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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28,444 | Biotin-Labelling of Immunoprecipitated RNA (v1pre) | null | dx.doi.org/10.17504/protocols.io.7z4hp8w | null | Steven Blue, Eric Van Nostrand, Gene Yeo | TITLE: Biotin-Labelling of Immunoprecipitated RNA (v1pre)
AUTHORS: Steven Blue, Eric Van Nostrand, Gene Yeo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">RNA binding proteins (RBPs) regulate a diverse array of RNA processing steps by binding RNAs through sequence and structural elements. The devel... | ["[Biotinylated Cytidine Ligation]\nIn an RNase-free 1.5 mL microcentrifuge tube, mix the following mix, volumes per sample:\n\n AB1 H2O 9.6 μL2 10X RNA Ligase Buffer (no DTT) 3.0 μL 3 0.1 M ATP 0.3 μL 4 100% DMSO 0.9 μL 5 1% Tween-20 0.6 μL 6 50% PEG 8000 9.0 μL 7 Murine RNase Inhibitor 0.4 μL 8 RNA Ligase Hig... |
78,850 | Procesador de tejidos | 1 | dx.doi.org/10.17504/protocols.io.rm7vzb9z5vx1/v1 | https://www.protocols.io/view/procesador-de-tejidos-cq9avz2e | Andrés AHJ Heredia Juyumaya | TITLE: Procesador de tejidos
AUTHORS: Andrés AHJ Heredia Juyumaya
[DESCRIPTION]
Descripción
Procese muestras biológicas desde fijación química hasta infiltración de parafina con el procesador de tejidos centrífugo Thermo Scientific™ STP 120. En carrusel, de sobremesa y compacto, su diseño exclusivo utiliza una fue... | ["[Modo de operación] Colocar los casetes histológicos con las muestras en cesta metálica, procurando dejar la tapa sobre ellos. Una vez hecho esto, levantar la tapa del carrusel pulsando el botón <ARRIBA-ABAJO>.", "Las cestas se sujetan por cuatro puntos. Para colocar la cesta, asegurarse de introducir los cuatro pivo... |
71,736 | GUARDS Statistical Analysis Plan Version 1.1 | 3 | dx.doi.org/10.17504/protocols.io.14egn7yzqv5d/v2 | https://www.protocols.io/view/guards-statistical-analysis-plan-version-1-1-ciayuafw | Professor Catherine Williamson, Dr Jose Blanco Carnero, Dr Catalina de Paco Matallana, Dr Alice Mitchell, Dr Caroline Ovadia, Professor David Wright, Monika Lewanczyk | TITLE: GUARDS Statistical Analysis Plan Version 1.1
AUTHORS: Professor Catherine Williamson, Dr Jose Blanco Carnero, Dr Catalina de Paco Matallana, Dr Alice Mitchell, Dr Caroline Ovadia, Professor David Wright, Monika Lewanczyk
[DESCRIPTION]
GUARDS is a double-blind randomised placebo-controlled single site trial. Th... | [] |
27,844 | Bodo saltans transfection with plasmid for tagging EF1alpha gene__IG BsTub | null | dx.doi.org/10.17504/protocols.io.7fchjiw | null | Fatma Gomaa, Roberto Docampo, Zhuhong Li, Peter Girguis, Virginia Edgcomb | TITLE: Bodo saltans transfection with plasmid for tagging EF1alpha gene__IG BsTub
AUTHORS: Fatma Gomaa, Roberto Docampo, Zhuhong Li, Peter Girguis, Virginia Edgcomb
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Stable transfection of </span><span style = "font-style:italic;">B. saltans</span... | [] |
91,485 | In vivo voltammetry and fiber photometry in the mouse striatum | 1 | dx.doi.org/10.17504/protocols.io.dm6gp32kpvzp/v1 | https://www.protocols.io/view/in-vivo-voltammetry-and-fiber-photometry-in-the-mo-c5j5y4q6 | Yan-Feng Zhang, Stephanie J Cragg | TITLE: In vivo voltammetry and fiber photometry in the mouse striatum
AUTHORS: Yan-Feng Zhang, Stephanie J Cragg
[DESCRIPTION]
This protocol describes how to measure extracellular dopamine concentrations and calcium dynamics in striatal dopaminergic axons in response to electrical stimulations using in vivo voltammetr... | ["[Preparing the mouse for surgery] Anesthetize the mouse in an induction chamber with urethane (1.4–1.9 g/kg, i.p.; Biolab), supplemented with additional urethane (0.2 g/kg) every 1-2 hr as required.", "[Preparing the mouse for surgery] Infiltrate all wounds and pressure points with bupivacaine (0.5%).", "[Preparing t... |
null | null | null | dx.doi.org/10.17504/protocols.io.eq2bdye | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in <a href="https://www.protocols.io/view/Polyacrylamide-Gel-System-For-Electrophoresis-Of-P-ep7bdrn" target="_blank">Polyacrylamide Gel System For Electrophoresis Of Proteins</a>.
[STEPS]
?.
?.
?.
?. | [] |
41,389 | Comparison of Two Lipid Emulsions on Interleukin-1β, Interleukin-8 and Plasma Fatty Acid Composition in Infants Post Gastrointestinal Surgery: A Randomized Trial | 1 | dx.doi.org/10.17504/protocols.io.bknmkvc6 | https://www.protocols.io/view/comparison-of-two-lipid-emulsions-on-interleukin-1-bknmkvc6 | Meta Herdiana Hanindita | TITLE: Comparison of Two Lipid Emulsions on Interleukin-1β, Interleukin-8 and Plasma Fatty Acid Composition in Infants Post Gastrointestinal Surgery: A Randomized Trial
AUTHORS: Meta Herdiana Hanindita
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Surgical intervention in infants is associated wi... | [] |
72,310 | iSeq Bacterial WGS Protocol using a quarter of the reagents | 1 | dx.doi.org/10.17504/protocols.io.6qpvr44rbgmk/v1 | https://www.protocols.io/view/iseq-bacterial-wgs-protocol-using-a-quarter-of-the-ciuwuexe | Sonsiray Alvarez Narvaez, Zhenyu Shen, Lifang Yan | TITLE: iSeq Bacterial WGS Protocol using a quarter of the reagents
AUTHORS: Sonsiray Alvarez Narvaez, Zhenyu Shen, Lifang Yan
[DESCRIPTION]
This is an adaptation of protocol https://dx.doi.org/10.17504/protocols.io.bij8kcrw in which initial the initial DNA concentration and library prep reagent volumes have been reduc... | ["[Bacterial propagation and DNA extraction] Frozen isolates should be sub-cultured on Trypticase Soy + 5% Sheep Blood Agar plates (BAPs) or equivalent media. If the culture appears pure, pick an isolated colony, and streak it on a fresh BAP; incubate at 35°C overnight (24±2 hours) in aerobic conditions.", "[Bacterial ... |
47,194 | Detection of cytosolic and mitochondrial ROS production using FlexStation 3 | 4 | dx.doi.org/10.17504/protocols.io.bsb2naqe | https://www.protocols.io/view/detection-of-cytosolic-and-mitochondrial-ros-produ-bsb2naqe | Nawel Zaibi; Pengyun Li; Shang-Zhong Xu | TITLE: Detection of cytosolic and mitochondrial ROS production using FlexStation 3
AUTHORS: Nawel Zaibi; Pengyun Li; Shang-Zhong Xu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is for the detection of cytosolic and mitochondrial ROS using FlexStation 3</div></div>
[STEPS]
?. | [] |
64,445 | Benefits and Challenges of Behavioral Health Treatment | 1 | dx.doi.org/10.17504/protocols.io.ewov1nmpogr2/v1 | https://www.protocols.io/view/benefits-and-challenges-of-behavioral-health-treat-ca65shg6 | coralynn.aracelly | TITLE: Benefits and Challenges of Behavioral Health Treatment
AUTHORS: coralynn.aracelly
[DESCRIPTION]
https://cutt.ly/7JFvsBE
[STEPS]
1. HardHS4 Male Enhancement Due to smooth availability and affordability, maximum guys opt for the fine male enhancement capsules. These pills incorporate herbal ingredients and a... | ["HardHS4 Male Enhancement Due to smooth availability and affordability, maximum guys opt for the fine male enhancement capsules. These pills incorporate herbal ingredients and are easily available for purchase with out the want of any prescription from a physician. You have to do extensive research for the top male en... |
40,378 | DNA Barcoded Hydrogel Bead Synthesis | 4 | null | https://www.protocols.io/view/dna-barcoded-hydrogel-bead-synthesis-bjn2kmge | Chris Cheshire | TITLE: DNA Barcoded Hydrogel Bead Synthesis
AUTHORS: Chris Cheshire
[STEPS]
?. [10% (vol/vol) Triton X-100]
Prepare 10% (vol/vol) Triton X-100Combine of NFW with of Triton X-100Store at for at least 6 months
90 mL
10 mL
0 Room temperature
?. [10% (vol/vol) Tween-20]
Prepare 10% (vol/vol) Tween-20Combine of NFW... | ["[10% (vol/vol) Triton X-100]\nPrepare 10% (vol/vol) Triton X-100Combine of NFW with of Triton X-100Store at for at least 6 months\n90 mL\n10 mL\n0 Room temperature", "[10% (vol/vol) Tween-20]\nPrepare 10% (vol/vol) Tween-20Combine of NFW with of Tween-20Store at for at least 6 months\n90 mL\n10 mL\n0 Room t... |
null | null | null | dx.doi.org/10.17504/protocols.io.pgtdjwn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This method adapted from instructions provided by Daiske Honda, Konan University. </p>
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.nemdbc6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong><em><span style="vertical-align: inherit;"><span style="vertical-align: inherit;">Antecedentes</span></span></em></strong><strong><span style="vertical-align: inherit;"><span style="vertical-align: inherit;"> : A</span></span></strong><span style="vertical-align: inhe... | [] |
62,274 | A novel laboratory method to simulate climatic stress with successful application to experiments with medically relevant ticks | 4 | dx.doi.org/10.17504/protocols.io.rm7vzyo8rlx1/v1 | https://www.protocols.io/view/a-novel-laboratory-method-to-simulate-climatic-str-b83aryie | Sang Hyo Kim, Caleb Nielebeck, Lauren Dedmon, Mark Pangilinan, Jahred Quan, William Ota, Javier D. Monzón | TITLE: A novel laboratory method to simulate climatic stress with successful application to experiments with medically relevant ticks
AUTHORS: Sang Hyo Kim, Caleb Nielebeck, Lauren Dedmon, Mark Pangilinan, Jahred Quan, William Ota, Javier D. Monzón
[DESCRIPTION]
This protocol details a novel method to isolate indivi... | ["[Set up] Place a single tick with one wooden skewer in each tube and seal with a cap, labelling each tube with an individual identifier", "[Set up] Place six tubes in each airtight container along with a humidity pack, labelling each container", "[Set up] Program the climate chamber", "[Set up] To cycle between 20 °C... |
48,260 | test/demo protocol | 1 | null | https://www.protocols.io/view/test-demo-protocol-btdcni2w | Josh Birlingmair | TITLE: test/demo protocol
AUTHORS: Josh Birlingmair
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Main protocol</div></div>
[STEPS]
?. This is a step | ["This is a step"] |
98,306 | From Taro Roots to Dental Roots | 0 | dx.doi.org/10.17504/protocols.io.261ge5okog47/v1 | https://www.protocols.io/view/from-taro-roots-to-dental-roots-db9a2r2e | Mistie T | TITLE: From Taro Roots to Dental Roots
AUTHORS: Mistie T
[DESCRIPTION]
This project aims to examine the impact of dietary shifts and cultural changes on dental health disparities. Through a literature review and field surveys, it will explore historical and contemporary dietary patterns, cultural practices, and their ... | ["[Literature Review] Identify relevant literature on historical dietary patterns, cultural practices, oral health knowledge, and the impact of colonialism on the South Pacific Islands' populations.", "[Data Collection] Pre-Colonial Era:", "[Data Collection] Gather historical data through archaeological findings, anthr... |
82,723 | Brain slice physiology and optogenetics | 4 | dx.doi.org/10.17504/protocols.io.eq2ly7m2rlx9/v1 | https://www.protocols.click/view/brain-slice-physiology-and-optogenetics-cu2bwyan | Hong-Yuan Chu | TITLE: Brain slice physiology and optogenetics
AUTHORS: Hong-Yuan Chu
[DESCRIPTION]
This protocol describes Chu Lab standard external solutions for electrophysiology.
[STEPS]
SECTION: Brain slice physiology: Setting up patch rig and environment
1. Turn on the MultiClamp 700B Amplifier, Axon Digidata 1550B digitizer, ... | ["[Brain slice physiology: Setting up patch rig and environment] Turn on the MultiClamp 700B Amplifier, Axon Digidata 1550B digitizer, PatchStar Micromanipulator, PatchStar Slicescope, computer tower and the associated software.", "[Brain slice physiology: Setting up patch rig and environment] Turn on O2/CO2 tank and b... |
40,767 | ELISA for quantification of IL-8 in human serum. | 6 | dx.doi.org/10.17504/protocols.io.bj27kqhn | https://www.protocols.io/view/elisa-for-quantification-of-il-8-in-human-serum-bj27kqhn | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-8 in human serum.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells. The... | ["An anti-human IL-8 coating antibody is adsorbed onto microwells by incubation overnight at 4°C.", "Add 50 µl of human serum. Human IL-8 present in the serum sample binds to antibodies adsorbed to the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and later wash to remove unbound proteins.",... |
17,729 | Default Fuhrman Lab Pipeline for Exact Amplicon Sequence Variant (eASV) Calling from SSU rRNA Amplicons Derived From 515Y/926R Primers | null | dx.doi.org/10.17504/protocols.io.vi9e4h6 | null | Jesse McNichol | TITLE: Default Fuhrman Lab Pipeline for Exact Amplicon Sequence Variant (eASV) Calling from SSU rRNA Amplicons Derived From 515Y/926R Primers
AUTHORS: Jesse McNichol
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Modern sequence analysis methods allow marker gene sequences to be resolved down to si... | ["[Removing primers and sorting 16s and 18s into two separate pools]\nMake sure you have the correct environment configuration for conda by typing \"which conda\" in your terminal. It should output \"/home/anaconda/miniconda2/bin/conda\". If not, please refer to Guidelines and Warnings to get set up properly, or instal... |
93,619 | Brain Histology - tissue sectioning and staining | 4 | null | https://www.protocols.io/view/brain-histology-tissue-sectioning-and-staining-c7ntzmen | Yiqin Shen | TITLE: Brain Histology - tissue sectioning and staining
AUTHORS: Yiqin Shen
[DESCRIPTION]
.
[STEPS]
SECTION: Sectioning
1. Turn on and set the water floating device to 37 °C .
Prepare a bucket of ice. Place the samples on ice before sectioning.
Check the blades by doing a few test sections. Change if they are not sha... | ["[Sectioning] Turn on and set the water floating device to 37 °C .\nPrepare a bucket of ice. Place the samples on ice before sectioning.\nCheck the blades by doing a few test sections. Change if they are not sharp.", "[Staining- Day 1] Place the slides onto the slide holder, and dip in xylene for 30 min.", "[Staining-... |
48,462 | SCC compressive strength test | 3 | dx.doi.org/10.17504/protocols.io.btjnnkme | https://www.protocols.io/view/scc-compressive-strength-test-btjnnkme | Guoqiang Du, Liangtao Bu, Qi Hou, Jing Zhou | TITLE: SCC compressive strength test
AUTHORS: Guoqiang Du, Liangtao Bu, Qi Hou, Jing Zhou
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This paper mainly introduces the test process of rebound method and ultrasonic method for high strength self-consolidating concrete with strength grade of C50,... | [] |
108,964 | RNAseq DEG analysis protocol for non-human samples using ONT reads | 0 | dx.doi.org/10.17504/protocols.io.5qpvokmbbl4o/v1 | https://www.protocols.io/view/rnaseq-deg-analysis-protocol-for-non-human-samples-dnnc5daw | Avni Arora | TITLE: RNAseq DEG analysis protocol for non-human samples using ONT reads
AUTHORS: Avni Arora
[DESCRIPTION]
Data analysis of short-read sequencing from ONT flow cells can be done in a multitude of ways depending on the type of analysis that needs to be done and the sequencer utilized for assembly. Packages like NanoPa... | ["[Data clean up and alignment] Obtain FASTQ files from flow cell (GridION, MinION, PromethION)", "[Data clean up and alignment] Upload FASTQ files to machine", "[Trimming] Utilize the Prowler options to build a script to trim your reads based on the adapter lengths produced by the Fasta file.", "[Trimming]", "[Alignme... |
null | null | null | dx.doi.org/10.17504/protocols.io.pb7dirn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocole provide guidance to detect<em> Mycobacterium ulcerans</em> in environmental samples. The protocole share the DNA extraction process using the FastDNA kit for soil samples and the amplification of gene based on a validated protocole published by Fyfe which is th... | [] |
65,023 | Increasing insulin measurement throughput by fluorescence anisotropy imaging immunoassays | 4 | dx.doi.org/10.17504/protocols.io.eq2lyn4kwvx9/v1 | https://www.protocols.io/view/increasing-insulin-measurement-throughput-by-fluor-cbq7smzn | Yao Wang, Damilola I. Adeoye, Yue J. Wang, Michael Roper | TITLE: Increasing insulin measurement throughput by fluorescence anisotropy imaging immunoassays
AUTHORS: Yao Wang, Damilola I. Adeoye, Yue J. Wang, Michael Roper
[DESCRIPTION]
Insulin secreted from islets of Langerhans is the main hormone to reduce blood glucose. Examination of insulin secretion patterns at the sing... | ["[Experimental] Chemicals and reagents\n\nSodium chloride, calcium chloride, sodium hydroxide, ethylenediaminetetraacetic acid (EDTA), Tween-20, and bovine serum albumin (BSA) were from EMD Chemicals (San Diego, CA). Dextrose, RPMI 1640, gentamicin, and fetal bovine serum were from Thermo Fisher Scientific (Waltham, M... |
107,027 | Study protocol: can viral load predict a symptomatic congenital CMV infection? A systematic review and meta-analysis | 0 | dx.doi.org/10.17504/protocols.io.14egn61qml5d/v1 | https://www.protocols.io/view/study-protocol-can-viral-load-predict-a-symptomati-dkrt4v6n | Serena Salomè, Roberta Gammella, Clara Coppola, Pasquale Dolce, Letizia Capasso, Daniel Blasquez-Gamero | TITLE: Study protocol: can viral load predict a symptomatic congenital CMV infection? A systematic review and meta-analysis
AUTHORS: Serena Salomè, Roberta Gammella, Clara Coppola, Pasquale Dolce, Letizia Capasso, Daniel Blasquez-Gamero
[DESCRIPTION]
CMV is the most common cause of congenital infection.
Although only ... | [] |
65,176 | DNA Extraction Microbiome Kit - Fecal | 1 | null | https://www.protocols.io/view/dna-extraction-microbiome-kit-fecal-cbvysn7w | Stephanie Clouser | TITLE: DNA Extraction Microbiome Kit - Fecal
AUTHORS: Stephanie Clouser
[DESCRIPTION]
DNA Extraction of fecal samples with the MagMAX Microbiome Kit from Applied Biosystems.
[STEPS]
SECTION: Before You Begin
1. Prepare your workspace
a. Turn on Biological Safety Cabinet blower, white light, and window alarm.
b. ... | ["[Before You Begin] Prepare your workspace\na. Turn on Biological Safety Cabinet blower, white light, and window alarm.\nb. Clean the cabinet with 70% ethanol, including the work surface, walls, and glass.\nc. Lower the sash and run the UV light for 15 minutes. ... |
55,514 | Ancient DNA extract purification (chunk samples/high volume) | 1 | dx.doi.org/10.17504/protocols.io.n92ldzbpxv5b/v2 | https://www.protocols.io/view/ancient-dna-extract-purification-chunk-samples-hig-b2f2qbqe | Marcel Keller, Christiana L Scheib | TITLE: Ancient DNA extract purification (chunk samples/high volume)
AUTHORS: Marcel Keller, Christiana L Scheib
[DESCRIPTION]
Protocol for the purification of extracts, modified from Dabney et al. (2013) PNAS (doi: 10.1073/pnas.1314445110).
[BEFORE_START]
Previous step:
This protocol follows the extraction protocol ... | ["[Preparation] Turn the hood on full power and open the glass.", "[Preparation] Spray hood and table bench surfaces with DNA Exitus, let sit a minute and wipe down with paper towels.", "[Preparation] Wipe down outside surfaces of reagents/tips with DNA Exitus and place in the hood.", "[Preparation] Check that the cent... |
null | null | null | dx.doi.org/10.17504/protocols.io.hg5b3y6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div>
<div>
<p>This protocol is from 'Flower Ca<sup>2+</sup> channel in CME and ADBE' of Yao CK et al.</p>
<div>
<div>
<p> </p>
<p>Please see the manuscript for the full method details.</p>
</div>
</div>
</div>
</div>
[BEFORE_START]
<p>You'll need: </p>
<p> </p>
<p><strong>0 mM... | [] |
90,294 | Quality of interactions between health workers and women, parents, caregivers and families using digital health technologies for maternal, newborn and child health: a scoping review | 1 | dx.doi.org/10.17504/protocols.io.x54v9pk4pg3e/v1 | https://www.protocols.io/view/quality-of-interactions-between-health-workers-and-c4ewytfe | Soha Karam, Katie Moore, Elizabeth Katwan, Anayda Gerarda Portela, Helen Smith | TITLE: Quality of interactions between health workers and women, parents, caregivers and families using digital health technologies for maternal, newborn and child health: a scoping review
AUTHORS: Soha Karam, Katie Moore, Elizabeth Katwan, Anayda Gerarda Portela, Helen Smith
[DESCRIPTION]
WHO/MCA has been working to ... | [] |
20,483 | Differentiation of NPC into cortical neurons | null | dx.doi.org/10.17504/protocols.io.x9bfr2n | null | Celeste Karch, Rita Martinez, Jacob Marsh | TITLE: Differentiation of NPC into cortical neurons
AUTHORS: Celeste Karch, Rita Martinez, Jacob Marsh
[STEPS]
?. Ensure cells are plated at an appropriate density (e.g.: 150K/well in 12-well plate; 75- 50K/well for 48 well plates; 30K/well for 8-well chamber slides) in NIM on pre-coated PLO/laminin plates.
?. After ,... | ["Ensure cells are plated at an appropriate density (e.g.: 150K/well in 12-well plate; 75- 50K/well for 48 well plates; 30K/well for 8-well chamber slides) in NIM on pre-coated PLO/laminin plates.", "After , replace with cortical neuron differentiation medium (Neurobasal medium, 1x B27, 20 ng/mL BDNF, 20 ng/mL GDNF, 0.... |
55,724 | Nanotrap® KingFisher™ Concentration/Extraction & MagMAX KingFisher™ Extraction | 4 | dx.doi.org/10.17504/protocols.io.b2nkqdcw | https://www.protocols.io/view/nanotrap-kingfisher-concentration-extraction-amp-m-b2nkqdcw | Orlando Sablon III, Jamie VanTassell, Julia Raymond, Marlene K Wolfe, Pengbo Liu, Christine Moe | TITLE: Nanotrap® KingFisher™ Concentration/Extraction & MagMAX KingFisher™ Extraction
AUTHORS: Orlando Sablon III, Jamie VanTassell, Julia Raymond, Marlene K Wolfe, Pengbo Liu, Christine Moe
[DESCRIPTION]
These protocols have been adapted from Ceres "Nanotrap® Wastewater Protocol using MagMAX Kits" (APP-030... | ["[Ceres Nanosciences Nanotrap® KingFisher™ Procedure] Label two KingFisher™ 24 Well Deep Well sample plates “Sample Plate 1” and “Sample Plate 2”. You will split the total sample volume to process across the two plates for each sample.", "[Ceres Nanosciences Nanotrap® KingFisher™ Procedure] Aliquot 10 µL of Bovine Res... |
75,376 | DNA Barcoding Standard Operating Protocol, Plants and Lichens at RBGE, Lab methods: DNA extraction | 1 | null | https://www.protocols.io/view/dna-barcoding-standard-operating-protocol-plants-a-cmuqu6vw | Laura L Forrest, Rebecca Yahr, Michelle Hart | TITLE: DNA Barcoding Standard Operating Protocol, Plants and Lichens at RBGE, Lab methods: DNA extraction
AUTHORS: Laura L Forrest, Rebecca Yahr, Michelle Hart
[DESCRIPTION]
This is part of the collection DToL Taxon-specific Standard Operating Procedures for the Plant Working Group (protocols.io). The SOP collection c... | ["[DNA extraction (Qiagen DNeasy plant mini kits)] Sampling. \n\nPlant DNA barcoding for the Darwin Tree of Life (DToL) project involves extraction of DNA from silica gel dried tissue that has been provided, along with the required metadata, following the collecting and submission SOPS available in the collection DToL... |
null | null | null | dx.doi.org/10.17504/protocols.io.c8czsv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Supplement to seawater for growth of cyanobacteria.
[GUIDELINES]
Matt suggested higher concentrations of NaH2PO4-H2O so only need to use 0.5 ml per 1 L seawater:<br />0.1 M NaH<sub>2</sub>PO<sub>4</sub>-H2O 0.345g/25ml or 1.38g/100ml<br />Use 500µl per 1L seawater
[STEPS]
?.... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.rt3d6qn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The anecdotal evidence is outstanding on the uses of <em>Aristolochia</em> plants as traditional medicines and dietary supplements in many regions of the world. However, herbal materials derived from <em>Aristolochia</em> species have been identified as potent human carcinoge... | [] |
50,510 | Expression and purification protocol of WIPI2d | 1 | dx.doi.org/10.17504/protocols.io.bvjnn4me | https://www.protocols.io/view/expression-and-purification-protocol-of-wipi2d-bvjnn4me | Chunmei Chang | TITLE: Expression and purification protocol of WIPI2d
AUTHORS: Chunmei Chang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details the expression and purification protocol of WIPI2d.</div></div>
[STEPS]
?. [Protein expression]
Transfect the DNA in cells using polyethylenimine (Poly... | ["[Protein expression]\nTransfect the DNA in cells using polyethylenimine (Polysciences).", "[Protein expression]\nAfter 48- to 72-hour expression, harvest the cells.", "[Protein purification]\nFollow the Strep-Tactin batch purification by Size Exclusion Chromatography.", "[Protein purification]\nIncubate the supernata... |
50,618 | Expression and purification protocol of ULK1 Complex wt or K46I mutant | 4 | dx.doi.org/10.17504/protocols.io.bvn2n5ge | https://www.protocols.io/view/expression-and-purification-protocol-of-ulk1-compl-bvn2n5ge | Xiaoshan Shi | TITLE: Expression and purification protocol of ULK1 Complex wt or K46I mutant
AUTHORS: Xiaoshan Shi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The Protocol describes the expression and purification of ULK1 Complex wt or K46I mutant.</div></div>
[STEPS]
?. [1- Protein expression:]
ULK1 and FIP2... | ["[1-\tProtein expression:]\nULK1 and FIP200/ATG13/ATG101 are transfected and expressed separately. Transfect DNA in cells at a concentration of 2.5–3 × 106/mL using polyethylenimine (Polysciences) and harvest after expression. Resuspend cells in PBS and harvest them by pelleting at for at , wash them with PBS once,... |
27,342 | Vandy - Mouse Blood Pressure Telemetry | null | dx.doi.org/10.17504/protocols.io.6xnhfme | null | Lin Zhong, Chee Lim | TITLE: Vandy - Mouse Blood Pressure Telemetry
AUTHORS: Lin Zhong, Chee Lim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">Imlantable radiotelemetry devices allow for long-term continous monitoring of blood pressure and... | ["Mice are anesthetized with pentobarbital (50 mg/kg, IP).", "The ventral neck and upper dorsum are shaved and disinfected with Betadine and then 70% alcohol.", "The mouse is positioned supineon a heating pad and a 1.5 cm midline incision is made through the skin underlying the trachea.", "The mouse is placed lateral d... |
36,559 | wisniewska_minimal_data_set | null | dx.doi.org/10.17504/protocols.io.bfxpjpmn | https://www.protocols.io/view/wisniewska-minimal-data-set-bfxpjpmn | Kinga Wisniewska | TITLE: wisniewska_minimal_data_set
AUTHORS: Kinga Wisniewska
[STEPS]
?.
?.
?. | [] |
82,665 | Confocal imaging and digital image analysis | 4 | dx.doi.org/10.17504/protocols.io.3byl4jmxzlo5/v1 | https://www.protocols.click/view/confocal-imaging-and-digital-image-analysis-cuyhwxt6 | Hong-Yuan Chu | TITLE: Confocal imaging and digital image analysis
AUTHORS: Hong-Yuan Chu
[DESCRIPTION]
This protocol describes confocal imaging on a Nikon A1R confocal microscope and digital image analysis.
[STEPS]
SECTION: Confocal imaging on a Nikon A1R confocal microscope
1. Turn on the power of laser, microscope, and computer.
... | ["[Confocal imaging on a Nikon A1R confocal microscope] Turn on the power of laser, microscope, and computer.", "[Confocal imaging on a Nikon A1R confocal microscope] Open the NIS-Elements AR software.", "[Confocal imaging on a Nikon A1R confocal microscope] Set lightpath to Eyepiece to locate brain slice under 10x len... |
null | null | null | dx.doi.org/10.17504/protocols.io.ccrsv5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
hMSC Basal Media
[STEPS]
?.
?.
?.
?.
?. | [] |
38,616 | Water Filtration with Peristaltic Pump or Syringe & DNA Preservation | 1 | dx.doi.org/10.17504/protocols.io.bhxyj7pw | https://www.protocols.io/view/water-filtration-with-peristaltic-pump-or-syringe-bhxyj7pw | Annette Engel, Audrey Paterson, Hannah Rigoni | TITLE: Water Filtration with Peristaltic Pump or Syringe & DNA Preservation
AUTHORS: Annette Engel, Audrey Paterson, Hannah Rigoni
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Cells, particulates, and fine sediment (i.e., clay) in water are retained on filters during filtration. Filtered water ca... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.s9ueh6w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>How to run MASH version (<a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x" target="_blank" rel="noopener noreferrer">Ondov <em>et al.</em> 2016</a>) through the <a href="https://www.imicrobe.us/" target="_blank" rel="noopener noreferrer">iM... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.vhde326 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Objective: To feed individual house flies a specific amount of bacteria in order to
determine bacteria “fate” (persistence, via enumeration; spatiotemporal location, via
microscopy) and house fly immune response (whole fly or tissue-specific, via downstream mRNA or protein expre... | ["[Preparing House Flies for Bacterial Feeding] {\"blocks\":[{\"key\":\"3g659\",\"text\":\"Collect pupae from colony and surface sanitize for 2 minutes each with gentle swirling in 10% bleach, sterile H2O, 100% ethanol, sterile\\u00a0H2O. \",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[{\"offset\":111,\"len... |
63,375 | k1 keto- ALERT - WHAT NO ONE TELLS YOU! | 1 | dx.doi.org/10.17504/protocols.io.14egn7jbyv5d/v1 | https://www.protocols.io/view/k1-keto-alert-what-no-one-tells-you-b95pr85n | MarcChipman , Subgenix Keto | TITLE: k1 keto- ALERT - WHAT NO ONE TELLS YOU!
AUTHORS: MarcChipman , Subgenix Keto
[DESCRIPTION]
| Get The bottle Home And Enjoy its Effective Working Of it | Order Now To Get the Best Results |
How Does Ketosis Work?
Ketosis is a metabolic condition in which fat replaces carbs as a source of energy. Carbohydrates... | [] |
66,342 | ProDentim Reviews 2022 - Does It Really Work Or Scam? | 3 | dx.doi.org/10.17504/protocols.io.36wgq7z73vk5/v1 | https://www.protocols.io/view/prodentim-reviews-2022-does-it-really-work-or-scam-cc2esybe | Ritarbritton | TITLE: ProDentim Reviews 2022 - Does It Really Work Or Scam?
AUTHORS: Ritarbritton
[DESCRIPTION]
ProDentim is an oral wellbeing supplement explicitly made to assist with advancing the oral cleanliness, forestall different gum sicknesses, keep a high populace of good microbes in your mouth and keep your mouth and in ... | [] |
54,043 | Transformation of E. coli with plasmid | 4 | dx.doi.org/10.17504/protocols.io.byz3px8n | https://www.protocols.io/view/transformation-of-e-coli-with-plasmid-byz3px8n | sanjana | TITLE: Transformation of E. coli with plasmid
AUTHORS: sanjana
[DESCRIPTION]
This protocol can be used to transform electrocompetent E. coli cells with a plasmid.
[STEPS]
SECTION: Preparation
1. Wash cuvette with 100 % (v/v) ethanol and UV in the hood for 20 min
SECTION: Preparation
2. Pre-thaw electrocompeten... | ["[Preparation] Wash cuvette with 100 % (v/v) ethanol and UV in the hood for 20 min", "[Preparation] Pre-thaw electrocompetent cells and plasmid on wet ice for 10 min", "[Electroporation] Add 1 µL of plasmid DNA to 50 µL electrocompetent cells", "[Electroporation] Transfer cell-DNA mixture into the cuvette and add equ... |
null | null | null | dx.doi.org/10.17504/protocols.io.dfq3mv | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<strong>Primers</strong> (Filée et al, 2005)<strong>:</strong><br /><br />MZIA1bis primer F: GAT ATT TGI GGI GTT CAG CCI ATG A<br />MZIA6 primer R: CGC GGT TGA TTT CCA GCA TGA TTT C<br /><br /><strong>Reaction Mix</strong> (using LA Takara)<strong>:</strong><br... | [] |
96,830 | MycoEd Lab: CU Denver Protocols | 0 | dx.doi.org/10.17504/protocols.io.261ge5pojg47/v1 | https://www.protocols.io/view/mycoed-lab-cu-denver-protocols-das62ehe | Andrew W. Wilson, sara.branco | TITLE: MycoEd Lab: CU Denver Protocols
AUTHORS: Andrew W. Wilson, sara.branco
[DESCRIPTION]
These lab protocols were written for the Fall 2023 Mycology course at University of Colorado Denver, Department of Integrative Biology instructed by Sara Branco and Andrew Wilson. The course is designed to guide students throug... | [] |
59,410 | Workflow for bulk RNAseq of human placenta | 1 | dx.doi.org/10.17504/protocols.io.b59sq96e | https://www.protocols.io/view/workflow-for-bulk-rnaseq-of-human-placenta-b59sq96e | Scott Lindsay-Hewett, Valentina Stanley, Mana Parast, Louise Laurent | TITLE: Workflow for bulk RNAseq of human placenta
AUTHORS: Scott Lindsay-Hewett, Valentina Stanley, Mana Parast, Louise Laurent
[DESCRIPTION]
Described here is the workflow used by the Female Reproductive Tissue Mapping Center at UCSD to generate RNAseq data from human placenta.
[STEPS]
SECTION: Tissue preparat... | ["[Tissue preparation] As soon as possible after Cesarean section or vaginal delivery, prepare tissue according to the following protocol:\n\nHuman Placenta Tissue Collection and Preservation Methods - UCSD Female Reproductive TMC\n\nFor this protocol, use tissue that has been stored in RNAlater.", "[Total RNA isolatio... |
41,104 | Dry Tissue sampling and DNA extraction with NEB monarch Kit | 4 | null | https://www.protocols.io/view/dry-tissue-sampling-and-dna-extraction-with-neb-mo-bkdqks5w | Alexander Bradshaw | TITLE: Dry Tissue sampling and DNA extraction with NEB monarch Kit
AUTHORS: Alexander Bradshaw
[STEPS]
?. [Tissue Sampling and Physical tissue disruption]
Flame sterilize a pair of fine-tip forceps in 70% ethanol
?. [Tissue Sampling and Physical tissue disruption]
With the sterilized forceps remove and weigh 10-15mg ... | ["[Tissue Sampling and Physical tissue disruption]\nFlame sterilize a pair of fine-tip forceps in 70% ethanol", "[Tissue Sampling and Physical tissue disruption]\nWith the sterilized forceps remove and weigh 10-15mg of Hymenium tissue into a bead bashing tube with a conical bottom (our bead beater cannot hold flat bott... |
42,298 | Solutions for CFPS (Version 1.1)- Haseloff Lab | 4 | null | https://www.protocols.io/view/solutions-for-cfps-version-1-1-haseloff-lab-bmi2k4ge | Fernando Guzman Chavez, Jim Haseloff | TITLE: Solutions for CFPS (Version 1.1)- Haseloff Lab
AUTHORS: Fernando Guzman Chavez, Jim Haseloff
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify">This protocol details the procedures for the preparation of individual cell-free protein synthesis (... | ["[1: Preparing Magnesium Glutamate Solution]\nThe following protocol describes the preparation of 22 mLof 1000 mM magnesium glutamate solution. Magnesium glutamate is kept as a separate addition because the magnesium concentration for maximum protein production varies from one lot of cell extract to another. The typic... |
79,566 | Viruses identification in metagenomes | 5 | dx.doi.org/10.17504/protocols.io.36wgqjk43vk5/v1 | https://www.protocols.io/view/viruses-identification-in-metagenomes-crxnv7me | Remi Denise | TITLE: Viruses identification in metagenomes
AUTHORS: Remi Denise
[DESCRIPTION]
This protocol shows how to use this virus identification workflow (doi: 10.5281/zenodo.7778392) and some manual curation criteria for viral sequence identification in metagenomes.
[BEFORE_START]
This tutorial requires Unix OS with "conda... | ["[Install dependencies and prep test data] Install dependencies\n\nWe need the following three tools for this SOP:\nsnakemake (version >= 7.25.0)\nsnakedeploy (version >= 0.8.6)\n\nFirst lets install mamba:\n\n \n\nSecond lets create new conda environment using mamba for this tutorial:\n\n \n\nNote: When you install t... |
57,133 | A validated protocol to UV-inactivate SARS-CoV-2 and herpesvirus-infected cells | 4 | dx.doi.org/10.17504/protocols.io.81wgb676qlpk/v1 | https://www.protocols.io/view/a-validated-protocol-to-uv-inactivate-sars-cov-2-a-b32mqqc6 | 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... | ["[Harvest cells]", "[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 i... |
null | null | null | dx.doi.org/10.17504/protocols.io.k73czqn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>VLP RT-qPCR</p>
[STEPS] | [] |
100,090 | Clinical features and management of VEXAS syndrome in critical care: a scoping review protocol | 0 | dx.doi.org/10.17504/protocols.io.14egn621ql5d/v1 | https://www.protocols.io/view/clinical-features-and-management-of-vexas-syndrome-ddy227ye | Kasumi Satoh, Yasushi Tsujimoto, Daisuke Kasugai, Kazuki Okura, Takao Ono, Yuki Miyamoto, Tasuku Matsuyama, Taketo Watase, Hajime Nakae, Tadahiro Goto | TITLE: Clinical features and management of VEXAS syndrome in critical care: a scoping review protocol
AUTHORS: Kasumi Satoh, Yasushi Tsujimoto, Daisuke Kasugai, Kazuki Okura, Takao Ono, Yuki Miyamoto, Tasuku Matsuyama, Taketo Watase, Hajime Nakae, Tadahiro Goto
[DESCRIPTION]
Objective: This study aims to understand th... | ["[Introduction] Vacuoles, E1 enzyme, X-linked, Autoinflammatory, Somatic (VEXAS) syndrome is an acquired autoinflammatory disorder that primarily affects men over 50 years of age and was identified in 2020 as a new disease concept associated with mutations in the Ubiquitin-like modifier activating enzyme 1 (UBA1) gene... |
null | null | null | dx.doi.org/10.17504/protocols.io.gitbuen | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 1">
<div class="layoutArea">
<div class="column">Highlights<br />
<ul>
<li>
<p>Quick (15 minute) high-yield recovery of ultra-pure DNA from agarose gels.</p>
</li>
<li>
<p>Column design permits DNA elution at high concentrations into minimal volumes... | [] |
92,708 | Generating Non-English IATs and Collecting Offline Samples | 5 | dx.doi.org/10.17504/protocols.io.kxygx34jdg8j/v1 | https://www.protocols.io/view/generating-non-english-iats-and-collecting-offline-c6sczeaw | João Oliveira Santos, Emerson Araújo Do Bú, Tomohiro Hara, Cristina Mendonça, Sara Hagá, Ruth Pogacar, Michal Kouril | TITLE: Generating Non-English IATs and Collecting Offline Samples
AUTHORS: João Oliveira Santos, Emerson Araújo Do Bú, Tomohiro Hara, Cristina Mendonça, Sara Hagá, Ruth Pogacar, Michal Kouril
[DESCRIPTION]
This protocol describes tools to: a) create non-English IATs using iatgen and R, b) build the repository of trans... | [] |
95,334 | ht-HiTE: High-Throughput DNA extraction from FFPE tissue | 1 | dx.doi.org/10.17504/protocols.io.6qpvr3jr3vmk/v1 | https://www.protocols.io/view/ht-hite-high-throughput-dna-extraction-from-ffpe-t-c9cez2te | Christoph Geisenberger | TITLE: ht-HiTE: High-Throughput DNA extraction from FFPE tissue
AUTHORS: Christoph Geisenberger
[DESCRIPTION]
This protocols outlines a high-throughput method for DNA extraction from FFPE material. The workflow has been automated on a Biomek i5 platform. 1 to 2 tissue scrolls (10 µm) or tissue macrodissected from glas... | ["[Preparation] Each well of a DNA lo-bind 96 deep-well plates is pre-loaded with 500 µl of mineral oil", "[Preparation] From each FFPE block, 1 thin section (2 µM) and 2 to 4 thicker sections (10 µM) are placed on glass slides. Thin sections are stained with hematoxylin and eosin (H&E) and used to select and mark regi... |
85,467 | Core Genome Multilocous Sequence Typing Development Workflow | 5 | dx.doi.org/10.17504/protocols.io.4r3l22o64l1y/v1 | https://www.protocols.io/view/core-genome-multilocous-sequence-typing-developmen-cxp3xmqn | made.krisna, William Monteith, odile.harrison, Martin C. J. Maiden | TITLE: Core Genome Multilocous Sequence Typing Development Workflow
AUTHORS: made.krisna, William Monteith, odile.harrison, Martin C. J. Maiden
[DESCRIPTION]
Core genome MLST (cgMLST) is a high-resolution typing approach that enables the evaluation of bacterial
population structure for research and public health-relat... | ["[Developing a computational pipeline for pangenome analysis tools using complete, reference genomes] Pangenome analysis 1: PIRATE (Pangenome Iterative Refinement and Threshold Evaluation)\n\n GFF file from annotation step using Prokka\n\nSoftware:\n \nCommand:\n \n\nKey output file: \n \nAlso available as csv file."... |
21,011 | UC Davis - Maximum passive stiffness (MPS) | null | dx.doi.org/10.17504/protocols.io.yrtfv6n | null | John Rutledge | TITLE: UC Davis - Maximum passive stiffness (MPS)
AUTHORS: John Rutledge
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">One index of arterial function that is compromised to a varying degree in individuals with cardi... | ["Mice are anesthetized with an intraperitoneal injection with 50 mg pentobarbital/kg weight.", "Either common carotid arteries or aorta are dissected as described in Macrovascular Permeability and Lipoprotein Flux protocol. Artery explants can be: a. Immediately utilized for analysis of vascular stiffness b. Stored in... |
54,390 | Agarose gel electrophoresis | 1 | null | https://www.protocols.io/view/agarose-gel-electrophoresis-bzcwp2xe | Yuichiroh Ikagawa | TITLE: Agarose gel electrophoresis
AUTHORS: Yuichiroh Ikagawa
[DESCRIPTION]
Electrophoresis is the most basic technique for identifying DNA amplified by PCR or restriction enzyme treatment. Agarose gels are used to separate the DNA by molecular weight. Here we describe the technique using a 1.5 % agarose gel.
[STEPS... | ["Weigh out 0.75 g of agarose powder and add it to the triangular flask.", "Add 49 ml of sterile water to the first flask and shake gently.", "Add 1 ml x50 TAE buffer to the flask and heat in the microwave.", "Allow the melted agarose to cool for 5 minutes before pouring it into a template set with a comb.", "Cover wit... |
36,580 | Hydrochloric Acid-Potassium Chloride Buffer (HCl-KCl) | null | dx.doi.org/10.17504/protocols.io.bfycjpsw | https://www.protocols.io/view/hydrochloric-acid-potassium-chloride-buffer-hcl-kc-bfycjpsw | Neilier Junior | TITLE: Hydrochloric Acid-Potassium Chloride Buffer (HCl-KCl)
AUTHORS: Neilier Junior
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A buffer solution has the function of resisting changes in pH even when adding powerful acids or bases. However, in the physiological environment the buffered system a... | ["[Hydrochloric Acid-Potassium Chloride Buffer (HCl-KCl)]\nMix and indicted volume of hydrochloric acid.\npH Range: to (a) 0.1 M Potassium chloride: 7.45 g L-1 (M.W.: 74.5 g mol-1)(b) 0.1 M Hydrochloric acid\n[potassium chloride]", "[Hydrochloric Acid-Potassium Chloride Buffer (HCl-KCl)]\nMix and adjust the final v... |
null | null | null | dx.doi.org/10.17504/protocols.io.ja3cign | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is to further process the sequences generated from ICE and Quiver.</p>
[BEFORE_START]
<p>Raw data from Pacbio Iso-Seq needs to be processed with RS IsoSeq (version 2.3) pipeline.</p>
[GUIDELINES]
<p><strong>Remove of the detected contaminant sequences</strong>... | [] |
50,695 | A General Guide To Generate Different Humanized Mouse Models | 4 | dx.doi.org/10.17504/protocols.io.bvrfn53n | https://www.protocols.io/view/a-general-guide-to-generate-different-humanized-mo-bvrfn53n | Mohsen Khosravi-Maharlooei, Markus Holzl, Austin Chen, Megan Sykes | TITLE: A General Guide To Generate Different Humanized Mouse Models
AUTHORS: Mohsen Khosravi-Maharlooei, Markus Holzl, Austin Chen, Megan Sykes
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol details how to create humanized mouse models from NSG mice. Four different variants of h... | ["NOD-scid common gamma chain knockout (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) (NSG) and NSG-(Kb Db)null (IA)null(NSG MHC KO) mice are obtained from the Jackson Laboratory or bred in-house and housed in a specific pathogen-free microisolator environment. Adult mice are used at 6–10 wk of age.", "Discarded human fetal thymus... |
68,588 | Using polyan: a Python package for modelling polysome profiles from ribosome density data | 5 | dx.doi.org/10.17504/protocols.io.5jyl8mz28g2w/v4 | https://www.protocols.io/view/using-polyan-a-python-package-for-modelling-polyso-ce8kthuw | Tobias von der Haar | TITLE: Using polyan: a Python package for modelling polysome profiles from ribosome density data
AUTHORS: Tobias von der Haar
[DESCRIPTION]
The assessment of transcriptome-wide ribosome binding to mRNAs is useful for studying the dynamic regulation of protein synthesis in living cells. Two methods frequently applied i... | ["[General Functionality] polyan accompanies a publication by Hedayioglu et al. (2022), Evaluating data integrity in ribosome footprinting datasets through modelled polysome profiles . \n\npolyan provides Python functions for modelling polysome profiles from input data on transcript abundance and ribosome occupancy of ... |
94,904 | SEM-EDS Protocol V1 | 1 | dx.doi.org/10.17504/protocols.io.5jyl8p7odg2w/v1 | https://www.protocols.io/view/sem-eds-protocol-v1-c8wyzxfw | Saylen Sofia Paz, David Bahamon-Pinzon, Dvanega | TITLE: SEM-EDS Protocol V1
AUTHORS: Saylen Sofia Paz, David Bahamon-Pinzon, Dvanega
[DESCRIPTION]
This protocol outlines the methodology for conducting Scanning Electron Microscopy (SEM) and Energy-Dispersive X-ray Spectroscopy (EDS) analysis of laser-inscribed graphene (LIG) electrodes using a SU5000 microscope. The ... | ["[Procedure] Step 1) Turn on the computer and equipment screens\nLogin from any device with internet access to iLab's website (iLabFacilityScheduling (clemson.edu))\nLog into your account\nClick on the start button \nNote: Automatically, the screens of the equipment will turn on (Figure 2)", "[Procedure] Step 2) Prepa... |
80,913 | Retrieving SSH Journals Citation Information from three datasets (COCI, META and ERIH-PLUS) - Workflow | 5 | dx.doi.org/10.17504/protocols.io.n92ldpeenl5b/v2 | https://www.protocols.io/view/retrieving-ssh-journals-citation-information-from-cs9rwh56 | Marta Soricetti, Sara Vellone, Olga Pagnotta, Lorenzo Paolini | TITLE: Retrieving SSH Journals Citation Information from three datasets (COCI, META and ERIH-PLUS) - Workflow
AUTHORS: Marta Soricetti, Sara Vellone, Olga Pagnotta, Lorenzo Paolini
[DESCRIPTION]
Purpose
The main purpose of our research is to answer to three different question and find out:
by looking at citations dat... | ["[Processing of Input Data] We tried to define a mapping of the datasets to understand which are the information that the three datasets have in common. By looking at the data and the column names, we have identified the following:\n\n \nTaking as a starting point META, we have identified the COCI columns \"citing\" a... |
27,994 | Transformation using Heat-Shock | null | dx.doi.org/10.17504/protocols.io.7j2hkqe | null | Alba Balletbó | TITLE: Transformation using Heat-Shock
AUTHORS: Alba Balletbó
[STEPS]
?. Add plasmid DNA (1 µL of miniprep/2 µL of ligation mixture/...µL of cesium-purified DNA).
?. Incubate on ice for 30 minutes.
?. Heat shock at exactly 42ºC for exactly 1:30 minutes, then chill on ice again for 5 minutes.
?. Culture in 1 mL SOC for... | ["Add plasmid DNA (1 µL of miniprep/2 µL of ligation mixture/...µL of cesium-purified DNA).", "Incubate on ice for 30 minutes.", "Heat shock at exactly 42ºC for exactly 1:30 minutes, then chill on ice again for 5 minutes.", "Culture in 1 mL SOC for 1 hour at 37ºC and pre-warm the agar plates in the meantime.", "Spin th... |
103,798 | Measuring the rate of NADPH consumption by glutathione reductase in the cytosol and mitochondria | 0 | dx.doi.org/10.17504/protocols.io.rm7vzjoy4lx1/v1 | https://www.protocols.io/view/measuring-the-rate-of-nadph-consumption-by-glutath-dhkw34xe | Kenneth Ting, Eric Floro, Riley Dow, Jenny Jongstra-Bilen, Myron Cybulsky, Jonathan Rocheleau | TITLE: Measuring the rate of NADPH consumption by glutathione reductase in the cytosol and mitochondria
AUTHORS: Kenneth Ting, Eric Floro, Riley Dow, Jenny Jongstra-Bilen, Myron Cybulsky, Jonathan Rocheleau
[DESCRIPTION]
Background: NADPH is an essential co-factor supporting the function of enzymes that participate in... | ["[Part I: Transfection of Apollo-NADP+ sensors in RAW264.7 Mφ cell lines] One week prior to nucleofection, passage cells in 15mL of DMEM media supplemented with 10% FBS for every 2-3 days in a T75 tissue culture treated flask.", "[Part I: Transfection of Apollo-NADP+ sensors in RAW264.7 Mφ cell lines] To passage cells... |
28,997 | Capture of Philaenus spumarius and Cicadella viridis | null | dx.doi.org/10.17504/protocols.io.8jdhui6 | null | Niels Appelman | TITLE: Capture of Philaenus spumarius and Cicadella viridis
AUTHORS: Niels Appelman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to capture spittlebugs (Philaenus spumarius) and Green Leafhoppers (Cicadella viridis)</div></div>
[STEPS]
?. It is recommended to familiarize yo... | ["It is recommended to familiarize yourself with the general characteristics of Spittlebugs and Green leafhoppers prior to attempting to capture the insects.", "Find a terrain in your vicinity with short (under 30 cm) herblike plants. No one source can be named, as both species are extremely polyphagous.", "Swipe an in... |
null | null | null | dx.doi.org/10.17504/protocols.io.ecnbave | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<strong>Viral Bioinformatic Resource Centre</strong>
<ul>
<li><strong>Provide databases of viral genomic information.</strong>
<ul>
<li>Please check the <strong><em>Organisms</em></strong> menu to see which viruses we support: we’re now focusing on large DNA viruses</li>
<li>The... | [] |
45,942 | Cell Harvesting Protocol | 4 | null | https://www.protocols.io/view/cell-harvesting-protocol-bq4wmyxe | Elizabeth Fozo | TITLE: Cell Harvesting Protocol
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A general procedure for harvesting bacterial cells for flow cytometry or fluorescence microscopy</div><div class = "text-block">Write up by S. Shore 11/17/2020 based on B. Bogati communications, p... | ["[Procedure]\nDilute the overnight culture to OD600 0.01 and grow cells in an appropriate medium to the desired time point/OD600 in at least 10mL of liquid culture.", "[Procedure]\nHarvest cells directly into pre-labeled falcon tubes (if running flow same-day) or Eppendorf tubes. Once cells have been harvested, minimi... |
21,814 | SYSB 3036 W08: Multi-Sequence Alignment and Phylogenetics | null | dx.doi.org/10.17504/protocols.io.ziwf4fe | null | Frank Aylward | TITLE: SYSB 3036 W08: Multi-Sequence Alignment and Phylogenetics
AUTHORS: Frank Aylward
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Get the data]
First we will download some files from GitHub from a repository called "phylogenetics_tutorial":git clone https://github.com/faylward/phylogenetics_tutorial... | ["[Get the data]\nFirst we will download some files from GitHub from a repository called \"phylogenetics_tutorial\":git clone https://github.com/faylward/phylogenetics_tutorialand then we will move into the new folder and see what files are present:cd phylogenetics_tutorialls -lhYou should see a file called SSU_seqs.fn... |
49,164 | Analysis of Islet Function in Dynamic Cell Perifusion System | 4 | dx.doi.org/10.17504/protocols.io.bt9knr4w | https://www.protocols.io/view/analysis-of-islet-function-in-dynamic-cell-perifus-bt9knr4w | IIDP-HIPP | TITLE: Analysis of Islet Function in Dynamic Cell Perifusion System
AUTHORS: IIDP-HIPP
[DESCRIPTION]
This Standard Operating Procedure (SOP) is based on the Vanderbilt Human Islet Phenotyping Program (HIPP) Islet Functional Analysis. This SOP provides HIPP procedure for dynamic perifusion and hormone secretion measu... | ["[Procedures] General Perifusion Startup", "[Procedures] Fill water bath with deionized water to about 1 inch from the top, and set the temperature to 37 °C .", "[Procedures] Label perifusion tubes with date, islet type, and any other identifying information, position the fraction collector trays for perifusion, and l... |
88,786 | Sample preparation and data collection for Serial Block Face Scanning Electron Microscopy of Mammalian Cell Monolayers | 4 | dx.doi.org/10.17504/protocols.io.e6nvwdz5zlmk/v1 | https://www.protocols.io/view/sample-preparation-and-data-collection-for-serial-c2xsyfne | Noelle Antao, Joseph Sall, Christopher Petzold, Damian C. Ekiert, Gira Bhabha, Feng-Xia Liang | TITLE: Sample preparation and data collection for Serial Block Face Scanning Electron Microscopy of Mammalian Cell Monolayers
AUTHORS: Noelle Antao, Joseph Sall, Christopher Petzold, Damian C. Ekiert, Gira Bhabha, Feng-Xia Liang
[DESCRIPTION]
Serial block face scanning electron microscopy (SBF-SEM) is volume EM techni... | ["[Culturing mammalian cells and sample fixation] Culture adherent mammalian cells for 24 - 48 h in a 60 mm or 100 mm tissue culture dish for cell pellet samples, or 35 mm tissue culture dish with a gridded glass bottom for CLEM samples (final density 3-6 x 105 cells) according to the standard protocol for the cell lin... |
35,042 | Lightsheet Microscope Acquisition Protocol | null | dx.doi.org/10.17504/protocols.io.begajbse | https://www.protocols.io/view/lightsheet-microscope-acquisition-protocol-begajbse | Marda Jorgensen, Seth Currlin | TITLE: Lightsheet Microscope Acquisition Protocol
AUTHORS: Marda Jorgensen, Seth Currlin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The </span><a href="https://www.zeiss.com/microscopy/int/cmp/lsc/20/light-sheet-microscopy/new-zeiss-lightsheet-7.html?utm_medium=cpc&utm_campaign=light-shee... | ["[Refractive Index (R.I.) Matching]\nPrepare 63% TDE, a refractive index matching solutions (RIMS). Prepare a 63% 2,2'-thiodiethanol (TDE) solution, diluted with 1xPBS adjusted to pH 7.2. One can use a refractometer to confirm the target refractive index (R.I.) of n = 1.45. Prepare a volume of solution at least 10 ti... |
null | null | null | dx.doi.org/10.17504/protocols.io.kwmcxc6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><em>Listeria monocytogenes</em> is a bacterial pathogen that enters and proliferates in the cytosol of mammalian cells. Following entry, bacteria disrupt the invasion vacuole and reach the cytoplasm, where they replicate and use the actin cytoskeleton to propel themselves fro... | [] |
44,313 | Capture RBP -RNA Complexes on Beads | 4 | dx.doi.org/10.17504/protocols.io.bphzmj76 | https://www.protocols.io/view/capture-rbp-rna-complexes-on-beads-bphzmj76 | Eric L. Van Nostrand, Thai B. Nguyen, Chelsea Gelboin-Burkhart, Ruth Wang, Steven M. Blue, Gabriel A. Pratt, Ashley L. Louie, Gene W. Yeo | TITLE: Capture RBP -RNA Complexes on Beads
AUTHORS: Eric L. Van Nostrand, Thai B. Nguyen, Chelsea Gelboin-Burkhart, Ruth Wang, Steven M. Blue, Gabriel A. Pratt, Ashley L. Louie, Gene W. Yeo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Profiling of RNA binding protein targets in vivo provides crit... | ["[Couple Antibody to Magnetic Beads (Start During Cell Lysis)]\nUse + per sample.\n[beads]\n[antibody]", "[Prewash Beads]\nMagnetically separate beads, remove the supernatant.", "[Prewash Beads]\nWash beads 2× in .\n[cold lysis buffer]", "[Prewash Beads]\nResuspend beads in .\n[cold lysis buffer]", "[Bind Antibody]\... |
23,800 | Histological Evaluation of Renal Fibrosis in Mice | null | dx.doi.org/10.17504/protocols.io.3gygjxw | null | Daisuke Katagiri, Takamune Takahashi | TITLE: Histological Evaluation of Renal Fibrosis in Mice
AUTHORS: Daisuke Katagiri, Takamune Takahashi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary </span></div><div class = "text-block">This protocol describes a protocol to evaluate histological fibrosis... | ["Tissue stain a. picrosiriusred stain Collagen including collagenand III were stained with the Picrosirius Red Stain kit (Polysciences Inc., PA, US) according to the manufacturers’ protocol.11. Dip in Xylene 5 min x 2 times 2. Dip in 100 % EtOH 5 min x 2 times 3. Dip in 90 % EtOH 5 min 4. Dip in 80 % EtOH 5 min 5.... |
null | null | null | dx.doi.org/10.17504/protocols.io.dqg5tv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
More than 40 years ago, Safferman and Morris (1963) used the plaque assay method to isolate the first cyanophage that infects a freshwater filamentous cyanobacterium, <em>Plectonema boryanum</em>. Since then, this approach has been used successfully to detect and isolate a numbe... | [] |
93,341 | Field Data Collection Protocols for NIJ Grant The Impact of Drugs on Human Decomposition and the Postmortem Interval: Insect, Scavenger and Microbial Evidence | 1 | dx.doi.org/10.17504/protocols.io.3byl4qy2jvo5/v1 | https://www.protocols.io/view/field-data-collection-protocols-for-nij-grant-the-c7d5zi86 | Hayden S. McKee-Zech, Erin A. Patrick, Allison R. Mason, Katha Hoeland, Charity Owings, Sarah T Schwing, Thomas Delgado, Amanda May, Mary C. Davis, Jennifer Debruyn, Shawn Campagna, Dawnie W Steadman | TITLE: Field Data Collection Protocols for NIJ Grant The Impact of Drugs on Human Decomposition and the Postmortem Interval: Insect, Scavenger and Microbial Evidence
AUTHORS: Hayden S. McKee-Zech, Erin A. Patrick, Allison R. Mason, Katha Hoeland, Charity Owings, Sarah T Schwing, Thomas Delgado, Amanda May, Mary C. Dav... | ["[Intake] Photographs - A standard sequence of photographs should be taken at intake for each enrolled donor, including: an overhead view of the exact condition in which the donor arrived, an overhead view with clothing and coverings removed, overhead views of the donor's body in overlapping thirds (head to nipples, ... |
23,278 | Characterization of Aloe Barbadensis Miller Leaves as a Potential Electrical Energy Source with Optimum Experimental Setup Conditions. | null | dx.doi.org/10.17504/protocols.io.2yngfve | null | Chong Peng Lean, Ajay Kumar Singh , Kok Swee Leong | TITLE: Characterization of Aloe Barbadensis Miller Leaves as a Potential Electrical Energy Source with Optimum Experimental Setup Conditions.
AUTHORS: Chong Peng Lean, Ajay Kumar Singh , Kok Swee Leong
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">E... | ["Brush the electrodes surface with sandpaper to remove any contaminant and oxidant. Then, wipe the surfaces with alchohol to further remove any micro-contaminant. Fig 2: Electrodes after been cleaned with sandpaper and alcohol. .", "First, prepare the number of desired electrode pairs, which consist of copper as catho... |
68,337 | Washing Protocol for Intact Proteoform MALDI on Human Kidney | 1 | null | https://www.protocols.io/view/washing-protocol-for-intact-proteoform-maldi-on-hu-ceyrtfv6 | Kevin J. Zemaitis, Dusan Velickovic, Ljiljana.PasaTolic | TITLE: Washing Protocol for Intact Proteoform MALDI on Human Kidney
AUTHORS: Kevin J. Zemaitis, Dusan Velickovic, Ljiljana.PasaTolic
[DESCRIPTION]
Scope:
A detailed protocol entailing the sample washing protocols developed for human kidney, this includes several timed washing steps for fixing the tissue, removing smal... | ["[Preparation] While the tissue is within the vacuum desiccator, pour all necessary solvents and solutions into the Coplin jar. These have a volume of approximately 75 mL and to reduce the variability in extraction fill the jars consistently.", "[Tissue fixation wash] Submerge the tissue section within a Coplin jar fi... |
54,759 | Metabolomics Preparation and Analysis | 4 | dx.doi.org/10.17504/protocols.io.bzqfp5tn | https://www.protocols.io/view/metabolomics-preparation-and-analysis-bzqfp5tn | Bryan Yoo, Jessica Griffiths, Sarkis Mazmanian | TITLE: Metabolomics Preparation and Analysis
AUTHORS: Bryan Yoo, Jessica Griffiths, Sarkis Mazmanian
[DESCRIPTION]
Protocol for metabolomics used in Yoo et al 2021
[STEPS]
SECTION: Sample Preparation
1. AAV-PHP.S:hSYN1-hM3Dq-mRuby2 (1012VGs) was delivered systemically to TH-Cre and ChAT-Cre mice. 3-4 week after in... | ["[Sample Preparation] AAV-PHP.S:hSYN1-hM3Dq-mRuby2 (1012VGs) was delivered systemically to TH-Cre and ChAT-Cre mice. 3-4 week after infection, C21 (3mg/kg) was administered daily for 10 consecutive days.", "[Sample Preparation] The samples were weighed out and an extraction solvent (1:1 methanol to water with an inter... |
71,819 | MAD4HatTeR | 4 | dx.doi.org/10.17504/protocols.io.14egn779mv5d/v3 | https://www.protocols.io/view/mad4hatter-cidjua4n | Andres Aranda-Diaz, eric.neubauervickers | TITLE: MAD4HatTeR
AUTHORS: Andres Aranda-Diaz, eric.neubauervickers
[DESCRIPTION]
This protocol has been adapted from Paragon Genomics CleanPlex® NGS Panel
Information about the primer pools can be found here
[STEPS]
SECTION: mPCR
2. Add DNA
SECTION: mPCR
3. Run PCR reaction on a thermocycler (in a separate room... | ["[mPCR] Add DNA", "[mPCR] Run PCR reaction on a thermocycler (in a separate room)\nInitial denaturation: 95 °C 10 min \nDenaturation: 98 °C 15 s with ramping 3 °C \nAnnealing/Extension: 60 °C 5 min with ramping 2 °C \nRepeat Denaturation and Annealing/Extension for X total cycles (see below). \n \nHold at 10 °C", "[Re... |
88,747 | HTTM : Transposon mutagenesis | 4 | dx.doi.org/10.17504/protocols.io.36wgq72n3vk5/v3 | https://www.protocols.io/view/httm-transposon-mutagenesis-c2wjyfcn | Antoine Champie, Amélie De Grandmaison | TITLE: HTTM : Transposon mutagenesis
AUTHORS: Antoine Champie, Amélie De Grandmaison
[DESCRIPTION]
Part of the HTTM protocol dedicated to the transposon mutagenesis of targets cells.
The last step in this version contains a supplemental video with extra context and tips, as part of the protocols.io Spotlight series... | ["[Day 1] (1-A) Make a 15 mL LB (Diaminopimelic acid [Dap], Ampicillin [Amp], Spectinomycin [Spec]) pre-culture ( 2 mL per plate minimum) of the donor strain eAC494 and incubate with agitation at 37 °C overnight.", "[Day 1] (1-B) Prepare the 96 deep-well plates for conjugation :", "[Day 1] Preheat the deep-well plates ... |
34,816 | Suitability Map of COVID-19 Virus Spread | null | dx.doi.org/10.17504/protocols.io.bd88i9zw | null | Gianpaolo Coro | TITLE: Suitability Map of COVID-19 Virus Spread
AUTHORS: Gianpaolo Coro
[DESCRIPTION]
<div class = "text-blocks"><div style = "text-align :; float : ;"><img style = "" src = "https://s3.amazonaws.com/protocols-files/public/d24555ea6537eeef4db42c4aa461f4a348d6f4fd099a232a2c61450ea74c051a/b27z7vcw.png" /></div><div clas... | [] |
34,617 | Making your own electrocompetent cells | 1 | dx.doi.org/10.17504/protocols.io.bd2zi8f6 | https://www.protocols.io/view/making-your-own-electrocompetent-cells-bd2zi8f6 | New England Biolabs | TITLE: Making your own electrocompetent cells
AUTHORS: New England Biolabs
[DESCRIPTION]
This protocol explains methods for making two 250 ml cultures of electrocompetent cells.
An Electroporation Protocol can be found here.
[BEFORE_START]
Sterile 10 % (can be autoclaved) is needed for the washes. The volume of ... | ["Innoculate 1 colony from a fresh plate of the strain to be made electrocompetent into 10 mL in a 125 ml flask.", "Incubate for 16-18 hours at 37 °C and 250 rpm.", "Pre-warm two 1 L flasks containing 250 mL pre-warmed to 37 °C.", "Add two drops of the overnight culture to each of the pre-warmed 250 ml flasks.", "Place... |
65,036 | Cell lysis and gel electrophoresis for protein analysis of HeLa cells (Provisional unformatted) | 4 | null | https://www.protocols.io/view/cell-lysis-and-gel-electrophoresis-for-protein-ana-cbrksm4w | OLIVIA HARDING, holzbaur | TITLE: Cell lysis and gel electrophoresis for protein analysis of HeLa cells (Provisional unformatted)
AUTHORS: OLIVIA HARDING, holzbaur
[DESCRIPTION]
Here, we present multiple protocols used for biochemical analysis of protein expression and association. First, we used a simple lysis technique to determine the ef... | ["- This protocol was developed to analyze protein expression and enrichment in cell culture, including HeLa-M cells and HeLa p62-/- cells", "- Option 2 was modified from a protocol used in Turco et al, Molec. Cell, 2019", "- Option 3 was modificed from a protocol used in Wurzer et al, eLife, 2015 Ma... |
null | null | null | dx.doi.org/10.17504/protocols.io.nv2de8e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p> Purpose of this overview is to isolate and clone genes of interest into an appropriate plasmid and then introduce the recombinant DNA molecule into E. coli</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?. | [] |
60,094 | MWP5 Final Project: 5 findability opportunities to access the portfolio dataset | 1 | dx.doi.org/10.17504/protocols.io.x54v9yr2qg3e/v1 | https://www.protocols.io/view/mwp5-final-project-5-findability-opportunities-to-b6w6rfhe | Anastasiia Iarkaeva | TITLE: MWP5 Final Project: 5 findability opportunities to access the portfolio dataset
AUTHORS: Anastasiia Iarkaeva
[DESCRIPTION]
This protocol was created as part of the Information Science Master's program project MWP5 Digital Information Management at the Humboldt University of Berlin.
It aims to help a potentia... | ["[DOI] Use the DOI to directly access the dataset.", "[PubMed Central] Searching via PubMed Central with the keywords “pubmed literature model” you will hit the data descriptor article as the first result.", "[Figshare] Use figshare repository where the data is located to find the dataset.\n\nFor that, open the reposi... |
null | null | null | dx.doi.org/10.17504/protocols.io.t5deq26 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Transcripts focus group interviews
[STEPS]
?. | ["null"] |
21,805 | Key protocols for chromosome-level genome assembly of the Scapharca (Anadara) broughtonii. | null | dx.doi.org/10.17504/protocols.io.zimf4c6 | null | Chang-Ming Bai, Lu-Sheng Xin, Umberto Rosani, Biao Wu, Qing-Chen Wang, Xiao-Ke Duan, Zhi-Hong Liu, Chong-Ming Wang | TITLE: Key protocols for chromosome-level genome assembly of the Scapharca (Anadara) broughtonii.
AUTHORS: Chang-Ming Bai, Lu-Sheng Xin, Umberto Rosani, Biao Wu, Qing-Chen Wang, Xiao-Ke Duan, Zhi-Hong Liu, Chong-Ming Wang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bol... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.rg9d3z6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A real-time PCR to broadly detect Rickettsia species DNA. This method has been adapted from a publication by Jiang et al 2012, and the oligonucleotides have been modified and a different PCR kit used.</p>
[GUIDELINES]
<ul>
<li>If using a different brand or model of real-tim... | [] |
63,333 | K1 Keto Life Reviews : Expert Opinions & Legit Reviews! | 1 | dx.doi.org/10.17504/protocols.io.81wgb6qj3lpk/v1 | https://www.protocols.io/view/k1-keto-life-reviews-expert-opinions-amp-legit-rev-b94dr8s6 | roxyhiml | TITLE: K1 Keto Life Reviews : Expert Opinions & Legit Reviews!
AUTHORS: roxyhiml
[DESCRIPTION]
➢ Product Name ⮞K1 Keto Reviews
➢ Composition ⮞Natural Organic Compound
➢ Side-Effects ⮞ NA
➢ Availability ⮞ Online
➢ Rating ⮞⭐⭐⭐⭐⭐
➢ Official Website⮞>>>K1KetoLife.com
➤ Price (for Sale) Buy Now Here
➤ Price (for Sale... | ["[K1 Keto Life Reviews] K1 Keto Reviews is an effective weight-loss supplement. It was developed as a consequence of extensive research and expert knowledge. Its formula contains nutrients, minerals, and other elements required for optimal physiological function.\n\nK1 Keto Reviews is a premium supplement that causes ... |
38,044 | Viral enrichment from wastewater samples | 4 | null | https://www.protocols.io/view/viral-enrichment-from-wastewater-samples-bhd4j28w | Iraola Lab | TITLE: Viral enrichment from wastewater samples
AUTHORS: Iraola Lab
[STEPS]
?. Wastewater samples are centrifuged at to remove debris
Centrifuge: 4500 33, 10 min, 4 10
Volume processed depends on user preferences and equipment. For information on sampling, check our previous protocol : Sampling and viral concentra... | ["Wastewater samples are centrifuged at to remove debris\nCentrifuge: 4500 33, 10 min, 4 10\nVolume processed depends on user preferences and equipment. For information on sampling, check our previous protocol : Sampling and viral concentration for SARS-CoV-2 detection in wastewater", "The supernatant is then filter... |
101,073 | Twist2 Snap Frozen Skeletal Muscle IF | 0 | null | https://www.protocols.io/view/twist2-snap-frozen-skeletal-muscle-if-dexr3fm6 | Griffen Wakelin | TITLE: Twist2 Snap Frozen Skeletal Muscle IF
AUTHORS: Griffen Wakelin
[DESCRIPTION]
This protocol details Twist2 immunofluorescent staining of fresh frozen mouse skeletal muscle.
[BEFORE_START]
Collect fresh muscle according to institution-specific guidelines and snap freeze in liquid nitrogen-cooled 2-methylbutane. ... | ["[Day 1] Thaw slides, dry for 30 mins, surround sections with , and label", "[Day 1] Fix with ice-cold 4 % (v/v) for 5 min", "[Day 1] Wash three times with 1X PBS for 5 min", "[Day 1] Permeabilize with 0.2 % (v/v) for 10 min", "[Day 1] Wash three times with 1X PBS for 5 min", "[Day 1] Block with 5 Mass / % volu... |
48,782 | SubARTIC ONT SARS-CoV-2 Spike sequencing protocol (LoCost) V3.2 | 1 | dx.doi.org/10.17504/protocols.io.btvnnn5e | https://www.protocols.io/view/subartic-ont-sars-cov-2-spike-sequencing-protocol-btvnnn5e | Paul J Parsons, Gavin Horsburgh, Kathryn Maher, Steve Paterson, Terry Burke | TITLE: SubARTIC ONT SARS-CoV-2 Spike sequencing protocol (LoCost) V3.2
AUTHORS: Paul J Parsons, Gavin Horsburgh, Kathryn Maher, Steve Paterson, Terry Burke
[DESCRIPTION]
This protocol describes a procedure for sequencing the Spike gene of SARS-CoV-2 using short amplicons (146-208bp) with Oxford Nanopore ... | ["[cDNA preparation] Prepare between 11 and 23 RNA samples plus a negative control (nuclease-free water) per library. If previously frozen, mix by briefly flicking and pulse spin to collect liquid. Keep samples on ice at all times.", "[cDNA preparation] Mix the following components in PCR strip-tubes/plate. Gently mix ... |
105,022 | Brain Tissue Samples and Mitochondrial extracts Samples Western Blot | 0 | dx.doi.org/10.17504/protocols.io.x54v92z2ql3e/v1 | https://www.protocols.io/view/brain-tissue-samples-and-mitochondrial-extracts-sa-dis64ehe | Livia Hecke Morais | TITLE: Brain Tissue Samples and Mitochondrial extracts Samples Western Blot
AUTHORS: Livia Hecke Morais
[DESCRIPTION]
Brain Tissue Samples and Mitochondrial extracts Samples Western Blot used in the Mazmanian Lab, Caltech.
[STEPS]
SECTION: Striatal tissue samples protein extraction
1. Prepare 1x RIPA Lysis Buffer (M... | ["[Striatal tissue samples protein extraction] Prepare 1x RIPA Lysis Buffer (Millipore, Cat #20-188) in PBS, adding one tablet of protease inhibitor (Sigma, Cat # 4693124001) per 50 mL. Add phosphatase inhibitor (Thermofisher, Cat #A32957) if testing for phosphorylated proteins.", "[Striatal tissue samples protein extr... |
64,898 | Vissentials Reviews – Active Ingredients | 1 | dx.doi.org/10.17504/protocols.io.rm7vzy998lx1/v1 | https://www.protocols.io/view/vissentials-reviews-active-ingredients-cbmask2e | vissentialmoz | TITLE: Vissentials Reviews – Active Ingredients
AUTHORS: vissentialmoz
[DESCRIPTION]
VissentialsWeight Loss can assist you with getting your fantasy body! At long last, you don't need to live with difficult muscle to fat ratio any longer. Chances are, you've most likely taken a stab at all that to dispose of it. You... | [] |
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