
The sputum samples were transferred to 1.5ml Eppendorf tubes for liquid nitrogen cell wall breakage, with a maximum of 600 µl of sputum per tube. Under full PPE conditions, the lid o... | ["[Breaking the cells with liquid nitrogen]\nThe sputum samples were transferred to 1.5ml Eppendorf tubes for liquid nitrogen cell wall breakage, with a maximum of 600 µl of sputum per tube. Under full PPE conditions, the lid of the tube was left open, and a small plastic pestle placed to sit inside. Liquid nitrogen wa... |
76,523 | Immunoprecipitation (IP) | 4 | dx.doi.org/10.17504/protocols.io.eq2ly79yelx9/v1 | https://www.protocols.io/view/immunoprecipitation-ip-cnyjvfun | nguyen.tha | TITLE: Immunoprecipitation (IP)
AUTHORS: nguyen.tha
[DESCRIPTION]
This protocol details about immunoprecipitation using anti-HA magnetic beads.
[STEPS]
SECTION: Procedures
1. Lyse cell pellets (5-7 mg) in 500 µL IP lysis buffer containing IP base buffer supplemented with 1x cOmplete, EDTA-free protease inhibitor cock... | ["[Procedures] Lyse cell pellets (5-7 mg) in 500 µL IP lysis buffer containing IP base buffer supplemented with 1x cOmplete, EDTA-free protease inhibitor cocktail and 0.1 µL of benzonase and incubate samples on ice for 30 min. Mix the sample by inverting the eppies gently every 5 min.", "[Procedures] Wash anti-HA beads... |
57,094 | Bacterial growth model | 1 | null | https://www.protocols.io/view/bacterial-growth-model-b3zeqp3e | Wolfram Moebius | TITLE: Bacterial growth model
AUTHORS: Wolfram Moebius
[DESCRIPTION]
Bacterial growth model
[STEPS]
1. RELEVANT TUTORIALS
https://www.comsol.com/model/microchannel-h-cell-19
https://www.comsol.com/model/hydrocarbon-dehalogenation-in-a-tortuous-microreactor-2182
To create the spatial aspect of our model, we use the G... | ["RELEVANT TUTORIALS\nhttps://www.comsol.com/model/microchannel-h-cell-19\nhttps://www.comsol.com/model/hydrocarbon-dehalogenation-in-a-tortuous-microreactor-2182\n\nTo create the spatial aspect of our model, we use the Geometry 1 menu to add blocks which represent individual channels or sheets of agar, and set the dim... |
75,571 | P7a.- Inscripción o modificación plan de investigación. | 1 | dx.doi.org/10.17504/protocols.io.eq2ly7enrlx9/v1 | https://www.protocols.io/view/p7a-inscripci-n-o-modificaci-n-plan-de-investigaci-cm2tu8en | cgarcia | TITLE: P7a.- Inscripción o modificación plan de investigación.
AUTHORS: cgarcia
[DESCRIPTION]
P7a.- Inscripción o modificación plan de investigación.
[STEPS]
SECTION: P7a.- Inscripción o modificación plan de investigación
1. INSCRIPCIÓN
Cada alumno admitido en un Programa de Doctorado de la EIDUCAM deberá presentar ... | ["[P7a.- Inscripción o modificación plan de investigación] INSCRIPCIÓN\n\nCada alumno admitido en un Programa de Doctorado de la EIDUCAM deberá presentar su Plan de Investigación antes de que transcurran 6 meses desde su matriculación en el programa. El doctorando presentará, con el visto bueno del director, un plan de... |
88,404 | Quality Control and Data Recording for DDNS | 3 | dx.doi.org/10.17504/protocols.io.5jyl8pe16g2w/v1 | https://www.protocols.io/view/quality-control-and-data-recording-for-ddns-c2juycnw | Alex Shaw, Joyce Akello, Catherine Troman, Aine.OToole, Erika Bujaki, c.ansley, Zoe Vance, rachel.colquhoun, Andrew Rambaut, Javier Martin, Nick Grassly | TITLE: Quality Control and Data Recording for DDNS
AUTHORS: Alex Shaw, Joyce Akello, Catherine Troman, Aine.OToole, Erika Bujaki, c.ansley, Zoe Vance, rachel.colquhoun, Andrew Rambaut, Javier Martin, Nick Grassly
[DESCRIPTION]
This standard operating procedure indicates how to perform quality control checks for DDNS a... | [] |
70,991 | Microwave digestion for microbes | 4 | dx.doi.org/10.17504/protocols.io.4r3l2747xg1y/v1 | https://www.protocols.io/view/microwave-digestion-for-microbes-chjpt4mn | An.Huang | TITLE: Microwave digestion for microbes
AUTHORS: An.Huang
[DESCRIPTION]
Before conducting inductively coupled plasma mass spectrometry (ICP-MS), all samples containing organic compounds need to be digested in order to eliminate all organic parts. Microwave digestion is a commonly used method for organism digestion. Th... | ["[Preparation of digestion vessels] Pick out digestion vessels from preservation boxes containing nitric acid (4%). Rinse and wash the vessels thoroughly. Also wash coordinated number of caps and plugs.", "[Preparation of digestion vessels] Put all vessels inside the oven and dried at 60 °C for at least 60 min.", "[Pr... |
94,530 | Pythium Zoospore Production Soaking Solution | 4 | null | https://www.protocols.io/view/pythium-zoospore-production-soaking-solution-c8jazuie | Nimalka Weerasuriya | TITLE: Pythium Zoospore Production Soaking Solution
AUTHORS: Nimalka Weerasuriya
[DESCRIPTION]
Creation and test of soaking solutions to be used for large-scale zoospore production for Pythium myriotylum. This is modified from methods in:
Nyochembeng, L. M., Pacumbaba, R. P., & Beyl, C. A. (2002). Calcium Enhanced Zo... | ["[Soaking Solutions] Make Soaking Solutions 1, 2, 3, and Control.\nPrep 4 x 1 L autoclavable bottles for each Soaking Solutions (1-3) and Control.", "[Preparation] Have mature colonies of verified Pythium myriotylum growing on CMA or 1.5-2% WA 90 mm plates. Colony maturity ~7-14 days, with visible oospores.", "[Soakin... |
null | null | null | dx.doi.org/10.17504/protocols.io.u3geyjw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Electroporation protocol
Weinstock paper:
Matthew T Weinstock, Eric D Hesek,Christopher M Wilson, Daniel G Gibson
Vibrio natriegens as a fast-growing host for molecular biology
Nature Methods volume 13, pages 849–851 (2016)
To prepare before:
recovery medium
(BHI + v2 sal... | [] |
34,726 | Protocol for Differentiation of Blood-Brain Barrier Endothelial Cells from Human Pluripotent Stem Cells | null | dx.doi.org/10.17504/protocols.io.bd6ei9be | null | Ethan Lippmann, Hannah Wilson, Emma Neal | TITLE: Protocol for Differentiation of Blood-Brain Barrier Endothelial Cells from Human Pluripotent Stem Cells
AUTHORS: Ethan Lippmann, Hannah Wilson, Emma Neal
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Human induced pluripotent stem cell (iPSC)-derived developmental lineages are key too... | ["[BBB differentiation (Day 0–4)]\nOn day 0, aspirate E8 medium and add of E6 per well.\nNote: Cells are seeded for differentiation in E8 medium according to the standardized single cell seeding protocol\n2 ml", "[BBB differentiation (Day 0–4)]\nChange medium every day using of E6 per well.\n2 ml", "[BBB expansion (D... |
41,526 | Clonal Amplification | 4 | dx.doi.org/10.17504/protocols.io.bkswkwfe | https://www.protocols.io/view/clonal-amplification-bkswkwfe | huiyi.chen , Sid Roy | TITLE: Clonal Amplification
AUTHORS: huiyi.chen , Sid Roy
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This user guide describes the protocol to produce template-loaded beads for one gCAS3 sequencing run by clonal amplification for the GenapSys system.</div></div>
[STEPS] | [] |
87,546 | A simple phototaxis assay for aquatic larvae | 4 | dx.doi.org/10.17504/protocols.io.x54v9p294g3e/v1 | https://www.protocols.io/view/a-simple-phototaxis-assay-for-aquatic-larvae-czq2x5ye | Julie M Butler, Lauren A O'Connell | TITLE: A simple phototaxis assay for aquatic larvae
AUTHORS: Julie M Butler, Lauren A O'Connell
[DESCRIPTION]
Phototaxis assays are utilized throughout neuroscience research to measure exploratory behaviors and visual capabilities. Here we detail a simple and low cost phototaxis assay for aquatic larvae. The assay cha... | ["[Arena construction] Obtain a large (15 cm diameter) petri dish and burn a hole in the middle of the petri dish just large enough to fit a screw through. This is the chamber base.", "[Arena construction] Paint half the base black on the inside of the dish. Repeat with two more paint layers until opaque.", "[Arena con... |
92,533 | Flow cytometry for TH-positive iPSC derived neurons | 1 | dx.doi.org/10.17504/protocols.io.81wgbxwkqlpk/v1 | https://www.protocols.io/view/flow-cytometry-for-th-positive-ipsc-derived-neuron-c6kvzcw6 | Ellen Hertz, Ellen Hertz, Gani Perez, Martha Kirby, Stacie Anderson, Yu Chen, Ellen Sidransky | TITLE: Flow cytometry for TH-positive iPSC derived neurons
AUTHORS: Ellen Hertz, Ellen Hertz, Gani Perez, Martha Kirby, Stacie Anderson, Yu Chen, Ellen Sidransky
[DESCRIPTION]
This protocol details the flow cytometry procedure.
[STEPS]
SECTION: Flow cytometry dopaminergic fraction
1. Wash the neurons in PBS and incub... | ["[Flow cytometry dopaminergic fraction] Wash the neurons in PBS and incubate with Membrite prestain solution, dilute 1:1000 in HBSS, for 5 min at 37 °C.", "[Flow cytometry dopaminergic fraction] Change the prestain solution to staining solution and incubate for another 5 min at 37 °C.", "[Flow cytometry dopaminergic f... |
null | null | null | dx.doi.org/10.17504/protocols.io.mc7c2zn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>We present a protocol for visualizing and quantifying single mRNA molecules in mammalian (mouse and human) tissues. In the approach described here, sets of about 50 short oligonucleotides, each labeled with a single fluorophore, are hybridized to target mRNAs in tissue sectio... | [] |
67,075 | Fluxactive Complete {SCAM & LEGIT} | 1 | dx.doi.org/10.17504/protocols.io.14egn7kwqv5d/v1 | https://www.protocols.io/view/fluxactive-complete-scam-amp-legit-cdrbs52n | fluxactiverate | TITLE: Fluxactive Complete {SCAM & LEGIT}
AUTHORS: fluxactiverate
[DESCRIPTION]
Prostate expansion and prostate illness are two of the most significant issues that men face as they age and near the uttermost furthest reaches of their lives. A large portion of men, up to 93 percent of men past 50 years of age, ha... | [] |
96,862 | REDI-NET T-1A ACTIVE VERTEBRATE TICK FIELD SAMPLING | 0 | dx.doi.org/10.17504/protocols.io.e6nvw1p5wlmk/v1 | https://www.protocols.io/view/redi-net-t-1a-active-vertebrate-tick-field-samplin-dat62ere | REDI-NET Consortium | TITLE: REDI-NET T-1A ACTIVE VERTEBRATE TICK FIELD SAMPLING
AUTHORS: REDI-NET Consortium
[DESCRIPTION]
To outline steps for properly collecting tick samples actively collected from cattle to evaluate the risk of zoonotic disease transmission by the detection of pathogens from invertebrate DNA (iDNA).
[BEFORE_START]
NO... | ["[SAMPLING TEAMS] This SOP assumes that the animals’ owners/handlers/veterinarians are on site to corral cattle, move them through the chute, and operate the chute. The three minute search time assumes at least three study personnel are available for tick collection. If only two individuals are present, increase searc... |
89,689 | Proteolytic Peptide Desalting with C18 Hydrophilic–Lipophilic Balance (HLB) Cartridges | 4 | dx.doi.org/10.17504/protocols.io.3byl4q382vo5/v1 | https://www.protocols.io/view/proteolytic-peptide-desalting-with-c18-hydrophilic-c3tzynp6 | J Bons, J P Rose, M A Watson, B Schilling | TITLE: Proteolytic Peptide Desalting with C18 Hydrophilic–Lipophilic Balance (HLB) Cartridges
AUTHORS: J Bons, J P Rose, M A Watson, B Schilling
[DESCRIPTION]
Desalting of proteolytic peptide elution using C18 Hydrophilic–Lipophilic Balance (HLB) Cartridges in preparation for downstream proteomic profiling.
[STEPS... | ["Centrifuge the samples at 1,850 x g for 5 minutes at room temperature to pellet insoluble material.", "Desalt the samples using Oasis HLB solid-phase extraction cartridges placed on top of a vacuum manifold as follows:", "Condition each cartridge two times with 800 µL of the condition buffer (50% ACN, 0.2% FA).", "Eq... |
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