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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74,313 | Trinity College Botanic Garden long-term monitoring program | 1 | dx.doi.org/10.17504/protocols.io.dm6gpjdedgzp/v1 | https://www.protocols.io/view/trinity-college-botanic-garden-long-term-monitorin-ckthuwj6 | Midori Yajima, Michelle Murray, Jennifer McElwain, Stephen Waldren | TITLE: Trinity College Botanic Garden long-term monitoring program
AUTHORS: Midori Yajima, Michelle Murray, Jennifer McElwain, Stephen Waldren
[DESCRIPTION]
Botanic gardens hold large, documented, and accessible collections of living plants. These represent unique subsets of taxa from different biogeographical region... | ["[Elemental analysis/ Water Use Efficiency] When\nImmediately after the last day of porometry\n\nCollection needs to be after a period of 5 to 10 days of no rain and low winds, to avoid particulates to being washed away", "[Stomatal conductance] When\nEnd of the growing season (July, not later than mid-August)", "[Sto... |
38,171 | Download Sequences from Eurofins - Edit Filenames for Use in Geneious | 5 | dx.doi.org/10.17504/protocols.io.eq2ly3bjegx9/v1 | https://www.protocols.io/view/download-sequences-from-eurofins-edit-filenames-fo-bhh3j38n | Dakota Betz | TITLE: Download Sequences from Eurofins - Edit Filenames for Use in Geneious
AUTHORS: Dakota Betz
[DESCRIPTION]
Our protocols are constantly evolving and old versions will be deleted.
The documents here are not intended to be cited in publications
[GUIDELINES]
This protocol is optimized for Macs for use with the bash... | ["Download sequences from Eurofins (you should have a link in your email). Once downloaded, unzip the folder.", "Optional: Search your four letter code (use command F in Finder) in the Eurofins folder and move all of your sequence files to another folder that is easy to navigate to. \n\nFor example, create a new folder... |
84,533 | Protocol for neurophysiological imaging in human iPSC-derived neurons | 4 | dx.doi.org/10.17504/protocols.io.81wgbxp8ylpk/v1 | https://www.protocols.click/view/protocol-for-neurophysiological-imaging-in-human-i-cwsvxee6 | Natalia Garcia Perez, Yi-Ning Kang, Emma Moles-Garcia, Tom Venneman, Pieter Vanden Berghe | TITLE: Protocol for neurophysiological imaging in human iPSC-derived neurons
AUTHORS: Natalia Garcia Perez, Yi-Ning Kang, Emma Moles-Garcia, Tom Venneman, Pieter Vanden Berghe
[DESCRIPTION]
The protocol describes how to perform neurophysiological imaging experiments on different types of human iPSC-derived neurons.
[... | ["[iPSC-derived neurons generation] Cells were differentiated from human iPSCs (WTC11, KOLF2.1 cell lines) according to published protocols, with some modifications to allow for easier live-cell imaging.", "[iPSC culture and maintenance] The iPSC cell lines (WTC11 and KOLF2.1J) are cultured in Essential 8 medium on Gel... |
43,577 | RNA Electrophoresis in Acrylamide Gels | 4 | dx.doi.org/10.17504/protocols.io.bnszmef6 | https://www.protocols.io/view/rna-electrophoresis-in-acrylamide-gels-bnszmef6 | Jonathan Houseley, Cristina Cruz | TITLE: RNA Electrophoresis in Acrylamide Gels
AUTHORS: Jonathan Houseley, Cristina Cruz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Over the past decade a plethora of noncoding RNAs (ncRNAs) have been identified, initiating an explosion in RNA research. Although RNA sequencing methods provide un... | ["[RNA Electrophoresis in Acrylamide Gels]\nIn a 15 mL tube (Falcon/Corning type), make of an 8% acrylamide, 1× TBE, 42% urea (w/v) solution, and warm to until urea dissolves. Let cool to .\n10 mL\n50 °C\n50 Room temperature", "[RNA Electrophoresis in Acrylamide Gels]\nMeanwhile, prepare the empty gel cassette. It is... |
33,703 | gRNA design and cloning with BbsI into Loop plasmid L1_lacZgRNA-Ck2/3 | null | dx.doi.org/10.17504/protocols.io.bc6fizbn | null | Eftychis Frangedakis, Marta Tomaselli, Susana Sauret-Gueto | TITLE: gRNA design and cloning with BbsI into Loop plasmid L1_lacZgRNA-Ck2/3
AUTHORS: Eftychis Frangedakis, Marta Tomaselli, Susana Sauret-Gueto
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol explains how to design and clone the guide RNA target sequence into a L1 plasmid ready to acc... | ["[Summary of design of gRNA and cloning into L1 with BbsI]", "[Protocol for design of gRNA and cloning into L1 with BbsI]\ngRNA oligo designOrder two oligos that contain the forward and reverse guide sequence plus the overhangs necessary for ligation (highlighted with bold) into L1_lacZgRNA-Ck2 or L1_lacZgRNA-Ck3:olig... |
57,732 | Feeder-free culturing of hPSCs | 2 | dx.doi.org/10.17504/protocols.io.b4mcqu2w | https://www.protocols.io/view/feeder-free-culturing-of-hpscs-b4mcqu2w | Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner | TITLE: Feeder-free culturing of hPSCs
AUTHORS: Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner
[DESCRIPTION]
This collection describes the standard procedure of feeder-free culturing of human pluripotent stem cells (hPSCs) using mTeSR-plus or StemFlex
Collection overview
Coating plates
A... | [] |
11,345 | mRNA purification with Ambion Dynabeads | null | dx.doi.org/10.17504/protocols.io.pbrdim6 | null | Magdalena Julkowska | TITLE: mRNA purification with Ambion Dynabeads
AUTHORS: Magdalena Julkowska
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The mRNA isolation that is usually used prior to RNAseq library preparation protocol</div></div>
[STEPS]
?. [Adjust the volume of 2 ug of RNA to 36 uL with distilled water]
?.... | ["[Adjust the volume of 2 ug of RNA to 36 uL with distilled water]", "[Heat to 65°C for 2 minutes to disrupt secondary structures]", "[Transfer 72 uL of well resuspended Dynabeads to microcentrifuge tube - place on magnet rack for 30 seconds or untill all Dynabeads migrate to the tube well]", "[Discard the supernatant,... |
56,469 | Characterizing the neighborhood risk environment in multisite clinic-based cohort studies: a practical geocoding and data linkages protocol for protected health information | 1 | dx.doi.org/10.17504/protocols.io.b3dvqi66 | https://www.protocols.io/view/characterizing-the-neighborhood-risk-environment-i-b3dvqi66 | Ariann Nassel, Marta G Wilson-Barthes, Chanelle J. Howe, Sonia Napravnik, Michael J. Mugavero, Deana Agil, Akilah J. Dulin | TITLE: Characterizing the neighborhood risk environment in multisite clinic-based cohort studies: a practical geocoding and data linkages protocol for protected health information
AUTHORS: Ariann Nassel, Marta G Wilson-Barthes, Chanelle J. Howe, Sonia Napravnik, Michael J. Mugavero, Deana Agil, Akilah J. Dulin
[DESCR... | [] |
91,218 | Human Placenta Tissue Collection and Preservation Methods - UCSD Female Reproductive TMC | 1 | dx.doi.org/10.17504/protocols.io.36wgq3ydklk5/v1 | https://www.protocols.io/view/human-placenta-tissue-collection-and-preservation-c5bsy2ne | Valentina Stanley, Scott Lindsay-Hewett, Donald P. Pizzo, Louise Laurent, Mana Parast | TITLE: Human Placenta Tissue Collection and Preservation Methods - UCSD Female Reproductive TMC
AUTHORS: Valentina Stanley, Scott Lindsay-Hewett, Donald P. Pizzo, Louise Laurent, Mana Parast
[DESCRIPTION]
Human Placenta Tissue collection and storage protocol for HuBMAP's UCSD Female Reproductive TMC.
[STEPS]
SECTION:... | ["[Preparation] Collect placenta from delivery room within 1 hour of delivery.", "[Preparation] Place placenta into bucket and photograph prior to sampling.", "[Preparation] Select 2 sites (A and B) from which samples will be collected. Aim for sites to be equidistant from the cord, avoid the edges, avoid areas with fi... |
97,097 | USDA LTAR Common Experiment measurement: Dissolved ammonia (NH3) concentration | 0 | dx.doi.org/10.17504/protocols.io.j8nlk8b61l5r/v1 | https://www.protocols.io/view/usda-ltar-common-experiment-measurement-dissolved-da3h2gj6 | Oliva Pisani, John L. Kovar, Robert W. Malone, Amy J. Morrow, Kevin J. Cole | TITLE: USDA LTAR Common Experiment measurement: Dissolved ammonia (NH3) concentration
AUTHORS: Oliva Pisani, John L. Kovar, Robert W. Malone, Amy J. Morrow, Kevin J. Cole
[DESCRIPTION]
Ammonia can form naturally from organic matter mineralization or can enter the aquatic environment via anthropogenic sources such as m... | ["[Sample collection and filtration] Return samples to the laboratory on ice and filter them on collection day if possible.", "[Sample collection and filtration] Filter samples through a 0.45 micrometer (µm) pore-size filter to minimize interference from particulates before chemical analysis.", "[Sample collection and ... |
101,755 | Survival Analysis | 0 | dx.doi.org/10.17504/protocols.io.q26g71m9kgwz/v1 | https://www.protocols.io/view/survival-analysis-dfk33kyn | Núria Peñuelas, Ariadna Laguna, Miquel Vila | TITLE: Survival Analysis
AUTHORS: Núria Peñuelas, Ariadna Laguna, Miquel Vila
[DESCRIPTION]
Mice Survival Analysis
[STEPS]
SECTION: Survival Analysis
1. Registerall births and follow the cohort of animals throughout their lifespan.
SECTION: Survival Analysis
2. Report all natural deaths in the followed cohort.
SECTI... | ["[Survival Analysis] Registerall births and follow the cohort of animals throughout their lifespan.", "[Survival Analysis] Report all natural deaths in the followed cohort.", "[Survival Analysis] Register all animals used for experimental purposes as censored animals, and do not include them in future follow-ups. It i... |
70,731 | Effectiveness of Functional Electrical Stimulation (FES) on Upper Limb Motor Functional Recovery in Stroke Patients: A Randomized Controlled Trial | 4 | dx.doi.org/10.17504/protocols.io.q26g7ybk8gwz/v1 | https://www.protocols.io/view/effectiveness-of-functional-electrical-stimulation-chbjt2kn | Ehsanur Rahman, Dr Hassan M Al-Emran | TITLE: Effectiveness of Functional Electrical Stimulation (FES) on Upper Limb Motor Functional Recovery in Stroke Patients: A Randomized Controlled Trial
AUTHORS: Ehsanur Rahman, Dr Hassan M Al-Emran
[DESCRIPTION]
Introduction:
Stroke is a global health problem that persists with sometimes serious or mild comorbidit... | ["[Fes protocol]"] |
null | null | null | dx.doi.org/10.17504/protocols.io.er3bd8n | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
7 hour IL-3A virus infected NC64A, pellets frozen at -80°C
[GUIDELINES]
<strong>MATERIALS AND ASSAY CONDITIONS:</strong> <br /><br /> 1) 7 hour IL-3A virus infected NC64A, pellets frozen at -80°C<br /> 2) Buffer A: <br />
<ul>
<li>10 mM Tris-Acetate, pH 8.0</li>
<li>10 mM 2-M<... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.cs9wh5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Drosophila melanogaster females' productive system has been an excellent model in studying many developmental events such as stem cell specification and cell migration. The ovaries are composed of a chain of egg chambers starting with the germaruim that buds of stage 1 egg chamb... | [] |
76,821 | DNA extraction from infected or not wheat leaf tissue | 4 | null | https://www.protocols.io/view/dna-extraction-from-infected-or-not-wheat-leaf-tis-cn9vvh66 | Benjamin Schwessinger | TITLE: DNA extraction from infected or not wheat leaf tissue
AUTHORS: Benjamin Schwessinger
[DESCRIPTION]
This protocols is part of the ANU Biosecurity mini-research project #1 "Plant Pathogen Diagnostics: Visuals, subcultures, and genomics".
You will be provided four pots of 3-4 week old wheat plants that have been... | ["[Week 2: Sampling of representative leaf tissue and tissue rupture] Label each 2ml Eppendorf tube containing 2-3 steal beads with the treatment group name and your research group name. Label both the top and the side of each tube clearly.", "[Week 2: Sampling of representative leaf tissue and tissue rupture] Carefull... |
96,568 | Preparation of viral sequencing library for Illumina using NEBNext ultra II | 1 | dx.doi.org/10.17504/protocols.io.kqdg3xrw1g25/v1 | https://www.protocols.io/view/preparation-of-viral-sequencing-library-for-illumi-daiy2cfw | Kenichi Komabayashi | TITLE: Preparation of viral sequencing library for Illumina using NEBNext ultra II
AUTHORS: Kenichi Komabayashi
[DESCRIPTION]
This method uses a metagenomic approach to analyze the genome sequence of RNA viruses. Nucleic acids outside the viral particles are reduced using nucleases and extracted to obtain template RNA... | ["[Reduction of nucleic acids derived from non-virus (pretreatment)] Collect 400 µL virus culture medium in a 1.5 mL tube.", "[Reduction of nucleic acids derived from non-virus (pretreatment)] Centrifuge 3 min at 17,000 x g and aspirate the supernatant with a 1 mL tuberculin syringe.", "[Reduction of nucleic acids der... |
65,163 | Image processing to investigate NEMO recruitment and involvement in mitophagy and inflammatory signaling | 1 | dx.doi.org/10.17504/protocols.io.n2bvj61xxlk5/v1 | https://www.protocols.io/view/image-processing-to-investigate-nemo-recruitment-a-cbvjsn4n | OLIVIA HARDING, Erika L.F. Holzbaur | TITLE: Image processing to investigate NEMO recruitment and involvement in mitophagy and inflammatory signaling
AUTHORS: OLIVIA HARDING, Erika L.F. Holzbaur
[DESCRIPTION]
Beautiful images are not sufficient to robustly characterize and interrogate a cellular mechanism. In order to show recruitment of NEMO and its rela... | ["[Blinded whole-cell recruitment assessment] Start with Z stack images of live cells collected with a 60X objective.", "[Blinded whole-cell recruitment assessment] Max project the Z stack fields of view by ~2 um to capture the center to upper half of the cell.", "[Blinded whole-cell recruitment assessment] Crop each c... |
57,226 | Overview of NCBI's SARS-CoV-2 submission process and the metadata required | 1 | dx.doi.org/10.17504/protocols.io.b35iqq4e | https://www.protocols.io/view/overview-of-ncbi-39-s-sars-cov-2-submission-proces-b35iqq4e | Ruth Timme, Emma Griffiths, Lee Katz, Michael Weigand, Technical Outreach and Assistance for States Team | TITLE: Overview of NCBI's SARS-CoV-2 submission process and the metadata required
AUTHORS: Ruth Timme, Emma Griffiths, Lee Katz, Michael Weigand, Technical Outreach and Assistance for States Team
[DESCRIPTION]
PURPOSE:
This protocol explains the metadata requirements for the following two protocols:
1. SARS... | ["[Three templates needed for NCBI SARS-CoV-2 submission] START HERE FIRST: Read the PHA4GE contextual data specification BEFORE populating your submission templates!\n\nDirect link to the PHA4GE GitHub repository: https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/tree/version_3_dev", "[Three template... |
93,532 | EBT buffer | 3 | dx.doi.org/10.17504/protocols.io.kxygx3x7zg8j/v1 | https://www.protocols.io/view/ebt-buffer-c7j4zkqw | Anna Schmidt, Sarah Nagel, Matthias Meyer | TITLE: EBT buffer
AUTHORS: Anna Schmidt, Sarah Nagel, Matthias Meyer
[DESCRIPTION]
EBT buffer (10 mM Tris-HCl, 0.05% Tween-20, pH 8.0) is used in various steps of sample preparation by the Ancient DNA Core Unit of the MPI-EVA.
[STEPS] | [] |
103,256 | Calcium chloride-mediated transformation of different Chlamydia species | 0 | dx.doi.org/10.17504/protocols.io.kxygxy53wl8j/v1 | https://www.protocols.io/view/calcium-chloride-mediated-transformation-of-differ-dg3y3ypw | Nadja Faessler, Kensuke Shima, Hanna Marti | TITLE: Calcium chloride-mediated transformation of different Chlamydia species
AUTHORS: Nadja Faessler, Kensuke Shima, Hanna Marti
[DESCRIPTION]
Summary
The genetic toolbox for the obligate intracellular bacterial species Chlamydia trachomatis and C. muridarum has rapidly expanded in recent years (Sixt and Valdivia, 2... | [] |
47,679 | High-molecular weight DNA extraction, clean-up and size selection for long-read sequencing | 2 | dx.doi.org/10.17504/protocols.io.bss7nehn | https://www.protocols.io/view/high-molecular-weight-dna-extraction-clean-up-and-bss7nehn | Ashley Jones, Cynthia Torkel, David Stanley, Jamila Nasim, Justin Borevitz, Benjamin Schwessinger | TITLE: High-molecular weight DNA extraction, clean-up and size selection for long-read sequencing
AUTHORS: Ashley Jones, Cynthia Torkel, David Stanley, Jamila Nasim, Justin Borevitz, Benjamin Schwessinger
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Rapid advancements in long-read sequencing tech... | [] |
45,861 | 3. LiCor_Blotting_Protocol | 4 | null | https://www.protocols.io/view/3-licor-blotting-protocol-bq2dmya6 | Elizabeth Fozo | TITLE: 3. LiCor_Blotting_Protocol
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Blotting Protocol for use on LiCor Odyssey imager.</div></div>
[STEPS]
?. [Blotting Protocol for use on LiCor Odyssey imager.]
Use only the Licor Immobilon FL PVDF membranes. Standard PVDF has... | ["[Blotting Protocol for use on LiCor Odyssey imager.]\nUse only the Licor Immobilon FL PVDF membranes. Standard PVDF has an unacceptable background signal in the IR. Handle the membranes with forceps at the very edges, and minimize contact with gloves. Damage to the membrane can show up on the image of the blot. Use ... |
62,491 | Cyanobacteria Total Lipid Extraction from Cell Pellets | 1 | dx.doi.org/10.17504/protocols.io.4r3l2oe3jv1y/v1 | https://www.protocols.io/view/cyanobacteria-total-lipid-extraction-from-cell-pel-b893rz8n | Robbie Martin, Steven W Wilhelm, Katarina A. Jones, Shawn Campagna | TITLE: Cyanobacteria Total Lipid Extraction from Cell Pellets
AUTHORS: Robbie Martin, Steven W Wilhelm, Katarina A. Jones, Shawn Campagna
[DESCRIPTION]
This protocol is designed/used for extraction of total cellular lipids from cyanobacteria samples (either lab cultures or field samples) collected via centrifugation f... | ["Prepare the three separate solutions needed for this extraction protocol as listed below.\n lipid extraction solvent (step 2) with a 1:1 ratio of butanol and lab purified water (water-saturated butanol, and lab purified water", "Prepare the three separate solutions needed for this extraction protocol as follows:\nlip... |
32,238 | Homology modeling for Biochemistry I | null | null | https://www.protocols.io/view/homology-modeling-for-biochemistry-i-bbqnimve | Michael Friedman, Chris Berndsen | TITLE: Homology modeling for Biochemistry I
AUTHORS: Michael Friedman, Chris Berndsen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for homology modeling proteins for use in Biochemistry I at James Madison University. Protocol guides students to use SWISS-Model and PHYRE2 web servers (cit... | ["[Homology Modeling]\nHaving identified the sequence and potential templates, now it is possible to start modeling the sequence to generate a potential sequence.", "[Homology Modeling]\nFollow the steps for the preferred server.\nFor the biochemistry course modeling project, both servers should be used.", "[Homology M... |
null | null | null | dx.doi.org/10.17504/protocols.io.gahbsb6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is provided by BioNano Genomics and was used in:</p>
<p> </p>
<p>Huang Zhihai, Xu Jiang, Xiao Shuiming, Liao Baosheng, Gao Yuan, Zhai Chaochao, Qiu Xiaohui, Xu Wen, Chen Shilin</p>
<p> (2016): Supporting data for 'Comparative optical genome analysis of two Pango... | [] |
44,334 | Biotinylation of Membrane Proteins for Binder Selections | 4 | dx.doi.org/10.17504/protocols.io.bpinmkde | https://www.protocols.io/view/biotinylation-of-membrane-proteins-for-binder-sele-bpinmkde | Benedikt T. Kuhn, Iwan Zimmermann, Pascal Egloff, Lea M. Hürlimann, Cedric A.J. Hutter, Christian Miscenic, Roger J.P. Dawson, Markus A. Seeger, Eric R. Geertsma | TITLE: Biotinylation of Membrane Proteins for Binder Selections
AUTHORS: Benedikt T. Kuhn, Iwan Zimmermann, Pascal Egloff, Lea M. Hürlimann, Cedric A.J. Hutter, Christian Miscenic, Roger J.P. Dawson, Markus A. Seeger, Eric R. Geertsma
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The selective i... | ["[3.1 FX Cloning]\nDesign FX-cloning compatible primers targeting your gene of interest. This is most conveniently done online at the https://www.fxcloning.org website using a FASTA-formatted sequence including a start and stop codon. Order the primer set optimized toward removal of stable hairpin structures (see Note... |
34,641 | Protocols for "Sequencing smart: De novo sequencing and assembly approaches for a non-model mammal" | null | dx.doi.org/10.17504/protocols.io.bd3ri8m6 | null | Graham J Etherington, Darren Heavens, David Baker, Ashleigh Lister, Rose McNelly, Gonzalo Garcia, Bernardo Clavijo, Iain Macaulay, Wilfried Haerty, Federica Di Palma | TITLE: Protocols for "Sequencing smart: De novo sequencing and assembly approaches for a non-model mammal"
AUTHORS: Graham J Etherington, Darren Heavens, David Baker, Ashleigh Lister, Rose McNelly, Gonzalo Garcia, Bernardo Clavijo, Iain Macaulay, Wilfried Haerty, Federica Di Palma
[DESCRIPTION]
<div class = "text-bloc... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.sqwedxe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Conflicting results have been obtained regarding the association between X-ray repair cross complementation group 1 (XRCC1) and susceptibility to hepatocellular carcinoma (HCC). In this study, associations between HCC and three polymorphisms (Arg194Trp, Arg280His, and Arg399G... | [] |
62,800 | Hi-C library construction from young Maize leaves | 4 | dx.doi.org/10.17504/protocols.io.bp2l61mkzvqe/v1 | https://www.protocols.io/view/hi-c-library-construction-from-young-maize-leaves-b9jqr4mw | Yikun Zhao, Yuancong Wang, De Ma, Guang Feng, Yongxue Huo, Zhihao Liu, Ling Zhou, Yunlong Zhang, Liwen Xu, Liang Wang, Han Zhao, Jiuran Zhao, Fengge Wang | TITLE: Hi-C library construction from young Maize leaves
AUTHORS: Yikun Zhao, Yuancong Wang, De Ma, Guang Feng, Yongxue Huo, Zhihao Liu, Ling Zhou, Yunlong Zhang, Liwen Xu, Liang Wang, Han Zhao, Jiuran Zhao, Fengge Wang
[DESCRIPTION]
In a recent study we constructed a high-quality chromosome-level reference genome for... | ["Approximately5 gleaf samples from seedling were cut into minute pieces and cross-linked by 4% formaldehyde solution at room temperature in a vacuum for30 min.", "Each sample was mixed with an excess of 2.5 Molarity (M) glycine to quench the crosslinking reaction for 5 min and then placed on ice for15 min.", "The cros... |
57,800 | Preparing MEF-cultured hPSCs for nucleofection | 4 | dx.doi.org/10.17504/protocols.io.b4pgqvjw | https://www.protocols.io/view/preparing-mef-cultured-hpscs-for-nucleofection-b4pgqvjw | Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner | TITLE: Preparing MEF-cultured hPSCs for nucleofection
AUTHORS: Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner
[DESCRIPTION]
This protocol describes the procedure or preparing MEF-cultured human pluripotent stem cells (hPSCs) for the delivery of plasmids, mRNA or ribonucleoprotein (RNP) using ... | ["When MEF-cultured hPSCs reach 50% confluency, change medium to hPSCs medium + Rock inhibitor, preparing for nucleofection the next day. For each 20 µl nucleofection reaction, prepare half to 1 well of cells.\n\nA detailed protocol on maintaining MEF-cultured hPSCs can be found in the collection \"Maintenance and inac... |
74,529 | Workflow for SNP genotyping using the Hi-Plex method | 4 | dx.doi.org/10.17504/protocols.io.8epv5jnnnl1b/v1 | https://www.protocols.io/view/workflow-for-snp-genotyping-using-the-hi-plex-meth-ckz9ux96 | Anne-Laure Besnard, Daniel J. Park, Bernard J. Pope, Fleur Hammet, Sophie Michon-Coudouel, Marine Biget, Stacy A. Krueger-Hadfield, Stéphane Mauger, Eric J. Petit | TITLE: Workflow for SNP genotyping using the Hi-Plex method
AUTHORS: Anne-Laure Besnard, Daniel J. Park, Bernard J. Pope, Fleur Hammet, Sophie Michon-Coudouel, Marine Biget, Stacy A. Krueger-Hadfield, Stéphane Mauger, Eric J. Petit
[DESCRIPTION]
Many research questions in ecology and evolution require balancing sampli... | ["[Gene Specific Primers (GSPs) and adaptator (TSITs) preparation] Gene Specific Primers (GSP) preparation\n\nGSP synthesis\n\nPrepare a fasta file with 145bp sequences that will be used to design GSPs. Sequence names should contain the position and polymorphism of the targeted SNP.\nAn example of one such sequence is:... |
44,729 | Corona Detective User Protocol V2.0 | 1 | dx.doi.org/10.17504/protocols.io.bpwzmpf6 | https://www.protocols.io/view/corona-detective-user-protocol-v2-0-bpwzmpf6 | Rachel Aronoff, Guy Aidelberg | TITLE: Corona Detective User Protocol V2.0
AUTHORS: Rachel Aronoff, Guy Aidelberg
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Corona Detective</span><span> is based upon a molecular amplification strategy inspired by the ‘</span><a href="https://gmodetective.com... | ["Sample Extraction: Two options are possible A: Direct reactions of inactivated sample (i.e. i.e. saliva, with the addition of 1/100 100x TCEP/EDTA inactivation reagent, and after incubation at for ) as in Rabe and CepkoB: RNA Concentration with 'Magnetic Beads' or other validated extraction methods as described o... |
109,153 | Acupuncture and the Acupoints Selections for Myopia: A Systematic Review and Meta-Analysis Protocol | 0 | dx.doi.org/10.17504/protocols.io.8epv5r4b6g1b/v1 | https://www.protocols.io/view/acupuncture-and-the-acupoints-selections-for-myopi-dnt95er6 | Lailatul Faizah, Guiping Zheng, Shuai Chang, Ming Meng | TITLE: Acupuncture and the Acupoints Selections for Myopia: A Systematic Review and Meta-Analysis Protocol
AUTHORS: Lailatul Faizah, Guiping Zheng, Shuai Chang, Ming Meng
[DESCRIPTION]
Myopia is a common worldwide disease and one of the leading factors of some severe visual impairments. Some systematic reviews have be... | ["[Objective] This study aimed to examine the therapeutic effect of traditional acupuncture on multi acupoints selection on myopia", "[Materials and Methods] Study Registration\nThe present systematic review will use Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) procedure and the Cochrane ... |
21,925 | 'Uniclear' water-based brain clearing for light sheet imaging of electrode tracks | null | dx.doi.org/10.17504/protocols.io.zndf5a6 | null | Susu Chen, Karel Svoboda | TITLE: 'Uniclear' water-based brain clearing for light sheet imaging of electrode tracks
AUTHORS: Susu Chen, Karel Svoboda
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">UniClear procedure for whole mouse brain clearing and refractive index matching. The advantages of this method are that t... | ["Perfuse mouse with cold 4% PFA. Post fix brain for at least at room temperature (RT). Wash brain in PBS to remove fixative. Fixed brain samples can be kept in PBS at before further processing.\n4 °C", "Delipidate brain with SBiP buffer: per adult mouse brain, shaking (70 RPM) at . On the first day: change buffer a... |
40,370 | Purification of the any avian IgY using chloroform, trichloroacetic acid and affinity purification using HiTrap™ Columns. | 4 | dx.doi.org/10.17504/protocols.io.bjnskmee | https://www.protocols.io/view/purification-of-the-any-avian-igy-using-chloroform-bjnskmee | Angel Justiz-Vaillant | TITLE: Purification of the any avian IgY using chloroform, trichloroacetic acid and affinity purification using HiTrap™ Columns.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This IgY purification technology can be used to purified IgY from the egg yolk of any bird ... | ["The IgY fraction of bantam hen was isolated by the chloroform-Trichloroacetic acid (TCA) -affinity chromatography method.", "The egg is washed with warm water and the egg yolk is separated from the egg white.", "The membrane is broken and the egg yolk collected.", "The egg yolk is then diluted 1:3 in phosphate buffer... |
63,897 | SOS Keto Pills! | 3 | dx.doi.org/10.17504/protocols.io.j8nlkk2zdl5r/v1 | https://www.protocols.io/view/sos-keto-pills-camzsc76 | SOS Keto | TITLE: SOS Keto Pills!
AUTHORS: SOS Keto
[DESCRIPTION]
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[STEPS] | [] |
57,864 | Thawing frozen hematopoietic stem cells (HPCs) | 4 | null | https://www.protocols.io/view/thawing-frozen-hematopoietic-stem-cells-hpcs-b4rgqv3w | Jessie Buth | TITLE: Thawing frozen hematopoietic stem cells (HPCs)
AUTHORS: Jessie Buth
[DESCRIPTION]
Protocol to thaw frozen hematopoietic stem cells made with the StemDiff Hematopoietic Kit for subsequent differentiation into microglia.
[BEFORE_START]
Make sure you have:
Enough GFR matrigel + DMEM/F12 to coat the plates
Micro... | ["[Prep Matrigel Plates] Coat tissue culture treated plates with 1 mg/mL GFR Matrigel (Growth GFR Matrigel (Growth factor reduced).", "[Prep Matrigel Plates] Get a frozen aliquot of GFR Matrigel from the hallway -30. The aliquots are typically labeled \"6.5\" or \"12.5\", this is the number of mL DMEM/F12 you will add.... |
57,273 | FACS isolation of intestine-specific C. elegans cells | 4 | dx.doi.org/10.17504/protocols.io.j8nlkk43dl5r/v1 | https://www.protocols.io/view/facs-isolation-of-intestine-specific-c-elegans-cel-b36zqrf6 | Robert TP Williams, Erin Osborne Nishimura | TITLE: FACS isolation of intestine-specific C. elegans cells
AUTHORS: Robert TP Williams, Erin Osborne Nishimura
[DESCRIPTION]
This protocol describes the steps necessary for FACS isolation of C. elegans intestine cells. Section 1 contains general guidelines and considerations to be made before performing a FACS exper... | ["[Before beginning] The starting material required to perform this procedure was generated with either of the following protocols:\nEmbryo Stage Dissociation\nL1 Stage Dissociation\nL3 Stage Dissociation", "[Before beginning] Ensure your cells do not exceed a concentration of . Cell suspensions exceeding this concent... |
57,774 | Measuring nitrate/nitrite (NOx) concentrations in water samples | 1 | dx.doi.org/10.17504/protocols.io.b4nnqvde | https://www.protocols.io/view/measuring-nitrate-nitrite-nox-concentrations-in-wa-b4nnqvde | Jacob Waldbauer, Amy Amy Zimmerman | TITLE: Measuring nitrate/nitrite (NOx) concentrations in water samples
AUTHORS: Jacob Waldbauer, Amy Amy Zimmerman
[DESCRIPTION]
Colorimetric (i.e., UV-visible spectroscopy) assay for measurements of nitrate/nitrite down to 0.5 µmol•L-1 concentration. Vanadium(III) reduces nitrate to nitrite prior to measurement wit... | ["Making standards (sodium nitrate and sodium nitrite)", "Prepare 200 µM stock solution: Dilute 1:500 from 0.1 M stock solution => 20 µL + 9.980 mL nanopure water.", "Dilute the stock solution to the following concentrations in nanopure water: 0, 10, 20, 30, 40, 60, 100, 150, 200 µM.", "Making Reagents and Solutions.",... |
42,665 | NLP of radiology reports: systematic review protocol | 3 | dx.doi.org/10.17504/protocols.io.bmwhk7b6 | https://www.protocols.io/view/nlp-of-radiology-reports-systematic-review-protoco-bmwhk7b6 | Beatrice Alex, Arlene Casey, Emma Davidson, Hang Dong, Daniel Duma, Andreas Grivas, Claire Grover, Victor Suarez Paniagua, Michael Tin Chung Poon, Richard Tobin, William Whiteley, Honghan Wu | TITLE: NLP of radiology reports: systematic review protocol
AUTHORS: Beatrice Alex, Arlene Casey, Emma Davidson, Hang Dong, Daniel Duma, Andreas Grivas, Claire Grover, Victor Suarez Paniagua, Michael Tin Chung Poon, Richard Tobin, William Whiteley, Honghan Wu
[STEPS] | [] |
81,103 | Neuromelanin-positive Neuron Density in Substantia Nigra Image Analysis | 1 | dx.doi.org/10.17504/protocols.io.14egn2kq6g5d/v1 | https://www.protocols.io/view/neuromelanin-positive-neuron-density-in-substantia-ctfpwjmn | Hemanth Ramesh Nelvagal, Toby J Curless, Zane Jaunmuktane | TITLE: Neuromelanin-positive Neuron Density in Substantia Nigra Image Analysis
AUTHORS: Hemanth Ramesh Nelvagal, Toby J Curless, Zane Jaunmuktane
[DESCRIPTION]
The protocol covers the steps to measure neuromelanin-positive neuron density in substantia nigra using image analysis tools including NZConnect (Hamamatsu), a... | ["[Annotation and Deconvolution] Manually annotate the substantia nigra on NZConnect (Hamamatsu), a web-based whole-slide image (WSI) viewer.", "[Annotation and Deconvolution] Download the annotations using a Python script, and then import into QuPath [1] using a Groovy script", "[Segmentation and Calculating Neuromela... |
68,933 | Quantification of various SARS-CoV-2 variant mutations (characteristic of Alpha, Beta, Gamma, Delta, Omicron and Omicron sublineages) in settled solids using digital RT-PCR | 1 | dx.doi.org/10.17504/protocols.io.14egnzrrzg5d/v8 | https://www.protocols.io/view/quantification-of-various-sars-cov-2-variant-mutat-cfjdtki6 | Bridgette Hughes, Bradley J. White, Marlene K. Wolfe, Alexandria B Boehm | TITLE: Quantification of various SARS-CoV-2 variant mutations (characteristic of Alpha, Beta, Gamma, Delta, Omicron and Omicron sublineages) in settled solids using digital RT-PCR
AUTHORS: Bridgette Hughes, Bradley J. White, Marlene K. Wolfe, Alexandria B Boehm
[DESCRIPTION]
This process instruction describes the step... | ["[Preparation] Retrieve all kit components from the One-Step RT-ddPCR advanced kit for probes from the -20 °C freezer and thaw the components on ice.", "[Preparation] Retrieve ddPCR positive control aliquots (50 copies per uL gRNA) from the -80 °C freezer and thaw on ice", "[Preparation] For re-running frozen plates o... |
23,891 | Neuropathy Phentoyping Protocols - Immuno-Electron Microscopy | null | dx.doi.org/10.17504/protocols.io.3jtgknn | null | Eva Feldman | TITLE: Neuropathy Phentoyping Protocols - Immuno-Electron Microscopy
AUTHORS: Eva Feldman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block"><span style = "font-weight:bold;">Phenotyping of Rodents for the Presence of Diab... | ["To perform immunohistochemical staining of the ultrathin sections, float the grid on 1-2 drops of buffer. Some of the grids may sink to the bottom of the drops—this is OK as long as there are no holes in the formvar itself (in this case the grid is worthless).", "Ultrathin sections are cut at the CBL (Cell Biology La... |
null | null | null | dx.doi.org/10.17504/protocols.io.s2regd6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Preparation of <em>Zymoseptoria tritici</em> long-term storage on silica gel. Rodney Pettway 1992, ed. Petteri Karisto 2018.</p>
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.n52dg8e | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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98,527 | CD34+ isolation from human bone marrow | 4 | dx.doi.org/10.17504/protocols.io.36wgq4p53vk5/v2 | https://www.protocols.io/view/cd34-isolation-from-human-bone-marrow-dcf72trn | Mohsen Khosravi-Maharlooei, Markus Holzl, Austin Chen, Megan Sykes | TITLE: CD34+ isolation from human bone marrow
AUTHORS: Mohsen Khosravi-Maharlooei, Markus Holzl, Austin Chen, Megan Sykes
[DESCRIPTION]
This protocol details the steps for isolating CD34+ cells from human bone marrow. The CD34+ cells isolated from this protocol can be used for generating humanized mice through reconst... | ["Transfer the content of the collection bag into a sterile flask", "Add 250 mLBM Medium to the bag and rinse it thoroughly", "Transfer the content of the collection bag into the sterile flask", "Layer 35 mLof the suspension over 15 mL of Histopaque", "Centrifuge the tubes for 30 minutes 500 g without brake at RT", "Co... |
104,533 | Transcription Factor Binding: Singleplex Assay for Function Measurements | 0 | dx.doi.org/10.17504/protocols.io.81wgbzq5qgpk/v1 | https://www.protocols.io/view/transcription-factor-binding-singleplex-assay-for-dibv4an6 | David Ross | TITLE: Transcription Factor Binding: Singleplex Assay for Function Measurements
AUTHORS: David Ross
[DESCRIPTION]
This protocol outlines an assay for measuring the function of plasmid variants in singleplex.
The inputs include separate E. coli glycerol stocks for each of 3 variants, distributed according to the prov... | ["[Fill in required Metadata] Next, select the step-case below that matches the type of transcription factor variants you are measuring. Below, you will see step cases for each of the transcription factor genes of interest. Please select the gene of interest you are investigating to ensure you follow the protocol with ... |
87,180 | Modeling acute visceral pain in adult zebrafish | 4 | dx.doi.org/10.17504/protocols.io.kxygx3ywog8j/v1 | https://www.protocols.io/view/modeling-acute-visceral-pain-in-adult-zebrafish-czdkx24w | Fabiano Costa, Denis Rosemberg | TITLE: Modeling acute visceral pain in adult zebrafish
AUTHORS: Fabiano Costa, Denis Rosemberg
[DESCRIPTION]
This protocol describes a reliable procedure for assessing acute pain responses in adult zebrafish (Danio rerio) based on the abdominal writhing-like phenotype following a single intraperitoneal injection of ac... | ["[ACCLIMATIZATION AND BASELINE BEHAVIORAL RECORDINGS ●TIMING ~ 1 h for acclimatization; 6 min per animal] Transport animals from their holding facility to the experimental room for acclimation 1 h prior to the experiments. Avoid low- or high density of fish to prevent social isolation or crowding stress (tanks must ha... |
22,617 | Bleach synchronisation of C. elegans | null | dx.doi.org/10.17504/protocols.io.2bzgap6 | null | Ida Barlow | TITLE: Bleach synchronisation of C. elegans
AUTHORS: Ida Barlow
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is for obtaining synchronised populations of </span><span style = "font-style:italic;">C. elegans</span><span>. Eggs are harvested from gravid hermaphrodites and allow ... | ["[Washing]\nWash hermaphrodites off plate with several ml of M9 solution and transfer to 15ml falcon tube (Fisher Scientific-Falcon 352096)", "[Washing]\nFill falcon tube up to 15ml with M9 solution", "[Washing]\nCentrifuge for 2 minutes at 1500 rpm (RCF:210, ascending 9; descending 7) – program 1Program 1 retains the... |
26,623 | Single worm lysis | null | dx.doi.org/10.17504/protocols.io.587g9zn | null | Ida Barlow | TITLE: Single worm lysis
AUTHORS: Ida Barlow
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Exraction of genomic DNA (gDNA) from single adult </span><span style = "font-style:italic;">C. elegans </span><span>suitable for downstream molecular biology applications such as PCR.</span></div></div... | ["Prepare 1mL 1X PCR buffer with 0.4mg/ml Proteinase K:nb. volumes can be scaled as required\n[water]\n[10X PCR buffer (pH8.3)]\n[20mg/ml Proteinase K solution]\n[Total volume]\n10X PCR buffer (pH8.3) preparation:AutoclaveCool (temperature affects pH)pH meter and add hydrochloric acid to achieve the correct pH", "Prepa... |
98,385 | Enterovirus D68 3C protease small scale expression and purification protocol | 1 | dx.doi.org/10.17504/protocols.io.dm6gpzrkdlzp/v1 | https://www.protocols.io/view/enterovirus-d68-3c-protease-small-scale-expression-dcbr2sm6 | Korvus Wang, michael fairhead, Eleanor Williams | TITLE: Enterovirus D68 3C protease small scale expression and purification protocol
AUTHORS: Korvus Wang, michael fairhead, Eleanor Williams
[DESCRIPTION]
This protocol details the expression and purification of enterovirus D68 3C protease construct bearing a C-terminal His-tag at small scale (<6L).
[GUIDELINES]
Con... | ["[Plasmid Transformation] Transform the D68EV3C construct (Addgene plasmid #204817) into BL21(DE3) and store a glycerol stock of this at -80 °C", "[Protein expression] When the OD600 reaches approximately 4.0, lower the temperature and shaker speed to and incubate 1440 min", "[Protein Purifcation] Perform IMAC to e... |
37,961 | HTAPP_Dissociation of human ovarian cancer resection to a single-cell suspension for single-cell RNA-seq | 1 | dx.doi.org/10.17504/protocols.io.bhbhj2j6 | https://www.protocols.io/view/htapp-dissociation-of-human-ovarian-cancer-resecti-bhbhj2j6 | Isaac Wakiro, Sara Napolitano, Jingyi Wu, Sébastien Vigneau, Asaf Rotem, Orit Rozenblatt-Rosen, Bruce Johnson, Aviv Regev | TITLE: HTAPP_Dissociation of human ovarian cancer resection to a single-cell suspension for single-cell RNA-seq
AUTHORS: Isaac Wakiro, Sara Napolitano, Jingyi Wu, Sébastien Vigneau, Asaf Rotem, Orit Rozenblatt-Rosen, Bruce Johnson, Aviv Regev
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Thi... | ["[Sample Description and Allocation]\nReport sample processing information.\n[Wet Ice]\nSample ID:Anatomical Site of Resection (e.g., Ovary, Omentum): \nDate: Media Used for Transportation:Person Processing:", "[Sample Description and Allocation]\nTransfer sample to a Petri dish with cold PBS (or RPMI 1640 without phe... |
24,518 | Golden Gate plasmids used for transfection of Perkinsus marinus | null | dx.doi.org/10.17504/protocols.io.37egrje | null | Elin Einarsson | TITLE: Golden Gate plasmids used for transfection of Perkinsus marinus
AUTHORS: Elin Einarsson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We have created plasmids for transfection of the parasite Perkinsus marinus using Golden Gate cloning. We have explored the possibility to either FACS sort (... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.c53y8m | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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40,248 | Polson method for IgY isolation with modification. | 6 | dx.doi.org/10.17504/protocols.io.bjiykkfw | https://www.protocols.io/view/polson-method-for-igy-isolation-with-modification-bjiykkfw | Angel Justiz-Vaillant | TITLE: Polson method for IgY isolation with modification.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Immunoglobulin Y (IgY) is the mayormolecule present in the avian egg yolk. This protein functions as antibody and fulfils important functions in the protection o... | ["Wash the egg with warm water and crack the eggshell carefully.", "Separate the egg yolk from the egg white manually and place the egg content on a tissue paper to help to remove as much egg white as possible.", "Wash four times the egg yolk with 100 ml of PBS, pH 7.4.", "Break the egg yolk membrane and pour it into a... |
34,273 | Adapter ligation with AMII | null | dx.doi.org/10.17504/protocols.io.bdp9i5r6 | null | Josh Quick | TITLE: Adapter ligation with AMII
AUTHORS: Josh Quick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a subprotocol for performing adapter ligation with AMII</div></div>
[STEPS]
?. Set up the following AMII adapter ligation reaction:Component ... | ["Set up the following AMII adapter ligation reaction:Component VolumeEnd-repaired amplicon pools NEBNext Quick Ligation Reaction Buffer (5X) Adapter Mix (AMII) ... |
37,804 | Selecting the correct transfer membrane for Western blot enhances detection of alpha-synuclein and tau proteins | 1 | dx.doi.org/10.17504/protocols.io.bg6kjzcw | https://www.protocols.io/view/selecting-the-correct-transfer-membrane-for-wester-bg6kjzcw | Gabriele Kaminski Schierle | TITLE: Selecting the correct transfer membrane for Western blot enhances detection of alpha-synuclein and tau proteins
AUTHORS: Gabriele Kaminski Schierle
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The ability to detect proteins by Western blot, particularly from tissue samples, can be hampered... | ["Protein samples were boiled for in 1x and ran on in using the at 200 V for .", "Three membranes were selected to test Western blot transfer and detection, PVDF 0.2 μm PVDF 0.45 μm and nitrocellulose 0.45 μm .", "PVDF membranes were first activated with methanol by incubating for . Nitrocellulose membranes do n... |
65,809 | Historical Samples Extraction | 1 | dx.doi.org/10.17504/protocols.io.81wgb68x1lpk/v1 | https://www.protocols.io/view/historical-samples-extraction-cchrst56 | Dakota Betz | TITLE: Historical Samples Extraction
AUTHORS: Dakota Betz
[DESCRIPTION]
Extraction protocol for historical samples. Requires overnight incubation and rotary mixer.
[GUIDELINES]
Important Safety Note: Complete extraction steps in a fume hood and be very careful about any skin contact. Extraction buffer contains hazard... | ["[Extraction Buffer Preparation] In a 50 mL conical:\n50 g guanidine isothiocyanate\n5.3 mL 1M Tris-HCl pH 7.5\n5.5 mL 0.2M EDTA\n10.6 mL 20% Sarkosyl\n1 mL B-mercaptoethanol\nAdd 50 mL of ddH2O.", "[Day 1 - Incubation] For each sample: place tissue in a 1.5 mL eppendorf tube with 200 uL of extraction buffer.", "[Day... |
33,648 | Extraction of Total Soluble Lipid from Ground Coral Samples | null | dx.doi.org/10.17504/protocols.io.bc4qiyvw | null | Rowan Mclachlan, Agus Munoz-Garcia, Andrea Grottoli | TITLE: Extraction of Total Soluble Lipid from Ground Coral Samples
AUTHORS: Rowan Mclachlan, Agus Munoz-Garcia, Andrea Grottoli
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This method is adapted and updated from methods originally published in Grottoli et al. (2004) and is based on the original ... | ["[Freeze dry ground coral samples]\nLoad samples into the freeze dryer. When freeze dryer is at the desired temperature and vacuum (Fig. 1), remove your samples (which are in the Freeze-Drying Vials) from the -80 °C freezer, and loosen the caps of each vial, but do not remove completely. A maximum of 60 samples can be... |
24,359 | RNAscope pretreatment optimized for fixed frozen retinas | null | dx.doi.org/10.17504/protocols.io.32fgqbn | null | Grace Burgin, Inbal Benhar | TITLE: RNAscope pretreatment optimized for fixed frozen retinas
AUTHORS: Grace Burgin, Inbal Benhar
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a pretreatment for RNAscope optimized for fixed frozen retina sections </div><div class = "text-block">(emphasizes adhesion of tissue to the sli... | [] |
44,295 | Immunohistochemical staining, vibratome sections | 4 | dx.doi.org/10.17504/protocols.io.eq2lypnkqlx9/v1 | https://www.protocols.io/view/immunohistochemical-staining-vibratome-sections-bphfmj3n | Joris Van Asselberghs, Veerle Baekelandt | TITLE: Immunohistochemical staining, vibratome sections
AUTHORS: Joris Van Asselberghs, Veerle Baekelandt
[DESCRIPTION]
This protocol outlines general procedures for Immunohistochemical staining, using vibratome sections.
[BEFORE_START]
This protocol uses floating sections in 24-well plate in 1 X.
[STEPS]
SECTION: ... | ["[Quench Endogenous Peroxidase Activity] Incubate samples in 1 x PBS 3% H2O2, for 10 min at Room temperature on the wobbler (to quench endogenous peroxidase activity) using 500 µL / well.", "[Quench Endogenous Peroxidase Activity] Rinse with 0.1 % (v/v).", "[Quench Endogenous Peroxidase Activity] Rinse with 0.1 % (v/v... |
59,185 | Determination of microglucosuria | 6 | dx.doi.org/10.17504/protocols.io.b52rq8d6 | https://www.protocols.io/view/determination-of-microglucosuria-b52rq8d6 | El Hadji Malick Ndour, Khuthala Mnika, Fatou Gueye Tall, Moussa Seck, Indou Deme Ly, Victoria Nembaware, Gaston Kuzamunu Mazandu, Helene Ange Therese Sagna-Bassene, Rokhaya Dione, Aliou Abdoulaye Ndongo, Jean Pascal Demba Diop, Nene Oumou Kesso Barry, Moustapha Djite, Rokhaya Ndiaye Diallo, Papa Madieye Gueye, Saliou D... | TITLE: Determination of microglucosuria
AUTHORS: El Hadji Malick Ndour, Khuthala Mnika, Fatou Gueye Tall, Moussa Seck, Indou Deme Ly, Victoria Nembaware, Gaston Kuzamunu Mazandu, Helene Ange Therese Sagna-Bassene, Rokhaya Dione, Aliou Abdoulaye Ndongo, Jean Pascal Demba Diop, Nene Oumou Kesso Barry, Moustapha Djite, Ro... | ["[DETERMINATION OF MICROGLUCOSURIA] . OBJECTIVE\nThe aim is to describe how microglucosuria is determined.", "[DETERMINATION OF MICROGLUCOSURIA] SAMPLING\n\nUrine \nA meadstream voiding urine sample at random at any time between 8 a.m. and 2 p.m. is collected. The urine sample is centrifuged before performing the tes... |
38,211 | mcSCRB-seq2 protocol | 1 | dx.doi.org/10.17504/protocols.io.n92ldyer9l5b/v1 | https://www.protocols.io/view/mcscrb-seq2-protocol-bhjbj4in | Lucas Esteban Wange, Johannes JWB Bagnoli, Aleksandar Janjic, Wolfgang Enard | TITLE: mcSCRB-seq2 protocol
AUTHORS: Lucas Esteban Wange, Johannes JWB Bagnoli, Aleksandar Janjic, Wolfgang Enard
[DESCRIPTION]
mcSCRB-seq2 is the improved version of our published protocol molecular crowding SCRB-seq (mcSCRB-seq) (https://www.nature.com/articles/s41467-018-05347-6/).
Following changes were introdu... | ["[Preparation] Before starting clean all surfaces and pipettes with RNase Away. \nApply RNase Away for 3-5 minutes and wipe away with a clean tissue.", "[Preparation] When running the protocol for the first time, prepare Cleanup Beads as described in Appendix 1.", "[Preparation] When running the protocol for the first... |
64,833 | https://www.facebook.com/primaweightlossdragonsdenUnitedKingdom/ | 1 | dx.doi.org/10.17504/protocols.io.81wgb6wqnlpk/v1 | https://www.protocols.io/view/https-www-facebook-com-primaweightlossdragonsdenun-cbi9skh6 | roxyhimb | TITLE: https://www.facebook.com/primaweightlossdragonsdenUnitedKingdom/
AUTHORS: roxyhimb
[DESCRIPTION]
Are you not satisfied with your Keto diet feature?
Not receiving actual weight loss results after spending too much time in the gym?
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Prima Weight Loss Dragon... | ["[Prima Weight Loss Dragons Den UK] This supplement can Prima Weight Loss Dragons Den UK help you to get a slim-fit figure with no side effects. Prima Weight loss supplement has received 4.6 ratings out of 5 which is fantastic. This product has Keto diet benefits along with herbal ingredients to burn excess fat to rel... |
69,056 | Fluorescent Immunolabelling for Alpha-Synuclein in neuronal primary culture (Testing PFF toxicity) | 4 | dx.doi.org/10.17504/protocols.io.kxygxzr6wv8j/v1 | https://www.protocols.io/view/fluorescent-immunolabelling-for-alpha-synuclein-in-cfn8tmhw | Sabina Marciano, Rong Chen, Ted Dawson, Roberta Marongiu | TITLE: Fluorescent Immunolabelling for Alpha-Synuclein in neuronal primary culture (Testing PFF toxicity)
AUTHORS: Sabina Marciano, Rong Chen, Ted Dawson, Roberta Marongiu
[DESCRIPTION]
This protocol is designed to perform fluorescent immunolabelling on neuronal primary culture after PFF incubation.
The labelling of ... | ["Aspirate the medium from coverslips (aspirate from only a few coverslips at a time).", "Add 4% (wt/vol) PFA /4% (wt/vol) sucrose (1 ml for a 12-well plate).", "Incubate the plate at Room temperature for 15 min.", "Wash 3 times 10 min with PBS/BSA/TWEEN solution.", "Proceed or store in the fridge in PBS, protected fr... |
44,701 | Allelic Exchange using pCJK218_1.3.17 | 4 | null | https://www.protocols.io/view/allelic-exchange-using-pcjk218-1-3-17-bpv5mn86 | Elizabeth Fozo | TITLE: Allelic Exchange using pCJK218_1.3.17
AUTHORS: Elizabeth Fozo
[STEPS]
?. [Markerless Genetic Exchange using p-Cl-Phe with temperature sensitive plasmid, pCJK218]
Design primers for overlap PCR to create deletion and for sequencing.
?. [Markerless Genetic Exchange using p-Cl-Phe with temperature sensitive plasmi... | ["[Markerless Genetic Exchange using p-Cl-Phe with temperature sensitive plasmid, pCJK218]\nDesign primers for overlap PCR to create deletion and for sequencing.", "[Markerless Genetic Exchange using p-Cl-Phe with temperature sensitive plasmid, pCJK218]\nUse overlap PCR to create in-frame deletion. Your deleted gene i... |
40,309 | nCoV-2019 McGill Nanopore LibPrep Protocol, 5 ng NB | 1 | dx.doi.org/10.17504/protocols.io.bjkvkkw6 | https://www.protocols.io/view/ncov-2019-mcgill-nanopore-libprep-protocol-5-ng-nb-bjkvkkw6 | Sarah Reiling, Anne-Marie Roy, Shu-Huang Chen, Josh Quick | TITLE: nCoV-2019 McGill Nanopore LibPrep Protocol, 5 ng NB
AUTHORS: Sarah Reiling, Anne-Marie Roy, Shu-Huang Chen, Josh Quick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Artic nCoV-2019 McGill modified Lunascript Reverse Transcriptase nanopore sequencing protocol.</div></div>
[STEPS]
?. [Native... | ["[Native barcoding]\nBarcode the amplicon pools using native barcodes.\nThis is a ‘one-pot ligation’ protocol for native barcoded ligation libraries. We have seen no reduction in performance compared to standard libraries, and is made faster by using the Ultra II® ligation module which is compatible with the Ultra II®... |
63,082 | Ex Vivo Electrophysiology | 4 | dx.doi.org/10.17504/protocols.io.b9uir6ue | https://www.protocols.io/view/ex-vivo-electrophysiology-b9uir6ue | Alexandra Nelson | TITLE: Ex Vivo Electrophysiology
AUTHORS: Alexandra Nelson
[DESCRIPTION]
This protocol describes preparation of brain slices, setup of electrophysiology rig, and solutions for collecting whole cell and cell attached recordings.
[STEPS]
SECTION: Preparing Brain Slices
1. Setup
SECTION: Preparing Brain Slices
1.1. Deca... | ["[Preparing Brain Slices] Setup", "[Preparing Brain Slices] Decant about 150 mL of 1X Glycerol-based ACSF solution into a small bottle or beaker and place in the freezer (see recipes for all solutions at bottom).", "[Preparing Brain Slices] Once mixed, decant some of the 1X ACSF into your slice storage chamber.\nPlace... |
99,747 | Diversity of bird communities and pressure from the recreational transformation | 0 | null | https://www.protocols.io/view/diversity-of-bird-communities-and-pressure-from-th-ddnb25an | Tatiana Shupova, Svetozar Dumenko | TITLE: Diversity of bird communities and pressure from the recreational transformation
AUTHORS: Tatiana Shupova, Svetozar Dumenko
[DESCRIPTION]
Recreational activity leads to a complex
transformation of the forest ecosystem. These disturbances taken together
affect the habitat conditions of birds.
The transformation ... | ["[Diversity of bird communities and pressure from the recreational transformation of riverbank tree biotopes of Siverskyi Donets River] Recreational activity leads to a complex\ntransformation of the forest ecosystem. These disturbances taken together\naffect the habitat conditions of birds. \nThe transformation of bi... |
null | null | null | dx.doi.org/10.17504/protocols.io.k45cyy6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>To amplify the target regions of GATA3 for studying rs3824662 polymorphism, a web-based primer designing tool available at <a href="http://bioinfo.ut.ee/primer3-0.4.0" target="_blank">http://bioinfo.ut.ee/primer3-0.4.0</a> facilitates crafting the set of outer primers [forwar... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.eygbftw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
A collection of protocols designed to guide the user in processing a viral metagenome from raw sequence data to assembly, and subsequent analysis. The user uses <em>actual</em> reads from <a href="https://github.com/MicroB3-IS/osd-analysis" target="_blank">Ocean Sampling Day (20... | [] |
94,081 | Quantification of area and optical density of intracellular neuromelanin with Image J | 1 | dx.doi.org/10.17504/protocols.io.81wgbxer1lpk/v1 | https://www.protocols.io/view/quantification-of-area-and-optical-density-of-intr-c749zqz6 | Camille Guillard-Sirieix, Thais Cuadros, Miquel Vila | TITLE: Quantification of area and optical density of intracellular neuromelanin with Image J
AUTHORS: Camille Guillard-Sirieix, Thais Cuadros, Miquel Vila
[DESCRIPTION]
Quantification of area and optical density of intracellular neuromelanin with Image J
[STEPS]
SECTION: Image Acquisition
1. Scan sections using 20x o... | ["[Image Acquisition] Scan sections using 20x objective (NA=0.8) with pre-set focusing and exposure parameters for optimal NM signal quality with an automated Slide Scanner Olympus (SLIDEVIEW VS200, Tokyo, Japan).", "[Image Acquisition] Acquire SNpc images with Qupath v0.5.0 software", "[Neuromelanin Quantification] Up... |
86,775 | CXCL2 and IL-1β: prognostic markers and immune cell infiltration targets of colorectal cancer | 5 | null | https://www.protocols.io/view/cxcl2-and-il-1-prognostic-markers-and-immune-cell-cyyxxxxn | Wen-Juan Zhang, Ke-Yun Li, Sheng Peng, Gao-Lu Cao, Sheng-Cheng Shi, Zi-Qing Xiao, Shui-Qin Chen, Shao-Gui Wan | TITLE: CXCL2 and IL-1β: prognostic markers and immune cell infiltration targets of colorectal cancer
AUTHORS: Wen-Juan Zhang, Ke-Yun Li, Sheng Peng, Gao-Lu Cao, Sheng-Cheng Shi, Zi-Qing Xiao, Shui-Qin Chen, Shao-Gui Wan
[DESCRIPTION]
Aims In this paper, the key genes in the occurrence and development of Colorectal car... | ["[Data preprocessing of colorectal cancer tissue transcriptome.] Download the Gene expression matrix of GSE178145 and convert them to blast databases. The GSE178145 is located on the Affymetrix GPL24247 platform (Affymetrix Illumina NovaSeq 6000) and is submitted by Wu M. \n\nAll raw data were processed using the R so... |
102,149 | Détection Directe du poliovirus par Séquencage Nanopore (DDNS) - Selle | 4 | dx.doi.org/10.17504/protocols.io.j8nlk8d9wl5r/v1 | https://www.protocols.io/view/d-tection-directe-du-poliovirus-par-s-quencage-nan-dfzd3p26 | Alex Shaw, Catherine Troman, Joyce Akello, Erika Bujaki, Manasi Majumdar, Shannon Fitz, Ben Bellekom, Aine OToole, c.ansley, rachel.colquhoun, arshady, khurshida, alammu, Andrew Rambaut, Javier Martin, Nick Grassly | TITLE: Détection Directe du poliovirus par Séquencage Nanopore (DDNS) - Selle
AUTHORS: Alex Shaw, Catherine Troman, Joyce Akello, Erika Bujaki, Manasi Majumdar, Shannon Fitz, Ben Bellekom, Aine OToole, c.ansley, rachel.colquhoun, arshady, khurshida, alammu, Andrew Rambaut, Javier Martin, Nick Grassly
[DESCRIPTION]
Ce... | ["[Premier tour PCR (semi-nest)] Préparer un mélange maître en utilisant les volumes de réaction détaillés dans le tableau ci-dessous pour le nombre d'échantillons que vous avez plus les contrôles négatifs. Le mélange réactionnel et l'enzyme SSIII sont fournis dans l'emballage suivant: \n\nAmorce avant: Y7 [GGGTTTGTGT... |
53,858 | Introducing GolgiTAG to Cells and Immunoprecipitation of Golgi | 4 | dx.doi.org/10.17504/protocols.io.6qpvrdjrogmk/v1 | https://www.protocols.io/view/introducing-golgitag-to-cells-and-immunoprecipitat-byuapwse | Rotimi Y. Fasimoye, Dario R. Alessi | TITLE: Introducing GolgiTAG to Cells and Immunoprecipitation of Golgi
AUTHORS: Rotimi Y. Fasimoye, Dario R. Alessi
[DESCRIPTION]
Golgi apparatus is essential to the secretory pathway of the cell and by extension helps to maintain cellular homeostasis. It is the main transportation hub of the cell, where molecules dest... | ["[Packaging GolgiTag and ControlTag construct into lentivirus system]", "[Packaging GolgiTag and ControlTag construct into lentivirus system] Grow 2 dishes of HEK293FT cells to 50-60% confluency in Growth media in 10cm Petri Dish.", "[Packaging GolgiTag and ControlTag construct into lentivirus system] Prepare a transf... |
63,849 | Condor CBD Gummies Amazon | 1 | dx.doi.org/10.17504/protocols.io.j8nlkk2qdl5r/v1 | https://www.protocols.io/view/condor-cbd-gummies-amazon-cakhsct6 | Condor CBD Gummies | TITLE: Condor CBD Gummies Amazon
AUTHORS: Condor CBD Gummies
[DESCRIPTION]
Condor CBD Gummies Para QueSirve - You plan to recuperate just as truly feel over and above anyone's expectations previously! However when you are encountering steady medical conditions, it tends to be hard to feel your ideal. This is the reas... | ["Condor CBD Gummies Amazon Shark TankReviews [HOAX OR SCAM]{Update 2022}- Benefits,Ingredients,side effects and Is it legitor Does it Really Work , What To Know Before Using It??", "Soothes Your Stress And Anxiety And Tension Quick", "Fantastic For Easing Discomfort/ Body Pains", "Helps In Reducing Back And Neck Pain ... |
27,734 | UC Davis - Atheroma Quantification | null | dx.doi.org/10.17504/protocols.io.7bwhipe | null | Amparo Villablanca | TITLE: UC Davis - Atheroma Quantification
AUTHORS: Amparo Villablanca
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Increased lipid accumulation in the artery wall and atherosclerotic lesion development are two hallm... | ["Mice are anesthetized with an intraperitoneal injection with 50 mg pentobarbital/kg weight.", "Immediately after sacrifice, aortas are perfused with phosphate-buffered saline to remove blood\nafter venting and nicking the heart.", "After careful removal of periadventitial fat, aortas are excised and fixed (4% followe... |
57,042 | S1 file | 6 | dx.doi.org/10.17504/protocols.io.b3xsqpne | https://www.protocols.io/view/s1-file-b3xsqpne | Évelyn Silva de Melo Soares, Camila Celeste Brandão Ferreira Ítavo, Luís Carlos Vinhas Ítavo, Geraldo Tadeu dos Santos, Carlos Eduardo Domingues Nazário, Israel Shekinah Souza Soares, Leandro Fontoura Cavalheiro | TITLE: S1 file
AUTHORS: Évelyn Silva de Melo Soares, Camila Celeste Brandão Ferreira Ítavo, Luís Carlos Vinhas Ítavo, Geraldo Tadeu dos Santos, Carlos Eduardo Domingues Nazário, Israel Shekinah Souza Soares, Leandro Fontoura Cavalheiro
[DESCRIPTION]
Studies comparing methodologies for fatty acids are very imp... | ["Step 1\n Lipid fraction extraction methods\n Total lipid extractions were performed in duplicate, and for a first direct attempt of extraction and derivatization (extraction method 1 – using HPLC-grade n-hexane), the following steps were performed: in a 15 mL centrifuge tube with screw cap and Teflon septum, 1 mL of ... |
51,711 | Preparation of Single Cell Suspensions of the Intra-Epithelial Layer and Lamina Propria from Human Intestinal Tissue | 1 | dx.doi.org/10.17504/protocols.io.bwq7pdzn | https://www.protocols.io/view/preparation-of-single-cell-suspensions-of-the-intr-bwq7pdzn | Steven B. Wells, Pranay Dogra, Peter A. Szabo, Joshua I. Gray, Daniel Caron, Yoonseung Lee, Rory Morrison-Colvin | TITLE: Preparation of Single Cell Suspensions of the Intra-Epithelial Layer and Lamina Propria from Human Intestinal Tissue
AUTHORS: Steven B. Wells, Pranay Dogra, Peter A. Szabo, Joshua I. Gray, Daniel Caron, Yoonseung Lee, Rory Morrison-Colvin
[DESCRIPTION]
This protocol describes a method for the isolation of the i... | ["[Preparing Mediums and Buffers] Create the following IMDM-FBS-PSQ Media in a 500mL bottle of IMDM by using the table below:\n \n Component Volume (mL) Starting Conc. Final Conc.* IMDM 500 - - Penicillin-Streptomycin-Glutamine 5 100X 1X FBS 50 100% 10%", "[Preparing Mediums and Buffers]... |
106,799 | NGAP Data Analysis Protocol | 0 | dx.doi.org/10.17504/protocols.io.14egn614pl5d/v1 | https://www.protocols.io/view/ngap-data-analysis-protocol-dkip4udn | Gordon Qian, Ryan Davis, Jennifer Johnston | TITLE: NGAP Data Analysis Protocol
AUTHORS: Gordon Qian, Ryan Davis, Jennifer Johnston
[DESCRIPTION]
Protocol for processing and analysis of data in the Neuronal Genome Atlas for Parkinsons (NGAP) on Illumina Connected Analytics (ICA). The protocol details the processing of data through the germline and somatic varia... | ["[Running Dragen Germline/Somatic Whole Genome 4.2.4 v2 pipeline] Running the Illumina Connected Analytics (ICA) DRAGEN pipeline can be done via a semi-automated python script that allows jobs to be submitted through the Command Line Interface (CLI).\nMake sure the following requirements are available:\n o ... |
101,559 | OSU TriState SenNet Processing and Storing of Normal Donor Lungs | 1 | dx.doi.org/10.17504/protocols.io.n92ld8r8nv5b/v1 | https://www.protocols.io/view/osu-tristate-sennet-processing-and-storing-of-norm-dfex3jfn | Sean D. Stacey, Brenda F. Reader, Lorena Rosas, Victor Peters, Ana L Mora, mauricio.rojas | TITLE: OSU TriState SenNet Processing and Storing of Normal Donor Lungs
AUTHORS: Sean D. Stacey, Brenda F. Reader, Lorena Rosas, Victor Peters, Ana L Mora, mauricio.rojas
[DESCRIPTION]
This protocol describes the processing and storing of normal donor lungs by the Comprehensive Transplant Center (CTC) Human Tissue Bio... | ["[Objective] To preserve lung tissue for further downstream cellular, protein, RNA, or DNA analyses.", "[Preparation]", "[Preparation] In the biosafety cell culture hood, place three underpads and all needed equipment, including biohazard receptacles, surgical kits, and specimen holders. Before beginning, check that a... |
79,629 | The extraction of cross-kingdom biofilm DNA using Zymo Reasearch Quick-DNA Fecal/Soil Microbe Kits. | 4 | null | https://www.protocols.io/view/the-extraction-of-cross-kingdom-biofilm-dna-using-crzmv746 | Lindsay Kate Newbold, Daniel S Read, Joetay, Jonathan Warren, kerry.walsh | TITLE: The extraction of cross-kingdom biofilm DNA using Zymo Reasearch Quick-DNA Fecal/Soil Microbe Kits.
AUTHORS: Lindsay Kate Newbold, Daniel S Read, Joetay, Jonathan Warren, kerry.walsh
[DESCRIPTION]
The extraction of DNA from environmental samples, including soils, sediments, water, and biofilms, is a crucial sta... | ["[Sample Preparation] In field samples are taken by the Environment Agency, and 5 mL biofilm suspension preserved in equal amounts of preservation buffer: 3.5 Molarity (M) ammonium sulphate, 17 millimolar (mM) sodium citrate, 13 millimolar (mM) EDTA. Samples are frozen in \n \n prior to laboratory preparation.", "[Sa... |
99,234 | Detection of Bordetella pertussis and Bordetella parapertussis Using the ABI 7500 Real-time PCR System | 0 | dx.doi.org/10.17504/protocols.io.6qpvr863zlmk/v1 | https://www.protocols.io/view/detection-of-bordetella-pertussis-and-bordetella-p-dc6a2zae | Martin Cheung, Tracy Lee, Robert B Azana, Loretta Janz, Natalie Prystajecky, Linda Hoang | TITLE: Detection of Bordetella pertussis and Bordetella parapertussis Using the ABI 7500 Real-time PCR System
AUTHORS: Martin Cheung, Tracy Lee, Robert B Azana, Loretta Janz, Natalie Prystajecky, Linda Hoang
[DESCRIPTION]
This procedure provides instructions for how to perform qualitative PCR (qPCR) for the detection... | ["[Procedure A: Preparing 20X PCR Master Mix] All primer and probe sequences are listed in the materials section of this protocol. \n\nOrder all necessary primers and probes; if received lyophilized reconstitute as per the manufacturers instructions before making desired stock dilutions.", "[Procedure A: Preparing 20X ... |
79,456 | Handling and Sampling Herpetofauna - ISL Peru | 1 | dx.doi.org/10.17504/protocols.io.kxygx98j4g8j/v1 | https://www.protocols.io/view/handling-and-sampling-herpetofauna-isl-peru-crt8v6rw | Zane Libke, Timothy Paine, Gideon Erkenswick, Mrinalini Watsa | TITLE: Handling and Sampling Herpetofauna - ISL Peru
AUTHORS: Zane Libke, Timothy Paine, Gideon Erkenswick, Mrinalini Watsa
[DESCRIPTION]
This protocol contains information on the safe capture and handling of a wide range of herpetofauna in general. It's focus however is on the Neotropics, and specifically it has been... | ["[VISUAL SURVEY] Before sampling begins, research coordinators designate transects. Distances can vary, but to allow for comparisons between different habitat types all transects should be the same distance and receive the same amount of sampling effort (measured as researchers * time, Eg. 4 researchers conducting 2 h... |
19,797 | An organotypic slice model for ex vivo study of neural, immune, and microbial interactions of mouse intestine | null | dx.doi.org/10.17504/protocols.io.xjvfkn6 | null | Luke Schwerdtfeger, Elizabeth Ryan, Stuart Tobet | TITLE: An organotypic slice model for ex vivo study of neural, immune, and microbial interactions of mouse intestine
AUTHORS: Luke Schwerdtfeger, Elizabeth Ryan, Stuart Tobet
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Organotypic tissue slices provide seminatural, three-dimensional microenviron... | ["[Intestinal Tissue Preparation ]\nAdult mice were deeply anesthe- tized with isoflurane and killed by cervical dislocation. The small intestine was removed from the pylorus-duodenal junction to the distal ileum, and the colon, excluding the cecum, was removed. Tissue was placed immediately in 4°C 1 Krebs buffer ... |
79,720 | Prevalencia de COVID-19 asociada con Dengue y Malaria en comunidades rurales y urbanas del norte de Perú | 1 | dx.doi.org/10.17504/protocols.io.kqdg39dk1g25/v1 | https://www.protocols.io/view/prevalencia-de-covid-19-asociada-con-dengue-y-mala-cr4gv8tw | Luz Moyano, Ricardo Gamboa | TITLE: Prevalencia de COVID-19 asociada con Dengue y Malaria en comunidades rurales y urbanas del norte de Perú
AUTHORS: Luz Moyano, Ricardo Gamboa
[DESCRIPTION]
Un nuevo coronavirus, llamado síndrome respiratorio agudo severo coronavirus 2 (SARS-CoV-2), surgió en China a fines de 2019 y, después de menos de 6 meses... | ["[PROCEDIMIENTOS PRE-INTERVENCIÓN] Nos comunicaremos con las autoridades de cada comunidad y las autoridades de salud que estén encargados de dicha localidades para explicar los objetivos del estudio de investigación, solicitaremos el visto bueno de la DIRESA-Tumbes e intituciones involucradas.", "[Enrolamiento y c... |
28,443 | Derivitization of polyphosphate with cystamine to facilitate secondary labeling with biotin | 1 | dx.doi.org/10.17504/protocols.io.7z3hp8n | https://www.protocols.io/view/derivitization-of-polyphosphate-with-cystamine-to-7z3hp8n | Catherine J. Baker, Stephanie A. Smith, James H. Morrissey | TITLE: Derivitization of polyphosphate with cystamine to facilitate secondary labeling with biotin
AUTHORS: Catherine J. Baker, Stephanie A. Smith, James H. Morrissey
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Investigation of the biological roles of inorganic polyphosphate has been facilitated... | ["Prepare and combine all materials in this order to a 1.5, 2 or 5 mL tube. ABC1 Volume (µL)Final Concentration2Water6593500 mM MOPS pH 8.0200100mM41M polyP (mode chain length: 1000)50100 µM ends (50 mM phosphate monomer)5500 mM Cystamine168 mM (80x ends)62M EDAC75150mM7total1000 At the last minute, dissolve dry E... |
91,689 | Tissue processing and freezing after surgery | 1 | null | https://www.protocols.io/view/tissue-processing-and-freezing-after-surgery-c5shy6b6 | Bettina Ergün | TITLE: Tissue processing and freezing after surgery
AUTHORS: Bettina Ergün
[DESCRIPTION]
The aim of this protocol is to document the processing of fresh tissue after surgery.
The collected tissue must also be documented in the files which are linked down below
The protocol descibes in detail how to process the res... | ["[Sample processing in the lab] Fresh tissue should be processed on the same day if possible, but can be stored at 4°C for a maximum of overnight.\nTo reduce pathogens, the tissue should be incubated for 60 min atRoom temperature", "[Sample processing in the lab]", "[Sample processing in the lab]", "[Sample processing... |
25,179 | NEBNext dA-Tailing Module (NEB #E6053) | null | dx.doi.org/10.17504/protocols.io.4t3gwqn | null | New England Biolabs, Menna Teffera | TITLE: NEBNext dA-Tailing Module (NEB #E6053)
AUTHORS: New England Biolabs, Menna Teffera
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The NEBNext dA-Tailing Module has been optimized to efficiently incorporate a non-templated dAMP on the 3 ́ end of a blunt DNA fragment (1). 3 ́-dA DNA tailing p... | ["[dA Tailing]\nMix the following components in a sterile microfuge tube: AB1ComponentVolume2End Repaired, Blunt DNAvariable3NEBNext dA-Tailing Reaction Buffer5 µl4Klenow Fragment (3'→5' exo-)3 µl5Sterile watervariable6Total Volume50 µl\nAB1ComponentVolume2End Repaired, Blunt DNAvariable3NEBNext dA-Tailing Reaction Bu... |
97,835 | SARS-CoV-2 nsp3 macrodomain Time-Resolved FRET peptide displacement assay | 1 | dx.doi.org/10.17504/protocols.io.eq2ly7r2mlx9/v3 | https://www.protocols.io/view/sars-cov-2-nsp3-macrodomain-time-resolved-fret-pep-dbsj2ncn | Haim Barr, Noa Lahav | TITLE: SARS-CoV-2 nsp3 macrodomain Time-Resolved FRET peptide displacement assay
AUTHORS: Haim Barr, Noa Lahav
[DESCRIPTION]
This protocol details the Time-Resolved FRET (TR-FRET) assay for SARS-CoV-2 nsp3 macrodomain (Mac1) binding of adenosine diphosphate (ADP)–ribosylated (ADPr) peptide. This method is intended to ... | ["[Prepare Reagents] PREPARE all of the reagents/buffers required for this experiment.\n\n Assay Buffer\n \n Reagents (dilute reagents in assay buffer for required volume)\n \nDetection Solution (dilute reagents in assay buffer for required volume)", "[Prepare 384-well Plate] PRIME Multi-Drop Combi Tube Dispensing Cass... |
70,240 | Modular Reconstruction and Co-registration of Imaging from Implanted ECoG and SEEG Electrodes | 5 | dx.doi.org/10.17504/protocols.io.5qpvornedv4o/v1 | https://www.protocols.io/view/modular-reconstruction-and-co-registration-of-imag-cgt8twrw | Daniel J Soper, Alex Ross, Dustine Reich, Sydney S. Cash, Ishita Basu, Noam Peled, Angelique C. Paulk | TITLE: Modular Reconstruction and Co-registration of Imaging from Implanted ECoG and SEEG Electrodes
AUTHORS: Daniel J Soper, Alex Ross, Dustine Reich, Sydney S. Cash, Ishita Basu, Noam Peled, Angelique C. Paulk
[DESCRIPTION]
This pipeline involves taking pre- and post-operative images to localized and visualize elect... | ["[Retrieving Images and Saving Files] Retrieve Images\n \nWhen retrieving imaging as DICOMs, you can download the entire imaging series or just the sequence of interest, whichever is easiest for your setup. If there is not a T1 MRI with high enough resolution, a T2/FLAIR image with good resolution can supplement (but ... |
50,134 | Expression and purification of PPM1H phosphatase | 1 | dx.doi.org/10.17504/protocols.io.bu7wnzpe | https://www.protocols.io/view/expression-and-purification-of-ppm1h-phosphatase-bu7wnzpe | Kerryn Berndsen, Axel Knebel, Pawel Lis, Amir Khan, Dario Alessi | TITLE: Expression and purification of PPM1H phosphatase
AUTHORS: Kerryn Berndsen, Axel Knebel, Pawel Lis, Amir Khan, Dario Alessi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A subset of small GTPases of the Rab family including Rab8A (Uniprot: P61006) and Rab10 (Uniprot: P61026) have been identi... | ["[Transformation of plasmid into competent bacteria]\nMix of pET15b 6HIS-SUMO-PPM1H 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 for .\n42... |
96,045 | Co-extraction of RNA and DNA from animal tissue | 4 | dx.doi.org/10.17504/protocols.io.ewov1qrkpgr2/v1 | https://www.protocols.io/view/co-extraction-of-rna-and-dna-from-animal-tissue-c92mz8c6 | Dominik Buchner | TITLE: Co-extraction of RNA and DNA from animal tissue
AUTHORS: Dominik Buchner
[DESCRIPTION]
This protocol describes how to co-extract RNA and DNA from animal tissue samples. Samples are homogenized and simultaneously lyzed by bead-beating. Cell debris is pelleted by centrifugation, the DNA is then subsequently bound... | ["[Sample preparation and lysis] For each sample prepare one 2 mL screwcap tube pre-filled with approximately 400 mg of 2 mm zirconia beads and 0.1 mm glass beads.", "[Sample preparation and lysis] Add up to 30 mg of animal tissue to the prepared tube.", "[Sample preparation and lysis] Add 1000 µL to the sample tube.",... |
81,458 | 10x Protocols: Visium v1 FFPE Library Construction -- University of Minnesota TMCs (CG000407 Rev C) | 1 | dx.doi.org/10.17504/protocols.io.6qpvr4jpogmk/v1 | https://www.protocols.io/view/10x-protocols-visium-v1-ffpe-library-construction-ctsswnee | IOx Genomics, Laura J Niedernhofer, David A Bernlohr | TITLE: 10x Protocols: Visium v1 FFPE Library Construction -- University of Minnesota TMCs (CG000407 Rev C)
AUTHORS: IOx Genomics, Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
Protocols from 10x Genomics for Visium Spatial Gene Expression v1 chemistry on FPPE samples without the CytAssist component.
Version o... | ["10x protocol CG000407, Rev C (Library construction)", "Additional Protocols/Resources\n \n \nhttps://www.10xgenomics.com/support/spatial-gene-expression-ffpe"] |
27,969 | Spot assay | null | dx.doi.org/10.17504/protocols.io.7i9hkh6 | null | Marijn Ceelen | TITLE: Spot assay
AUTHORS: Marijn Ceelen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A variant of the plaque assay in which entire phage dilution ranges can be tested on a single plate. </div></div>
[STEPS]
?. Streak LB plate with E. coli (strain should susceptible to phage lambda. Strains that... | ["Streak LB plate with E. coli (strain should susceptible to phage lambda. Strains that include a prophage lambda are likely to be resistant. Strains LE392 and DH10B have been used with this protocol) and incubate overnight at\n37 °C", "Pick a colony from this plate and use it to inoculate of LB. Incubate this culture... |
79,827 | IHC and image analysis | 4 | dx.doi.org/10.17504/protocols.io.14egn2ojzg5d/v1 | https://www.protocols.click/view/ihc-and-image-analysis-cr7tv9nn | michela.deleidi, Bianca Marchetti, Federico Bertoli, Carmela Giachino | TITLE: IHC and image analysis
AUTHORS: michela.deleidi, Bianca Marchetti, Federico Bertoli, Carmela Giachino
[DESCRIPTION]
A laboratory method that uses antibodies to check for certain antigens (markers) in a sample of tissue. The antibodies are usually linked to an enzyme or a fluorescent dye.
[STEPS]
SECTION: IMMUN... | ["[IMMUNOHYSTOCHEMISTRY AND IMAGE ANALYSIS] For CNS analyses, each brain was cut in the coronal plane and serially-sectioned at 14 μm with a freezing sliding microtome (Leica). For the SNpc, every section from the rostral hippocampus to the anterior aspects of the cerebellar-midbrain junction was saved, coded and mount... |
63,426 | Oplexx Keto - REVIEWS, PRICE, SCAM OR LEGIT? | 3 | dx.doi.org/10.17504/protocols.io.rm7vzy28rlx1/v1 | https://www.protocols.io/view/oplexx-keto-reviews-price-scam-or-legit-b97ar9ie | Tzachi H | TITLE: Oplexx Keto - REVIEWS, PRICE, SCAM OR LEGIT?
AUTHORS: Tzachi H
[DESCRIPTION]
Leading to an early stage dementia triggered by partial brain damage. It’s no wonder scientists nicknamed Alzheimer’s disease as the type 3 diabetes.
[STEPS] | [] |
53,234 | Human Thymus single cell dissociation protocol - Teichmann Lab | 4 | dx.doi.org/10.17504/protocols.io.bx8sprwe | https://www.protocols.io/view/human-thymus-single-cell-dissociation-protocol-tei-bx8sprwe | Jongeun Park, Veronika Kedlian, Chenqu Suo, Liam Bolt, Alexander Steemers, Nadav Yayon, Sarah Teichmann | TITLE: Human Thymus single cell dissociation protocol - Teichmann Lab
AUTHORS: Jongeun Park, Veronika Kedlian, Chenqu Suo, Liam Bolt, Alexander Steemers, Nadav Yayon, Sarah Teichmann
[DESCRIPTION]
This Protocol is intended for human Thymus single cell dissociation.
It includes tissue preservation and handling... | ["[Materials and reagents] 'mso-list:Ignore'>d.", "[Materials and reagents] Enzymes \n1. Liberase TH stock 2.5 mg/mL – Roche, 05401135001\n2. Trypsin – EDTA (0.25%) – Gibco, 25200056\n3. DNaseI (1000X) – Roche, 4716728001\n4. Collagenase type IV (stock 50mg/ml current stock might be different) – Gibco, 1710... |
null | null | null | dx.doi.org/10.17504/protocols.io.gujbwun | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Purpose:</strong> To reproducibly generate fresh preparations of virus for independent experiments.</p>
<p><strong>Summary:</strong> Fresh virus sample for an experiment is generated by a primary infection of exponentially growing host cells from a master stock of vir... | [] |
57,466 | Making LB NGM Plates | 1 | dx.doi.org/10.17504/protocols.io.b4c2qsye | https://www.protocols.io/view/making-lb-ngm-plates-b4c2qsye | Priota Islam | TITLE: Making LB NGM Plates
AUTHORS: Priota Islam
[DESCRIPTION]
C. elegans is maintained in the laboratory on Nematode Growth Medium (NGM) agar which has been aseptically poured into petri plates. Sometimes they can also be grown on LB-NGM, where the LB in the media will promote better growth of the bacteria the worm... | ["[Pre-Autoclave:] Book the autoclave (notebook on top of the machine).", "[Pre-Autoclave:] Take clean flasks from the glass kitchen (Only the ones with autoclave tape on are sterile)", "[Pre-Autoclave:] Measure all the pre-autoclave reagents and add to the flask (Use a new weighing boat and spatula for each reagent. A... |
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