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 |
|---|---|---|---|---|---|---|---|
18,272 | SYSB 3036 W03: Gene Prediction | null | dx.doi.org/10.17504/protocols.io.v38e8rw | null | Frank Aylward | TITLE: SYSB 3036 W03: Gene Prediction
AUTHORS: Frank Aylward
[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 sure to unzip it so that we can access t... | ["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 \... |
92,952 | Acute thermal tolerance | 1 | dx.doi.org/10.17504/protocols.io.5jyl8pxerg2w/v1 | https://www.protocols.io/view/acute-thermal-tolerance-c6zyzf7w | Leah A. Turner, Anne Easton, Moira M. Ferguson, Roy G. Danzmann | TITLE: Acute thermal tolerance
AUTHORS: Leah A. Turner, Anne Easton, Moira M. Ferguson, Roy G. Danzmann
[DESCRIPTION]
Understanding the mechanisms that underlie the adaptive response of ectotherms to rising temperatures is key to mitigate the effects of climate change. We assessed the molecular and physiological proc... | ["[Fish rearing] Rear embryos in vertical incubating racks at 8°C until approx. 1 week post-hatching", "[Fish rearing] Move fish to 0.5m tanks according to family until 45 days post-fertilization (dpf). Feed daily and maintain at 8°C with constant aeration with an air stone to maintain oxygen at ~9-10 mg L-1 O2. Period... |
93,207 | Head-fixed behavior | 1 | dx.doi.org/10.17504/protocols.io.q26g7p7k9gwz/v1 | https://www.protocols.io/view/head-fixed-behavior-c69xzh7n | Mai-Anh Vu, mwhowe | TITLE: Head-fixed behavior
AUTHORS: Mai-Anh Vu, mwhowe
[DESCRIPTION]
We have developed a new micro-fiber array approach capable of chronically measuring and optogenetically manipulating local dynamics across over 100 targeted locations simultaneously in head-fixed and freely moving mice, enabling investigation of cell... | ["[Water reward] For reward experiments, mice were water-schedule: they received 0.8-1.5mL water daily, calibrated so they could maintain a body weight 85-90% of their free-water body weight, as described previously (Howe and Dombeck, 2016).", "[Head-fixed setup] Mice were headfixed over a hollow styrofoam ball treadmi... |
63,356 | MS2 Plaque Assay | 4 | null | https://www.protocols.io/view/ms2-plaque-assay-b944r8yw | Daniel Ma | TITLE: MS2 Plaque Assay
AUTHORS: Daniel Ma
[DESCRIPTION]
MS2 plaque assay based on EPA Method 1601 and modified as a spot plating assay (Beck et al., 2009).
[STEPS]
SECTION: MS2 Plaque Assay
2. E. coli Famp Overnight Culture: Add 10 µL E. coli Famp (ATCC 700891) cyrostock to 10 mL sterile Tryptic Soy Broth (30 g/L... | ["[MS2 Plaque Assay] E. coli Famp Overnight Culture: Add 10 µL E. coli Famp (ATCC 700891) cyrostock to 10 mL sterile Tryptic Soy Broth (30 g/L). Incubate . to obtain stationary phase.", "[MS2 Plaque Assay] E. coli Famp Morning Culture: Add 0.75 mL E. coli Overnight Culture to fresh 100 mL sterile Tryptic Soy Broth (3... |
101,795 | Retrospective study of biochemical and haematological changes in diabetes mellitus: The protocol | 0 | dx.doi.org/10.17504/protocols.io.eq2lyw65evx9/v1 | https://www.protocols.io/view/retrospective-study-of-biochemical-and-haematologi-dfnb3man | Jovita Mbah, Phillip Bwititi, Prajwal Gyawali, Ezekiel U Nwose | TITLE: Retrospective study of biochemical and haematological changes in diabetes mellitus: The protocol
AUTHORS: Jovita Mbah, Phillip Bwititi, Prajwal Gyawali, Ezekiel U Nwose
[DESCRIPTION]
The research will analyze 10 years clinical laboratory data to evaluate the changes in routine hematological parameters and haemo... | ["[Abstract] The research will analyze 10 years clinical laboratory data to evaluate the changes in routine hematological parameters and haemorrheology, as well as routine dyslipidemia and liver function test, in diabetes management. This is a laboratory-based clinical observational study involving retrospective\nlongi... |
90,851 | Pre-processing of a textual corpus for a lexicographic analysis with Iramuteq | 1 | null | https://www.protocols.io/view/pre-processing-of-a-textual-corpus-for-a-lexicogra-c4ybyxsn | Wendeline Swart, Guillaume Cabanac, Cécile Crespy | TITLE: Pre-processing of a textual corpus for a lexicographic analysis with Iramuteq
AUTHORS: Wendeline Swart, Guillaume Cabanac, Cécile Crespy
[DESCRIPTION]
This protocol presents a lexicographic analysis of a textual corpus composed of documents. In our case, we applied that method to a corpus of 41 OECD reports ini... | ["Reformatting the input files.", "Convert input files. Open each PDF with Acrobat Reader Pro and convert into the Microsoft Word format (File, Save as… DOCX format).", "Manual pre-processing of the DOCX documents.", "Correct OCR errors. For each DOCX file, open it, spot the OCR errors (most of them are underlined in r... |
55,862 | rNTPs Stock Preparation / IVT Standard Reaction | 4 | dx.doi.org/10.17504/protocols.io.e6nvwkpx2vmk/v1 | https://www.protocols.io/view/rntps-stock-preparation-ivt-standard-reaction-b2swqefe | Felipe Navarro Martínez, Anibal Arce Medina, Fernan Federici | TITLE: rNTPs Stock Preparation / IVT Standard Reaction
AUTHORS: Felipe Navarro Martínez, Anibal Arce Medina, Fernan Federici
[DESCRIPTION]
This protocol describes the preparation of rNTPs stock solutions for their use on IVT and other molecular reactions.
The rNTPs preparation is adapted from a protocol by Berglun... | ["[rNTPs Preparation] Determine the mass of rNTPs that is going to be used. In this case, 100 mg of each rNTP are recommended.", "[rNTPs Preparation] Calculate the necessary volume to obtain a 100 millimolar (mM) solution of each rNTP.\n\nWe did this by estimating how many mmoles are in 100mg and used that value to est... |
null | null | null | dx.doi.org/10.17504/protocols.io.uscewaw | null | null | TITLE: No Title
AUTHORS:
[STEPS] | [] |
39,143 | Open Field Test | 1 | null | https://www.protocols.io/view/open-field-test-bigfkbtn | Lani Tieu | TITLE: Open Field Test
AUTHORS: Lani Tieu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The open field test measures locomotor activity and anxiety-like behavior in rodents.</div></div>
[STEPS]
?. [Open Field Maze Setup]
Arrange open field boxes like this:
?. [Open Field Maze Setup]
Hang the trip... | ["[Open Field Maze Setup]\nArrange open field boxes like this:", "[Open Field Maze Setup]\nHang the tripod on hook that is located on ceiling right above the open field boxes", "[Open Field Maze Setup]\nClean each box with quatricide", "[Open Field Maze Setup]\nConnect camera to computer with USB cord, then attach the ... |
63,411 | Oplexx Keto - Trusted Diet Formula or Cheap Brand? | 3 | dx.doi.org/10.17504/protocols.io.n92ldzjy9v5b/v1 | https://www.protocols.io/view/oplexx-keto-trusted-diet-formula-or-cheap-brand-b96tr9en | H Douglas Morris | TITLE: Oplexx Keto - Trusted Diet Formula or Cheap Brand?
AUTHORS: H Douglas Morris
[DESCRIPTION]
OpleXX Keto Diet Reviews leave risks of operation, as this thing will get the basic advance of fat melting achieved for you!
[STEPS] | [] |
88,986 | Isolated Mitochondria Characterization | 4 | dx.doi.org/10.17504/protocols.io.e6nvwdz87lmk/v1 | https://www.protocols.io/view/isolated-mitochondria-characterization-c252yg8e | Megan Lee, Neal Bennett, Ken Nakamura | TITLE: Isolated Mitochondria Characterization
AUTHORS: Megan Lee, Neal Bennett, Ken Nakamura
[DESCRIPTION]
This protocol is used to isolate mitochondria from cells. Isolated mitochondria can then be further analyzed, as described here, with a complex I enzyme activity assay, and/or blue native PAGE to quantify amounts... | ["[Isolating Mitochondria] Make mitochondrial isolation buffers - starting buffer, mitochondrial resuspension buffer.", "[Isolating Mitochondria] 100 mM EGTA, pH 7.4:\n3.8 g EGTA\n70 mL water \nAdjusted pH KOH\nBring to 100 mL with water", "[Isolating Mitochondria] Starting Buffer (225 mM mannitol, 75 mM sucrose, 30 mM... |
99,659 | QTL Mapping via GeneNetwork.org | 0 | dx.doi.org/10.17504/protocols.io.n92ld8pb7v5b/v1 | https://www.protocols.io/view/qtl-mapping-via-genenetwork-org-ddjj24kn | Dow Michael Glikman, Dennis de Bakker, Rob W. Williams | TITLE: QTL Mapping via GeneNetwork.org
AUTHORS: Dow Michael Glikman, Dennis de Bakker, Rob W. Williams
[DESCRIPTION]
The use of GeneNetwork.org for identifying quantitative trait loci. Rich datasets available for mapping a wide range of traits to genomic variation.
[STEPS]
SECTION: Introduction
1. Quantitative trait ... | ["[Introduction] Quantitative trait loci (QTL) mapping using GeneNetwork.org:\n\nQTL mapping is a method to identify genomic regions that influence variation in a phenotypic trait.\nGeneNetwork.org is a data and analytic resource for interrogating linked multimodal data, with integrating functionality for QTL mapping. ... |
33,843 | Neutralizing antibody detection | 1 | dx.doi.org/10.17504/protocols.io.bdati2en | https://www.protocols.io/view/neutralizing-antibody-detection-bdati2en | Shihong Fu, Wenjing Liu | TITLE: Neutralizing antibody detection
AUTHORS: Shihong Fu, Wenjing Liu
[DESCRIPTION]
Neutralizing antibodies of serum samples were detected by 90% plaque reduction neutralization test (PRNT90).
[BEFORE_START]
the serum samples should be inactived (56℃，30min,in water)before the test.
[STEPS]
SECTION: Neutralizing a... | ["[Neutralizing antibody detection] 1. \t Diluted serum: dilute the serum sample in a 96-well plate. Take 24 μl of inactivated serum and mix it with 96 μl of MEM culture medium to complete the 5-fold dilution of serum,the Serum samples were serially diluted two-fold beginning at a 1:5 dilution and ending at 1: 160 .", ... |
41,487 | Granulate formulation protocol | 1 | dx.doi.org/10.17504/protocols.io.bkrpkv5n | https://www.protocols.io/view/granulate-formulation-protocol-bkrpkv5n | Andreea S | TITLE: Granulate formulation protocol
AUTHORS: Andreea S
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Bioformulation</span><span> is used in agriculture for various reasons like soil fertility, plant growth promotion, and suppression of phytopathogens. The bacter... | ["[Bacterium Inoculum]\nGrow a single colony of bacteria in an assay tube with of Luria Broth (LB) medium\n5 mL", "[Bacterium Inoculum]\nIncubate it in an orbital shaker at 200 rev.min-1 at for .\n30 °C", "[Bacterium Inoculum]\nAfter bacterial growth, take a Erlenmeyer flask and add of LB medium in it.\n500 mL... |
97,973 | Primary Neuron Culture from Embryonic Rats | 0 | dx.doi.org/10.17504/protocols.io.j8nlk8eewl5r/v1 | https://www.protocols.io/view/primary-neuron-culture-from-embryonic-rats-dbwv2pe6 | Lucas Hampton, Paul Temkin | TITLE: Primary Neuron Culture from Embryonic Rats
AUTHORS: Lucas Hampton, Paul Temkin
[GUIDELINES]
This protocol may also be used with P0 or neonatal mouse pups.
[STEPS]
SECTION: Procedure
2. Sacrifice time-pregnant rat (E18) by CO2 asphyxiation followed by secondary method (thoracotomy or cervical dislocation).
Not... | ["[Procedure] Sacrifice time-pregnant rat (E18) by CO2 asphyxiation followed by secondary method (thoracotomy or cervical dislocation).\n\nNote: All procedures are performed in compliance with AAALAC guidelines and are approved by the Biogen Institutional Animal Care and Use Committee.", "[Procedure] Wash lower abdomen... |
20,294 | Cell dissociation from airway biopsies with cold-active protease for single-cell RNA-seq | null | dx.doi.org/10.17504/protocols.io.x3efqje | null | Laure-Emmanuelle Zaragosi, Pascal Barbry | TITLE: Cell dissociation from airway biopsies with cold-active protease for single-cell RNA-seq
AUTHORS: Laure-Emmanuelle Zaragosi, Pascal Barbry
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol provides details on the cell dissociation that should be performed to obtain single-cell sus... | ["Perform bronchial biopsy at the desired level of the airways (to be performed by a medical doctor)", "Put the biopsy in 1 mL DPBS in a well of a 6-well plate, observe aspect, and then transfer into 1 mL of ice-cold dissociation buffer in a 1.5 mL eppendorf tube. Use wide-bore 1 mL pipet tip for all biopsy transfers.\... |
60,503 | FQ-LAMP Assay for Detection of CoV2 in Clinical Nasal Swabs | 1 | dx.doi.org/10.17504/protocols.io.14egn74bpv5d/v1 | https://www.protocols.io/view/fq-lamp-assay-for-detection-of-cov2-in-clinical-na-b7bxripn | Les Jones, Hemant K. Naikare, Yung-Yi C. Mosley, and Ralph A. Tripp | TITLE: FQ-LAMP Assay for Detection of CoV2 in Clinical Nasal Swabs
AUTHORS: Les Jones, Hemant K. Naikare, Yung-Yi C. Mosley, and Ralph A. Tripp
[DESCRIPTION]
COVID-19 is a public health challenge requiring rapid testing for detecting infections and transmission. Nucleic acid amplification tests (NAAT) targeting SARS-C... | ["[FQ-LAMP Sample Preparation] mix 20ul of clinical swab material with 20 ul of SPS buffer containing Proteinase K.", "[FQ-LAMP Sample Preparation] Incubate at 37C for 15 minutes, then 95C for 5 minutes", "[FQ-LAMP Sample Preparation] Sample is ready to use in FQ-LAMP at 2ul / 25ul reaction", "[Prepare FQ-LAMP Master M... |
55,693 | Quantification of SARS-CoV-2 variant mutations (HV69-70, E484K/N501Y, and del156-157/R158G) in settled solids using digital RT-PCR | 1 | dx.doi.org/10.17504/protocols.io.b2mmqc46 | https://www.protocols.io/view/quantification-of-sars-cov-2-variant-mutations-hv6-b2mmqc46 | Bridgette Hughes, Bradley J. White, Marlene K. Wolfe, Krista Wigginton, Alexandria B B Boehm | TITLE: Quantification of SARS-CoV-2 variant mutations (HV69-70, E484K/N501Y, and del156-157/R158G) in settled solids using digital RT-PCR
AUTHORS: Bridgette Hughes, Bradley J. White, Marlene K. Wolfe, Krista Wigginton, Alexandria B B Boehm
[DESCRIPTION]
This process instruction describes the steps for quantitative ... | ["[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... |
19,740 | UC Davis - Receipt of Vendor and Courier Mice | null | dx.doi.org/10.17504/protocols.io.xh4fj8w | null | K.C. Kent Lloyd | TITLE: UC Davis - Receipt of Vendor and Courier Mice
AUTHORS: K.C. Kent Lloyd
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">The purpose of this document is to describe the procedure for accepting commercial vendor an... | ["Daily Tasks – Refer to MBPVIV-20-105 Daily Observations/Action for further details1.1 Receipt of mice from commercial vendors 1.1.1 Mice arriving from the following commercial vendors of mice are considered “clean”: Charles River Laboratory ... |
null | null | null | dx.doi.org/10.17504/protocols.io.qzwdx7e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Background:</strong> The neutrophil-lymphocyte ratio (NLR) is increasingly known as an indicator of systemic inflammation. It is used as a predictor for clinical outcomes in cancers and cardiovascular disease. However, its relationship with intracerebral hemorrhage (I... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.mvhc636 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Marine protists are important in all marine ecosystems, but many are not culturable and therefore difficult to study. The increasing development of single-cell techniques is allowing for more marine protists to be studied, but many single-cell protocols are only optimized for... | [] |
88,550 | Conventional methods for isolation and Identification of Streptococcus pyogenes | 1 | dx.doi.org/10.17504/protocols.io.rm7vzx6e2gx1/v1 | https://www.protocols.io/view/conventional-methods-for-isolation-and-identificat-c2qeydte | melissa.kalladeen | TITLE: Conventional methods for isolation and Identification of Streptococcus pyogenes
AUTHORS: melissa.kalladeen
[DESCRIPTION]
The protocol outlines the steps for isolating and identifying Group A streptococci (Streptococcus pyogenes) from growth on primary culture media.
[STEPS]
SECTION: Culture and identification ... | ["[Culture and identification of Streptococcus pyogenes] Upon receipt, a beta-haemolytic colony was streaked onto a new 5% blood agar (HiMedia Laboratories Limited, Mumbai, In.) plate to obtain isolated colonies and incubated at 35-37ºC for 24 hours in an anerobic jar.", "[Culture and identification of Streptococcus py... |
96,996 | Procedure for EEG surgery | 4 | dx.doi.org/10.17504/protocols.io.kxygx3dxog8j/v2 | https://www.protocols.io/view/procedure-for-eeg-surgery-dayc2fsw | daniel.dautan daniel, Per Svenningsson | TITLE: Procedure for EEG surgery
AUTHORS: daniel.dautan daniel, Per Svenningsson
[DESCRIPTION]
Standard Operating Procedure for EEG surgery
[STEPS]
SECTION: Preparation of EEG transponder (DSI)
1. Prepare the transponder by twisting the excess wire in the ribs holder.
SECTION: Anesthesia and Animal Preparation
4. Ind... | ["[Preparation of EEG transponder (DSI)] Prepare the transponder by twisting the excess wire in the ribs holder.", "[Anesthesia and Animal Preparation] Induce anesthesia using isoflurane in an induction chamber. We recommend to use between 2-3% isoflurane in 02.", "[Preparation of EEG transponder (DSI)] The transponder... |
23,165 | Enhanced convolutional neural network for plankton identification and enumeration | null | dx.doi.org/10.17504/protocols.io.2u5gey6 | null | Kaichang CHENG, Xuemin Cheng, Yuqi Wang, Hongsheng Bi, Mark C. Benfield | TITLE: Enhanced convolutional neural network for plankton identification and enumeration
AUTHORS: Kaichang CHENG, Xuemin Cheng, Yuqi Wang, Hongsheng Bi, Mark C. Benfield
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is an automatic plankton image recognition and enumeration system using an en... | ["[The whole procedure]\nThe whole procedure for the proposed method.This is a flow chart illustrating the different steps and modules in the proposed automated plankton identification and enumeration procedure.", "[Substeps in this procedure]\nThe several substeps for the proposed method.", "[Substeps in this proced... |
40,446 | Protocols for "The draft genome assembly of the critically endangered Nyssa yunnanensis, a plant species with extremely small populations endemic to Yunnan Province, China" | 2 | dx.doi.org/10.17504/protocols.io.bjq6kmze | https://www.protocols.io/view/protocols-for-34-the-draft-genome-assembly-of-the-bjq6kmze | Weixue Mu, Jinpu Wei, Ting Yang, Yannan Fan, Le Cheng, Jinlong Yang, Ranchang Mu, Jie Liu, Jianming Zhao, Weibang Sun, Xun Xu, Xin Liu, Radoje Drmanac, Huan Liu | TITLE: Protocols for "The draft genome assembly of the critically endangered Nyssa yunnanensis, a plant species with extremely small populations endemic to Yunnan Province, China"
AUTHORS: Weixue Mu, Jinpu Wei, Ting Yang, Yannan Fan, Le Cheng, Jinlong Yang, Ranchang Mu, Jie Liu, Jianming Zhao, Weibang Sun, Xun Xu, Xin ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.fepbjdn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Amalgam from various places.</p>
[BEFORE_START]
<p>This protcol is designed/re-optimized for staining 5e6 cells. However, sytoxgreen is supposed to be fairly robust to cell number changes, so variation from this should be tolerated (see Haase and Reed 2002). Remember, PBS me... | [] |
91,273 | Protocol: A Systematic Review and Meta-Analysis of HLA-DR in Onychomycosis Susceptibility | 1 | dx.doi.org/10.17504/protocols.io.j8nlko2m5v5r/v1 | https://www.protocols.io/view/protocol-a-systematic-review-and-meta-analysis-of-c5dhy236 | Andrew C Cook, nathancohen, Rishi Patel, Shannon South, Marcia Ballantyne | TITLE: Protocol: A Systematic Review and Meta-Analysis of HLA-DR in Onychomycosis Susceptibility
AUTHORS: Andrew C Cook, nathancohen, Rishi Patel, Shannon South, Marcia Ballantyne
[DESCRIPTION]
Onychomycosis is a significant health concern for many populations. Onychomycosis is known to have environmental and genetic ... | ["[Title] A Systematic Review and Meta-Analysis of HLA-DR in Onychomycosis Susceptibility", "[Registration] Protocols.io", "[Authors] Andrew C Cook: Lake Erie College of Osteopathic Medicine - Bradenton OMS-III\nACook28563@med.lecom.edu \nORCID: 0000-0001-6332-1993\n\nNathan Cohen: Lake Erie College of Osteopathic Medi... |
28,818 | DNA/RNA Radiolabeling Protocol | null | dx.doi.org/10.17504/protocols.io.8dshs6e | null | Liz O'Brien, Connor Tsuchida | TITLE: DNA/RNA Radiolabeling Protocol
AUTHORS: Liz O'Brien, Connor Tsuchida
[STEPS]
?. Incubate at for .
37 °C
?. Prepare G25 columns (from GE, green box): vortex thoroughly, twist cap ¼ turn, snap off bottom, spin for at to get rid of liquid.
Centrifuge: 3000 33
?. Add H2O to each labeling reaction after heat ina... | ["Incubate at for .\n37 °C", "Prepare G25 columns (from GE, green box): vortex thoroughly, twist cap ¼ turn, snap off bottom, spin for at to get rid of liquid.\nCentrifuge: 3000 33", "Add H2O to each labeling reaction after heat inactivation is done.\n25 µl", "Since 50 μl H2O were in bottom of tube and you add your... |
null | null | null | dx.doi.org/10.17504/protocols.io.cruv6v | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol may be used with electrocompetent cells prepared by you according to <a href="https://www.protocols.io/view/Making-your-own-electrocompetent-cells-imsv6m" target="_blank">this protocol.</a>
[BEFORE_START]
For control electroporation dilute pUC19 to 10 pg/µl ... | [] |
30,789 | In vitro infection of PBMCs with dengue and Zika virus | null | dx.doi.org/10.17504/protocols.io.babdiai6 | null | Yujao Zhao | TITLE: In vitro infection of PBMCs with dengue and Zika virus
AUTHORS: Yujao Zhao
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details in vitro infection of human PBMCs with dengue/zika virus followed by multiparameter antibody labeling and data acquisition using CyTOF.The data usin... | [] |
94,822 | Protocols from Kilfeather, Khoo et al., 2024 | 2 | dx.doi.org/10.17504/protocols.io.36wgqj75kvk5/v2 | https://www.protocols.io/view/protocols-from-kilfeather-khoo-et-al-2024-c8uezwte | Peter Kilfeather, Maria Claudia Caiazza | TITLE: Protocols from Kilfeather, Khoo et al., 2024
AUTHORS: Peter Kilfeather, Maria Claudia Caiazza
[DESCRIPTION]
This protocol collection includes immunohisto/chemical staining methods, DAT-TRAP methods and the protocol for the Fura-2 assay in Kilfeather, Khoo et al., 2024.
[STEPS] | [] |
99,219 | Expression and purification of Syp-VAMP2 complex into native nanodiscs | 0 | dx.doi.org/10.17504/protocols.io.4r3l2qo24l1y/v1 | https://www.protocols.io/view/expression-and-purification-of-syp-vamp2-complex-i-dc5t2y6n | Caroline Brown, Snehasish Ghosh, Kallol Gupta | TITLE: Expression and purification of Syp-VAMP2 complex into native nanodiscs
AUTHORS: Caroline Brown, Snehasish Ghosh, Kallol Gupta
[DESCRIPTION]
This is a protocol for the purification of Syp-VAMP2 complex into native nanodiscs.
[STEPS]
SECTION: Mammalian expression constructs
1. Thaw Expi-HEK293 cells and passage ... | ["[Mammalian expression constructs] Thaw Expi-HEK293 cells and passage 3 times", "[Mammalian expression constructs] Using a T2A polycistronic vector containing the VAMP2 and Synaptophysin (Syp) genes with FLAG tag, express VAMP2 and Syp in Expi-HEK293 cells using ExpiFectamine transfection reagent for 2880 min hours.",... |
63,566 | Production of 10000x TO-DMSO DNA gel stain | 5 | null | https://www.protocols.io/view/production-of-10000x-to-dmso-dna-gel-stain-cabnsame | Shalo Minette, Stephane Fadanka, Nadine Mowoh | TITLE: Production of 10000x TO-DMSO DNA gel stain
AUTHORS: Shalo Minette, Stephane Fadanka, Nadine Mowoh
[DESCRIPTION]
DNA dyes stain deoxyribonucleic acid for laboratory purposes such as detection and quantification. Many DNA dyes also bind to RNA and could be more broadly described as nucleic acid stains. Com... | ["[Preparing a 13mg/ml stock of DNA gel stain (1ml)] Use a weighing balance to carefully measure0.013 g of into a 1.5ml Eppendorf tube or opaque screw cap tube.", "[Preparing a 13mg/ml stock of DNA gel stain (1ml)] Use a micropipette to pipette 1000 µL of into the same Eppendorf tube.", "[Preparing a 13mg/ml stock ... |
28,994 | LAMP assay | null | dx.doi.org/10.17504/protocols.io.8jahuie | null | Niels Appelman | TITLE: LAMP assay
AUTHORS: Niels Appelman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is a protocol used to perform LAMP assays. It was adapted to </span><a href="https://international.neb.com/protocols/2016/08/15/warmstart-colorimetric-lamp-2x-master-mix-typical-lamp-protocol-m1800" ... | ["Prepare a 10X primermix according to the following scheme: AB1PrimerConcentration2FIP16 uM3BIP16 uM4F32 uM5B32 uM6LOOP F8 uM7LOOP B8 uM\nAB1PrimerConcentration2FIP16 uM3BIP16 uM4F32 uM5B32 uM6LOOP F8 uM7LOOP B8 uM", "Add the following components to a microcentrifuge tube ABC1ComponentVolume added (25 uL reaction)V... |
42,122 | Isolation of bacteria associated with mucus on shark skin | 1 | dx.doi.org/10.17504/protocols.io.bmdik24e | https://www.protocols.io/view/isolation-of-bacteria-associated-with-mucus-on-sha-bmdik24e | Claudia Pogoreutz, Gabriela Perna, Mauvis A. Gore, Rupert F. Ormond, Christopher R. Clarke, Christian Voolstra | TITLE: Isolation of bacteria associated with mucus on shark skin
AUTHORS: Claudia Pogoreutz, Gabriela Perna, Mauvis A. Gore, Rupert F. Ormond, Christopher R. Clarke, Christian Voolstra
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Animals and plants are metaorganisms or holobionts associated... | ["Sampling: Collect replicate swab samples to potentially increase diversity of isolates. If sampling is vessel-based, and circumstances permit, let the skin of the shark first dry for a couple of seconds, and then swab the desired skin area (approx. 8 – 10 strokes, if feasible) using a sterile cotton swab. Use a new s... |
85,330 | Gewebesammlung Frischgewebe Prostatektomie | 1 | null | https://www.protocols.io/view/gewebesammlung-frischgewebe-prostatektomie-cxjsxkne | Annika Fendler, Bettina Ergün | TITLE: Gewebesammlung Frischgewebe Prostatektomie
AUTHORS: Annika Fendler, Bettina Ergün
[DESCRIPTION]
Dieses Protokoll beschreibt die Schritte für die Sammlung von Frischgewebe, Gefriergewebe (Fresh-frozen), und Blut von Patienten mit Prostatakarzinom bei Prostatektomie.
Verwandte Dokumente:
Protokoll zur Blutaufa... | ["[Gewebesammlung im OP] Frischgewebe :\nDie erste 6 mm Stanze sollte für Frischgewebe verwendet werden und wird direkt in Medium überführt. \nRöhrchen mit Gewebenummer und falls nötig T1 und T2 beschriften.", "[Gewebesammlung im OP] Fresh-frozen tissue:\nDie zweite Stanze sollte direkt neben der Frischgewebestanze erf... |
83,840 | Library Aligner | 5 | dx.doi.org/10.17504/protocols.io.5qpvo3n89v4o/v1 | https://www.protocols.click/view/library-aligner-cv48w8zw | ckremitz | TITLE: Library Aligner
AUTHORS: ckremitz
[DESCRIPTION]
Protocol on how to run Library Aligner in FIVTools once sequencing data has been returned to us from the Sequencing Core. It also has an option for checking the Representation of a gRNA library.
[STEPS]
1. Open FIVTools and click on the LA tab in the upper left ... | ["Open FIVTools and click on the LA tab in the upper left section of the program.", "Enter in your returned NGS link into the HTCF Link tab and the destination to download the files into Dest.", "Press Download UZ to download the files and automatically unzip them. This will deposit reads into your destination folder ... |
null | null | null | dx.doi.org/10.17504/protocols.io.kw7cxhn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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16,802 | In vivo assessment of S. scimitus predation upon bee brood | null | dx.doi.org/10.17504/protocols.io.unaevae | null | Sabrina Rondeau, Pierre Giovenazzo, Valérie Fournier | TITLE: In vivo assessment of S. scimitus predation upon bee brood
AUTHORS: Sabrina Rondeau, Pierre Giovenazzo, Valérie Fournier
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify"><span>In order to investigate the potential of predatory mites to contro... | ["[Experimental design]\nA) Randomly assign each hive to a treatment (control or treated) and identify the hives.Note: Refer to both the Guidelines and the Materials sections for more information about colony and apiary requirements.", "[Egg laying monitoring]\nAs described in Human et al. (2013). doi: 10.3896/IBRA.1.5... |
54,370 | Growth Curves of S. elongatus under salt stress and low carbon | 4 | dx.doi.org/10.17504/protocols.io.bzcap2se | https://www.protocols.io/view/growth-curves-of-s-elongatus-under-salt-stress-and-bzcap2se | Akashdutta | TITLE: Growth Curves of S. elongatus under salt stress and low carbon
AUTHORS: Akashdutta
[DESCRIPTION]
When liquid media is inoculated with bacteria and the cell population is counted at intervals, it is possible to plot a typical bacterial growth curve that shows the increase in the number of cells over time. Suc... | ["Take 100 mL culture in BG-11 . Add 150 milimolar (mM) Nacl and note the time of addition.", "3 hours after salt acclimation, take 2 1 mL samples from each flask in 2 microcentrifuge tubes", "Use one set of samples to take the OD measurements", "Take the other set of samples and centrifuge at 4000 rpm, 7 min, 25 °C",... |
27,293 | Biocatalytic Enzymes Have Wide Applications in the Real World | null | dx.doi.org/10.17504/protocols.io.6v5he86 | null | Bingly Fiona, Laisa Liane Paineiras-Domingos, Caio Maximino | TITLE: Biocatalytic Enzymes Have Wide Applications in the Real World
AUTHORS: Bingly Fiona, Laisa Liane Paineiras-Domingos, Caio Maximino
[STEPS] | [] |
73,333 | Synthesis of Silver Nanoparticles | 6 | dx.doi.org/10.17504/protocols.io.q26g7yywkgwz/v2 | https://www.protocols.io/view/synthesis-of-silver-nanoparticles-cjuvunw6 | Raphael D. Ayivi, Bukola Adesanmi, Eric S McLamore, Sherine O. Obare | TITLE: Synthesis of Silver Nanoparticles
AUTHORS: Raphael D. Ayivi, Bukola Adesanmi, Eric S McLamore, Sherine O. Obare
[DESCRIPTION]
This protocol describes the synthesis of silver nanoparticles for colorimetric sensing of environmental samples and for other biochemical applications. The protocol requires 110 minutes ... | ["[SECTION 1) Preparation] Prepare stabilizer solution (0.01 M Sodium citrate; Na3C6H5O7) \nPrepare a glass beaker with 50 ml of deionized water and label\nWeigh 0.1290 g of trisodium citrate on scale\nDissolve sodium citrate powder in prepared glass beaker with deionized water\nPlace magnetic stir bar in beaker and pl... |
38,751 | SPARC_Duke_Grill_OT2-OD025340_HumanVagusNerve_Claudin1IHC_Morphology | 1 | dx.doi.org/10.17504/protocols.io.bh37j8rn | https://www.protocols.io/view/sparc-duke-grill-ot2-od025340-humanvagusnerve-clau-bh37j8rn | Nicole A. Pelot, J. Ashley Ezzell, Gabriel B. Goldhagen, Jake E. Cariello, Kara A. Clissold, Warren M. Grill | TITLE: SPARC_Duke_Grill_OT2-OD025340_HumanVagusNerve_Claudin1IHC_Morphology
AUTHORS: Nicole A. Pelot, J. Ashley Ezzell, Gabriel B. Goldhagen, Jake E. Cariello, Kara A. Clissold, Warren M. Grill
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The protocol describes immunohistochemistry with anti-clau... | ["[Immunohistochemistry]\nBake slides with sections of paraffin-embedded vagus nerve at 50oC overnight.", "[Immunohistochemistry]\nDeparaffinize the slides and hydrate them to distilled water: xylene (2x 6 min), 100% ethanol (5 min), 95% ethanol (4 min), 70% ethanol (3 min), deionized water (2x 1 min).", "[Immunohistoc... |
45,756 | mynetsohbet | 1 | dx.doi.org/10.17504/protocols.io.bqw4mxgw | https://www.protocols.io/view/mynetsohbet-bqw4mxgw | sohbet | TITLE: mynetsohbet
AUTHORS: sohbet
[STEPS]
?. http://www.sohbet.world Eski mynet sohbet odaları omegla sohbet yazılı omegla chat 18 sohbet odaları yaş grupları akıllı telefon ve tablet uyumlu üyelij gerekmeyen ücretsiz resimli sesli görüntülü sohbet ve cgat seçenekleri.
?.
?. | ["http://www.sohbet.world Eski mynet sohbet odaları omegla sohbet yazılı omegla chat 18 sohbet odaları yaş grupları akıllı telefon ve tablet uyumlu üyelij gerekmeyen ücretsiz resimli sesli görüntülü sohbet ve cgat seçenekleri."] |
36,313 | Differentiation of iPSC into dopaminergic neurons | null | dx.doi.org/10.17504/protocols.io.bfpzjmp6 | https://www.protocols.io/view/differentiation-of-ipsc-into-dopaminergic-neurons-bfpzjmp6 | Elisangela Bressan, Melanie Cobb, on behalf of the Foundational Data Initiative for Parkinson's Disease (FOUNDIN-PD) | TITLE: Differentiation of iPSC into dopaminergic neurons
AUTHORS: Elisangela Bressan, Melanie Cobb, on behalf of the Foundational Data Initiative for Parkinson's Disease (FOUNDIN-PD)
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Induced pluripotent stem cell (iPSC)-derived dopaminergic neurons is ... | ["[iPSC preparation for differentiation]\nGrow iPSC on matrigel-coated plates with Essential E8 Flex medium until they cover 70-80% of the well area.", "[iPSC preparation for differentiation]\nCheck if iPSC appear pluripotent and undifferentiated using a bright-field microscope. The iPSC should show a typical morpholog... |
86,208 | Preparation of soluble and insoluble mitochondrial protein fractions for mass spectrometry analysis | 1 | dx.doi.org/10.17504/protocols.io.kxygx394kg8j/v1 | https://www.protocols.io/view/preparation-of-soluble-and-insoluble-mitochondrial-cye8xthw | Louise Uoselis | TITLE: Preparation of soluble and insoluble mitochondrial protein fractions for mass spectrometry analysis
AUTHORS: Louise Uoselis
[DESCRIPTION]
Preparation of soluble and insoluble mitochondrial protein fractions from HeLa cells for mass spectrometry analysis.
[STEPS]
SECTION: Day 1
1. Thaw mitochondrial stocks on i... | ["[Day 1] Thaw mitochondrial stocks on ice, and aliquot out one tube of 60 µg of mitochondria for each sample.", "[Day 1] Centrifuge samples at 10000 rcf for 10 min at 4 °C, and carefully aspirate the supernatant.", "[Day 1] Add 60 µL of ice cold 0.5% TX-100 in PBS, vortex each sample for ~5 seconds, and leave samples ... |
62,999 | XR Massive Male Enhancement | 1 | dx.doi.org/10.17504/protocols.io.14egn7n9pv5d/v1 | https://www.protocols.io/view/xr-massive-male-enhancement-b9rxr57n | XRMassiveMaleEnhanc | TITLE: XR Massive Male Enhancement
AUTHORS: XRMassiveMaleEnhanc
[DESCRIPTION]
►Product Name–XR Massive Male Enhancement
►Category- Male Enhancement
►Main Benefits– Improve Libido & Sex Drive, Increase Stamina & Sexual Confidence
►Availability– Online[Official Website]
Erectile dysfunction is a common problem among... | [] |
85,961 | Differentiation of SH-SY5Y cells | 4 | dx.doi.org/10.17504/protocols.io.dm6gp3jj1vzp/v1 | https://www.protocols.io/view/differentiation-of-sh-sy5y-cells-cx7hxrj6 | Shenjie Wu, Nancy C. Hernandez Villegas, schekman | TITLE: Differentiation of SH-SY5Y cells
AUTHORS: Shenjie Wu, Nancy C. Hernandez Villegas, schekman
[DESCRIPTION]
This protocol describes a standard procedure to differentiate SH-SY5Y cells into dopaminergic neurons using retinoic acid
[STEPS]
SECTION: Differentiation of SH-SY5Y cells
1. SH-SY5Y neuroblastoma cells ... | ["[Differentiation of SH-SY5Y cells] SH-SY5Y neuroblastoma cells were maintained in DMEM supplemented with 1× nonessential amino\nacid (NEAA), 1× sodium pyruvate, and 10% FBS.", "[Differentiation of SH-SY5Y cells] Differentiation was induced by lowering the FBS in culture medium to 1% plus 10 μM RA.", "[Differentiation... |
18,298 | DALEX NonTox PAGE Stain | null | dx.doi.org/10.17504/protocols.io.v42e8ye | null | David Frommholz, Alexandra Ehl, Nadine Stefanczyk | TITLE: DALEX NonTox PAGE Stain
AUTHORS: David Frommholz, Alexandra Ehl, Nadine Stefanczyk
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">DALEX NonTox PAGE Stain is a non-toxic Commassie based protein dye for the detection of bands in SDS and Native PAGE. The easy and fast staining procedure does no... | ["[Washing]\nRemove the gel from the cassette and place it into a tray e.g. a weighing pan.Immerse the gel in distilled water (50 ml for an 8 x 8 cm gel) and microwave for 30 s at 500 W.Incubate with gentle shaking for 5 minutes and discard the water afterwards.Repeat two more times.\nNative PAGE gels do not require wa... |
90,866 | Genomic DNA extraction from STERIVEX filter within capsule using QIAGEN´s DNeasy Blood and Tissue kit | 6 | null | https://www.protocols.io/view/genomic-dna-extraction-from-sterivex-filter-within-c4ysyxwe | delphine.vanhaecke | TITLE: Genomic DNA extraction from STERIVEX filter within capsule using QIAGEN´s DNeasy Blood and Tissue kit
AUTHORS: delphine.vanhaecke
[DESCRIPTION]
This is our protocol for extracting environmental DNA from STERIVEX filters using QIAGEN´s Dneasy Blood and Tissue KIT. The protocol is a combination of previously des... | ["Clean the laminar flow hood surface and pipettes with DNAZAP and rinse with ddH2O.", "Place gloves and 1.5 mL low bind tubes (for receiving DNA extract elution 1, elution 2 and one DNA extraction control) in the flow hood and expose to UV for 10 minutes.", "While exposing to UV in step 2 in the PRE-PCR room, in the P... |
83,638 | Single cell dissociation of healthy paediatric skin | 1 | dx.doi.org/10.17504/protocols.io.e6nvwd6kwlmk/v1 | https://www.protocols.click/view/single-cell-dissociation-of-healthy-paediatric-ski-cvwww7fe | Emily Stephenson, Chloe Admane, Keval Sidhpura | TITLE: Single cell dissociation of healthy paediatric skin
AUTHORS: Emily Stephenson, Chloe Admane, Keval Sidhpura
[DESCRIPTION]
This protocol outlines the method for the enzymatic dissociation of healthy paediatric skin >3mm into a single cell suspension.
[BEFORE_START]
Do not forget to record the metadata for this... | ["[Day 1 - Begin protocol late afternoon] Empty sample onto petri dish and wash sample with PBS", "[Day 1 - Begin protocol late afternoon] Cut off lower dermis and fat and place in well of 48-well plate with 1ml RPMI", "[Day 1 - Begin protocol late afternoon] Place epidermis and upper dermis sample in a 48 well V-botto... |
58,954 | Overall protocol for top-down CZE-MS/MS of human spleen tissue | 1 | dx.doi.org/10.17504/protocols.io.b5tiq6ke | https://www.protocols.io/view/overall-protocol-for-top-down-cze-ms-ms-of-human-s-b5tiq6ke | Jeannie Camarillo, Bryon Drown, Neil Kelleher | TITLE: Overall protocol for top-down CZE-MS/MS of human spleen tissue
AUTHORS: Jeannie Camarillo, Bryon Drown, Neil Kelleher
[DESCRIPTION]
Overview description of the process for acquiring top-down CZE-MS/MS data on human spleen tissue
[STEPS]
SECTION: Tissue Collection
1. Spleen tissue was provided by University ... | ["[Tissue Collection] Spleen tissue was provided by University of Florida TMC. Tissue was collected and prepared according to the following:", "[Sample Preparation]", "[Data Acquisition]", "[Data Analysis]"] |
41,866 | T4H protocol | 1 | dx.doi.org/10.17504/protocols.io.bk5iky4e | https://www.protocols.io/view/t4h-protocol-bk5iky4e | Ophir Auslaender, kalle.levon | TITLE: T4H protocol
AUTHORS: Ophir Auslaender, kalle.levon
[STEPS]
?. Clean Au chip: insert in piranha solution (75% H2SO4, 25% H2O2), wash with DI water, dry with nitrogen gas.
?. Mix the solution for imprinting in 19/1 volume ratio: 19 for the analyte, 1 for the monolayer former at self-assembled monolayer (SAM) ... | ["Clean Au chip: insert in piranha solution (75% H2SO4, 25% H2O2), wash with DI water, dry with nitrogen gas.", "Mix the solution for imprinting in 19/1 volume ratio: 19 for the analyte, 1 for the monolayer former at self-assembled monolayer (SAM) concentration.", "Place Au chip in the imprinting solution. Incubate ov... |
null | null | null | dx.doi.org/10.17504/protocols.io.m8kc9uw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is a modification of a previously published method by Wilgenburg et al (<a href="https://www.ncbi.nlm.nih.gov/pubmed/23951090" target="_blank">PLoS One, 2013</a>) to obtain monocytes and macrophages from induced Pluripotent Stem Cells (iPSCs) lines. </p>
[BEFOR... | [] |
53,419 | d1 21/09 | 3 | dx.doi.org/10.17504/protocols.io.byejptcn | https://www.protocols.io/view/d1-21-09-byejptcn | name go test surname, mariia guliakina | TITLE: d1 21/09
AUTHORS: name go test surname, mariia guliakina
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">test</div></div>
[STEPS] | [] |
14,543 | Free radical scavenging activity | null | dx.doi.org/10.17504/protocols.io.sfpebmn | null | Jorge Carlos Ruiz Ruiz | TITLE: Free radical scavenging activity
AUTHORS: Jorge Carlos Ruiz Ruiz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Free radical scavenging assay was measured using 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical test. To each aqueous extract 3 mL of 0.1 mM solution of DPPH in methanol... | ["To each aqueous extract 3 mL of 0.1 mM solution of DPPH in methanol was added. Tubes were shaken vigorously and allowed to stand for 30 min at room temperature in the dark.", "Absorbance was measured at 517 nm. Distilled water was the control and ascorbic acid served as the standard.", "Free radical scavenging activi... |
61,193 | Isolation and identification of potential probiotic bacteria from the soil of Saint Martin's island Bangladesh | 4 | dx.doi.org/10.17504/protocols.io.ewov1nzokgr2/v1 | https://www.protocols.io/view/isolation-and-identification-of-potential-probioti-b7zhrp36 | Md. Mahbubur Rahman, Sulav Indra Paul | TITLE: Isolation and identification of potential probiotic bacteria from the soil of Saint Martin's island Bangladesh
AUTHORS: Md. Mahbubur Rahman, Sulav Indra Paul
[DESCRIPTION]
Soil bacteria of Saint Martin’s Island modulates gut microbiota and prevents Enterococcus faecalis infection in tilapia (Oreochromis ni... | ["[Collection of soil sample.] the marine soil samples were collected from the shore of Saint Martin’s Island (20°37'40.3\"N’ 92°19'22.3\"E) of the Bay of Bengal, Bangladesh", "[Collection of soil sample.] the samples were collected from 6-15 inch depth using an auger", "[Collection of soil sample.] immediately transfe... |
79,003 | dead or alive | 4 | dx.doi.org/10.17504/protocols.io.14egn21zqg5d/v1 | https://www.protocols.io/view/dead-or-alive-crd3v28n | Angela Belulia, Kalani Alcala, James Fermelia, Clairey Yang, Richard Klein | TITLE: dead or alive
AUTHORS: Angela Belulia, Kalani Alcala, James Fermelia, Clairey Yang, Richard Klein
[DESCRIPTION]
Objective: Identifying and quantifying the effect of live & dead corals on species diversity.
[BEFORE_START]
Bring your swim gear. Wear sunscreen.
[STEPS]
SECTION: Coral Head Colonization Protoc... | ["[Coral Head Colonization Protocol] Remove coral head from placement block by detaching the PVC plate with the coral head, then immediately place it into a large bucket underwater. Bring to the surface and bring back to the boat without letting new water enter the bucket or releasing any organisms.", "[Coral Head Colo... |
70,176 | CUT&RUN with Drosophila tissues-9-17 modifided | 1 | null | https://www.protocols.io/view/cut-amp-run-with-drosophila-tissues-9-17-modifided-cgr8tv9w | lilyli | TITLE: CUT&RUN with Drosophila tissues-9-17 modifided
AUTHORS: lilyli
[DESCRIPTION]
We have modified the Cleavage Under Targets and Release Using Nuclease (CUT&RUN) method for epigenomic profiling of histone modifications and chromatin proteins to use dissected Drosophila tissues. In CUT&RUN, cells or tissues are ... | ["[Prepare solutions and beads] Prepare a fresh 5% digitonin solution as follows:\n \n\nWeigh out 50 mg digitonin powder in a 2 ml microcentrifuge tube. Boil some water in a small beaker in a microwave oven, and pipette in and out to warm the 1000 μL pipette tip. Pipette the hot water into the tube with the digitonin p... |
58,103 | Purification of the PE2 nCas9-RT protein | 4 | dx.doi.org/10.17504/protocols.io.b4yxqxxn | https://www.protocols.io/view/purification-of-the-pe2-ncas9-rt-protein-b4yxqxxn | Donald Rio | TITLE: Purification of the PE2 nCas9-RT protein
AUTHORS: Donald Rio
[DESCRIPTION]
This protocol describes the process of expressing and purifying the nicking Cas9-MMLV RT fusion protein for prime editing.
Protocol overview
A. Heat-shock Transformation
B. Protein Expression
C. Protein Purification
[STEPS]
SECTION: ... | ["[A. Heat-shock Transformation] Thaw frozen competent cells on ice until just thawed.", "[A. Heat-shock Transformation] Gently mix the thawed competent cells (Rosetta 2 (pLysS)) by flicking the tube.", "[A. Heat-shock Transformation] Transfer 100 μl competent cells to a chilled culture tube.", "[A. Heat-shock Transfo... |
45,237 | Hair cortisol analysis protocol | 1 | dx.doi.org/10.17504/protocols.io.bqevmte6 | https://www.protocols.io/view/hair-cortisol-analysis-protocol-bqevmte6 | Katy Parker, Matt Bristow | TITLE: Hair cortisol analysis protocol
AUTHORS: Katy Parker, Matt Bristow
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">There has been considerable interest in the measurement of cortisol in hair as a biomarker of stress since work by Davenport et al. (2006). The methodology developed by our la... | ["[Hair cutting/weighing]\nEnsure analytical balance is calibrated.", "[Hair cutting/weighing]\nPlace clean beaker on balance.", "[Hair cutting/weighing]\nScan sample id into spreadsheet.", "[Hair cutting/weighing]\nPlace corresponding barcoded 4.5ml sample tube (ThermoFisher Scientific 342800-0045) in beaker and tare.... |
23,054 | Top2 Chromatin Accessibility by Etoposide Cross-linking | null | dx.doi.org/10.17504/protocols.io.2rngd5e | null | Jacob Kirkland | TITLE: Top2 Chromatin Accessibility by Etoposide Cross-linking
AUTHORS: Jacob Kirkland
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">The best way to determine TOP2 specific accessibility to chromatin is via etoposide treatment, which leads to a covalent cross-link... | ["Cell Culture:Trypsinize and count cellsTransfer 0.75e6-1e6 cells to (4) different eppendorfsSave (1) eppendorf for your input sample for step 4Bring volumes to 1ml with media (If volume is already more than 1ml you can transfer to a 15ml conical and bring volume up to known amount where all cell lines are at the same... |
97,338 | Conditioned Media Concentration with Amicon Ultra Centrifugal Filters | 0 | dx.doi.org/10.17504/protocols.io.e6nvw1px7lmk/v1 | https://www.protocols.io/view/conditioned-media-concentration-with-amicon-ultra-dba22ige | Joanna Bons, J P Rose, M A Watson, B Schilling | TITLE: Conditioned Media Concentration with Amicon Ultra Centrifugal Filters
AUTHORS: Joanna Bons, J P Rose, M A Watson, B Schilling
[DESCRIPTION]
Conditioned media has to be concentrated for downstream processing. To do this, complete media was removed the day before the study endpoint from cultured cells/tissue, and... | ["Insert the Amicon Ultra 0.5 mL Centrifugal Filter into one of the provided microcentrifuge tubes.", "Add up to 0.5 mL of conditioned media to the filter device and cap it.", "Place the capped filter device into the centrifuge rotor and align the cap strap toward the center of the rotor; counterbalance with a similar ... |
101,678 | Preparation of Sera-Mag SpeedBeads | 0 | dx.doi.org/10.17504/protocols.io.261ge5r2jg47/v1 | https://www.protocols.io/view/preparation-of-sera-mag-speedbeads-dfin3kde | Nina Alperovich | TITLE: Preparation of Sera-Mag SpeedBeads
AUTHORS: Nina Alperovich
[DESCRIPTION]
This protocol describes the preparation of Sera-mag SpeedBeads with PEG-salt buffer for downstream use in the Automated Bar-Seq Library Preparation protocol.
[STEPS]
SECTION: Prepare SpeedBeeds in tubes
1. Vortex 15 mL Sera-mag SpeedBead... | ["[Prepare SpeedBeeds in tubes] Vortex 15 mL Sera-mag SpeedBeads solution until beads are uniformly distributed.", "[Prepare SpeedBeeds in tubes] Place all 15 of the tubes on the tube magnetic separation rack until beads are drawn to magnet.", "[Prepare SpeedBeeds in tubes] Remove the supernatant from each tube.", "[Pr... |
93,476 | Acute testing of temporal patterns of vagus nerve stimulation on physiological outcomes in mouse | 1 | dx.doi.org/10.17504/protocols.io.5jyl8pop7g2w/v1 | https://www.protocols.io/view/acute-testing-of-temporal-patterns-of-vagus-nerve-c7iczkaw | William Huffman, Nicole A Pelot, Warren Grill | TITLE: Acute testing of temporal patterns of vagus nerve stimulation on physiological outcomes in mouse
AUTHORS: William Huffman, Nicole A Pelot, Warren Grill
[DESCRIPTION]
This protocol outlines the process for an anesthetized in vivo mouse study to electrically stimulate the cervical vagus nerve while recording EMG ... | ["[Animal preparation] Gas flow on 1\nAnesthesia induction - place animal in induction chamber and apply anesthesia (5% sevoflurane)\nPlace animal on heated pad in supine position and apply anesthesia using nose cone (2-5% sevoflurane)\nInsert rectal thermometer\nUse paper tape to secure upper extremities\nPlace pulse ... |
51,514 | Additional information for the creation of a high-quality draft genome for Melaleuca alternifolia (tea tree) | 5 | dx.doi.org/10.17504/protocols.io.bwi2pcge | https://www.protocols.io/view/additional-information-for-the-creation-of-a-high-bwi2pcge | Julia Voelker | TITLE: Additional information for the creation of a high-quality draft genome for Melaleuca alternifolia (tea tree)
AUTHORS: Julia Voelker
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol provides additional information to be read together with the publication about the genome ass... | ["[DNA extraction]\nIn order to yield high-quality DNA for PacBio sequencing, the CTAB extraction protocol from Healey et al. (2014) was used with the following modifications. DNA was extracted in a buffer containing 100 mM Tris-HCl (pH 8), 25 mM EDTA, 1.4 M NaCl, 2% (w/v) CTAB, and 1% (v/v) β-mercaptoethanol. After th... |
20,676 | Supplement Figure | null | dx.doi.org/10.17504/protocols.io.yfcftiw | null | Lijun Zhang, lijun zhang | TITLE: Supplement Figure
AUTHORS: Lijun Zhang, lijun zhang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = ":;"> </span><a style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;"> </span></a><span style = ":;:;"> </span><a style = "text-decoration:underline;co... | [] |
29,668 | Isolation of mononuclear cells using Septmate | null | dx.doi.org/10.17504/protocols.io.88chzsw | null | Ajit N Shah | TITLE: Isolation of mononuclear cells using Septmate
AUTHORS: Ajit N Shah
[STEPS]
?. Add density gradient medium to the SepMateTM tube by carefully pipetting it through the central hole of the SepMateTM insert. Refer to step 2 for required volumes. The top of the density gradient medium will be above the insert.N... | ["Add density gradient medium to the SepMateTM tube by carefully pipetting it through the central hole of the SepMateTM insert. Refer to step 2 for required volumes. The top of the density gradient medium will be above the insert.NOTE: Small bubbles may be present in the density gradient medium after pipetting. These b... |
84,195 | Nuclei Isolation from Tissue for 10x Multiome by Iodixanol | 1 | dx.doi.org/10.17504/protocols.io.eq2lyj3nplx9/v1 | https://www.protocols.click/view/nuclei-isolation-from-tissue-for-10x-multiome-by-i-cwgbxbsn | Li Wang, arnoldkriegstein | TITLE: Nuclei Isolation from Tissue for 10x Multiome by Iodixanol
AUTHORS: Li Wang, arnoldkriegstein
[DESCRIPTION]
We are using the iodixanol gradient method to extract nuclei for 10X single cell and Multiome assays. We have tested this protocols with a range of primary brain samples, developing, postnatal and adult. ... | ["[Before you start the protocol:] 1) All steps should be performed on ice or at 4°C. Pre-chill a swinging bucket centrifuge and a fixed angle centrifuge to 4°C. \n2) Pre-chill all Dounces and pestles to 4°C on ice.\n3) Pre-chill all tubes.\n4) Prepare all buffers. For faster dissolution, crush protease inh... |
37,432 | A randomized clinical trial of exenatide onT2D | null | dx.doi.org/10.17504/protocols.io.bgsyjwfw | https://www.protocols.io/view/a-randomized-clinical-trial-of-exenatide-ont2d-bgsyjwfw | Jing Xu | TITLE: A randomized clinical trial of exenatide onT2D
AUTHORS: Jing Xu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Among the Chinese adults with diabetes, the proportion of overweight is 41.0%, the proportion of obesity is 24.3%, and the proportion of abdominal obesity is as high as 45.4% ... | [] |
75,582 | PROCEDIIENTO PARA LA SOLICITUD DE ADMISIÓN A UN PROGRAMA DE DOCTORADO DE LA EIUCAM (PREINSCRIPCIÓN) | 1 | dx.doi.org/10.17504/protocols.io.6qpvr4m43gmk/v1 | https://www.protocols.io/view/procediiento-para-la-solicitud-de-admisi-n-a-un-pr-cm26u8he | cgarcia | TITLE: PROCEDIIENTO PARA LA SOLICITUD DE ADMISIÓN A UN PROGRAMA DE DOCTORADO DE LA EIUCAM (PREINSCRIPCIÓN)
AUTHORS: cgarcia
[DESCRIPTION]
La solicitud de admisión será on-line y permanecerá abierta durante todo el curso académico.
Preinscripción on-line
Podrán preinscribirse quienes cumplan los requisitos de acceso a... | ["[PROCEDIIENTO PARA LA SOLICITUD DE ADMISIÓN A UN PROGRAMA DE DOCTORADO DE LA EIUCAM (PREINSCRIPCIÓN)] Realizar la preinscripción on-line, anexando a la misma (exclusivamente en formato pdf) los documentos exigidos en la aplicación, que son:\n\n·Documento acreditativo de su identidad y nacionalidad.\n·Títulos que dan ... |
65,597 | Nuclease Test (OpenVent polymerase, PCR Master Mix, DNA loading dye) | 4 | null | https://www.protocols.io/view/nuclease-test-openvent-polymerase-pcr-master-mix-d-cca5ssg6 | Nadine Mowoh, Stephane Fadanka | TITLE: Nuclease Test (OpenVent polymerase, PCR Master Mix, DNA loading dye)
AUTHORS: Nadine Mowoh, Stephane Fadanka
[DESCRIPTION]
Quality control involves incubating the enzymes or reagents in reconstituted recombination assays to eliminate the possibility of relevant protein or nucleic acid contaminants that may i... | ["[Nuclease activity]", "[Nuclease activity] Pipetting\n\nPipette the following reagents into 0.2ml reaction tubes as shown in the table below, while working on ice\n\n \n\n\nIncubate reaction tubes for the specified times and briefly place tubes on ice to stop the reaction.\n\nChecking and interpreting results:\n\nAft... |
42,606 | Insects and DNA metabarcoding - InsectMobile laboratory protocols | 1 | dx.doi.org/10.17504/protocols.io.bmunk6ve | https://www.protocols.io/view/insects-and-dna-metabarcoding-insectmobile-laborat-bmunk6ve | Cecilie Svenningsen, Lene Bruhn Pedersen | TITLE: Insects and DNA metabarcoding - InsectMobile laboratory protocols
AUTHORS: Cecilie Svenningsen, Lene Bruhn Pedersen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This document is a collection of laboratory protocols for the citizen science and DNA metabarcoding research project 'InsectMobi... | ["[Purifying digest]\nPurify the aliquots in the QIASymphony robot. 24 samples can be purified each time and always include one extraction blank aliquot as a robot blank. The robot runs 24 samples in one hour. The protocol draws on the following resources:·DNA Handbook: EN-QIAsymphony-DNA-Handbook.pdf·Low content puri... |
19,792 | U Cinn - Meal Pattern Analysis Food Intake Procedure | null | dx.doi.org/10.17504/protocols.io.xjqfkmw | null | Patrick Tso, Dana Lee | TITLE: U Cinn - Meal Pattern Analysis Food Intake Procedure
AUTHORS: Patrick Tso, Dana Lee
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block"><span style = "font-weight:bold;">
</span><span style = "font-weight:bold;">Food... | ["Meal Pattern Analysis Protocol (Columbus Instruments)\n1. Take Body Composition via QMR before you put animals in this experiment.\n2. Set up cages (this can be done at any time before starting an experiment)\n a. Weigh animals and place into Food Intake chambers b. Supply food and water\n i. To fill fo... |
45,814 | Ce3D™ Tissue Clearing Protocol | 1 | null | https://www.protocols.io/view/ce3d-tissue-clearing-protocol-bqywmxxe | Ken Lau | TITLE: Ce3D™ Tissue Clearing Protocol
AUTHORS: Ken Lau
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Biological tissues are generally composed of proteins, lipids, and water, each of which has a different refractive index (RI). Differences in refractive indices, or RI mismatch, cause the sca... | ["[Whole Animal Perfusion]\nPrepare fresh heparin/ PBS solution at the indicated dosage: Add 10 units of heparin per mL of PBS. Use ≥ 50 mL per mouse. Keep chilled at 4°C.! It is recommended to prepare fresh heparin/ PBS solution. Steps 1-7 and step 10 must be carried out using chilled buffers.", "[Whole Animal Perfusi... |
68,024 | Preparation of qPCR standards for AAV titering | 3 | dx.doi.org/10.17504/protocols.io.bp2l61jndvqe/v1 | https://www.protocols.io/view/preparation-of-qpcr-standards-for-aav-titering-cenytdfw | Roberta Marongiu, Santiago Unda, Michael G. Kaplitt | TITLE: Preparation of qPCR standards for AAV titering
AUTHORS: Roberta Marongiu, Santiago Unda, Michael G. Kaplitt
[DESCRIPTION]
qPCR standards for AAV tittering
document annex to protocol "AAV Purification Protocol with Iodixanol gradient"
[STEPS] | [] |
69,445 | éêëēėę çćč ñń áâ | 1 | null | https://www.protocols.io/view/protocol-cf3dtqi6 | Maria Gul, katarina | TITLE: éêëēėę çćč ñń áâ
AUTHORS: Maria Gul, katarina
[DESCRIPTION]
Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Quis autem vel eum iure reprehenderit qui in ea voluptate velit esse quam nihil molestiae consequatur, vel illum qui dolorem eum fugiat quo voluptas nulla pariatur? Vivamus porttitor turpis ac l... | ["Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Quis autem vel eum iure reprehenderit qui in ea voluptate velit esse quam nihil molestiae consequatur, vel illum qui dolorem eum fugiat quo voluptas nulla pariatur? Vivamus porttitor turpis ac leo. Quisque porta. Cras pede libero, dapibus nec, pretium sit amet... |
24,140 | Mimulus in planta Transformation | null | dx.doi.org/10.17504/protocols.io.3tkgnkw | null | Yaowu Yuan | TITLE: Mimulus in planta Transformation
AUTHORS: Yaowu Yuan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This collection consists of three protocols: </div><div class = "text-block">1. Agro Transformation </div><div class = "text-block"> a) Using Electropotator </div><div class = "text-block">... | [] |
60,672 | Pasteuria farm protocol | 3 | null | https://www.protocols.io/view/pasteuria-farm-protocol-b7g8rjzw | Meghan Duffy, Katherine Hunsberger, Rebecca Bilich | TITLE: Pasteuria farm protocol
AUTHORS: Meghan Duffy, Katherine Hunsberger, Rebecca Bilich
[DESCRIPTION]
This is a protocol to infect and maintain Daphnia with Pasteuria ramosa for use in laboratory experiments.
[STEPS] | [] |
36,084 | Drug Liquid Imaging | null | dx.doi.org/10.17504/protocols.io.bfgujjww | https://www.protocols.io/view/drug-liquid-imaging-bfgujjww | Ida Barlow, Adam Mcdermott-Rouse | TITLE: Drug Liquid Imaging
AUTHORS: Ida Barlow, Adam Mcdermott-Rouse
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">For imaging drug-treated young adult C. elegans in liquids using the Multiworm tracker. Worms are synchronised by picking L4s, and then the young adults are exposed to drugs for 4 hou... | ["[Worm Synchronisation (-4 days) eg Friday PM]\nFour days before the experiment date, transfer 6 N2 adult gravid worms from a maintenance plate to a new 60mm NGM plates with bacterial food (OP50) present. This will give approximately 100 L4 worms on the morning of the third day (eg Monday).", "[Worm Synchronisation (-... |
30,658 | Immunocytochemistry Staining for Methanol Fixed Cells | null | dx.doi.org/10.17504/protocols.io.97ah9ie | null | Sam Li | TITLE: Immunocytochemistry Staining for Methanol Fixed Cells
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Sterilzation:]
Transfer a single cover slip into a 12-well plate, then add 1 mL of 70% Ethanol into a well for 20 minutes at room temperature.
?. [Sterilzation:]
Wash quickly three ... | ["[Sterilzation:]\nTransfer a single cover slip into a 12-well plate, then add 1 mL of 70% Ethanol into a well for 20 minutes at room temperature.", "[Sterilzation:]\nWash quickly three times with PBS.", "[Poly-Lysine Coating for 12-Well Plates (optional; for loosely attached cells):]\nAdd 1 mL of 0.1 mg/mL Poly-D-lysi... |
87,555 | Prozedere Bacterial stabs in Kultur nehmen bis Übernachtkultur ernten | 1 | null | https://www.protocols.io/view/prozedere-bacterial-stabs-in-kultur-nehmen-bis-ber-czrbx52n | Bettina Ergün | TITLE: Prozedere Bacterial stabs in Kultur nehmen bis Übernachtkultur ernten
AUTHORS: Bettina Ergün
[DESCRIPTION]
Das Protokoll beschreibt die In-Kulturnahme von Bacterial stabs zur Anreicherung einzelner Klone und zur Produktion von ausreichend Bakterien zur Gewinnung der gewünschten Plasmide mittels Maxi Prep.
[GUI... | ["[Before Start] Ampicillin:\n100 mg/ml in sterilem H2O lösen; sterilfiltrieren, aliq.; - 20 °C\n1:1000 zu dem Platten bzw. Medium => 100 µg/ml", "[Before Start] Agarplatten gießen:\n10 cm Greiner-Schalen\n1,5 g Agar auf 100 ml LB-Broth-Medium o. 3,5 g LB Agar auf 100 ml ddH2O\naufkochen, abkühlen auf 50 °C im Wasserba... |
44,769 | Cell DIVE™ Platform | Antibody Purification Chemistry | 4 | dx.doi.org/10.17504/protocols.io.bpx9mpr6 | https://www.protocols.io/view/cell-dive-platform-antibody-purification-chemistry-bpx9mpr6 | Anup Sood, Eric Williams, Liz McDonough | TITLE: Cell DIVE™ Platform | Antibody Purification Chemistry
AUTHORS: Anup Sood, Eric Williams, Liz McDonough
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpose of the protocol is to purify antibodies that will be conjugated to Cy dyes as per the Cell DIVE™ technology. Affinity chromatograp... | ["[Evaluate Need for Purification as per Formulation]\nTo determine the formulation of the vendor antibody solution refer to the vendor data sheet for product specifications. Refer to Table 7.1, for additives that require the antibody to be purified. ABCD1FormulationAdditiveBufferNeeds purification2Tissue culture supe... |
65,012 | HeLa culture, transfection, and labeling of Halo-fusion proteins | 1 | dx.doi.org/10.17504/protocols.io.yxmvmnb66g3p/v1 | https://www.protocols.io/view/hela-culture-transfection-and-labeling-of-halo-fus-cbqusmww | OLIVIA HARDING, Erika L.F. Holzbaur | TITLE: HeLa culture, transfection, and labeling of Halo-fusion proteins
AUTHORS: OLIVIA HARDING, Erika L.F. Holzbaur
[DESCRIPTION]
High-throughput, predictable systems that are easily modulated are ideal for the study of cell biology. Here we developed a protocol to investigate the role of the Nuclear Factor kappa-B E... | ["[Day 1: Plating] Follow plating protocol as described in dx.doi.org/10.17504/protocols.io.bt7wnrpe.", "[Day 2: Transfection] Examine cells by compound microscope 1080 min-1440 min after plating to confirm 80-90% confluence.", "[Day 2: Transfection] For each dish, prepare the mixture of desired plasmids in 1.5 mL tube... |
38,413 | PMN- 03 Culture of Human PMN - Migration | 4 | dx.doi.org/10.17504/protocols.io.bhrmj546 | https://www.protocols.io/view/pmn-03-culture-of-human-pmn-migration-bhrmj546 | Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino | TITLE: PMN- 03 Culture of Human PMN - Migration
AUTHORS: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Published work using this protocol:</div><div class = "text-block"><span sty... | ["Separation of PMN (at least 7 million PMN).", "Preparation of 6 Boyden chambers: Cut the bottom part of the vial and apply the filter (with holes of 3-5 μm in diameter) with glue / mastic (fig. 1). With paper scotch, name all Boyden chambers (fig. 2).", "Preparation of the solutions for: IL-8 10 ng/ml (2 μL stock in ... |
28,731 | Plantar Analgesia Test for Hind Paw and Tail | null | dx.doi.org/10.17504/protocols.io.8a3hsgn | null | Eva Feldman | TITLE: Plantar Analgesia Test for Hind Paw and Tail
AUTHORS: Eva Feldman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This protocol measures and quantifies the animals sensitivity to pain in the hind paw. These meas... | ["[Setup:]\n- Must clean equipment with sporeklenz before entering the animal room\n- All restrainers need to be exclusively used in same room. If restrainer has been in another animal room, it CANNOT be used!\n- The True Tail Temp cannot be used for the paw test. It must be disabled.\n Press 6000E on keypad of CP... |
null | null | null | dx.doi.org/10.17504/protocols.io.sazeaf6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
36,453 | Human Fallopian Tube and Ovary Dissociation for Single Cell RNA-Seq | 1 | dx.doi.org/10.17504/protocols.io.bfudjns6 | https://www.protocols.io/view/human-fallopian-tube-and-ovary-dissociation-for-si-bfudjns6 | Melissa Javellana, Mark Eckert, Ernst Lengyel | TITLE: Human Fallopian Tube and Ovary Dissociation for Single Cell RNA-Seq
AUTHORS: Melissa Javellana, Mark Eckert, Ernst Lengyel
[DESCRIPTION]
This protocol provides a procedure for human fallopian tube and ovary dissociation into single cell suspension prior to single cell RNA-sequencing. It involves removing the ... | ["[Solution Preparation] Prepare 10 mL of Pronase solution per sample in 50ml LoBind conical :", "[Solution Preparation] Prepare 10 mL of digestion buffer per sample in a 50 mL LoBind conical:", "[Dissociation] Rinse gross blood off samples with DMEM/10% FBS.", "[Dissociation] Place each sample into 10 mL of Pronase so... |
97,442 | The culture-independent Bcc NAD method for the rapid detection and quantification of Bcc in water | 4 | dx.doi.org/10.17504/protocols.io.rm7vzxox8gx1/v2 | https://www.protocols.io/view/the-culture-independent-bcc-nad-method-for-the-rap-dbea2jae | Huong Thu Duong, Shannon Fullbrook, Kate Reddington, Elizabeth Minogue, Thomas Barry | TITLE: The culture-independent Bcc NAD method for the rapid detection and quantification of Bcc in water
AUTHORS: Huong Thu Duong, Shannon Fullbrook, Kate Reddington, Elizabeth Minogue, Thomas Barry
[DESCRIPTION]
Here we present a rapid (<4 hours from sample in to result out) culture-independent Bcc NAD method, incor... | ["[WATER FILTRATION] Water preparation:\nWater is collected in a sterile container containing sterile 0.1% v/v sodium thiosulfate pentahydrate solution to inactivate any residual disinfectant chlorine (if needed) and immediately used for experimental analysis upon arrival in the laboratory (within approximately 2 hours... |
63,683 | Sky Islands Collection 2022 | 1 | dx.doi.org/10.17504/protocols.io.rm7vz39krgx1/v4 | https://www.protocols.io/view/sky-islands-collection-2022-cafbsbin | Lauren Ponisio | TITLE: Sky Islands Collection 2022
AUTHORS: Lauren Ponisio
[DESCRIPTION]
This protocol details the Ponisio Lab's collecting protocol for the 2022 Sky Islands season.
[STEPS]
SECTION: Field station prep
1. Prior to collection, it is important to make sure that the following preparations are made:
Shared sampling b... | ["[Field station prep] Prior to collection, it is important to make sure that the following preparations are made:\n\nShared sampling box:\nGPS\nspare batteries \nflagging tape\npin flags \nspare sharpies, microns etc \n\nShared collection equipment/consumables:\nsterile, snap cap collection vials for bees \nnon-steril... |
88,565 | Inclusion and Exclusion criteria | 1 | dx.doi.org/10.17504/protocols.io.3byl4qzyjvo5/v1 | https://www.protocols.io/view/inclusion-and-exclusion-criteria-c2qvydw6 | pooja.devrukhkar, hannah.anvari, asma.giornazi Asma Giornazi, shriya.shah, maryellen.pavone, francesca.e.duncan francesca.duncan | TITLE: Inclusion and Exclusion criteria
AUTHORS: pooja.devrukhkar, hannah.anvari, asma.giornazi Asma Giornazi, shriya.shah, maryellen.pavone, francesca.e.duncan francesca.duncan
[DESCRIPTION]
The purpose of this protocol is to describe the inclusion/exclusion criteria for collection of human follicular fluid, ovarian... | ["[Collection of Research Specimens for U54/UG3 – Done by Pathology] Human ovaries and follicular fluid are obtained following informed consent from the Northwestern University Reproductive Tissue Library (NU-RTL).", "[Collection of Research Specimens for U54/UG3 – Done by Pathology] NU-RTL uses an established IRB-appr... |
100,687 | Refractive index adjusted imaging medium: Glycerol (RI ~ 1.4) - Yeast | 0 | dx.doi.org/10.17504/protocols.io.n2bvjn3wngk5/v1 | https://www.protocols.io/view/refractive-index-adjusted-imaging-medium-glycerol-dejp3cmn | Mathias Hammer, Ammeret Rossouw, Azra Lari, Ben Montpetit, David Grunwald | TITLE: Refractive index adjusted imaging medium: Glycerol (RI ~ 1.4) - Yeast
AUTHORS: Mathias Hammer, Ammeret Rossouw, Azra Lari, Ben Montpetit, David Grunwald
[DESCRIPTION]
This protocol describes the steps to prepare imaging medium for Saccharomyces cerevisiae with adjusted refractive index. This medium is optimized... | ["[Preparation of 30ml refractive index adjusted imaging medium with Glycerol] Compound medium for autoclave", "[Preparation of 30ml refractive index adjusted imaging medium with Glycerol] Fill a 50 ml flask with 14.5 mLddH2O\nAdd a magnetic stirring bar and place the flask on a stirring hot plate.", "[Preparation of 3... |
66,552 | Designing Knockout Oligonucleotides | 5 | null | https://www.protocols.io/view/designing-knockout-oligonucleotides-cc8yszxw | Brian P Teague | TITLE: Designing Knockout Oligonucleotides
AUTHORS: Brian P Teague
[DESCRIPTION]
The Yeast ORFan CURE is a project to "knock out" (disable) a bunch of yeast genes of unknown function. Doing so requires small synthetic pieces of DNA called "oligonucleotides" or "oligos". This protocol walks you through selecting a gene... | ["[Choose a gene to knock out] Point your web browser to the Saccharomyces Genome Database at https://www.yeastgenome.org/.", "[Choose a gene to knock out] In the purple menu bar at the top, choose \"Analyze\", then \"Gene Lists\"", "[Choose a gene to knock out] In the light-blue menu bar on the upper-left, choose \"V... |
52,859 | RNA extraction for Karlodinium veneficum PLY720 | 4 | dx.doi.org/10.17504/protocols.io.n92ld9xe7g5b/v1 | https://www.protocols.io/view/rna-extraction-for-karlodinium-veneficum-ply720-bxu3pnyn | Will Lewis | TITLE: RNA extraction for Karlodinium veneficum PLY720
AUTHORS: Will Lewis
[DESCRIPTION]
A methodology for cell harvesting and RNA extraction from Karlodinium veneficum for the purposes of RNA-seq.
[BEFORE_START]
Cool centrifuges to 4°C.
[GUIDELINES]
Clean all pipettes and bench with ethanol and then RNase Zap befor... | ["[Cell harvesting] Grow 200 ml of Karlodinium veneficum PLY720 culture in L1 medium. Once cultures have grown to a density between 50,000 and 300,000 cells/ml (corresponding to exponential growth phase) they can be harvested.", "[Cell harvesting] For each culture being processed, gently invert the culture flask severa... |
86,931 | scRNA Delivery | 1 | null | https://www.protocols.io/view/scrna-delivery-cy5txy6n | Tyler Stahl | TITLE: scRNA Delivery
AUTHORS: Tyler Stahl
[DESCRIPTION]
Overview of GRC scRNA delivery links and folders
[STEPS]
SECTION: Overview of the Analysis
1. To analyze scRNA data, we use the cellRanger software provided by 10X. In brief, after sequencing, we demultiplex samples using cellRanger mkfastq. For each sample, w... | ["[Overview of the Analysis] To analyze scRNA data, we use the cellRanger software provided by 10X. In brief, after sequencing, we demultiplex samples using cellRanger mkfastq. For each sample, we then run cellRanger counts. CellRanger counts performs cell counting, read alignment and gene expression quantification.", ... |
69,172 | Mouse perfusions and brain tissue processing | 1 | dx.doi.org/10.17504/protocols.io.bp2l69kn1lqe/v1 | https://www.protocols.io/view/mouse-perfusions-and-brain-tissue-processing-cfsutnew | Ayse Ulusoy, Shirley Lee, Angela Rollar, Michael Helwig, Michael Klinkenberg, Sinead O'Sullivan, Rita Pinto-Costa, Donato Di Monte | TITLE: Mouse perfusions and brain tissue processing
AUTHORS: Ayse Ulusoy, Shirley Lee, Angela Rollar, Michael Helwig, Michael Klinkenberg, Sinead O'Sullivan, Rita Pinto-Costa, Donato Di Monte
[DESCRIPTION]
The protocol describes tissue processing for histological analyses and includes perfusions, brain fixation, and t... | ["Inject sodium pentobarbital (600 mg/kg, i.p.) to sacrifice the mouse", "Once the respiration is stopped, open the chest and place the cannula connected to a peristaltic pump into the heart. Make sure that the cannula has access to the ascending aorta.", "Perfuse, first with 20 ml saline solution, kept at room tempera... |
62,734 | Structural prediction of VPS13C with AlphaFold2 | 1 | dx.doi.org/10.17504/protocols.io.6qpvr6rjbvmk/v1 | https://www.protocols.io/view/structural-prediction-of-vps13c-with-alphafold2-b9hnr35e | Shujun Cai, Pietro De Camilli | TITLE: Structural prediction of VPS13C with AlphaFold2
AUTHORS: Shujun Cai, Pietro De Camilli
[DESCRIPTION]
This protocol describes the procedure of structural prediction of full-length human VPS13C and its truncation mutant with AlphaFold2 and the procedure to combine each segments into one structure.
[STEPS]
SEC... | ["[Structure prediction] Separate Full-length VPS13C and truncation mutant into three pieces and two pieces, respectively, i.e., a.a. 1-1860, 1201-2340, 1801-3753 for full-length VPS13C and a.a. 1-1762, 1277-3240 for VPS13CΔ1235-1748.", "[Structure prediction] Install AlphaFold 2.0 on the Yale Farnam high performance c... |
17,923 | rev-ChIP | null | dx.doi.org/10.17504/protocols.io.vrbe52n | null | Lorane Texari, Carlos Guzman, Sven Heinz | TITLE: rev-ChIP
AUTHORS: Lorane Texari, Carlos Guzman, Sven Heinz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify">Understanding the precise regulation of transcriptional programs in human health and disease requires the accurate identification and ... | ["[Lysis and Sonication]\nThaw cell pellet on ice and resuspend cells in of lysis buffer.\n500 µl\nWe do not recommend using of lysis buffer or tip sonication when sonicating less than 500K cells. In this case we suggest using Covaris ( ) or PIXUL ( ).", "[Lysis and Sonication]\nSonicate samples for 7 cycles.\nThis s... |
47,120 | Neurolucida 360: Importing a 3D Organ Scaffold Model for Fiducial Marking | 1 | null | https://www.protocols.io/view/neurolucida-360-importing-a-3d-organ-scaffold-mode-br9qm95w | Maci Heal | TITLE: Neurolucida 360: Importing a 3D Organ Scaffold Model for Fiducial Marking
AUTHORS: Maci Heal
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">How to import a generic 3D organ scaffold model into Neurolucida 360. </div></div>
[STEPS]
?. [Loading an Image, Adding Metadata, and Accessing Vocabul... | ["[Loading an Image, Adding Metadata, and Accessing Vocabularies ]\nLaunch Neurolucida 360 with SPARC-mode enabled.", "[Loading an Image, Adding Metadata, and Accessing Vocabularies ]\nOpen a microscopy image via the Open icon, File>Open, or dragging and dropping into the program window.", "[Loading an Image, Adding Me... |
34,644 | Long Mate Pair Library Construction Protocol | null | dx.doi.org/10.17504/protocols.io.bd3ui8nw | null | Graham J Etherington, Darren Heavens, David Baker, Ashleigh Lister, Rose McNelly, Gonzalo Garcia, Bernardo Clavijo, Iain Macaulay, Wilfried Haerty, Federica Di Palma | TITLE: Long Mate Pair Library Construction Protocol
AUTHORS: Graham J Etherington, Darren Heavens, David Baker, Ashleigh Lister, Rose McNelly, Gonzalo Garcia, Bernardo Clavijo, Iain Macaulay, Wilfried Haerty, Federica Di Palma
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Long Mate Pair Library Co... | ["For the Tagmentation reactions and of Genomic DNA was prepared in and then 5x Tagment Buffer Mate Pair (Illumina) added followed by Mate Pair Tagmentation Enzyme (Illumina) and the reaction gently vortexed to mix.\n3 µg\n3 µg\n308 µl\n80 µl\n12 µl", "This was then incubated for at , 100μl of Neutralize Tagment ... |
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