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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68,512 | Diagnostic Restriction Digest | 4 | null | https://www.protocols.io/view/diagnostic-restriction-digest-ce58tg9w | Brian Teague | TITLE: Diagnostic Restriction Digest
AUTHORS: Brian Teague
[DESCRIPTION]
In this restriction digest, you'll use an enzyme that cuts DNA to cut your miniprepped plasmid. This can give you some evidence as to whether your plasmid is what you expected or not.
You'll also use Benchling to predict the result of you... | ["[Perform the diagnostic digest] For each miniprep, compute the volume that contains 1 µg of DNA.", "[Perform the diagnostic digest] In the PCR tube, mix:\nThe volume of DNA you computed in step 1, up to a maximum of 5 µL\n2 µL of CutSmart enzyme buffer\n2 µL of PvuII enzyme\nEnough nuclease-free water for a total vol... |
null | null | null | dx.doi.org/10.17504/protocols.io.rswd6fe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<p>The protocol aims explicitly to amplify BFV viruses and not other viruses.</p>
<p>The assay targets the E2 gene region and is designed as a qualitative test for investigating BFV infection of humans... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.pifdkbn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Here is a short intro on short read assembly using the SPAdes assembler. </p>
<p> </p>
<p>Some notes on tool installation:</p>
<p>To install SPAdes or other tools into your PATH you may wish to use a package manager called Miniconda. For this go to the website here and downlo... | [] |
63,833 | Via Keto Gummies Expert Reviews – Official Report Analysis | 1 | dx.doi.org/10.17504/protocols.io.81wgb69eolpk/v1 | https://www.protocols.io/view/via-keto-gummies-expert-reviews-official-report-an-cajzscp6 | D D | TITLE: Via Keto Gummies Expert Reviews – Official Report Analysis
AUTHORS: D D
[DESCRIPTION]
This is definitively what the new and progressiveVia Keto Gummiesis about. It's a ketogenic supplement planned explicitly to assist you with arriving at ketosis faster. At the end of the day, the ideal answer for anybody need... | [] |
25,247 | How to Prepare a Single Cell Suspension from Mouse Spleen | null | dx.doi.org/10.17504/protocols.io.4v7gw9n | null | STEMCELL Technologies | TITLE: How to Prepare a Single Cell Suspension from Mouse Spleen
AUTHORS: STEMCELL Technologies
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The spleen is an important organ of the immune system responsible for filtering blood and initiating immune responses to blood-borne antigens. Various blood... | ["[Mechanical Digestion of a Spleen Sample]\nTransfer the spleen to be processed into a sterile 35 mm culture dish containing 5 mL of recommended dissociation medium for downstream isolation. If you are not using an isolation kit following dissociation please use phosphate buffered saline (PBS) + 1 mM EDTA.Recommended ... |
88,915 | Simulating the modal analysis of hyperelastic membranes immersed in fluid using FE software ANSYS | 5 | dx.doi.org/10.17504/protocols.io.bp2l6x7dklqe/v2 | https://www.protocols.io/view/simulating-the-modal-analysis-of-hyperelastic-memb-c23tygnn | samuel.vorlet | TITLE: Simulating the modal analysis of hyperelastic membranes immersed in fluid using FE software ANSYS
AUTHORS: samuel.vorlet
[DESCRIPTION]
This protocol provides step-by-step guidelines to perform the modal analysis of pre-strained hyperelastic rectangular membrane accounting for fluid-structure interactions using ... | ["[Hyperelastic material definition using the Mooney-Rivlin formulation from uniaxial test data] Open Engineering Data.", "Ad a new material and define the material name. Verify the units.", "Define the hyperelastic material properties.", "In the Hyperelastic toolbox, choose the Mooney-Rivlin material model with the ap... |
104,376 | Sinai SCENT TMC - FFPE Blocking, Sectioning, and TMA Construction | 0 | null | https://www.protocols.io/view/sinai-scent-tmc-ffpe-blocking-sectioning-and-tma-c-dh6y39fw | Sojin Kim | TITLE: Sinai SCENT TMC - FFPE Blocking, Sectioning, and TMA Construction
AUTHORS: Sojin Kim
[DESCRIPTION]
FFPE Blocking and Sectioning protocol
[GUIDELINES]
Comply with Universal Precautions when handling all specimens.
Use personal protective equipment according to the institution’s guidelines.
[STEPS]
SECTION: FF... | ["[FFPE Blocking and Sectioning] Rince the collected tissues in PBS to remove blood.", "[FFPE Blocking and Sectioning] Place tissues in at least 10 volumes of buffered formalin or buffered paraformaldehyde", "[FFPE Blocking and Sectioning] Incubate for the necessary fixation time\n1. 1-2 mm thick: 2-3 hours RT\n2. 5-10... |
null | null | null | dx.doi.org/10.17504/protocols.io.ruhd6t6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This assay is used to measure cell viability. Dead cells have damage membranes. The ethidium homodimer-1 enters damaged cells and is fluorescent when bound to nucleic acids, producing a bright red fluorescence in damaged or dead cells.</p>
[STEPS] | [] |
72,965 | Untargeted lipidomics analysis for Golgi immunopurification (Golgi-IP) | 4 | dx.doi.org/10.17504/protocols.io.3byl4jq6jlo5/v1 | https://www.protocols.io/view/untargeted-lipidomics-analysis-for-golgi-immunopur-cjhduj26 | Wentao Dong, Eshaan S Rawat, Monther Abu-Remaileh | TITLE: Untargeted lipidomics analysis for Golgi immunopurification (Golgi-IP)
AUTHORS: Wentao Dong, Eshaan S Rawat, Monther Abu-Remaileh
[DESCRIPTION]
The Golgi apparatus functions as a central hub in the cell that processes, packages, and distributes proteins. Despite its critical cellular function, there has been ch... | ["[LC/MS lipidomics settings] Set an ID-X tribrid mass spectrometer (Thermo Fisher Scientific) with a heated electrospray ionization (HESI) probe, for initial nonpolar lipid profiling.\n\nPrepare an Ascentis Express C18 150 x 2.1 mm column (Millipore Sigma 53825-U) coupled with a 5 x 2.1 mm guard (Sigma-Aldrich 53500-U... |
24,556 | Hiseq 2000 Library Construction and Sequencing for RNA Seq | null | dx.doi.org/10.17504/protocols.io.38kgruw | null | Eric J. Carpenter, Naim Matasci, Shuangxiu Wu, Jing Sun, Jun Yu, Fabio Rocha Jimenez Vieira, Chris Bowler, Richard G. Dorrell, Matt Gitzendanner, Ling Li, Wensi Du, Kristian Ullrich, Michael S. Barker, James H. Leebens-Mack, Gane Ka-Shu Wong | TITLE: Hiseq 2000 Library Construction and Sequencing for RNA Seq
AUTHORS: Eric J. Carpenter, Naim Matasci, Shuangxiu Wu, Jing Sun, Jun Yu, Fabio Rocha Jimenez Vieira, Chris Bowler, Richard G. Dorrell, Matt Gitzendanner, Ling Li, Wensi Du, Kristian Ullrich, Michael S. Barker, James H. Leebens-Mack, Gane Ka-Shu Wong
[D... | ["Isolate polyA RNA from of total RNA treated by using .It is best to use up to 50 µg as the use of a lower mass (typically 20 µg) has been insufficient for successful library construction. This can be assessed by running final PCR products on an agarose gel; the library construction is considered to have failed when... |
71,727 | Rapid Sequencing gDNA | 1 | dx.doi.org/10.17504/protocols.io.14egn27eyg5d/v1 | https://www.protocols.io/view/rapid-sequencing-gdna-ciapuadn | Carlos Goller | TITLE: Rapid Sequencing gDNA
AUTHORS: Carlos Goller
[DESCRIPTION]
ONT Rapid sequencing kit use in a classroom setting.
[STEPS]
SECTION: Library Preparation
1. DNA tagmentation
Thaw kit components at Room temperature , spin down briefly using a microfuge and mix by pipetting as indicated below:
Lambda DNA (50 μg/ml... | ["[Library Preparation] DNA tagmentation\n\nThaw kit components at Room temperature , spin down briefly using a microfuge and mix by pipetting as indicated below:\n\nLambda DNA (50 μg/ml): thaw at RT, briefly spin down, mix well by pipetting\nFragmentation Mix (FRA): not frozen, briefly spin down, mix well by pipetting... |
44,042 | Vivarium Population Spenser: Internal migration module | 5 | dx.doi.org/10.17504/protocols.io.bn9imh4e | https://www.protocols.io/view/vivarium-population-spenser-internal-migration-mod-bn9imh4e | Camila Rangel Smith, Kasra Hosseini | TITLE: Vivarium Population Spenser: Internal migration module
AUTHORS: Camila Rangel Smith, Kasra Hosseini
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Description of the steps followed by Vivarium Population Spenser library when running the Internal migration module. </div></div>
[STEPS]
?. Thi... | ["This module models the [internal_migration](src/vivarium_population_spenser/internal_migration.py) between MSOAs (and theirrespective LADs) of individuals based on their gender, age, initial location (local authority level) and ethnicity.The input table to establish the pool of migrants that internally migrate based... |
40,798 | ELISA for quantification of IL-34 in human serum. | 6 | dx.doi.org/10.17504/protocols.io.bj36kqre | https://www.protocols.io/view/elisa-for-quantification-of-il-34-in-human-serum-bj36kqre | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-34 in human serum.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells.... | ["An anti-human IL-34 coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.", "Add 50 µl of human serum. Human IL-34 present in the serum sample binds to antibodies adsorbed into the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and... |
107,221 | Multicellular Circulating Co-Culture | 0 | dx.doi.org/10.17504/protocols.io.ewov19b47lr2/v1 | https://www.protocols.io/view/multicellular-circulating-co-culture-dkxv4xn6 | Bianca Cruz Pachane, Pedro Henrique Teixeira Bottaro, Wanessa Fernanda Altei, Heloisa Sobreiro Selistre de Araujo | TITLE: Multicellular Circulating Co-Culture
AUTHORS: Bianca Cruz Pachane, Pedro Henrique Teixeira Bottaro, Wanessa Fernanda Altei, Heloisa Sobreiro Selistre de Araujo
[DESCRIPTION]
A novel method to study the tumor microenvironment (TME) in vitro, using the quasi-vivo technology from Kirstall to survey the individual ... | ["[Preparation of matrix-coated coverslips] Clean round glass coverslips (13 mm ø) with 70% ethanol wipes before use. Maintain slips in a clean container.", "[Preparation of matrix-coated coverslips] Prepare a 0.5% solution of glutaraldehyde in H2O and maintain it at 4 °C protected from light.", "[Preparation of matrix... |
null | null | null | dx.doi.org/10.17504/protocols.io.mpqc5mw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?. | [] |
80,233 | Generation of stable cell lines using retroviral system | 4 | dx.doi.org/10.17504/protocols.io.81wgbyez1vpk/v1 | https://www.protocols.io/view/generation-of-stable-cell-lines-using-retroviral-s-cskhwct6 | nguyen.tha | TITLE: Generation of stable cell lines using retroviral system
AUTHORS: nguyen.tha
[DESCRIPTION]
This protocol details generation of stable cell lines using retroviral system.
[GUIDELINES]
Attention
The HEK293T cells detach very easily, be extra gentle when changing the media.
[STEPS]
SECTION: Day 1
1. Seed NIH HE... | ["[Day 1] Seed NIH HEK293T cells into a 6-well plate (900k cells/well if set up in the morning, 950k cells/well if set up in the afternoon).", "[Day 2: The following protocol is designed for one well of the 6-well plate] Transfect cells with viral and helper vectors using lipofectamine LTX. Combine the following in a 1... |
88,854 | PCR based amplicon sequencing of P. vivax antigens | 4 | dx.doi.org/10.17504/protocols.io.261gedwddv47/v1 | https://www.protocols.io/view/pcr-based-amplicon-sequencing-of-p-vivax-antigens-c2zwyf7e | Paolo Bareng | TITLE: PCR based amplicon sequencing of P. vivax antigens
AUTHORS: Paolo Bareng
[STEPS]
SECTION: Primer pool(s) preparation
1. Prepare the primer pools 1, 2, and 3 by reconstituting lyophilized primers to a concentration of 100µM using nuclease-free water
SECTION: Primer pool(s) preparation
1.1. The tables below show ... | ["[Primer pool(s) preparation] Prepare the primer pools 1, 2, and 3 by reconstituting lyophilized primers to a concentration of 100µM using nuclease-free water", "[Primer pool(s) preparation] The tables below show the volume of each 100µM forward and reverse primers stock to be added in the respective pools. The total ... |
null | null | null | dx.doi.org/10.17504/protocols.io.hbvb2n6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Current long read sequencing, e. g. PacBio and Nanopore, requires high molecular weight (HMW) and highly pure DNA. Many fungal and plant species have high content of polysaccharides and other contaminants that are co-precipitated with DNA during ethanol precipitation. This pr... | [] |
64,751 | Standard Operating Procedure for assembly and deployment of ovitraps | 1 | dx.doi.org/10.17504/protocols.io.14egn7r4pv5d/v1 | https://www.protocols.io/view/standard-operating-procedure-for-assembly-and-depl-cbgpsjvn | Tanya L Russell, Kyran Staunton, Thomas R. Burkot | TITLE: Standard Operating Procedure for assembly and deployment of ovitraps
AUTHORS: Tanya L Russell, Kyran Staunton, Thomas R. Burkot
[DESCRIPTION]
The purpose of this Standard Operating Procedure (SOP) is to outline the materials and processes required to assemble, deploy and service an ovitrap.
Description: Ovit... | ["[Trap assembly] Collect trap components. Ovistrips made from cloth or paper should be cut to roughly 6 cm wide x 12 cm long.", "[Trap assembly] Pour water into the bucket until it is about 2/3 full. For example, fill a 1 L bucket with ~660 ml of water.", "[Trap assembly] Insert organic material (0.5 g/L) of such as a... |
null | null | null | dx.doi.org/10.17504/protocols.io.r4xd8xn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The Modified Ziehl-Neelsen stain (mZN stain) is a type of differential bacteriological stain used to identify acid-fast organisms, mainly <em>Mycobacteria</em>. Acid fast organisms are those which are capable of retaining the primary stain when treated with an acid (<em>fast=... | [] |
34,482 | Extracellular DNA extraction | null | dx.doi.org/10.17504/protocols.io.bdwsi7ee | null | Charline Giguet-Covex, Pierre Taberlet, Francesco Gentile Ficetola | TITLE: Extracellular DNA extraction
AUTHORS: Charline Giguet-Covex, Pierre Taberlet, Francesco Gentile Ficetola
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Over the past decade, an increasing number of studies has used environmental DNA from lake sediments to trace past lake ecosystem and landsc... | ["[exDNA extraction]\nPhosphate buffer preparation:The phosphate buffer must be prepared the same day, before starting the extraction protocol. Calculate the quantity of phosphate buffer required for the extractions. Prepare a little more especially for the extraction control. You will add the same volume of phosphate ... |
35,883 | Successful and cost-effective DNA extraction method from insects with small amount of tissue | null | dx.doi.org/10.17504/protocols.io.bfajjicn | https://www.protocols.io/view/successful-and-cost-effective-dna-extraction-metho-bfajjicn | Rahul Jamdade | TITLE: Successful and cost-effective DNA extraction method from insects with small amount of tissue
AUTHORS: Rahul Jamdade
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">DNA extraction from insects is an initial and critical step that might affect the molecular taxonomy. There are several protoc... | [] |
44,640 | Dip-C (Part 2: Whole-genome Amplification with Nextera) | 4 | dx.doi.org/10.17504/protocols.io.bpt8mnrw | https://www.protocols.io/view/dip-c-part-2-whole-genome-amplification-with-nexte-bpt8mnrw | Longzhi Tan | TITLE: Dip-C (Part 2: Whole-genome Amplification with Nextera)
AUTHORS: Longzhi Tan
[STEPS]
?. [Oligos]
Carrier ssDNA (same as in LIANTI and META):TCAGGTTTTCCTGAAPurification: standard desaltingDissolve in 0.1 X TE (made from ) to a final concentration of .Store at .
-20 °C
?. [Oligos]
Nextera i7 Index Primers:701: C... | ["[Oligos]\nCarrier ssDNA (same as in LIANTI and META):TCAGGTTTTCCTGAAPurification: standard desaltingDissolve in 0.1 X TE (made from ) to a final concentration of .Store at .\n-20 °C", "[Oligos]\nNextera i7 Index Primers:701: CAAGCAGAAGACGGCATACGAGATTCGCCTTAGTCTCGTGGGCTCGG702: CAAGCAGAAGACGGCATACGAGATCTAGTACGGTCTCGTG... |
50,414 | Protocol for Image processing and analysis of VPS13D recruitment to mitochondria | 1 | dx.doi.org/10.17504/protocols.io.bvgnn3ve | https://www.protocols.io/view/protocol-for-image-processing-and-analysis-of-vps1-bvgnn3ve | Marianna Leonzino, Andrés Guillén-Samander, Ni Tang, Pietro De Camilli | TITLE: Protocol for Image processing and analysis of VPS13D recruitment to mitochondria
AUTHORS: Marianna Leonzino, Andrés Guillén-Samander, Ni Tang, Pietro De Camilli
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol details the image processing and analysis of VPS13D recruitment ... | ["[For the analysis of optogenetic experiments:]\nBuild kymographs tracing a line ROI across the mitochondria that was illuminated with Blue Light.", "[For the analysis of optogenetic experiments:]\nMeasure an intensity profile by tracing a line ROI across the center of the mitochondrial signal on the kymograph. Take a... |
94,189 | Sucrose preference test | 4 | dx.doi.org/10.17504/protocols.io.3byl4q4xrvo5/v1 | https://www.protocols.io/view/sucrose-preference-test-c78mzru6 | mariangela.massarocenere | TITLE: Sucrose preference test
AUTHORS: mariangela.massarocenere
[DESCRIPTION]
The sucrose preference test assesses the animal’s interest in a sweet-tasting sucrose solution relative to unsweetened
water
[STEPS]
1. Place one animalper cage during the test duration and habituate them to drinking from two equally acce... | ["Place one animalper cage during the test duration and habituate them to drinking from two equally accessible bottles", "Refill each bottle with fresh water or 1% sucrose solution and inverte to its original position every day for two consecutive days", "To avoid side preference, place the sucrose bottle on the left f... |
null | null | null | dx.doi.org/10.17504/protocols.io.d9m945 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol has been modified from the original method developed and reported by Steward and Culley (2010) and Mueller et al. (2014). As a starting point we assume that viruses have been collected from the environment on 0.02 µm syringe filters (Anotop, Whatman).</p>
[STEP... | [] |
51,102 | Flow CyTOF Using Single Cells From Human Islets | 4 | dx.doi.org/10.17504/protocols.io.bv56n89e | https://www.protocols.io/view/flow-cytof-using-single-cells-from-human-islets-bv56n89e | Klaus H. Kaestner Lab, Suzanne Shapira | TITLE: Flow CyTOF Using Single Cells From Human Islets
AUTHORS: Klaus H. Kaestner Lab, Suzanne Shapira
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Cytometry by time-of-flight (CyTOF) is an application of mass cytometry using antibodies conjugated to rare heavy m... | ["[II. CyTOF barcoding and labelling]\nThaw the cells in quickly, and immediately add the Perm bufferRemove the barcodes (Fluidigm 201060) from freezer and allow them to warm up to RT for at least 10 min.\n37 °C\n-20 °C", "[II. CyTOF barcoding and labelling]\nWash cells 2x with Foxp3 perm buffer (eBioscience, 00-5523... |
null | null | null | dx.doi.org/10.17504/protocols.io.etxbepn | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<strong>Materials:</strong><br /><br />
<ol>
<li>Reagent “A” - 2.0% Na<sub>2</sub>CO<sub>3</sub> in 0.1 N NaOH</li>
<li>Reagent “B” - 0.5% CuSO<sub>4</sub><sup>.</sup>5H<sub>2</sub>O in 1.0% Na citrate</li>
<li>Reagent “C” - 50.0 mL reagent “A” + 1.0 mL reagent “B”</li>
<li>Reage... | [] |
59,738 | Total RNA and DNA from Microalgae (24 samples per day) | 1 | null | https://www.protocols.io/view/total-rna-and-dna-from-microalgae-24-samples-per-d-b6j2rcqe | Yingyu Hu, Zoe V Finkel | TITLE: Total RNA and DNA from Microalgae (24 samples per day)
AUTHORS: Yingyu Hu, Zoe V Finkel
[DESCRIPTION]
Here we describe a protocol for extracting and quantifying bulk RNA and DNA from microalgae, which is adapted from Berdalet E. et al. (2005).
RNA and DNA are extracted from microalgae samples and then quant... | ["[Day 1: Freeze-dry samples] Freeze dry samples and blank filters. Freeze at -80 °C until processed.", "[Day 1: Prepare primary solutions] Turn on UV light in biosafety cabinet for 15 min and clean working surface with decontamination solution.", "[Day 1: Prepare primary solutions] Prepare Tris buffer 5 mM pH 8.0", ... |
23,764 | CODEX Oligo-labeled Antibody Conjugation | null | dx.doi.org/10.17504/protocols.io.3fugjnw | null | Yury Goltsev, Nikolay Samusik, Julia Kennedy-Darling, Salil Bhate, Matthew Hale, Gustavo Vazquez, Sarah Black, Garry Nolan | TITLE: CODEX Oligo-labeled Antibody Conjugation
AUTHORS: Yury Goltsev, Nikolay Samusik, Julia Kennedy-Darling, Salil Bhate, Matthew Hale, Gustavo Vazquez, Sarah Black, Garry Nolan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>CODEX is a technology that uses oligo labeled antibodies, speciali... | ["[Antibody Disulfide Reduction Reaction]\nRetrieve one MWCO filter column for each antibody to be conjugated. Block nonspecific antibody binding to the MWCO filter columns by adding 500ul Filter Blocking Solution to the top of each column and spinning down at 12,000g for 2 minutes.\n0 Room temperature", "[Antibody Di... |
40,889 | Removal of Melanin | 1 | dx.doi.org/10.17504/protocols.io.bj6zkrf6 | https://www.protocols.io/view/removal-of-melanin-bj6zkrf6 | Jason Stajich | TITLE: Removal of Melanin
AUTHORS: Jason Stajich
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Principle is that CTAB is charging the anionic nucleotides whereby neutral polysaccharides/ melanins are remaining in supernatant. This method also uses urea with the idea that the presence of urea helps... | ["Add to ~- DNA/RNA solution until a volume of is reached.\n100 µl\n200 µl\n400 µl", "Add\n130 µl", "Add mL of CTAB-Urea solution\n1.6 mL\n{\"blocks\":[{\"key\":\"7ul3n\",\"text\":\"\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]}],\"entityMap\":[]}", "Mix samples (by han... |
61,598 | Human fibroblast culturing | 4 | dx.doi.org/10.17504/protocols.io.rm7vzy542lx1/v1 | https://www.protocols.io/view/human-fibroblast-culturing-b8d6rs9e | Laura Smith, David C | TITLE: Human fibroblast culturing
AUTHORS: Laura Smith, David C
[DESCRIPTION]
Fibroblasts are cultured in Dulbecco’s modified eagle media (DMEM) 4500 (mg/L) growth medium supplemented with Glutamax (Gibco), 10% foetal bovine serum (FBS), non-essential amino acids (NEAA: 0.1 mM of: glycine, L-alanine, L-asparagine, L... | ["[Characteristics] Characteristics\nObtained /developed from human adult dermal biopsies\nProliferative until p20\nDoubling time ~ 24h\nMaintain between 60 – 90% confluent", "[Complete growth medium] DMEM (LT # 61965-059; 4500 mg/L and no pyruvate) Glutamax medium\nFetal bovine serum (FBS, 10% final) – 1 / 1... |
null | null | null | dx.doi.org/10.17504/protocols.io.c3iykd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Last optimized January 2006, updated by Matt on March 16 2009
[GUIDELINES]
This protocol comes from a group of other protocols.This protocol is (1) of (4): <br />1. <a href="https://www.protocols.io/view/Large-Volume-Marine-Cyanophage-Phage-Protocols-c3iykd" target="_blank">'La... | [] |
47,834 | Modified EMP ITS Illumina Amplicon Protocol | 1 | dx.doi.org/10.17504/protocols.io.6qpvrdmeogmk/v1 | https://www.protocols.io/view/modified-emp-its-illumina-amplicon-protocol-bsx2nfqe | Dylan P. Smith, Kabir G. Peay, Gail Ackermann, Amy Apprill, Markus Bauer, Donna Berg-Lyons, Jason Betley, T. D. Bruns, J. Greg Caporaso, Noah Fierer, Louise Fraser, Jed A. Fuhrman, M. Gardes, Jack A. Gilbert, Niall Gormley, Greg Humphrey, James Huntley, Janet K. Jansson, Rob Knight, Chris L. Lauber, S. Lee, Sarah M. Ow... | TITLE: Modified EMP ITS Illumina Amplicon Protocol
AUTHORS: Dylan P. Smith, Kabir G. Peay, Gail Ackermann, Amy Apprill, Markus Bauer, Donna Berg-Lyons, Jason Betley, T. D. Bruns, J. Greg Caporaso, Noah Fierer, Louise Fraser, Jed A. Fuhrman, M. Gardes, Jack A. Gilbert, Niall Gormley, Greg Humphrey, James Huntley, Janet... | ["[Amplification Protocol] Amplify samples in triplicate.", "[Amplification Protocol] Pool triplicate PCR reactions for each sample into a single volume (75 µL). Do not combine amplicons from different samples at this point.", "[Amplification Protocol] Run amplicons from each sample on an agarose gel.", "[Amplification... |
40,922 | ELISA for quantification of human C3 in serum or plasma. | 6 | dx.doi.org/10.17504/protocols.io.bj72krqe | https://www.protocols.io/view/elisa-for-quantification-of-human-c3-in-serum-or-bj72krqe | Angel Justiz-Vaillant, Belkis Ferrer-Cosme | TITLE: ELISA for quantification of human C3 in serum or plasma.
AUTHORS: Angel Justiz-Vaillant, Belkis Ferrer-Cosme
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. An anti-human C3 coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.
?.... | ["An anti-human C3 coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.", "Add 50 µl of human serum or plasma. Human C3 present in the serum or plasma binds to antibodies adsorbed into the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buf... |
101,063 | 12S rRNA-Gene Metabarcoding Library Prep: Dual-PCR Method | 1 | dx.doi.org/10.17504/protocols.io.n2bvjnn25gk5/v1 | https://www.protocols.io/view/12s-rrna-gene-metabarcoding-library-prep-dual-pcr-dexf3fjn | rute.carvalho Carvalho, Colleen Kellogg, Matt Lemay | TITLE: 12S rRNA-Gene Metabarcoding Library Prep: Dual-PCR Method
AUTHORS: rute.carvalho Carvalho, Colleen Kellogg, Matt Lemay
[DESCRIPTION]
This protocol is used for eDNA metabarcoding of the mitochondrial 12S rRNA gene (Miya et al 2015) using Pair-End Illumina Miseq Sequencing. As part of the Hakai Institute Ocean Ob... | ["[Preparations] Ensure that the laboratory is appropriately configured and that staff has appropriate training. See \"Guidelines\" for more information. Pay attention to the separation of pre and post-PCR spaces and equipment.", "[Triplicate PCR Amplification (1st PCR)] Preparations\n\n \n\n Reagents:\n (Or equal)\n ... |
83,165 | Concentration and nucleic acid extraction of viruses from wastewater influent | 4 | null | https://www.protocols.io/view/concentration-and-nucleic-acid-extraction-of-virus-cvf5w3q6 | Ari N Machtinger, Olivia S Hershey, William J Bradshaw, Michael R McLaren | TITLE: Concentration and nucleic acid extraction of viruses from wastewater influent
AUTHORS: Ari N Machtinger, Olivia S Hershey, William J Bradshaw, Michael R McLaren
[DESCRIPTION]
In this protocol, 200 mL of raw influent wastewater is concentrated to a final volume of 400 uL using the Innovaprep Concentrating Pipet... | ["[Part 1: Influent Handling, Dissociation, Centrifugation, Filtration] In the fume hood, add 400 uL of 10% Tween 20 stock solution each to the seven centrifuge tubes.", "[Part 1: Influent Handling, Dissociation, Centrifugation, Filtration] Prepare the negative control. Add 40 mL of PBS to two of the centrifuge tubes.... |
93,627 | Practical Guide to Live Sampling of Livestock and Wildlife for Infectious Disease Surveillance | 1 | dx.doi.org/10.17504/protocols.io.rm7vzxro8gx1/v2 | https://www.protocols.io/view/practical-guide-to-live-sampling-of-livestock-and-c7n3zmgn | Stefano Catalano | TITLE: Practical Guide to Live Sampling of Livestock and Wildlife for Infectious Disease Surveillance
AUTHORS: Stefano Catalano
[DESCRIPTION]
Under- or misdiagnosed cases of disease caused by especially dangerous pathogens present public health and proliferation risks. Numerous studies have demonstrated that in low-re... | [] |
54,317 | Consistency in Identity Related Sequential Decisions | 2 | null | https://www.protocols.io/view/consistency-in-identity-related-sequential-decisio-bzamp2c6 | Dikla Perez, Yael Steinhart, Amir Grinstein, Meike Morren | TITLE: Consistency in Identity Related Sequential Decisions
AUTHORS: Dikla Perez, Yael Steinhart, Amir Grinstein, Meike Morren
[DESCRIPTION]
We conducted four lab and online experiments, and a field experiment to test our hypotheses and to rule out an alternative explanation. The design of each of the five experimen... | [] |
97,050 | Introduction to flux balance analysis (FBA) | 0 | null | https://www.protocols.io/view/introduction-to-flux-balance-analysis-fba-daz22f8e | Cailean Carter, Dipali Singh, Gemma Langridge | TITLE: Introduction to flux balance analysis (FBA)
AUTHORS: Cailean Carter, Dipali Singh, Gemma Langridge
[DESCRIPTION]
Flux balance analysis (FBA) is a mathematical approach to finding an optimal net flow of mass through a metabolic network that follows a set of instructions defined by the user. This protocol covers ... | ["[Background] Flux balance analysis (FBA) is a mathematical approach to finding an optimal net flow of mass through a metabolic network that follows a set of instructions defined by the user. This protocol covers the mathematical principles behind FBA and provides coding examples that can be followed using Python3. A ... |
null | null | null | dx.doi.org/10.17504/protocols.io.cp8vrv | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.erabd2e | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p>Components:<br /><br />2.25 M DTT, 40 mM KOAc, pH 6.0.</p>
[STEPS]
?.
?.
?. | [] |
41,181 | manu 3 | 1 | null | https://www.protocols.io/view/manu-3-bkf5ktq6 | Monica Hassan | TITLE: manu 3
AUTHORS: Monica Hassan
[STEPS]
?. | [] |
32,624 | Single molecule FISH | null | dx.doi.org/10.17504/protocols.io.bb4qiqvw | null | Thuc Nguyen, Emma Garren | TITLE: Single molecule FISH
AUTHORS: Thuc Nguyen, Emma Garren
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Updated This protocol describes multiround hybrization of directly-conjugated FISH probes for single molecule RNA detection. Thin tissue sections (10-μm) are placed onto silanized coverslips... | ["[Coverslip Preparation]\nClean coverslips (Thorlabs #CG15KH) with lens paper and 70% ethanol. With minimal handling of the coverslips (touch edges with clean gloves is ok), load them into a coverslip rack compatible with a plasma cleaning oven. We use a quartz coverslip rack. Placing coverslips in a clean glass conta... |
83,013 | Microscopy-based bead protein-protein interaction assay | 1 | dx.doi.org/10.17504/protocols.io.dm6gp3erpvzp/v1 | https://www.protocols.io/view/microscopy-based-bead-protein-protein-interaction-cvbdw2i6 | Elisabeth Holzer | TITLE: Microscopy-based bead protein-protein interaction assay
AUTHORS: Elisabeth Holzer
[DESCRIPTION]
This protocol describes how to perform microscopy-based bead protein-protein interaction assay with GST- or mCherry-tagged proteins as baits and fluorescently-tagged proteins as preys. The protocol requires to have p... | ["[Prepare bait-coated beads] Equilibrate 20 µL Glutathione Sepharose 4B or RFP-Trap Agarose beads with 200 µL SEC buffer", "[Prepare bait-coated beads] Incubate equilibrated beads with GST- or mCherry-tagged bait protein for a final concentration of 5 micromolar (µM) in SEC buffer for 60 min at 4 °C with gentle rotati... |
28,245 | MojoSort™ Selection Kits Column Protocol - 3 | null | dx.doi.org/10.17504/protocols.io.7tvhnn6 | null | Sam Li | TITLE: MojoSort™ Selection Kits Column Protocol - 3
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) ... |
97,425 | RNA Slide Preparation Protocol (FFPE) for nanostring DSP - GeoMx - Human Ovary U54 Native Tissue v2 | 4 | dx.doi.org/10.17504/protocols.io.bp2l624bdgqe/v2 | https://www.protocols.io/view/rna-slide-preparation-protocol-ffpe-for-nanostring-dbdr2i56 | Nicolas Martin, Tommy Tran | TITLE: RNA Slide Preparation Protocol (FFPE) for nanostring DSP - GeoMx - Human Ovary U54 Native Tissue v2
AUTHORS: Nicolas Martin, Tommy Tran
[DESCRIPTION]
This protocol is designed for RNA slide preparation for formalin-fixed tissue.
[GUIDELINES]
This is the default protocol for slide preparation by Nanostring.
... | ["Prepare reagents\n\nPrepare the reagents using the dilution instructions (see Table 1).\nUse DEPC- treated water for all dilutions. The actual volume of\nreagents used in the protocol will vary – the volumes to prepare in Table 1 are suggestions.\n\nTable 1: Reagent prep for RNA slide preparation\n\n Reagent ... |
38,666 | Intravenous Jugular Catheterization for Rats | 1 | null | https://www.protocols.io/view/intravenous-jugular-catheterization-for-rats-bhzij74e | Sharona Sedighim, Lani Tieu, Olivier George | TITLE: Intravenous Jugular Catheterization for Rats
AUTHORS: Sharona Sedighim, Lani Tieu, Olivier George
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the step-by-step setup and procedure of the pre-op, surgery, and post-op for intravenous jugular cathetarization for rats in... | ["[Animal Preparation for Surgery]\nPlace rat in the knock-down chamber. Set isoflurane vaporizer dial on 5 to begin anesthetizing rat.", "[Animal Preparation for Surgery]\nOnce breathing is constant (about 2 breaths every 3 seconds) and deep, turn off isoflurane and take the animal out for preparation.", "[Animal Prep... |
50,058 | PEI/Laminin Coating | 1 | dx.doi.org/10.17504/protocols.io.bu5iny4e | https://www.protocols.io/view/pei-laminin-coating-bu5iny4e | Zoe | TITLE: PEI/Laminin Coating
AUTHORS: Zoe
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to prepare plates for iPSC-derived neuron maturation. It is a part of the NGN2 cortical neuron differentiation protocol: coat plates in preparation for Day 7 dissociation and replating.</di... | ["[PEI Coating]\nAt least one day before plating, make 2x borate buffer with 20x borate buffer (Thermo, cat. no. 28341) in water in a Falcon tube.\n4 mL\n36 mL\n50 mL", "[PEI Coating]\nDilute 5% PEI (poly-ethylenimine; stored at ) in 2x borate buffer to make 0.1% PEI.\n800 µl\n4 °C\n40 mL", "[PEI Coating]\nFilter-... |
22,183 | Euplotes crassus micronuclear enrichment by PFGE | null | dx.doi.org/10.17504/protocols.io.zwff7bn | null | Rachele Cesaroni, Angela Piersanti | TITLE: Euplotes crassus micronuclear enrichment by PFGE
AUTHORS: Rachele Cesaroni, Angela Piersanti
[STEPS]
?. Starved Euplotes crassus cells (treated overnight with ampicillin 100 mg/ml) were filtered and harvested by centrifugation at 400 rcf for 3 min.
?. As much as possible of the sea water was removed and cells w... | ["Starved Euplotes crassus cells (treated overnight with ampicillin 100 mg/ml) were filtered and harvested by centrifugation at 400 rcf for 3 min.", "As much as possible of the sea water was removed and cells were resuspended in 1V of 1XTE buffer and mixed with 1V of 2% Certified Low-Melt Agarose (Bio-Rad) in 1XTE buf... |
77,722 | In situ CD79a detection in formalin-fixed, paraffin-embedded (FFPE) pig tissues | 4 | dx.doi.org/10.17504/protocols.io.x54v9dzq1g3e/v1 | https://www.protocols.io/view/in-situ-cd79a-detection-in-formalin-fixed-paraffin-cp52vq8e | Jayne E Wiarda, Crystal Loving | TITLE: In situ CD79a detection in formalin-fixed, paraffin-embedded (FFPE) pig tissues
AUTHORS: Jayne E Wiarda, Crystal Loving
[DESCRIPTION]
An immunohistochemistry (IHC) staining protocol for in situ identification of porcine CD79a
[BEFORE_START]
Starting specimens:
Starting samples = FFPE tissues cut to 4 micron th... | ["[Baking] Before starting the assay: \nPreheat a dry oven to 60℃ \nLoad slides for assay into vertical slide rack\n\nBaking\nBake slides 20 min 60℃\n\nWhile slides bake:\nPrepare 0.05% PBS-T (can store at RT up to 1 month)", "[Deparaffinizing & Rehydrating] Immediately before deparaffinizing:\nAdd ~200 mL xylenes ... |
62,752 | Regulation of mitophagy by the NSL complex underlies genetic risk for Parkinson’s disease: Cell-Based in vitro Assays | 4 | dx.doi.org/10.17504/protocols.io.5jyl89648v2w/v1 | https://www.protocols.io/view/regulation-of-mitophagy-by-the-nsl-complex-underli-b9h8r39w | Marc P.M. Soutar, Daniela Melandri, Benjamin O'Callaghan, Emily Annuario, Amy E. Monaghan, Paul J. Whiting, Helene Plun-Favreau | TITLE: Regulation of mitophagy by the NSL complex underlies genetic risk for Parkinson’s disease: Cell-Based in vitro Assays
AUTHORS: Marc P.M. Soutar, Daniela Melandri, Benjamin O'Callaghan, Emily Annuario, Amy E. Monaghan, Paul J. Whiting, Helene Plun-Favreau
[DESCRIPTION]
Impaired mitophagy is a key causative pat... | ["[Cell Culture and siRNA Transfection] Culture cells in Dulbecco’s Modified Eagle Medium (DMEM, Gibco, 11995-0 65) supplemented with 10% heat-inactivated foetal bovine serum (FBS, Gibco) in a humidified chamber at 37 °C with 5% CO2.", "[Cell Culture and siRNA Transfection] For siRNA transfection, transfect cells using... |
46,098 | My new protocol | 1 | dx.doi.org/10.17504/protocols.io.bq9smz6e | https://www.protocols.io/view/my-new-protocol-bq9smz6e | Monica Hassan | TITLE: My new protocol
AUTHORS: Monica Hassan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">any</div></div>
[STEPS]
?. Pressure:
?. | ["Pressure:"] |
62,525 | OcuPrime - 100% Safe And Effective For Eyes! | 3 | dx.doi.org/10.17504/protocols.io.j8nlkkn6wl5r/v1 | https://www.protocols.io/view/ocuprime-100-safe-and-effective-for-eyes-b9a5r2g6 | OcuPrime | TITLE: OcuPrime - 100% Safe And Effective For Eyes!
AUTHORS: OcuPrime
[DESCRIPTION]
OcuPrime
[STEPS] | [] |
66,100 | Monitoring the point spread function for quality control of confocal microscopes | 1 | dx.doi.org/10.17504/protocols.io.bp2l61ww1vqe/v1 | https://www.protocols.io/view/monitoring-the-point-spread-function-for-quality-ccsuswew | Glyn Nelson, Ioannis Alexopoulos, Maria Azevedo, Fabio Barachati, Yury Belyaev, Mariana T Carvalho, Yann Cesbron, Aurelien Dauphin, Alexander D Corbett, Ian M Dobbie, Laurent Gelman, Nadia Halidi, Xiang Hao, Hella Hartmann, Rainer Heintzmann, Peter Hemmerich, Marcel Kirchner, Judith Lacoste, Penghuan Liu, Laure Planta... | TITLE: Monitoring the point spread function for quality control of confocal microscopes
AUTHORS: Glyn Nelson, Ioannis Alexopoulos, Maria Azevedo, Fabio Barachati, Yury Belyaev, Mariana T Carvalho, Yann Cesbron, Aurelien Dauphin, Alexander D Corbett, Ian M Dobbie, Laurent Gelman, Nadia Halidi, Xiang Hao, Hella Hartmann... | ["[Bead Slide Preparation] The bead slide preparation described below contains steps previously published in the following protocols:\n \nas well as another:", "[Bead Slide Preparation] Bead dilution", "[Bead Slide Preparation] Bead slide mounting", "[Bead Slide Preparation] The bead slides can be stored at room temper... |
65,392 | Pure Calms CBD Gummies – Reviews & Price 2022 | 1 | dx.doi.org/10.17504/protocols.io.kqdg3pn71l25/v1 | https://www.protocols.io/view/pure-calms-cbd-gummies-reviews-amp-price-2022-cb4qsqvw | purecalmot | TITLE: Pure Calms CBD Gummies – Reviews & Price 2022
AUTHORS: purecalmot
[DESCRIPTION]
Pure Calms CBD Gummies is the item that is ideal to accomplish calming, cleaning, and mitigating properties for muscle joints, nerves, nails, hair, skin, joints, and some more. This item is particularly alright for outside uti... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.cicuav | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?. | [] |
50,425 | Plankton DNA extraction from Sterivex filter units | 4 | dx.doi.org/10.17504/protocols.io.bvgzn3x6 | https://www.protocols.io/view/plankton-dna-extraction-from-sterivex-filter-units-bvgzn3x6 | Marine Vautier, Cécile Chardon, Camilla Capelli, Rainer Kurmayer, Nico Salmaso, Isabelle Domaizon | TITLE: Plankton DNA extraction from Sterivex filter units
AUTHORS: Marine Vautier, Cécile Chardon, Camilla Capelli, Rainer Kurmayer, Nico Salmaso, Isabelle Domaizon
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The objective of this protocol is to provide a reliable and replicable method for the... | ["Take the Sterivex™ filter unit (previously stored at after filtration). Remove the Inlet Cap (Figure 1) and add of Solution ST1B using a pipette tip. Note: Insert the tip completely into the inlet so that the pipette tip is visible inside the unit just above the membrane. Note: Solution ST1A must be added to bottl... |
99,621 | Protocol for development and temporal in vivo imaging of RVO mouse models | 0 | dx.doi.org/10.17504/protocols.io.ewov19nrplr2/v1 | https://www.protocols.io/view/protocol-for-development-and-temporal-in-vivo-imag-ddid24a6 | Xu Xiaowei | TITLE: Protocol for development and temporal in vivo imaging of RVO mouse models
AUTHORS: Xu Xiaowei
[DESCRIPTION]
This is an protocol for development and temporal in vivo imaging of RVO mouse models.
[STEPS]
SECTION: Animals and Anesthesia
1. Male C57BL/6J mice, aged 6-8 weeks and weighing 19-21g, were purchased fr... | ["[Animals and Anesthesia] Male C57BL/6J mice, aged 6-8 weeks and weighing 19-21g, were purchased from DOSSY EXPERIMENTAL ANIMALS CO. LTD, Chengdu, China. The mice were adaptively raised in an environment with a 12h/12h light/dark cycle, constant room temperature of 26°C, and adequate water and food for one week before... |
18,106 | New version of protocol 2 images pokipoki | null | dx.doi.org/10.17504/protocols.io.vw2e7ge | null | Darja Darja | TITLE: New version of protocol 2 images pokipoki
AUTHORS: Darja Darja
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Between May and June 1993, Slovenia competed in the qualifiers for the EuroBasket 1993, where the team won all seven games and therefore qualified for its first EuroBasket. At the ... | ["[1. ball ]\nBetween May and June 1993, Slovenia competed in the qualifiers for the EuroBasket 1993, where the team won all seven games and therefore qualified for its first EuroBasket. At the main tournament, held in Germany, Slovenia finished in 14th place out of 16 teams with one win and two defeats. Between Ma... |
53,981 | Thawing primary leukemia cells | 4 | dx.doi.org/10.17504/protocols.io.byx5pxq6 | https://www.protocols.io/view/thawing-primary-leukemia-cells-byx5pxq6 | Kathrin Bernt | TITLE: Thawing primary leukemia cells
AUTHORS: Kathrin Bernt
[DESCRIPTION]
This protocol is used to thaw primary cells. Key points are the addition of DNAse, which helps to preserve viability.
[STEPS]
1. Transfer the contents to a 15ml conical tube.
2. Add DNase. 1/10 of the volume of liquid in the tube (100µl/1ml o... | ["Transfer the contents to a 15ml conical tube.", "Add DNase. 1/10 of the volume of liquid in the tube (100µl/1ml of sample). Do not pipette. Gently shake the sample to mix in the DNase.", "Incubate sample in 37˚C water bath for 90 seconds.", "Add media. 10ml, Drop for drop or very slowly while again gently mixing the ... |
98,951 | Immunofluorescence Staining in Mouse Brain Tissue Sections | 0 | dx.doi.org/10.17504/protocols.io.14egn6zopl5d/v1 | https://www.protocols.io/view/immunofluorescence-staining-in-mouse-brain-tissue-dcvf2w3n | madalynn.erb Erb | TITLE: Immunofluorescence Staining in Mouse Brain Tissue Sections
AUTHORS: madalynn.erb Erb
[DESCRIPTION]
This protocol details the immunofluorescence staining in mouse brain tissue sections.
[STEPS]
SECTION: Day 1
1. Staining of 35μm free-floating mouse brain sections is performed in glass staining dishes (Pyrex 367... | ["[Day 1] Staining of 35μm free-floating mouse brain sections is performed in glass staining dishes (Pyrex 36754-60) using 8-section staining nets (Ted Pella 36154-64). dx.doi.org/10.17504/protocols.io.5jyl8pzk9g2w/v1", "[Day 1] The sections can be transferred between wells using a paint brush.", "[Day 1] Volume of sol... |
40,375 | MPAPASS - Creating an MPAPASS database | 1 | dx.doi.org/10.17504/protocols.io.bjnxkmfn | https://www.protocols.io/view/mpapass-creating-an-mpapass-database-bjnxkmfn | Joshua Welsh, Sean Cook, Jennifer Jones | TITLE: MPAPASS - Creating an MPAPASS database
AUTHORS: Joshua Welsh, Sean Cook, Jennifer Jones
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is collection contains the protocols required for each step in the mpapass software pipeline for performing stitched multiplex analysis. This is one of ... | ["[Open New Dataset Window]\nOpen the MPAPASS software and navigate to the Menu tab in the upper left-hand corner. Under the Menu tab, choose the New Dataset option and a new window will pop-up as shown below:", "[Select CSV Directory]\nTo construct the database, follow the steps outlined on the right side of the windo... |
74,334 | QIAGEN DNeasy PowerMax Soil Kit | 4 | dx.doi.org/10.17504/protocols.io.6qpvr4ke3gmk/v1 | https://www.protocols.io/view/qiagen-dneasy-powermax-soil-kit-ckt6uwre | QIAGEN | TITLE: QIAGEN DNeasy PowerMax Soil Kit
AUTHORS: QIAGEN
[DESCRIPTION]
For the isolation of microbial DNA from large quantities of soil - great for samples with low microbial load
The DNeasy PowerMax Soil Kit comprises a novel and proprietary method for isolating genomic DNA from environmental samples using Inhibitor R... | ["[Sample preparation & cell lysis] ADD 15 mL of PowerBead Solution to a PowerMax Bead Pro Tube\n\nADD up to 10 g of soil sample to the PowerMax Bead Pro Tube containing PowerBead Solution\n\nVORTEX vigorously for 1 min", "[Sample preparation & cell lysis] ADD 1.2 mL of Solution C1 to the PowerMax Bead Pro Tube... |
62,244 | Forti Prime Italy : How To Use It In 2022! {UPDATED NEWS} | 1 | dx.doi.org/10.17504/protocols.io.kqdg3p747l25/v1 | https://www.protocols.io/view/forti-prime-italy-how-to-use-it-in-2022-updated-ne-b82cryaw | hooksrobs | TITLE: Forti Prime Italy : How To Use It In 2022! {UPDATED NEWS}
AUTHORS: hooksrobs
[DESCRIPTION]
Forti Prime Reviews: Forti Prime is an all-natural immune booster formula that includes a powerful combination of the world’s best immune-boosting ingredients. 100% safe to use a supplement, Check out its dosage, benefi... | ["[Forti Prime]"] |
null | null | null | dx.doi.org/10.17504/protocols.io.dh338m | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Combine<br />2mls glacial acetic acid<br />1L distilled water
[STEPS] | [] |
79,780 | Gcase co-immunoprecipitation | 1 | dx.doi.org/10.17504/protocols.io.kxygx9xozg8j/v1 | https://www.protocols.io/view/gcase-co-immunoprecipitation-cr6cv9aw | michela.deleidi, Federico Bertoli | TITLE: Gcase co-immunoprecipitation
AUTHORS: michela.deleidi, Federico Bertoli
[DESCRIPTION]
We developed this protocol to identify protein-protein interactions between the enzyme glucocerebrosidase (GCase) and other proteins in human iPSC-derived Neural Precursor Cells.
[STEPS]
SECTION: Gcase co-immunoprecipitatio... | ["[Gcase co-immunoprecipitation] Wash cells 1X with phosphate-buffered saline (PBS, Sigma‒Aldrich) and detach using Accutase.", "[Gcase co-immunoprecipitation] Pellet the cell suspension at 280 rcf, 5 min, 23 °C.", "[Gcase co-immunoprecipitation] Lyse the pellets in IP/lysis buffer (Thermo Fisher, #87787) supplemented ... |
81,154 | 5' RACE for RNA fragments with 5' phosphate | 4 | dx.doi.org/10.17504/protocols.io.261ge3mzwl47/v1 | https://www.protocols.io/view/5-39-race-for-rna-fragments-with-5-39-phosphate-cthawj2e | Marta.Gaglia | TITLE: 5' RACE for RNA fragments with 5' phosphate
AUTHORS: Marta.Gaglia
[DESCRIPTION]
This protocol will allow identification of fragments of RNA that have a 5' phosphate. It relies on ligation of an RNA adapter to the 5' end of the fragment and amplification with primers that bind the adapter and gene-specif... | ["RNA purification:\nExtract RNA and elute/resuspend in 50 µl H2O", "DNase treatment: \n\nTo each 50 µl sample, add 10 µl of DNase reaction mix containing:\n6 µl DNase buffer\n1.2 µl Turbo DNase\n1.5 µl RNasin\n1.3 µl H2O\n(total volume = 60 µl)\n\nIncubate for 15 min at 37°C (waterbath or heatblock).", "RNA extraction... |
28,181 | Aortic Banding in Mice | null | dx.doi.org/10.17504/protocols.io.7rvhm66 | null | Dale Abel | TITLE: Aortic Banding in Mice
AUTHORS: Dale Abel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This protocol describes the procedure used by the DiaComp for inducing pressure overload hypertrophy in mice.</div><div c... | ["Mice are anesthetized with 1% isoflurane delivered via nose cone. A topical depilatory agent is applied to the neck and chest and the area is cleaned with betadine and alcohol. Mice are placed supine and temperature maintained at 37ºC with a heating pad. A horizontal skin incision ~ 0.5 - 1.0 cm in length is made at ... |
68,593 | Targeted isolation of circular extrachromosomal DNA by CRISPR-CATCH | 4 | dx.doi.org/10.17504/protocols.io.ewov1ne8ygr2/v1 | https://www.protocols.io/view/targeted-isolation-of-circular-extrachromosomal-dn-ce8rthv6 | King L Hung, Howard Y. Chang | TITLE: Targeted isolation of circular extrachromosomal DNA by CRISPR-CATCH
AUTHORS: King L Hung, Howard Y. Chang
[DESCRIPTION]
This protocol enables targeted isolation of circular extrachromosomal DNA using CRISPR-Cas9-mediated linearization followed by pulsed field gel electrophoresis. Isolated DNA products can be su... | ["[Embedding cells in agarose plugs] Melt 1% Certified Low Melt Agarose solution in PBS, place in 45C water bath.", "[Embedding cells in agarose plugs] Pellet 1 million cells per agarose plug at 300g for 5 minutes. (for example, spin down 10 million cells to make 10 agarose plugs)", "[Embedding cells in agarose plugs] ... |
54,433 | Adult mouse kidney dissociation (on ice) | 1 | dx.doi.org/10.17504/protocols.io.bzd9p296 | https://www.protocols.io/view/adult-mouse-kidney-dissociation-on-ice-bzd9p296 | Andrew Potter | TITLE: Adult mouse kidney dissociation (on ice)
AUTHORS: Andrew Potter
[DESCRIPTION]
Protocol for adult (8-10 week) mouse kidney dissociation performed on ice to reduce artifact gene expression. The protocol is based on our protocol published in Development for P1 mouse kidney, however this protocol includes two layer... | ["[Isolate kidney] Coarsely mince tissue in PBS. \n\n2 min", "[Layer 1] Weigh out 25 mg coarsely minced tissue for each set of kidneys (remove PBS before weighing).\n\n25 5", "[Layer 1] Incubate digest mix for 10 min on ice with trituration and shaking. Triturate 15 strokes using 1 mL pipet set to 600 µL every 2 min; s... |
25,002 | Plasmid used for transfection trails of Hematodinium | null | dx.doi.org/10.17504/protocols.io.4nigvce | null | Imen Lassadi | TITLE: Plasmid used for transfection trails of Hematodinium
AUTHORS: Imen Lassadi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Attempts to transfect</span><span style = "font-style:italic;"> Hematodinium </span><span>was performed using a plasmid that will express eGFP under the control o... | [] |
69,810 | Testing the effect of paraquat on C. elegans behaviour when on Keio E. coli mutants (6-well plates) | 1 | dx.doi.org/10.17504/protocols.io.6qpvr4e6zgmk/v1 | https://www.protocols.io/view/testing-the-effect-of-paraquat-on-c-elegans-behavi-cgesttee | Saul Moore | TITLE: Testing the effect of paraquat on C. elegans behaviour when on Keio E. coli mutants (6-well plates)
AUTHORS: Saul Moore
[DESCRIPTION]
Protocol for screening candidate behaviour-modifying E. coli BW25113 single-gene deletion mutants from the 'Keio Collection', to investigate their differential effects on Caeno... | ["[Preparing NGM agar + pouring plates] Prior to screening, prepare the materials needed for screening C. elegans on selected Keio E. coli mutants:\n\n- 6-well plates (aka. 'imaging plates')\n- 15 mL Falcon tubes\n- 50 mL Erlenmeyer flasks\n- 90 mm Petri plates (aka. 'maintenance plates')\n- 150 mm Petri plates (aka. '... |
24,353 | Step-by-step protocol for high resolution respirometry for human heart homogenates | null | dx.doi.org/10.17504/protocols.io.3z9gp96 | null | Adéla Krajčová, Tomáš Urban, Petr Waldauf, František Duška | TITLE: Step-by-step protocol for high resolution respirometry for human heart homogenates
AUTHORS: Adéla Krajčová, Tomáš Urban, Petr Waldauf, František Duška
[STEPS]
?. [Step-by-step protocol for high resolution respirometry for human heart homogenates]
Firstly, wash properly all tubes, scissors, forceps, teflon pestl... | ["[Step-by-step protocol for high resolution respirometry for human heart homogenates]\nFirstly, wash properly all tubes, scissors, forceps, teflon pestles and glassware (including Dounce Tissue homogenizer and glass pestles) with 70% ethanol and tap water and keep them on ice to cool to 0°C. Immediatelly, before use, ... |
45,555 | 2. Gel run and transfer -Tricine | 4 | null | https://www.protocols.io/view/2-gel-run-and-transfer-tricine-bqqtmvwn | Elizabeth Fozo | TITLE: 2. Gel run and transfer -Tricine
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Western Blot</span></div></div>
[STEPS]
?. [Buffers:]
Tricine SDSRunningBuffer- dilute from 10 X to 1X Composition 10X/L100... | ["[Buffers:]\nTricine SDSRunningBuffer- dilute from 10 X to 1X Composition 10X/L100 mM Tris base (121 g)100 mM Tricine (179 g)0.1% SDS (10g)pH 8.3The pH of the 1X solution is 8.3. Do not use acid or base to adjust pH (Novex, 2003)St... |
50,781 | Large scale screening of SARS-CoV-2 variants of worldwide concern by RT-qPCR | 1 | dx.doi.org/10.17504/protocols.io.bvt5n6q6 | https://www.protocols.io/view/large-scale-screening-of-sars-cov-2-variants-of-wo-bvt5n6q6 | Katja Spiess , Ellinor Marving, Alonzo Alfaro-Núñez, Vithiagaran Gunalan, Sofie Holdflod Nielsen, Michelle G. P. Jørgensen, Anna S. Fomsgaard, Søren M. Karst, Shila Mortensen, Ria Lassaunière, Jannik Fonager, Morten Rasmussen, Maiken Worsøe Rosenstierne, Charlotta Polacek Strandh, Anne-Marie Vangsted, Claus Nielsen, A... | TITLE: Large scale screening of SARS-CoV-2 variants of worldwide concern by RT-qPCR
AUTHORS: Katja Spiess , Ellinor Marving, Alonzo Alfaro-Núñez, Vithiagaran Gunalan, Sofie Holdflod Nielsen, Michelle G. P. Jørgensen, Anna S. Fomsgaard, Søren M. Karst, Shila Mortensen, Ria Lassaunière, Jannik Fonager, Morten Rasmussen,... | ["Protocol for 96 and 384 well PCR formatPrepare three different mastermixes. Make sure to vortex all reagents before use.Mastermix 1, for detection of H69/V70 and N501Y, contains the following: Mastermix 2, for detection of E484K, contains the following: Mastermix 3, for detection of L452R, contains the following: Add... |
80,628 | Neural differentiation on EM grids - iNeurons sample preparation for cryo-ET and CLEM | 4 | null | https://www.protocols.io/view/neural-differentiation-on-em-grids-ineurons-sample-csyuwfww | Cristina Capitanio, Victoria Trinkaus, Melissa Hoyer | TITLE: Neural differentiation on EM grids - iNeurons sample preparation for cryo-ET and CLEM
AUTHORS: Cristina Capitanio, Victoria Trinkaus, Melissa Hoyer
[DESCRIPTION]
This is a protocol for differentiating AAVS1-TRE3G-NGN2 iPSCs and hESCs to iNeurons directly on EM grids for cryo-ET and cryo-CLEM. The protocol co... | ["[Starting the neural differentiation (Day 0-Day6)] We based our neural differentiation protocol, for both iPSCs and hESCs AAVS1-TRE3G-NGN2 cells, on: \n \nWe also refer to that protocol for a complete list of media and reagents. \n\nFollow the neural differentiation protocol until cell splitting on Day 6;\nOne well o... |
60,358 | Highly Parallel Droplet Sample Preparation for Single Cell Proteomics | 1 | dx.doi.org/10.17504/protocols.io.b67erhje | https://www.protocols.io/view/highly-parallel-droplet-sample-preparation-for-sin-b67erhje | Andrew Leduc, Richard Huffman, Joshua Cantlon, Saad Khan, Nikolai Slavov | TITLE: Highly Parallel Droplet Sample Preparation for Single Cell Proteomics
AUTHORS: Andrew Leduc, Richard Huffman, Joshua Cantlon, Saad Khan, Nikolai Slavov
[DESCRIPTION]
Protocol for preparing single cells for mass-spec analysis by nPOP as described by Leduc et al., 2021, 2022 DOI: 10.1101/2021.04.24.441211. n... | ["[Carrier and Reference Preparation (***Only if Carrier is used***)] Prepare cell pellets of at least 500,000 cells for all relevant cell types . Add 100% DMSO to cells to a cellular concentration of 6000 cells/ul. Incubate cells in DMSO for 20 minutes to lyse cells. Add mass spectrometry grade water to bring solution... |
36,056 | SARS-CoV-2 Sequencing on Illumina MiSeq Using ARTIC Protocol: Part 2 - Illumina DNA Flex Protocol | null | dx.doi.org/10.17504/protocols.io.bffyjjpw | https://www.protocols.io/view/sars-cov-2-sequencing-on-illumina-miseq-using-arti-bffyjjpw | Joel Sevinsky, Arian Nassiri, Heather Blankenship, Erin Young, Kevin Libuit, Kelly Oakeson, Lauren Turner, StaPH-B Consortium | TITLE: SARS-CoV-2 Sequencing on Illumina MiSeq Using ARTIC Protocol: Part 2 - Illumina DNA Flex Protocol
AUTHORS: Joel Sevinsky, Arian Nassiri, Heather Blankenship, Erin Young, Kevin Libuit, Kelly Oakeson, Lauren Turner, StaPH-B Consortium
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protoco... | ["[DNA Flex - Dilution Plate Preparation]\nDilution Plate Preparation Date/Initials:_________________Prior to starting your DNA Flex library prep, samples should be diluted into a 96 well plate as described below. Ideally, you would like each sample to be diluted such that the final volulme of sample contains ... |
null | null | null | dx.doi.org/10.17504/protocols.io.dpf5jm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
The modified dilution assay aims to partition phytoplankton mortality into virus- versus grazing-induced fractions and has previously been applied to several different environments to determine viral lysis rates of natural phytoplankton. The method involves creating a gradient o... | [] |
62,496 | Caltech-SCFA-methods fecal | 1 | dx.doi.org/10.17504/protocols.io.bp2l61rrkvqe/v1 | https://www.protocols.io/view/caltech-scfa-methods-fecal-b898rz9w | rabdelha | TITLE: Caltech-SCFA-methods fecal
AUTHORS: rabdelha
[DESCRIPTION]
This protocol details the Caltech-SCFA-methods for measurement of short-chain fatty acids in mouse fecal samples.
[STEPS]
SECTION: Sample preparation
2.
Briefly add, ice-cold extraction solvent (1:1 v/v ACN/water) to fecal sample at a ratio of 2 µL:... | ["[Sample preparation] Briefly add, ice-cold extraction solvent (1:1 v/v ACN/water) to fecal sample at a ratio of 2 µL: 1 mg sample and internal standard mix to a final concentration of 100 micromolar (µM) and subject to vortex mixing for 3 min at Room temperature and sonicate for 15 min.", "[Sample preparation] Centri... |
null | null | null | dx.doi.org/10.17504/protocols.io.jsycnfw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Secreted protein, acidic and rich in cysteine (SPARC) is differentially associated with cell proliferation and extracellular matrix (ECM) assembly. We show here the effect of exogenous SPARC inhibition/induction on ECM and mitochondrial proteins expression and on the differen... | [] |
48,981 | How to increase the number of simultaneous users allowed in an R Shiny App | 5 | null | https://www.protocols.io/view/how-to-increase-the-number-of-simultaneous-users-a-bt3vnqn6 | Sonia García-Ruiz | TITLE: How to increase the number of simultaneous users allowed in an R Shiny App
AUTHORS: Sonia García-Ruiz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">There are multiple ways of hosting a Shiny App in production. When it is required to do so over a specific URL domain, RStudio Server combined ... | ["Install ShinyProxy.ShinyProxy is a java-based open-source tool to deploy Shiny apps in a production or enterprise context https://www.shinyproxy.io/.To install it on CentOS 7:sudo yum install shinyproxy_2.3.0_x86_64.rpm", "Configure ShinyProxy.Before executing any docker image, ShinyProxy first needs to be able to co... |
76,263 | Implant Surgery: Chronic recoverable Neuropixels in mice | 1 | dx.doi.org/10.17504/protocols.io.yxmvmnn2bg3p/v5 | https://www.protocols.io/view/implant-surgery-chronic-recoverable-neuropixels-in-cnqfvdtn | Emily A Aery Jones | TITLE: Implant Surgery: Chronic recoverable Neuropixels in mice
AUTHORS: Emily A Aery Jones
[DESCRIPTION]
This protocol collection explains how to build a low-cost, lightweight system to implant 1 Neuropixels 1.0 probe or 2 Neuropixels 2.0 probes into mice, record during freely moving behavior, then recover the probes... | ["[Prepare surgical tools and field] Sterilize tips of metal instruments, ground screw, and headbar in autoclave 25 min or hot bead sterilizer 5 s . Disinfect cotton swabs, toothpick, and a weigh boat under UV light 30 min .", "[Prepare surgical tools and field] Disinfect surgical field with 10% bleach. Lay absorbent ... |
20,627 | Case - Intraperitoneal Glucose Tolerance Test | null | dx.doi.org/10.17504/protocols.io.ydtfs6n | null | Henri Brunengraber | TITLE: Case - Intraperitoneal Glucose Tolerance Test
AUTHORS: Henri Brunengraber
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This is the standard protocol for most routine glucose tolerance testing. It is performe... | ["Fast mice overnight or for 6 hours. Remove mouse from cage and put into a clean cage with water and no food (5:00PM). Next day begin GTT by 9:00AM.", "Weigh each mouse and record weight.", "Insert glucose strip into glucometer and check that the code matches for the strip being used.", "Take fasting blood glucose by ... |
32,997 | Testing repetitive tDCS on daily smoking behaviour: A placebo controlled EMA study | null | dx.doi.org/10.17504/protocols.io.bcgdits6 | https://www.protocols.io/view/testing-repetitive-tdcs-on-daily-smoking-behaviour-bcgdits6 | Ilse Verveer, Danielle Remmerswaal, Joran Jongerling, Frederik M. van der Veen, Ingmar H. A. Franken | TITLE: Testing repetitive tDCS on daily smoking behaviour: A placebo controlled EMA study
AUTHORS: Ilse Verveer, Danielle Remmerswaal, Joran Jongerling, Frederik M. van der Veen, Ingmar H. A. Franken
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The aim of the study was to explore the effect... | [] |
81,613 | TS Procure 812 - primary fixation formalin/wet tissue (TM - 013) | 4 | dx.doi.org/10.17504/protocols.io.bp2l61qbdvqe/v2 | https://www.protocols.io/view/ts-procure-812-primary-fixation-formalin-wet-tissu-ctxmwpk6 | sandra.crameri | TITLE: TS Procure 812 - primary fixation formalin/wet tissue (TM - 013)
AUTHORS: sandra.crameri
[DESCRIPTION]
The method is used to process formalin fixed histological tissues to Procure 812 resin blocks.
[GUIDELINES]
Sample is not optimal for EM, best to dissect and use only the outer 2mm of tissue mass. Sample is ... | ["[HEADER] SAN:\n\n\n\n\nSPEC No:\n\n\n\n\nOPERATOR & STEPS:\n\n\n\n\nOPERATOR & STEPS:", "[Primary fixation] Formalin for undefined extended period of time at Room temperature", "[Conventional] 2.5 % volume in 0.1 Molarity (M) Sorenson's Phosphate buffer (pH 7.2, 300mosmol/kg) for at least 40 min or overnight", "[C... |
34,600 | DNA Fragmentation & Library Construction | 2 | dx.doi.org/10.17504/protocols.io.bp2l6nr4zgqe/v1 | https://www.protocols.io/view/dna-fragmentation-amp-library-construction-bd2gi8bw | Marina McCowin | TITLE: DNA Fragmentation & Library Construction
AUTHORS: Marina McCowin
[DESCRIPTION]
The KAPA HyperPlus Kit provides a versatile, streamlined DNA fragmentation and library construction protocol for the rapid preparation of libraries for Illumina sequencing. The one-tube chemistry and protocol improves the efficie... | [] |
108,556 | Chemical fixation of Solarion arianae for transmission electron microscopy | 0 | dx.doi.org/10.17504/protocols.io.kxygxyd5zl8j/v1 | https://www.protocols.io/view/chemical-fixation-of-solarion-arianae-for-transmis-dm9k494w | Marek Valt, Pavla Hrubá | TITLE: Chemical fixation of Solarion arianae for transmission electron microscopy
AUTHORS: Marek Valt, Pavla Hrubá
[DESCRIPTION]
This is an optimized version of the protocol for standard chemical fixation for transmission electron microscopy that was used for the fixation of the culture of Solarion arianae.
[STEPS]
... | ["[Cell harvest] Centrifuge a well-grown culture at 1250 g at 4 °C.", "[Chemical cell fixation] Immerse pellet with 2,5% glutaraldehyde fixative in 0,1M cacodylate buffer solution for 1h. Work on ice.", "[Cell harvest] Discard supernatant and collect pellet.", "[Chemical cell fixation] Wash with 0,1M cacodylate buffer,... |
66,881 | Fluorescence size exclusion chromatography (FSEC) from ATP13A2 microsomes | 6 | dx.doi.org/10.17504/protocols.io.81wgb6bpolpk/v1 | https://www.protocols.io/view/fluorescence-size-exclusion-chromatography-fsec-fr-cdi9s4h6 | Sue Sim, eunyong_park | TITLE: Fluorescence size exclusion chromatography (FSEC) from ATP13A2 microsomes
AUTHORS: Sue Sim, eunyong_park
[DESCRIPTION]
Using fluorescence size exclusion chromatography (FSEC) to analyze ATP13A2 expression in microsomes
[STEPS]
1. Thaw 100 μg microsomes on ice
2. Resuspend microsomes in Lysis Buffer and fina... | ["Thaw 100 μg microsomes on ice", "Resuspend microsomes in Lysis Buffer and final volume 1% DDM/0.2% CHS (1X pellet, 3X Lysis Buffer, 1X 5% DDM/1% CHS) at 4 °C", "DDM: n-dodecyl-β-D-maltopyranoside (Anatrace)", "CHS: cholesteryl hemisuccinate (Anatrace)", "Solubilize by rotating end-over-end for 2 h at 4C", "Clarify ly... |
36,591 | Phosphate Buffered Saline (PBS) | null | dx.doi.org/10.17504/protocols.io.bfypjpvn | https://www.protocols.io/view/phosphate-buffered-saline-pbs-bfypjpvn | Neilier Junior | TITLE: Phosphate Buffered Saline (PBS)
AUTHORS: Neilier Junior
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A buffer solution has the function of resisting changes in pH even when adding powerful acids or bases. However, in the physiological environment the buffered system also provides cofactors... | ["[Phosphate Buffered Saline (PBS)]\nPrepare by dissolving , and in .\n150 mM NaCl10 mM Potassium Phosphate buffer\n[PBS]\n[NaCl]\n[K2HPO4 • 3H2O]\n[KH2PO4]\n[distilled water]", "[Phosphate Buffered Saline (PBS)]\nAdjust the pH before use.", "[Phosphate Buffered Saline (PBS)]\nA variation of PBS can also be prepared... |
86,540 | NucBarcoder - a bioinformatic pipeline to characterise the genetic basis of plant species differences | 5 | dx.doi.org/10.17504/protocols.io.5qpvo33rzv4o/v1 | https://www.protocols.io/view/nucbarcoder-a-bioinformatic-pipeline-to-characteri-cyrkxv4w | Wu Huang, Alex Twyford, Peter Hollingsworth | TITLE: NucBarcoder - a bioinformatic pipeline to characterise the genetic basis of plant species differences
AUTHORS: Wu Huang, Alex Twyford, Peter Hollingsworth
[DESCRIPTION]
There are now a significant number of studies that have sequenced multiple loci from the nuclear genomes of plants and these are available in p... | ["[Overview of the data management and the structure of NucBarcoder]", "[Data cleaning and filtering] Data cleaning and filtering were performed at both the individual and locus levels. \nDifferent clean-up and filtering tools were used for aligned sequence formats and SNP matrices. VCFtools (0.1.17) (Danecek et al., 2... |
null | null | null | dx.doi.org/10.17504/protocols.io.e2tbgen | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The cells targeted by the Nanobeads are either selected or depleted by incubating your sample with the directly conjugated magnetic particles. The magnetically labeled fraction is retained by the use of a magnetic separator. After collection of the targeted cells, downstream ... | [] |
54,914 | Starlet Sea Anemone (Nematostella vectensis) 2021 Environmental Summary, Reptile & Aquatics, Stowers Institute for Medical Research | 3 | dx.doi.org/10.17504/protocols.io.bzvap62e | https://www.protocols.io/view/starlet-sea-anemone-nematostella-vectensis-2021-en-bzvap62e | Shane C. Miller, Diana P Baumann, M. Shane Merryman | TITLE: Starlet Sea Anemone (Nematostella vectensis) 2021 Environmental Summary, Reptile & Aquatics, Stowers Institute for Medical Research
AUTHORS: Shane C. Miller, Diana P Baumann, M. Shane Merryman
[DESCRIPTION]
The starlet sea anemone (Nematostella vectensis) is an emerging model organism, and we have maintai... | [] |
52,731 | ADP-Glo kinase assay | 4 | dx.doi.org/10.17504/protocols.io.bxq3pmyn | https://www.protocols.io/view/adp-glo-kinase-assay-bxq3pmyn | Chunmei Chang | TITLE: ADP-Glo kinase assay
AUTHORS: Chunmei Chang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">An assay for measuring ULK1 kinase activity</div></div>
[STEPS]
?. Make a mixture of 100 nM purified wild-type or kinase dead ULK1 complex with 5 µM ULKtide in the presence or absence of 100 µM ATP. ... | ["Make a mixture of 100 nM purified wild-type or kinase dead ULK1 complex with 5 µM ULKtide in the presence or absence of 100 µM ATP. The total volume is 50 µL.", "Add 50 µL ATP-depletion reagent to terminate the reaction and deplete the unconsumed ATP.", "Incubate at room temperature for 40 min.", "Add 10 µL of kinase... |
null | null | null | dx.doi.org/10.17504/protocols.io.ftjbnkn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Yeast is a well-characterized genome due to its small size and historical significance in genetics. The website http://yeastgenome.org/ is a dedicated resource for yeast genomics.</p>
<p> </p>
<p>For this exercise, I want you to create a "Makefile" that will execute this ent... | [] |
78,441 | Protein Transfer using Bio-rad TransBlot Turbo with Turbo RTA Transfer Kit | 4 | null | https://www.protocols.io/view/protein-transfer-using-bio-rad-transblot-turbo-wit-cquhvwt6 | Lynn Doran, Steven J Burgess | TITLE: Protein Transfer using Bio-rad TransBlot Turbo with Turbo RTA Transfer Kit
AUTHORS: Lynn Doran, Steven J Burgess
[DESCRIPTION]
A protocol for transfer of proteins from acrylamide gels onto nitrocellulose membrane for immunoblot analysis. This protocol is based on the assumption that TGX pre-cast gels have bee... | ["Place the gel in the middle of the membrane and roll to remove air-bubbles.", "Place the top stack on top of the gel, gently roll", "Close the cassette lid, taking care not to disturb the gel", "Place the cassette in the Trans-Blot Turbo and follow the instructions on the machine (Fast protocol TGX gel - 3 minutes)... |
null | null | null | dx.doi.org/10.17504/protocols.io.i35cgq6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?. | [] |
84,802 | LRRK1 expression and purification | 4 | dx.doi.org/10.17504/protocols.io.rm7vzx3b5gx1/v1 | https://www.protocols.click/view/lrrk1-expression-and-purification-cw3axgie | Yu Xuan Lin, janice reimer | TITLE: LRRK1 expression and purification
AUTHORS: Yu Xuan Lin, janice reimer
[DESCRIPTION]
Protein purification protocol for full-length LRRK1 as done by Leschziner and Reck-Peterson Labs.
Original protocol by Janice M. Reimer and Yu Xuan Lin.
[STEPS]
SECTION: His6-Z-TEV-LRRK1 Purification
1. N-terminally tagged Hi... | ["[His6-Z-TEV-LRRK1 Purification] N-terminally tagged His6-Z-TEV-LRRK1(FL) was expressed in Sf9 insect cells. Insect cells were infected with baculovirus and grown at 27°C for 3 days.", "[His6-Z-TEV-LRRK1 Purification] Cells were harvested and then resuspended in lysis buffer (50mM HEPES pH 7.4, 500 mM NaCl, 20 mM imid... |
24,779 | 96-well Plate Growth Curve Setup | null | dx.doi.org/10.17504/protocols.io.4fjgtkn | null | Norman van Rhijn, Panagiotis Papastamoulis, Takanori Furukawa, Magnus Rattray, Elaine Bignell, Mike Bromley | TITLE: 96-well Plate Growth Curve Setup
AUTHORS: Norman van Rhijn, Panagiotis Papastamoulis, Takanori Furukawa, Magnus Rattray, Elaine Bignell, Mike Bromley
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Generally, growth assays for filamentous fungi have been performed on solid media, either... | ["[Plate preparation]\nHarvest and dilute spores in PBS+0.01% Tween to 4*105 spores/mL.", "[Plate preparation]\nAliquot 5 uL of this spore stock per well of a CytoOne 96-well plate (Starlab) non-coated, this will be overlayed with 195 uL of liquid media to a total volume of 200 uL.\nThis equals to 2000 spores (absolute... |
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