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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73,114 | Detection of phospho IRF3 and p65 in PBMCs by flow cytometry | 4 | null | https://www.protocols.io/view/detection-of-phospho-irf3-and-p65-in-pbmcs-by-flow-cjm2uk8e | Andrea Bausch | TITLE: Detection of phospho IRF3 and p65 in PBMCs by flow cytometry
AUTHORS: Andrea Bausch
[DESCRIPTION]
This protocol describes a method to detect phosphorylated IRF3 and phosphorylated p65 (subunit of NFkB) in PBMCs by flow cytometry. An extracellular staining to identify different immune subsets is followed by an i... | ["[Preparation and stimulation of cells] Thaw PBMCs and adjust concentration to 1.11*10^7 cells/ml", "[Preparation and stimulation of cells] Seed 90 µL in 96-well round bottom plate (1x10^6 cells per well).", "[Preparation and stimulation of cells] Prepare a 10x stock solution of your stimulus.", "[Preparation and stim... |
75,021 | Enteric neuron activity during spontaneous motor complexes in mouse colon | 4 | dx.doi.org/10.17504/protocols.io.6qpvr4oz3gmk/v1 | https://www.protocols.io/view/enteric-neuron-activity-during-spontaneous-motor-c-cmhmu346 | Kristen Smith-Edwards | TITLE: Enteric neuron activity during spontaneous motor complexes in mouse colon
AUTHORS: Kristen Smith-Edwards
[DESCRIPTION]
This protocol describes the steps to prepare mouse colon and image GCaMP calcium activity in myenteric neurons during spontaneous colonic motor complexes.
[STEPS]
1. Euthanize EIIa-GCaMP mice... | ["Euthanize EIIa-GCaMP mice (offspring from the pairing of B6.FVB-Tg(EIIa-cre)C5379Lmgd/J [RRID:IMSR_JAX:003724;cat. 003724; Jax Labs] and B6J.Cg-Gt(ROSA)26Sortm95.1(CAG-GCaMP6f)Hze/MwarJ [RRID:IMSR_JAX:028866;cat. 028865; Jax Labs]), by inhalation of isoflurane and thoracotomy. Remove the entire colon from mouse and p... |
63,175 | Tokuyasu processing and immuno-electron microscopy of cells | 4 | dx.doi.org/10.17504/protocols.io.14egn7nr6v5d/v1 | https://www.protocols.io/view/tokuyasu-processing-and-immuno-electron-microscopy-b9xfr7jn | Jillian C Danne, Viola Oorschot, Georg Ramm | TITLE: Tokuyasu processing and immuno-electron microscopy of cells
AUTHORS: Jillian C Danne, Viola Oorschot, Georg Ramm
[DESCRIPTION]
Ultrastructural morphological information is routinely obtained from the processing of cells and tissue into plastics for transmission electron microscopy imaging. This technique invo... | ["[Fixation] All fixation steps must be performed in a fume hood wearing the appropriate personal protective equipment (PPE). The Material Safety Data Sheet (MSDS) for each chemical must be read before commencing.\n\nAdherent cells grown in a petri dish must be submerged in solution at all times to prevent desiccation.... |
84,108 | MED-JET H4 MULTIJET (MJH4M) Transfection Protocol | 1 | dx.doi.org/10.17504/protocols.io.kxygx3ekog8j/v1 | https://www.protocols.click/view/med-jet-h4-multijet-mjh4m-transfection-protocol-cwdkxa4w | Nathan Liu, Hani Abd-Ul-Salam, Noemie Joannette-Lafrance, Jingjing Li, Karim Menassa, Monzur Murshed | TITLE: MED-JET H4 MULTIJET (MJH4M) Transfection Protocol
AUTHORS: Nathan Liu, Hani Abd-Ul-Salam, Noemie Joannette-Lafrance, Jingjing Li, Karim Menassa, Monzur Murshed
[DESCRIPTION]
Transfection, a non-viral method of nucleic acid delivery, often shows poor efficiency in vivo. The needle-based in vivo delivery of trans... | ["Prepare transfection reagent by diluting renilla-luciferase plasmid DNA (pR-Luc) in 5% glucose (w/v) to a final concentration of 0.1 μg/μl.", "Insert the transfection reagent cartridge into the MED-JET H4 MULTIJET (MJH4M) device.", "MJH4M device parameters were set to 80 psi and 75 µl.", "Adult wild-type C57BL/6 mice... |
null | null | null | dx.doi.org/10.17504/protocols.io.sk6ecze | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Objective: This study aimed to determine the predictive value of the neutrophil to lymphocyte ratio (NLR) in patients with acute exacerbation of chronic obstructive pulmonary disease (AECOPD).</p>
<p> Methods: A retrospective study was conducted from March 2012 to May 2016... | [] |
57,736 | Implant Surgery: Chronic recoverable Neuropixels in mice | 1 | null | https://www.protocols.io/view/implant-surgery-chronic-recoverable-neuropixels-in-b4mgqu3w | Emily A Aery Jones | TITLE: Implant Surgery: Chronic recoverable Neuropixels in mice
AUTHORS: Emily A Aery Jones
[DESCRIPTION]
This protocol collection explains how to build a low-cost, lightweight system to implant Neuropixels 1.0 probes into mice, record during freely moving behavior, then recover the probe for future use. This protocol... | ["[Prepare surgical tools and field] Sterilize tips of metal instruments, ground screw, and headbar in autoclave 25 min or hot bead sterilizer 5 s . Disinfect cotton swabs, toothpick, and a weigh boat under UV light 30 min .", "[Prepare surgical tools and field] Disinfect surgical field with 10% bleach. Lay absorbent ... |
49,366 | Protocol: "Investigating DOIs classes of errors" V.2 | 5 | dx.doi.org/10.17504/protocols.io.bufwntpe | https://www.protocols.io/view/protocol-34-investigating-dois-classes-of-errors-3-bufwntpe | Ricarda Boente, Deniz Tural, Cristian Santini, Arcangelo Massari | TITLE: Protocol: "Investigating DOIs classes of errors" V.2
AUTHORS: Ricarda Boente, Deniz Tural, Cristian Santini, Arcangelo Massari
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpose of this protocol is to provide an automated process to repair invalid DOIs that have been collected by the... | ["[DATA IMPORT]\nWe import a CSV containing invalid DOI-to-DOI citations. The CSV is provided on public license by Peroni, Silvio. (2021). Citations to invalid DOI-identified entities obtained from processing DOI-to-DOI citations to add in COCI (Version 1.0) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.4625300. Th... |
null | null | null | dx.doi.org/10.17504/protocols.io.pg8djzw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><u>Goal</u>:</p>
<p>This document aims to standardize the protocol used for labeling intracellular or extracellular antigens in eukaryotic cells, using antibodies already associated with fluorochromes, and quantifying them by flow cytometry.</p>
<p><u> </u></p>
<p><u>General ... | [] |
63,602 | K1 Keto Reviews - (Ingredients, Side Effects) Does Pills Work Without Keto Diet! | 3 | dx.doi.org/10.17504/protocols.io.rm7vzy258lx1/v1 | https://www.protocols.io/view/k1-keto-reviews-ingredients-side-effects-does-pill-cacssawe | thomsalonzo | TITLE: K1 Keto Reviews - (Ingredients, Side Effects) Does Pills Work Without Keto Diet!
AUTHORS: thomsalonzo
[DESCRIPTION]
Why am I exhausted on K1 keto Life Diet?
K1 keto Life Reviews - The most widely recognized oftentimes asked question on the web. You probably paid attention to great weight reduction examples o... | [] |
51,046 | Protocol for RNAseq analysis of identified gastric vagal afferent neurons | 4 | dx.doi.org/10.17504/protocols.io.x54v9j5zqg3e/v1 | https://www.protocols.io/view/protocol-for-rnaseq-analysis-of-identified-gastric-bv4en8te | Martin Stebbing, Juan C Molero | TITLE: Protocol for RNAseq analysis of identified gastric vagal afferent neurons
AUTHORS: Martin Stebbing, Juan C Molero
[DESCRIPTION]
This protocol describes methods to dissociate nodose ganglion neurons from rats, identify and specifically collect neurons previously labeled using retrograde tracing, and then perform... | ["[Tissue harvesting] Vagal neurons innervating either the muscle layers or the mucosa in various stomach regions in Sprague Dawley rats (RRID: RGD_10395233), are identified using injections of fluorescent beads as described in a separate protocol (see below)", "[Tissue harvesting] Rats that have received tracer inject... |
22,300 | Scanning electron microscopy | null | dx.doi.org/10.17504/protocols.io.zz4f78w | null | Sue Lin | TITLE: Scanning electron microscopy
AUTHORS: Sue Lin
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Double fixation: The specimen was first fixed with 2.5% glutaraldehyde in phosphate buffer (pH7.0) for more than 4 hours; washed three times in the phosphate buffer; then postfixed with 1% OsO4 in phosphate... | ["Double fixation: The specimen was first fixed with 2.5% glutaraldehyde in phosphate buffer (pH7.0) for more than 4 hours; washed three times in the phosphate buffer; then postfixed with 1% OsO4 in phosphate buffer (pH7.0) for 1 hour and washed three times in the phosphate buffer.", "Dehydration: The specimen was firs... |
55,910 | Visualizing lower urinary tract afferent projections in the lumbosacral spinal cord in rats | 2 | dx.doi.org/10.17504/protocols.io.b2ueqete | https://www.protocols.io/view/visualizing-lower-urinary-tract-afferent-projectio-b2ueqete | John-Paul Fuller-Jackson, Peregrine B Osborne, Janet R Keast | TITLE: Visualizing lower urinary tract afferent projections in the lumbosacral spinal cord in rats
AUTHORS: John-Paul Fuller-Jackson, Peregrine B Osborne, Janet R Keast
[DESCRIPTION]
This collection includes the protocols required to map the lower urinary tract afferent projections to the lumbosacral spinal cord of m... | [] |
52,504 | Microfluidics 2 - Mold Fabrication: UV Lithography | 1 | dx.doi.org/10.17504/protocols.io.bxhypj7w | https://www.protocols.io/view/microfluidics-2-mold-fabrication-uv-lithography-bxhypj7w | Serhat Sevli, C. Yunus Sahan | TITLE: Microfluidics 2 - Mold Fabrication: UV Lithography
AUTHORS: Serhat Sevli, C. Yunus Sahan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">Su8 is a photoresist resin used in MEMS technology for thick structures. PDMS microfluidic chips fabrica... | ["[Direct UV Laser Lithography Setup]\nLithography on photoresists is mostly performed by 2 methods; UV exposure using a mask and direct UV exposure on the material. NehirBT uses a maskless direct UV laser lithography method. It transfers drawings by CAD software to channels on mold. The important parameters arranged a... |
61,610 | Preparation of Triton X-100 soluble and insoluble fractions of SH-SY5Y cells | 4 | dx.doi.org/10.17504/protocols.io.6qpvr6p1ovmk/v1 | https://www.protocols.io/view/preparation-of-triton-x-100-soluble-and-insoluble-b8eirtce | Laura Smith, Matthew Gegg | TITLE: Preparation of Triton X-100 soluble and insoluble fractions of SH-SY5Y cells
AUTHORS: Laura Smith, Matthew Gegg
[DESCRIPTION]
SH-SY5Y cells are trypsinised and lysed in 1% (v/v) Triton X 100, 50 mM Tris, pH 7.5, 750 mM NaCl, 5 mM EDTA, 4 units RQ1 RNase-free DNase (Promega), protease and phosphatase inhibitor... | ["The detergent Triton X-100 is a good general purpose detergent for preparing lysates. However, it cannot solubilise lipid rafts, proteins that have aggregated and become insoluble, or lyse nuclei. Therefore to investigate insoluble proteins (e.g. a-synuclein that has taken on insoluble/aggregating forms) or proteins ... |
null | null | null | dx.doi.org/10.17504/protocols.io.in5cdg6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Please contact Dr. Steven Wilhelm (wilhelm@utk.edu) for additional information regarding this protocol.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
85,947 | A Simple Exploration of Simulated Annealing: Protocol | 5 | dx.doi.org/10.17504/protocols.io.eq2lyj77plx9/v1 | https://www.protocols.io/view/a-simple-exploration-of-simulated-annealing-protoc-cx63xrgn | Chasz Griego | TITLE: A Simple Exploration of Simulated Annealing: Protocol
AUTHORS: Chasz Griego
[DESCRIPTION]
This protocol describes technical steps to understand the computational environment for A Simple Exploration of Simulated Annealing hosted on Code Ocean.
[STEPS]
SECTION: Reproducing the Data Analysis
2. The analysis was ... | ["[Reproducing the Data Analysis] The analysis was completed with Python in a Jupyter Notebook. The following notebook is found in the code folder in the file manager:", "[Reproducing the Data Analysis] Access the capsule for this project at Code Ocean. Select \"Edit Capsule\" to work with your own copy.", "[Reproducin... |
90,313 | Intrinsic water use efficiency estimate: an isotopic method | 4 | dx.doi.org/10.17504/protocols.io.dm6gp3xk8vzp/v1 | https://www.protocols.io/view/intrinsic-water-use-efficiency-estimate-an-isotopi-c4fhytj6 | Flavie Gerle, Pauline Malherbe, Christelle Boisselet, David Lafleuriel, Julien Godfroy, Pierre Lochin, Baptiste Marteau, Hervé Piegay, Sara Puijalon, Antoine Vernay | TITLE: Intrinsic water use efficiency estimate: an isotopic method
AUTHORS: Flavie Gerle, Pauline Malherbe, Christelle Boisselet, David Lafleuriel, Julien Godfroy, Pierre Lochin, Baptiste Marteau, Hervé Piegay, Sara Puijalon, Antoine Vernay
[DESCRIPTION]
Protocol summary and key steps
This protocol describes in deta... | [] |
20,178 | rotocol for data collection for association data between VEMP in the time domain and the frequency domain. | 1 | dx.doi.org/10.17504/protocols.io.xxsfpne | https://www.protocols.io/view/rotocol-for-data-collection-for-association-data-b-xxsfpne | Aline Tenório Lins Carnaúba, Kelly Andrade, Pedro Menezes | TITLE: rotocol for data collection for association data between VEMP in the time domain and the frequency domain.
AUTHORS: Aline Tenório Lins Carnaúba, Kelly Andrade, Pedro Menezes
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for data collection for association data between VEMP in the... | [] |
106,970 | Publishing Generic Organ Scaffold as a SPARC Dataset | 0 | dx.doi.org/10.17504/protocols.io.6qpvr8q72lmk/v4 | https://www.protocols.io/view/publishing-generic-organ-scaffold-as-a-sparc-datas-dkp24vqe | Mabelle Lin, Hugh Sorby | TITLE: Publishing Generic Organ Scaffold as a SPARC Dataset
AUTHORS: Mabelle Lin, Hugh Sorby
[DESCRIPTION]
In this protocol, we will demonstrate how to prepare a generic organ scaffold for publication as a SPARC dataset using the Scaffold mapping tools. This protocol will ensure that a generic organ scaffold is made a... | ["Use the latest official version of the Scaffold mapping tools to generate your organ scaffold. Do not use a developer installation to generate a scaffold.", "Use the standard generic organ scaffold workflow to generate organ scaffold files. The workflow is installed by default with the mapping tools MAP Client instal... |
null | null | null | dx.doi.org/10.17504/protocols.io.c82zyd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in <a href="http://protocols.io/view/Wet-mount-Method-for-Enumeration-of-Aquatic-Viruse-c8pzvm" target="_blank">Wet-mount Method for Enumeration of Aquatic Viruses</a>
[STEPS]
?. | [] |
47,211 | Fluoxetine as an Anti-Inflammatory Therapy in SARS-CoV-2 Infection - Protocol v1.1 | 5 | dx.doi.org/10.17504/protocols.io.bscjnaun | https://www.protocols.io/view/fluoxetine-as-an-anti-inflammatory-therapy-in-sars-bscjnaun | Justin Fortune Creeden, Ali Sajid Imami, Hunter M. Eby, Cassidy Gillman, Kathryn N. Becker, Jim Reigle, Elissar Andari, Zhixing K Pan, Sinead M O’Donovan, Robert E McCullumsmith, Cheryl B McCullumsmith | TITLE: Fluoxetine as an Anti-Inflammatory Therapy in SARS-CoV-2 Infection - Protocol v1.1
AUTHORS: Justin Fortune Creeden, Ali Sajid Imami, Hunter M. Eby, Cassidy Gillman, Kathryn N. Becker, Jim Reigle, Elissar Andari, Zhixing K Pan, Sinead M O’Donovan, Robert E McCullumsmith, Cheryl B McCullumsmith
[DESCRIPTION]
<div... | ["[Workflow]\nIdentify Drug SignaturesWe searched iLINCS for the L1000 drug signatures for Fluoxetine, Paroxetine, Bupropion and Dexamethasone.", "[Workflow]\nDownload Drug SignaturesWe downloaded all the 436 identified signatures for further processing.", "[Workflow]\nGenerating High Confidence SignaturesWe filtered a... |
96,998 | Gut-PFF Surgery | 0 | null | https://www.protocols.io/view/gut-pff-surgery-daye2fte | daniel.dautan daniel, Per Svenningsson | TITLE: Gut-PFF Surgery
AUTHORS: daniel.dautan daniel, Per Svenningsson
[DESCRIPTION]
Methods for injection of alpha-synuclein preformed fibrils in the gut in a mice.
[STEPS]
SECTION: Surgery Preparation
1. Prepare the needle.
We are using a 20µl Hamilton syringe that we polish the tip to a 20–30-degree angle with Tho... | ["[Surgery Preparation] Prepare the needle.\nWe are using a 20µl Hamilton syringe that we polish the tip to a 20–30-degree angle with Thorlabs 30µm diamond sandpaper. Flush the syringe with ethanol and distilled water.", "[Surgery Preparation] Prepare the mouse.\nWe recommend placing the mice on the back with a 10ml sy... |
90,382 | Mouse Perfusions | 1 | dx.doi.org/10.17504/protocols.io.6qpvr3rjbvmk/v1 | https://www.protocols.io/view/mouse-perfusions-c4hnyt5e | Asta Zane, Nicole J Corbin-Stein, Gabrielle Childers, Jhodi Webster, Vickie Yang, Woong-Jai Won, Rajesh Gupta, Ashley Harms | TITLE: Mouse Perfusions
AUTHORS: Asta Zane, Nicole J Corbin-Stein, Gabrielle Childers, Jhodi Webster, Vickie Yang, Woong-Jai Won, Rajesh Gupta, Ashley Harms
[DESCRIPTION]
This protocol outlines the procedure to ethically euthanize/sacrifice a mouse using sterile, cold PBS and paraformaldehyde (4%). Following this perf... | ["[PROCEDURE] Pick the mouse up by its tail, place it into the isofluorane box, wait ~5 min. Assess if the mouse has reached a surgical plane of anesthesia by loss of response to toe pinch. Do not wait too long, since the heart may stop, and you need the heart beating to get a good perfusion.", "[PROCEDURE] Connect the... |
66,238 | MBP Pulldown Assay of ATG9A Truncations | 4 | dx.doi.org/10.17504/protocols.io.e6nvwk7xwvmk/v1 | https://www.protocols.io/view/mbp-pulldown-assay-of-atg9a-truncations-ccw6sxhe | Adam Yokom, Xuefeng Ren | TITLE: MBP Pulldown Assay of ATG9A Truncations
AUTHORS: Adam Yokom, Xuefeng Ren
[DESCRIPTION]
MBP Pulldown Assay of ATG9A Truncations
[STEPS]
1. Equilibrate 30 μl of Amylose resin (New England Biolabs, Ipswich, MA). Add >500mL of wash buffer (25 mM HEPES pH 7.5, 150mM NaCl, 1mM MgCl2, 1mM TCEP). Slow spin to pelle... | ["Equilibrate 30 μl of Amylose resin (New England Biolabs, Ipswich, MA). Add >500mL of wash buffer (25 mM HEPES pH 7.5, 150mM NaCl, 1mM MgCl2, 1mM TCEP). Slow spin to pellet resin. ~1000rpm for 1 minute should be good. Repeat X3", "Add recombinant MBP protien (~1 uM) and ATG13:ATG101 dimer (~3 uM) to Amylose resin", "I... |
64,033 | Ree Drummond CBD Gummies Reviews & Shark Tank 2022 | 1 | dx.doi.org/10.17504/protocols.io.81wgb6k61lpk/v1 | https://www.protocols.io/view/ree-drummond-cbd-gummies-reviews-amp-shark-tank-20-car9sd96 | reedrummondgummiesasa | TITLE: Ree Drummond CBD Gummies Reviews & Shark Tank 2022
AUTHORS: reedrummondgummiesasa
[DESCRIPTION]
Ree Drummond CBD Gummies Reviews & Shark Tank 2022
[STEPS]
1. Ree Drummond CBD Gummies Reviews & Shark Tank 2022
Duringmid-age suffering not being suitable to perform in bed is commodity that most men face th... | ["Ree Drummond CBD Gummies Reviews & Shark Tank 2022\nDuringmid-age suffering not being suitable to perform in bed is commodity that most men face these days. After the age of 30s men generally start having reduction in testosterone position but the unhealthy and sedentary life plays a major part in that. While utmost ... |
54,225 | Environmental DNA sampling protocols for the surveillance of marine non-indigenous species | 1 | dx.doi.org/10.17504/protocols.io.by7rpzm6 | https://www.protocols.io/view/environmental-dna-sampling-protocols-for-the-surve-by7rpzm6 | Luca Mirimin, Dulaney Miller, Sara Fernandez | TITLE: Environmental DNA sampling protocols for the surveillance of marine non-indigenous species
AUTHORS: Luca Mirimin, Dulaney Miller, Sara Fernandez
[DESCRIPTION]
This document describes a series of protocols for the collection of environmental samples intended for the monitoring and surveillance of marine inva... | ["[HEALTH AND SAFETY]", "[Protocol for collection of water samples (low volume water)] SAMPLING", "[Protocol for collection of water samples (low volume water)] Put on clean, single-use gloves.\n\nChange gloves if a glove has contacted anything except the sampled water body or decontaminated equipment. For example, if ... |
90,986 | A validated protocol to UV-inactivate SARS-CoV-2 and herpesvirus-infected cells | 4 | dx.doi.org/10.17504/protocols.io.81wgb676qlpk/v2 | https://www.protocols.io/view/a-validated-protocol-to-uv-inactivate-sars-cov-2-a-c44iyyue | Timothy K. Soh, Susanne Pfefferle, Stephanie Wurr, Ronald von Possel, Lisa Oestereich, Toni Rieger, Maria Rosenthal, Jens B. Bosse | TITLE: A validated protocol to UV-inactivate SARS-CoV-2 and herpesvirus-infected cells
AUTHORS: Timothy K. Soh, Susanne Pfefferle, Stephanie Wurr, Ronald von Possel, Lisa Oestereich, Toni Rieger, Maria Rosenthal, Jens B. Bosse
[DESCRIPTION]
Downstream analysis of virus-infected cell samples, such as reverse transcript... | ["[UV inactivate infected cells] Wash each well with 1 mL PBS", "[UV inactivate infected cells] Scrape each well (2x106 cells) into 1 mL PBS", "[UV inactivate infected cells] Transfer cells into a 1.5 mL tube", "[UV inactivate infected cells] Pellet cells at 16000 x g, 1 min, 4 °C", "[UV inactivate infected cells] Resu... |
89,225 | Heart Rate Variability Parameters for Assessing Autonomic Responses to Brief Rectal Distention in Patients with Irritable Bowel Syndrome | 1 | dx.doi.org/10.17504/protocols.io.j8nlko3x1v5r/v1 | https://www.protocols.io/view/heart-rate-variability-parameters-for-assessing-au-c3dhyi36 | M Khawar Ali, Shiyuan Gong, Jiande Chen, Borko Nojkov, Colin Burnett | TITLE: Heart Rate Variability Parameters for Assessing Autonomic Responses to Brief Rectal Distention in Patients with Irritable Bowel Syndrome
AUTHORS: M Khawar Ali, Shiyuan Gong, Jiande Chen, Borko Nojkov, Colin Burnett
[DESCRIPTION]
Heart rate variability (HRV) has been used to measure autonomic nervous system (ANS... | ["[Methods] Twenty-two patients with IBS (constipation-dominant or IBS-C) were recruited initially. Nineteen patients had completed all five visits and recordings throughout the study. Out of the nineteen patients, two patients were excluded because of their HRV data were considered outliers. \nSince each patient will ... |
null | null | null | dx.doi.org/10.17504/protocols.io.h2rb8d6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes the preparation of Illumina libraries for high through-put sequencing of full-length SSU rRNA sequences from all domains of life without primer bias.</p>
<p> </p>
<p>Sequences for primers and adaptor used can be found under guidelines.</p>
[GUIDELINES... | [] |
42,658 | Emergency Department Management of AcuteAsthma Exacerbation in Childhood | 4 | dx.doi.org/10.17504/protocols.io.bmwak7ae | https://www.protocols.io/view/emergency-department-management-of-acuteasthma-exa-bmwak7ae | Wilson Rocha MD | TITLE: Emergency Department Management of AcuteAsthma Exacerbation in Childhood
AUTHORS: Wilson Rocha MD
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Goal: Establish a protocol focusing on the first care of asthma exacerbation in children under 12 years old attending the emergency department of o... | [] |
54,343 | StyroStone: A protocol for scanning and extracting three-dimensional meshes of stone artefacts using Micro-CT scanners | 1 | dx.doi.org/10.17504/protocols.io.bzbfp2jn | https://www.protocols.io/view/styrostone-a-protocol-for-scanning-and-extracting-bzbfp2jn | Dominik Göldner, Fotios Alexandros Karakostis, Armando Falcucci | TITLE: StyroStone: A protocol for scanning and extracting three-dimensional meshes of stone artefacts using Micro-CT scanners
AUTHORS: Dominik Göldner, Fotios Alexandros Karakostis, Armando Falcucci
[DESCRIPTION]
This protocol presents the first detailed step-by-step pipeline for the 3D scanning and post processin... | ["[Part 1 - Styrofoam preparation] Note: Depending on the number of lithics that need to be scanned, this section might take several hours.\n\nSelect a blank Styrofoam body (or similar material) to hold the artefacts. It should be thick enough to carve holes on both sides (Face A and Face B).", "[Part 1 - Styrofoam pre... |
49,783 | An mHealth app intervention for self-management of knee osteoarthritis: a protocol for a scoping review | 1 | dx.doi.org/10.17504/protocols.io.buuxnwxn | https://www.protocols.io/view/an-mhealth-app-intervention-for-self-management-of-buuxnwxn | Takashi Kitagawa, Homare Hirokawa, Nanako Otake, Takumi Denda, Kaede Hiraya | TITLE: An mHealth app intervention for self-management of knee osteoarthritis: a protocol for a scoping review
AUTHORS: Takashi Kitagawa, Homare Hirokawa, Nanako Otake, Takumi Denda, Kaede Hiraya
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Objective:</span><span... | [] |
55,902 | Measuring growth rates of diatom cells in culture | 4 | dx.doi.org/10.17504/protocols.io.rm7vzynnxlx1/v1 | https://www.protocols.io/view/measuring-growth-rates-of-diatom-cells-in-culture-b2t6qere | Phoebe Argyle, Jana Hinners, Nathan G. Walworth, Sinéad Collins, Naomi M. Levine, Martina A. Doblin | TITLE: Measuring growth rates of diatom cells in culture
AUTHORS: Phoebe Argyle, Jana Hinners, Nathan G. Walworth, Sinéad Collins, Naomi M. Levine, Martina A. Doblin
[DESCRIPTION]
A method for measuring growth rates in diatoms, based on work with Thalassiosira spp. Used in:
Argyle, P. A., Walworth, N. G., Hinners, J.... | ["[Using manual cell counts] Take an aliquot of culture:\n\nTake daily aliquots of culture and take measurements immediately or fix using .\n\nThe size of the aliquot depends on a number of things:\n-Total volume of culture\n-Approximate concentration\n\nAs multiple aliquots will be taken, it is important to not remov... |
72,671 | LAMP - Kit WarmStart Colorimetric LAMP 2x Master Mix (DNA & RNA), marca New England Biolabs | 1 | null | https://www.protocols.io/view/lamp-kit-warmstart-colorimetric-lamp-2x-master-mi-ci77uhrn | marcellaa | TITLE: LAMP - Kit WarmStart Colorimetric LAMP 2x Master Mix (DNA & RNA), marca New England Biolabs
AUTHORS: marcellaa
[DESCRIPTION]
Reação de LAMP para identificação de isolados de Sporothrix brasiliensis - Kit WarmStart Colorimetric LAMP 2x Master Mix (DNA & RNA), marca New England Biolabs.
[STEPS]
SECTION: Pre... | ["[Preparo] Identifique corretamente os eppendorfs com a ID das amostras a serem testadas;", "[Preparo] Pipete 5 μL do mix de LAMP em cada eppendorf;", "[Preparo] Pipete 1 μL do mix de primers de LAMP;", "[Preparo] Pipete 3 μL de água miliq;", "[Preparo] Nos controles negativos adicione mais 1 μL de água miliq (total d... |
105,093 | LTEE Media Recipes | 1 | dx.doi.org/10.17504/protocols.io.81wgbyr31vpk/v5 | https://www.protocols.io/view/ltee-media-recipes-divd4e26 | Jesus E Chavarria-Palma, Zachary D Blount, Jeffrey E Barrick | TITLE: LTEE Media Recipes
AUTHORS: Jesus E Chavarria-Palma, Zachary D Blount, Jeffrey E Barrick
[DESCRIPTION]
This protocol describes recipes to prepare growth media and reagents used in the E. coli long-term evolution experiment (LTEE).
Section 1: DM-glucose, Davis-Mingioli liquid medium supplemented with glucose
... | ["[DM-glucose: Davis-Mingioli liquid medium supplemented with glucose] To prepare 1 L of DM, follow these steps.", "[DM-glucose: Davis-Mingioli liquid medium supplemented with glucose] Weigh dry components:\na. 5.34 g of or 7 gof \nb. 2 g of \nc. 1 g of \nd. 0.5 g of", "[DM-glucose: Davis-Mingioli liquid medi... |
68,073 | Preparing 1x PCR Master Mix | 4 | dx.doi.org/10.17504/protocols.io.14egn737zv5d/v2 | https://www.protocols.io/view/preparing-1x-pcr-master-mix-ceqhtdt6 | Jenny Molloy, Stephane Fadanka, Nadine Mowoh, Cordellia Cordellia Fulai | TITLE: Preparing 1x PCR Master Mix
AUTHORS: Jenny Molloy, Stephane Fadanka, Nadine Mowoh, Cordellia Cordellia Fulai
[DESCRIPTION]
This protocol documents the production of BenBio 1X PCR Master Mix "Wet" and "Dry" formulations including the different colors of the Wet formulations (Rubis or oink and Saphir... | ["[Cellular reagents preparation] Prepare a fresh batch of cellular reagents (OpenVent) following BenBio protocol for plate protein expression on autoinduction media.", "[Functionality test] Remove the enzymes from storage, reconstitute and test for functionality as described in the BenBio protocol using the specific t... |
41,107 | fastGRO-LI (Low-input fastGRO) | 1 | dx.doi.org/10.17504/protocols.io.bkdtks6n | https://www.protocols.io/view/fastgro-li-low-input-fastgro-bkdtks6n | Elisa Barbieri, Connor Hill, Alessandro Gardini | TITLE: fastGRO-LI (Low-input fastGRO)
AUTHORS: Elisa Barbieri, Connor Hill, Alessandro Gardini
[STEPS]
?. [Nuclei isolation]
Harvest cells and wash in cold 1X PBS
?. [Nuclei isolation]
Resuspend cells in of ice-cold SB. Incubate for . Spin .
10 mL
Centrifuge: 400 34, 10 min
?. [Nuclei isolation]
Remove supernatant a... | ["[Nuclei isolation]\nHarvest cells and wash in cold 1X PBS", "[Nuclei isolation]\nResuspend cells in of ice-cold SB. Incubate for . Spin .\n10 mL\nCentrifuge: 400 34, 10 min", "[Nuclei isolation]\nRemove supernatant and resuspend in GSB\n10 mL\nVolume of GSB should be at least 5 times the volume of cell pellet", "[N... |
78,391 | Bone Decalcification Protocol Using 14% EDTA Buffer Solution pH 7.2 - 7.4 | 1 | dx.doi.org/10.17504/protocols.io.4r3l2718qg1y/v1 | https://www.protocols.io/view/bone-decalcification-protocol-using-14-edta-buffer-cqsxvwfn | Donna Peehl, Renuka Sriram, Rosalie Nolley | TITLE: Bone Decalcification Protocol Using 14% EDTA Buffer Solution pH 7.2 - 7.4
AUTHORS: Donna Peehl, Renuka Sriram, Rosalie Nolley
[DESCRIPTION]
This protocol describes the steps required for successful decalcification. Decalcification describes the technique for removing minerals from bone or other calcified tissu... | ["[Preparation of Ethylenediaminetetraacetic acid (EDTA)] Make 14% EDTA solution fresh\na. Add 140 g free acid EDTA to 700 mL distilled H2O\nb. On stir plate in the fume hood, add ammonium hydroxide, 30 mL at a time, until solution clears (about 90 mL total)\nc. Add H2O to almost 1 L. Check pH and adjust with ammon... |
28,924 | Characterization of two thermophilic cellulases from Talaromyces leycettanus JCM12802 and their synergistic action on cellulose hydrolysis | null | dx.doi.org/10.17504/protocols.io.8g4htyw | null | Yuan Gu, Fei Zheng, Yuan Wang, Xiaoyun Su, Yingguo Bai, Bin Yao, Huoqing Huang, Huiying Luo | TITLE: Characterization of two thermophilic cellulases from Talaromyces leycettanus JCM12802 and their synergistic action on cellulose hydrolysis
AUTHORS: Yuan Gu, Fei Zheng, Yuan Wang, Xiaoyun Su, Yingguo Bai, Bin Yao, Huoqing Huang, Huiying Luo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span... | ["Cloning of the cellulase-encoding genes", "The full length cellulase-encoding genes,Tlcel5A and Tlcel6A, were identified in the genome sequence of T. leycettanusJCM12802, and obtained by PCR amplification with specific primers GH5F/GH5R and GH6F/GH6R (Table 1).", "The PCR conditions were as follows: 95°C for 3min, fo... |
null | null | null | dx.doi.org/10.17504/protocols.io.irhcd36 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Background & Aims </strong>Hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) is prevalent worldwide. Despite its limitations, serum alpha-fetoprotein (AFP) remains the most widely-used biomarker for the diagnosis of HCC. This study aimed to assess whe... | [] |
107,070 | Tomogram Reconstruction and Gold Fiducial Removal with WarpTools, Etomo, and Fidder | 0 | dx.doi.org/10.17504/protocols.io.6qpvr8qbblmk/v2 | https://www.protocols.io/view/tomogram-reconstruction-and-gold-fiducial-removal-dks64whe | Connor Garrels, Benjamin Barad, Steve Reichow | TITLE: Tomogram Reconstruction and Gold Fiducial Removal with WarpTools, Etomo, and Fidder
AUTHORS: Connor Garrels, Benjamin Barad, Steve Reichow
[DESCRIPTION]
While gold nanoparticle fiducials greatly improve tilt-series alignment in cryo-electron tomography data, they can cause artifacts during later image processin... | ["[Install Software] Make sure you have these packages installed.\n\n- IMOD\n- WarpTools \n- Fidder", "[WarpTools Preprocessing] We will be using WarpTools for the bulk of our processing. This section follows this warptools tutorial. \n\nValues shown are data-specific (i.e. exposure, pixel size, paths), so please be ca... |
104,983 | SARS-CoV-2 nsp3 macrodomain His-SUMO tagged expression and purification protocol for crystallization (c004) | 1 | dx.doi.org/10.17504/protocols.io.n92ld8jm8v5b/v1 | https://www.protocols.io/view/sars-cov-2-nsp3-macrodomain-his-sumo-tagged-expres-dirx4d7n | Korvus Wang, michael fairhead, Eleanor Williams | TITLE: SARS-CoV-2 nsp3 macrodomain His-SUMO tagged expression and purification protocol for crystallization (c004)
AUTHORS: Korvus Wang, michael fairhead, Eleanor Williams
[DESCRIPTION]
This protocol details the expression and purification of SARS-CoV-2 nsp3 macrodomain crystallization construct bearing a N-terminal ... | ["[Plasmid Transformation] CVNSP3mac1 N-terminal His-SUMO-tagged construct was inoculated from its BL21(DE3)-RR glycerol stock.", "[Protein expression] When the OD600 approximately 2.0, lower the temperature and shaker speed to . Incubate overnight.", "[Protein Purifcation] Perform IMAC to extract target protein from ... |
78,371 | Plate Count Agar | 4 | dx.doi.org/10.17504/protocols.io.eq2ly74delx9/v1 | https://www.protocols.io/view/plate-count-agar-cqsbvwan | Andreas Sagen | TITLE: Plate Count Agar
AUTHORS: Andreas Sagen
[DESCRIPTION]
Plate Count Agar (PCA), is a microbiological growth medium to assess viable bacterial growth of a sample.
The total number of living aerobic bacteria can be determined using PCA which is a substrate for bacteria to grow on. The medium contains casein which p... | ["[500 mL Plate Count Agar] In a bottle, add approx. 400 mL deionized water", "[500 mL Plate Count Agar] Measure and add:\n 5 g Tryptone\n 2.5 g Yeast extract\n 1 g Glucose\n 15 g Agar\n\nMaterials:", "[500 mL Plate Count Agar] Adjust pH to pH 7.0 using sodium hydroxide", "[500 mL Plate Count Agar] Fill bot... |
99,390 | Immune Saturation Genome Editing (Immune SGE): Variant Analysis in T cells | 0 | dx.doi.org/10.17504/protocols.io.36wgqn7e3gk5/v1 | https://www.protocols.io/view/immune-saturation-genome-editing-immune-sge-varian-dda622he | Nathan Camp, Sam Dawson | TITLE: Immune Saturation Genome Editing (Immune SGE): Variant Analysis in T cells
AUTHORS: Nathan Camp, Sam Dawson
[DESCRIPTION]
This protocol details immune saturation genome editing (Immune SGE) and variant analysis in T cells. In brief, primary T cells are isolated from donor PBMCs, edited with a variant library ce... | ["[OVERVIEW: ssODN repair template and oPool design notes] Determine your editing region of interest, trying to stay within 20bp on either side of the cut site.", "[OVERVIEW: ssODN repair template and oPool design notes] Add respective homology arms to both the 5’ and 3’ ends of the editing region such that ssODN is at... |
15,461 | High-Throughput Library Pooling for NGS | null | dx.doi.org/10.17504/protocols.io.tcdeis6 | null | Madeline Mayday, Lillian Khan, Eric D. Chow, Matt S. Zinter, Joseph L. DeRisi | TITLE: High-Throughput Library Pooling for NGS
AUTHORS: Madeline Mayday, Lillian Khan, Eric D. Chow, Matt S. Zinter, Joseph L. DeRisi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">Preparation of high-quality sequencing libraries is a costly and time... | ["[POOLING PREP]\nTransfer the libraries into a new 384 well Echo source plate. Skip if samples already complete. Make sure to dilute samples if needed to contain enough dead volume. Samples should be between 22-25uL to be able to dispense accurately using the Echo.\nWells of the source plate containing samples should ... |
74,870 | Protocol for staining of urinary cells for flow cytometric analysis | 4 | dx.doi.org/10.17504/protocols.io.x54v9d79zg3e/v1 | https://www.protocols.io/view/protocol-for-staining-of-urinary-cells-for-flow-cy-cmcwu2xe | luka.prskalo | TITLE: Protocol for staining of urinary cells for flow cytometric analysis
AUTHORS: luka.prskalo
[DESCRIPTION]
This protocol outlines the specific steps required to stain different cell population in urine samples using fluorescence-labeled antibodies for subsequent flow cytometric analysis. The focus of the protocol ... | ["[Defrosting and sample distribution] Quickly defrost urine sediments in1 mL PBE and filter into small Falcon tubes using a 30 µl mesh. Flush filter with 9 mLPBE and spin the sample (600xg, 8min, 4°C). Aspirate supernatant.", "[Defrosting and sample distribution] Resuspend each sample in 400 µL PBE and divide them int... |
21,182 | UC Davis - Urea Protocol | null | dx.doi.org/10.17504/protocols.io.yw6fxhe | null | Peter Havel | TITLE: UC Davis - Urea Protocol
AUTHORS: Peter Havel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">
The enzyme methodology employed in this reagent is based on the reaction first described by Talke and Schubert. To sh... | ["Add 3 μl of calibrator and sample to each well.", "Add 300 μl of reagent to each well. Incubate at 37°C for 30 seconds. Read at 340 nm.IMPORTANT: Make sure not to add any bubbles to the wells when dispensing reagents, this will interfere with reading in the platereader.", "Incubate at 37°C for 60 seconds. Read at 340... |
108,301 | Lentivirus production & concentration | 4 | null | https://www.protocols.io/view/lentivirus-production-amp-concentration-dmzm4746 | Allan JW Lui | TITLE: Lentivirus production & concentration
AUTHORS: Allan JW Lui
[DESCRIPTION]
Lentivirus production protocol based on official protocol for Lipofectamine 3000 and TransIT-Lenti
[BEFORE_START]
Prepare culture media for HEK293T:
supplemented with 10%
[STEPS]
SECTION: HEK293T seeding density titration
1. D... | ["[HEK293T seeding density titration] Detach, count & seed HEK293T cells into T75 flasks at:\n4 x 10E6 cells\n6 x 10E6 cells\n8 x 10E6 cells\n10 x 10E6 cells", "[HEK293T seeding density titration] Incubate plates at 37 °C for up to 1440 min \nObserve confluence of cells under a microscope at 18 - 24 hours after plating... |
null | null | null | dx.doi.org/10.17504/protocols.io.mzuc76w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Immunohistochemistry (IHC) is a method that combines biochemical, histological and immunological techniques into a simple but powerful assay for protein detection. IHC provides valuable information as it visualizes the distribution and localization of specific cellular compon... | [] |
28,271 | genotyping_PCR | null | dx.doi.org/10.17504/protocols.io.7uphnvn | null | Ida Barlow | TITLE: genotyping_PCR
AUTHORS: Ida Barlow
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for doing PCR on single worm lysate. This is a basic protocol that can be adapted according to specific primers and amplicon size.</div></div>
[STEPS]
?. [Prepare reagents]
Get primers out of freezer ... | ["[Prepare reagents]\nGet primers out of freezer or prepare new primers", "[Prepare reagents]\nIf primers are ordered new, resuspend lypholised oligo to (== 100 μmol/l). Volume of water (in μl) to add is calculated as Volume =nmol*10Eg. for primer provided as 28.5nmol, add 285 μl of MQ water", "[Prepare reagents]\nIf d... |
81,182 | Multi-Step Ancient DNA Extraction Protocol For Bone And Teeth | 4 | null | https://www.protocols.io/view/multi-step-ancient-dna-extraction-protocol-for-bon-cth6wj9e | Valeria Mattiangeli, cassidl, Kevin Daly, mullinv, Marta Verdugo | TITLE: Multi-Step Ancient DNA Extraction Protocol For Bone And Teeth
AUTHORS: Valeria Mattiangeli, cassidl, Kevin Daly, mullinv, Marta Verdugo
[DESCRIPTION]
The protocol described here is a multi-day extraction protocol for the recovery of fragment DNA molecules from bone or teeth powder obtained from ancient or histo... | ["[Stage 1 - Preparation (day 1)] In advance of extraction, prepare bone powder. Measure 0.09 mg to 0.120 mg of bone powder into a 2 mL Eppendorf tube", "[Stage 1 - Preparation (day 1)] Prepare the extraction buffer where n is the number of sample and control tubes plus one (for pipetting error). In the example below ... |
null | null | null | dx.doi.org/10.17504/protocols.io.ezybf7w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a collection of BioLegend T Cell Activation with anti-CD3ε Antibodies protocols, for human and mouse.</p>
[STEPS]
?. | [] |
69,247 | OMS Atlas OCT Spatial Mapping | 1 | dx.doi.org/10.17504/protocols.io.261ge677dl47/v4 | https://www.protocols.io/view/oms-atlas-oct-spatial-mapping-cfu7tnzn | Brett Johnson, Danielle Galipeau, George Thomas | TITLE: OMS Atlas OCT Spatial Mapping
AUTHORS: Brett Johnson, Danielle Galipeau, George Thomas
[DESCRIPTION]
This protocol describes the procedure by which the OMS Atlas serially sections an OCT block, prepares the resulting slides and samples, and then distributes the specimens for downstream analysis.
[BEFORE_STAR... | ["[Preparation] Verify the identity of the OCT block to be cut against written request for sectioning.", "[Preparation] Remove OCT block from -80 °C freezer and acclimate to cryostat (-20 °C ) for minimum of 180 min.", "[Preparation] Label all slides and cryotubes with a unique BEMS ID and Part#, corresponding to the w... |
66,885 | Via Keto Apple Gummies Canada, UK & Australia [Reviews] – Top Weight loss supplement of 2022 | 3 | dx.doi.org/10.17504/protocols.io.dm6gpbnrplzp/v1 | https://www.protocols.io/view/via-keto-apple-gummies-canada-uk-amp-australia-rev-cdjds4i6 | viaketocanada | TITLE: Via Keto Apple Gummies Canada, UK & Australia [Reviews] – Top Weight loss supplement of 2022
AUTHORS: viaketocanada
[DESCRIPTION]
Via Keto Apple Gummies Canada are potentially the best-tasting supplement when it relates to keto diet regimens.
[STEPS] | [] |
86,013 | Juego de rol para el fomento de habilidades comunicativas. Debate. | 1 | dx.doi.org/10.17504/protocols.io.dm6gp3jzpvzp/v1 | https://www.protocols.io/view/juego-de-rol-para-el-fomento-de-habilidades-comuni-cx85xry6 | Diana Eguía Armenteros | TITLE: Juego de rol para el fomento de habilidades comunicativas. Debate.
AUTHORS: Diana Eguía Armenteros
[DESCRIPTION]
Este trabajo propone un ejercicio educativo destinado a enseñar a los alumnos dos habilidades fundamentales: el arte del debate oral y la búsqueda de información veraz. Para ello, se ha desarrollado ... | ["Eres un experto en educación llamado por la Conserjería de Educación de Castilla y León para convencer a la Consejera Diana Eguía de la jornada escolar más beneficiosa para los niños. Debes debatir con otros expertos y respaldar tus argumentos con información veraz.", "Previamente al debate, cada estudiante revisará ... |
42,330 | System Dynamics (SD) Model of the HIV Care Continuum | 1 | dx.doi.org/10.17504/protocols.io.bmj2k4qe | https://www.protocols.io/view/system-dynamics-sd-model-of-the-hiv-care-continuum-bmj2k4qe | Margaret Weeks, David W. Lounsbury, Jianghong Li, H. Danielle Green, Marcie Berman, Lucy Rohena, Rosely Gonzalez, Heather I. Mosher, Gary Hirsch | TITLE: System Dynamics (SD) Model of the HIV Care Continuum
AUTHORS: Margaret Weeks, David W. Lounsbury, Jianghong Li, H. Danielle Green, Marcie Berman, Lucy Rohena, Rosely Gonzalez, Heather I. Mosher, Gary Hirsch
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the developmen... | [] |
98,469 | Preparation of Glycerol Stocks from storing microbes from Petri Dishes | 1 | null | https://www.protocols.io/view/preparation-of-glycerol-stocks-from-storing-microb-dced2ta6 | Stephane Fadanka, Shalo Minette, Nadine Mowoh | TITLE: Preparation of Glycerol Stocks from storing microbes from Petri Dishes
AUTHORS: Stephane Fadanka, Shalo Minette, Nadine Mowoh
[DESCRIPTION]
This protocol is meant to provide researchers with a step by step procedure on how to prepare glycerol stocks in order to preserve and store bacteria for long term.
Bacter... | ["[From the plate to a PBS eppendorf] If you have colonies already growing in a Petri dish you can simply collect them using an inoculating wire loop and transfer to a eppendorf tube with 500 µL of 1x PBS\nOnce you have collect enough pure colonies you can go to the next step.", "[Diluting Pure Glycerol to 50% with D... |
30,442 | sci-RNA-seq3 | 1 | dx.doi.org/10.17504/protocols.io.9yih7ue | https://www.protocols.io/view/sci-rna-seq3-9yih7ue | Junyue Cao, Jay Shendure | TITLE: sci-RNA-seq3
AUTHORS: Junyue Cao, Jay Shendure
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Single-cell combinatorial indexing (‘sci-’) is a methodological framework that employs split-pool barcoding to uniquely label the nucleic acid contents of large numbers of single cells or nuclei. Al... | ["[Buffer preparation]\n500ml Nuclei buffer (Stored in 4C): 10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2 in nuclease-free water: ABCD1ReagentStock concentrationFinal concentrationVolume (ml)2Tris-HCl (pH 7.5)1M10mM53NaCl5M10mM14MgCl21M3mM1.55Nuclease-free waterNANA492.56Final volume500Filter the buffer through 0.22u... |
44,956 | Genetic mechanisms associated with floral initiation and the repressive effect of fruit on flowering in apple (Malus x domestica Borkh.) | 5 | dx.doi.org/10.17504/protocols.io.bp54mq8w | https://www.protocols.io/view/genetic-mechanisms-associated-with-floral-initiati-bp54mq8w | Chris Gottschalk, Songwen Zhang, Phil Schwallier, Sean Rogers, M. John Bukovac, Steve van Nocker | TITLE: Genetic mechanisms associated with floral initiation and the repressive effect of fruit on flowering in apple (Malus x domestica Borkh.)
AUTHORS: Chris Gottschalk, Songwen Zhang, Phil Schwallier, Sean Rogers, M. John Bukovac, Steve van Nocker
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><s... | ["[Read Alignment]\nRetrieve RNAseq librariesFiles are locally maintained but can be retrieved from NCBI SRA database", "[Read Alignment]\nFilter RNAseq reads for quality and removal of the adapter sequences", "[Read Alignment]\nAlign RNAseq reads to reference genome assembly", "[Transcriptome Assembly]\nConvert SAM al... |
null | null | null | dx.doi.org/10.17504/protocols.io.pa7dihn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The ITS protocol detailed here is designed to amplify fungal microbial eukaryotic lineages using paired-end community sequencing on the Illumina platform with primers ITS1f-ITS2 (EMP.ITSkabir).</p>
[BEFORE_START]
<p>For running these libraries on the MiSeq and HiSeq, please ... | [] |
35,518 | Laser microdissection for regional transcriptomics and proteomics | null | dx.doi.org/10.17504/protocols.io.bew6jfhe | 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: Laser microdissection for regional transcriptomics and proteomics
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">Recent advance... | ["[Cryosectioning for Regional Transcriptomics]\nAll work is performed in a manner that limits RNA contamination and necessitates use of clean disposable gloves and face mask, as well as ensuring the cleanliness of all surfaces (RNAse Away, Ambion, Cat #10328011). This protocol is to be used with kidney tissue preserve... |
31,861 | Appendix for Spleen SOP | null | dx.doi.org/10.17504/protocols.io.bbcviiw6 | null | Marda Jorgensen, Jerelyn Nick | TITLE: Appendix for Spleen SOP
AUTHORS: Marda Jorgensen, Jerelyn Nick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is an appendix diagram for spleen tissue cutting. </div></div>
[STEPS] | [] |
19,184 | Detection of anti-phytopathogenic fungal activity | null | dx.doi.org/10.17504/protocols.io.wyqffvw | null | Cecilia Monica Rodriguez García, Leticia Peraza Echeverría | TITLE: Detection of anti-phytopathogenic fungal activity
AUTHORS: Cecilia Monica Rodriguez García, Leticia Peraza Echeverría
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Here we describe the detection of in vitro anti-phytopathogenic fungal activity using the broth dilution method to find the MIC... | ["[Dilution of the aqueous extract of leaves ]\nABCDEF1Dilution numberAE (μL)CS \n(μL)\nH2O\n(μL)\n final volume\n(μL)\nconcentration\n(%)\n21 500 100 400 1000532 250 100 650 10002.543 125 100 775 10001.255 --- --- --- 10001... |
72,299 | Western Blot | 4 | dx.doi.org/10.17504/protocols.io.14egn22emg5d/v1 | https://www.protocols.io/view/western-blot-ciujueun | Addgene The Nonprofit Plasmid Repository | TITLE: Western Blot
AUTHORS: Addgene The Nonprofit Plasmid Repository
[DESCRIPTION]
Western blot is a technique used to separate proteins by size followed by detection using antibodies specific to the protein of interest. This protocol describes the basic steps for lysing cells, determining total protein concentration... | ["[Lyse cells] Centrifuge for 5 min at 100 x g.", "[Lyse cells] Gently remove supernatant.", "[Lyse cells] Resuspend cell pellet in 1 mL of 1X PBS and transfer to a microcentrifuge tube.", "[Lyse cells] Centrifuge for 5 min at 100 x g.", "[Lyse cells] Carefully remove supernatant.", "[Lyse cells] Resuspend cell pelle... |
50,499 | Expression and purification protocol of linear GST-4xUbiquitin | 1 | dx.doi.org/10.17504/protocols.io.bvjbn4in | https://www.protocols.io/view/expression-and-purification-protocol-of-linear-gst-bvjbn4in | Chunmei Chang | TITLE: Expression and purification protocol of linear GST-4xUbiquitin
AUTHORS: Chunmei Chang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details the expression and purification of linear GST-4x Ubiquitin.</div></div>
[STEPS]
?. [Protein purification]
Resuspend the pellets in Lysi... | ["[Protein purification]\nResuspend the pellets in Lysis Buffer, sonicate for cell lysis and clear at at for\nCentrifuge: 16000 33\n4 °C", "[Protein purification]\nIncubate the supernatant with Glutathione Sepharose 4B (GE Healthcare) at with gentle shaking for , apply to a gravity flow column, and wash extensively ... |
27,362 | University Published Paper Reproducibility Assessment Protocol - For students | null | dx.doi.org/10.17504/protocols.io.6yahfse | null | Scott Edmunds, Jesse Xiao, Hongling Zhou | TITLE: University Published Paper Reproducibility Assessment Protocol - For students
AUTHORS: Scott Edmunds, Jesse Xiao, Hongling Zhou
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is for students carrying out a literature/data curation exercise to crowdsource and determining whether... | ["Find the assigned papersEach student should have been assigned a number of papers in a spreadsheet that they need to assess.", "Find your assignments, and start the exercise by looking at the first assigned paper, clicking on the identifier (handle, URL, etc.) and locating the paper to assess via its DOI.", "Assess ... |
22,874 | Teacher Sense of Efficacy Scale Short Form | null | dx.doi.org/10.17504/protocols.io.2j2gcqe | null | Kevin Crouse | TITLE: Teacher Sense of Efficacy Scale Short Form
AUTHORS: Kevin Crouse
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Teachers’ Sense of Efficacy is the beliefs in their capability to make a difference in student learning, to be able to get through even to students who are difficult or unmotiva... | ["How much can you do to control disruptive behavior in the classroom?", "How much can you do to motivate students who show low interest in school work?\n212 °C", "How much can you do to calm a student who is disruptive or noisy?BUG (for social science use): GOTO does not allow you to skip, only to go back. Also, no h... |
62,782 | 18S+16S library preparation for Illumina MiSeq eDNA metabarcoding - rocky intertidal seawater samples | 1 | dx.doi.org/10.17504/protocols.io.6qpvr6r1bvmk/v1 | https://www.protocols.io/view/18s-16s-library-preparation-for-illumina-miseq-edn-b9i6r4he | Mary McElroy | TITLE: 18S+16S library preparation for Illumina MiSeq eDNA metabarcoding - rocky intertidal seawater samples
AUTHORS: Mary McElroy
[DESCRIPTION]
This protocol describes library preparation for combined 18S+16S amplicon metabarcoding with the Illumina MiSeq system. Seawater samples were collected from California rocky ... | ["[18S Amplicon PCR] Dilute primers to 10 uM in PCR water. Dilute BSA to 4 mg/ml in PCR water. Set up triplicate PCRs for each sample.", "[18S Amplicon PCR] Perform PCRs in 25 ul volumes with the following reaction chemistry:\n\n12.5 ul NEBNext Ultra II Q5 Master Mix (#M0544)\n0.5 ul 4 mg/ml bovine serum albumin ... |
85,525 | Measurement of GLP-1 release in cell supernatant from Hutu-80 enteroendocrine cells via ELISA | 1 | dx.doi.org/10.17504/protocols.io.j8nlkokm6v5r/v1 | https://www.protocols.io/view/measurement-of-glp-1-release-in-cell-supernatant-f-cxrvxm66 | r.mezabrovschi, rachel.bates | TITLE: Measurement of GLP-1 release in cell supernatant from Hutu-80 enteroendocrine cells via ELISA
AUTHORS: r.mezabrovschi, rachel.bates
[DESCRIPTION]
This protocol describes the method of use for the Glucagon-Like Peptide-1 (Active) ELISA Kit
96-Well Plate (Cat. # EGLP-35K) to measure GLP-1 release (pM) from super... | ["[Day 2] Make up the Wash Buffer using the 10X Wash Buffer Concentrate and dilute 1:10 with deionised water.", "[Day 2] In each well of the ELISA plate, add 300 µL of diluted Wash Buffer (or in two intervals of 150 µL). Incubate at Room temperature for 5 min. Decant excess buffer and blot with absorbent towels.", "[... |
50,648 | CELL STORAGE-01-Freezing and Thawing Protocol for Adherent Cell Lines | 4 | dx.doi.org/10.17504/protocols.io.bvpyn5pw | https://www.protocols.io/view/cell-storage-01-freezing-and-thawing-protocol-for-bvpyn5pw | Marco Cosentino, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Mariagiulia Albizzati, Marco Ferrari, Franca Marino, Alessandra Luini, Alessandra Luini | TITLE: CELL STORAGE-01-Freezing and Thawing Protocol for Adherent Cell Lines
AUTHORS: Marco Cosentino, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Mariagiulia Albizzati, Marco Ferrari, Franca Marino, Alessandra Luini, Alessandra Luini
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In o... | ["[CELL FREEZING PROCEDURE FOR ADHERENT CELLS (MCF7, HUVEC, A549, SYNOVIAL FIBROBLAST)]\nAdd of complete medium to inactivate trypsin, recover the cell suspension in 15 mL conical tube and centrifuge for at .\n4 mL\nCentrifuge: 200 34\n0 Room temperature", "[CELL FREEZING PROCEDURE FOR ADHERENT CELLS (MCF7, HUVEC, A54... |
73,893 | Chromic acid assay for quantification of total lipids in pollen | 6 | dx.doi.org/10.17504/protocols.io.ewov1odqplr2/v1 | https://www.protocols.io/view/chromic-acid-assay-for-quantification-of-total-lip-ckeduta6 | Mark J. Carroll | TITLE: Chromic acid assay for quantification of total lipids in pollen
AUTHORS: Mark J. Carroll
[DESCRIPTION]
This protocol quantifies total lipid contents of pollen through colorimetric oxidation of lipids by chromic acid (adapted from Amenta, 1970). Small pollen samples (10 mg) are fractured by cell homogenization ... | ["[Folch Extraction and Partition of Lipids] Add 1.0 mm zirconia beads to a 2 mL homogenizer tube and fill approximately 1/4 full.", "[Folch Extraction and Partition of Lipids] Pulverize the pollen in the homogenizer tube with the BeadBeater homogenizer for 30 seconds. Tough materials may require additional 30 second ... |
16,853 | Verification of protein changes by parallel reaction monitoring (PRM) | null | dx.doi.org/10.17504/protocols.io.upvevn6 | null | Lihui Li | TITLE: Verification of protein changes by parallel reaction monitoring (PRM)
AUTHORS: Lihui Li
[STEPS]
?. 200ug protein was taken from each sample of each group separately, and 10fmol heavy isotope-labeled peptide DSPSAPVNVTVR (Thermo Fisher Scientific Inc.) was incorporated as internal standard.
?. DTT was added to a... | ["200ug protein was taken from each sample of each group separately, and 10fmol heavy isotope-labeled peptide DSPSAPVNVTVR (Thermo Fisher Scientific Inc.) was incorporated as internal standard.", "DTT was added to a final concentration of 10 mM, and then heated on the boiling water bath for 15min following cooling it t... |
null | null | null | dx.doi.org/10.17504/protocols.io.e5qbg5w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is designed for high sensitivity miRNA library generation for the Illumina sequencing platform. Our protocol and the enhanced reagent kit enables the discovery and profiling of small RNAs from a variety of sources including FFPE, exosome, serum, and whole blood.... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.mwnc7de | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is aimed at amplifying the cytochrome c oxidase subunit I (COI) mitochondrial gene in eukaryotes. The primers (forward: mlCOIintF, reverse: HCO2198) utilized in this protocol are based on the primers utilized in Leray et al. 2013 (forward) and Folmer et al. 1994... | [] |
88,978 | GFP-sacB Characterization | 4 | dx.doi.org/10.17504/protocols.io.261gedwxwv47/v1 | https://www.protocols.io/view/gfp-sacb-characterization-c25syg6e | NUS iGEM | TITLE: GFP-sacB Characterization
AUTHORS: NUS iGEM
[DESCRIPTION]
2023 NUS-Singapore iGEM team followed this protocol to characterise their New Composite Part "GFP-sacB" with IPTG and sucrose solution at various concentrations.
[STEPS]
SECTION: Cell Inoculation and Incubation (Day Before Characterization)
1. Inoculat... | ["[Cell Inoculation and Incubation (Day Before Characterization)] Inoculate cells with GFP-sacB gene from the cell stock.", "[Cell Inoculation and Incubation (Day Before Characterization)] Add 5 mL of LB media and 5 µL of the appropriate antibiotic to a Falcon tube.", "[Cell Inoculation and Incubation (Day Before Chara... |
null | null | null | dx.doi.org/10.17504/protocols.io.eigbcbw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Stains the nucleus of budding or fission yeast with DAPI in order to see it with a fluorescence microscope.
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?. | [] |
64,432 | Immunofluorescence Staining of Sea Urchin Embryos | 1 | dx.doi.org/10.17504/protocols.io.5jyl8no8rl2w/v2 | https://www.protocols.io/view/immunofluorescence-staining-of-sea-urchin-embryos-ca6qshdw | David Booth | TITLE: Immunofluorescence Staining of Sea Urchin Embryos
AUTHORS: David Booth
[DESCRIPTION]
In this lab, you will use immunofluroescence staining to visualize the wondrous cellular transformations that occur throughout sea urchin development. The goals of this module:
1. To learn about marine organisms at Marine Res... | ["[Fix Cells] Prepare cells for fixation\n• Place 225 µl of embryos in filtered seawater in 1 well of a 96-well, round-bottom dish.", "[Fix Cells] Fix cells with paraformaldeyde\n• Add 75 µl of 16% (w/v) paraformaldehydle to 225 µl of embryos in seawater\n• Gently rock cells for 1 h at room temperature", "[Fix Cells] R... |
68,530 | DNA Purification (NEB) | 4 | null | https://www.protocols.io/view/dna-purification-neb-ce6sthee | Brian Teague | TITLE: DNA Purification (NEB)
AUTHORS: Brian Teague
[DESCRIPTION]
This protocol purifies DNA from an enzymatic reaction (like a PCR or a digestion with a restriction enzyme.) It is NOT an miniprep -- if you are trying to purify DNA from a culture of E. coli, you are in the wrong place!
[STEPS]
1. Make sure you are... | ["Make sure you are using the \"Monarch PCR & DNA Cleanup Kit\", not the Monarch Plasmid Miniprep Kit. They come in identical boxes -- read the label!", "Mix the ENTIRE DNA sample with 5 times its volume of Binding Buffer. Pipette up and down several times to mix the sample thoroughly.", "Insert the column into the col... |
89,550 | Polysomnography | 1 | dx.doi.org/10.17504/protocols.io.rm7vzx77xgx1/v1 | https://www.protocols.io/view/polysomnography-c3pnymme | Núria Peñuelas | TITLE: Polysomnography
AUTHORS: Núria Peñuelas
[DESCRIPTION]
Polysomnography in mice
[STEPS]
1. Anesthetize the animals (ketamine and xylazine,100/10 mg/kg. i.p.) for polysomnography.
2. Screw 3 electrodes to skull above parietal and frontal cortex and cerebellum as the reference for electroencephalogram (EEG).
3. Sl... | ["Anesthetize the animals (ketamine and xylazine,100/10 mg/kg. i.p.) for polysomnography.", "Screw 3 electrodes to skull above parietal and frontal cortex and cerebellum as the reference for electroencephalogram (EEG).", "Slip 2 wire electrodes between neck muscles for electromyogram (EMG).", "Braze thebleads to a mini... |
86,897 | A recombinant retroviral expression vector (pLXSN-HygR) based on pLXSN that confers resistance to hygromycin and pLXSN-HygR derivatives that encode EGFR, ERBB2, or ERBB3 | 1 | dx.doi.org/10.17504/protocols.io.j8nlkooq1v5r/v1 | https://www.protocols.io/view/a-recombinant-retroviral-expression-vector-plxsn-h-cy4rxyv6 | David J Riese II, Vipasha VD Dwivedi | TITLE: A recombinant retroviral expression vector (pLXSN-HygR) based on pLXSN that confers resistance to hygromycin and pLXSN-HygR derivatives that encode EGFR, ERBB2, or ERBB3
AUTHORS: David J Riese II, Vipasha VD Dwivedi
[DESCRIPTION]
Here we describe the construction of a derivative of pLXSN, called pLXSN-HygR, th... | ["[Introduction] Recombinant retroviruses are commonly used to direct the ectopic expression of genes in infected cells. There are two significant advantages to this approach. Following infection of the target cell, the recombinant retroviral genome is reverse-transcribed and subsequently integrated into the host cell... |
90,317 | ŌGI Bio Oxygen Flask Cleaning | 1 | dx.doi.org/10.17504/protocols.io.261ged277v47/v2 | https://www.protocols.io/view/gi-bio-oxygen-flask-cleaning-c4fmytk6 | Jack Hocking | TITLE: ŌGI Bio Oxygen Flask Cleaning
AUTHORS: Jack Hocking
[DESCRIPTION]
This protocol is for the cleaning of your OGI BioReactor Oxygen Measurement Flasks.
[BEFORE_START]
Ensure protocol is carried out in sterile conditions.
Ensure you have familiarised yourself with the guidelines and warnings for this protocol.
[... | ["[Cleaning Oxygen Measurement Flask] Retaining the magnetic stir bar, empty the contents of each flask into the waste flask.", "[Cleaning Oxygen Measurement Flask] Remove stir bars and wipe thoroughly with 70% ethanol. Leave aside.", "[Cleaning Oxygen Measurement Flask] Vigorously swill 10-20 mL of 70% ethanol around... |
61,709 | Nuclei Prep from Frozen Mouse Brain Tissues with Optional Sucrose Column for single nuclei RNA-seq | 4 | dx.doi.org/10.17504/protocols.io.81wgb657ylpk/v1 | https://www.protocols.io/view/nuclei-prep-from-frozen-mouse-brain-tissues-with-o-b8hmrt46 | Greggory A Perry, Sandra L Daigle, Paul Gabriel, Diane Luo, Jessica Grassmann, William F F Flynn, Elise T Courtois, Paul Robson | TITLE: Nuclei Prep from Frozen Mouse Brain Tissues with Optional Sucrose Column for single nuclei RNA-seq
AUTHORS: Greggory A Perry, Sandra L Daigle, Paul Gabriel, Diane Luo, Jessica Grassmann, William F F Flynn, Elise T Courtois, Paul Robson
[DESCRIPTION]
This SOP aims to extract nuclei from unfixed snap-frozen ... | ["[Procedure- gentleMAC] Miltenyi gentleMACS Procedure for Tissue Lysis and nuclei extraction\n\nPlease see the Guidelines & Warnings section before beginning. This protocol was optimized to process up to 8 samples simultaneously. Some practice is required to process 8 samples at once. Work fast but cautiously..", "[Su... |
55,252 | Rescue Intracranial Stenting in acute Ischemic Stroke | 3 | dx.doi.org/10.17504/protocols.io.bz7up9nw | https://www.protocols.io/view/rescue-intracranial-stenting-in-acute-ischemic-str-bz7up9nw | Minh Thang Le, Chi Cuong Tran, Luu Giang Nguyen, Dao Nhat Huy Nguyen, Minh Tuan Ngo, Hoang Linh Duong, Minh Luan Tran | TITLE: Rescue Intracranial Stenting in acute Ischemic Stroke
AUTHORS: Minh Thang Le, Chi Cuong Tran, Luu Giang Nguyen, Dao Nhat Huy Nguyen, Minh Tuan Ngo, Hoang Linh Duong, Minh Luan Tran
[DESCRIPTION]
Abstract
Background
In acute ischemic stroke (AIS) caused by intracranial large vessel occlusion, rescue intr... | [] |
98,046 | Test 1 - two-day protocol | 0 | dx.doi.org/10.17504/protocols.io.x54v92mdpl3e/v1 | https://www.protocols.io/view/test-1-two-day-protocol-dby62pze | Gabriel Gasque | TITLE: Test 1 - two-day protocol
AUTHORS: Gabriel Gasque
[DESCRIPTION]
Abstract here for second protocol
[STEPS]
SECTION: Day 1
1. Step 1
SECTION: Day 1
2. Step 2
SECTION: Day 2
3. Step 4
SECTION: Day 2
4. Step 5 | ["[Day 1] Step 1", "[Day 1] Step 2", "[Day 2] Step 4", "[Day 2] Step 5"] |
57,630 | Primary cortical mixed culture | 4 | dx.doi.org/10.17504/protocols.io.b4h6qt9e | https://www.protocols.io/view/primary-cortical-mixed-culture-b4h6qt9e | Xiqun Chen, Qing Ye | TITLE: Primary cortical mixed culture
AUTHORS: Xiqun Chen, Qing Ye
[DESCRIPTION]
To obtain cortical culture, pregnant mice were anesthetized, embryos were dissected, and cortex was collected in PBS. Tissues were incubated in 0.25% trypsin–EDTA at 37°C for 15 min. Trypsinized tissue was transferred into a high-glucose ... | ["For primary cortical mixed culture - Use C57BL/6J mice at embryonic day 17", "Anesthetized pregnant mice (1% sodium pentobarbital, 80mg/kg), dissect their embryos and collect the cortex. \n(Separate and remove the soft membrane and blood vessels, rinse the cerebral cortex in PBS, and use the ophthalmic scissor to cut... |
77,175 | Purification of ACOD1 expressed in E. coli | 4 | null | https://www.protocols.io/view/purification-of-acod1-expressed-in-e-coli-cpkxvkxn | Konrad Büssow | TITLE: Purification of ACOD1 expressed in E. coli
AUTHORS: Konrad Büssow
[DESCRIPTION]
This protocol describes the purification of the human enzyme cis-aconitate decarboxylase (ACOD1) from recombinant E. coli cells.
[BEFORE_START]
The expression plasmid pCAD29 (pCAD29_hIRG1_4-461_pvp008, Addgene #124843) is used. It... | ["[Protein expression] Inoculate 20 ml MDAG-135 containing 100 mg/L kanamycin and chloramphenicol with a colony and shake over night at 37°C.", "[Protein expression] Prepare 4×1 L ZYM-5052 medium with 100 mg/L kanamycin and 34 mg/L chloramphenicol in 2.8 L baffled Fernbach flasks. Inoculate each Fernbach flask with 4 m... |
null | null | null | dx.doi.org/10.17504/protocols.io.pdwdi7e | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
<p>Checklist:</p>
<p> </p>
<p>1. FASTA file containing the proteins to analyze.</p>
<p>2. FASTX toolkit installed</p>
<p>3. phobius installed</p>
<p>4. pandas installed in python</p>
[GUIDELINES]
<p>This protocol was executed via ssh on a Ubuntu machine using the command line.... | [] |
102,406 | Preparation of SARS-CoV-2 Saliva Samples Using an ARTIC V4.1 Tiled Amplicon Approach for Sequencing on Illumina Platforms | 0 | null | https://www.protocols.io/view/preparation-of-sars-cov-2-saliva-samples-using-an-df9e3r3e | Leah Lariscy, Amanda Sullivan, Katie Dillon, Megan Lott, Travis Glenn, Erin Lipp | TITLE: Preparation of SARS-CoV-2 Saliva Samples Using an ARTIC V4.1 Tiled Amplicon Approach for Sequencing on Illumina Platforms
AUTHORS: Leah Lariscy, Amanda Sullivan, Katie Dillon, Megan Lott, Travis Glenn, Erin Lipp
[DESCRIPTION]
This protocol describes how to prepare purified SARS-CoV-2 RNA from positive saliva sa... | ["[cDNA Synthesis] Prepare the cDNA synthesis reactions as follows:", "[cDNA Synthesis] For purified RNA samples, combine the following components in a 96-well plate:", "[cDNA Synthesis] For no template controls, combine the following components in a 96-well plate:", "[cDNA Synthesis] Pipet up and down 10 times to mix.... |
32,731 | Viral isolation for SAR11 and OM43 hosts | null | dx.doi.org/10.17504/protocols.io.bb73irqn | https://www.protocols.io/view/viral-isolation-for-sar11-and-om43-hosts-bb73irqn | Holger Buchholz, Michelle Michelsen, Michael Allen, Ben Temperton | TITLE: Viral isolation for SAR11 and OM43 hosts
AUTHORS: Holger Buchholz, Michelle Michelsen, Michael Allen, Ben Temperton
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Working protocol</div></div>
[STEPS]
?. [Sample Preparation ]
Take 2 liter water samples of environmental water you wish to isol... | ["[Sample Preparation ]\nTake 2 liter water samples of environmental water you wish to isolate viruses from. To remove larger plankton and particles, filter through a GF/D filter membrane (14.2 cm Whatman GF/D filter) using a peristaltic pump. Collect filtrate in a sterile, acid-washed 2 liter Polycarbonate bottle.", "... |
19,780 | SSH Amazon EC2 | null | dx.doi.org/10.17504/protocols.io.xjcfkiw | null | Mihai IONITA | TITLE: SSH Amazon EC2
AUTHORS: Mihai IONITA
[STEPS]
?. Log in to Amazon EC2
?. Select Instances, Actions, Instance State, Start (YES, Confirm)Copy IPv4 Public IP
?. Run software:Add:IPv4 Public IP and port 22your .ppk file (SSH, Auth.)run command:
?. | ["Log in to Amazon EC2", "Select Instances, Actions, Instance State, Start (YES, Confirm)Copy IPv4 Public IP", "Run software:Add:IPv4 Public IP and port 22your .ppk file (SSH, Auth.)run command:"] |
50,837 | Multiplex Real-Time PCR for genotyping Glutathione S-Transferase deletion polymorphisms | 1 | dx.doi.org/10.17504/protocols.io.bvvvn666 | https://www.protocols.io/view/multiplex-real-time-pcr-for-genotyping-glutathione-bvvvn666 | Rayana Pereira Dantas de Oliveira, Kamilla de Faria Santos, Wandelisa Cançado Flores Menezes, Rodrigo da Silva Santos, Angela Adamski da Silva Reis | TITLE: Multiplex Real-Time PCR for genotyping Glutathione S-Transferase deletion polymorphisms
AUTHORS: Rayana Pereira Dantas de Oliveira, Kamilla de Faria Santos, Wandelisa Cançado Flores Menezes, Rodrigo da Silva Santos, Angela Adamski da Silva Reis
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">... | ["[Samples collection and DNA extraction]\nPeripheral blood samples from diabetic patients and health control group were collected in tubes containing heparin and stored at -80°C to preserve the characteristics of nucleic acid for genotyping. The DNA extraction was performed using the PureLink ™ Genomic DNA Mini Kit (T... |
66,023 | GoKeto Gummies – Check Its Advantages + Side-Effects | 1 | dx.doi.org/10.17504/protocols.io.eq2lynb2mvx9/v1 | https://www.protocols.io/view/goketo-gummies-check-its-advantages-side-effects-ccqfsvtn | truketoosm | TITLE: GoKeto Gummies – Check Its Advantages + Side-Effects
AUTHORS: truketoosm
[DESCRIPTION]
Do you continually feel yourself succumbing to mental and actual wellbeing illnesses? The increment of unfamiliar particles in the encompassing region has made us defenseless against different medical problems. To address t... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.vhue36w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Liver Tissue dissociation of single-cell RNA-seq (10x Single-cell RNA-seq)
[STEPS]
SECTION: Buffers
?.
SECTION: Enrichment of Hepatocytes
?.
SECTION: Dissociation
?.
SECTION: Dead Cell Removal
?.
SECTION: MACS depletion of CD45 positive cells
?. | ["[Buffers] {\"blocks\":[{\"key\":\"76jf3\",\"text\":\"**Before tumor arrives** \",\"type\":\"align-center\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"1655t\",\"text\":\"\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"cunj2... |
32,983 | A protocol to address the study of microplastic intake in stranded cetaceans | 1 | dx.doi.org/10.17504/protocols.io.bcfxitpn | https://www.protocols.io/view/a-protocol-to-address-the-study-of-microplastic-in-bcfxitpn | Tania Montoto-Martinez, Raquel Puig-Lozano, Nuno Marques, Antonio Fernández, Jesús De La Fuente, Maria Dolores Gelado Caballero | TITLE: A protocol to address the study of microplastic intake in stranded cetaceans
AUTHORS: Tania Montoto-Martinez, Raquel Puig-Lozano, Nuno Marques, Antonio Fernández, Jesús De La Fuente, Maria Dolores Gelado Caballero
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Marine debris can impact biodiv... | ["[Extraction of the digestive tract during the necropsy]\nAfter opening the thoracic cavity, locate the final part of the oesophagus (between both lungs) before passing through the diaphragm by the oesophageal hiatus. Separate a little bit of the connective tissue that holds it in place and with some string (or ties) ... |
49,745 | Collection and processing of intertidal seagrass tissues for bacterial and fungal culturing | 1 | dx.doi.org/10.17504/protocols.io.butrnwm6 | https://www.protocols.io/view/collection-and-processing-of-intertidal-seagrass-t-butrnwm6 | Cassie Ettinger | TITLE: Collection and processing of intertidal seagrass tissues for bacterial and fungal culturing
AUTHORS: Cassie Ettinger
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details collection and processing of intertidal seagrass tissues for bacterial and fungal culturing.</div></div>
... | ["[Field collections]\nPut on gloves.", "[Field collections]\nWalk to a location that is submerged (~0.5 m).", "[Field collections]\nUsing a coring device, take a sample of an individual seagrass plant and its associated sediment.", "[Field collections]\nPlace core in dark box until transport back to the lab.\non ice"... |
73,397 | Procedure for Aflatoxin M1 and B1 in Liver by HPLC-Fluorescence Detection with Pre-column Derivatization | 6 | dx.doi.org/10.17504/protocols.io.j8nlkw83wl5r/v1 | https://www.protocols.io/view/procedure-for-aflatoxin-m1-and-b1-in-liver-by-hplc-cjwvupe6 | duey | TITLE: Procedure for Aflatoxin M1 and B1 in Liver by HPLC-Fluorescence Detection with Pre-column Derivatization
AUTHORS: duey
[DESCRIPTION]
The current procedure is for quantitative determination of aflatoxin M1 (AFM1) and B1(AFB1) in animal liver by HPLC-fluorescence detection at concentrations 0.2-10 ng/g (ppb). Not... | ["[PREPARATION OF REAGENTS AND STANDARDS] The standard stock solutions of each aflatoxin is prepared by dissolving the pre-weighed standards in chloroform (AFM1) or methanol (AFB1) and stored in -20 °C when not in use.", "A mixed standard solution (250 ng/mL for each aflatoxin) is prepared. Quantitatively transfer 1 mL... |
42,943 | Photographing Agave for 3D reconstruction using Structure From Motion | 1 | dx.doi.org/10.17504/protocols.io.bm67k9hn | https://www.protocols.io/view/photographing-agave-for-3d-reconstruction-using-st-bm67k9hn | David Lebauer | TITLE: Photographing Agave for 3D reconstruction using Structure From Motion
AUTHORS: David Lebauer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol was used in 2014 to capture 3D models of plant canopies. The technology has certainly advanced since this time! </div><div class = "text-... | ["place sheets of newspaper, sheets, or other material on the ground around the base of the plant, and in the background. It is most important to obscure other plants.", "take a photograph from eye level in which the plant takes up most of the frame.", "move approximately 20 degrees ( two steps to the side) around the ... |
null | null | null | dx.doi.org/10.17504/protocols.io.jpbcmin | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Background: The two most common surgical approaches to total hip arthroplasty are the posterior approach and lateral approach. The surgical approach may influence cup positioning and restoration of the offset, which may affect the biomechanical properties of the hip joint.<br... | [] |
31,382 | Self-Perception: A view into the mind of Self-Imaging | null | dx.doi.org/10.17504/protocols.io.bavwie7e | null | Hunter Duval | TITLE: Self-Perception: A view into the mind of Self-Imaging
AUTHORS: Hunter Duval
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">When a person looks into a mirror, three reflections appear the reflection that only they see, the reflection that everyone else sees, and the reflection that is truly t... | ["Choose Population — Be sure to choose an unbiased population, meaning do not choose a population that is known for being over or under-confident.", "Set Up Questions — What are the subjects going to be asked? How will these questions pertain to the experiment?", "Collect Data — Ask the population the selected questio... |
66,309 | Protocol for intracellular recording from mouse intrinsic cardiac neurons | 1 | dx.doi.org/10.17504/protocols.io.81wgb6ep3lpk/v1 | https://www.protocols.io/view/protocol-for-intracellular-recording-from-mouse-in-cczdsx26 | John D Tompkins | TITLE: Protocol for intracellular recording from mouse intrinsic cardiac neurons
AUTHORS: John D Tompkins
[DESCRIPTION]
Basic protocol for isolation and intracellular recording from mouse intrinsic cardiac neurons is presented. The intrinsic cardiac ganglia, containing hundreds of intrinsic cardiac neurons (ICNs), ... | ["[Isolation of intrinsic cardiac ganglia] Adult mice (M/F; 12±2 weeks of age) are sacrificed under deep isoflurane (5%) anesthesia by cervical dislocation and exsanguination.", "[Isolation of intrinsic cardiac ganglia] The thorax is removed and placed in ice-cold physiologic salt solution (PSS) containing in mM: 121 N... |
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