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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null | null | null | dx.doi.org/10.17504/protocols.io.qyjdxun | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes how to perform PCR on extracted <em>Symbiodinium</em> DNA to amplify a fragment of the chloroplast 23S rRNA gene. It is based on the method describes in Pochon <em>et al.</em>, 2006. The protocol then explains how to perform an RFLP (restriction fragme... | [] |
100,510 | Fetal and neonatal outcomes in syphilis infected pregnant women in Reunion Island | 0 | dx.doi.org/10.17504/protocols.io.6qpvr83mblmk/v1 | https://www.protocols.io/view/fetal-and-neonatal-outcomes-in-syphilis-infected-p-ded63a9e | Camille CRAMEZ, Phuong Lien TRAN | TITLE: Fetal and neonatal outcomes in syphilis infected pregnant women in Reunion Island
AUTHORS: Camille CRAMEZ, Phuong Lien TRAN
[DESCRIPTION]
Abstract
Objectives :
To evaluate the fetal and neonatal morbidity and mortality in pregnant women with syphilis during their pregnancy in Reunion Island, population benefi... | ["[METHODS] We conducted a multicenter retrospective observational study in the four hospital centers of Reunion Island (Centre Hospitalier Universitaire Nord et Sud - CHU, Centre Hospitalier Ouest Réunion - CHOR, Groupe Hospitalier Est Réunion - GHER), between January 1, 2017 and December 31, 2022, on fetal and neonat... |
68,784 | CRISPR puromycin | 4 | dx.doi.org/10.17504/protocols.io.yxmvmndpog3p/v1 | https://www.protocols.io/view/crispr-puromycin-cfeqtjdw | Rebecca Berrens | TITLE: CRISPR puromycin
AUTHORS: Rebecca Berrens
[DESCRIPTION]
This protocol is for CRISPR knock-in generation in mouse embryonic stem cells
[BEFORE_START]
Have ES cells ready growing happily. Mostly 2 passages after thawing
[STEPS]
1. Plate cells on 6-well plate on SNL a day before transfection (number of cells sh... | ["Plate cells on 6-well plate on SNL a day before transfection (number of cells shown in the table below).", "A day after transfection cells were passaged from 6-well plate into 10cm Petri dishes with SNL. Cells from each well were split into 3 Petri dishes in 3 different densities (1/2, 1/3 and 1/5 of the cells).", "2... |
33,947 | PCR Protocol for Phusion High-Fidelity DNA Polymerase (M0530) | 1 | dx.doi.org/10.17504/protocols.io.bdd3i28n | https://www.protocols.io/view/pcr-protocol-for-phusion-high-fidelity-dna-polymer-bdd3i28n | New England Biolabs | TITLE: PCR Protocol for Phusion High-Fidelity DNA Polymerase (M0530)
AUTHORS: New England Biolabs
[DESCRIPTION]
This is the PCR protocol for Phusion® High-Fidelity DNA Polymerase (M0530).
[BEFORE_START]
Annealing temperatures should be determined using the NEB Annealing Temp Calculator.
Please note that protocols... | ["Set up the following reaction on ice:\n Component 20 µl Reaction 50 µl Reaction Final Concentration Nuclease-free water to 20 µl to 50 µl 5X Phusion HF or GC Buffer 4 µl 10 µl 1X 10 mM dNTPs 0.4 µl 1 µl 200 µM 10 µM Forward Primer 1 µl 2.5 µl 0.5 µM 10 µM Reverse Primer 1 µl 2.5 µl 0.5 µM Template DNA... |
39,257 | Recombinant Protein Expression of MMLV-RT H+ (SkiBar H+ RT) V2 | 1 | dx.doi.org/10.17504/protocols.io.bijzkcp6 | https://www.protocols.io/view/recombinant-protein-expression-of-mmlv-rt-h-skibar-bijzkcp6 | Alex Brown | TITLE: Recombinant Protein Expression of MMLV-RT H+ (SkiBar H+ RT) V2
AUTHORS: Alex Brown
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">About:</span></div><div class = "text-block">This protocol has been optimized for recombinant expression of molony virus based r... | ["[Protein Expression]\nStreak CarbrCamr LB plate supplemented with from frozen stock of Rosetta DE3 . Grow plate overnight at 37°C.", "[Protein Expression]\nSelect single colony from overnight streak plate and inoculate 5mL of LB broth supplemented with Carb and Cam. Grow overnight at 37°C shaking at 250rpm.Prepare 50... |
29,648 | FACS staining PBMCs for TLR and intracellular staining | null | dx.doi.org/10.17504/protocols.io.87qhzmw | null | Marloes van Splunter | TITLE: FACS staining PBMCs for TLR and intracellular staining
AUTHORS: Marloes van Splunter
[STEPS] | [] |
42,450 | McGill Nanopore Native Barcoding LibPrep Protocol,10 ng NB | 1 | dx.doi.org/10.17504/protocols.io.bmpsk5ne | https://www.protocols.io/view/mcgill-nanopore-native-barcoding-libprep-protocol-bmpsk5ne | Sarah Reiling, Anne-Marie Roy, Shu-Huang Chen, Ioannis Ragoussis | TITLE: McGill Nanopore Native Barcoding LibPrep Protocol,10 ng NB
AUTHORS: Sarah Reiling, Anne-Marie Roy, Shu-Huang Chen, Ioannis Ragoussis
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol works for 12 native barcodes, 24 native barcodes, and 96 native barcodes.</div></div>
[STEPS]
?. ... | ["[Before you start]\nFor native barcoding library preparations, it is highly recommended to always add a libprep negative control. Because we have two subsequenc ligation reactions, any leftover native barcodes from the first ligation step may bind to end-prepped DNA strands in the second ligation step. To reduce the ... |
93,166 | ssDNA2.0: Ligation mix II | 3 | dx.doi.org/10.17504/protocols.io.36wgq311xlk5/v1 | https://www.protocols.io/view/ssdna2-0-ligation-mix-ii-c68nzhve | Sarah Nagel, Anna Schmidt, Matthias Meyer | TITLE: ssDNA2.0: Ligation mix II
AUTHORS: Sarah Nagel, Anna Schmidt, Matthias Meyer
[DESCRIPTION]
Protocol for the preparation of Ligation mix II for automated single-stranded DNA library preparation using the ssDNA2.0 method (Gansauge et al. 2020).
References
Gansauge, M.-T., Aximu-Petri, A., Nagel, S., & Meyer, M.... | [] |
47,023 | Working Theory of Flow Cytometry | 4 | null | https://www.protocols.io/view/working-theory-of-flow-cytometry-br6pm9dn | 181830691 | TITLE: Working Theory of Flow Cytometry
AUTHORS: 181830691
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Flow Cytometry (FCM) is a scientific technology developed in the 1970s. In the 1980s, its application rangewas developing from basic research to clinical medical research and disease diagnosis... | [] |
98,819 | Subcellular Fractionation | 0 | dx.doi.org/10.17504/protocols.io.4r3l2q4y3l1y/v1 | https://www.protocols.io/view/subcellular-fractionation-dcrb2v2n | Szu-Chi Liao, Mohamed Taha Moutaoufik, Ken Nakamura | TITLE: Subcellular Fractionation
AUTHORS: Szu-Chi Liao, Mohamed Taha Moutaoufik, Ken Nakamura
[DESCRIPTION]
To isolate total cell lysate into cytosolic and mitochondrial, soluble vs insoluble fractions.
[STEPS]
1. Harvest cells with a scraper.
2. Resuspend PBS and centrifuge at 500g for 5 min.
3. Homogenize using a g... | ["Harvest cells with a scraper.", "Resuspend PBS and centrifuge at 500g for 5 min.", "Homogenize using a glass pestle in isolation medium.", "Centrifuge at 600 g for 10 min at 4°C.", "Transfer the supernatant to a new microcentrifuge tube and centrifuge at 9,000 g for 10 min at 4°C.", "Transfer the supernatant (cytosol... |
null | null | null | dx.doi.org/10.17504/protocols.io.gs9bwh6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for seamless, scarless, homology-based cloning of vectors using an enzyme-free technique. </p>
<p>The method was published by Zurbriggen et al., 2015, doi: <a href="https://dx.doi.org/10.1371%2Fjournal.pone.0137652" target="_blank">10.1371/journal.pone.0137652</a></p... | [] |
46,957 | Zebrafish (Danio rerio) Environmental Summary, Aquatic Resources Program, Boston Children's Hospital 2020a | 1 | dx.doi.org/10.17504/protocols.io.br4mm8u6 | https://www.protocols.io/view/zebrafish-danio-rerio-environmental-summary-aquati-br4mm8u6 | Christian Lawrence, Jason Best, Althea James, Shane Hurley, Mitchel Shia, Michelle Urh, Brady Hirshfeld, Nina Bakker, Hugo Perdomo, Aaron Krueger | TITLE: Zebrafish (Danio rerio) Environmental Summary, Aquatic Resources Program, Boston Children's Hospital 2020a
AUTHORS: Christian Lawrence, Jason Best, Althea James, Shane Hurley, Mitchel Shia, Michelle Urh, Brady Hirshfeld, Nina Bakker, Hugo Perdomo, Aaron Krueger
[DESCRIPTION]
<div class = "text-blocks"><div ... | [] |
73,494 | NHS-ester-protein-labeling | 1 | dx.doi.org/10.17504/protocols.io.x54v9d2zpg3e/v1 | https://www.protocols.io/view/nhs-ester-protein-labeling-cjzwup7e | Liv Jensen | TITLE: NHS-ester-protein-labeling
AUTHORS: Liv Jensen
[DESCRIPTION]
Protocol for labeling a purified protein with an NHS ester fluorescent dye.
[STEPS]
1. Mix 40μM unlabeled protein with 80μM ATTO 565 NHS ester dye in labeling buffer.
2. Incubate 1 hr at room temperature.
3. Buffer exchange the reaction into quench b... | ["Mix 40μM unlabeled protein with 80μM ATTO 565 NHS ester dye in labeling buffer.", "Incubate 1 hr at room temperature.", "Buffer exchange the reaction into quench buffer over a pre-equilibrated G-25 desalting\ncolumn.", "Assess labeling efficiency by measuring the ratio of absorbance at 280 and 564 nm,\ncorrecting for... |
null | null | null | dx.doi.org/10.17504/protocols.io.ifccbiw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is adapted from that detailed in the <em>International Course on Laboratory methods for the Diagnosis of Leptospirosis</em>, by Dr. R.A. Hartskeerl, Dr. H.L. Smits, Mr. H. Korver, Dr. M.G.A. Goris and Dr. W.J. Terpstra from the Leptospirosis Reference Center in ... | [] |
54,750 | Tissue preparation, immunohistochemistry, Imaging, and Quantification | 4 | dx.doi.org/10.17504/protocols.io.bzp6p5re | https://www.protocols.io/view/tissue-preparation-immunohistochemistry-imaging-an-bzp6p5re | Bryan Yoo, Jessica Griffiths, Sarkis Mazmanian | TITLE: Tissue preparation, immunohistochemistry, Imaging, and Quantification
AUTHORS: Bryan Yoo, Jessica Griffiths, Sarkis Mazmanian
[DESCRIPTION]
Protocol for neuronal imaging used in Yoo et al 2021
[STEPS]
SECTION: Tissue Preparation
1. 100mg/kg of pentobarbital (Euthasol - Virbac, Carros, France) was administer... | ["[Tissue Preparation] 100mg/kg of pentobarbital (Euthasol - Virbac, Carros, France) was administered intraperitoneally (IP), and tissues were perfused with 30mL of phosphate buffer solution (PBS) and next with cold 4% paraformaldehyde (PFA) in PBS.", "[Tissue Preparation] GI tract was post-fixed in 4% PFA overnight at... |
85,925 | sample_prep_urine.nan | 4 | dx.doi.org/10.17504/protocols.io.j8nlkowkwv5r/v1 | https://www.protocols.io/view/sample-prep-urine-nan-cx6dxra6 | NAN KB, Mario Uchimiya, John Glushka, Leandro I Ponce, Saraa Al Jawad, Laura Morris, Arthur Edison | TITLE: sample_prep_urine.nan
AUTHORS: NAN KB, Mario Uchimiya, John Glushka, Leandro I Ponce, Saraa Al Jawad, Laura Morris, Arthur Edison
[DESCRIPTION]
This is a modified protocol for NMR metabolomics for urine samples. This method was originally proposed by:
See also:
[BEFORE_START]
This protocol assumes that... | ["[Day-1/1] Add 600 µL of 100% cold methanol to 300 µL of samples on ice \nUse 1.5-mL tubes", "[Day-1/1] Vortex the samples for 10 s", "[Day-1/1] Incubate the samples at -20 °C for 20 min", "[Day-1/1] Centrifuge the samples at for 30 min", "[Day-1/1] Transfer the supernatant of each sample to a new tube\nUse 1.5-mL t... |
null | null | null | dx.doi.org/10.17504/protocols.io.i9zch76 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<h2>Introduction</h2>
<p>The incidence of thyroid cancer is increasing and histological test by itself cannot differentiate thyroid cancer from some benign nodules. Our immediate goal is to meta-analysis and determines the impact of promoter methylation of eight selected candida... | [] |
97,884 | FSCV and Ephys Recording Setup | 0 | dx.doi.org/10.17504/protocols.io.yxmvme785g3p/v1 | https://www.protocols.io/view/fscv-and-ephys-recording-setup-dbt42nqw | Raymond Murray, Helen Schwerdt | TITLE: FSCV and Ephys Recording Setup
AUTHORS: Raymond Murray, Helen Schwerdt
[DESCRIPTION]
Methods detailing the recording setup using both electrophysiological (Ephys) and fast-scan cyclic voltammetry (FSCV) are described.
[STEPS]
SECTION: Recording Setup
1. One to four selected probes were utilized to record dop... | ["[Recording Setup] One to four selected probes were utilized to record dopamine concentrations using fast scan cyclic voltammetry (FSCV) while electrophysiological (Ephys) activity was recorded from all other implanted probes not connected to FSCV. Probes used to record dopamine in a given recording session were switc... |
82,327 | Immunocytochemistry | 3 | dx.doi.org/10.17504/protocols.io.14egn2556g5d/v1 | https://www.protocols.io/view/immunocytochemistry-cumxwu7n | Shiyi Wang | TITLE: Immunocytochemistry
AUTHORS: Shiyi Wang
[DESCRIPTION]
Immunocytochemistry
[STEPS] | [] |
41,020 | Soil Bioassay | 4 | dx.doi.org/10.17504/protocols.io.bka4ksgw | https://www.protocols.io/view/soil-bioassay-bka4ksgw | Andreea S | TITLE: Soil Bioassay
AUTHORS: Andreea S
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Neuropeptide-like proteins (NLPs) are a type of neuropeptides that influence and regulate the neuronal behaviour of the nematodes. Altering of the levels of the NLPs lead to a changed behavioural output. Wi... | ["[Soil Bioassay]\nTwo medium sized, tubs of top diameter approximately are to be used for this experiment which will assess the responses of second stage infective juveniles responses to chemical stimuli. One is to contain a young potato plant cultivar which secretes the neuropeptide-like proteins (NLPs) from the b... |
91,207 | Closed-chamber hydroponics for whole-plant phenotyping | 1 | dx.doi.org/10.17504/protocols.io.q26g7p6m1gwz/v1 | https://www.protocols.io/view/closed-chamber-hydroponics-for-whole-plant-phenoty-c5bfy2jn | Daniel Ginzburg, Jack Cox, Seung Yon Rhee | TITLE: Closed-chamber hydroponics for whole-plant phenotyping
AUTHORS: Daniel Ginzburg, Jack Cox, Seung Yon Rhee
[DESCRIPTION]
Noninvasive phenotyping can quantify dynamic plant growth processes at higher temporal resolution than destructive phenotyping and can reveal phenomena that would be missed by end-point analy... | ["[Closed-system hydroponic growth apparatus construction] Using a 21/64 inch drill bit, drill holes into the centers of 50mL Falcon tube caps.", "[Pre-phenotyping hydroponic growth conditions] Ensure that the drainage height of the ebb & flow system reaches the bottom ~2-3cm of the cut pipette tips during irrigation."... |
98,215 | U2OS Nucleofection & Analysis Protocol for MSPH Validation | 0 | null | https://www.protocols.io/view/u2os-nucleofection-amp-analysis-protocol-for-msph-db6f2rbn | Jason Waligorski, Colin Kremitzki, Graham Bachman, Mallory Wright, William J Buchser | TITLE: U2OS Nucleofection & Analysis Protocol for MSPH Validation
AUTHORS: Jason Waligorski, Colin Kremitzki, Graham Bachman, Mallory Wright, William J Buchser
[DESCRIPTION]
Validation steps.
[STEPS]
SECTION: Design
1. Choosing synGRNA sequence
This is the method utilized in 2023 for the MSPH library in U2OS ce... | ["[Design] Choosing synGRNA sequence\n\nThis is the method utilized in 2023 for the MSPH library in U2OS cells for validating Raft-Seq hits. This is NOT the tandem gRNA method.\n\nChoose one gRNA that was a hit from the primary screen, usually from a published library (Brunello)\nDesign a 2nd 'backup' gRNA sequenced wh... |
92,577 | Visium CytAssist FFPE v3 -- University of Minnesota TMCs | 1 | dx.doi.org/10.17504/protocols.io.n92ldmn99l5b/v3 | https://www.protocols.io/view/visium-cytassist-ffpe-v3-university-of-minnesota-t-c6m9zc96 | Laura J Niedernhofer, David A Bernlohr | TITLE: Visium CytAssist FFPE v3 -- University of Minnesota TMCs
AUTHORS: Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
The Visium CytAssist Spatial Gene Expression for FFPE assay is designed to analyze mRNA in
tissue sections derived from formalin fixed & paraffin embedded (FFPE) tissue samples. The Visium
CytA... | ["[Deparaffinization, H&E Staining, Imaging & Decrosslinking]", "[Library Preparation & Sequencing]", "[FASTQ Generation] BCL data from Illumina sequencer is demultiplexed and converted into FASTQ format using bcl2fastq software version 2.20.0"] |
44,436 | Protocol 2: CRISPR Transformation | 4 | dx.doi.org/10.17504/protocols.io.bpmumk6w | https://www.protocols.io/view/protocol-2-crispr-transformation-bpmumk6w | TITLE: Protocol 2: CRISPR Transformation
AUTHORS:
[STEPS]
?. Mix Bacterial transformation solution with cultured E coli. Pipette 100uL of Bacterial Transformation mix into a microcentrifuge tube. Use an inoculation loop to lightly scrape E coli and transfer to the microcentrifuge tube. Use pipetting technique of asp... | ["Mix Bacterial transformation solution with cultured E coli. Pipette 100uL of Bacterial Transformation mix into a microcentrifuge tube. Use an inoculation loop to lightly scrape E coli and transfer to the microcentrifuge tube. Use pipetting technique of aspirating and dispensing to homogenize the mixture.", "Add CRISP... | |
55,263 | Evaluation of entomopathogenic fungi by larval and adult immersion method | 1 | dx.doi.org/10.17504/protocols.io.bz77p9rn | https://www.protocols.io/view/evaluation-of-entomopathogenic-fungi-by-larval-and-bz77p9rn | Lissette Torres-Torres, Carlos Espinel-Correal, Adriana Santos-Díaz | TITLE: Evaluation of entomopathogenic fungi by larval and adult immersion method
AUTHORS: Lissette Torres-Torres, Carlos Espinel-Correal, Adriana Santos-Díaz
[DESCRIPTION]
The search for commercially viable entomopathogenic fungi for use in integrated pest management programs involves several steps. Fungal species mus... | ["[Reagent preparation] 0.1%Tween® 80 (preparation to 1000 mL):\n\n1 mL Tween® 80 (comercial concentration)\nComplete volume with water up to 1000 mL\nAutoclave at 121 °C ± 3 °C for 15 minutes at 15 psi\n\n\n0.05% Sodium hypoclorite (NaClO) (preparation to 1000 mL):\n\n3.33 mL Sodium hypoclorite(comercial concentration... |
51,276 | Processamento de actígrafos pós-coleta - ActTrust - V.2 | 1 | dx.doi.org/10.17504/protocols.io.bwbkpakw | https://www.protocols.io/view/processamento-de-act-grafos-p-s-coleta-acttrust-v-bwbkpakw | Daniel Vartanian | TITLE: Processamento de actígrafos pós-coleta - ActTrust - V.2
AUTHORS: Daniel Vartanian
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Este protocolo faz parte do processo de coleta de dados actigráficos do Grupo Interdisciplinar de Pesquisa em Sono (GIPSO). Ele foi desenhado para os actígra... | ["[Kanban]\nAdicione o cartão da tarefa no quadro de trabalho do seu projeto (somente para projetos que usam Kanban)\nAbra o quadro de trabalho de seu projeto e adicione um cartão chamado Realizar o processamento de actígrafos pós-coleta na lista Em andamento. Ao clicar sobre o cartão, vá em Etiquetas e selecione (ou a... |
54,191 | PCR and gel electrophoresis | 4 | dx.doi.org/10.17504/protocols.io.by6ppzdn | https://www.protocols.io/view/pcr-and-gel-electrophoresis-by6ppzdn | Ashwinuday | TITLE: PCR and gel electrophoresis
AUTHORS: Ashwinuday
[DESCRIPTION]
This protocol can be used to confirm genes or DNA of interest from a template using PCR. Also to amplify required amount of genes to larger amounts.
[STEPS]
1. Prepare the working stock solution of all the reagents required. If already prepared a... | ["Prepare the working stock solution of all the reagents required. If already prepared and stored, takeout from the refrigerator and thaw on ice.", "Prepare the following mixes each of total 50 µL : -", "Perform PCR using a Thermo cycler with the following temperature settings (All temperatures are in degree Celcius) :... |
69,816 | 城市微生物相調查計畫—採集土壤教學 | 1 | dx.doi.org/10.17504/protocols.io.4r3l2oxzpv1y/v3 | https://www.protocols.io/view/protocol-cgeyttfw | Hsin-Mao Wu | TITLE: 城市微生物相調查計畫—採集土壤教學
AUTHORS: Hsin-Mao Wu
[DESCRIPTION]
吳昕懋
[STEPS]
SECTION: 如何加入專案
1. 開啟Line app，將頁面切換成「聊天」，並按下頂部的掃描圖示(紅框處)
SECTION: 如何加入專案
2. 掃描以下QR code或點選此連結微生物公民科學
SECTION: 如何加入專案
3. 加入成功後會顯示以下畫面
SECTION: 如何加入專案
4. 接著等待採集工具包寄送即可開始採集！
SECTION: 採土與iNaturalist紀錄教學
5. 移除表土，取距離土表5~7公分之處的土，裝入塑膠夾鏈袋中
... | ["[如何加入專案] 開啟Line app，將頁面切換成「聊天」，並按下頂部的掃描圖示(紅框處)", "[如何加入專案] 掃描以下QR code或點選此連結微生物公民科學", "[如何加入專案] 加入成功後會顯示以下畫面", "[如何加入專案] 接著等待採集工具包寄送即可開始採集！", "[採土與iNaturalist紀錄教學] 移除表土，取距離土表5~7公分之處的土，裝入塑膠夾鏈袋中", "[採土與iNaturalist紀錄教學] 將塑膠袋中的土均勻混合，倒入採集罐之中", "[採土與iNaturalist紀錄教學] 在採集紀錄紙上勾選採樣地點、採樣種類，以及填寫日期、城市、鄉鎮、地點、採集者等資訊", "[採土與iNatural... |
97,906 | Protocol OCPRIP | 0 | dx.doi.org/10.17504/protocols.io.261ge56qwg47/v1 | https://www.protocols.io/view/protocol-ocprip-dbus2nwe | Chiara Parravicini, Daniele Spedicati, Matteo Guenci, Nicole Liggeri | TITLE: Protocol OCPRIP
AUTHORS: Chiara Parravicini, Daniele Spedicati, Matteo Guenci, Nicole Liggeri
[DESCRIPTION]
We present a step-by-step methodology for the systematic extraction, alignment, and analysis of peer review data from Crossref to enhance the OpenCitations Index.
The protocol delineates four key phases:... | ["[Gathering Data from Crossref] The first step is to isolate all objects described in Crossref as peer-review. In Crossref, these entities are registered with the type \"peer-review\".\n\nMore specifically, for each entity we want to annotate:\n- The DOI value of the peer-review\n- The type of peer-review\n- The year ... |
40,346 | UAV DSLR photogrammetry with PPK processing | 1 | dx.doi.org/10.17504/protocols.io.bjm2kk8e | https://www.protocols.io/view/uav-dslr-photogrammetry-with-ppk-processing-bjm2kk8e | Oliver Lucanus, Margaret Kalacska | TITLE: UAV DSLR photogrammetry with PPK processing
AUTHORS: Oliver Lucanus, Margaret Kalacska
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The following protocol details the steps needed to acquire UAV based photographs with a DSLR and generate geotags through a PPK workflow. The protocol requir... | ["[UAV Preparation]\nThe following steps apply to most UAV systems, but this protocol is written specifically for the use of a DJI Matrice 600 Pro. Use of a D-RTK system, while optional, greatly improves the UAV's accuracy and precision in following the pre-planned mission.", "[Mission Planning]\nSteps for GS Pro 2.0 (... |
null | null | null | dx.doi.org/10.17504/protocols.io.ja2cige | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Polyploidization contributes to the complexity of gene expression resulting in numerous related but different transcripts. This study explored the transcriptome diversity and complexity of tetraploid Arabica coffee (Coffea arabica) bean. Long-read sequencing (LRS) by Pacbio I... | [] |
12,621 | Fluorescence microscopy with the marine heterotrophic flagellate Cafeteria roenbergensis | null | dx.doi.org/10.17504/protocols.io.qjmduk6 | null | Monica Berjon-Otero, Sarah Duponchel, Matthias Fischer | TITLE: Fluorescence microscopy with the marine heterotrophic flagellate Cafeteria roenbergensis
AUTHORS: Monica Berjon-Otero, Sarah Duponchel, Matthias Fischer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Fluorescence microscopy is essential to understand, between others, the cell organizat... | ["[Remove bacteria from Cafeteria roenbergensis culture]\nFollow the protocol: \"Lysozyme-based removal of bacteria from cultures of the marine heterotrophic flagellate Cafeteria roenbergensis\"\nIf the culture is to be treated with other reagents, for example L-Azidohomoalanine, dilute the cells without bacteria to th... |
56,750 | Keio Acute Response Antioxidant Rescue | 1 | dx.doi.org/10.17504/protocols.io.b3nnqmde | https://www.protocols.io/view/keio-acute-response-antioxidant-rescue-b3nnqmde | Saul Moore | TITLE: Keio Acute Response Antioxidant Rescue
AUTHORS: Saul Moore
[DESCRIPTION]
Phenotyping the acute behavioural response of Caenorhabditis elegans (N2 Bristol) to E. coli single-gene deletion mutants (BW25113), in both the presence and absence of antioxidants (Trolox, NAC, vitamin C and resveratrol).
Videos ar... | ["[Preparing maintenance plates] Make 500mL normal Nematode Growth Media (NGM) agar, following the protocol", "[Preparing maintenance plates] Under a hood, pour 20ml NGM agar into each of 10 x 60mm Petri plates (maintenance plates), and leave to dry for apprximately 1 hour. Once dry, store at 4°C until seeding bacteria... |
null | null | null | dx.doi.org/10.17504/protocols.io.gznbx5e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for western blot to detect strep-tagged constructs, using chromogenic detection with Strep-Tactin AP (Alkaline Phosphatase) conjugate. Based on protocol from iba life sciences.</p>
[STEPS]
?.
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?.
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?. | [] |
69,808 | simpleISM - A straight forward guide to upgrade from confocal to ISM | 1 | dx.doi.org/10.17504/protocols.io.kxygx9mz4g8j/v1 | https://www.protocols.io/view/simpleism-a-straight-forward-guide-to-upgrade-from-cgeqttdw | Monalisa Goswami, René Lachmann, Robert Kretschmer, Rainer Heintzmann | TITLE: simpleISM - A straight forward guide to upgrade from confocal to ISM
AUTHORS: Monalisa Goswami, René Lachmann, Robert Kretschmer, Rainer Heintzmann
[DESCRIPTION]
A hands-on guide to convert a confocal microscopy (here Olympus FluorView 300) into an image scanning microscopy (ISM) using a fast CMOS camera (here ... | ["Replace the dichromatic beam splitter slider of the confocal microscope (Supplementary Figure 1) with a custom-made slider that has a mirror at a 45-degree angle to reflect the beam out of the confocal microscope and a hole to let the beam pass and get detected with PMT channel 2. The slider will be used to switch be... |
47,921 | F0 knockout—single gene | 1 | dx.doi.org/10.17504/protocols.io.bs2rngd6 | https://www.protocols.io/view/f0-knockout-single-gene-bs2rngd6 | Francois Kroll, J Rihel | TITLE: F0 knockout—single gene
AUTHORS: Francois Kroll, J Rihel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Remember to cite the publication if you use this protocol!</div><div class = "text-block">Get in touch for questions</div><div class = "text-block">twitter – @francois_kroll</div><div clas... | ["crRNA selectionThis protocol is to disrupt one gene at three target sites.We ordered all components from Integrated DNA Technologies (IDT).For the published work, we used the predesigned crRNAs from IDT (https://eu.idtdna.com/site/order/designtool/index/CRISPR_PREDESIGN).Wherever possible, crRNAs targeted three disti... |
25,122 | Tache_Yuan_OT2OD024899_CLARITYAnd3DImagingOfColonicENSintheMouseAndPig_1_2019-Mouse_Protocol (Annotation Copy) | null | dx.doi.org/10.17504/protocols.io.4sagwae | null | Pu-Qing Yuan, Lixin Wang, Yvette Taché | TITLE: Tache_Yuan_OT2OD024899_CLARITYAnd3DImagingOfColonicENSintheMouseAndPig_1_2019-Mouse_Protocol (Annotation Copy)
AUTHORS: Pu-Qing Yuan, Lixin Wang, Yvette Taché
[STEPS]
?. The male adult C57BL/6J mice (6-8 weeks, 25.4-28.6g, n=4) were used for CLARITY by PARS (perfusion-assisted agent release in situ) technique, ... | ["The male adult C57BL/6J mice (6-8 weeks, 25.4-28.6g, n=4) were used for CLARITY by PARS (perfusion-assisted agent release in situ) technique, a method for whole-body clearing and immunolabeling. The mice were perfused transcardially with 10 ml of ice cold PBS followed by 20 mL of the ice cold hydrogel solution at a s... |
45,887 | 'Frankenstein’ protocol for nuclei isolation from FRESH and FROZEN tissue for snRNA-Seq (10x Genomics Platform) | 1 | dx.doi.org/10.17504/protocols.io.bq27myhn | https://www.protocols.io/view/39-frankenstein-protocol-for-nuclei-isolation-fro-bq27myhn | Luciano Martelotto | TITLE: 'Frankenstein’ protocol for nuclei isolation from FRESH and FROZEN tissue for snRNA-Seq (10x Genomics Platform)
AUTHORS: Luciano Martelotto
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is the result of the combination of various nuclei isolation protocols for single cell ... | ["[Tissue Homogenization]\nMince/chop tissue with a razor blade to small pieces. The tissue may be as small as a grain of rice.\nFor mincing the tissue, you may take the tube out of ice, however, be quick and return to ice.", "[Tissue Homogenization]\nAdd chilled Nuclei EZ Lysis Buffer to the tissue in 1.5 mL tube.\n5... |
22,280 | Spectral photogrammetry protocol | null | dx.doi.org/10.17504/protocols.io.zzgf73w | null | Aurore Mathys | TITLE: Spectral photogrammetry protocol
AUTHORS: Aurore Mathys
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Acquisition]
Place de specimen at the center of the turntable with scales, photogrammetry marker and MSI calibration card (CHSOS).
?. [Acquisition]
Setup the correct exposure for each wavelenght ... | ["[Acquisition]\nPlace de specimen at the center of the turntable with scales, photogrammetry marker and MSI calibration card (CHSOS).", "[Acquisition]\nSetup the correct exposure for each wavelenght and verify that the exposure is correct in spectrashoot using the MSI calibration card. Adjust exposure until the specim... |
20,986 | Genomic mapping of transformed DNA fragments | null | dx.doi.org/10.17504/protocols.io.yq2fvye | null | Oskar Johansson, Adrian Clarke | TITLE: Genomic mapping of transformed DNA fragments
AUTHORS: Oskar Johansson, Adrian Clarke
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Mapping of transformed DNA within mutated diatoms. A stepwise specific PCR reaction that allow for identification of genome location of transformed fragments su... | ["Primary, 25uL PCR reactionVol. Component5uL 5x SuperFi Buffer0.8uL dNTP - Mix (10mM Each)3uL Internal Primer (10uL)0.2uL SuperFi12.5uL Water2.5uL Degenerate Primer (40uM)1uL gDNA (100ng/uL)Primary PCR programStep Temp Time1 96 5 min2 ... |
42,232 | Influenza A Virus Infection | 4 | dx.doi.org/10.17504/protocols.io.bmgyk3xw | https://www.protocols.io/view/influenza-a-virus-infection-bmgyk3xw | Timothy S C Hinks, Bonnie van Wilgenburg, Huimeng Wang, Liyen Loh, Marios Koutsakos, Katherine Kedzierska, Alexandra J. Corbett, Zhenjun Chen | TITLE: Influenza A Virus Infection
AUTHORS: Timothy S C Hinks, Bonnie van Wilgenburg, Huimeng Wang, Liyen Loh, Marios Koutsakos, Katherine Kedzierska, Alexandra J. Corbett, Zhenjun Chen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is part 3.3 of the "Study of MAIT Cell Activation in Viral In... | ["Thaw virus vial rapidly in a water bath until all ice crystals have melted.\n37 °C", "Decontaminate the outer surface of the vial with .\n[ethanol]", "Perform serial dilutions in sterile PBS to achieve the desired inoculum. For example:(a) If titer of PR8 stock = 1.0 × 109 plaque-forming units (PFU)/mL, require 25 P... |
86,091 | Preparation of soluble and insoluble mitochondrial protein fractions for immunoblotting | 1 | null | https://www.protocols.io/view/preparation-of-soluble-and-insoluble-mitochondrial-cybjxskn | Louise Uoselis | TITLE: Preparation of soluble and insoluble mitochondrial protein fractions for immunoblotting
AUTHORS: Louise Uoselis
[DESCRIPTION]
Preparation of soluble and insoluble mitochondrial protein fractions from HeLa cells for immunoblotting.
[STEPS]
1.
Thaw mitochondrial stocks on ice, and take two aliquots of 15 ug o... | ["Thaw mitochondrial stocks on ice, and take two aliquots of 15 ug of mitochondria each for each sample (one aliquot will be the ‘total’ sample fraction, and one aliquot will represent the ‘fractionation’ sample).", "Centrifuge samples at 10,000x rcf for 10 min at 4 deg C, and carefully aspirate the supernatant", "Add ... |
51,001 | Creating a Frankenstein's Genome | 5 | dx.doi.org/10.17504/protocols.io.bv2zn8f6 | https://www.protocols.io/view/creating-a-frankenstein-39-s-genome-bv2zn8f6 | Helena Pound, Eric Gann, Steven Wilhelm | TITLE: Creating a Frankenstein's Genome
AUTHORS: Helena Pound, Eric Gann, Steven Wilhelm
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This short, command-line protocol is used to combine coding sequences (nucleic acids) from reference genomes into a single file with all coding sequences, wit... | ["Download the nucleic acid coding sequences from all reference genomes you wish to include in your Frankenstein's genome in a .fasta format.", "X1 is the concatenated reference .fasta file, X2 is the output folder name, X3 is the clustering threshold, and X4 is the word size.", "Fu, L., Niu, B., Zhu, Z., Wu, S., and L... |
106,443 | Viral Enumeration of Microbial Mat Samples Using Wet Mount Epifluorescence Microscopy | 0 | null | https://www.protocols.io/view/viral-enumeration-of-microbial-mat-samples-using-w-dj7j4rkn | Madeline Bellanger, Pieter Visscher, Richard Allen White III | TITLE: Viral Enumeration of Microbial Mat Samples Using Wet Mount Epifluorescence Microscopy
AUTHORS: Madeline Bellanger, Pieter Visscher, Richard Allen White III
[DESCRIPTION]
Epifluorescence microscopy (EFM) has been the gold standard method for environmental viral enumeration for over 25 years. Currently, standard ... | ["[Sample Collection and Cleaning] Tare a 1.5 mL low protein binding nuclease free tube on a top loading balance.", "[Sample Collection and Cleaning] Collect approximately 100 mg of mat using a scoopula or similar tool cleaned with 70% ethanol and transfer to the tube. Record the mass of the mat sample.", "[Sample Coll... |
35,530 | main title | null | dx.doi.org/10.17504/protocols.io.bexijfke | null | Cui Jian | TITLE: main title
AUTHORS: Cui Jian
[STEPS]
?. | [] |
18,293 | Comparative transcriptome analysis reveals osmotic-regulated genes in the gill of Chinese mitten crab (Eriocheir sinensis) | null | dx.doi.org/10.17504/protocols.io.v4ve8w6 | null | Junyu Zhou | TITLE: Comparative transcriptome analysis reveals osmotic-regulated genes in the gill of Chinese mitten crab (Eriocheir sinensis)
AUTHORS: Junyu Zhou
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">To reveal the genes and pathways involved in osmoregulation of Chinese mitten crab, adult male crabs w... | ["[Crabs acclimation]\nChinese mitten crabs (body weight 110±5g) were obtained from the Chongming Research Base of Shanghai Ocean University and kept in a freshwater tank for 1 week for acclimation.\nCleaning the tank, oxygenating, changing water everyday", "[Osmotic pressure of crabs under salinity stress]\nAfter a we... |
48,980 | child publication 1 7.4 | 1 | null | https://www.protocols.io/view/child-publication-1-7-4-bt3unqnw | Mariia Guliakina | TITLE: child publication 1 7.4
AUTHORS: Mariia Guliakina
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">test </div></div>
[STEPS]
?. test 1
?. est 2 | ["test 1", "est 2"] |
35,800 | Multiplexed assay for detection of cell culture EV surface membrane proteins | 1 | dx.doi.org/10.17504/protocols.io.be7yjhpw | https://www.protocols.io/view/multiplexed-assay-for-detection-of-cell-culture-ev-be7yjhpw | Joshua Welsh, Bryce Killingsworth, Julia Kepley, Tim Traynor, Alexis Barfield, Jennifer Jones | TITLE: Multiplexed assay for detection of cell culture EV surface membrane proteins
AUTHORS: Joshua Welsh, Bryce Killingsworth, Julia Kepley, Tim Traynor, Alexis Barfield, Jennifer Jones
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for using Miltenyi Biotec's human MACSplex Exosome Kit ... | ["[Experiment planning]\nDetermine which antibodies to use to detect EV surface membrane proteins in addition to the included CD9, CD63 and CD81 antibodies. All additional antibodies must be either APC or AF647 conjugated. Ensure you know the concentration of the antibodies, and if you are using an antibody conjugated ... |
null | null | null | dx.doi.org/10.17504/protocols.io.mntc5en | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes the preparation of cryogenic cultures from liquid cultures of <em>Synechocystis</em> sp. PCC 6803 for a further storage under -80 °C.</p>
<p>The protocol was handed over by Anna Behle MSc.</p>
<p>You can also check the recipe for cyanobacteria in gener... | [] |
80,923 | DNA extraction and purification from dermatophytes using the Qiagen DNEasy™ UltraClean Microbial kit (Qiagen, 12224-50) | 4 | dx.doi.org/10.17504/protocols.io.q26g74d79gwz/v2 | https://www.protocols.io/view/dna-extraction-and-purification-from-dermatophytes-cs93wh8n | Khalid El Moussaoui | TITLE: DNA extraction and purification from dermatophytes using the Qiagen DNEasy™ UltraClean Microbial kit (Qiagen, 12224-50)
AUTHORS: Khalid El Moussaoui
[DESCRIPTION]
This protocol describes the steps to extract and purify genomic DNA from dermatophytes (and more specifically from dermatophytes of the genus Trichop... | ["[Medium preparation] Dissolve 30 g of in 1 L \nof and let mix on the heated magnetic stirrer for 5 min(temperature and mixing speed knob at mid-step).", "[Medium preparation] Cover the flask with glass wool and aluminium foil. Autoclave it at 121 °C 121 °C for 30 min.", "[Cultivation of the strains] After allowin... |
45,007 | Creare baseurl per harvesting di repository OAI con OpenRefine | 5 | dx.doi.org/10.17504/protocols.io.bp7pmrmn | https://www.protocols.io/view/creare-baseurl-per-harvesting-di-repository-oai-co-bp7pmrmn | Andrea Marchitelli | TITLE: Creare baseurl per harvesting di repository OAI con OpenRefine
AUTHORS: Andrea Marchitelli
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Il protocollo descrive il metodo per creare le baseurl per l'harvesting di un repository OAI-PMH a partire da una lista di identificatori.</div></div>
[... | ["Aprire il progetto OpeRefine contenente la lista degli identificatori OAI predisposta per l'harvesting.La lista può essere predisposta seguendo le indicazioni del protocollo collegato Come importare identificatori OAI-PMH in OpenRefine.\n{\"blocks\":[{\"data\":[],\"depth\":0,\"entityRanges\":[],\"inlineStyleRanges\":... |
37,951 | Q5® Site-Directed Mutagenesis (E0552) | 1 | dx.doi.org/10.17504/protocols.io.bha7j2hn | https://www.protocols.io/view/q5-site-directed-mutagenesis-e0552-bha7j2hn | New England Biolabs | TITLE: Q5® Site-Directed Mutagenesis (E0552)
AUTHORS: New England Biolabs
[DESCRIPTION]
The Q5 Site-Directed Mutagenesis Kit (Without Competent Cells) enables rapid, site-specific mutagenesis of double-stranded plasmid DNA in less than 2 hours (Figure 1). The kit utilizes the robust Q5 Hot Start High-Fidelity DNA P... | ["[Exponential Amplification (PCR)] Assemble the following reagents in a thin-walled PCR tube:\n 25 μl RXN FINAL CONC. Q5 Hot Start High-Fidelity 2X Master Mix 12.5 μl 1X 10 μM Forward Primer 1.25 μl 0.5 μM 10 μM Reverse Primer 1.25 μl 0.5 μM Template DNA (1–25 ng/μl) 1 μl 1-25 ng Nuclease-free water 9.0 ... |
92,571 | Visium CytAssist FFPE v2 -- University of Minnesota TMCs | 1 | dx.doi.org/10.17504/protocols.io.n92ldmn99l5b/v2 | https://www.protocols.io/view/visium-cytassist-ffpe-v2-university-of-minnesota-t-c6m3zc8n | Laura J Niedernhofer, David A Bernlohr | TITLE: Visium CytAssist FFPE v2 -- University of Minnesota TMCs
AUTHORS: Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
The Visium CytAssist Spatial Gene Expression for FFPE assay is designed to analyze mRNA in
tissue sections derived from formalin fixed & paraffin embedded (FFPE) tissue samples. The Visium
CytA... | ["[Deparaffinization, H&E Staining, Imaging & Decrosslinking]", "[Library Preparation & Sequencing]", "[FASTQ Generation] BCL data from Illumina sequencer is demultiplexed and converted into FASTQ format using bcl2fastq software version 2.20.0"] |
null | null | null | dx.doi.org/10.17504/protocols.io.ntqdemw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol was adapted from Chiyoda et al., 2007 and Boehm et al., 2015 </p>
<p> </p>
<p> </p>
<p> </p>
<p> </p>
[BEFORE_START]
<p>-filter sterilise the CaCl<sub>2</sub> solution and store aliquots in -20 °C</p>
<p>-store spermidine aliquots at -80 °C</p>
<p>-wash stoppin... | [] |
105,818 | GEARBOCS protocols | 0 | dx.doi.org/10.17504/protocols.io.36wgqnq15gk5/v1 | https://www.protocols.io/view/gearbocs-protocols-djj24kqe | Justin T Savage, Luke Bradley, Nicholas Brose | TITLE: GEARBOCS protocols
AUTHORS: Justin T Savage, Luke Bradley, Nicholas Brose
[DESCRIPTION]
Protocols for AAV production and use of the GEARBOCS system.
[STEPS] | [] |
101,455 | Three-dimensional models of skeletal muscle under tension and methods to induce traumatic injury: systematic review search protocol | 0 | dx.doi.org/10.17504/protocols.io.q26g71m81gwz/v1 | https://www.protocols.io/view/three-dimensional-models-of-skeletal-muscle-under-dfbp3imn | Kunal Bhanot, Robert Staruch | TITLE: Three-dimensional models of skeletal muscle under tension and methods to induce traumatic injury: systematic review search protocol
AUTHORS: Kunal Bhanot, Robert Staruch
[DESCRIPTION]
Volumetric
muscle loss (VML) is defined as the significant loss of skeletal muscle as a result of traumatic injury or surgical i... | ["[Methods] This systematic review was reported in compliance with the PRISMA 2020 checklist. The protocol was developed prospectively in collaboration with a research librarian (NT) at the Nuffield Department of Rheumatology and Musculoskeletal Sciences (NDORMS).", "All databases were searched from inception until 13/... |
22,891 | SPARC Serotonin 7 Receptor (5-HT7) Immunohistochemistry Protocol in Rat Tissues Labeled with Cholera Toxin B-fragment | null | dx.doi.org/10.17504/protocols.io.2kjgcun | null | Elisa Gonzalez-Rothi, Yasin Seven, Latoya Allen, Marissa Ciesla, Gordon Mitchell | TITLE: SPARC Serotonin 7 Receptor (5-HT7) Immunohistochemistry Protocol in Rat Tissues Labeled with Cholera Toxin B-fragment
AUTHORS: Elisa Gonzalez-Rothi, Yasin Seven, Latoya Allen, Marissa Ciesla, Gordon Mitchell
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the immunoflu... | ["Day 1: primary antibodies required:5-HT7 Receptor: Rabbit anti-5-HT7R (Immunostar #244430)Cholera toxin B-fragment: Goat anti-CT-B (Millipore #227040)", "Place 40um transverse spinal cord sections into 1xPBS in 12 well cell culture plates", "3x washes in 1xPBS for 5 minutes each at room temperature", "Antigen retrie... |
28,212 | Measurement of XylE (Catechol 2,3-Dioxygenase) enzyme activity by microplate reader | null | dx.doi.org/10.17504/protocols.io.7suhnew | null | Ji Gao | TITLE: Measurement of XylE (Catechol 2,3-Dioxygenase) enzyme activity by microplate reader
AUTHORS: Ji Gao
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Simple measurement of XylE (Catechol 2,3-Dioxygenase) enzyme activity by microplate reader. Catechol 2,3-Dioxygenase can catalyze catechol (1,2-D... | ["[Protocol for the instrument]\nShake the plate for at .\nCentrifuge: 600 33", "[Protocol for the instrument]\nMeasure the absorbance of cell culture at 600 nm as the estimation of cell amounts.", "[Protocol for the instrument]\nPlate out and add catechol () to every well, then plate in immediately.\n2.5 µl\nThe w... |
41,957 | Mikro SARS-CoV-2 Multiplex Protocol | 4 | dx.doi.org/10.17504/protocols.io.bk8dkzs6 | https://www.protocols.io/view/mikro-sars-cov-2-multiplex-protocol-bk8dkzs6 | Toby Overmaat | TITLE: Mikro SARS-CoV-2 Multiplex Protocol
AUTHORS: Toby Overmaat
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Sample Collection]
Remove the lid of sample collector. Direct the sample provider to expel saliva into the collector until 0.5 mL has been collected. Replace lid.
Teeth brushing, mouthwash, dr... | ["[Sample Collection]\nRemove the lid of sample collector. Direct the sample provider to expel saliva into the collector until 0.5 mL has been collected. Replace lid.\nTeeth brushing, mouthwash, drinks, food, and nasal sprays should be avoided for half an hour before sample collection.", "[Heat Pre-Treatment]\nLoad sam... |
104,107 | CTLR-Seq Protocol | 0 | dx.doi.org/10.17504/protocols.io.q26g71d7kgwz/v1 | https://www.protocols.io/view/ctlr-seq-protocol-dhwj37cn | Bo Zhou, GiWon Shin, Yiling Huang, Raegan N. Wood, Hanlee P. Ji, Alexander E. Urban | TITLE: CTLR-Seq Protocol
AUTHORS: Bo Zhou, GiWon Shin, Yiling Huang, Raegan N. Wood, Hanlee P. Ji, Alexander E. Urban
[DESCRIPTION]
We developed a generally applicable method CRISPR/Cas9-targeted long read sequencing (CTLR-Seq) to resolve, haplotype-specifically, and at base-pair resolution, large, complex, and highly... | ["[Sample Handling:] Count number of cells in sample.", "[Sample Handling:] Wash cells 3X with phosphate-buffer\n\n\n\n saline (PBS). Centrifugation should be done at 100 g-200 g for 5 min-10 min, depending on cell type.", "[Sample Handling:] Resuspend pellet in 60 µL of Sage Science M2 Buffer per million cells counted... |
34,553 | RDH | null | dx.doi.org/10.17504/protocols.io.bdyzi7x6 | https://www.protocols.io/view/rdh-bdyzi7x6 | Irfan Uddin, Taeeb Ahmad, Furqan Aziz | TITLE: RDH
AUTHORS: Irfan Uddin, Taeeb Ahmad, Furqan Aziz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This algorithm implements Reversible Data Hiding (RDH) technique by rearranging the columns (or rows) of the image in a way that enhances the smooth regions of an image. Any difference based tec... | [] |
79,051 | In vitro excystment of Juvenile Fasciola hepatica | 4 | dx.doi.org/10.17504/protocols.io.14egn212qg5d/v1 | https://www.protocols.io/view/in-vitro-excystment-of-juvenile-fasciola-hepatica-crfjv3kn | Paul McCusker, Rebecca Armstrong, Duncan Wells, Emily Robb, Paul McVeigh, Aaron Maule, Erin McCammick, Nathan Clarke, Erica Gardiner | TITLE: In vitro excystment of Juvenile Fasciola hepatica
AUTHORS: Paul McCusker, Rebecca Armstrong, Duncan Wells, Emily Robb, Paul McVeigh, Aaron Maule, Erin McCammick, Nathan Clarke, Erica Gardiner
[DESCRIPTION]
This protocol describes our excystment protocol for Fasciola hepatica supplied by Ridgeway Research Ltd. F... | ["[Outer metacercariae (met) wall removal] Pipette 300 µL 50% chicken serum (CS50) onto large petri dish base and lid, spread with finger.", "[Outer metacercariae (met) wall removal] Fill petri dish base with 10 mL RO water.", "[Outer metacercariae (met) wall removal] Gently lift rolled-up met sheet out of tube, place ... |
28,655 | Isolation of nuclei from paraffin-embedded tissue with subsequent immunostaining | null | dx.doi.org/10.17504/protocols.io.78phrvn | null | Dorothe Moellmann | TITLE: Isolation of nuclei from paraffin-embedded tissue with subsequent immunostaining
AUTHORS: Dorothe Moellmann
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how individual nuclei are isolated from paraffin tissue and then stained immunhistochemically</div></div>
[STEPS... | ["cut 60µm sections from paraffin material and add to an 1,5ml tube", "dewaxing by addition of xylene; 99%; 96%: 70% Ethanol each forremove and replace after incubation\n0 Room temperature", "after removing the last rehydration step add Target Retrieval Solution\n400 µl", "add 0,2mm diameter stainless steel beadsplace... |
null | null | null | dx.doi.org/10.17504/protocols.io.ex9bfr6 | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<strong>Solutions and Buffers: </strong><br /><strong>Note:</strong> Do not use sodium azide in any buffers or solutions, as sodium azide inactivates the horseradish-peroxidase enzyme. <br /><br /><strong>Carbonate Coating Buffer </strong><br />BioLegend Cat. No. 421701 or… <br /... | [] |
35,373 | Tissue Quality Evaluation for Brain Perfusion/Dissection Specimens | null | dx.doi.org/10.17504/protocols.io.besmjec6 | null | Allen Institute for Brain Science | TITLE: Tissue Quality Evaluation for Brain Perfusion/Dissection Specimens
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol provides guidance in the assessment of quality of tissues post perfusion and dissection and applies to all such procedure... | [] |
78,235 | Time-lapse killing assay (monolayer - IncuCyte) | 1 | dx.doi.org/10.17504/protocols.io.q26g7b6x8lwz/v2 | https://www.protocols.click/view/time-lapse-killing-assay-monolayer-incucyte-cqm3vu8n | Philippa R Kennedy, Peter Hinderlie | TITLE: Time-lapse killing assay (monolayer - IncuCyte)
AUTHORS: Philippa R Kennedy, Peter Hinderlie
[DESCRIPTION]
Fluorescent target cells are plated in a monolayer in a 96 well plate. Effector cells are added to that plate and time-lapse imaging in combination with fluorescent indicators of cell death reveal the dyna... | ["[Overview] Target cells are fluorescently labelled to differentiate them from effector cells.", "[Overview] Option 1: Target cells are labeled using an amine-reactive dye (CellTrace Far Red Proliferation Kit, Cat. No:C34564, Thermo Fisher) according to the manufacturer's instructions.", "[Overview] Option 2: Target c... |
26,868 | 16 High Throughput Screening with Fluorescent Probe | null | dx.doi.org/10.17504/protocols.io.6guhbww | null | TJUSLS China | TITLE: 16 High Throughput Screening with Fluorescent Probe
AUTHORS: TJUSLS China
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">High Throughput Screens (HTS) are recent scientific methods relevant to the field of chemistry and biology, in which hundreds of thousands of experimental samples are subj... | ["[Sample preparation]\nSoak the 96-well plates in 75% ethanol and put the container in ultrasonic cleaner for 30min to 1 hour, then use ddH2O to wash these plates several times. Put clean plates in drying oven at 55°C.\n55 °C", "[Sample preparation]\nDilute the enzyme using its buffer. There we pipet 1 μL protein stoc... |
63,396 | Prima Weight Loss Pills Dragons Den Uk Buy Now? | 1 | dx.doi.org/10.17504/protocols.io.bp2l61p4rvqe/v1 | https://www.protocols.io/view/prima-weight-loss-pills-dragons-den-uk-buy-now-b96cr9aw | ericyoungzs | TITLE: Prima Weight Loss Pills Dragons Den Uk Buy Now?
AUTHORS: ericyoungzs
[DESCRIPTION]
Prima Weight Loss Pills Dragons Den Uk
is a company that helps people who are interested in using their fitness knowledge to make more money. They offer an online blog and video courses, which provide tools for health and welln... | ["[Prima Weight Loss Pills Dragons Den Uk Buy Now?]"] |
80,505 | Production of Neuron-Preferential Lentiviral Vectors Protocol | 4 | dx.doi.org/10.17504/protocols.io.8epv5jqpnl1b/v1 | https://www.protocols.io/view/production-of-neuron-preferential-lentiviral-vecto-csuzwex6 | creative-biogene | TITLE: Production of Neuron-Preferential Lentiviral Vectors Protocol
AUTHORS: creative-biogene
[DESCRIPTION]
This protocol provides a method that allows the production of high titer lentivectors that preferentially transduce neurons. The lentiviral vectors produced using this protocol were used in previous studies, in... | ["[Experiment Summary] This protocol provides a method that allows the production of high titer lentivectors that preferentially transduce neurons. The lentiviral vectors produced using this protocol were used in previous studies, including re-introduction of CD38 gene expression into the hypothalamic neurons of CD38 k... |
47,302 | (ILLUMINA MENU) Protocols for SARS-CoV-2 Library Prep with ARTIC Primers, Bioinformatic Analysis, and Database Submission | 2 | null | https://www.protocols.io/view/illumina-menu-protocols-for-sars-cov-2-library-pr-bsfenbje | Technical Outreach and Assistance for States Team | TITLE: (ILLUMINA MENU) Protocols for SARS-CoV-2 Library Prep with ARTIC Primers, Bioinformatic Analysis, and Database Submission
AUTHORS: Technical Outreach and Assistance for States Team
[DESCRIPTION]
This collection of protocols covers library preparation and sequencing on Illumina platforms as well as bioinformat... | [] |
43,336 | Manual Tracing Study: Tibetan Knot | 3 | dx.doi.org/10.17504/protocols.io.bnjgmcjw | https://www.protocols.io/view/manual-tracing-study-tibetan-knot-bnjgmcjw | Jamin Pelkey, Sari Park, Zahra Vahedi, Stephanie Walsh Matthews | TITLE: Manual Tracing Study: Tibetan Knot
AUTHORS: Jamin Pelkey, Sari Park, Zahra Vahedi, Stephanie Walsh Matthews
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Lab Study Script and Protocols for manual tracing study using Tibetan knot pattern (Prime) and asymmetrical pattern (Anti-prime) and Con... | [] |
85,884 | DengueSeq: A pan-serotype whole genome amplicon sequencing protocol for dengue virus | 4 | dx.doi.org/10.17504/protocols.io.kqdg39xxeg25/v3 | https://www.protocols.io/view/dengueseq-a-pan-serotype-whole-genome-amplicon-seq-cx44xqyw | Chantal Vogels, Verity Hill, Mallery I Breban, Chrispin Chaguza, Afeez Sodeinde, Emma Taylor-Salmon, Abigail J. Porzucek, Nathan D Grubaugh | TITLE: DengueSeq: A pan-serotype whole genome amplicon sequencing protocol for dengue virus
AUTHORS: Chantal Vogels, Verity Hill, Mallery I Breban, Chrispin Chaguza, Afeez Sodeinde, Emma Taylor-Salmon, Abigail J. Porzucek, Nathan D Grubaugh
[DESCRIPTION]
Version 3 updates:
Updated abstract
Included link to preprint an... | ["[Dengue Serotype Identification / Plate Setup] There are options available for use: Serotype-specific and Pan-serotype approach. \n\nVarious library prep kits can be used with the DengueSeq primers, following the manufacturer's protocol. Below we describe detailed steps for the Illumina COVIDSeq Test Kit (RUO version... |
53,380 | Agarose Gel Electrophoresis for quality control of DNA aptamers in biosensor assays | 4 | dx.doi.org/10.17504/protocols.io.bydcps2w | https://www.protocols.io/view/agarose-gel-electrophoresis-for-quality-control-of-bydcps2w | Geisianny AM Moreira, Diana Vanegas, Eric S McLamore | TITLE: Agarose Gel Electrophoresis for quality control of DNA aptamers in biosensor assays
AUTHORS: Geisianny AM Moreira, Diana Vanegas, Eric S McLamore
[DESCRIPTION]
This protocol describes the procedure for electrophoresis in agarose gel to check the quality, purity, and size of DNA aptamers. The general objective i... | ["Prepare the agarose gel (Timing: 30 minutes)\nAssemble the gel casting\nPrepare the 1X TAE working solution. To make 1X TAE from 10X TAE stock solution, dilute 100 ml of the stock solution into 900 mL of DI water.\nPrepare 3% agarose gel\nAdjust the mass of agarose in a given buffer volume (1X TAE) to make gels in 3%... |
91,215 | Fluorescein diacetate assay - for plastic degrading enzymes in algae | 4 | dx.doi.org/10.17504/protocols.io.n2bvj3j9blk5/v1 | https://www.protocols.io/view/fluorescein-diacetate-assay-for-plastic-degrading-c5bpy2mn | Joao Vitor Molino | TITLE: Fluorescein diacetate assay - for plastic degrading enzymes in algae
AUTHORS: Joao Vitor Molino
[DESCRIPTION]
Fluorescein diacetate (FDA) hydrolysis assays can be used to measure the enzyme activity of cells in a sample. A bright yellow-green glow is produced and is strongest when enzymatic activity is greatest... | ["[Checking cell density] Sample 160 µL of culture in a 96-well-clear plate.", "[Checking cell density] Measure the absorbance at 750 nm and Chlorophyll fluorescence at 440/680nm. For example, in Infinite‱ M200 PRO plate reader, set the gain to 100, sensor distance 18000um, and top reading.", "[Sample preparation] Spin... |
52,873 | MultiQuas (Multiple reference quasispecies reconstruction protocol) | 5 | null | https://www.protocols.io/view/multiquas-multiple-reference-quasispecies-reconstr-bxvhpn36 | Marco Cacciabue | TITLE: MultiQuas (Multiple reference quasispecies reconstruction protocol)
AUTHORS: Marco Cacciabue
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The following protocol summarizes the major steps to run the MultiQuas pipeline to evaluate viral variability and reconstruct the viral quasispecies fr... | ["[Brief pipeline description]\nReads are trimmed and filtered using", "[Brief pipeline description]\nFiltered and trimmed reads are aligned to a set of user-defined references (multifasta format) with", "[Brief pipeline description]\nReads are then split into different classes (one for each reference and one for the u... |
null | null | null | dx.doi.org/10.17504/protocols.io.eupbevn | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
6ml of 0.1% Oil Red O in isopropanol<br />4ml ddH2O<br /><br />Mix well and filter through 0.45 micron filter
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.n7idhke | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol was designed and developed at this laboratory.</p>
<p>The assay targets the capsid peptide coding region of DENV 1-4 and is desigend as a qualitative screening test for human cases of DENV infection.</p>
[BEFORE_START]
<div>
<ul>
<li>If using a different brand ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ge9bth6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Stock<em> vitamin solution</em> for ESAW Media for Marine Phytoplankton</p>
[STEPS]
?.
?.
?.
?. | [] |
97,517 | Tissue Fixation | HubMAP | JHU-TMC | 0 | dx.doi.org/10.17504/protocols.io.3byl4929jgo5/v1 | https://www.protocols.io/view/tissue-fixation-hubmap-jhu-tmc-dbgm2ju6 | Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Miklhail James, Sashank Reddy, Denis Wirtz | TITLE: Tissue Fixation | HubMAP | JHU-TMC
AUTHORS: Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Miklhail James, Sashank Reddy, Denis Wirtz
[DESCRIPTION]
First and most important - the original tissue sample must be of good quality. Factors such as warm
ischemic time, the time delay between tissue excisio... | ["[Tissue Fixation] Tissue is harvested using our protocol (Tissue Harvesting Protocol)", "[Tissue Fixation] The rate of penetration of formaldehyde depends on the size of the biopsy. Trimming is often required to facilitate fixation. Tissues placed in the tissue cassettes should be no thicker than 3-4mm because the in... |
null | null | null | dx.doi.org/10.17504/protocols.io.u4ceysw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Extraction of tissue metaboilites for untargeted LC-MS on LC-QTOF.
[BEFORE_START]
The tissue, disposable pestle and 1.5 ml-centrifuge tube in liquid nitrogen were chilled in liquid nitrogen.
[STEPS]
SECTION: Metabolite extraction
?.
SECTION: Untargeted metabolomics by LC/MS
?... | ["[Metabolite extraction] The tissue was pulverized in the presence of liquid nitrogen to fine powder. \n100 ml of chloroform and 200 ml of methanol were added to the fine powder and resuspended by vigorous vortexing.\nThe mixture was stored at room temperature for 30 min. \nSubsequently, 100 ml of chloroform and 100 m... |
82,035 | Desalting of Peptides to Prepare for Mass Spectrometry Analysis | 4 | dx.doi.org/10.17504/protocols.io.6qpvr4n3ogmk/v2 | https://www.protocols.io/view/desalting-of-peptides-to-prepare-for-mass-spectrom-cuctwswn | jconsi, Ikram Isa, Alexandra Naba | TITLE: Desalting of Peptides to Prepare for Mass Spectrometry Analysis
AUTHORS: jconsi, Ikram Isa, Alexandra Naba
[DESCRIPTION]
Prior to proteomic analysis, peptide samples are desalted and eluted with freshly prepared 50% acetonitrile, 0.1% trifluoroacetic acid, followed by concentration in a vacuum concentrator. Pep... | ["[Column Preparation] Column Preparation", "[Column Preparation] Take a Pierce peptide desalting spin column and remove the white tip (do not remove the screw cap of the tube). Place in a 2mL tube and spin column at for 1 min.", "[Column Preparation] Add 300 µLof acetonitrile. Spin at for 1 minand discard flow-thro... |
76,423 | Heat-inactivation of Fetal Bovine Serum (FBS) | 4 | null | https://www.protocols.io/view/heat-inactivation-of-fetal-bovine-serum-fbs-cnvfve3n | Andreas Sagen | TITLE: Heat-inactivation of Fetal Bovine Serum (FBS)
AUTHORS: Andreas Sagen
[DESCRIPTION]
The objective of heat inactivation is to destroy complement activity in the serum without affecting the growth-promoting characteristics of the product. Removal of complement activity from serum, such as fetal bovine serum, is no... | ["[FBS heat-inactivation procedure] Slow thaw FBS at 4 °C overnight", "[FBS heat-inactivation procedure] Aliquot FBS into 50 mL units in a sterile environment", "[FBS heat-inactivation procedure] Prepare a volumetrically equal blank container with distilled water", "[FBS heat-inactivation procedure] Let FBS equilibrate... |
62,485 | Intestinal Lamina Propria and Spleen Immune Cell Isolation | 1 | dx.doi.org/10.17504/protocols.io.dm6gpbxo5lzp/v1 | https://www.protocols.io/view/intestinal-lamina-propria-and-spleen-immune-cell-i-b89vrz66 | rabdelha | TITLE: Intestinal Lamina Propria and Spleen Immune Cell Isolation
AUTHORS: rabdelha
[DESCRIPTION]
This protocol details isolation of immune cells from intestinal lamina propria/spleen and flow cytometry.
[STEPS]
SECTION: Isolation of Immune Cells from Intestinal Lamina Propria/Spleen
1. Dissect the small and larg... | ["[Isolation of Immune Cells from Intestinal Lamina Propria/Spleen] Dissect the small and large intestines for isolation of intestinal lamina propria cells, place the small and large intestines immediately on ice cold PBS.", "[Isolation of Immune Cells from Intestinal Lamina Propria/Spleen] Open the intestines longit... |
57,192 | dsDNA quantification using Sybr Green I | 4 | dx.doi.org/10.17504/protocols.io.b34gqqtw | https://www.protocols.io/view/dsdna-quantification-using-sybr-green-i-b34gqqtw | James JN Kitson | TITLE: dsDNA quantification using Sybr Green I
AUTHORS: James JN Kitson
[DESCRIPTION]
This is a simple protocol that uses Sybr Green 1 and a microplate reader to quantify dsDNA concentrations in unknown samples. This is best suited for situations where a high number of samples need to be quantified (e.g. normalisation... | ["[Part 1 - Make a dilution series of a Lambda DNA standard:] Select which standards we need to make and use based on the strength of the samples being tested.", "[Part 1 - Make a dilution series of a Lambda DNA standard:] Serially dilute this as below:\n \t\t\t \t\t\t\tDilution \t\t\t \t\t\t \t\t\t\tlambda \t... |
83,241 | Halo-LC3B processing assay to assess autophagy | 4 | dx.doi.org/10.17504/protocols.io.3byl4qexzvo5/v1 | https://www.protocols.click/view/halo-lc3b-processing-assay-to-assess-autophagy-cvihw4b6 | Xuefeng Ren | TITLE: Halo-LC3B processing assay to assess autophagy
AUTHORS: Xuefeng Ren
[DESCRIPTION]
This protocol details Halo-LC3B processing assay to assess autophagy.
[GUIDELINES]
Reference: DOI: 10.7554/eLife.78923
[STEPS]
SECTION: Halo-LC3B processing assay to assess autophagy
1. Generating HeLa cells expressing HaloTag-L... | ["[Halo-LC3B processing assay to assess autophagy] Generating HeLa cells expressing HaloTag-LC3B using pMRX-IP-HaloTag7-LC3 from Mizushima lab (Addgene #184899; DOI: 10.7554/eLife.78923).", "[Halo-LC3B processing assay to assess autophagy] Seed HeLa cells at 100-150K cells/well in 12-well plate one day before.", "[Halo... |
98,623 | Immune stimulation of human induced pluripotent stem cells (hiPSC)-derived glia with lipopolysaccharide (LPS) | 0 | dx.doi.org/10.17504/protocols.io.eq2lywp7wvx9/v1 | https://www.protocols.io/view/immune-stimulation-of-human-induced-pluripotent-st-dci72uhn | Yasmine Nonose, Gist Croft | TITLE: Immune stimulation of human induced pluripotent stem cells (hiPSC)-derived glia with lipopolysaccharide (LPS)
AUTHORS: Yasmine Nonose, Gist Croft
[DESCRIPTION]
Human induced pluripotent stem cells (hiPSC) are widely used as a human development and disease model system. However, for the development of optimized ... | ["[REAGENT INFORMATION AND PREPARATION] Lipopolysaccharide (LPS) aliquot preparation", "[REAGENT INFORMATION AND PREPARATION] LPS resuspension and aliquot preparation", "[REAGENT INFORMATION AND PREPARATION] LPS solubility: LPS are molecules that form micelles in every solvent. This explains the hazy solutions observed... |
29,273 | Biolistic transformation of Emiliania huxleyi | null | dx.doi.org/10.17504/protocols.io.8tzhwp6 | null | Glen Wheeler, Rowena Stern | TITLE: Biolistic transformation of Emiliania huxleyi
AUTHORS: Glen Wheeler, Rowena Stern
[STEPS]
?. [Preparing tungsten beads]
Weigh out 60 mg tungsten into a microfuge tube
?. [Preparing tungsten beads]
Wash in 1 mL 100% ethanol. Vortex. Centrifugation at 13000rpm for 1 minute then remove ethanol
?. [Preparing tungst... | ["[Preparing tungsten beads]\nWeigh out 60 mg tungsten into a microfuge tube", "[Preparing tungsten beads]\nWash in 1 mL 100% ethanol. Vortex. Centrifugation at 13000rpm for 1 minute then remove ethanol", "[Preparing tungsten beads]\nWash four times in 1 mL molecular grade water. Centrifugation at 13000rpm for 1 minute... |
null | null | null | dx.doi.org/10.17504/protocols.io.guhbwt6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This script is used for northern blotting with the Roche DIG Northern Starter Kit.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
49,738 | Expression and purification of Rab8A (1-181) stoichiometrically phosphorylated at pThr72 (the LRRK2 site) | 1 | dx.doi.org/10.17504/protocols.io.butinwke | https://www.protocols.io/view/expression-and-purification-of-rab8a-1-181-stoichi-butinwke | Axel Knebel, Kerryn Berndsen, Pawel Lis, Paul Davies, Dario Alessi | TITLE: Expression and purification of Rab8A (1-181) stoichiometrically phosphorylated at pThr72 (the LRRK2 site)
AUTHORS: Axel Knebel, Kerryn Berndsen, Pawel Lis, Paul Davies, Dario Alessi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A subset of small GTPases of the Rab family including Rab8A (U... | ["[Transformation of plasmid into competent bacteria]\nMix of pET28a 6HIS Thrombin Rab8a 1-181 plasmid (around ) with - of the competent BL21(DE3) cells and incubate for .\n10 µl\n50 µl\n100 µl\non ice", "[Transformation of plasmid into competent bacteria]\nTransfer the vial to a heat block equilibrated at and leave... |
83,661 | Environmental DNA (eDNA) Sample Shipping Protocol | 1 | dx.doi.org/10.17504/protocols.io.dm6gp38jpvzp/v1 | https://www.protocols.io/view/environmental-dna-edna-sample-shipping-protocol-cvxmw7k6 | Meghan M. Shea, Alexandria B Boehm | TITLE: Environmental DNA (eDNA) Sample Shipping Protocol
AUTHORS: Meghan M. Shea, Alexandria B Boehm
[DESCRIPTION]
This is a protocol for mailing PCR amplicons generated from eDNA samples, specifically via the following earlier sampling & filtration, extraction, and PCR protocols, e.g.:
While this protocol was... | ["[Preparing Samples for Shipping] Clean bench area with 10% bleach, 70% ethanol, and RNase Away", "[Preparing Samples for Shipping] Wipe down 20 µL multichannel pipette and several PCR tube holders with RNase away. Run in UV Crosslinker for 10 minutes on each side.", "[Preparing Samples for Shipping] Wipe down ice bin... |
106,298 | DNA EXTRACTION Protocol Template | 1 | null | https://www.protocols.io/view/dna-extraction-protocol-template-dj224qge | Kathleen Pitz, Raïssa Meyer | TITLE: DNA EXTRACTION Protocol Template
AUTHORS: Kathleen Pitz, Raïssa Meyer
[DESCRIPTION]
A protocol template created through the BeBOP project for DNA Extraction. For more information please visit our github site at https://github.com/BeBOP-OBON.
[STEPS]
SECTION: MIOP: Minimum Information about an Omics Protocol
1.... | ["[MIOP: Minimum Information about an Omics Protocol] MIOP Term\nValue\n \nmethodology category\n\n \nproject\n\n \npurpose\n\n \nanalyses\n\n \ngeographic location\n\n \nbroad-scale environmental context\n\n \nlocal environmental context\n\n \nenvironmental medium\n\n \ntarget\n\n \ncreator\n\n \nmaterials required\... |
85,699 | High-Yield Monocyte/Macrophage Differentiation from hiPSC | 4 | dx.doi.org/10.17504/protocols.io.14egn37oql5d/v1 | https://www.protocols.io/view/high-yield-monocyte-macrophage-differentiation-fro-cxxbxpin | Lilia Rodriguez, Florence Petit, Janelle Drouin-Ouellet | TITLE: High-Yield Monocyte/Macrophage Differentiation from hiPSC
AUTHORS: Lilia Rodriguez, Florence Petit, Janelle Drouin-Ouellet
[DESCRIPTION]
Here, a highly efficient method for differentiating monocytes/macrophages from hiPSC is described. The process utilizes commercially-available materials to derive CD34+ progen... | ["[Differentiation of iPSCs to Hematopoietic Progenitor Cells (HPCs)] Start with large cultures of pluripotent stem cells around 50–70% confluence cultured on Matrigel hESC.", "[Differentiation of iPSCs to Hematopoietic Progenitor Cells (HPCs)] Coat 6-well plates with fresh Matrigel (1 mg/plate) 1 h to 60 min at 37 °C.... |
40,080 | De-salting of tryptic digested peptides | 3 | dx.doi.org/10.17504/protocols.io.bjdqki5w | https://www.protocols.io/view/de-salting-of-tryptic-digested-peptides-bjdqki5w | avinash.kale | TITLE: De-salting of tryptic digested peptides
AUTHORS: avinash.kale
[STEPS] | [] |
34,970 | Image Registration of MALDI IMS to Microscopy | null | dx.doi.org/10.17504/protocols.io.bed2ja8e | null | Nathan Heath Patterson, Elizabeth Neumann, Jamie Allen, Danielle Gutierrez, Jeff Spraggins | TITLE: Image Registration of MALDI IMS to Microscopy
AUTHORS: Nathan Heath Patterson, Elizabeth Neumann, Jamie Allen, Danielle Gutierrez, Jeff Spraggins
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Scope:</div><div class = "text-block">To process to register MALDI IMS images to different types of... | ["Generate a MALDI imaging mass spectrometry (IMS) pixel map using regToolboxMSRChttps://github.com/nhpatterson/regtoolboxmsrc", "Using FIJI ImageJ, select corresponding laser ablation marks and IMS pixels in the post-acquisition autofluorescence (post-AF) and IMS pixel map, respectively.https://fiji.sc", "Use a \"Land... |
48,709 | The effects of long-term oral antithrombotic agents after intracranial haemorrhage: protocol for a prospective individual participant data meta-analysis of randomised controlled trials | 1 | dx.doi.org/10.17504/protocols.io.bttdnni6 | https://www.protocols.io/view/the-effects-of-long-term-oral-antithrombotic-agent-bttdnni6 | Rustam Al-Shahi Salman, Craig S. Anderson, Oscar R. Benavente, Barbara Casolla, Chen Chen, Xin Cheng, Stuart J. Connolly, Charlotte Cordonnier, Eva-Lotta Glader, Graeme J. Hankey, Peter U. Heuschmann, Jeannette Hofmeijer, Hooman Kamel, Henk Kerkhoff, Catharina J.M. (Karin) Klijn, Christina Kruuse, Kristin Tveitan Larse... | TITLE: The effects of long-term oral antithrombotic agents after intracranial haemorrhage: protocol for a prospective individual participant data meta-analysis of randomised controlled trials
AUTHORS: Rustam Al-Shahi Salman, Craig S. Anderson, Oscar R. Benavente, Barbara Casolla, Chen Chen, Xin Cheng, Stuart J. Connoll... | [] |
98,023 | Behavior: Analysis Protocol | 0 | dx.doi.org/10.17504/protocols.io.eq2lyw3nwvx9/v1 | https://www.protocols.io/view/behavior-analysis-protocol-dbyf2ptn | Sasha Burwell | TITLE: Behavior: Analysis Protocol
AUTHORS: Sasha Burwell
[DESCRIPTION]
This protocol details visualisation and analysis of the collected reward learning behavior data.
[STEPS]
SECTION: Analysis Protocol
1. To visualize licks around reward delivery times (ex, Fig. 2b), load a
file into the workspace and run
SE... | ["[Analysis Protocol] To visualize licks around reward delivery times (ex, Fig. 2b), load a \n \n file into the workspace and run", "[Analysis Protocol] Move all the collected data from a mouse (one \n \n file per day of behavior) into the same subfolder (ex, called ‘Data’).", "[Analysis Protocol] Run the Matlab code",... |
49,419 | Investigating Invalid DOIs in COCI | 5 | dx.doi.org/10.17504/protocols.io.buhjnt4n | https://www.protocols.io/view/investigating-invalid-dois-in-coci-buhjnt4n | Nooshin Shahidzadeh, Alessia Cioffi, Arianna Moretti, Sara Coppini | TITLE: Investigating Invalid DOIs in COCI
AUTHORS: Nooshin Shahidzadeh, Alessia Cioffi, Arianna Moretti, Sara Coppini
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">A preliminary note</span></div><div class = "text-block"><span>This protocol illustrates the workflo... | ["[Reading the CSV Data]\nFirst we read the CSV of the invalid DOIs, containing all the invalid cited DOIs in one column and their valid citing counterparts in another.", "[Creating the Output JSON File]\nWe create a JSON file for the output data that strictly answer the research questions and data for the visualizatio... |
null | null | null | dx.doi.org/10.17504/protocols.io.i8ichue | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is for isolation of high quality, high molecular weight DNA (20 kb and larger) that is suitable for PacBio library preparation. This protocol has been tested on lyophilized conidia from multiple isolates of <em>Fusarium oxysporum, </em>including f. sp. <em>apii<... | [] |
93,621 | Guide Pratique sur l'Échantillonage des Animaux Vivants (Domestiques, Peridomestiques et Sauvages) pour la Surveillance des Maladies Infectieuses | 1 | dx.doi.org/10.17504/protocols.io.ewov1qb5pgr2/v1 | https://www.protocols.io/view/guide-pratique-sur-l-39-chantillonage-des-animaux-c7nvzme6 | Stefano Catalano | TITLE: Guide Pratique sur l'Échantillonage des Animaux Vivants (Domestiques, Peridomestiques et Sauvages) pour la Surveillance des Maladies Infectieuses
AUTHORS: Stefano Catalano
[DESCRIPTION]
Les cas de maladies causées par des agents pathogènes particulièrement dangereux ou mal diagnostiquées présentent des risq... | [] |
27,721 | MojoSort™ Mouse NK Cell Isolation Kit Column Protocol | null | dx.doi.org/10.17504/protocols.io.7bhhij6 | null | Sam Li | TITLE: MojoSort™ Mouse NK Cell Isolation Kit Column Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>BioLegend MojoSort™ nanobeads work in commonly used separation columns, based on our internal research as well as validation by external testing by academic labs. This s... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes.", "In the final wash of your sample preparation, resuspend the cells in MojoSort™ Buffer by adding up to 4 mL in a 5 mL (12 x 75 mm) polypropylene tube.Note: Keep MojoSort™ Buffer on ice throughout the procedure.", "Filter the cells with... |
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