id float64 1.55k 110k ⌀ | title stringlengths 1 256 ⌀ | template_id float64 0 6 ⌀ | doi stringlengths 39 49 ⌀ | url stringlengths 40 92 ⌀ | authors stringlengths 1 933 ⌀ | protocol_text stringlengths 34 1.08M | steps_list stringlengths 2 269k |
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45,436 | 1 | 6 | dx.doi.org/10.17504/protocols.io.bqk4muyw | https://www.protocols.io/view/1-bqk4muyw | Daniela Patricia Rueda Quintero | TITLE: 1
AUTHORS: Daniela Patricia Rueda Quintero
[STEPS]
?.
?. LABORATORIO 1. DETERMINACIÓN PUNTO DE EBULLICIÓNINTRODUCCIÓN
?. | ["LABORATORIO 1. DETERMINACIÓN PUNTO DE EBULLICIÓNINTRODUCCIÓN"] |
null | null | null | dx.doi.org/10.17504/protocols.io.rifd4bn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol, developed in 2011 by Angela Poole while in the Weis lab, is a quick prep for protein extraction from Aiptasia adults.</p>
[BEFORE_START]
<p><strong>RIPA extraction buffer:</strong></p>
<ul>
<li>100mM Tris, pH 7.4</li>
<li>100mM NaCl</li>
<li>10mM EDTA, pH 8.0<... | [] |
91,869 | A universal protocol for high-quality DNA and RNA isolation from diverse plant species | 4 | dx.doi.org/10.17504/protocols.io.8epv5xj86g1b/v3 | https://www.protocols.io/view/a-universal-protocol-for-high-quality-dna-and-rna-c5x5y7q6 | Farhad Masoomi-Aladizgeh, Leila Jabbari, Reza Khayam Nekouei, Ali Aalami, Brian J Atwell, Paul A Haynes | TITLE: A universal protocol for high-quality DNA and RNA isolation from diverse plant species
AUTHORS: Farhad Masoomi-Aladizgeh, Leila Jabbari, Reza Khayam Nekouei, Ali Aalami, Brian J Atwell, Paul A Haynes
[DESCRIPTION]
Next-generation sequencing demands high-quality nucleic acid, yet isolating DNA and RNA from plant... | ["[Lysis Buffer for DNA and RNA Isolation] The lysis buffer contains 0.5% CTAB, 1% EDTA, 2.5% Tris base and 5% NaCl. These are the four main components of the lysis buffer for DNA and RNA isolation from plant tissues. \n\nExample: Add CTAB (125 mg), EDTA (250 mg), Tris base (625 mg), and NaCl (1250 mg) to 25 ml nucleas... |
29,543 | SNP Calling and VCF Filtering Pipeline | 1 | dx.doi.org/10.17504/protocols.io.84fhytn | https://www.protocols.io/view/snp-calling-and-vcf-filtering-pipeline-84fhytn | M Renee Bellinger | TITLE: SNP Calling and VCF Filtering Pipeline
AUTHORS: M Renee Bellinger
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">SNP-calling and genotype filtering using bowtie2, samtools, bcftools, and vcftools</div><div class = "text-block"><span>This pipeline was used for calling SNPs using GBS data obt... | ["[CALL SNPS]\n# copy the genome to a working folder and unzip it to be a \"working copy\"cp /your/path/to/genome/genome.gz genome.fasta.gzgunzip genome.fasta.gz", "[CALL SNPS]\n# index genomesamtools faidx genome.fastabowtie2-build genome.fasta genome", "[CALL SNPS]\n# Map demultiplexed GBS reads with bowtie2 or a pro... |
38,784 | Long-Term Storage of Bacteria | 4 | null | https://www.protocols.io/view/long-term-storage-of-bacteria-bh48j8zw | Huan Jui Chang, Hung Liang Pai | TITLE: Long-Term Storage of Bacteria
AUTHORS: Huan Jui Chang, Hung Liang Pai
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is suitable for preparing bacterial storage for -80 degree Celsius with glyceral as the solvent. It is usually performed after the overnight incubation of transf... | ["[Preparation]\nTurn on the UV light of the laminar flow for to in order to sterilize it.", "[Protocol]\nAdd 300 μL of 50% glycerol into an eppendorf.", "[Protocol]\nAdd 600 μL of bacterial media prepared in a procedure like \"Bacterial Culture for Plasmid Extraction\" to an eppendorf.", "[Protocol]\nStore the eppe... |
null | null | null | dx.doi.org/10.17504/protocols.io.grtbv6n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 1">
<div class="layoutArea">
<div class="column">
<p>This is an In-Cell Western™ Assay protocol for the detection of Phospho-p53 in COS cells in response to Hydroxyurea.</p>
<p> </p>
<p><strong>Developed for:</strong></p>
<p> </p>
<p>Aerius,<br /> O... | [] |
48,660 | Protocol for variant calling in SARS-Cov-2 enabling long indel detection | 5 | dx.doi.org/10.17504/protocols.io.btrunm6w | https://www.protocols.io/view/protocol-for-variant-calling-in-sars-cov-2-enablin-btrunm6w | Juanjo Bermúdez | TITLE: Protocol for variant calling in SARS-Cov-2 enabling long indel detection
AUTHORS: Juanjo Bermúdez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for SARS-Cov-2 variant calling departing from raw reads in a run. First, we will de-novo assemble the genome using s-aligner, then we will... | ["Assemble the genome\n{\"blocks\":[{\"key\":\"amjfu\",\"text\":\"This is a protocol for using Contignant s-aligner to de-novo assemble SARS-Cov-2 genomes. S-aligner outperforms common open-source software for de novo-assembly of viruses by 110% increased performance.\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRa... |
67,411 | Diaetoxil kaufen (Diettoxil,Test & chris tall) Bewertungen DE – Funktionieren diese Kapseln? Diaetoxil kaufen Update! | 1 | dx.doi.org/10.17504/protocols.io.n92ldzkbxv5b/v1 | https://www.protocols.io/view/diaetoxil-kaufen-diettoxil-test-amp-chris-tall-bew-cd3ts8nn | metcarter | TITLE: Diaetoxil kaufen (Diettoxil,Test & chris tall) Bewertungen DE – Funktionieren diese Kapseln? Diaetoxil kaufen Update!
AUTHORS: metcarter
[DESCRIPTION]
Produktname: Dietoxil (Diaetoxil Test,kaufen & chris tall)
Nebenwirkung: Keine größeren Nebenwirkungen bekannt
Erwartete Ergebnisse: In 2 – 3 Monaten
Be... | ["[Diaetoxil kaufen (Diettoxil,Test & chris tall) Bewertungen DE – Funktionieren diese Kapseln? Diaetoxil kaufen Update!]"] |
78,865 | SARS-CoV-2 inactivation and scRNAseq sample preparation protocol | 4 | dx.doi.org/10.17504/protocols.io.kqdg3999eg25/v2 | https://www.protocols.io/view/sars-cov-2-inactivation-and-scrnaseq-sample-prepar-cq9rvz56 | Raven M Osborn, Justin Leach, Michelle Zanche, John M. Ashton, ChinYi Chu, Juilee Thakar, Stephen Dewhurst, Sonia Rosenberger, Martin Pavelka, Gloria S Pryhuber, Thomas J. Mariani, Christopher Anderson | TITLE: SARS-CoV-2 inactivation and scRNAseq sample preparation protocol
AUTHORS: Raven M Osborn, Justin Leach, Michelle Zanche, John M. Ashton, ChinYi Chu, Juilee Thakar, Stephen Dewhurst, Sonia Rosenberger, Martin Pavelka, Gloria S Pryhuber, Thomas J. Mariani, Christopher Anderson
[DESCRIPTION]
Coronavirus disease (C... | ["[Lifting cells from tissue culture plate] Set up the biosafety cabinet according to your institution’s BSL3 biosafety cabinet setup standard operating procedure or the \"Basic Biosafety Cabinet Setup” supplied in this protocol.", "[Lifting cells from tissue culture plate] Transfer the tissue culture plates, in a seco... |
35,709 | Sample preparation to mass spectrometer using ZipTipC18 | null | dx.doi.org/10.17504/protocols.io.be45jgy6 | https://www.protocols.io/view/sample-preparation-to-mass-spectrometer-using-zipt-be45jgy6 | Neilier Junior | TITLE: Sample preparation to mass spectrometer using ZipTipC18
AUTHORS: Neilier Junior
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">ZipTip is a 10 µL pipette tip that aims to concentrate and purify from femtomols to picomols protein and oligopeptide .</div></div>
[STEPS]
?. [Prepae the materials... | ["[Prepae the materials and workspace]\nCalibrate the P-10 pipette to 10 μL.", "[Prepae the materials and workspace]\nName 4 microtubes of 1.5 mL with the respective reagents:ACN100% (I)TFA0.1% (I)TFA 0.1% (II)ACN100% (II)Add 1 mL of the respective solutions to the tubes above.", "[Prepae the materials and workspace]\n... |
86,422 | Preparation of human iPSC-derived cortical neuronal progenitors for transplantation into the rodent brain | 4 | dx.doi.org/10.17504/protocols.io.x54v9ppeqg3e/v1 | https://www.protocols.io/view/preparation-of-human-ipsc-derived-cortical-neurona-cymwxu7e | louise.cottle, Clare Parish | TITLE: Preparation of human iPSC-derived cortical neuronal progenitors for transplantation into the rodent brain
AUTHORS: louise.cottle, Clare Parish
[DESCRIPTION]
This protocol describes how we prepare human iPSC-derived cells, that have been differentiated into cortical neuronal
progenitors, for transplantation into... | ["[Preparation of cell suspension] Prepare a Falcon tube with 2 mLbase cortical media plus Rock inhibitor (Ri, 1:1000\ndilution)\nWash cells with 300 µL PBS -/- (gently run PBS down the side of each well)\nIncubate cells in 300 µL Accutase (per well) at 37 °C to lift cells off wells in small\nclumps\n - Monitor... |
18,863 | Baited live-trapping of triatomines in semi-arid environments | null | dx.doi.org/10.17504/protocols.io.wnpfddn | null | Carezza Botto-Mahan, Antonella Bacigalupo, Viviana Estadella, Berenice Cornejo-Villar, Juana P. Correa, Pedro E. Cattan | TITLE: Baited live-trapping of triatomines in semi-arid environments
AUTHORS: Carezza Botto-Mahan, Antonella Bacigalupo, Viviana Estadella, Berenice Cornejo-Villar, Juana P. Correa, Pedro E. Cattan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Includes a list of materials, baits, references, and r... | ["[Triatomine trapping]\nVisually prospect the areas where is intended to collect triatomines, searching for suitable locations to find these insects; for example, rocky outcrops, bromeliads, rock piles, animals burrows, etc.", "[Triatomine trapping]\nSet the traps with adequate bait: in the hot season during the day, ... |
99,508 | Live-cell imaging of the plasma membrane of Jurkat T cells | 0 | dx.doi.org/10.17504/protocols.io.kxygxyzxzl8j/v1 | https://www.protocols.io/view/live-cell-imaging-of-the-plasma-membrane-of-jurkat-ddeu23ew | Ezra Bruggeman, Markus Körbel | TITLE: Live-cell imaging of the plasma membrane of Jurkat T cells
AUTHORS: Ezra Bruggeman, Markus Körbel
[DESCRIPTION]
This is a protocol for the preparation of a Jurkat T cells for live imaging of the plasma membrane. This protocol was used to generate the data shown in Figure 6 of the following publication:
Bruggem... | ["[Cell culture] J8 LFA-1 cells were incubated overnight (approximately 1080 min) in complete-RPMI (StableCell RPMI-1640 media, Sigma) supplemented with 10 % (v/v) fetal calf serum (FCS), 1 % (v/v) HEPES buffer, and 1 % (v/v) pen/strep antibiotics.", "[Cell culture] 1 mL of cells were collected by centrifugation and re... |
null | null | null | dx.doi.org/10.17504/protocols.io.cnzvf5 | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
It is important to plan the timing of the embryo collection in advance. To select a specific genotype, be sure to cross in the selectable balancer that will allow you to distinguish mutants from non-mutants. To prevent the collection of unfertilized animals into sample, it is h... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ssxeefn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Background: </strong>The spotted sea bass (<em>Lateolabrax maculatus</em>) is a valuable commercial fish that is widely cultured in China. While analyses using molecular markers and population genetics have been conducted, genomic resources are lacking.</p>
<p><strong... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.gz8bx9w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This method describes the preparation of Illumina sequencing libraries with a 1/20 scale Nextera protocol. Typically, yeast or E. coli plasmid DNA is the input. </p>
<p> </p>
<p> </p>
<p>Method derived from: </p>
<p>Baym M, Kryazhimskiy S, Lieberman TD, Chung H, Desai MM, Ki... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.hdfb23n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for DNase I digestion of nuclei for 'double hit' DNase-SEQ analysis adapted from doi:10.1038/nmeth.2762</p>
<p> </p>
<p>As a general guide DNA should show moderate to light smearing after completing the protocol as seen the gel image in Figure 1.</p>
<p> </p>
<p><img... | [] |
85,076 | Anti oxidant and apoptotic activities of sitagliptin | 4 | dx.doi.org/10.17504/protocols.io.5jyl8p587g2w/v1 | https://www.protocols.click/view/anti-oxidant-and-apoptotic-activities-of-sitaglipt-cxbuxinw | ruqaya alameen, ahsan f. bairam | TITLE: Anti oxidant and apoptotic activities of sitagliptin
AUTHORS: ruqaya alameen, ahsan f. bairam
[DESCRIPTION]
Abstract
Background: Hepatocellular carcinoma (HCC) is the most common and aggressive
type of liver cancer. Most chemotherapeutic medications nowadays imply
oxidative stress leading to toxicity, which... | ["The cell were cultured into a 96-well plate with RPMI-1640 and then incubated for 24 hours", "The old medium was discarded and 200 μL of medium containing the test medicines was added", "Five primary groups were utilized including the control group, which were: control group, cisplatin-treated HepG2 group, sitaglipti... |
34,743 | CRITERIA TO EVALUATE NEUROGENIC BOWEL IN CHILDREN WITH CONGENITAL ZIKA SYNDROME | null | dx.doi.org/10.17504/protocols.io.bd6xi9fn | null | Valeria Azevedo De Almeida, Nancy Sotero, Lilian Lira Lisboa, Rafael Pauletti Gonçalves, Edgard Morya, Lucia Monteiro, Reginaldo Antônio de Oliveira Freitas Júnior | TITLE: CRITERIA TO EVALUATE NEUROGENIC BOWEL IN CHILDREN WITH CONGENITAL ZIKA SYNDROME
AUTHORS: Valeria Azevedo De Almeida, Nancy Sotero, Lilian Lira Lisboa, Rafael Pauletti Gonçalves, Edgard Morya, Lucia Monteiro, Reginaldo Antônio de Oliveira Freitas Júnior
[DESCRIPTION]
<div class = "text-blocks"><div class = "text... | ["Initial Assessment:\nIt must contain detailed clinical history, describing bowel habits, including continence, water intake and diet type, current medications and any special regimen for bowel emptying, as well as frequency of bowel emptying and stool characteristics.", "Bristol Stool Scale:It is recommended the use ... |
35,262 | River biofilms sampling for both downstream DNA analysis and microscopic counts | 1 | dx.doi.org/10.17504/protocols.io.ben6jdhe | https://www.protocols.io/view/river-biofilms-sampling-for-both-downstream-dna-an-ben6jdhe | Frederic Rimet, Marine Vautier, Rainer Kurmayer, Nico Salmaso, Camilla Capelli, Agnès Bouchez, Peter Hufnagl, Isabelle Domaizon | TITLE: River biofilms sampling for both downstream DNA analysis and microscopic counts
AUTHORS: Frederic Rimet, Marine Vautier, Rainer Kurmayer, Nico Salmaso, Camilla Capelli, Agnès Bouchez, Peter Hufnagl, Isabelle Domaizon
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" styl... | ["[When & where to sample]\nChoice of the sampling season an period- Season: Sampling in the framework of national river monitoring networks is usually carried out during low flow season, optimally during the natural low-water period of the respective water body under clear water conditions (i.e. summer in Europe).-... |
82,508 | DQ-BSA assay | 4 | dx.doi.org/10.17504/protocols.io.kxygx9r9dg8j/v1 | https://www.protocols.click/view/dq-bsa-assay-cutkwwkw | Narayana Yadavalli, Shawn M. Ferguson | TITLE: DQ-BSA assay
AUTHORS: Narayana Yadavalli, Shawn M. Ferguson
[DESCRIPTION]
This protocol describes the DQ BSA assay for measuring the lysosomal proteolytic activity.
[STEPS]
SECTION: DQ-BSA assay
1. Plate 100,000 mature macrophages or microglia or BMDM were seeded on Mattek glass bottom dishes.
SECTION: DQ-BSA ... | ["[DQ-BSA assay] Plate 100,000 mature macrophages or microglia or BMDM were seeded on Mattek glass bottom dishes.", "[DQ-BSA assay] Next day treat cells with 50 nanomolar (nM) MLi2 or 250 nanomolar (nM) LRRK2-IN-1 for 120 min followed by 60 min treatment with 10 µg/mL DQ-BSA (Thermo Fisher Scientific, #D12051) and 50 µ... |
27,416 | Peripheral Blood Mononuclear Cells Preparation | null | dx.doi.org/10.17504/protocols.io.6zyhf7w | null | John Davis Coakley | TITLE: Peripheral Blood Mononuclear Cells Preparation
AUTHORS: John Davis Coakley
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">How to prepare PBMCs for Stimulation experiment</div></div>
[STEPS]
?. Dilute whole blood 1:1 with 1% FCS HBSS Medium
?. Layer this diluted blood onto 10mls LymphoprepTM... | ["Dilute whole blood 1:1 with 1% FCS HBSS Medium", "Layer this diluted blood onto 10mls LymphoprepTM", "Centrifuge for 25 minutes at 400G with acceleration and brake off", "Discard the plasma and obtain the buffy coat", "Top up buffy coat with 1% FCS, vortex and Centrifuge for 8 minutes at 1500RPM with brake on. Discar... |
60,110 | TMA-TNP Section Map and Slide Processing - Phase 3 | 1 | dx.doi.org/10.17504/protocols.io.6qpvr6992vmk/v1 | https://www.protocols.io/view/tma-tnp-section-map-and-slide-processing-phase-3-b6xnrfme | Heidi S Feiler | TITLE: TMA-TNP Section Map and Slide Processing - Phase 3
AUTHORS: Heidi S Feiler
[DESCRIPTION]
Human Tumor Atlas Tissue MicroArrary TNP (TMA-TNP)
The Tissue MicroArray (TMA) TNP will extend the SARDANA-TNP characterization and analytics methodologies for evaluation and validation on a large array of breast tumor ... | ["[Preparation] Verify the identity of the FFPE block to be cut against written request for sectioning. The FFPE block (TMA1) will be utilized for TMA-TNP Phase 3.", "[Preparation] Each slide was labeled with a unique OHSU Slide ID corresponding to the FFPE section map (below).\n\n Slide ID ... |
91,663 | Open field test | 1 | dx.doi.org/10.17504/protocols.io.n2bvj3bxnlk5/v1 | https://www.protocols.io/view/open-field-test-c5rpy55n | Pranay Srivastava | TITLE: Open field test
AUTHORS: Pranay Srivastava
[DESCRIPTION]
Open field test can be used to evaluate locomotor activity in rodents.
[STEPS]
1. Prepare the open field arena.
2. Allow the animal to acclimate to the testing environment for one hour.
3. The mice were placed in the plexiglass chamber (11 × 11 in with c... | ["Prepare the open field arena.", "Allow the animal to acclimate to the testing environment for one hour.", "The mice were placed in the plexiglass chamber (11 × 11 in with clear 8-in high walls) and were allowed to explore for a period of 10 min.", "The total distance travelled was measured with software Ethovision XT... |
42,929 | Gene Regulatory Network | 5 | dx.doi.org/10.17504/protocols.io.bm6rk9d6 | https://www.protocols.io/view/gene-regulatory-network-bm6rk9d6 | Amin Mohamed, Antonio Reverter, James Kijas | TITLE: Gene Regulatory Network
AUTHORS: Amin Mohamed, Antonio Reverter, James Kijas
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Gene regulatory networks (GRNs) provide a platform for integrating multiomic data and can be used to characterize the dynamics of perturbations during biological ... | ["Master regulator analysis was performed using regulatory impact factor (RIF) metrics (Reverter et al., 2010) to identify key regulators contributing to the differential expression in the T4 vs T1 comparison in each tissue. Data for potential transcription factors (TFs) in Atlantic salmon were retrieved (Mohamed et al... |
37,904 | Quick Protocol for Monarch® Plasmid Miniprep Kit (NEB #T1010) | 1 | dx.doi.org/10.17504/protocols.io.bg9qjz5w | https://www.protocols.io/view/quick-protocol-for-monarch-plasmid-miniprep-kit-ne-bg9qjz5w | New England Biolabs | TITLE: Quick Protocol for Monarch® Plasmid Miniprep Kit (NEB #T1010)
AUTHORS: New England Biolabs
[DESCRIPTION]
This is the quick version of the Monarch® Plasmid DNA Miniprep Kit Protocol (NEB #T1010). For the full protocol, please click here.
[BEFORE_START]
All centrifugation steps should be carried out at 16000 x g... | ["Pellet 1 mL–5 mL (not to exceed 15 OD units) bacterial culture by centrifugation at 16000 x g for 30 s. Discard supernatant.", "Resuspend pellet in 200 µL.", "Add 200 µL, gently invert tube 5–6 times, and incubate at 4 Room temperature for 1 min. Do not vortex.", "Add 400 µL, gently invert tube until neutralized, and... |
22,764 | 03: Gene Prediction | null | dx.doi.org/10.17504/protocols.io.2gkgbuw | null | Frank Aylward | TITLE: 03: Gene Prediction
AUTHORS: Frank Aylward
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Let's start by downloading a Staphylococcus aureus genome from NCBI:wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/009/585/GCF_000009585.1_ASM958v1/GCF_000009585.1_ASM958v1_genomic.fna.gzand let's make su... | ["Let's start by downloading a Staphylococcus aureus genome from NCBI:wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/009/585/GCF_000009585.1_ASM958v1/GCF_000009585.1_ASM958v1_genomic.fna.gzand let's make sure to unzip it so that we can access the .fna file directly (gunzip command). Make sure to use \"head\" and \... |
null | null | null | dx.doi.org/10.17504/protocols.io.g93bz8n | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
17,458 | CHROMagar Malassezia Medium (CHROM) | 1 | dx.doi.org/10.17504/protocols.io.6qpvre38plmk/v1 | https://www.protocols.click/view/chromagar-malassezia-medium-chrom-vase2ee | Amy Gladfelter | TITLE: CHROMagar Malassezia Medium (CHROM)
AUTHORS: Amy Gladfelter
[DESCRIPTION]
Media recipe for growth of Malassezia species.
[STEPS]
1. CHROMagar Malassezia basal medium 56.3 g
2. Tween 40 10 mL
3. dH2O 1 L
4. Sterilize by autoclaving. | ["CHROMagar Malassezia basal medium 56.3 g", "Tween 40 10 mL", "dH2O 1 L", "Sterilize by autoclaving."] |
106,542 | Annotation for Fungi | 0 | dx.doi.org/10.17504/protocols.io.e6nvw14nwlmk/v2 | https://www.protocols.io/view/annotation-for-fungi-dkan4sde | Sebastian Bassi, Virginia Gonzalez, Tristan Yang | TITLE: Annotation for Fungi
AUTHORS: Sebastian Bassi, Virginia Gonzalez, Tristan Yang
[DESCRIPTION]
Protocol to annotate a fungi genome
[STEPS]
SECTION: Setup
1. Install Docker
If you don't have Docker already, install it. There are two versions, Docker Engine (also known as CE) and Docker Desktop. The Desktop versi... | ["[Setup] Install Docker\n\nIf you don't have Docker already, install it. There are two versions, Docker Engine (also known as CE) and Docker Desktop. The Desktop version is more user friendly but since may require commercial license for large enterprise, this tutorial is based on the Docker engine. Both version will w... |
55,219 | Effect of antioxidants agents on Dentinal Tubular Penetration of EndoREZ sealer on sodium hypochlorite-treated root canal dentin: A Scanning electron microscopic study | 4 | dx.doi.org/10.17504/protocols.io.bz6tp9en | https://www.protocols.io/view/effect-of-antioxidants-agents-on-dentinal-tubular-bz6tp9en | Sudhir Varma | TITLE: Effect of antioxidants agents on Dentinal Tubular Penetration of EndoREZ sealer on sodium hypochlorite-treated root canal dentin: A Scanning electron microscopic study
AUTHORS: Sudhir Varma
[DESCRIPTION]
According to ISO, the canals were enlarged to a size 30, 6% taper with ProTaper gold (Dentsply Sirona, Ball... | ["[Methodology] Extracted mandibular premolars (n=50) were taken. The samples were randomly divided into 5 groups. These samples were autoclaved, later decoronated using a sectioning disc to attain a 14-mm length of the root from the apex, segregated into five groups.To prevent apical extrusion, sticky wax was used to ... |
40,491 | Binding properties of immunoglobulin-binding protein by double immunodiffusion (Ouchterlony) technique. | 4 | dx.doi.org/10.17504/protocols.io.bjsjkncn | https://www.protocols.io/view/binding-properties-of-immunoglobulin-binding-prote-bjsjkncn | Angel Justiz-Vaillant | TITLE: Binding properties of immunoglobulin-binding protein by double immunodiffusion (Ouchterlony) technique.
AUTHORS: Angel Justiz-Vaillant
[STEPS]
?. The binding of SpLAG, SpLG and SpAG with animal sera, avian IgY, and purified mammalian IgG are investigated by double immunodiffusion.
?. Briefly, 1% agarose gels... | ["The binding of SpLAG, SpLG and SpAG with animal sera, avian IgY, and purified mammalian IgG are investigated by double immunodiffusion.", "Briefly, 1% agarose gels are prepared and wells cut into the gel using a template.", "Initially, aliquots of 25 µl each of the immunoglobulin-bacterial protein SpLAG, SpLG or SpA... |
null | null | null | dx.doi.org/10.17504/protocols.io.ha8b2hw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?. | [] |
57,217 | mPSM protocol | 4 | null | https://www.protocols.io/view/mpsm-protocol-b349qqz6 | Takehito Tomita | TITLE: mPSM protocol
AUTHORS: Takehito Tomita
[DESCRIPTION]
Protocol to perform 2D ex vivo segmentation assay (Lauschke et al. 2013).
[STEPS]
4.
Extract mouse embryos and collect tails in dissection medium.
3. Wash the dried wells with ~200μL culture medium per well. Apply fresh culture medium (160uL ~ 300μL per ... | ["Extract mouse embryos and collect tails in dissection medium.", "Wash the dried wells with ~200μL culture medium per well. Apply fresh culture medium (160uL ~ 300μL per well) and equilibrate in 37°C 5% CO2 until use.", "Prepare dissection medium and culture medium.", "Coat dishes/plates with fibronectin.", "Cut the t... |
35,982 | Time-lapse killing assay (spheroid - IncuCyte) | 1 | dx.doi.org/10.17504/protocols.io.6qpvro2m3vmk/v1 | https://www.protocols.io/view/time-lapse-killing-assay-spheroid-incucyte-bfdnji5e | Philippa R Kennedy, Peter Hinderlie | TITLE: Time-lapse killing assay (spheroid - IncuCyte)
AUTHORS: Philippa R Kennedy, Peter Hinderlie
[DESCRIPTION]
Many tumors exist in vivo as three-dimensional masses. In order to better model the dynamics of three-dimensional tumor growth and immune cell invasion, cancer cell lines are grown in low-adhesion plates t... | ["Resuspend target cells in their preferred media. Seed 2x104 target cells in 100 μL/well into a 96 well U-bottom low adhesion plate (ULA plate, Cat. No. 7007, Corning).", "Spin the plate at 40 g (500 RPM) in one orientation and then 80 g (700 RPM) in the opposite orientation without any brake applied to the centrifuge... |
78,092 | single-cell Micro-C protocol | 1 | dx.doi.org/10.17504/protocols.io.kqdg39wbzg25/v1 | https://www.protocols.io/view/single-cell-micro-c-protocol-cqhkvt4w | Honggui Wu, Longzhi Tan | TITLE: single-cell Micro-C protocol
AUTHORS: Honggui Wu, Longzhi Tan
[DESCRIPTION]
Here we present a single-cell 3D genome mapping assay with improved spatial resolution with the help of micrococcal nuclease (MNase), termed single-cell Micro-C (scMicro-C). To achieve scMicro-C, we made three improvements. First, we ti... | ["[Prepare Micro-C Buffers] Prepare Micro-C Buffers", "[Prepare Micro-C Buffers] 10 mL Prepare Micro-C Buffer 1 (300 µL)\n50 µL 5 M NaCl (Invitrogen AM9760G; final 50 mM)\n50 µL 1 M Tris pH 7.5 (Invitrogen 15567027; final 10 mM)\n25 µL 1 M MgCl2 (Invitrogen AM9530G; final 5 mM)\n5 µL 1 M CaCl2 (Sigma 21115; final 1 mM)... |
null | null | null | dx.doi.org/10.17504/protocols.io.s8fehtn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>To extract plasmid DNA from <em>Agrobacterium</em>, to confirm the correct plasmid has been taken-up, this protocol allows you to directly perform a mini-prep on transformed <em>Agrobacterium</em>, digest this DNA and visualize it on a gel. This is without the need of rescuin... | [] |
29,791 | Polyacrylamide Gel Electrophoresis (SDS-PAGE) | null | dx.doi.org/10.17504/protocols.io.9b7h2rn | null | Neilier Junior | TITLE: Polyacrylamide Gel Electrophoresis (SDS-PAGE)
AUTHORS: Neilier Junior
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Parameters adjusted for gels 7 cm and 1.5 mm thick.</div></div>
[STEPS]
?. [Preparation of solutions and workspace]
Separation Gel Buffer (150 mL)1.5 M Tris-HCl, pH 8.8Tris (... | ["[Preparation of solutions and workspace]\nSeparation Gel Buffer (150 mL)1.5 M Tris-HCl, pH 8.8Tris (18,15 g/100 mL) ............................................................... 27,23 gdiH2O ......................................................................................... 80 mLAdjust pH to 8.8 with HCldiH2O... |
53,120 | Analysis of Lysophagic Flux in Cultured Induced Neurons using RFP-GFP-galectin3 | 4 | dx.doi.org/10.17504/protocols.io.bx48pqzw | https://www.protocols.io/view/analysis-of-lysophagic-flux-in-cultured-induced-ne-bx48pqzw | Vinay Eapen, Harper JW, Melissa Hoyer, sharan_swarup | TITLE: Analysis of Lysophagic Flux in Cultured Induced Neurons using RFP-GFP-galectin3
AUTHORS: Vinay Eapen, Harper JW, Melissa Hoyer, sharan_swarup
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Lysophagy-the selective elimination of damaged lysosomes by the autophagy pathway-is a critical hou... | ["[Electroporation of PB vectors. Use ThermoFisher kit and ThermoFisher Neon Electroporator to electroporate ES cells with PB vector and PB helper vector.]\nAdd 10ml buffer R to a sterile 1.5ml tube. Add 0.5µg of pAC150 GFP-RFP-LGALS3 or pAC150 GFP-RFP-LGALS3 R186S vector and 0.5µg of pCMV-hyPBase hyperactive piggyBac ... |
86,926 | Sensor Synthesis and Storage Protocol | 1 | dx.doi.org/10.17504/protocols.io.rm7vzxxz4gx1/v1 | https://www.protocols.io/view/sensor-synthesis-and-storage-protocol-cy5nxy5e | Nikita Srinivasan, Heather.Ann.Clark, Kristine Y Ma, James Monaghan | TITLE: Sensor Synthesis and Storage Protocol
AUTHORS: Nikita Srinivasan, Heather.Ann.Clark, Kristine Y Ma, James Monaghan
[DESCRIPTION]
This protocol explains the fabrication of DNA nanosensors with pHAb dye used for stability analysis, its characterization, and the detailed protocol of the DNA scaffold stability stud... | ["[Conjugation of pHAb to single-stranded DNA oligonucleotides] As shown in Figure 1, the buffer exchange was performed for the strands L2 and L4 (20 nmole each) for the pHAb conjugation in 0.1M NAHCO3 solution of pH= 8.1 using a 3k centrifugal filter (Amicon Ultra-0.5mL). Followed by that, strands (L2 and L4) are plac... |
92,797 | GT-seq protocol EFGL | 1 | dx.doi.org/10.17504/protocols.io.j8nlko1e6v5r/v1 | https://www.protocols.io/view/gt-seq-protocol-efgl-c6u5zey6 | EagleFish GeneticsLab | TITLE: GT-seq protocol EFGL
AUTHORS: EagleFish GeneticsLab
[DESCRIPTION]
The purpose of this protocol is to prepare extracted samples of DNA to be read on a NextSeq 2000. This will be achieved through SNP-PCR, barcoding, SequalPrep Normalization, Ampure bead size selection, and Qubit quantification. This will result ... | ["[SNP-PCR] Prepare SNP-PCR master mix using species specific primer panel.", "[SNP-PCR] Vortex and spin down aliquots of Qiagen Multiplex Master Mix and panel specific GT-seq primers, keep them in benchtop coolers. The table has been formulated to account for pipette errors. \n\n \n\nCombine the ingredients in a non- ... |
48,551 | HuBMAP - STANFORD RTI Multiplex Ion Beam Imaging (MIBI) MODALITY OVERVIEW | 1 | dx.doi.org/10.17504/protocols.io.btnfnmbn | https://www.protocols.io/view/hubmap-stanford-rti-multiplex-ion-beam-imaging-mib-btnfnmbn | Marc Bosse, Ferda Filiz, Noah Greenwald, Christine Camacho, Alex Kong, Adam Kagel, Sean Bendall, Mike Angelo | TITLE: HuBMAP - STANFORD RTI Multiplex Ion Beam Imaging (MIBI) MODALITY OVERVIEW
AUTHORS: Marc Bosse, Ferda Filiz, Noah Greenwald, Christine Camacho, Alex Kong, Adam Kagel, Sean Bendall, Mike Angelo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We aim to provide high resolution, high dimensional ... | ["[Sample collection and preparation]\nFormalin fixation and paraffin embedding of specimens dx.doi.org/10.17504/protocols.io.bqp6mvre", "[Sample collection and preparation]\nSectioning of FFPE specimens https://dx.doi.org/10.17504/protocols.io.bfz4jp8w MIBI slide specifications is detailed in MIBI staining dx.doi.o... |
36,080 | Overviews on adverse events in pharmacological interventions | null | dx.doi.org/10.17504/protocols.io.bfgqjjvw | https://www.protocols.io/view/overviews-on-adverse-events-in-pharmacological-int-bfgqjjvw | Elena Dorando, Thilo Sachse, Tim Matthes, Simone Heß, Petra Thürmann, Sven Schmiedl, Salmaan Kanji, Carole Lunny, Pierre Thabet, Dawid Pieper | TITLE: Overviews on adverse events in pharmacological interventions
AUTHORS: Elena Dorando, Thilo Sachse, Tim Matthes, Simone Heß, Petra Thürmann, Sven Schmiedl, Salmaan Kanji, Carole Lunny, Pierre Thabet, Dawid Pieper
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Please find detailed information ... | [] |
67,426 | InstaHard Reviews: InstaHard Male Enhancement Reviews! | 1 | dx.doi.org/10.17504/protocols.io.rm7vzyzn5lx1/v1 | https://www.protocols.io/view/instahard-reviews-instahard-male-enhancement-revie-cd4as8se | InstaHard Reviews | TITLE: InstaHard Reviews: InstaHard Male Enhancement Reviews!
AUTHORS: InstaHard Reviews
[DESCRIPTION]
InstaHard Reviews
[STEPS]
1. Official WebSite Of InstaHard:- https://wintersupplement.com/instahard-reviews/
InstaHard Reviews Male Enhancement
Product Name :-InstaHard Male Enhancement
Product Type:- Prostate sup... | ["Official WebSite Of InstaHard:- https://wintersupplement.com/instahard-reviews/\n\nInstaHard Reviews Male Enhancement\nProduct Name :-InstaHard Male Enhancement\nProduct Type:- Prostate support formula for better urine flow\nFormulator/Developer:- Dr. Leo Shub\nManufacturer & Distributor:- Pure Body Innovations\nIngr... |
40,800 | ELISA for quantification of IL-36 in human serum. | 6 | dx.doi.org/10.17504/protocols.io.bj38kqrw | https://www.protocols.io/view/elisa-for-quantification-of-il-36-in-human-serum-bj38kqrw | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-36 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-36 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-36 present in the serum sample binds to antibodies adsorbed into the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and... |
44,649 | Preparo de meio de LB e LB ágar em placa 11/11/20 | 1 | null | https://www.protocols.io/view/preparo-de-meio-de-lb-e-lb-gar-em-placa-11-11-20-bpuhmnt6 | Mariana Jacques | TITLE: Preparo de meio de LB e LB ágar em placa 11/11/20
AUTHORS: Mariana Jacques
[STEPS]
?. [Preparo do LB]
Dissolver 25 g de LB em 1 L de H2O filtrada
?. [Preparo do LB ágar]
Dissolver 12 g de LB ágar 300 mL de H2O filtrada
?. Depois de pronto autoclavar os meios LB e LB em placa, em temperatura- controlada.
?.... | ["[Preparo do LB]\nDissolver 25 g de LB em 1 L de H2O filtrada", "[Preparo do LB ágar]\nDissolver 12 g de LB ágar 300 mL de H2O filtrada", "Depois de pronto autoclavar os meios LB e LB em placa, em temperatura- controlada.", "Ao retirar e o meio atingir uma temperatura ideal ( ) adicionar , Ampicilina.", "Colocar ... |
99,706 | Scoping Review Protocol: Changes in Skin Microbiome Post-Dermatological Interventions | 0 | dx.doi.org/10.17504/protocols.io.261ge53owg47/v1 | https://www.protocols.io/view/scoping-review-protocol-changes-in-skin-microbiome-ddk224ye | Eron J. Powell, Jeremy R. Ellis | TITLE: Scoping Review Protocol: Changes in Skin Microbiome Post-Dermatological Interventions
AUTHORS: Eron J. Powell, Jeremy R. Ellis
[DESCRIPTION]
This scoping review protocol aims to systematically map the existing literature on the effects of common dermatological procedures on the skin microbiome. Adhering to PRIS... | ["[Introduction] The skin microbiome is an ecosystem of microorganisms residing on the human skin which play a crucial role in maintaining skin health and protecting against pathogens(1). This community includes bacteria, fungi, viruses, and mites, which interact with each other and the host forming a dynamic equilibri... |
52,821 | Generation of functional induced DA neurons (iDANs) from dermal fibroblasts of adult donors | 1 | dx.doi.org/10.17504/protocols.io.ewov14w1pvr2/v1 | https://www.protocols.io/view/generation-of-functional-induced-da-neurons-idans-bxtvpnn6 | Janelle Drouin-Ouellet | TITLE: Generation of functional induced DA neurons (iDANs) from dermal fibroblasts of adult donors
AUTHORS: Janelle Drouin-Ouellet
[DESCRIPTION]
This describes the steps for direct DA neurons reprogramming of patient’s fibroblasts.
[GUIDELINES]
Notes
It is recommended to prepare the ENM and LNM fresh. Both these medi... | ["[1. Seeding of fibroblasts for conversion to induced DA neurons] Thaw a vial containing fibroblasts in a water bath at 37 °C, until only a small piece of frozen congelation medium is remaining (See Notes 2 and 3).", "[1. Seeding of fibroblasts for conversion to induced DA neurons] Quickly transfer the content of the ... |
76,945 | Sequencing fungal and bacterial metabarcodes with native barcoding and Nanopore | 1 | null | https://www.protocols.io/view/sequencing-fungal-and-bacterial-metabarcodes-with-cpdrvi56 | Carlos Goller, Benjamin Schwessinger, Carly Sjogren | TITLE: Sequencing fungal and bacterial metabarcodes with native barcoding and Nanopore
AUTHORS: Carlos Goller, Benjamin Schwessinger, Carly Sjogren
[DESCRIPTION]
This protocols is part of the ANU Biosecurity mini-research project #1 "Plant Pathogen Diagnostics: Visuals, subcultures, and genomics".
You will be provid... | ["[Preparation Before Starting] Prepare for your experiment (done bye the demonstrators for you).", "[Preparation Before Starting] Purify your PCR amplicons with AMPure beads or similar and measure concentrations (Step 1+2 in Abstract Overview).", "[Preparation Before Starting] Ensure you have your sequencing kit, the ... |
null | null | null | dx.doi.org/10.17504/protocols.io.ssseeee | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a protocol from the <a href="http://doudnalab.org/" target="_blank" rel="noopener noreferrer">Doudna Lab</a> for His10-MBP-Cas9 purification. </p>
[BEFORE_START]
<p><strong>DAY 1 materials</strong></p>
<p> </p>
<table style="height: 186px; width: 332px;">
<tbody>
<tr... | [] |
99,230 | Seawater Filtration for Microbial or Environmental DNA | 1 | null | https://www.protocols.io/view/seawater-filtration-for-microbial-or-environmental-dc562y9e | Colleen Kellogg | TITLE: Seawater Filtration for Microbial or Environmental DNA
AUTHORS: Colleen Kellogg
[DESCRIPTION]
This protocol describes water filtrations using 0.22μl sterivex filters. The protocol is part of the Hakai Institute's pipeline to analyze microbial and environmental DNA from seawater samples and is implemented as a s... | ["[SETUP OF FILTRATION APPARATUS] Line counter with lab diapers.", "[SETUP OF FILTRATION APPARATUS] For extra cleanliness, you can place an autoclave or otherwise plastic bin on one side of the pump.", "[SETUP OF FILTRATION APPARATUS] Place the waste flask or container on the other side of the pump.", "[SETUP OF FILTRA... |
75,812 | Quantification of various SARS-CoV-2 variant mutations (characteristic of Alpha, Beta, Gamma, Delta, Omicron and Omicron sublineages) in settled solids using digital RT-PCR | 1 | dx.doi.org/10.17504/protocols.io.14egnzrrzg5d/v10 | https://www.protocols.io/view/quantification-of-various-sars-cov-2-variant-mutat-cnacvaaw | Bridgette Hughes, Bradley J. White, Marlene K. Wolfe, Alexandria B Boehm | TITLE: Quantification of various SARS-CoV-2 variant mutations (characteristic of Alpha, Beta, Gamma, Delta, Omicron and Omicron sublineages) in settled solids using digital RT-PCR
AUTHORS: Bridgette Hughes, Bradley J. White, Marlene K. Wolfe, Alexandria B Boehm
[DESCRIPTION]
This process instruction describes the step... | ["[Preparation] Retrieve all kit components from the One-Step RT-ddPCR advanced kit for probes from the -20 °C freezer and thaw the components on ice.", "[Preparation] Retrieve ddPCR positive control aliquots (50 copies per uL gRNA) from the -80 °C freezer and thaw on ice", "[Preparation] For re-running frozen plates o... |
17,657 | Matrix-Assisted Laser Desorption/Ionization – time of flight mass spectrometry (MALDI-TOF) | null | dx.doi.org/10.17504/protocols.io.vgze3x6 | null | PALOMA VARELA | TITLE: Matrix-Assisted Laser Desorption/Ionization – time of flight mass spectrometry (MALDI-TOF)
AUTHORS: PALOMA VARELA
[STEPS] | [] |
24,242 | Quantification of atherosclerosis at the aortic sinus | null | dx.doi.org/10.17504/protocols.io.3wsgpee | null | Daniel Teupser, Jan Breslow | TITLE: Quantification of atherosclerosis at the aortic sinus
AUTHORS: Daniel Teupser, Jan Breslow
[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 procedures for fixing, sectioning and staini... | ["Preparation of Aortic Root and Brachiocephalic Artery for Lesion Quantitation:1. Prepare a 1 ml syringe by filling with 15µl 0.5 M EDTA ph 8.0 and then capping with a 23g needle. The syringe will be used for drawing blood from the heart. 2. Prepare a 10 ml syringe with 50-100 µl of heparin (1000 units per ml), then f... |
20,412 | Primary Ventral Midbrain Culture | null | dx.doi.org/10.17504/protocols.io.x64frgw | null | Douglas Miller, Min Lin, Joseph Lebowitz, Danielle Sambo, Kaustuv Saha, Habibeh Khoshbouei | TITLE: Primary Ventral Midbrain Culture
AUTHORS: Douglas Miller, Min Lin, Joseph Lebowitz, Danielle Sambo, Kaustuv Saha, Habibeh Khoshbouei
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Primary ventral midbrain cultures provide a reproducible medium to explore neuronal dynamics that are expe... | ["[Washing Coverslips]\nBoil cloverslips in 1M HCL for 5 minutes, allow to cool.Wash 3X with ddH2O.Wash for 30 min in 100% ethanol. Wash 3X with ddH2O. Cover flask with aluminum foil and autoclave.Wash for 30 min in 100% ethanol.Wash 3X with ddH2O. Cover flask with aluminum foil and autoclave.", "[Coating Coverslips]\n... |
104,257 | Seizures – like behavior assay for D. melanogaster | 0 | dx.doi.org/10.17504/protocols.io.81wgbzqd1gpk/v1 | https://www.protocols.io/view/seizures-like-behavior-assay-for-d-melanogaster-dh2938h6 | Natalie Kaempf, Patrik Verstreken | TITLE: Seizures – like behavior assay for D. melanogaster
AUTHORS: Natalie Kaempf, Patrik Verstreken
[DESCRIPTION]
This protocol allows to assess the susceptibility of flies to seizure-like behavior based on mechanically
hyper-stimulating sensory inputs and assessing seizure-like activity.
[STEPS]
SECTION: Seizures –... | ["[Seizures – like behavior assay] prepare groups of 5 ± 1 flies and transfer them to transparent empty vials", "[Seizures – like behavior assay] let them rest for at least 30 min after CO2 anesthesia", "[Seizures – like behavior assay] mechanically stimulate the flies by vortexing the vial for 10 s at maximum intensit... |
88,628 | Production of GTPase Deficient RAB1A(Q70L) Protein | 4 | null | https://www.protocols.io/view/production-of-gtpase-deficient-rab1a-q70l-protein-c2suyeew | Annan SI Cook | TITLE: Production of GTPase Deficient RAB1A(Q70L) Protein
AUTHORS: Annan SI Cook
[DESCRIPTION]
Bacterial expression of the GTPase deficient Q70L mutant of human RAB1A.
[STEPS]
SECTION: Transformation and Colony Selection
1. Transform E. coli BL21 cells with the pET vector containing 6x-His-RAB1A(Q70L) by heat shock.
... | ["[Transformation and Colony Selection] Transform E. coli BL21 cells with the pET vector containing 6x-His-RAB1A(Q70L) by heat shock.", "[Transformation and Colony Selection] Plate the transformed cells on ampicillin-resistant plates.", "[Transformation and Colony Selection] Incubate the plates at 37 °C.", "[Pre-cult... |
83,260 | U54 SCENT Pediatric Colonoscopy Tissue Collection Procedure | 1 | null | https://www.protocols.click/view/u54-scent-pediatric-colonoscopy-tissue-collection-cvi4w4gw | Mary Jordan* | TITLE: U54 SCENT Pediatric Colonoscopy Tissue Collection Procedure
AUTHORS: Mary Jordan*
[DESCRIPTION]
This document outlines the required criteria for pediatric colonoscopy inclusion of colon specimens collected at Duke University Hospital through the Biorepository and Precision Pathology Center (BRPC) in the Departm... | ["[Inclusion and Exclusion Criteria] Inclusion Criteria:\n • Healthy patients age 5-18 years of age presenting for outpatient colonoscopy. \n • Screening may wish to focus on the following indications: abdominal pain, constipation, diarrhea, \n bloating/gas, patients with normal labs and/or imaging.... |
50,699 | Design and validation of a low-cost sugar-feeder for resource-poor insectaries. | 4 | dx.doi.org/10.17504/protocols.io.14egnzrbmg5d/v1 | https://www.protocols.io/view/design-and-validation-of-a-low-cost-sugar-feeder-f-bvrjn54n | Zachary Thomas Stavrou - Dowd, Clair Rose, Alvaro Acosta Serrano, Lee R Haines | TITLE: Design and validation of a low-cost sugar-feeder for resource-poor insectaries.
AUTHORS: Zachary Thomas Stavrou - Dowd, Clair Rose, Alvaro Acosta Serrano, Lee R Haines
[DESCRIPTION]
Background
The emergence of insecticide resistance in insects has led researchers to develop new control
tools so that historic ga... | ["Collect materials required for construction of feeder. See \"Materials\"", "Using either your hands or a pair of pliers, unravel the outer loop of a paperclip and twist it into a hanger.", "Mould the outer loop around the bottom of the tube and leave the inner loop free to construct hanging hook", "Tape down the pape... |
72,986 | Thickness and width of the menisci of adult knee joint, a cadaveric study | 1 | dx.doi.org/10.17504/protocols.io.3byl4jjprlo5/v1 | https://www.protocols.io/view/thickness-and-width-of-the-menisci-of-adult-knee-j-cjh2uj8e | Bv Murlimanju, S Vikram, VANISHRI S. NAYAK, Nandini P Bhat, mangala.pai, Rajanigandha Vadgaonkar, Latha V Prabhu, Sunil S Nayak | TITLE: Thickness and width of the menisci of adult knee joint, a cadaveric study
AUTHORS: Bv Murlimanju, S Vikram, VANISHRI S. NAYAK, Nandini P Bhat, mangala.pai, Rajanigandha Vadgaonkar, Latha V Prabhu, Sunil S Nayak
[DESCRIPTION]
Background:The goal is to determine the thickness and width of the knee joint meniscus ... | ["[Thickness and width of the menisci of adult knee joint: a descriptive cross-sectional observational study in cadavers] Review of Literature\nThe first meniscal allograft transplantation in human was reported by Milachowski and Wirth in 1984 (10). However the concept of meniscal replacement could be traced back to Le... |
30,760 | Sympathetic chain ganglia dissection_Protocol | 1 | dx.doi.org/10.17504/protocols.io.baagiabw | https://www.protocols.io/view/sympathetic-chain-ganglia-dissection-protocol-baagiabw | Rui Zhang, Heike Muenzberg | TITLE: Sympathetic chain ganglia dissection_Protocol
AUTHORS: Rui Zhang, Heike Muenzberg
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The study goal is to identify the gene expression profile of interscapular brown fat (iBAT)-related ganglia (SG/T1 & T3) and inguinal white fat (Iwat)-related gang... | ["Weigh mouse, then euthanize via CO2 inhalation method, and record start time", "Perfusion - mice will be perfused with cold, sterile saline to remove the blood from the animal tissues.", "Prepare the 50 ml syringe for perfusion by filling up with at least 30 ml ice-cold sterile saline, and connecting it with the vacu... |
106,495 | KAPP-Sen TMC: Whole human kidney preparation | 0 | dx.doi.org/10.17504/protocols.io.eq2lyw4kwvx9/v1 | https://www.protocols.io/view/kapp-sen-tmc-whole-human-kidney-preparation-dj874rzn | Juliana Alcoforado Diniz, Ramalakshmi Ramasamy, Alejandro Peña, Qian Wu, Jillian L. Woodworth, Vladislav Bugay, Manpreet Semwal, Paul Robson | TITLE: KAPP-Sen TMC: Whole human kidney preparation
AUTHORS: Juliana Alcoforado Diniz, Ramalakshmi Ramasamy, Alejandro Peña, Qian Wu, Jillian L. Woodworth, Vladislav Bugay, Manpreet Semwal, Paul Robson
[DESCRIPTION]
This protocol describes removal, shipping, dissection, formalin preservation of a whole human kidney fr... | ["Remove the whole kidney from a brain-dead donor. Flush the kidney with UW solution and perfuse with 1 liter of Waters IGL Pulsatile Perfusion Solution (PPS) for shipping.", "Once received, bring the sample still on ice to the pathology department at UConn Health for dissection. The whole process was performed at room... |
89,094 | Archived Human Tissue Collection Sept 2015 - 2019 -- University of Minnesota TMCs | 1 | dx.doi.org/10.17504/protocols.io.x54v9p15pg3e/v1 | https://www.protocols.io/view/archived-human-tissue-collection-sept-2015-2019-un-c29eyh3e | Laura J Niedernhofer, David A Bernlohr | TITLE: Archived Human Tissue Collection Sept 2015 - 2019 -- University of Minnesota TMCs
AUTHORS: Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
Tissue collection and processing protocols for liver and adipose tissue samples obtained and archived by the UMN Biospecimen Repository from Sept 2015 to 2019.
[STEPS... | ["[BioNet Gross Room SOP for tissue acquisition] The following document the correct procedure for tissue acquisition in the\nUniversity of Minnesota Medical Center, Fairview/ East Bank Gross Room.", "[BioNet Tissue Processing SOP] The purpose of this document is to describe BioNet’s current tissue processing procedure ... |
75,538 | TSST | 1 | dx.doi.org/10.17504/protocols.io.e6nvwj85zlmk/v1 | https://www.protocols.io/view/tsst-cmzsu76e | Johannes Bodo Heekerens | TITLE: TSST
AUTHORS: Johannes Bodo Heekerens
[DESCRIPTION]
This protocol details about Trier Social Stress Test (TSST).
[GUIDELINES]
Instructions for investigators (German)
Vor dem TSST (Raum A)
Vor dem TSST zeigt und erklärt der Versuchsleiter dem Probanden die drei mobilen Geräte zur kontinuierlichen Erfassung v... | ["[Before the TSST] Before the TSST, the investigator shows and explains to the subject the two devices for continuous recording of heart rate (Vivalink ECG Patch) and blood pressure (Vivalink BP Cuff). The devices are cleaned with 70% alcohol cleaning solution and the subject will be instructed to put the devices on."... |
37,939 | Separation of Human Neutrophils (PMN) from Whole Blood | 4 | null | https://www.protocols.io/view/separation-of-human-neutrophils-pmn-from-whole-blo-bhatj2en | Marco Cosentino, Elisa Storelli, Alessandra Luini, Emanuela Rasini, Massimiliano Legnaro, Marco Ferrari, Franca Marino | TITLE: Separation of Human Neutrophils (PMN) from Whole Blood
AUTHORS: Marco Cosentino, Elisa Storelli, Alessandra Luini, Emanuela Rasini, Massimiliano Legnaro, Marco Ferrari, Franca Marino
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Separation of Human Neutrophils (PMN) from Buffy Coat: list of... | ["Place of whole blood into a 10 ml volume centrifuge tube.\n5 mL", "Add of dextran solution and mix well by drawing in and out of a pipette.\n2 mL", "Incubate in the dark for at\n37 °C", "Place of Fycoll-HyPaque media solution into a 10 ml volume centrifuge tube.\n3 mL", "Slowly and carefully layer the supernatant... |
21,060 | SYSB 3036 W06: Annotating a Complete Genome with HMMs | null | dx.doi.org/10.17504/protocols.io.ytcfwiw | null | Frank Aylward | TITLE: SYSB 3036 W06: Annotating a Complete Genome with HMMs
AUTHORS: Frank Aylward
[STEPS]
?. First let's download some files from GitHub:git clone https://github.com/faylward/hmm_tutorialAnd move inside the new folder and see what is there:cd hmm_tutorialls
?. In the new file you should see a gzipped file that conta... | ["First let's download some files from GitHub:git clone https://github.com/faylward/hmm_tutorialAnd move inside the new folder and see what is there:cd hmm_tutorialls", "In the new file you should see a gzipped file that contains proteins from a mystery genome. We can gunzip it now:gunzip mystery_genome_proteins.faa.gz... |
109,202 | 384 Well PicoGreen | 1 | dx.doi.org/10.17504/protocols.io.36wgq5ekxgk5/v3 | https://www.protocols.io/view/384-well-picogreen-dnvs5e6e | Allen Institute for Brain Science | TITLE: 384 Well PicoGreen
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
Quant-iT™ PicoGreen® dsDNA Assay is used for detection and quantitation of double stranded DNA products.
Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes o... | [] |
30,989 | Conducting Dynamic BH3 Profiling Adapted From Letai Lab | 1 | dx.doi.org/10.17504/protocols.io.3byl47j4jlo5/v1 | https://www.protocols.io/view/conducting-dynamic-bh3-profiling-adapted-from-leta-bahmib46 | Dennis Juarez | TITLE: Conducting Dynamic BH3 Profiling Adapted From Letai Lab
AUTHORS: Dennis Juarez
[DESCRIPTION]
Dynamic BH3 Profiling is used to test cellular proximity to apoptosis after treatment by exposure of in situ mitochondria with the BH3 domain of apoptotic proteins to induce mitochondrial cytochrome C release. Cytochrom... | ["[BH3 Peptide Exposure] Count your cells and take 2,000,000 cells per treatment condition in a 1.7mL tube use in the assay.", "[BH3 Peptide Exposure] During the spin, prepare your 2x peptide solutions in MEB2- P25. The peptide stocks are made at 100x and should be diluted 1:50. Prepare enough for every cell line and t... |
98,495 | Differentiation between different soft hammers stigmats, quantitative and traceological approach | 0 | dx.doi.org/10.17504/protocols.io.eq2lyw3mmvx9/v1 | https://www.protocols.io/view/differentiation-between-different-soft-hammers-sti-dce72thn | Jean-Thomas Vie, zixuan shen | TITLE: Differentiation between different soft hammers stigmats, quantitative and traceological approach
AUTHORS: Jean-Thomas Vie, zixuan shen
[DESCRIPTION]
Many studies in archaeology focus on the traces associated with stone knapping during prehistory, debating their correlation with the techniques used (Clément, 202... | ["[Selection of a specific raw material] Select Raw material : Sandstone quartzite, Quartzite, Flint, Quartz", "[Knapping with different hammers in order to produce flakes] Use hammer from low to high hardness to produce flakes : \nSoft rock percussor, volcanic rock percussor.\nWe plan to knap in the order of Sandstone... |
null | null | null | dx.doi.org/10.17504/protocols.io.nk4dcyw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
44,599 | Isolation and Fixation of Nuclei from the Mouse Brain for Dip-C | 4 | dx.doi.org/10.17504/protocols.io.bpsxmnfn | https://www.protocols.io/view/isolation-and-fixation-of-nuclei-from-the-mouse-br-bpsxmnfn | Longzhi Tan | TITLE: Isolation and Fixation of Nuclei from the Mouse Brain for Dip-C
AUTHORS: Longzhi Tan
[STEPS]
?. [Reagents]
Prepare 1.5 M sucrose (): (final: , ) waterHeat and vortex to mix.Filter to sterilize.Store at .
40 mL
20.538 g
40 mL
4 °C
?. [Reagents]
Prepare Nuclei Isolation Medium 1 (; note that Tris is replaced wi... | ["[Reagents]\nPrepare 1.5 M sucrose (): (final: , ) waterHeat and vortex to mix.Filter to sterilize.Store at .\n40 mL\n20.538 g\n40 mL\n4 °C", "[Reagents]\nPrepare Nuclei Isolation Medium 1 (; note that Tris is replaced with HEPES): 1.5 M sucrose (final: , ) (final: ) (final: ) (final: ) waterStore at .\n45 mL\n7.5 m... |
81,365 | 10x Protocols: Visium v1 FFPE Deparaffinization, H&E staining, and Imaging-- University of Minnesota TMCs (CG000409 Rev C) | 1 | dx.doi.org/10.17504/protocols.io.3byl4joqjlo5/v1 | https://www.protocols.io/view/10x-protocols-visium-v1-ffpe-deparaffinization-h-a-ctpvwmn6 | IOx Genomics, Laura J Niedernhofer, David A Bernlohr | TITLE: 10x Protocols: Visium v1 FFPE Deparaffinization, H&E staining, and Imaging-- University of Minnesota TMCs (CG000409 Rev C)
AUTHORS: IOx Genomics, Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
Protocols from 10x Genomics for Visium Spatial Gene Expression v1 chemistry on FPPE samples without the CytA... | ["Additional Protocols/Resources\n \n \nhttps://www.10xgenomics.com/support/spatial-gene-expression-ffpe", "10x protocol CG000409, Rev C (Deparaffinization, H&E, etc)"] |
27,824 | DNaseI and flowcell clearing for increasing long read yields and multi-sample sequencing | null | dx.doi.org/10.17504/protocols.io.7eqhjdw | null | John Tyson | TITLE: DNaseI and flowcell clearing for increasing long read yields and multi-sample sequencing
AUTHORS: John Tyson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">DNaseI and flowcell clearing for increasing long read yields and multi-sample sequencing</span></div><... | ["Mix together FB + CaCl2 + DNaseI (2U per ul) to form DNaseI flowcell digestion buffer\n200 µl\n2 µl\n2 µl", "Add 200ul of DNaseI Digestion buffer to the flowcell through the sample port and close", "Incubate for 20mins to 2hrs depending on sample, monitoring the Single Pore : Strand numbers reported in MinKNOW", ... |
92,555 | Synthesis of 1-(3-chlorophenethyl)-3-cyclopentylpyrimidine-2,4,6-(1H,3H,5H)-trione (CP8) | 6 | dx.doi.org/10.17504/protocols.io.bp2l6xd71lqe/v2 | https://www.protocols.io/view/synthesis-of-1-3-chlorophenethyl-3-cyclopentylpyri-c6mjzc4n | Carole JR Bataille, Katherine Brimblecombe, Stephanie J Cragg | TITLE: Synthesis of 1-(3-chlorophenethyl)-3-cyclopentylpyrimidine-2,4,6-(1H,3H,5H)-trione (CP8)
AUTHORS: Carole JR Bataille, Katherine Brimblecombe, Stephanie J Cragg
[DESCRIPTION]
A structure-activity relationship-based modification of pyrimidine-2,4,6-triones led to 1-(3-chlorophenethyl)-3-cyclopentylpyrimidine-2,4,... | ["[Synthesis of 1-(3-chlorophenethyl)-3-cyclopentylpyrimidine-2,4,6-(1H,3H,5H)-trione (CP8)] Add 357 µL 2-(3-chlorophenyl)ethylamine (2.58 mmol, 1.0 eq.) to a solution of 290 mg of Cyclopentaneisocyanate (2.58 mmol, 1.0 eq.) in 10 mL of dichloromethane.", "[Synthesis of 1-(3-chlorophenethyl)-3-cyclopentylpyrimidine-2,4... |
56,679 | Bogus Safety Protocol | 3 | dx.doi.org/10.17504/protocols.io.b3kfqktn | https://www.protocols.io/view/bogus-safety-protocol-b3kfqktn | Abby Moore | TITLE: Bogus Safety Protocol
AUTHORS: Abby Moore
[DESCRIPTION]
The purpose of this document is to act as a placeholder for a real safety protocol.
[STEPS] | [] |
37,683 | SARS-CoV-2 NCBI assembly submission protocol: GenBank | 1 | dx.doi.org/10.17504/protocols.io.bg2tjyen | https://www.protocols.io/view/sars-cov-2-ncbi-assembly-submission-protocol-genba-bg2tjyen | Ruth Timme, Heather Blankenship, Erin Young, Emma Griffiths, Duncan MacCannell, Stacia Wyman | TITLE: SARS-CoV-2 NCBI assembly submission protocol: GenBank
AUTHORS: Ruth Timme, Heather Blankenship, Erin Young, Emma Griffiths, Duncan MacCannell, Stacia Wyman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">PURPOSE: </span></div><div class = "text-block"><span s... | ["[\"Ingredients\" to have in place before starting your submissions]\n1.1: Ensure you have a working NCBI user account1.2: Identify your NCBI submission user group or establish a new one if necessary. 1.3: Bookmark the link to your submission portal1.4. BioSample + BioProject assessions in-handAfter these steps are co... |
38,829 | Saliva Collection and RNA Extraction for SARS-CoV-2 Detection | 1 | dx.doi.org/10.17504/protocols.io.bh6mj9c6 | https://www.protocols.io/view/saliva-collection-and-rna-extraction-for-sars-cov-bh6mj9c6 | Isabel Ott, Chantal Vogels, Nathan Grubaugh, Anne Wyllie | TITLE: Saliva Collection and RNA Extraction for SARS-CoV-2 Detection
AUTHORS: Isabel Ott, Chantal Vogels, Nathan Grubaugh, Anne Wyllie
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details recommendations for collecting and processing saliva for SARS-CoV-2 detection, as used in </div... | ["[Sample Collection]\nSaliva can either be collected independently by the individual providing the sample ('Self-collection') or with the assistance of a healthcare worker ('Assisted').", "[Sample Collection]\nThe sample collector must don PPE (at minimum, mask and gloves) prior to contact with the sample provider.", ... |
29,194 | Cryopreservation | null | dx.doi.org/10.17504/protocols.io.8rihv4e | null | Michael Eadon, Daria Barwinska, Ying-Hua Cheng, Michael J. Ferkowicz, Samir V. Parikh, Brad H. Rovin, John P. Shapiro, Pierre C. Dagher, Tarek M. El-Achkar | TITLE: Cryopreservation
AUTHORS: Michael Eadon, Daria Barwinska, Ying-Hua Cheng, Michael J. Ferkowicz, Samir V. Parikh, Brad H. Rovin, John P. Shapiro, Pierre C. Dagher, Tarek M. El-Achkar
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Samples of kidney tissues are cryopreserved, sectioned an... | ["[Cryopreservation]\nKidney tissues are acclimated to OCT for and then transferred to a cryomold with partially frozen OCT in the bottom (on a block of dry ice).\nThis protocol is to be used for 0.5-10mm3 pieces of kidney tissue, including local nephrectomies and biopsies.", "[Cryopreservation]\nThe tissue is complet... |
40,894 | ELISA for quantification of RANTES (Regulated on Activation, Normal T cell Expressed and Secreted) in human serum or plasma. | 6 | dx.doi.org/10.17504/protocols.io.bj66krhe | https://www.protocols.io/view/elisa-for-quantification-of-rantes-regulated-on-a-bj66krhe | Angel Justiz-Vaillant | TITLE: ELISA for quantification of RANTES (Regulated on Activation, Normal T cell Expressed and Secreted) in human serum or plasma.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">RANTES (Regulated on Activation, Normal T cell Expressed and Secreted) also known... | ["An anti-human RANTES 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 RANTES (CCL5) present in the serum or plasma binds to antibodies adsorbed into the microwells.", "The microplate is blocked with 3% non-f... |
25,526 | Steady-state cell-free gene expression with microfluidic chemostats | null | dx.doi.org/10.17504/protocols.io.46wgzfe | null | Nadanai Laohakunakorn, Barbora Lavickova, Zoe Swank, Julie Laurent, Sebastian Maerkl | TITLE: Steady-state cell-free gene expression with microfluidic chemostats
AUTHORS: Nadanai Laohakunakorn, Barbora Lavickova, Zoe Swank, Julie Laurent, Sebastian Maerkl
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Cell-free synthetic biology offers an approach to building and testing gene circuit... | ["[Design of Microfluidic Devices]\nDesign the device (see Note 2) on AutoCAD 2019 or other software with similar functionality. A specific example is shown in Figure 1, and other designs are available on our webpage (see Note 3). Export the final design as a .dxf file.", "[Design of Microfluidic Devices]\nUsing CleWin... |
67,634 | Protein Extraction and Western Blot of Human Lung Organoids | 1 | dx.doi.org/10.17504/protocols.io.81wgb6peylpk/v3 | https://www.protocols.io/view/protein-extraction-and-western-blot-of-human-lung-ceastaee | Morris Baumgardt, Maren Hülsemann, Diana Fatykhova, Stefan Hippenstiel, Andreas C. Hocke, Katja Hönzke | TITLE: Protein Extraction and Western Blot of Human Lung Organoids
AUTHORS: Morris Baumgardt, Maren Hülsemann, Diana Fatykhova, Stefan Hippenstiel, Andreas C. Hocke, Katja Hönzke
[DESCRIPTION]
This protocol describes the protein extraction from human alveolar-like organoids followed by western blotting. It gives a de... | ["[Prepare cell lysate of alveolar-like organoids] You need a sufficient amount of organoids (approx. 300,000 cells per well) and organoids should be collected from minimum two wells of a 24-well plate (total ~600,000 cells).", "[Prepare cell lysate of alveolar-like organoids] From here all steps on ice. \n\nKeep tubes... |
103,752 | Generation of Myelinating Oligodendrocytes from Pluripotent Stem Cells | 0 | dx.doi.org/10.17504/protocols.io.5jyl8265rl2w/v1 | https://www.protocols.io/view/generation-of-myelinating-oligodendrocytes-from-pl-dhjg34jw | Melanie Gil, Vivian Gama | TITLE: Generation of Myelinating Oligodendrocytes from Pluripotent Stem Cells
AUTHORS: Melanie Gil, Vivian Gama
[DESCRIPTION]
This document contains two separate differentiation protocols, one to generate oligodendrocyte progenitor cells (OPCs) and the other to generate motor neurons. For co-culture, both protocols mu... | ["[Day -3: Replating hESCs] When the cells reach 70–90% confluency, remove the medium and add 1 mL of accutase.", "[Day -3: Replating hESCs] Incubate the plate in a 37 °C incubator for 5 min.", "[Day -3: Replating hESCs] Plate 8 × 104 cells per well on a Matrigel-coated six-well plate with mTeSR1 supplemented with 10 m... |
73,121 | Bat Measurements - ISL Peru | 1 | dx.doi.org/10.17504/protocols.io.ewov1oqrklr2/v1 | https://www.protocols.io/view/bat-measurements-isl-peru-cjm9uk96 | Cristian Tirapelle, Gideon Erkenswick, Jorge Luis Mendoza-Silva, Pamela Sánchez-Vendizú, Mrinalini Watsa | TITLE: Bat Measurements - ISL Peru
AUTHORS: Cristian Tirapelle, Gideon Erkenswick, Jorge Luis Mendoza-Silva, Pamela Sánchez-Vendizú, Mrinalini Watsa
[DESCRIPTION]
This protocol describes the external morphological measurements taken on bats prior to release and is actively used by Field Projects International at the E... | ["[Bat Anatomical References] Noseleaf length: The noseleaf is a membranous fold of skin of variable size located on or around the nostrils. This length is measured from the base of the horseshoe until the tip of the spear.", "[Bat Anatomical References] Tragus length: The tragus is a small flap of skin in front of the... |
null | null | null | dx.doi.org/10.17504/protocols.io.fitbken | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol details the use of various unix commands commonly used in bioinformatics.
[GUIDELINES]
<p><strong>Unix Commands<br /></strong></p>
<table>
<tbody>
<tr>
<td>pwd</td>
<td>rm</td>
<td>grep</td>
<td>tail</td>
<td>install</td>
</tr>
<tr>
<td>ls</td>
<td>'>'</td>
<td... | [] |
25,308 | Hornwort sporophyte induction -OXF | null | dx.doi.org/10.17504/protocols.io.4x4gxqw | null | Eftychis Frangedakis | TITLE: Hornwort sporophyte induction -OXF
AUTHORS: Eftychis Frangedakis
[STEPS]
?. To induce sporophytes, plants were grown for one month in petri dishes on Lorbeer’s medium.
?. Afterwards, plants were transferred to Magenta pots on 1/10 Knop medium (2.5 g/L K2HPO4, 2.5 g/L KH2PO4, 2.5 g/L KCL, 2.5 g/L MgSO4.7H2O, 10 ... | ["To induce sporophytes, plants were grown for one month in petri dishes on Lorbeer’s medium.", "Afterwards, plants were transferred to Magenta pots on 1/10 Knop medium (2.5 g/L K2HPO4, 2.5 g/L KH2PO4, 2.5 g/L KCL, 2.5 g/L MgSO4.7H2O, 10 g/L Ca(NO3)2.4H2O, 37 mg/L FeSO4.7H2O) at pH 6.2 and containing 0.7% (w/v) agar.",... |
94,756 | Open field test in rats | 1 | dx.doi.org/10.17504/protocols.io.kxygx3dozg8j/v1 | https://www.protocols.io/view/open-field-test-in-rats-c8sczwaw | eduard.bentea, María Sanchiz Calvo, Veerle Baekelandt | TITLE: Open field test in rats
AUTHORS: eduard.bentea, María Sanchiz Calvo, Veerle Baekelandt
[DESCRIPTION]
Protocol for performing the open field test in rats. The open field test measures spontaneous locomotion during 5-min free exploration of an open field arena (1m x 1m), and can be used to measure hypolocomotion ... | ["[Test] Bring cages to the behavioral room for at least 60 min prior to the test for habituation", "[Test] Place rat individually in a clean open field arena (1m x 1m)", "[Test] Video tape from above for 5 min and record parameters of spontaneous activity (distance traveled, movement time, immobility) using an activit... |
28,107 | Preparation of LB Agar | null | dx.doi.org/10.17504/protocols.io.7pjhmkn | null | NUS iGEM | TITLE: Preparation of LB Agar
AUTHORS: NUS iGEM
[STEPS]
?. Weigh of LB agar powder.
32 g
?. Add the powder into 1 of deionized water.
1 L
?. Autoclave entire bottle of LB media. | ["Weigh of LB agar powder.\n32 g", "Add the powder into 1 of deionized water.\n1 L", "Autoclave entire bottle of LB media."] |
47,643 | High-throughput Sars-CoV-2 detection from self-collected saline gargle samples | 1 | dx.doi.org/10.17504/protocols.io.bsr3nd8n | https://www.protocols.io/view/high-throughput-sars-cov-2-detection-from-self-col-bsr3nd8n | Noel Rouven Stierlin, Laura Laks, Regina Reimann, Miodrag Savic, Fabian Rudolf, Adriano Aguzzi, Karl Frontzek | TITLE: High-throughput Sars-CoV-2 detection from self-collected saline gargle samples
AUTHORS: Noel Rouven Stierlin, Laura Laks, Regina Reimann, Miodrag Savic, Fabian Rudolf, Adriano Aguzzi, Karl Frontzek
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The corona virus disease 19 (COVID19) p... | ["[Prepare reagents and instruments for nucleic acid extraction]\nPrepare GdnHCl / Chelex mix. Note: GdnHCl helps to stablize the RNA at 65°C during Chelex incubation. Prepare per sample plus 15% overage: GdnHCl + Chelex 30%.\n250 µl\n900 µl\nCHELEX beads settle quickly and need to be resuspended directly prior to... |
18,156 | Decision Support System for assessing management interventions in a Mental Health ecosystem | null | dx.doi.org/10.17504/protocols.io.vyke7uw | null | Carlos Garcia-Alonso | TITLE: Decision Support System for assessing management interventions in a Mental Health ecosystem
AUTHORS: Carlos Garcia-Alonso
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Here it is included the pseudocode for the Decision Support System for assessing management interventions in a Mental Healt... | ["DSS procedure", "The solution pool (SP) is cleaned", "Forj=1 to do → being j the simulation number and the maximum number of simulations", "Fori=1 to do → being i the scenario number and the maximum number of scenarios", "Fork=1 to do → being k the SHA (DMU) number and the number of SHA", "Original dataset Sijk→ the ... |
28,184 | Protocol for removing ssDNA from dsDNA or RNA Samples (NEB #M0568) | null | dx.doi.org/10.17504/protocols.io.7ryhm7w | https://www.protocols.io/view/protocol-for-removing-ssdna-from-dsdna-or-rna-samp-7ryhm7w | New England Biolabs | TITLE: Protocol for removing ssDNA from dsDNA or RNA Samples (NEB #M0568)
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The protocol described below will enable degradation of up to 20 pmol of a 25 nt ssDNA (~ 200 ng). </div><div class = "text-block">In order to degra... | ["Prepare a reaction as follows: AB1Sample containing ssDNA (up to 20 pmol of a 25-mer)x μl2NEBuffer 3.1 (NEB #B7203)*2 μl**3Thermolabile Exonuclease I 1 μl4Nuclease-free water to 20 μl****Most PCR buffers are compatible. **No reaction buffer is necessary if enzyme is added to a PCR reaction.***Scale large... |
73,519 | HuBMAP Lung TMC UCSD & URMC Protocol Overall for Multimodal Single Cell/Nucleus Assays | 1 | dx.doi.org/10.17504/protocols.io.4r3l27qpqg1y/v1 | https://www.protocols.io/view/hubmap-lung-tmc-ucsd-amp-urmc-protocol-overall-for-cj2puqdn | Gloria S Pryhuber, Elizabeth Duong, Blue Lake, Cory Poole, heidie_huyck, Ravi Misra, Xin Sun, Jim Hagood, Dinh H Diep, Kun Zhang | TITLE: HuBMAP Lung TMC UCSD & URMC Protocol Overall for Multimodal Single Cell/Nucleus Assays
AUTHORS: Gloria S Pryhuber, Elizabeth Duong, Blue Lake, Cory Poole, heidie_huyck, Ravi Misra, Xin Sun, Jim Hagood, Dinh H Diep, Kun Zhang
[DESCRIPTION]
This protocol is an overview of the protocols in use for the single ... | ["Screen and accept donor organs, gross and preserve the tissues into samples for analysis using the protocols: \n \n602.2 Donor Acceptance Criteria for URMC HTC HuBMAP and LungMAP Inclusion dx.doi.org/10.17504/protocols.io.bjuxknxn\n603.3 & 604.5_URMC_HTC_Whole Lung and Lobe Processing\ndx.doi.org/10.17504/protocols.... |
null | null | null | dx.doi.org/10.17504/protocols.io.i9gch3w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<h1> </h1>
<h1> </h1>
<h1> </h1>
<p> </p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.d2x8fm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Protocol to fix marine samples for flow cytometry sorting of phytoplankton. <br />Fix at least 2 samples per depth sampled and at least 6 to 10 depths per vertical profile.<br /><br />Back to the laboratory, pico and nano-plankton populations can be sorted and used for clone lib... | [] |
79,946 | MERS Main Protease (Mpro) Fluorescence Dose Response | 1 | null | https://www.protocols.io/view/mers-main-protease-mpro-fluorescence-dose-response-csbiwake | Haim Barr, Noa Lahav | TITLE: MERS Main Protease (Mpro) Fluorescence Dose Response
AUTHORS: Haim Barr, Noa Lahav
[DESCRIPTION]
This is a functional, biochemical assay used to identify treatments for viral infectious disease in MERS 3C-like protease.
Utilizing a direct enzyme activity measurement method, the experiment was performed in a 3... | ["[Prepare 384 Well Plate] PRIME with Assay Buffer by Multi-Drop Combi Tube Dispensing Cassette by selecting the PRIME button on the Combi Dispenser until the tubes are filled completely.", "[Prepare 384 Well Plate] DISPENSE 10 µL to Columns 1 and 23 of assay plate\nNote: These will represent the inhibitor control colu... |
92,469 | Preservation method for long-term storage of fluorescently labeled cells for microscopy | 4 | dx.doi.org/10.17504/protocols.io.ewov1q15pgr2/v1 | https://www.protocols.io/view/preservation-method-for-long-term-storage-of-fluor-c6ivzce6 | Jacob Robertson, Erin Garza | TITLE: Preservation method for long-term storage of fluorescently labeled cells for microscopy
AUTHORS: Jacob Robertson, Erin Garza
[DESCRIPTION]
This method can be used to preserve fluorescently labeled bacterial cells for long-term storage before imaging on a fluorescent microscope. Using this protocol, samples can... | ["[Sample] Collect your cells (up to 500 μl) in a sterile microfuge tube.\n- This protocol can also be used on solid material containing biofilms.", "[Preserve] To your sample tube, add 250 µL sterile 10% glycerol and 250 µL sterile 4% paraformaldehyde in PBS (pH 7.4).\n- If preserving solid material, make sure the ent... |
28,379 | MojoSort™ Human anti-PE Nanobeads Protocol | null | dx.doi.org/10.17504/protocols.io.7x3hpqn | null | Sam Li | TITLE: MojoSort™ Human anti-PE Nanobeads Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Product description and procedure summary:</span><span> Target cells are positively selected or depleted by incubating the sample with an anti-human PE ... | ["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) ... |
99,850 | Ultra-Long Sequencing of Yeast Cells (S. cerevisiae) on ONT Sequencers – A Modified FindingNemo Protocol | 4 | dx.doi.org/10.17504/protocols.io.rm7vzjbk5lx1/v1 | https://www.protocols.io/view/ultra-long-sequencing-of-yeast-cells-s-cerevisiae-ddri254e | Inswasti Cahyani | TITLE: Ultra-Long Sequencing of Yeast Cells (S. cerevisiae) on ONT Sequencers – A Modified FindingNemo Protocol
AUTHORS: Inswasti Cahyani
[DESCRIPTION]
This protocol is a bespoke modification of the FindingNemo protocol (LongRead Club) to enable ultra-long (UL) sequencing of yeast on Nanopore sequencers.
We have test... | ["[Spheroplasting] In a 2 ml DNA LoBind tube, pellet ~200 million cells (50 µL volume of pellet per reaction).", "[Spheroplasting] Wash cells in cold PBS and centrifuge at 10.000 x g, 1 min", "[Spheroplasting] Remove supernatant.", "[Spheroplasting] Repeat step 2-3 once more.", "[Spheroplasting] Resuspend pellet in 480... |
70,106 | Protocol for ex vivo patch clamping | 4 | dx.doi.org/10.17504/protocols.io.261ge361ol47/v1 | https://www.protocols.io/view/protocol-for-ex-vivo-patch-clamping-cgp2tvqe | Maia Datunashvili | TITLE: Protocol for ex vivo patch clamping
AUTHORS: Maia Datunashvili
[DESCRIPTION]
Protocol for ex vivo patch clamping
[STEPS]
SECTION: Preparation of acute brain slices
1. Chill sucrose aCSF up to 4 degrees and then keep it on the ice and bubble continuously by carbogen.
SECTION: Preparation of acute brain slices
2... | ["[Preparation of acute brain slices] Chill sucrose aCSF up to 4 degrees and then keep it on the ice and bubble continuously by carbogen.", "[Preparation of acute brain slices] Place 150 ml standard aCSF in holding chamber. Warm it up to 34oC in water bath and bubble continuously by carbogen.", "[Preparation of acute b... |
null | null | null | dx.doi.org/10.17504/protocols.io.fv7bn9n | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
62,600 | How to Create an Awesome Instagram Video About Dragons Den Keto Slimming Pills UK | 1 | dx.doi.org/10.17504/protocols.io.bp2l61rzdvqe/v1 | https://www.protocols.io/view/how-to-create-an-awesome-instagram-video-about-dra-b9dgr23w | Ericaluceros | TITLE: How to Create an Awesome Instagram Video About Dragons Den Keto Slimming Pills UK
AUTHORS: Ericaluceros
[DESCRIPTION]
“Grab Available Discount Price For Prima Weight Loss Pills UK Today”
When it comes to losing excess weight and fat, there are many medications, exercises, treatments, and supplements that are... | ["[How to Create an Awesome Instagram Video About Dragons Den Keto Slimming Pills UK]"] |
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