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 |
|---|---|---|---|---|---|---|---|
47,151 | Micro-C protocol for frozen tissue using the Dovetail® Micro-C Kit | 4 | dx.doi.org/10.17504/protocols.io.14egnz4kyg5d/v1 | https://www.protocols.io/view/micro-c-protocol-for-frozen-tissue-using-the-dovet-bsapnadn | Eric RA Pederson | TITLE: Micro-C protocol for frozen tissue using the Dovetail® Micro-C Kit
AUTHORS: Eric RA Pederson
[DESCRIPTION]
micro-C protocol from Dovetail for the use on frozen tissue, in this case
[BEFORE_START]
Complete everything in the pre-epxerimentation section
[GUIDELINES]
The amount of mononuclease content must be be... | ["[pre-experimentation] All steps should be performed on ice or at 4 °C.", "[pre-experimentation] Autoclave cryogrinder pieces wrapped in foil", "[pre-experimentation] pre-cool the cryogrinder pieces", "[pre-Step 1] Stage 1: Crosslinking, Digestion and Lysis \n\nAs you prepare for Stage 1, keep the following in mind: \... |
68,123 | Sex Work and Sexual Violence Research Study Protocol 2022 | 1 | dx.doi.org/10.17504/protocols.io.eq2lynojevx9/v1 | https://www.protocols.io/view/sex-work-and-sexual-violence-research-study-protoc-cer3td8n | Scoular, Jane, Sanders, Teela, Abel, Gillian, Brents, Barbara, Ellison, Graham, Susie Balderston, Marriott, Nigel | TITLE: Sex Work and Sexual Violence Research Study Protocol 2022
AUTHORS: Scoular, Jane, Sanders, Teela, Abel, Gillian, Brents, Barbara, Ellison, Graham, Susie Balderston, Marriott, Nigel
[DESCRIPTION]
Globally, the most important public health issue that sex workers face is their experience of high levels of violence... | [] |
45,764 | RNA Extraction of SARS-CoV-2 from Wastewater | 4 | null | https://www.protocols.io/view/rna-extraction-of-sars-cov-2-from-wastewater-bqxcmxiw | Neha Mittal, Vbarua , Nick Stark, Cynthia Gibas, jschluet , Mariya Munir | TITLE: RNA Extraction of SARS-CoV-2 from Wastewater
AUTHORS: Neha Mittal, Vbarua , Nick Stark, Cynthia Gibas, jschluet , Mariya Munir
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Modified protocol from RNA-extraction of SARS-CoV-2 from wastewater using the Qiagen QIAmp Viral RNA extraction kit. <... | ["The biosafety cabinet should be properly sterilized (UV light for 20 minutes and the surface should be cleaned with 70% ethanol). Clean the area with RNA Zap. All extraction work will be done inside the biosafety cabinet. Clean the equipment/instruments to be used including the centrifuges and pipettes with 70% alcoh... |
31,165 | Flow cytometry based monocyte adhesion assay for quantification of endothelial activation in vitro | null | dx.doi.org/10.17504/protocols.io.ban5idg6 | null | Vinnyfred Vincent, Himani Thakkar, Anjali Verma, Atanu Sen, Nikhil Chandran, Archna Singh | TITLE: Flow cytometry based monocyte adhesion assay for quantification of endothelial activation in vitro
AUTHORS: Vinnyfred Vincent, Himani Thakkar, Anjali Verma, Atanu Sen, Nikhil Chandran, Archna Singh
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Endothelial pro inflammatory activation is a ke... | ["[Preparation of human umbilical vein endothelial cell (HUVEC) monolayer ]\nAdd 1 ml of 0.2% gelatin in PBS to each well of a 6 well plate and keep inside a CO2 incubator at 37oC for 1 hour.", "[Fluorescent labeling of THP1 monocytes ]\nTHP1 cells are cultured in RPMI 1640 medium with 10% FBS and antibiotics. Count TH... |
18,349 | Usage of EMBL2checklists | null | dx.doi.org/10.17504/protocols.io.v6me9c6 | null | Michael Gruenstaeudl | TITLE: Usage of EMBL2checklists
AUTHORS: Michael Gruenstaeudl
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The submission of DNA sequences to public sequence databases is an essential, but insufficiently automated step in the process of generating and disseminating novel DNA sequence data. A use... | ["Annotation of DNA sequencesAdd sequence features and feature qualifiers to each DNA sequence using INSDC-compatible feature table keywords.Use any of the following software tools:", "Saving sequences as flat fileSave multiple DNA sequences of the same barcoding marker as an single, multi-sequence flat file in EMBL or... |
104,282 | Construction of individuals ddRADseq libraries for macro-algae (Kelp) V.2 | 0 | dx.doi.org/10.17504/protocols.io.rm7vzjo68lx1/v2 | https://www.protocols.io/view/construction-of-individuals-ddradseq-libraries-for-dh3238qe | Stéphane Mauger, Komlan Avia | TITLE: Construction of individuals ddRADseq libraries for macro-algae (Kelp) V.2
AUTHORS: Stéphane Mauger, Komlan Avia
[DESCRIPTION]
This protocol describes a double digested restriction-site associated DNA (ddRADseq) procedure, that is a variation on the original RAD sequencing method (Davey & Blaxter 2011), which is... | ["[Solutions and buffers preparations] Annealing buffer stock (10x)\nAnnealing buffer composed 100 mM Tris-HCl, pH8; 500 mM NaCl and 10 mM EDTA \n5 mL\n5 mL\n1 mL \n39 mL \n \nHomogenize and autoclave.\n\nStore at Room temperature", "[Solutions and buffers preparations] 5 M sodium chloride solution (NaCl)\n29.2 g \nDis... |
108,063 | Rodent Gait Analysis Using Linear Track Protocol | 0 | dx.doi.org/10.17504/protocols.io.n2bvjnwjbgk5/v1 | https://www.protocols.io/view/rodent-gait-analysis-using-linear-track-protocol-dmr7459n | Rose B. Creed, Alexandra Nelson | TITLE: Rodent Gait Analysis Using Linear Track Protocol
AUTHORS: Rose B. Creed, Alexandra Nelson
[DESCRIPTION]
This protocol is used to evaluate quantitative aspects of mouse locomotor behavior (gait).
[STEPS]
SECTION: Procedure
1. There is no need to habituate mice to the apparatus; mice will walk across volunta... | ["[Procedure] There is no need to habituate mice to the apparatus; mice will walk across voluntarily to enter the black box.", "[Procedure] Start video recording.", "[Procedure] Place mouse on open end of the catwalk; observe to make sure mouse walks towards the black “home” box.", "[Procedure] When mouse reaches “home... |
92,223 | Cryopreservation of intestinal/colonic biopsies | 4 | dx.doi.org/10.17504/protocols.io.eq2lyj43qlx9/v1 | https://www.protocols.io/view/cryopreservation-of-intestinal-colonic-biopsies-c6a7zahn | Tatiana Karakasheva | TITLE: Cryopreservation of intestinal/colonic biopsies
AUTHORS: Tatiana Karakasheva
[DESCRIPTION]
This is a protocol for cryopreservation of biopsies, optimized for maximum viability and establishment of primary lines at a later point. Specific notes included for cryopreservation of samples for future scRNA-seq.
[STE... | [] |
100,535 | DNA Extraction - Qiagen DNeasy Blood and Tissue Kit UCC & IMR eWHALE | 0 | dx.doi.org/10.17504/protocols.io.n92ld8m2ov5b/v1 | https://www.protocols.io/view/dna-extraction-qiagen-dneasy-blood-and-tissue-kit-deex3bfn | Lauren Rodriguez, Lorenzo De Bonis, James McKenna | TITLE: DNA Extraction - Qiagen DNeasy Blood and Tissue Kit UCC & IMR eWHALE
AUTHORS: Lauren Rodriguez, Lorenzo De Bonis, James McKenna
[DESCRIPTION]
This DNA extraction protocol was used in Rodriguez et al., 2024 (in prep) for the extraction of environmental DNA from samples collected off of the coast of Ireland (... | ["[Lysis] Remove filters from the freezer and allow to thaw at room temperature for 45 min . Ensure that all filter capsules are properly closed and labeled.", "[Lysis] Invert filters a couple of times to agitate lysate.", "[Lysis] Incubate filter capsules at 56 °C for 180 min . Invert filters every 30 minutes.", "[Lys... |
null | null | null | dx.doi.org/10.17504/protocols.io.ri7d4hn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A real-time PCR to detect RNA in mouse liver tissue. This method has been adapted from a<br />publication by Liu XJ et al 2014, and the oligonucleotides have been modified and a different PCR kit<br />used.</p>
[BEFORE_START]
<p>If using a different brand or model of real-ti... | [] |
19,791 | Lymphocyte proliferation in poultry species | null | dx.doi.org/10.17504/protocols.io.xjpfkmn | null | Ahmed O.Abass, Gamal Mehaisen | TITLE: Lymphocyte proliferation in poultry species
AUTHORS: Ahmed O.Abass, Gamal Mehaisen
[STEPS]
?. The heparinized blood samples were added to separation medium Histopaque®-1077 (cat# 10771, Sigma, USA).
?. Samples were centrifuged at 1030 xg for 20 min at 4°C.
?. Peripheral blood mononuclear cells (PBMCs) were isol... | ["The heparinized blood samples were added to separation medium Histopaque®-1077 (cat# 10771, Sigma, USA).", "Samples were centrifuged at 1030 xg for 20 min at 4°C.", "Peripheral blood mononuclear cells (PBMCs) were isolated and washed twice with RPMI-1640 (Invitrogen Corp., Grand Island, NY, USA) and then re-suspended... |
53,897 | Chelex DNA extraction Protocol | 1 | dx.doi.org/10.17504/protocols.io.byvhpw36 | https://www.protocols.io/view/chelex-dna-extraction-protocol-byvhpw36 | Sarah Chang, Michael Russello | TITLE: Chelex DNA extraction Protocol
AUTHORS: Sarah Chang, Michael Russello
[DESCRIPTION]
Laboratory protocol for DNA extraction from animal tissue with Chelex.
[STEPS]
1. Make up enough 10% Chelex for entire plate (195 µL /individual + slop) (ie. 1 g Chelex: 9 mL dH2O)
2. Place a magnetic stir bar in the jar c... | ["Make up enough 10% Chelex for entire plate (195 µL /individual + slop) (ie. 1 g Chelex: 9 mL dH2O)", "Place a magnetic stir bar in the jar containing your 10% Chelex solution. The Chelex powder is very heavy and needs to be constantly stirred in order to maintain consistency.", "Pipette 195 µL of Chelex into each w... |
null | null | null | dx.doi.org/10.17504/protocols.io.c9jz4m | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
The following are media recipes necessary for isolating and maintaining <em>Synechococcus</em> isolates.
[GUIDELINES]
<strong>SN MEDIUM</strong> (used for maintenance of culture stocks)<br /><br />
<table>
<tbody>
<tr>
<td>75% Seawater </td>
<td>(750 mL)</td>
</tr>
<tr>
<td>2... | [] |
67,424 | InstaHard Male Enhancement Reviews | 1 | dx.doi.org/10.17504/protocols.io.bp2l61q4dvqe/v1 | https://www.protocols.io/view/instahard-male-enhancement-reviews-cd38s8rw | S S | TITLE: InstaHard Male Enhancement Reviews
AUTHORS: S S
[DESCRIPTION]
InstaHard Reviews
[STEPS]
1. Official website:-https://wintersupplement.com/instahard-reviews/
InstaHard Reviews Male Enhancement
Product Name :-InstaHard Male Enhancement
Product Type:-Prostate support formula for better urine flow
Formulator/De... | ["Official website:-https://wintersupplement.com/instahard-reviews/\nInstaHard Reviews Male Enhancement\n\n\nProduct Name :-InstaHard Male Enhancement\nProduct Type:-Prostate support formula for better urine flow\nFormulator/Developer:-Dr. Leo Shub\nManufacturer & Distributor:-Pure Body Innovations\nIngredients:-Saw Pa... |
59,611 | FLASH-seq protocol | 4 | dx.doi.org/10.17504/protocols.io.kxygxzkrwv8j/v2 | https://www.protocols.io/view/flash-seq-protocol-b6f3rbqn | Simone Picelli, Vincent Hahaut | TITLE: FLASH-seq protocol
AUTHORS: Simone Picelli, Vincent Hahaut
[DESCRIPTION]
The single-cell RNA-sequencing (scRNA-seq) field has evolved tremendously since the first paper was published back in 2009. While the first methods analysed just a handful of cells, the throughput and performance rapidly increased over... | ["[Prepare lysis mix] Prepare the following lysis mix:\n ReagentReaction concentrationVolume (µl)384-well plateTriton-X100 (10% v/v)0.2%0.0208.448dNTP mix (25 mM each)6 mM0.240101.376SMART dT30VN (100 µM)1.8 mM0.0187.603RNAse inhibitor (40 U/µL)1.2 U/µL0.03012.672DTT (100 mM)1.2 mM0.0125.069FS TSO (100 µM)9.2 µM0.09... |
76,318 | Building a SpikeGLX Rig with camera: Chronic recoverable Neuropixels in mice | 1 | dx.doi.org/10.17504/protocols.io.kxygxzzxkv8j/v2 | https://www.protocols.io/view/building-a-spikeglx-rig-with-camera-chronic-recove-cnr6vd9e | Emily A Aery Jones | TITLE: Building a SpikeGLX Rig with camera: Chronic recoverable Neuropixels in mice
AUTHORS: Emily A Aery Jones
[DESCRIPTION]
This protocol collection explains how to build a low-cost, lightweight system to implant 1 Neuropixels 1.0 probe or 2 Neuropixels 2.0 probes into mice, record during freely moving behavior, the... | ["[Set up acquisition hardware] Load the PCIe module into your computer", "[Set up acquisition hardware] Load the PXIe modules and the IMEC module into the NIDAQ chassis", "[Set up acquisition hardware] Connect the PXIe modules to the BNC breakout board and the computer. Connect the IMEC SMA to the BNC board (analog sl... |
32,873 | Ligation Protocol with T4 DNA Ligase (M0202) | 1 | dx.doi.org/10.17504/protocols.io.bcchist6 | https://www.protocols.io/view/ligation-protocol-with-t4-dna-ligase-m0202-bcchist6 | New England Biolabs | TITLE: Ligation Protocol with T4 DNA Ligase (M0202)
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This product can be used for the following applications:</div><div class = "text-block"><ul style = "list-style-type:disc;"><li style = "counter-reset:ol0;list-style-type... | ["Set up the following reaction in a microcentrifuge tube . AB1COMPONENT20 μl REACTION2T4 DNA Ligase Buffer (10X)*2 μl3Vector DNA (4 kb)50 ng (0.020 pmol)4Insert DNA (1 kb)37.5 ng (0.060 pmol)5Nuclease-free waterto 20 μl6T4 DNA Ligase1 μl\non ice\nAB1COMPONENT20 μl REACTION2T4 DNA Ligase Buffer (10X)*2 μl3Vector DNA (... |
44,602 | Quantitative real-time PCR for the four Lactobacillus species | 4 | dx.doi.org/10.17504/protocols.io.bps2mnge | https://www.protocols.io/view/quantitative-real-time-pcr-for-the-four-lactobacil-bps2mnge | Chen Chen | TITLE: Quantitative real-time PCR for the four Lactobacillus species
AUTHORS: Chen Chen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Quantitative Real-time Polymerase Chain Reaction(qPCR) for the four </span><span style = "font-style:italic;">Lactobacillus</span><span> species, including </... | ["The primers for the four Lactobacillus species used in this study were performed as Backer et al. (2007). Pick some vaginal DNA samples at random, and perform PCR reactions using these four sets of primers, respectively. Then use electrophoresis to identify the PCR products, and purify the final PCR product by gel ex... |
76,633 | TEST - manual DNA Purification via magnetic beads | 4 | null | https://www.protocols.io/view/test-manual-dna-purification-via-magnetic-beads-cn3zvgp6 | Carla Jungkunz | TITLE: TEST - manual DNA Purification via magnetic beads
AUTHORS: Carla Jungkunz
[DESCRIPTION]
manual purification of DNA/PCRs via magnetic beads
[BEFORE_START]
bring magnetic beads to room temperature (at least 30min)
[STEPS]
SECTION: prepare magnetic beads
1. 30 min bring magnetic beads to room temperature (RT)
... | ["[prepare magnetic beads] 30 min bring magnetic beads to room temperature (RT)", "[prepare magnetic beads] vortex until homogeneous", "[Binding of DNA] Add beads ... |
87,591 | Protocol for Deep Learning-Based Classification of Vitreomacular Adhesion in Diabetic Macular Edema using SD-OCT. | 1 | dx.doi.org/10.17504/protocols.io.4r3l2295pl1y/v1 | https://www.protocols.io/view/protocol-for-deep-learning-based-classification-of-czsfx6bn | Brughanya Subramanian, A. Q. M Sala Uddin Pathan, Maitreyee Roy, Dhanashree Ratra, Salil S. Kanhere, Matthew P Simunovic, Rajiv Raman | TITLE: Protocol for Deep Learning-Based Classification of Vitreomacular Adhesion in Diabetic Macular Edema using SD-OCT.
AUTHORS: Brughanya Subramanian, A. Q. M Sala Uddin Pathan, Maitreyee Roy, Dhanashree Ratra, Salil S. Kanhere, Matthew P Simunovic, Rajiv Raman
[DESCRIPTION]
This study is a continuation of our previ... | ["[Introduction] VMA describes residual adhesion between the vitreous and macula, occurring within the context of an incomplete posterior vitreous detachment. It might not lead to any retinal abnormality but may exert traction on the underlying macula, distorting the retinal architecture and leading to\nVMT. [2] VMA ca... |
null | null | null | dx.doi.org/10.17504/protocols.io.tkkekuw | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p>Use with Ultra Streptavidin Detection Kit (<a href="https://antibody.biolegend.com/datasheet.php?UpProd=&catalogno=SIG-32250" target="_blank">SIG-32250)</a> or (<a href="https://antibody.biolegend.com/datasheet.php?UpProd=&catalogno=SIG-32248" target="_blank">SIG-32248... | ["[Clear Slides] {\"blocks\":[{\"key\":\"6qb09\",\"text\":\"Clear Slides: Removes paraffin and hydrates the tissue.\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"76h2v\",\"text\":\" \",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":... |
95,428 | Making Agarose for use in acute in vivo Electrophysiology Experiments | 1 | dx.doi.org/10.17504/protocols.io.5jyl8py89g2w/v1 | https://www.protocols.io/view/making-agarose-for-use-in-acute-in-vivo-electrophy-c9fcz3iw | Ryan Gillis, Mikayla Carlson, Severine Durand | TITLE: Making Agarose for use in acute in vivo Electrophysiology Experiments
AUTHORS: Ryan Gillis, Mikayla Carlson, Severine Durand
[DESCRIPTION]
This protocol describes the procedure for making agarose used in acute in vivo Electrophysiology Experiments with Neuropixels probes. This exact methodology is crucial to t... | ["[Create Agarose Aliquot] Place a piece of weigh paper on scale", "[Create Agarose Aliquot] Make sure the scale is tared and display is showing grams.", "[Create Agarose Aliquot] Measure out .42 g of Certified Low-Melt Agarose and transfer powder to 2mL centrifuge tube.", "[Create Agarose Aliquot] On the same paper, m... |
null | null | null | dx.doi.org/10.17504/protocols.io.tffejjn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A maternal cardiovascular profile was assessed in every pregnant woman combining three non-invasive techniques to obtain information about arteries, veins, heart and body fluid content (Table 1). A standardized protocol was used as reported in previous studies, as enlisted be... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.etjbekn | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<strong>Reaction Conditions and Buffer, Materials:</strong><br /><br />
<ul>
<li>Reaction conditions: 50 mM Tris-HCl, pH 7.8, 10 mM EDTA, 0.5 mM DTT, 2 µCi Adenosyl-L-Methionine, S-Methyl (<sup>3</sup>H), 3 µg DNA</li>
</ul>
<br />
<ul>
<li>Preparation of reaction buffer, 10X</li... | [] |
93,394 | Akoya Biosciences PhenoCycler Fusion (formerly CODEX) User Guide | 1 | dx.doi.org/10.17504/protocols.io.x54v9p4j1g3e/v1 | https://www.protocols.io/view/akoya-biosciences-phenocycler-fusion-formerly-code-c7fszjne | Andrew Houston | TITLE: Akoya Biosciences PhenoCycler Fusion (formerly CODEX) User Guide
AUTHORS: Andrew Houston
[DESCRIPTION]
Link to PhenoCycler User Guide to allow for multi-plex spatial proteomic detection on fresh frozen and FFPE tissue sections
[STEPS]
1. Staining/slide prep protocol can be found here:
FFPE tissue staining ... | ["Staining/slide prep protocol can be found here:\n \n\nFFPE tissue staining pgs. 45-56\nReporter plate preparation pgs. 70-75", "Imaging protocol can be found here:\n \n\nFlow cell assembly pgs. 29-39\nInstrument set-up for PhenoCycler scan pgs. 57-71"] |
49,480 | Total nucleic acid extraction - Maxwell(R) HT Environmental TNA Kit, custom (Promega) | 4 | dx.doi.org/10.17504/protocols.io.bujgnujw | https://www.protocols.io/view/total-nucleic-acid-extraction-maxwell-r-ht-environ-bujgnujw | Adélaïde Roguet | TITLE: Total nucleic acid extraction - Maxwell(R) HT Environmental TNA Kit, custom (Promega)
AUTHORS: Adélaïde Roguet
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Total nucleic acid extraction from wastewater using Maxwell(R) HT Environmental TNA Kit, custom (Promega)</div></div>
[STEPS]
?. [Tot... | ["[Total nucleic acid extraction]\nFor HA filter extraction, let the sample thaw on ice and go to step 2. For BCoV/BRSV extraction (in duplicate), add 5 µL of BCoV/BRSV solution to the 2-mL tube containing 250 µL CTAB. Vortex for 15 seconds (speed 7 out of 10) and flash freeze the tube. Go to step 4.For Direct extracti... |
102,313 | Decálogo de cómo escribir ciencia (Torres-Gordillo, 2020) | 0 | dx.doi.org/10.17504/protocols.io.dm6gpzdq8lzp/v1 | https://www.protocols.io/view/dec-logo-de-c-mo-escribir-ciencia-torres-gordillo-df6h3rb6 | Juan Jesus Torres-Gordillo | TITLE: Decálogo de cómo escribir ciencia (Torres-Gordillo, 2020)
AUTHORS: Juan Jesus Torres-Gordillo
[DESCRIPTION]
Decálogo de aprender a escribir ciencia (v2), del profesor Juan Jesús Torres-Gordillo (2020)
[STEPS]
1. | [] |
59,164 | Preparing multiplexed WGS/MetaG libraries with the Illumina DNA Prep kit for the Illumina NextSeq or MiSeq | 4 | dx.doi.org/10.17504/protocols.io.5qpvob31bl4o/v1 | https://www.protocols.io/view/preparing-multiplexed-wgs-metag-libraries-with-the-b5z4q78w | André M Comeau, Gina V Filloramo | TITLE: Preparing multiplexed WGS/MetaG libraries with the Illumina DNA Prep kit for the Illumina NextSeq or MiSeq
AUTHORS: André M Comeau, Gina V Filloramo
[DESCRIPTION]
The preparation of (meta)genomic libraries using the Illumina Nextera Flex (now "DNA Prep") kit with CD/UDI indices at the IMR.
Based upon Illumin... | ["[Prepare and Quantify gDNA] Using two 96-well PCR plates, prepare 30 µL of 1:10 dilution using nuclease-free water (NFW) for up to 192 gDNA samples.", "[Prepare and Quantify gDNA] Quantify 5 µL of the 1:10 diluted gDNA using the Invitrogen Quant-iT dsDNA HS assay kit on the fluorescent 96-well plate reader.", "[Perfo... |
26,545 | UC Davis - Immunohistochemistry BODIPY | null | dx.doi.org/10.17504/protocols.io.56rg9d6 | null | Jennifer Rutkowsky | TITLE: UC Davis - Immunohistochemistry BODIPY
AUTHORS: Jennifer Rutkowsky
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">BODIPY® 493/503 can be used as a stain for neutral lipids and as a tracer for oil and other nonp... | ["Frozen tissue sections (10µM) on slides (tissues embedded in OCT) are then fixed in 4% paraformaldehyde for 5 minutes. a. Alternatively paraffin embedded sections are deparaffinized through 3 100% xylene 3 min wash b. Sections were rehydrated through 100%, 95%, 70%, 50%, and 30% then into deionized water (3min each).... |
91,372 | Wheat leaf high-molecular weight (HMW) DNA extraction | 1 | dx.doi.org/10.17504/protocols.io.bp2l6xpy1lqe/v1 | https://www.protocols.io/view/wheat-leaf-high-molecular-weight-hmw-dna-extractio-c5gky3uw | Maximillian RW Jones, Nikolai Adamski, Cristobal Uauy | TITLE: Wheat leaf high-molecular weight (HMW) DNA extraction
AUTHORS: Maximillian RW Jones, Nikolai Adamski, Cristobal Uauy
[DESCRIPTION]
This protocol is for the extraction of high-molecular weight DNA from wheat leaf tissue. The product is suitable for long-read sequencing such as PacBio. The protocol may also be ef... | ["[Buffer preparation] Prepare 10x HB", "[Buffer preparation]", "[Buffer preparation]", "[Buffer preparation]", "[Tissue collection] Sanitise scissors and/or other tools, plus gloved hands, with 70% ethanol. Collect 2-5 g leaf blade tissue into a 50 mL Falcon tube. Do not use leaf sheath tissue. Avoid using diseased, b... |
95,601 | eDNA extraction from water samples filtered through 47 mm diameter filters (NucleoMag DNA/RNA Water Kit - MACHEREY NAGEL). | 4 | dx.doi.org/10.17504/protocols.io.j8nlkox7dv5r/v1 | https://www.protocols.io/view/edna-extraction-from-water-samples-filtered-throug-c9krz4v6 | Marine Vautier, Cecile Chardon, Cyrielle Galiegue, Isabelle Domaizon | TITLE: eDNA extraction from water samples filtered through 47 mm diameter filters (NucleoMag DNA/RNA Water Kit - MACHEREY NAGEL).
AUTHORS: Marine Vautier, Cecile Chardon, Cyrielle Galiegue, Isabelle Domaizon
[DESCRIPTION]
The objective of this protocol is the environmental DNA (eDNA) extraction from water samples fil... | ["[Material preparation] To limit contamination of the kit buffers, it is recommended to aliquote them:\n- Into 50 mL tubes for MWA1, MWA2, MWA3 and MWA4\n- Into 2 mL tubes for NucleoMag B-Beads solution and DNase-free H2O\n\nTubes annotation \n- one 2 mL tube per sample for lysate collection\n- one 1.5 mL tube per sam... |
36,646 | Hematoxylin & Eosin Protocol For Leica ST5020 Automated Stainer | 1 | dx.doi.org/10.17504/protocols.io.bf2ejqbe | https://www.protocols.io/view/hematoxylin-amp-eosin-protocol-for-leica-st5020-au-bf2ejqbe | Angela Denn | TITLE: Hematoxylin & Eosin Protocol For Leica ST5020 Automated Stainer
AUTHORS: Angela Denn
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This Hematoxylin and Eosin protocol is for the Leica ST5020 Automated multistainer. You can use it as a guide to developing your own protocol, catered to the ne... | ["[H&E Stain]\nABCDEF1STEPSTATIONDYE/REAGENT STATIONDURATIONEXACTDIP2138Oven station5:00nono3237Oven station5:00nono431Pro-Par5:00noyes542Pro-Par5:00noyes653Pro-Par5:00noyes764100% IPA1:30noyes875100% IPA1:30noyes98690% IPA1:30noyes10912DI Water Wash1:30nono111021SelectTech Hematoxylin 5601:30yesyes121111DI Water Wash1... |
87,580 | 10X Multiome TST Nuclei Isolation | 4 | dx.doi.org/10.17504/protocols.io.kxygx3wmzg8j/v1 | https://www.protocols.io/view/10x-multiome-tst-nuclei-isolation-czr4x58w | Sébastien Vigneau, Yashika_Rustagi | TITLE: 10X Multiome TST Nuclei Isolation
AUTHORS: Sébastien Vigneau, Yashika_Rustagi
[DESCRIPTION]
This protocol describes the process of nuclei isolation from frozen tissue. The protocol has been slightly modified from the Nature Medicine RNA-Seq toolbox manuscript (Slyper et al., 2020) and applied to frozen melanoma... | ["[PREPARATION] Clean off bench space with RNAse away, then 70% EtOH.", "[PREPARATION] Set swing-bucket centrifuge to 4°C.", "[PREPARATION] Prepare tissue culture hood by turning off UV light, opening the sash, and allowing for the 3-minute ventilation. Clean off work area with 70% EtOH and check for any supplies neede... |
null | null | null | dx.doi.org/10.17504/protocols.io.kt8cwrw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol details the steps to annotate Anvi'o gene calls for function using Uproc. </p>
[STEPS]
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27,436 | Protocol for detect Trypanosoma cruzi by indirect methods as IIF, ELISA and IHA from serological samples | null | dx.doi.org/10.17504/protocols.io.62khgcw | null | Claudia Méndez, Maria Clara Duque, Yanira Romero, Julie Pérez, Omaira Rodríguez, Camilo A. Correa-Cárdenas, Maria Teresa Alvarado, Omar Cantillo-Barraza | TITLE: Protocol for detect Trypanosoma cruzi by indirect methods as IIF, ELISA and IHA from serological samples
AUTHORS: Claudia Méndez, Maria Clara Duque, Yanira Romero, Julie Pérez, Omaira Rodríguez, Camilo A. Correa-Cárdenas, Maria Teresa Alvarado, Omar Cantillo-Barraza
[DESCRIPTION]
<div class = "text-blocks"><div... | ["[Indirect Immunofluorescent (IIF) staining]\nIndirect Immunofluorescent (IIF) staining 1. Antigen-Antibody formation: The IIF staining was performed using antigen glass slides impregnated with trypomastigote forms of Chagas obtained from culture in house. A volume of 12 µL of the serum patients and controls (previous... |
null | null | null | dx.doi.org/10.17504/protocols.io.h4ib8ue | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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52,931 | Qiagen DNeasy 96 blood & tissue protocol for bee guts | 4 | dx.doi.org/10.17504/protocols.io.q26g78k23lwz/v1 | https://www.protocols.io/view/qiagen-dneasy-96-blood-amp-tissue-protocol-for-bee-bxxbppin | Lauren Ponisio, Jocelyn Zorn | TITLE: Qiagen DNeasy 96 blood & tissue protocol for bee guts
AUTHORS: Lauren Ponisio, Jocelyn Zorn
[DESCRIPTION]
Tissue protocol for bee guts.
[STEPS]
SECTION: Day 1
1. UV sterilize supplies for 2 96 well plates worth of extractions: 1 50mL centrifuge tube, 1 15mL centrifuge tube, 1 box 1,000uL pipette tips, 2... | ["[Day 1] UV sterilize supplies for 2 96 well plates worth of extractions: 1 50mL centrifuge tube, 1 15mL centrifuge tube, 1 box 1,000uL pipette tips, 2 boxes 200uL pipette tips, 24 elution microtube strip caps, steel beads, zirconia beads, and 1 reagent reservoir", "[Day 1] Combine 36 mL and 4000 µL in 50mL centri... |
54,179 | Experiment 3 | 1 | null | https://www.protocols.io/view/experiment-3-by6bpzan | Dikla Perez , Yael Steinhart , Amir Grinstein, Meike Morren | TITLE: Experiment 3
AUTHORS: Dikla Perez , Yael Steinhart , Amir Grinstein, Meike Morren
[DESCRIPTION]
This experiment had two main goals. First, it aimed to replicate and extend our previous results regarding H1 by using a different product category (a mouse pad) and a different expected-visibility manipulation. Spe... | ["Experimental design:\nWe have employed two expected-visibility conditions (high vs. low) in a between-subjects design.", "Sample:\nn = 154 panel participants (Mage= 29.14, SDage= 3.91, 55.2% women) were paid to take part in an online study. All participants were residents of Metropolis and had lived there for an av... |
40,074 | Toxicity assay for mosquito larvicidal activity | 3 | dx.doi.org/10.17504/protocols.io.bjdiki4e | https://www.protocols.io/view/toxicity-assay-for-mosquito-larvicidal-activity-bjdiki4e | avinash.kale | TITLE: Toxicity assay for mosquito larvicidal activity
AUTHORS: avinash.kale
[STEPS] | [] |
16,891 | Manual dissection of the Schistosoma mansoni and S. japonicum head and back end for transcriptomic analysis | null | dx.doi.org/10.17504/protocols.io.uq3evyn | null | null | TITLE: Manual dissection of the Schistosoma mansoni and S. japonicum head and back end for transcriptomic analysis
AUTHORS:
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Schistosomes are intravenous parasites with ability to survive in the mammalian host for decades, using its blood as a so... | ["[Place the Petri dish with worms on the microscope]\nTake the Petri dish out of the ice bath, touch it against a paper to remove the excess of water, place it under the stereomicroscope and adjust the focus.", "[Zoom in at the head of a worm]\nLook for a parasite with uncurled head/esophagus. Increase the lenses magn... |
37,477 | Axenic Diatoms cultures protocol | null | dx.doi.org/10.17504/protocols.io.bgudjws6 | https://www.protocols.io/view/axenic-diatoms-cultures-protocol-bgudjws6 | Mariella Ferrante, Rossella Annunziata, Monia Teresa Russo, Francesco Manfellotto | TITLE: Axenic Diatoms cultures protocol
AUTHORS: Mariella Ferrante, Rossella Annunziata, Monia Teresa Russo, Francesco Manfellotto
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Axenic cultures protocol</div><div class = "text-block">Axenicity of cultures is obtained by multi-antibiotic treatment: ... | ["[antibiotics concentration]\nThe antibiotics used are ampicillin, streptomycin and penicillin; We used the following final concentration:Ampicillin 0,7 mg/mlStreptomycin 0,1 mg/mlPenicillin 0,5 mg/ml", "[antibiotics concentration]\nAdd antibiotics in F/2 medium.Start from 20/50.000 cells in 25 ml of F/2 medium with a... |
20,162 | U Mass - Glucose Tolerance Test | null | dx.doi.org/10.17504/protocols.io.xxafpie | null | Jason Kim | TITLE: U Mass - Glucose Tolerance Test
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Glucose tolerance test measures systemic clearance of glucose following an intraperitoneal bolus injection of 20... | ["Mice may be fasted overnight (~15 hours) or for 5 hours prior to the start of experiment.", "Collect plasma sample (10 µl) before the start of experiment (basal-0 min) to measure basal glucose levels.", "Administer intraperitoneal injection of 20% dextrose (1 or 2 g/kg body weight) using an insulin syringe.", "Collec... |
44,688 | PCR Cleanup | 3 | dx.doi.org/10.17504/protocols.io.bpvqmn5w | https://www.protocols.io/view/pcr-cleanup-bpvqmn5w | Caroline Storer, Jiri Hulcr | TITLE: PCR Cleanup
AUTHORS: Caroline Storer, Jiri Hulcr
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol explain how to clean PCR products.</div></div>
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.icmcau6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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74,533 | Population relationships of Oomyzus scaposus (Hymenoptera: Eulophidae) | 1 | dx.doi.org/10.17504/protocols.io.81wgbynnqvpk/v1 | https://www.protocols.io/view/population-relationships-of-oomyzus-scaposus-hymen-ck2duya6 | nedved, Lida Fekrat | TITLE: Population relationships of Oomyzus scaposus (Hymenoptera: Eulophidae)
AUTHORS: nedved, Lida Fekrat
[DESCRIPTION]
Comparison of COI DNA barcodes from Iranian and other populations of Oomyzus scaposus and other species of Oomyzus.
[STEPS]
SECTION: Population relationships of Oomyzus scaposus (Thomson) (Hymenop... | ["[Population relationships of Oomyzus scaposus (Thomson) (Hymenoptera: Eulophidae)] We extracted DNA from the wasps using Tissue DNA genomic DNA extraction mini kit (Favorgen) according to the manufacturer’s instructions.", "[Population relationships of Oomyzus scaposus (Thomson) (Hymenoptera: Eulophidae)] Partial seq... |
82,671 | Cylinder behavior test | 4 | dx.doi.org/10.17504/protocols.io.eq2ly7m9qlx9/v1 | https://www.protocols.click/view/cylinder-behavior-test-cuypwxvn | Hong-Yuan Chu | TITLE: Cylinder behavior test
AUTHORS: Hong-Yuan Chu
[DESCRIPTION]
This protocol describes cylinder behavior test.
[STEPS]
SECTION: Procedure
1. Move the test mice from their housing room to the testing room and allow to acclimate for around 120 min.
SECTION: Procedure
2. Keep the test environment under dim white-lig... | ["[Procedure] Move the test mice from their housing room to the testing room and allow to acclimate for around 120 min.", "[Procedure] Keep the test environment under dim white-light illumination (around 150 lux).", "[Procedure] Place two mirrors perpendicular to each other to form a ninety-degree angle.", "[Procedure]... |
99,982 | Preparation of acid-washed glass coverslips for immunofluorescence microscopy | 0 | dx.doi.org/10.17504/protocols.io.6qpvr847blmk/v1 | https://www.protocols.io/view/preparation-of-acid-washed-glass-coverslips-for-im-ddvn265e | Jenna Ekstrom | TITLE: Preparation of acid-washed glass coverslips for immunofluorescence microscopy
AUTHORS: Jenna Ekstrom
[DESCRIPTION]
Rizzardi Lab (Adapted from Schwer Lab- UCSF)
[STEPS]
1. Add coverslips to 10cm culture dish
2. Add ~20 mL of 1 N HCl; swirl on orbital shaker for 2 h at RT.Room temperature
3. Remove acid, rinse... | ["Add coverslips to 10cm culture dish", "Add ~20 mL of 1 N HCl; swirl on orbital shaker for 2 h at RT.Room temperature", "Remove acid, rinse with 2 x 25 mL PBS until pH is at least 6.0.", "Rinse 1 x 25 mL water.", "Add ~20 mL of 70% EtOH; swirl on orbital shaker for 10 min, RT.Room temperature", "Remove ethanol, transf... |
76,915 | Periodic acid Schiff hematoxylin (PASH) staining for human retina | 4 | dx.doi.org/10.17504/protocols.io.n2bvj8qzwgk5/v1 | https://www.protocols.io/view/periodic-acid-schiff-hematoxylin-pash-staining-for-cpctviwn | Dongfeng Cao, Jeff D. Messinger, Angela Kruse, Jamie Allen, David Anderson, Christine A. Curcio, Jeff Spraggins | TITLE: Periodic acid Schiff hematoxylin (PASH) staining for human retina
AUTHORS: Dongfeng Cao, Jeff D. Messinger, Angela Kruse, Jamie Allen, David Anderson, Christine A. Curcio, Jeff Spraggins
[DESCRIPTION]
Periodic acid Schiff hematoxylin (PASH) staining protocol is adapted from other tissues to identify carb... | ["[PASH Staining] Remove glass slides with human retinal cryosections from -80 °C, keep on ice during transfer from freezer to bench.", "[PASH Staining] Put glass slides on slide warmer (Fisher, Cat# 120594) at 37 °C overnight to dehydrate.", "[PASH Staining] Label slides with PASH, date, and additional relevant inform... |
38,580 | PONE-S-20-05322-2 DATA SETS, BOX PLOTS and GRAPHS | 2 | dx.doi.org/10.17504/protocols.io.bhwuj7ew | https://www.protocols.io/view/pone-s-20-05322-2-data-sets-box-plots-and-graphs-bhwuj7ew | Kameran Lashkari, Gianna Teague, Ursula Beattie, Joanna Betts, Megan M McLaughlin, Francisco J Lopez | TITLE: PONE-S-20-05322-2 DATA SETS, BOX PLOTS and GRAPHS
AUTHORS: Kameran Lashkari, Gianna Teague, Ursula Beattie, Joanna Betts, Megan M McLaughlin, Francisco J Lopez
[STEPS] | [] |
92,648 | Fiber Photometry Acquisition | 1 | dx.doi.org/10.17504/protocols.io.bp2l6xz5dlqe/v1 | https://www.protocols.io/view/fiber-photometry-acquisition-c6qgzdtw | Jonathan Tang | TITLE: Fiber Photometry Acquisition
AUTHORS: Jonathan Tang
[DESCRIPTION]
Fiber Photometry Acquisition parameters and protocol for Tang et al 2023.
[BEFORE_START]
Mice have undergone surgery 1 month prior to the acquisition.
[GUIDELINES]
Closed-Loop Optogenetics Setup and Parameters:
For close loop optogenetics,... | ["[Habituation] One-month post-surgery, mice were habituated to head-mounted equipment for 2 days. \n\nOn day 1, an actual or mock wireless inertial sensor(~2.5 cm H x 1 cm L x 0.5 cm W with ~ 2.5-3.0 cm antennae, ~1.8 g weight)glued to the 4-position connector(Harwin Inc., M52-040023V0445) was attached to the implante... |
70,233 | Preparation of 1L of Nematode Growth Medium (NGM) | 4 | dx.doi.org/10.17504/protocols.io.81wgby1jnvpk/v1 | https://www.protocols.io/view/preparation-of-1l-of-nematode-growth-medium-ngm-cgtztwp6 | Alfonso Pérez Escudero, gabrielmadirolas, Alid Al-Asmar | TITLE: Preparation of 1L of Nematode Growth Medium (NGM)
AUTHORS: Alfonso Pérez Escudero, gabrielmadirolas, Alid Al-Asmar
[DESCRIPTION]
Original source of the protocol: WormBook Methods http://www.wormbook.org/chapters/www_strainmaintain/strainmaintain.html.
This protocol is for making Nematode Growth Medium (NGM), a... | ["In order to perform this protocol, you will need the following solutions:\n 5mg/mL cholesterol in absolute ethanol (do not autoclave) (stored in freezer)\npH=6 phosphate buffer (as prepared in: https://www.protocols.io/view/preparation-of-0-5l-of-phosphate-buffer-ph-6-0-n2bvj8r7bgk5/v1)\n1M magnesium sulfate (as prep... |
53,314 | 0.05 M Glycine | 4 | dx.doi.org/10.17504/protocols.io.bybapsie | https://www.protocols.io/view/0-05-m-glycine-bybapsie | Jacquelina.Woods | TITLE: 0.05 M Glycine
AUTHORS: Jacquelina.Woods
[DESCRIPTION]
This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wastewater. Protocols developed for this project cover wastewater collection, concentratio... | ["Mix 3.75 g in deionized or ultrapure water to 1 L", "Adjust pH 9.5", "Autoclave 121 °C15 min", "Store at 2-8 °C"] |
null | null | null | dx.doi.org/10.17504/protocols.io.jhxcj7n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>In order to determine the consequence of <em>ILDR1</em> reported mutations on splicing and translation initiation, we used Human Splicing Finder (version 3.0) (http://www.umd.be/HSF3/) and ORF finder (http://www.geneinfinity.org/sms/sms_orffinder.html) respectively.</p>
[STE... | [] |
80,348 | PotatoMASH library construction | 4 | dx.doi.org/10.17504/protocols.io.e6nvw53zdvmk/v2 | https://www.protocols.io/view/potatomash-library-construction-csp4wdqw | Maria de la O Leyva Perez, Lea Vexler, Dan Milbourne | TITLE: PotatoMASH library construction
AUTHORS: Maria de la O Leyva Perez, Lea Vexler, Dan Milbourne
[DESCRIPTION]
We have developed PotatoMASH (Potato Multi-Allele Scanning Haplotags), a novel low cost, genome-scanning marker platform. We designed a panel of 339 multi-allelic regions placed at 1 Mb intervals througho... | ["[Organize your samples in 96 well plates, quantitate template DNA, and normalize at 20ng/uL.] Quantification with PicoGreen\nIn the preparation for the library construction, the first step is to quantify the template DNA. We used Quant-iT™ PicoGreen ® dsDNA assay kit (Invitrogen, P7589)as detailed below: \n\nThe Quan... |
null | null | null | dx.doi.org/10.17504/protocols.io.dar2d5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<strong>Purpose:</strong> This protocol describes how to adsorb viruses onto TEM (transmission electron microscopy) grids. The sample is allowed to sit on a hydrophilic grid and viruses adsorb onto the surface of the grid. This technique is generally used for viral lysates with ... | [] |
60,387 | TELEvir Field Protocol | 1 | dx.doi.org/10.17504/protocols.io.n2bvj694xlk5/v1 | https://www.protocols.click/view/televir-field-protocol-b68brhsn | Anna S Fomsgaard | TITLE: TELEvir Field Protocol
AUTHORS: Anna S Fomsgaard
[DESCRIPTION]
The TELE-Vir project key aim is to develop a fast point-of-incidence (poi) toolbox for identification and characterisation of emerging virus threats for humans and/or domestic and wildlife animals.
Presented here is a protocol including sample pre... | ["[Pretreatment] 400 µL \n50 µL \n50 µL \n15 min", "[Pretreatment] Add 500 µL (or equivalent to 1 ml sample material in total)", "[Pretreatment] Poor the diluted sample into the lid of the Syringe Filter (Minsart). The filter can be placed on a sterile surface meanwhile e.g. the Syringe Filter paper lid (inner side)."... |
46,346 | TD test protocol 9/26/19 | 4 | null | https://www.protocols.io/view/td-test-protocol-9-26-19-brhim34e | Elizabeth Fozo | TITLE: TD test protocol 9/26/19
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Tolerance detection test</div><div class = "text-block">Bikash(Adapted from(Gefen et al. 2017), Scientific reports)</div></div>
[STEPS]
?. [TD test: Step 1 - Day 1]
Preparation of Mueller-Hinton... | ["[TD test: Step 1 - Day 1]\nPreparation of Mueller-Hinton plate (Hudzicki n.d.)", "[TD test: Step 1 - Day 1]\nAllow an MH agar plate (one for each organism to be tested) to come to room temperature. It is preferable to allow the plates to remain in the plastic sleeve while they warm to minimize condensation.", "[TD ... |
45,686 | Topological indexes and community structure for urban mobility networks: variations in a business day | 5 | null | https://www.protocols.io/view/topological-indexes-and-community-structure-for-ur-bquwmwxe | Jessica Domingues Lamosa, Lívia R Tomás, Marcos G. Quiles, Luciana R. Londe, Leonardo B L Santos, Elbert E. Macau | TITLE: Topological indexes and community structure for urban mobility networks: variations in a business day
AUTHORS: Jessica Domingues Lamosa, Lívia R Tomás, Marcos G. Quiles, Luciana R. Londe, Leonardo B L Santos, Elbert E. Macau
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This work fo-cused i... | ["[The whole procedure]\nThe whole procedure used:", "The mobility data:", "[Preprocessing]\nPreprocessing in C++", "[Preprocessing]\nInput data: csv file with 5 columns: ZONE_ORIGIN, STARTING_TIME, ZONE_DESTINATION, ARRIVAL_TIME, SAMPLING", "[Preprocessing]\nTime, origin and destination represented in a matrix form ... |
77,653 | MoDC immunogenicity assay | 4 | null | https://www.protocols.io/view/modc-immunogenicity-assay-cp3vvqn6 | Annabel J Curle, Sarah Howlett, Joanne Jones | TITLE: MoDC immunogenicity assay
AUTHORS: Annabel J Curle, Sarah Howlett, Joanne Jones
[DESCRIPTION]
The monocyte-derived dendritic cell (moDC) immunogenicity assay can be utilised to test immunogenicity of different cell types. Similar to the mixed lymphocyte reaction (MLR) assay, cells of interest are co-cultured wi... | ["[Cell preparations and moDC differentiation - Day 0-7] Make PBMCs using preferred method from whole blood", "[Cell preparations and moDC differentiation - Day 0-7] Take whole PBMCs and enrich for CD14+ cells using magnetic activated cell sorting (MACS) with CD14+ microbeads", "[Cell preparations and moDC differentiat... |
68,870 | Measuring tension and calcium imaging within cell subtypes of the colon in response to vagus nerve stimulation | 4 | dx.doi.org/10.17504/protocols.io.x54v9y9wzg3e/v1 | https://www.protocols.io/view/measuring-tension-and-calcium-imaging-within-cell-cfhetj3e | Dante Heredia, Thomas Gould | TITLE: Measuring tension and calcium imaging within cell subtypes of the colon in response to vagus nerve stimulation
AUTHORS: Dante Heredia, Thomas Gould
[DESCRIPTION]
Protocol for measuring tension and activity in distinct cell types of the colon in response to stimulation of the vagus nerve in an ex vivo preparatio... | ["The entire gut, including esophagus with vagus nerve trunks attached, and stomach and intestines and mesentery, is dissected and placed in a dish with oxygenated Krebs-Ringers solution. The small intestine, as well as pancreas and spleen, are removed carefully. The colon is pinned and gently flushed of its contents... |
49,990 | Prediction of COVID-19 prognosis using machine learning techniques: a systematic review | 1 | dx.doi.org/10.17504/protocols.io.bu3enyje | https://www.protocols.io/view/prediction-of-covid-19-prognosis-using-machine-lea-bu3enyje | Alexandre Negrao Pantaleao, Carolina Sant' Anna Filipin, Larissa Braga Costa, Luiza Coimbra Teixeira, Renata Araujo Avendanha, Tainara Lima Fernandes, Zilma Reis | TITLE: Prediction of COVID-19 prognosis using machine learning techniques: a systematic review
AUTHORS: Alexandre Negrao Pantaleao, Carolina Sant' Anna Filipin, Larissa Braga Costa, Luiza Coimbra Teixeira, Renata Araujo Avendanha, Tainara Lima Fernandes, Zilma Reis
[DESCRIPTION]
<div class = "text-blocks"><div class =... | ["[METHODS]\nCritérios de elegibilidade/ Elegibility CriteriaEstudos relatando o uso de tecnologias de aprendizado de máquina para a previsão do prognóstico de pacientes com COVID-19.Os critérios de inclusão foram:(1) Pacientes com diagnóstico de COVID-19 confirmado por exame RT-PCR;(2) Pacientes hospitalizados;(3) Uso... |
100,108 | KAT8 compound inhibition inhibits the initial steps of PINK1-dependant mitophagy | 4 | dx.doi.org/10.17504/protocols.io.eq2ly7m8qlx9/v3 | https://www.protocols.io/view/kat8-compound-inhibition-inhibits-the-initial-step-ddzk274w | Capucine de Talhouet, Benjamin O'Callaghan, Helene Plun-Favreau, Noemi Esteras, Marc P. M. Soutar | TITLE: KAT8 compound inhibition inhibits the initial steps of PINK1-dependant mitophagy
AUTHORS: Capucine de Talhouet, Benjamin O'Callaghan, Helene Plun-Favreau, Noemi Esteras, Marc P. M. Soutar
[DESCRIPTION]
It has recently been shown that KAT8, a genome-wide association study candidate risk gene for Parkinson’s Dise... | ["[Cell Culture] Maintain cells in culture in a humified 5% CO2 incubator at 37 °C in Dulbecco's modified Eagle's medium (DMEM, Gibco, 11995-065) supplemented with 10% heat-inactivated foetal bovine serum (FBS, Gibco). Change cell medium every 3 days.", "[Cell Culture] Split cells at 75% to 90% confluency using 2 mL of... |
20,025 | SPARC RNEL Bladder January 2019 protocol | 1 | dx.doi.org/10.17504/protocols.io.xszfnf6 | https://www.protocols.io/view/sparc-rnel-bladder-january-2019-protocol-xszfnf6 | Max Novelli | TITLE: SPARC RNEL Bladder January 2019 protocol
AUTHORS: Max Novelli
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;"> </span><span style = "font-weight:bold;">Protocol for dataset “RNEL Bladder January 2019”</span><span></span></div><div class = "text-block">Lower u... | ["[Surgical Preparation]\nAnesthetize animal and maintain physiological parameters throughout procedure", "[Surgical Preparation]\nPlace animal in the supine position, place tracheostomy tube and place invasive blood pressure measurement catheter.", "[Surgical Preparation]\nMake a midline abdominal incision to expose b... |
88,453 | DNA Cloning (Gibson Assembly, Transformation, Plating and Incubation) | 1 | dx.doi.org/10.17504/protocols.io.8epv5xnddg1b/v1 | https://www.protocols.io/view/dna-cloning-gibson-assembly-transformation-plating-c2mdyc26 | NUS iGEM | TITLE: DNA Cloning (Gibson Assembly, Transformation, Plating and Incubation)
AUTHORS: NUS iGEM
[DESCRIPTION]
2023 NUS-Singapore iGEM Team followed this protocol to construct the plasmid of interest or to clone the plasmid of interest.
[STEPS]
SECTION: Gibson Assembly
1. Calculate the volumes of respective DNA fragmen... | ["[Gibson Assembly] Calculate the volumes of respective DNA fragments to assemble based on their length and concentration. (The maximum final volume of the mixed fragments is 5 µL for each reaction.)", "[Gibson Assembly] Add the DNA fragments into a PCR tube according to the volumes obtained from the calculation.", "[G... |
null | null | null | dx.doi.org/10.17504/protocols.io.dkm4u5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol is suitable for both endogeneous and overexpressed protein immunoprecipitations.
[STEPS]
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76,076 | RNA isolation protocol from unwilling plant tissue | 4 | dx.doi.org/10.17504/protocols.io.5jyl8j6n7g2w/v1 | https://www.protocols.io/view/rna-isolation-protocol-from-unwilling-plant-tissue-cnikvccw | Samuel Parra | TITLE: RNA isolation protocol from unwilling plant tissue
AUTHORS: Samuel Parra
[DESCRIPTION]
This protocol is intended for HIGH quality RNA extraction from plan tissues
We used this protocol after several attempts with Trizol, Qiagen RNeasy plant kit and other protocols with no ressults.
This procedure redered us be... | ["[RNA isolation protocol] This protocol is an adaptation of https://doi.org/10.1007/BF02670468 designed for extraction of RNA from pine needles with high polyphenolic compounds or high sugar content.\n\nFor all buffers use DEPC treated water or Nuclease free ddH2O", "[RNA isolation protocol] Reagents", "[RNA isolation... |
54,102 | Steps for setup of AWS organization, S3 data storage, and EC2 computing for using Python notebooks | 5 | dx.doi.org/10.17504/protocols.io.rm7vz3z4xgx1/v1 | https://www.protocols.io/view/steps-for-setup-of-aws-organization-s3-data-storag-by3wpype | Daniel J. Pollak, Gautam Chawla, Andrey Andreev, David A. Prober | TITLE: Steps for setup of AWS organization, S3 data storage, and EC2 computing for using Python notebooks
AUTHORS: Daniel J. Pollak, Gautam Chawla, Andrey Andreev, David A. Prober
[DESCRIPTION]
With the oncoming age of big data, biologists are encountering more use cases for cloud-based computing to streamline data pr... | ["[Setting organization and budget management] Setting up a Root account", "[Setting organization and budget management] Create “root” account for your organization, using Business account type", "[Setting organization and budget management] If you are using GMail account to manage other services in your lab, for examp... |
102,273 | Retrospective observational study in patients with onychomycosis treated with Mycoclear and ciclopirox | 0 | dx.doi.org/10.17504/protocols.io.j8nlk8d6dl5r/v1 | https://www.protocols.io/view/retrospective-observational-study-in-patients-with-df493qz6 | Michela Valeria Rita Starace, Bianca Maria Piraccini, Aurora Alessandrini | TITLE: Retrospective observational study in patients with onychomycosis treated with Mycoclear and ciclopirox
AUTHORS: Michela Valeria Rita Starace, Bianca Maria Piraccini, Aurora Alessandrini
[DESCRIPTION]
The prevalence of onychomycosis in adults varies considerably between countries. In
a recent survey conducted in... | ["[Authors] Dr. Michela Valeria Rita Starace\nProf. Bianca Maria Piraccini\nDr. Aurora Alessandrini", "[Code and version] Code of the study: ONYCO/23\nProtocol version: 1.0\nDate: May 15, 2024", "[Title] Retrospective, observational study in patients with onychomycosis treated with Mycoclear and ciclopirox", "[Backgrou... |
76,951 | Antiangiogenic research using AgNPs-FD | 1 | dx.doi.org/10.17504/protocols.io.14egn2nj6g5d/v1 | https://www.protocols.io/view/antiangiogenic-research-using-agnps-fd-cpdxvi7n | Rudy Agung Nugroho | TITLE: Antiangiogenic research using AgNPs-FD
AUTHORS: Rudy Agung Nugroho
[DESCRIPTION]
Background: Ficus deltoidea L. Jack is a folk medicinal plant known for its pharmacological properties, including anti-inflammatory, anticancer, and anti-angiogenic. This study aimed to evaluate the anti-angiogenic properties of si... | ["[Biosynthesis of AgNPs-Fd] Aqueous silver nitrate (AgNO3) (100 mL, 1 mM) was combined with 100 mL 0.1%F. deltoidealeaf extract.", "[Characterization of AgNPs-Fd] To determine phytochemicals surrounding the AgNPs-Fd, FTIR spectroscopy (Agilent, Cary 630 model, US) was performed", "[Characterization of AgNPs-Fd] The TE... |
91,659 | Visium CytAssist FFPE -- University of Minnesota TMCs | 1 | dx.doi.org/10.17504/protocols.io.n92ldmn99l5b/v1 | https://www.protocols.io/view/visium-cytassist-ffpe-university-of-minnesota-tmcs-c5rjy54n | Laura J Niedernhofer, David A Bernlohr | TITLE: Visium CytAssist FFPE -- University of Minnesota TMCs
AUTHORS: Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
The Visium CytAssist Spatial Gene Expression for FFPE assay is designed to analyze mRNA in
tissue sections derived from formalin fixed & paraffin embedded (FFPE) tissue samples. The Visium
CytAssi... | ["[Deparaffinization, H&E Staining, Imaging & Decrosslinking]", "[Library Preparation & Sequencing]", "[FASTQ Generation] BCL data from Illumina sequencer is demultiplexed and converted into FASTQ format using bcl2fastq software version 2.20.0"] |
63,406 | Prima Slimming Pills UK : Expert Reviews Of This Product? | 1 | dx.doi.org/10.17504/protocols.io.261genj6yg47/v1 | https://www.protocols.io/view/prima-slimming-pills-uk-expert-reviews-of-this-pro-b96nr9de | roxyhime | TITLE: Prima Slimming Pills UK : Expert Reviews Of This Product?
AUTHORS: roxyhime
[DESCRIPTION]
Prima Slimming Pills UK Obesity issues are growing rapidly in the world. If you will not take care of your health and will keep on eating unhealthy food regularly, then it may affect your health in several negative ways.... | ["[Prima Slimming Pills UK] There are many times when you purchase a product and while you are using it, you observe that it is not being useful to you and all the promises which manufacturers made while selling this product were all fake? So if you're having the same queries with the Prima Slimming Pills UK product, t... |
76,485 | Labeling of Dense Light Data in Amira 3D 2022.1 Classic Segmentation Workroom | 1 | dx.doi.org/10.17504/protocols.io.dm6gpjx6pgzp/v1 | https://www.protocols.io/view/labeling-of-dense-light-data-in-amira-3d-2022-1-cl-cnxdvfi6 | Alyson Petruncio, CellMap Project Team | TITLE: Labeling of Dense Light Data in Amira 3D 2022.1 Classic Segmentation Workroom
AUTHORS: Alyson Petruncio, CellMap Project Team
[DESCRIPTION]
This protocol is optimized for densely labeling high dynamic range light data subvolumes requiring unique identification of each expressed structure.
Segmentation Summary
... | ["[Amira Project and Segmentation Setup] After opening a new Amira project, select File → Open Data, or click and drag the raw data tiff to the empty space under the Project tab. Confirm coordinates and voxel size in the Image Read Parameters window. \n\nFor higher label resolution: Select the arrow of the raw data obj... |
65,363 | Twin Elements CBD Gummies (NEW 2022!) Does It Work Or Just Scam? | 3 | dx.doi.org/10.17504/protocols.io.n2bvj61pplk5/v1 | https://www.protocols.io/view/twin-elements-cbd-gummies-new-2022-does-it-work-or-cb3tsqnn | Twin Elements CBD Gummies | TITLE: Twin Elements CBD Gummies (NEW 2022!) Does It Work Or Just Scam?
AUTHORS: Twin Elements CBD Gummies
[DESCRIPTION]
MUST CHECK: *Special Discounted Pricing Available For The First 50 Customers Only! (ORDER Twin Elements CBD Gummies)
[STEPS] | [] |
28,246 | MojoSort™ Selection Kits Column Protocol - 4 | null | dx.doi.org/10.17504/protocols.io.7twhnpe | null | Sam Li | TITLE: MojoSort™ Selection Kits Column Protocol - 4
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>BioLegend MojoSort™ nanobeads work in commonly used separation columns, based on our internal research as well as validation by external testing by academic labs. This simple pro... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes. 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) ... |
67,555 | Dilutions and Pipetting Practice (Instructor Protocol) | 4 | null | https://www.protocols.io/view/dilutions-and-pipetting-practice-instructor-protoc-cd8bs9sn | Brian P Teague | TITLE: Dilutions and Pipetting Practice (Instructor Protocol)
AUTHORS: Brian P Teague
[DESCRIPTION]
This is the instructor protocol for
It contains setup instructions and instructor tips for running the lab.
[STEPS]
SECTION: Lab Setup
1. In the conical tubes, add 500 µl of food coloring to 9.5 ml of tap water to ma... | ["[Lab Setup] In the conical tubes, add 500 µl of food coloring to 9.5 ml of tap water to make the \"10X stocks.\" Make a stock for each color.", "[Lab Setup] Transfer 500 µLof each stock into a microcentrifuge tubes. Label them appropriately.", "[Instructor Tips & Common Student Errors] Instructor Tips\nI often st... |
78,167 | High-throughput physiological profiling of endosymbiotic dinoflagellates (Symbiodiniaceae) using flow cytometry | 4 | dx.doi.org/10.17504/protocols.io.dm6gpjr2jgzp/v2 | https://www.protocols.io/view/high-throughput-physiological-profiling-of-endosym-cqjxvupn | Colin J Anthony, Colin Lock, Bastian Bentlage | TITLE: High-throughput physiological profiling of endosymbiotic dinoflagellates (Symbiodiniaceae) using flow cytometry
AUTHORS: Colin J Anthony, Colin Lock, Bastian Bentlage
[DESCRIPTION]
This protocol quantifies light-harvesting complex (LHC) and antioxidant pigments, while simultaneously determining cell density of ... | ["[Sample Preservation] Sample tissue from cnidarian\nIf calcifying coral, we suggest 3 pieces at around 2 cm3 sampled with wire cutters or hammer and chisel \nIf gelatinous cnidarian, 0.05 - 0.1 g of tissue sampled with sterile scissors works well", "[Sample Preservation] Store tissue in bag or tube\nFor calcifiers, W... |
108,394 | Studying viscerofugal neurons in human colon | 0 | dx.doi.org/10.17504/protocols.io.x54v92xy1l3e/v1 | https://www.protocols.io/view/studying-viscerofugal-neurons-in-human-colon-dm4i48ue | Bao Nan Chen, Adam G Humenick, Simon Brookes | TITLE: Studying viscerofugal neurons in human colon
AUTHORS: Bao Nan Chen, Adam G Humenick, Simon Brookes
[DESCRIPTION]
This protocol explains how viscerofugal neurons can be studied in ex vivo specimens of human colon. Viscerofugal neurons are characterized by having cell bodies in myenteric ganglia and axons that p... | ["[Collecting tissue] All handling of un-fixed (live) human tissue must be exclusively done by staff trained in occupational health and safety requirements for handling hazardous material, wearing appropriate PPE (personal protective equipment) (gloves, gowns and masks) and working in areas designated for human tissue,... |
49,682 | Generation of an isogenic set of HD model hESC lines | 1 | dx.doi.org/10.17504/protocols.io.bursnv6e | https://www.protocols.io/view/generation-of-an-isogenic-set-of-hd-model-hesc-lin-bursnv6e | Albert Ruzo, Gist F. Croft, Jakob J. Metzger, Szilvia Galgoczi, Lauren J. Gerber, Cecilia Pellegrini, Hanbin Wang Jr, Maria Fenner, Stephanie Tse, Adam Marks, Corbyn Nchako, Ali H. Brivanlou | TITLE: Generation of an isogenic set of HD model hESC lines
AUTHORS: Albert Ruzo, Gist F. Croft, Jakob J. Metzger, Szilvia Galgoczi, Lauren J. Gerber, Cecilia Pellegrini, Hanbin Wang Jr, Maria Fenner, Stephanie Tse, Adam Marks, Corbyn Nchako, Ali H. Brivanlou
[DESCRIPTION]
<div class = "text-blocks"><div class = "text... | ["[Generation of an isogenic set of HD model hESC lines]\nIn order to establish an optimal platform for understanding the effects of HD mutations, use CRISPR/Cas9 technology to generate a set of isogenic hESC lines that would differ only in the HTT locus, bearing different lengths of the CAG tract.", "[Generation of an... |
47,308 | UCSF CAT COVID-19 Tailed 275bp v3 ARTIC protocol v1 | 1 | null | https://www.protocols.io/view/ucsf-cat-covid-19-tailed-275bp-v3-artic-protocol-v-bsfknbkw | Delsy Martinez, Tyler Miyasaki, Eric Chow | TITLE: UCSF CAT COVID-19 Tailed 275bp v3 ARTIC protocol v1
AUTHORS: Delsy Martinez, Tyler Miyasaki, Eric Chow
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left"><span>This is a tailed amplicon method similar to </span><a href="https://www.protocols.i... | ["[cDNA generation]\nImportant! This step must be performed in a RNase free, pre-PCR environment in which post PCR COVID-19 amplicons are not present, to minimise risk of sample contamination.Decontaminate bench surfaces, pipettes and gloves with RNase ZAP before starting work. Keep reagents and samples chilled through... |
101,975 | EB Formation using Aggrewell 400/800 | 0 | dx.doi.org/10.17504/protocols.io.14egn64bpl5d/v1 | https://www.protocols.io/view/eb-formation-using-aggrewell-400-800-dftx3npn | Niraj Sawarkar, Regine Tipon, Yasmine Nonose, Gist Croft | TITLE: EB Formation using Aggrewell 400/800
AUTHORS: Niraj Sawarkar, Regine Tipon, Yasmine Nonose, Gist Croft
[DESCRIPTION]
Embryoid body formation is the aggregate formation of hPS cells in a three-dimensional format to differentiate into specific lineages. In this,protocol we would discuss some important steps to en... | ["[A. PREPARATION OF EBs using AGGREWEL 400/800 PLATES] Add 2 mL of AggreWell Anti-adherence reagent Solution to each well to be used.", "[A. PREPARATION OF EBs using AGGREWEL 400/800 PLATES] Centrifuge plate at 2000 x g (or maximum speed) for 5 minutes. Check for bubbles under the microscope, and spin again if needed.... |
null | null | null | dx.doi.org/10.17504/protocols.io.kghctt6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Assay to obtain plaque forming units of mammalian orthoreovirus</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ue8ethw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
The following protocol pools miniaturized PCR replicates from (2) different 384-well plates into (1) final 384-well plate using the epMotion 5075. The miniaturized PCR reaction was done in triplicate across (3) 384-well plates and the third PCR plate will be the final storage pl... | ["[Prepare PCR plates] If needed, thaw PCR plates, then centrifuge them.", "[Setup epMotion automation platform] {\"blocks\":[{\"key\":\"6kdmg\",\"text\":\"\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"a41oc\",\"text\":\" \",\"type\":\"atomic\",\"depth\":0,\"i... |
28,772 | DNA Extraction | null | dx.doi.org/10.17504/protocols.io.8cchssw | null | Stefania Konstantinidi, Hana Samet | TITLE: DNA Extraction
AUTHORS: Stefania Konstantinidi, Hana Samet
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The goal is to extract DNA from plant leaves using a microneedle patch.</div></div>
[STEPS]
?. [Application of microneedle patch]
Place the microneedle patch between the base and the mi... | ["[Application of microneedle patch]\nPlace the microneedle patch between the base and the midrib of the leaf and apply pressure for a few seconds.", "[Application of microneedle patch]\nCarefully remove the microneedle and put is in a petri dish.", "[Application of microneedle patch]\nAdd 100uL of EB buffer on the mic... |
103,474 | Nuclei Isolation from Human Cartilage for 10x Multiome | 0 | dx.doi.org/10.17504/protocols.io.rm7vzj7q5lx1/v1 | https://www.protocols.io/view/nuclei-isolation-from-human-cartilage-for-10x-mult-dhas32ee | Takuya Sakamoto, Erpei Wang, Merissa Olmer, Martin Lotz | TITLE: Nuclei Isolation from Human Cartilage for 10x Multiome
AUTHORS: Takuya Sakamoto, Erpei Wang, Merissa Olmer, Martin Lotz
[DESCRIPTION]
This protocol describes isolation of nuclei from fresh-frozen human knee cartilage for use in Omics analyses, including RNA-sequencing of ATAC-sequencing. Tissue dissociation was... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ta4eigw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div>
<p>In the study we have used a standard Thermo Scientific TaqMan protocol which can be found under this link:</p>
</div>
<div> </div>
<div>http://tools.thermofisher.com/content/sfs/brochures/taqman-assay-genetic-variation-research-br.pdf</div>
[GUIDELINES]
<div>
<p>In the... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.eycbfsw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
K-mer-based approaches to determining sequence similiarity can be faster than traditional use of BLAST. This application uses <a href="http://www.genome.umd.edu/jellyfish.html" target="_blank">Jellyfish</a> to index host FASTA files, then uses the mode value (default 2) of the ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.nwadfae | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><span style="font-weight: 400;">Este protocolo describe como aislar bacterias mótiles del género P</span><em><span style="font-weight: 400;">aenibacillus</span></em><span style="font-weight: 400;"> a partir de muestras ambientales. El protocolo no involucra material de labora... | [] |
68,889 | Electron microscopy (EM) analysis of LRRK2-Nanotube assembles | 1 | dx.doi.org/10.17504/protocols.io.3byl4bmdzvo5/v1 | https://www.protocols.io/view/electron-microscopy-em-analysis-of-lrrk2-nanotube-cfhztj76 | Xinbo Wang, Pietro De Camilli | TITLE: Electron microscopy (EM) analysis of LRRK2-Nanotube assembles
AUTHORS: Xinbo Wang, Pietro De Camilli
[DESCRIPTION]
This protocol details methods for the analysis of LRRK2-Nanotube assembles by negative stained EM and Cryo-EM.
[STEPS]
SECTION: Negative stained EM analysis
1. Prepare samples in a PCR tube with 3... | ["[Negative stained EM analysis] Prepare samples in a PCR tube with 300 nanomolar (nM) LRKK2, 20 micromolar (µM) lipid nanotubes and 1 millimolar (mM) GMPPNP.", "[Negative stained EM analysis] Incubate samples at 37 °C for 30 min.", "[Negative stained EM analysis] Glow-discharge carbon-coated grids (25 mA, 45 s) during... |
95,633 | Sleep scoring using Neuroscore | 0 | dx.doi.org/10.17504/protocols.io.81wgbxjdolpk/v1 | https://www.protocols.io/view/sleep-scoring-using-neuroscore-c9mrz456 | daniel.dautan daniel, Per Svenningsson | TITLE: Sleep scoring using Neuroscore
AUTHORS: daniel.dautan daniel, Per Svenningsson
[DESCRIPTION]
Analysis of sleep data using Neuroscore v.30
[STEPS]
1. Open the file using File – Open Recording – Browse – Open
2. Remove unused signals using the right side tools “signal & data” and unselect all markers:
3. Ide... | ["Open the file using File – Open Recording – Browse – Open", "Remove unused signals using the right side tools “signal & data” and unselect all markers:", "Identify the EEG and EMG signals by adjusting the time windows:", "If the signal is unusable, just move to another recording. Here the top signal is EMG and bottom... |
63,859 | Via Keto Gummies | 3 | dx.doi.org/10.17504/protocols.io.n92ldzjdxv5b/v1 | https://www.protocols.io/view/via-keto-gummies-caktscwn | PelterBugs | TITLE: Via Keto Gummies
AUTHORS: PelterBugs
[DESCRIPTION]
Via keto Gummies Weight Loss If you want to lose weight naturally. It is made up of all-natural ingredients that help the users in losing healthy and faster weight.
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.f5ebq3e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="column">The steps for preparing the lysate are different depending on the starting material. Please ensure you follow the correct procedure for your starting material (see the section <a href="https://www.protocols.io/view/genomic-dna-removal-and-total-rna-purificati... | [] |
63,861 | Via Keto Gummies | 3 | dx.doi.org/10.17504/protocols.io.dm6gpb2nplzp/v1 | https://www.protocols.io/view/via-keto-gummies-cakvscw6 | PelterBugs | TITLE: Via Keto Gummies
AUTHORS: PelterBugs
[DESCRIPTION]
Via keto Gummies Weight Loss If you want to lose weight naturally. It is made up of all-natural ingredients that help the users in losing healthy and faster weight.
[STEPS] | [] |
77,991 | Drug treatment in Zebrabox | 4 | dx.doi.org/10.17504/protocols.io.4r3l27p6pg1y/v1 | https://www.protocols.io/view/drug-treatment-in-zebrabox-cqefvtbn | FishFloorUCL | TITLE: Drug treatment in Zebrabox
AUTHORS: FishFloorUCL
[DESCRIPTION]
How to do a standard Rihel lab behaviour tracking experiment with drug treatment.
[STEPS]
SECTION: Design your experiment
1. Figure out if the drug you will use has good solubility in water.
Ideal case is to find a publication which has used the d... | ["[Design your experiment] Figure out if the drug you will use has good solubility in water.\n\nIdeal case is to find a publication which has used the drug in zebrafish larvae. Alternatively, you will often be able to find the solubility on PubChem.\n\nThe present protocol will assume the drug is soluble in water.", "[... |
39,570 | Mass testing equity during infectious disease outbreaks: a scoping review. | 1 | dx.doi.org/10.17504/protocols.io.bivske6e | https://www.protocols.io/view/mass-testing-equity-during-infectious-disease-outb-bivske6e | Katarina Ost, Kate Zinszer, Isadora Mathevet, Lola Traverson, Valery Ridde | TITLE: Mass testing equity during infectious disease outbreaks: a scoping review.
AUTHORS: Katarina Ost, Kate Zinszer, Isadora Mathevet, Lola Traverson, Valery Ridde
[STEPS]
?. [Title and author identification]
Mass testing equity during infectious disease outbreaks: a scoping review.Katarina Ost1, Isadora Mathevet2,... | ["[Title and author identification]\nMass testing equity during infectious disease outbreaks: a scoping review.Katarina Ost1, Isadora Mathevet2, Lola Traverson2, Valéry Ridde2, Kate Zinszer1,31. Centre de recherche en santé publique, Montréal, Canada.2. CEPED, Institute for Research on Sustainable Development, IRD-Univ... |
48,199 | Chimeric Protein-LAG and Protein-AG sandwich ELISA | 1 | dx.doi.org/10.17504/protocols.io.btbfnijn | https://www.protocols.io/view/chimeric-protein-lag-and-protein-ag-sandwich-elisa-btbfnijn | Angel Justiz-Vaillant | TITLE: Chimeric Protein-LAG and Protein-AG sandwich ELISA
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This ELISA was used to study the interactions between protein-LAG (PLAG) and protein-AG (SpAG) with different immunoglobulin preparations from mammalian and avi... | ["This ELISA was used to study the interactions between protein-LAG (PLAG) and protein-AG (SpAG) with different immunoglobulin preparations from mammalian and avian species. The 96 well microtiter plate was coated overnight at 4°C with 2 µg/µl per well of PLAG in carbonate-bicarbonate buffer pH 9.6.", "The plate was th... |
20,442 | Soil Sampling and Preparation for Soil Chemical Analysis | null | dx.doi.org/10.17504/protocols.io.x72frqe | null | Matema Imakumbili | TITLE: Soil Sampling and Preparation for Soil Chemical Analysis
AUTHORS: Matema Imakumbili
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to collect and prepare a soil sample for various soil chemical analyses. </div></div>
[STEPS]
?. [Soil sampling design]
When you com... | ["[Soil sampling design]\nWhen you come to a field from which you want to collect a soil sample from, first observe the field for any gradients/slopes. If the field is relatively even, i.e. with no obvious slopes, randomly select 10 to 20 points from which you will collect sub-samples of the fields’ soil. Random sampli... |
53,333 | Fungal Mounting and Staining Procedure | 1 | null | https://www.protocols.io/view/fungal-mounting-and-staining-procedure-bybvpsn6 | Yin-Tse Huang | TITLE: Fungal Mounting and Staining Procedure
AUTHORS: Yin-Tse Huang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Fungal Mounting and Staining Procedure</span></div></div>
[STEPS]
?. [Staining]
Commercial Lugol’s Iodine (5%): to examine amyloid, inamyloid, and ... | ["[Staining]\nCommercial Lugol’s Iodine (5%): to examine amyloid, inamyloid, and dextrinoid reaction of basidios (mostly spores) and ascos (mostly asci). Dilute the commercial (5%): distilled water = 1:4 as working solution. (c.a. 1/6)Pictures from mushroomexpert.com & Wikipedia", "[Staining]", "[Mounting]\nPermanent m... |
92,998 | Integrated Indexing One-Step RT-PCR with NEB LunaScript: Influenza A Virus Sequencing with Native Oxford Nanopore Software Compatibility | 4 | null | https://www.protocols.io/view/integrated-indexing-one-step-rt-pcr-with-neb-lunas-c63ezgje | Abhinaya Srikanth, Brian Merritt, Peter Thielen | TITLE: Integrated Indexing One-Step RT-PCR with NEB LunaScript: Influenza A Virus Sequencing with Native Oxford Nanopore Software Compatibility
AUTHORS: Abhinaya Srikanth, Brian Merritt, Peter Thielen
[DESCRIPTION]
This integrated indexing RT-PCR protocol has been optimized for whole genome sequencing of influenza A v... | ["[Protocol for Integrated Indexing of Influenza A Virus] Prepare the One-Step Reverse Transcriptase Multi-Segment PCR for Influenza A Virus as described below:", "[Protocol for Integrated Indexing of Influenza A Virus] Flick the tube or pipet up and down to mix at minimum 10 times followed by a short spin", "[Protocol... |
null | null | null | dx.doi.org/10.17504/protocols.io.phpdj5n | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
45,519 | Optogenetically inhibiting enteric neurons in the murine large intestine | 4 | dx.doi.org/10.17504/protocols.io.bqppmvmn | https://www.protocols.io/view/optogenetically-inhibiting-enteric-neurons-in-the-bqppmvmn | Dante Heredia, Thomas Gould | TITLE: Optogenetically inhibiting enteric neurons in the murine large intestine
AUTHORS: Dante Heredia, Thomas Gould
[DESCRIPTION]
Protocol for optogenetically inhibiting neuronal subtypes in murine colonic myenteric plexus.
[GUIDELINES]
This protocol applies to transgenic animals expressing the optogenetic protei... | ["Dissection and experiments are done in the dark under infrared illumination. A ventral midline incision is made and the whole colon is carefully excised into a Sylguard lined dissection dish containing oxygenated Krebs-ringer solution.", "The colon is then drawn over a 1.5-mm diameter fire-polished capillary tube, wh... |
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