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.jkackse | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Zika Virus propagation</p>
[STEPS]
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73,818 | Amplicon multiplex PCR sequencing of Rift Valley fever virus (RVFV) on Illumina MiSeq | 4 | null | https://www.protocols.io/view/amplicon-multiplex-pcr-sequencing-of-rift-valley-f-ckb2usqe | John Juma, Samuel O. Oyola, Samson Konongoi, Isidore Nsengimana [Rwanda Inspectorate, Competition and Consumer Protection Authority], r.k.mwangi, James Akoko, Richard Nyamota, c.muli, e.kiritu, p.dobi, s.osiany, Amos Onwong'a, rwanja8, Rosemary Sang, Alan Christoffels, Kristina Roesel, Bernard Bett, Samuel O. Oyola | TITLE: Amplicon multiplex PCR sequencing of Rift Valley fever virus (RVFV) on Illumina MiSeq
AUTHORS: John Juma, Samuel O. Oyola, Samson Konongoi, Isidore Nsengimana [Rwanda Inspectorate, Competition and Consumer Protection Authority], r.k.mwangi, James Akoko, Richard Nyamota, c.muli, e.kiritu, p.dobi, s.osiany, Amos ... | ["[RNA extraction] Extract viral RNA from serum or cell-culture supernatants using QIAamp Viral RNA kit (QIAGEN, Hilden, Germany), according to the manufacturer’s instructions. Begin with a volume of 140 µL", "[RT-qPCR] Determine cycle threshold (Ct) values on RNA samples using probe-based reverse transcription quantit... |
88,643 | A small scale of Fusarium oxysporum protoplast generation | 4 | dx.doi.org/10.17504/protocols.io.4r3l226w3l1y/v1 | https://www.protocols.io/view/a-small-scale-of-fusarium-oxysporum-protoplast-gen-c2tbyein | Jun-Ze Zheng, Tao-Ho Chang | TITLE: A small scale of Fusarium oxysporum protoplast generation
AUTHORS: Jun-Ze Zheng, Tao-Ho Chang
[DESCRIPTION]
The generation of fungal protoplasts is crucial for advancing fungal gene editing methods. We aim to implement the ribonucleoprotein (RNP) method for gene editing (Wang et al., 2018). Generating protoplas... | ["[Fungus single spore isolation] Rinse Fusarium oxysporum fungal spores from the two-week-old culture plate with 7 mL distilled water, and filter the spore suspension with sterilized filter paper or 4 layers of Miracloth.", "[Mycelium collection] The 700 µL of germinated spores were added into the filter column.", "[E... |
null | null | null | dx.doi.org/10.17504/protocols.io.iv9ce96 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Please contact Dr. Steven Wilhelm (wilhelm@utk.edu) for additional information regarding this protocol.</p>
[STEPS]
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42,815 | LAMP Master Mix + Reaction Protocol | 3 | dx.doi.org/10.17504/protocols.io.bm27k8hn | https://www.protocols.io/view/lamp-master-mix-reaction-protocol-bm27k8hn | Caterina Villari | TITLE: LAMP Master Mix + Reaction Protocol
AUTHORS: Caterina Villari
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the LAMP (Loop-mediated isothermal amplification) master mix and reaction.</div><div class = "text-block"><span>This protocol is part of the Bark Beetle Mycobi... | [] |
52,672 | Day 1: Background and Fieldwork | 3 | dx.doi.org/10.17504/protocols.io.bxn8pmhw | https://www.protocols.io/view/day-1-background-and-fieldwork-bxn8pmhw | Tom Little | TITLE: Day 1: Background and Fieldwork
AUTHORS: Tom Little
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">ADE 2021 description of work to be done on Day 1 of the practical work</div></div>
[STEPS] | [] |
70,161 | Elevated plus maze protocol | 1 | dx.doi.org/10.17504/protocols.io.dm6gpj8kdgzp/v1 | https://www.protocols.io/view/elevated-plus-maze-protocol-cgrrtv56 | Archana Venkataraman, Holly Ingraham | TITLE: Elevated plus maze protocol
AUTHORS: Archana Venkataraman, Holly Ingraham
[DESCRIPTION]
This protocol describes steps for assessing anxiety-like behavior in rodents using an elevated plus maze test.
The elevated plus maze (EPM) is one of the widely used behavioral assays to measure anxiety-like behaviors in r... | ["Make sure the equipment is clean and dry before use.", "The time spent and distance traveled in the open and closed arms were determined using ANY-maze software and these measures serve as an index of anxiety-like behavior.", "Once ready to start the experiment, place a mouse in the center area of the maze.", "Set up... |
37,042 | Mutational Spectra of SARS-CoV-2 orf1ab polyprotein and Signature mutations in the United States of America | null | dx.doi.org/10.17504/protocols.io.bgesjtee | https://www.protocols.io/view/mutational-spectra-of-sars-cov-2-orf1ab-polyprotei-bgesjtee | Shuvam Banerjee, Sohan Seal, Riju Dey, Kousik Kr. Mondal, Pritha Bhattacharjee | TITLE: Mutational Spectra of SARS-CoV-2 orf1ab polyprotein and Signature mutations in the United States of America
AUTHORS: Shuvam Banerjee, Sohan Seal, Riju Dey, Kousik Kr. Mondal, Pritha Bhattacharjee
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Pandemic COVID-19 outbreak has been caused ... | ["[ORF1ab protein sequence retrieval from the database]\nRetrieve the protein sequences through the NCBI Virus database.\nSpecific input was \"SARS-CoV-2\"", "[ORF1ab protein sequence retrieval from the database]\nRefine the output with a sequence length of 7100 from the initial 7050.\nThe length of the target orf1ab p... |
86,327 | Mito and Glycolysis Stress Tests for Enteroendocrine Cells - Hutu-80 | 4 | dx.doi.org/10.17504/protocols.io.14egn32kpl5d/v1 | https://www.protocols.io/view/mito-and-glycolysis-stress-tests-for-enteroendocri-cyixxufn | Jan-Willem Taanman, r.mezabrovschi | TITLE: Mito and Glycolysis Stress Tests for Enteroendocrine Cells - Hutu-80
AUTHORS: Jan-Willem Taanman, r.mezabrovschi
[DESCRIPTION]
The Seahorse XFp Extracellular Flux Analyzer is designed to compare two different cultures or treatments. Culture cells as usual in either cell culture dishes or flasks as preferred. I... | ["[Day 1 - Harvesting, Counting and Diluting] Harvest two cell cultures flasks - work in a laminar flow hood.", "[Day 1 - Harvesting, Counting and Diluting] Aspirate off medium; rinse each flask with 5 mL of PBS; aspirate off PBS; add 1 mL of accuitase solution to each flask; incubate 5 min at 37 °C; add 9 mL of med... |
46,662 | Quantifying % Cover with ImageJ: An Analysis Tool for Image-based Assessments in Grazing Experiment Studies | 4 | dx.doi.org/10.17504/protocols.io.e6nvw5epdvmk/v1 | https://www.protocols.click/view/quantifying-cover-with-imagej-an-analysis-tool-for-brtem6je | Clara Arboleda-Baena, Claudia Pareja, Javiera Poblete, Eric Berlow, Hugo Sarmento, Ramiro Logares, Rodrigo De La Iglesia, Sergio navarrate | TITLE: Quantifying % Cover with ImageJ: An Analysis Tool for Image-based Assessments in Grazing Experiment Studies
AUTHORS: Clara Arboleda-Baena, Claudia Pareja, Javiera Poblete, Eric Berlow, Hugo Sarmento, Ramiro Logares, Rodrigo De La Iglesia, Sergio navarrate
[DESCRIPTION]
Protocol used in the article “Unifying mic... | ["[PROTOCOL] We analyzed 10 rocks for each treatment, examining the effects of epilithic biofilm grazing by five different species: the chiton Chiton granosus (Frembly 1828), the littorinid Echinolittorina peruviana (Lamarck 1822), the keyhole limpet Fissurella crassa (Lamarck 1822), the scurrinid limpet Scurria arauca... |
62,859 | Standard Operating Procedure for human baited tent traps to sample host-seeking mosquitoes | 1 | dx.doi.org/10.17504/protocols.io.n92ldzq99v5b/v1 | https://www.protocols.io/view/standard-operating-procedure-for-human-baited-tent-b9mjr44n | Kyran Staunton, Tanya L Russell, Thomas Burkot | TITLE: Standard Operating Procedure for human baited tent traps to sample host-seeking mosquitoes
AUTHORS: Kyran Staunton, Tanya L Russell, Thomas Burkot
[DESCRIPTION]
The purpose of this SOP is to outline the materials and processes required to deploy human baited traps to collect host-seeking adult mosquitoes.
Des... | ["[Sampling procedure] Erect the outer mesh structure in the middle of the selected sampling site.\n\nThe specific instructions to set up the structure will vary for different configurations. It is essential that the walls of the outer structure are taut, without loose folds in the fabric where mosquitoes can hide.", "... |
89,886 | Reference Kidney Sample Collection | 1 | null | https://www.protocols.io/view/reference-kidney-sample-collection-c3z6yp9e | Nicholas Lucarelli | TITLE: Reference Kidney Sample Collection
AUTHORS: Nicholas Lucarelli
[DESCRIPTION]
Inclusion:
Minimal pathologic changes
Exclusion:
Evidence of hydronephrosis
Evidence of infectious disease
Proteinuria
Image artifacts
>5% Interstitial Fibrosis and Tubular Atrophy (IFTA)
[STEPS]
SECTION: Sample Collection
1. Patien... | ["[Sample Collection] Patient samples will be obtained from human kidneys, using nephrectomies from renal cancer patients. Tissue sections will be uninvolved and away from tumor areas. Sections will be screened by a pathologist to ensure minimal pathologic changes, and minimal image artifacts.", "[Sample Collection] In... |
67,176 | Dilutions and Pipetting Practice | 4 | null | https://www.protocols.io/view/dilutions-and-pipetting-practice-cdugs6tw | Brian P Teague | TITLE: Dilutions and Pipetting Practice
AUTHORS: Brian P Teague
[DESCRIPTION]
Nowadays, doing molecular biology frequently boils down to "mixing small volumes of clear liquids." The volumes we're working with are very small indeed: down to one or two microliters (a microliter, abbreviated µl, is one one-thousandth of ... | ["[Pipetting Practice] Adjusting the volume of the micropipettor correctly is the most important part of the process. Refer to the image below for how to set each of the micropipettors.", "[Pipetting Practice] Grab the P-1000. \nSet it to transfer 400 µL of liquid. (DO NOT TRY TO MAKE IT READ 4-0-0 - YOU WILL BREAK T... |
85,173 | Capturing and Processing Slaking Images With a Multi-Well Plate | 6 | null | https://www.protocols.click/view/capturing-and-processing-slaking-images-with-a-mul-cxevxje6 | Claire Phillips, Robert E Meadows III, Joaquin Casanova, Bryan Emmett | TITLE: Capturing and Processing Slaking Images With a Multi-Well Plate
AUTHORS: Claire Phillips, Robert E Meadows III, Joaquin Casanova, Bryan Emmett
[DESCRIPTION]
This describes a process to measure soil wet aggregate stability through slaking, or rapid immersion it water. It uses a multi-well plate to process many a... | ["[Sample preparation] Establish how you will count the wells (across or down) and create a spreadsheet identifying the sample in each well. \nExample Document:", "[Sample preparation] The well plate we provided a 3D print file for has a notch in the upper left corner to identify the first column and row.", "[Sample pr... |
47,950 | Analysis of the reproducibility, transparency and quality of economic studies on pharmacological interventions in health included in clinical practice guidelines in Spain 2000-2020 | 3 | dx.doi.org/10.17504/protocols.io.bp2l6b395gqe/v2 | https://www.protocols.io/view/analysis-of-the-reproducibility-transparency-and-q-bs3nngme | juanruanoruiz , Pedro J Gómez Arias, Jesús Gay-Mimbrera, Macarena Aguilar-Luque, Beatriz Isla-Tejera | TITLE: Analysis of the reproducibility, transparency and quality of economic studies on pharmacological interventions in health included in clinical practice guidelines in Spain 2000-2020
AUTHORS: juanruanoruiz , Pedro J Gómez Arias, Jesús Gay-Mimbrera, Macarena Aguilar-Luque, Beatriz Isla-Tejera
[DESCRIPTION... | [] |
28,394 | Human primary T cell culture media | null | dx.doi.org/10.17504/protocols.io.7yihpue | null | Bulent Arman Aksoy, Pınar Aksoy, Megan Wyatt, Chrystal M. Paulos, Jeff Hammerbacher | TITLE: Human primary T cell culture media
AUTHORS: Bulent Arman Aksoy, Pınar Aksoy, Megan Wyatt, Chrystal M. Paulos, Jeff Hammerbacher
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Mix components]
Mix all in a 500 ml 0.22 um filter bottle in the hood:
?. [Mix components]
500 ml RPMI-1640 (Corning™ cellg... | ["[Mix components]\nMix all in a 500 ml 0.22 um filter bottle in the hood:", "[Mix components]\n500 ml RPMI-1640 (Corning™ cellgro™ RPMI 1640 Medium (Mod.) 1X with L-Glutamine)", "[Mix components]\n25 ul of EMD Millipore™ Calbiochem™ β-Mercaptoethanol, Molecular Biology Grade (715 uM)", "[Mix components]\n12.5 ml of Hy... |
40,786 | ELISA for quantification of IL-24 in human serum. | 6 | dx.doi.org/10.17504/protocols.io.bj3skqne | https://www.protocols.io/view/elisa-for-quantification-of-il-24-in-human-serum-bj3skqne | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-24 in human serum.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells. ... | ["An anti-human IL-24 coating antibody is adsorbed onto the microwells by incubation overnight at 4°C.", "Add 50 µl of human serum. Human IL-24 present in the serum sample binds to antibodies adsorbed to the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and later wash to remove unbound protei... |
71,304 | Cell lysis and immunoblotting for protein and phospho-protein quantification | 1 | dx.doi.org/10.17504/protocols.io.5jyl8j5zrg2w/v1 | https://www.protocols.io/view/cell-lysis-and-immunoblotting-for-protein-and-phos-chvgt63w | Dan Dou, C. Alexander Boecker, Erika L.F. Holzbaur | TITLE: Cell lysis and immunoblotting for protein and phospho-protein quantification
AUTHORS: Dan Dou, C. Alexander Boecker, Erika L.F. Holzbaur
[DESCRIPTION]
Here, we describe the procedure by which human iPSC-derived neurons or mouse embryonic fibroblasts (MEFs) were lysed and probed for levels of proteins of intere... | ["[Preparation of cell lysates] Quickly wash cells twice with ice-cold PBS. After the second wash, tilt the dish and completely aspirate all residual PBS.", "[Preparation of cell lysates] Immediately add ice-cold lysis buffer, ensuring that the entire surface is covered by lysis buffer. Place cells on ice.", "[Preparat... |
84,017 | Pressure measurement in intact mouse fundus | 1 | dx.doi.org/10.17504/protocols.io.3byl4q2n8vo5/v1 | https://www.protocols.io/view/pressure-measurement-in-intact-mouse-fundus-cwarxad6 | Maryrose Sullivan, Vivian Cristofaro | TITLE: Pressure measurement in intact mouse fundus
AUTHORS: Maryrose Sullivan, Vivian Cristofaro
[DESCRIPTION]
Each region of the stomach has distinct functional characteristics to ensure coordinated gastric storage and emptying. Inhibitory and excitatory enteric neurotransmission plays an important role in the adapt... | ["[Isolation of Gastric Fundus] Euthanize mice according to IACUC approved method (i.e., CO2 asphyxiation).", "[Isolation of Gastric Fundus] After abdominal incision, excise the stomach by transecting the lower esophagus and the pylorus.", "[Isolation of Gastric Fundus] Quickly place stomach in Sylgard-coated dissectin... |
94,451 | Rotarod-Test for Mice | 4 | dx.doi.org/10.17504/protocols.io.14egn3qpml5d/v1 | https://www.protocols.io/view/rotarod-test-for-mice-c8gtztwn | Cristian González-Cabrera, Katharina Draggendorf, Matthias Prigge | TITLE: Rotarod-Test for Mice
AUTHORS: Cristian González-Cabrera, Katharina Draggendorf, Matthias Prigge
[DESCRIPTION]
The Rotarod Test Protocol for Mice assesses their motor coordination and balance. Mice are trained to walk on a rotating rod in a dimly lit environment and then tested for their ability to maintain bal... | ["[Objective] To assess motor coordination and balance in mice", "[Apparatus] A suitable Rotarod system for mice, including a rotating rod with separate lanes and fall sensors (e.g., SD Instruments or Med Associates).\nDim red lighting for the test environment - not more the 50lux", "[Preparation] Acclimate mice to the... |
22,832 | High resolution labeling of vagal efferent fibers using Dextran-Biotin with counterstaining | null | dx.doi.org/10.17504/protocols.io.2iqgcdw | null | Deborah Jaffey, Terry Powley, Jennifer McAdams, Robert Phillips | TITLE: High resolution labeling of vagal efferent fibers using Dextran-Biotin with counterstaining
AUTHORS: Deborah Jaffey, Terry Powley, Jennifer McAdams, Robert Phillips
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the methods used to trace and enable morphometric quanti... | ["[Animals]\nTwo to four month old malerats in the weight range of 180g to 360g at the time of tracer injection were housed individually in wire hanging cages or in vented rack plastic cages in an Association for Assessment and Accreditation of Laboratory Animal Care-approved temperature (22–24 °C) and humidity (40–60%... |
85,393 | Using MultiQuant and Excel software to evaluate and report multi-analyte targeted LC-MS/MS data | 5 | null | https://www.protocols.click/view/using-multiquant-and-excel-software-to-evaluate-an-cxmrxk56 | Natalie ZM Homer | TITLE: Using MultiQuant and Excel software to evaluate and report multi-analyte targeted LC-MS/MS data
AUTHORS: Natalie ZM Homer
[DESCRIPTION]
This protocol describes how to evaluate and report targeted LC-MS/MS data that has been collected in Analyst software on AB Sciex mass spectrometers. It describes using a Proce... | ["[Using MultiQuant to evaluate Analyst acquired LC-MS/MS data] Create a result file in MultiQuant 3.0.3 by opening the software, selecting an LC-MS/MS data file acquired in Analyst software, that has been acquired following extraction using a protocol with carefully designed calibration curve and known calibration uni... |
35,520 | RTPCR Amplification of SARS-CoV2 Whole Genome for Illumina NGS | null | dx.doi.org/10.17504/protocols.io.bew8jfhw | https://www.protocols.io/view/rtpcr-amplification-of-sars-cov2-whole-genome-for-bew8jfhw | Monica Galiano, Shahjahan Miah, Angie Lackenby, Omolola Akinbami, Joanna Ellis, Maria Zambon | TITLE: RTPCR Amplification of SARS-CoV2 Whole Genome for Illumina NGS
AUTHORS: Monica Galiano, Shahjahan Miah, Angie Lackenby, Omolola Akinbami, Joanna Ellis, Maria Zambon
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">SUMMARY</div></div><div class ... | ["A total amount of 140 µl of RNA (includes some excess) are needed to set up the necessary volume of RT reactions. RNA should be kept on ice or stored at if not immediately used.\n-80 °C", "To ensure uniform heat distribution, we aliquot this mix into 7 x 0.2 (strip) tubes.Cycling program: Hold at Keep cDNA on ice o... |
38,278 | MIBI and IHC solutions | 1 | dx.doi.org/10.17504/protocols.io.bhmej43e | https://www.protocols.io/view/mibi-and-ihc-solutions-bhmej43e | Marc Bosse, Christine Camacho, Sean Bendall, Mike Angelo | TITLE: MIBI and IHC solutions
AUTHORS: Marc Bosse, Christine Camacho, Sean Bendall, Mike Angelo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">These protocols are designed to prepare solutions to be used for the Multiplex Ion Beam Imaging Time of Flight instrument (MIBI_TOF) and IHC related protoco... | ["[Target retrieval solution (Antigen retrieval)]\nMake a fresh 1:10 dilution of target retrieval solution 10x (3-in-1) pH 9 (Dako)in of ultrapure (type 1, >18 MOhms) water ABC1Total volume (mL)Volume (mL) Target retrievalVolume (mL) H2O2252.522.535054541001090\n2.5 mL\n22.5 mL\nABC1Total volume (mL)Volume (mL) Ta... |
null | null | null | dx.doi.org/10.17504/protocols.io.eskbecw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in <a href="https://www.protocols.io/view/CviJI-Purification-From-IL-3A-Virus-Infected-NC64A-er3bd8n" target="_blank">CviJI Purification From IL-3A Virus Infected NC64A Chlorella</a>.
[STEPS]
?.
?.
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100,748 | 709.1 Staining of Dissociated Lung Cells for Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE sequencing) | 0 | dx.doi.org/10.17504/protocols.io.e6nvw1jk7lmk/v2 | https://www.protocols.io/view/709-1-staining-of-dissociated-lung-cells-for-cellu-demk3c4w | Gautam Bandyopadhyay, Jeffrey Malik, Heidie Huyck, Ravi Misra, John Ashton, Gloria S Pryhuber | TITLE: 709.1 Staining of Dissociated Lung Cells for Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE sequencing)
AUTHORS: Gautam Bandyopadhyay, Jeffrey Malik, Heidie Huyck, Ravi Misra, John Ashton, Gloria S Pryhuber
[DESCRIPTION]
This article describes step by step protocol for antibody-staining fr... | ["[Thawing of frozen dissociated human lung cells] Frozen cells were thawed in 37°C water bath and soon after the freezing medium melted cells were transferred into a 15 ml conical tube and the tubes were filled with staining buffer [1% BSA (w/v, Millipore) in DPBS (Biowhittaker)] to dilute the DMSO in freezing medium.... |
null | null | null | dx.doi.org/10.17504/protocols.io.np7ddrn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Human tyrosinase, a protein involved in the melanogenesis pathway, has various mutations in its corresponding gene <em>(TYR)</em> which have been linked to Oculocutaneous Albinism type 1 (OCA1), an autosomal recessive disease. Naturally, this inherited disorder leads to decre... | [] |
48,492 | FCMPASS - Mac - Providing Read and Write Permission | 5 | null | https://www.protocols.io/view/fcmpass-mac-providing-read-and-write-permission-btkknkuw | Joshua Welsh | TITLE: FCMPASS - Mac - Providing Read and Write Permission
AUTHORS: Joshua Welsh
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">If you hear/receive error messages when opening FCMPASS or trying to create a database it likely due to you Mac not providing FCMPASS read and write permissions by default... | ["Close FCMPASS before performing any of the following steps.", "On the top menu bar click 'Go'.", "Hold down the 'Option' key and 'Library' will appear on the menu.", "Click 'Library'", "In the finder window that pops up, click 'Application Support' and scroll down to 'Mathworks'.", "Inside the 'Mathworks' folder, cli... |
11,822 | Overlap extension PCR | null | dx.doi.org/10.17504/protocols.io.psndnde | null | Anna Behle | TITLE: Overlap extension PCR
AUTHORS: Anna Behle
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Linear assembly of PCR fragments.</div><div class = "text-block">Can be used to quickly and efficiently fuse promoters, terminators, fusion proteins etc. without time-consuming sub-cloning steps.</div></... | ["[Primer design]\nBefore starting, thoroughly design and plan your experiment in silico, ideally using cloning software such as SnapGene.Make sure all primers anneal only once in the actual template (e.g. when using a whole genome) and separate parts are able to anneal to each other after PCR. I recommend going throug... |
22,266 | 1M Potassium Citrate Buffer, pH 6.0 | 1 | null | https://www.protocols.io/view/1m-potassium-citrate-buffer-ph-6-0-zy2f7ye | Adrien Assie, Buck Samuel | TITLE: 1M Potassium Citrate Buffer, pH 6.0
AUTHORS: Adrien Assie, Buck Samuel
[DESCRIPTION]
Potassium Citrate Buffer recipe
[STEPS]
1. 700 mL
2. 268.8 g tripotassium citrate or 293.5 g tripotassium citrate monohydrate (880 mM)
3. 26.3 g citric acid monohydrate (125 mM)
4. Adjust pH to 6.0 with 5 M KOH
5. Adjust to10... | ["700 mL", "268.8 g tripotassium citrate or 293.5 g tripotassium citrate monohydrate (880 mM)", "26.3 g citric acid monohydrate (125 mM)", "Adjust pH to 6.0 with 5 M KOH", "Adjust to1000 mL", "Autoclave"] |
90,325 | Multi-electrode array (MEA) | 1 | dx.doi.org/10.17504/protocols.io.j8nlkonj6v5r/v1 | https://www.protocols.io/view/multi-electrode-array-mea-c4fvytn6 | Leonardo A Parra-Rivas | TITLE: Multi-electrode array (MEA)
AUTHORS: Leonardo A Parra-Rivas
[DESCRIPTION]
Multi-electrode array (MEA)
[STEPS]
1. One day before plating, 6-well MEA plates (Axion Biosystems, M384-tMEA-6W) were coated with poly-D-lysine (Millipore Sigma P6407-5MG) in borate buffer
2. ,then washed six times with sterile water a... | ["One day before plating, 6-well MEA plates (Axion Biosystems, M384-tMEA-6W) were coated with poly-D-lysine (Millipore Sigma P6407-5MG) in borate buffer", ",then washed six times with sterile water and aspirated prior use.", "150,000 cells in a 15 µl drop were plated on a 6-well MEA plate. Cultures were maintained for ... |
82,687 | Quantification of TH immunoreactivity | 1 | dx.doi.org/10.17504/protocols.io.n2bvj85qngk5/v1 | https://www.protocols.click/view/quantification-of-th-immunoreactivity-cuy7wxzn | Hong-Yuan Chu, Hong-yuan Chu | TITLE: Quantification of TH immunoreactivity
AUTHORS: Hong-Yuan Chu, Hong-yuan Chu
[DESCRIPTION]
This protocol describes quantification of TH immunoreactivity.
[STEPS]
SECTION: Procedure
1. TH signals from bilateral striatum and cortex are imaged under a 20x objective lens using identical imaging settings.
SECTION: P... | ["[Procedure] TH signals from bilateral striatum and cortex are imaged under a 20x objective lens using identical imaging settings.", "[Procedure] Open the confocal files in Image J software.", "[Procedure] Using the “Rectangle” function to select an area (width x high = 150 x 150) in striatum sections from both hemisp... |
null | null | null | dx.doi.org/10.17504/protocols.io.h6yb9fw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
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?.
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82,394 | 13. Taxon Group: Pycnogonida | 4 | dx.doi.org/10.17504/protocols.io.x54v9d98mg3e/v1 | https://www.protocols.click/view/13-taxon-group-pycnogonida-cup2wvqe | Kesella Scott-Somme, Chris Fletcher, Inez Januszczak | TITLE: 13. Taxon Group: Pycnogonida
AUTHORS: Kesella Scott-Somme, Chris Fletcher, Inez Januszczak
[DESCRIPTION]
This is part of the collection "DToL Taxon-specific Standard Operating Procedures (SOPs) for Marine Metazoa", lead by the Other Metazoa Working Group. The SOP collection contains guidance on how to process t... | [] |
43,311 | Fluorescent Molecular Beacons Mimicking RNA Secondary Structures to Study RNA Chaperone Activity | 2 | dx.doi.org/10.17504/protocols.io.bnipmcdn | https://www.protocols.io/view/fluorescent-molecular-beacons-mimicking-rna-second-bnipmcdn | Pilar Menendez-Gil, Carlos J. Caballero, Cristina Solano, Alejandro Toledo-Arana | TITLE: Fluorescent Molecular Beacons Mimicking RNA Secondary Structures to Study RNA Chaperone Activity
AUTHORS: Pilar Menendez-Gil, Carlos J. Caballero, Cristina Solano, Alejandro Toledo-Arana
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Molecular beacons (MBs) are oligonucleotide probes w... | [] |
86,555 | Immunocytochemistry (ICC) for Progenitor markers FOXA2 and OTX2 | 1 | dx.doi.org/10.17504/protocols.io.q26g7ppp3gwz/v1 | https://www.protocols.io/view/immunocytochemistry-icc-for-progenitor-markers-fox-cyr3xv8n | Ning Xia | TITLE: Immunocytochemistry (ICC) for Progenitor markers FOXA2 and OTX2
AUTHORS: Ning Xia
[DESCRIPTION]
This is the protocol for Immunocytochemistry (ICC) for Progenitor markers FOXA2 and OTX2.
[STEPS]
1. Grow the cells on either 8µm chamber slide or 48-well plate. (1x105cells/well)
- Coating and plating densi... | ["Grow the cells on either 8µm chamber slide or 48-well plate. (1x105cells/well)\n- Coating and plating densities can be found in the differentiation kit", "Aspirate medium and rinse with 1x PBS", "Fixation: Cover cells with warm 4% PFA and fix for 20 min at RT.\n- Cover the vessel and place in the hood... |
null | null | null | dx.doi.org/10.17504/protocols.io.jjjckkn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Introduction</strong></p>
<p>In conventional MR examination glioblastomas multiforme (GBM), metastases and primary CNS lymphomas (PCNSLs) may show very similar appearance. The aim of the study was to evaluate usefulness of multiparametric DSC perfusion and diffusion M... | [] |
99,399 | Implementation outcomes for agitation detection technologies in people with dementia: A systematic review protocol | 0 | dx.doi.org/10.17504/protocols.io.14egn67nyl5d/v1 | https://www.protocols.io/view/implementation-outcomes-for-agitation-detection-te-ddbf22jn | Lorna Smith, Nicolas Farina, Sube Banerjee | TITLE: Implementation outcomes for agitation detection technologies in people with dementia: A systematic review protocol
AUTHORS: Lorna Smith, Nicolas Farina, Sube Banerjee
[DESCRIPTION]
Experiencing agitation can be particularly distressing for people living with dementia and their caregivers. Using technologies to ... | [] |
70,339 | Live-cell imaging: cell death assay | 1 | dx.doi.org/10.17504/protocols.io.n2bvj8yywgk5/v1 | https://www.protocols.io/view/live-cell-imaging-cell-death-assay-cgxbtxin | gurvir.virdi | TITLE: Live-cell imaging: cell death assay
AUTHORS: gurvir.virdi
[DESCRIPTION]
Examining cell death in midbrain dopaminergic neurons using SYTOX Green
[STEPS]
1. Cell death is detected using SYTOX™ Green (SYTOX, Thermo Fisher Scientific) which is excluded from viable cells but exhibits green (SYTOX) fluorescence foll... | ["Cell death is detected using SYTOX™ Green (SYTOX, Thermo Fisher Scientific) which is excluded from viable cells but exhibits green (SYTOX) fluorescence following a loss of membrane integrity. \n\nHoechst 33342 (Hoechst, Thermo Fisher Scientific) is used as a nuclear cell stain.", "Cells were incubated with 500 nM SYT... |
80,239 | Digitization of data from published plots v1.0 | 1 | dx.doi.org/10.17504/protocols.io.n2bvj8wnngk5/v1 | https://www.protocols.io/view/digitization-of-data-from-published-plots-v1-0-cskpwcvn | Gustav Nilsonne, Love Ahnström | TITLE: Digitization of data from published plots v1.0
AUTHORS: Gustav Nilsonne, Love Ahnström
[DESCRIPTION]
Purpose
This is a protocol for digitizing data that have been published in diagrams available as image files (such as .img or .png). The typical use-case is to extract data from published scientific papers for s... | ["[Protocol] Create a folder with a descriptive name to identify the data that are being digitized and the date, for example the first author and year of the published paper, the year of publication, the figure number, and the date of creating the folder, for example: nilsonne_2022_fig1A_digitized_2023-04-22.", "[Proto... |
63,870 | Via Keto Gummies Reviews [SCAM & LEGIT] | Does It Work? | 1 | dx.doi.org/10.17504/protocols.io.x54v9yz6pg3e/v1 | https://www.protocols.io/view/via-keto-gummies-reviews-scam-amp-legit-does-it-wo-cak6scze | viaketobenefit | TITLE: Via Keto Gummies Reviews [SCAM & LEGIT] | Does It Work?
AUTHORS: viaketobenefit
[DESCRIPTION]
Might it be said that you are feeling like your perseverance and energy have decreased? Is it true or not that you are depleted or unmotivated to finish things? Might it be said that you are stressed over your we... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.iascaee | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?. | [] |
20,634 | Adult mouse liver dissociation (on ice) | null | dx.doi.org/10.17504/protocols.io.yd2fs8e | null | Andrew Potter | TITLE: Adult mouse liver dissociation (on ice)
AUTHORS: Andrew Potter
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is used to dissociate adult (10 week) CD-1 mouse liver "on ice", preserving authentic gene expression profiles. The first layer consists of 3.5 hours rotation at ... | ["[Isolate tissue]\nDissect out liver tissue and immerse/transport in ice-cold PBS.", "[Isolate tissue]\nUsing sterile forceps, place tissue on petri dish on ice. Remove excess DPBS using pipet. Mince tissue thoroughly on petri dish on ice (~2 min) until fine paste. Manipulate tissue with forceps while mincing with raz... |
93,218 | Brimblecombe, K.R. et al. (2023) Inhibition of striatal dopamine release by the L-type calcium channel inhibitor isradipine, co-varies with risk factors for Parkinson’s. | 2 | dx.doi.org/10.17504/protocols.io.4r3l27dxxg1y/v3 | https://www.protocols.io/view/brimblecombe-k-r-et-al-2023-inhibition-of-striatal-c7aaziae | Katherine Brimblecombe, Stephanie J Cragg | TITLE: Brimblecombe, K.R. et al. (2023) Inhibition of striatal dopamine release by the L-type calcium channel inhibitor isradipine, co-varies with risk factors for Parkinson’s.
AUTHORS: Katherine Brimblecombe, Stephanie J Cragg
[DESCRIPTION]
This collection contains five protocols detailing methods used in Brimblecom... | [] |
27,689 | MojoSort™ Human CD14 Nanobeads Column Protocol | null | dx.doi.org/10.17504/protocols.io.7ahhib6 | null | Sam Li | TITLE: MojoSort™ Human CD14 Nanobeads 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 simple p... | ["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... |
47,316 | document 16/2 2 | 3 | null | https://www.protocols.io/view/document-16-2-2-bsfunbnw | Maria Guliakina | TITLE: document 16/2 2
AUTHORS: Maria Guliakina
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS] | [] |
69,784 | Structural, biochemical, and cellular characterization of MIGA2 | 4 | dx.doi.org/10.17504/protocols.io.yxmvm27kbg3p/v1 | https://www.protocols.io/view/structural-biochemical-and-cellular-characterizati-cgdyts7w | Zhouping Hong, Karin Reinisch | TITLE: Structural, biochemical, and cellular characterization of MIGA2
AUTHORS: Zhouping Hong, Karin Reinisch
[DESCRIPTION]
Mitoguardin-2, a newly discovered mitochondrial protein at contact with the ER and/or lipid droplets (LDs) was characterized as a lipid transporter and its lipid transfer ability is essential fo... | ["[Structural determination of mitoguardin-2: protein prep, crystallization, MR, and structure determination] Expression, Purification of C.elegans MIGA (106-496)", "[Biochemical experiments: lipid binding and competition assay, lipid transfer assay (FRET or end point), aLD preparation, lipid transfer between aLD and L... |
73,305 | Phage DNA extraction with phenol-chloroform and digestion to single nucleosides | 1 | dx.doi.org/10.17504/protocols.io.8epv5jrxnl1b/v1 | https://www.protocols.io/view/phage-dna-extraction-with-phenol-chloroform-and-di-cjtzunp6 | Adair Borges | TITLE: Phage DNA extraction with phenol-chloroform and digestion to single nucleosides
AUTHORS: Adair Borges
[DESCRIPTION]
This protocol details high-molecular-weight DNA extraction from bacteriophages using phenol-chloroform. Following DNA extraction, DNA is digested down to single nucleosides using the NEB Nucleosi... | ["[Degradation of host nucleic acids] To degrade any non-encapsulated nucleic acids, treat the concentrated phage lysate with 10 µg/mL RNase A (NEB T3018) and 10 µg/mL DNase I (NEB M0303). Digest for 1 h at room temperature or 4 °C overnight. Store phage at 4 °C.", "[Phage DNA extraction (using phenol-chloroform)] Stri... |
90,998 | Ex vivo mouse brain patch clamp recordings combined with uncaging and optogenetic stimulation | 4 | null | https://www.protocols.io/view/ex-vivo-mouse-brain-patch-clamp-recordings-combine-c44wyyxe | enrico.zampese | TITLE: Ex vivo mouse brain patch clamp recordings combined with uncaging and optogenetic stimulation
AUTHORS: enrico.zampese
[DESCRIPTION]
In this protocol we detail the steps to perform ex-vivo brain slices electrophysiology and optogenetic stimulation and/or 2-photon uncaging recordings.
[BEFORE_START]
Please note ... | ["[Prepare patch pipettes] Turn on the Sutter P-1000 puller and enter the desired pull protocol.", "[Prepare patch pipettes] Insert a thick-walled borosilicate glass capillary and press pull.", "[Prepare patch pipettes] Pipette resistance must be of 3 to 5 megaohms.", "[Setting up patch rig and environment] Turn on the... |
87,044 | Protocol SAM-Seq Zea Mays | 4 | dx.doi.org/10.17504/protocols.io.kqdg3x25zg25/v1 | https://www.protocols.io/view/protocol-sam-seq-zea-mays-cy9cxz2w | basile.leduque, Quadrana Leandro | TITLE: Protocol SAM-Seq Zea Mays
AUTHORS: basile.leduque, Quadrana Leandro
[DESCRIPTION]
Background: Epigenetic modifications, including chromatin accessibility, nucleosome positioning, and DNA methylation (5mC), are pivotal in shaping genome function. However, current short read sequencing approaches present chall... | ["[Plant nuclei purification and permeabilization] Add the powder to 12.5 ml of Extraction Buffer (EB) 1 in a 50 ml falcon tube. Let sit on ice for 5 min.", "[Plant nuclei purification and permeabilization] Add 1% Formaldehyde for crosslinking (i.e. 338 µl Formaldehyde 37% in 12.5ml of EB1). Incubate 5 minutes", "[Pl... |
27,684 | MojoSort™ Mouse anti-PE Nanobeads Column Protocol | null | dx.doi.org/10.17504/protocols.io.7achiaw | null | Sam Li | TITLE: MojoSort™ Mouse anti-PE Nanobeads 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 simpl... | ["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... |
17,863 | Y Choice test invertebrate | null | dx.doi.org/10.17504/protocols.io.vpfe5jn | null | Freddie-Jeanne Richard | TITLE: Y Choice test invertebrate
AUTHORS: Freddie-Jeanne Richard
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Y choice test designed for terrestrial invertebrase</div></div>
[STEPS]
?. [Device ]
Tests were performed using a Y-shaped choice chamber built in a plastic Petri dish (diameter: 8.7 c... | ["[Device ]\nTests were performed using a Y-shaped choice chamber built in a plastic Petri dish (diameter: 8.7 cm; height: 1.2 cm; lid included) (Fig 2, from Beauché and Richard 2013 in Plos One). Rigid plastic tunnels were also used to create the device, and two plastic pipettes were sealed at the end of these tunnels... |
62,205 | https://urbanmatter.clubeo.com/news/2022/05/07/keto-start-acv-gummies-is-it-scam-or-real-product | 1 | dx.doi.org/10.17504/protocols.io.8epv593w4g1b/v1 | https://www.protocols.io/view/https-urbanmatter-clubeo-com-news-2022-05-07-keto-b8y5rxy6 | sailbabolsh | TITLE: https://urbanmatter.clubeo.com/news/2022/05/07/keto-start-acv-gummies-is-it-scam-or-real-product
AUTHORS: sailbabolsh
[DESCRIPTION]
Shop Now:- https://supplement24hours.com/keto-start-acv-gummies/
[STEPS]
1. What are Keto Start ACV Gummies?The ketogenic diet has become popular with many individuals across th... | ["What are Keto Start ACV Gummies?The ketogenic diet has become popular with many individuals across the globe for its adequacy as a method for getting thinner. The ketogenic diet is described by an expanded admission of fat and protein, and lower utilization of carbs. The ketogenic diet can support the utilization of ... |
27,951 | Basal cortisol | null | dx.doi.org/10.17504/protocols.io.7iphkdn | null | Worapaka Manosroi | TITLE: Basal cortisol
AUTHORS: Worapaka Manosroi
[STEPS] | [] |
15,421 | Nucleic Acid Purification: Bead Clean | 1 | dx.doi.org/10.17504/protocols.io.ta5eig6 | https://www.protocols.io/view/nucleic-acid-purification-bead-clean-ta5eig6 | Madeline Mayday, Lillian Khan, Eric D. Chow, Matt S. Zinter, Joseph L. DeRisi | TITLE: Nucleic Acid Purification: Bead Clean
AUTHORS: Madeline Mayday, Lillian Khan, Eric D. Chow, Matt S. Zinter, Joseph L. DeRisi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">Preparation of high-quality sequencing libraries is a costly and time-c... | ["[Add Beads]\nAspirate desired volume of Ampure beads from reservoir and mix well into sample plate by mixing total volume minus one microliter less -- 20 times.\nBead volumes for each bead clean are available in the High-Throughput Echo Library Prep Protocol.", "[Incubate]\nTransfer plate onto Alpaqua 384 Post Magne... |
47,527 | Bulk RNA Isolation (Ding) | 4 | dx.doi.org/10.17504/protocols.io.bsnfndbn | https://www.protocols.io/view/bulk-rna-isolation-ding-bsnfndbn | Reyka Jayasinghe, Feng Chen, Satok, Li Ding | TITLE: Bulk RNA Isolation (Ding)
AUTHORS: Reyka Jayasinghe, Feng Chen, Satok, Li Ding
[DESCRIPTION]
Bulk RNA Isolation - Ding Lab
[STEPS]
1. Add 1 ml Trizol to ~10 mg tissue.
2. Add 200 µL chloroform
3. Vortex for 1 min until homogenous.
4. Incubate at room temperature for 5 min
5. Spin samples in microcentrifuge at ... | ["Add 1 ml Trizol to ~10 mg tissue.", "Add 200 µL chloroform", "Vortex for 1 min until homogenous.", "Incubate at room temperature for 5 min", "Spin samples in microcentrifuge at 12,000 rpm for 20 min. at 4°C", "Transfer ~500 µL of clear (aqueous) top phase to a new 1.5 mL tube.", "Add 500 µL of cold 2-propanol to the ... |
63,756 | Mitochondrial Quality and Membrane Potential Detection | 4 | dx.doi.org/10.17504/protocols.io.kxygxz24ov8j/v1 | https://www.protocols.io/view/mitochondrial-quality-and-membrane-potential-detec-cahksb4w | mitsjoecohen | TITLE: Mitochondrial Quality and Membrane Potential Detection
AUTHORS: mitsjoecohen
[DESCRIPTION]
A large number of studies have shown that mitochondria are closely related to apoptosis, in which the decrease of mitochondrial transmembrane potential (MMP) is considered one of the earliest events in the cascade of ap... | [] |
20,091 | E. coli Optical Quantification | null | dx.doi.org/10.17504/protocols.io.xu3fnyn | null | Kenneth Schackart, Kattika Kaarj | TITLE: E. coli Optical Quantification
AUTHORS: Kenneth Schackart, Kattika Kaarj
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This procedure details how to culture </span><span style = "font-style:italic;">E. coli</span><span> K-12 in suspension and quantify cultured bacteria using a spectr... | ["[Inoculate Culture]\nPipette BHI broth into 15 mL centrifuge tube.\n10 ml", "[Inoculate Culture]\nPlace tube in incubator or water bath to warm.", "[Inoculate Culture]\nAdd lyophilized E. coli K-12 to warm BHI broth.\n2 mg", "[Inoculate Culture]\nClose lid and shake gently.", "[Inoculate Culture]\nIncubate at for sev... |
64,378 | Eagle Hemp CBD Gummies [USA Official]: Why It is in Demand? | 1 | dx.doi.org/10.17504/protocols.io.261gen87wg47/v1 | https://www.protocols.io/view/eagle-hemp-cbd-gummies-usa-official-why-it-is-in-d-ca42sgye | ieaglehemp | TITLE: Eagle Hemp CBD Gummies [USA Official]: Why It is in Demand?
AUTHORS: ieaglehemp
[DESCRIPTION]
Your wellbeing is the underpinning of your satisfaction. In the event that you're not healthy and satisfaction, it will influence your temperament and you'll begin to feel that you'll at absolutely no point in the fu... | [] |
49,365 | Past human stone tool performance: experiments to test the influence of raw material variability and edge angle design on tool function | 1 | dx.doi.org/10.17504/protocols.io.3byl4kr6ovo5/v1 | https://www.protocols.click/view/past-human-stone-tool-performance-experiments-to-t-bufvntn6 | Lisa Schunk, Ivan Calandra, Anja Cramer, Walter Gneisinger, Joao Marreiros | TITLE: Past human stone tool performance: experiments to test the influence of raw material variability and edge angle design on tool function
AUTHORS: Lisa Schunk, Ivan Calandra, Anja Cramer, Walter Gneisinger, Joao Marreiros
[DESCRIPTION]
The goal of this sequential experiment was to test tool performance of Late M... | ["[Sample preparation] Standardised tools \n24 experimental standard samples were produced for the experiment: \n\n6 x 35 ° \n6 x 35 ° \n6 x 45 ° \n6 x 45 °", "[Sample preparation] Raw material \n\nBaltic flint: \nSouthern Sweden (secondary deposit):\n \n\nSilicified schist: \nBalver Höhle \n \nBuhlen", "[Sample ... |
35,776 | Quality control for metagenomics data | null | dx.doi.org/10.17504/protocols.io.be68jhhw | https://www.protocols.io/view/quality-control-for-metagenomics-data-be68jhhw | Qi Wang | TITLE: Quality control for metagenomics data
AUTHORS: Qi Wang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Quality control for metagenomics data,including: remove low quality reads and host contamination reads.</div></div>
[STEPS]
?. Step1: remove low quality reads：We firstly calculate the accur... | ["Step1: remove low quality reads：We firstly calculate the accuracy probabilities of each base using the following equations:1)Q = -10 log10E2)P = 1 - EWhereQ is thePhred quality score of each base,Eis the error probability of each base.Then we calculate the overall accuracy probability(OA)of each readusing the followi... |
null | null | null | dx.doi.org/10.17504/protocols.io.e2abgae | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p><strong>Tips</strong>:</p>
<p><strong>High background</strong></p>
<p>1. Transfer buffers may have become contaminated. Contamination can be transferred to the blots from electrophoresis and related equipment used in blot preparation.</p>
<p>2. Post-antibody washes may not hav... | [] |
40,887 | Detection and Sorting of Extracellular Vesicles and Viruses using nanoFACS | 1 | dx.doi.org/10.17504/protocols.io.bj6xkrfn | https://www.protocols.io/view/detection-and-sorting-of-extracellular-vesicles-an-bj6xkrfn | Aizea Morales-Kastresana, Joshua Welsh, Jennifer Jones | TITLE: Detection and Sorting of Extracellular Vesicles and Viruses using nanoFACS
AUTHORS: Aizea Morales-Kastresana, Joshua Welsh, Jennifer Jones
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Recent advances in high resolution flow cytometry (HRFC), which show improvements in both light scat... | ["[Basic Protocol 1]\n{\"blocks\":[{\"key\":\"ekhom\",\"text\":\"Carboxyfluorescein Diacetate Succynidimil Esther (CFDA-SE) is a small molecule that has been used extensively for labeling and tracking cells by flow cytometry, along with other imaging techniques(Lyons, Blake, & Doherty, 2013; Perfetto, Ambrozak, Roedere... |
null | null | null | dx.doi.org/10.17504/protocols.io.hwzb7f6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes MesoScale Discovery (MSD) assays for measurement of proinflammatory cytokines in supernatants collected from T cell dependent cytotoxicity (TDCC) cultures after BiTE® treatment.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
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91,358 | Tail Suspension Test | 1 | dx.doi.org/10.17504/protocols.io.6qpvr3222vmk/v1 | https://www.protocols.io/view/tail-suspension-test-c5f6y3re | Marina Lorente Picón, Núria Peñuelas, Ariadna Laguna, Miquel Vila | TITLE: Tail Suspension Test
AUTHORS: Marina Lorente Picón, Núria Peñuelas, Ariadna Laguna, Miquel Vila
[DESCRIPTION]
Tail Suspension Test for mice
[STEPS]
1. Suspend animals by their tails with tape in a suspension bar.
2. To avoid the tail climbing behavior, pass a 2cm methacrylate tube through the tail before suspe... | ["Suspend animals by their tails with tape in a suspension bar.", "To avoid the tail climbing behavior, pass a 2cm methacrylate tube through the tail before suspending the animal.", "Quantify the escape-oriented behaviors (i.e. fore and hind limbs movement) during six minutes.", "Calculate the total immobilization time... |
105,853 | RNA Isolation of Human Meniscus | 0 | dx.doi.org/10.17504/protocols.io.8epv5ropdg1b/v1 | https://www.protocols.io/view/rna-isolation-of-human-meniscus-djk54ky6 | Takuya Sakamoto, Merissa Olmer, Martin Lotz | TITLE: RNA Isolation of Human Meniscus
AUTHORS: Takuya Sakamoto, Merissa Olmer, Martin Lotz
[DESCRIPTION]
This protocol demonstrates how to perform RNA isolation from fresh snapfrozen and AllProtect preserved human meniscus tissue.
[BEFORE_START]
This protocol works with both fresh snapfrozen and AllProtect preserved... | ["[Tissue Homogenization] Precool Benchtop Centrifuge and make sure temperature is at 4℃.", "[Tissue Homogenization] Prepare tools, mortar and pestle, and work surface by spraying down with RNAse Away.", "[Tissue Homogenization] Weigh out 100mg of preserved tissue. If you have to cut a smaller piece of tissue to get 10... |
33,929 | Competition in Aedes aegypti larvae: the effects of distributing food inputs over time | null | dx.doi.org/10.17504/protocols.io.bddhi236 | null | Kurt Steinwascher | TITLE: Competition in Aedes aegypti larvae: the effects of distributing food inputs over time
AUTHORS: Kurt Steinwascher
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details the three experiments analyzed in the manuscript, "Competition in Aedes aegypti larvae: the effects of distri... | ["[Experiment one]\nFor experiment 1: Obtain mosquito eggs from an A. aegypti colony after feeding females on a mouse.", "[Experiment one]\nHatch the eggs in distilled water, immersing them for at least 2 hours.", "[Experiment one]\nAssign random numbers to treatments: 16 treatments (2 food levels, 2 densities, 2 aliqu... |
null | null | null | dx.doi.org/10.17504/protocols.io.reqd3dw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<p>This protocol was designed and developed at this laboratory.</p>
<p>The protocol specifically aims to amplify strains of Influenza B VICTORIA virus lineage and not strains of the YAMAGATA virus lineage or... | [] |
70,100 | Headplate surgery protocol for in vivo electrophysiological and optogenetic manipulation of basal ganglia neurons in awake head-fixed mice | 4 | dx.doi.org/10.17504/protocols.io.bp2l694z5lqe/v1 | https://www.protocols.io/view/headplate-surgery-protocol-for-in-vivo-electrophys-cgputvnw | Mark Bevan | TITLE: Headplate surgery protocol for in vivo electrophysiological and optogenetic manipulation of basal ganglia neurons in awake head-fixed mice
AUTHORS: Mark Bevan
[DESCRIPTION]
Step by step protocol for headplate surgery for in vivo electrophysiological and optogenetic manipulation of basal ganglia neurons in awake... | ["[Surgical preparation] Before and after any procedures, spray down working lab surfaces and equipment with 5% Nolvasan to disinfect the surgical area.", "[Surgical preparation] Autoclave all surgical instruments and ensure that sterility is maintained throughout the surgery. If multiple surgeries are required, a micr... |
26,948 | Spatial metabolomics of in situ, host-microbe interactions (practical guide for combining MALDI-MSI and FISH microscopy on the same section) | null | dx.doi.org/10.17504/protocols.io.6jchciw | null | Benedikt Geier, Emilia Sogin , Dolma Michellod, Moritz Janda, Mario Kompauer, Bernhard Spengler, Nicole Dubilier, Manuel Liebeke | TITLE: Spatial metabolomics of in situ, host-microbe interactions (practical guide for combining MALDI-MSI and FISH microscopy on the same section)
AUTHORS: Benedikt Geier, Emilia Sogin , Dolma Michellod, Moritz Janda, Mario Kompauer, Bernhard Spengler, Nicole Dubilier, Manuel Liebeke
[DESCRIPTION]
<div class = "text-... | ["Cryo-fixation and Embeddinga) Dissect tissue samples and submerge in precooled (4°C) 2% w/v carboxymethyl cellulose gel (CMC, Mw ~ 700'000, Sigma-Aldrich Chemie GmbH) and snap-freeze in liquid N2\nMake sure the sample is fully covered in CMC gelAvoid air bubbles in CMC gel--> this will cause holes in the frozen block... |
91,545 | Primary hippocampal and cortical neuronal culture and transfection | 4 | dx.doi.org/10.17504/protocols.io.ewov1qxr2gr2/v1 | https://www.protocols.io/view/primary-hippocampal-and-cortical-neuronal-culture-c5mzy476 | Ryan J. Farrell, Alexandros C Kokotos, Timothy A. Ryan | TITLE: Primary hippocampal and cortical neuronal culture and transfection
AUTHORS: Ryan J. Farrell, Alexandros C Kokotos, Timothy A. Ryan
[DESCRIPTION]
Neurons consist some of the most complex cells. The culture of primary neurons from murine brains has advanced the understanding of neuronal function at the cellular a... | ["[Preparing Dishes, 1 Day before]", "[Preparing dishes, 1 Day before] For each dish, place a coverslip in a p35.", "[Preparing dishes, 1 Day before] Take an 100X poly-L-ornithine aliquot and dilute in 10 mL ultrapure water (final conc. 10000 µg/µL).", "[Preparing dishes, 1 Day before] Add ~ 200 µL of poly-L-ornithine ... |
25,873 | Protocol for Robot-Assisted Progressive Muscle Strength Training | null | dx.doi.org/10.17504/protocols.io.5hrg356 | https://www.protocols.io/view/protocol-for-robot-assisted-progressive-muscle-str-5hrg356 | Azeemsha Thacham Poyil, Farshid Amirabdollahian | TITLE: Protocol for Robot-Assisted Progressive Muscle Strength Training
AUTHORS: Azeemsha Thacham Poyil, Farshid Amirabdollahian
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a protocol for an progressive muscle strength training in a new domain of adaptive robot-assisted training interact... | ["[Preparation Stage]\nParticipants were assisted to fix the EMG electrodes on three specific upper limb muscles (Biceps Brachii (BB), Anterior Deltoid (DLTF), and Middle Deltoid (DLTM)). The ground electrode was connected to a bony area near the elbow.", "[Initial Measurements]\nThe most feasible and highest robotic ... |
62,121 | Keto Extreme Fat Burner South Africa 2022: The Truth Revealed by Customers | 3 | dx.doi.org/10.17504/protocols.io.ewov1n362gr2/v1 | https://www.protocols.io/view/keto-extreme-fat-burner-south-africa-2022-the-trut-b8whrxb6 | health | TITLE: Keto Extreme Fat Burner South Africa 2022: The Truth Revealed by Customers
AUTHORS: health
[DESCRIPTION]
Keto Extreme Fat Burner South Africa is a weight loss supplement that claims to be the most powerful and effective fat burner on the market. It’s made from natural ingredients clinically studied and prov... | [] |
51,075 | Quantification of SARS-CoV-2 variant mutations (HV69-70 and E484K/N501Y) in settled solids using digital RT-PCR | 1 | dx.doi.org/10.17504/protocols.io.bv5bn82n | https://www.protocols.io/view/quantification-of-sars-cov-2-variant-mutations-hv6-bv5bn82n | Bridgette Hughes, Bradley J. White, Marlene K. Wolfe, Krista Wigginton, Alexandria Boehm | TITLE: Quantification of SARS-CoV-2 variant mutations (HV69-70 and E484K/N501Y) in settled solids using digital RT-PCR
AUTHORS: Bridgette Hughes, Bradley J. White, Marlene K. Wolfe, Krista Wigginton, Alexandria Boehm
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This process instruction describes ... | ["[Preparation ]\nRetrieve the ddPCR One-Step RT Supermix for probes from the freezer and thaw the components .\n-20 °C\non ice", "[Preparation ]\nRetrieve ddPCR positive control aliquots (50 copies per uL gRNA) from the freezer and thaw\n-80 °C\non ice", "[Preparation ]\nFor re-running frozen plates only: Thaw the R... |
50,941 | “Skeeter Pheeder”: inexpensive 3D printed, battery-powered blood feeder for mosquitoes and other haematophagous arthropods | 1 | null | https://www.protocols.io/view/skeeter-pheeder-inexpensive-3d-printed-battery-po-bvy5n7y6 | Philip Stoddard | TITLE: “Skeeter Pheeder”: inexpensive 3D printed, battery-powered blood feeder for mosquitoes and other haematophagous arthropods
AUTHORS: Philip Stoddard
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>A portable heated feeder for blood-feeding arthropods, the Skeeter Pheeder, has been design... | ["[Materials Needed]\nSee Materials section A table is include with details, approximate costs, and possible suppliers.Note: One can purchase blunt #20 hypodermic needles at a premium price or make them by grinding the tips off sharp hypodermic needles (I used a Dremel hand grinder). The needle shaft should be about 2... |
null | null | null | dx.doi.org/10.17504/protocols.io.idnca5e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol was used to compute figures 7 and 8 in the manuscript: 'High precision detection of conserved segments from synteny blocks'</p>
[STEPS]
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.c3vyn5 | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
(using GIBCO LM agarose = now called Invitrogen Life Technologies LMP agarose, 1-800-955-6288, cat# 1-5517-014 for 50 g, 1-5517-022 for 100 g)<br /><strong>Note:</strong> new catalog number is16520-050.
[STEPS]
?.
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25,667 | Ribosome Purification for OnePot PURE cell-free system | null | dx.doi.org/10.17504/protocols.io.5bbg2in | null | Konstantinos Ragios | TITLE: Ribosome Purification for OnePot PURE cell-free system
AUTHORS: Konstantinos Ragios
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In this protocol we explain the procedure of ribosomes purification with the method of hydrophobic interaction chromatography (HIC) so they can be used for a PUR... | ["[Small cell culture]\nAdd 100ml of LB medium to the 1L Erlenmeyer flask\nWork under flame Sterilize the bench with 70% Ethanol", "[Small cell cultu]", "[Small cell culture]\nInoculate the LB with 10μl of A19 E. coli strain kept in glycerol stock", "[Small cell culture]\nIncubate overnight (at least 12 hours) at 37oC ... |
null | null | null | dx.doi.org/10.17504/protocols.io.ieecbbe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol explains how to prepare, load and run cell-free RNAPT7 transcription/translation coupled reactions. To be able to follow this protocol it is necessary to have prepared all the solutions needed including <strong>amino acids and Energy solutions</strong> and <stro... | [] |
25,249 | Marchantia chloroplast transformation | null | dx.doi.org/10.17504/protocols.io.4v9gw96 | null | Eftychis Frangedakis, Kasey Markel | TITLE: Marchantia chloroplast transformation
AUTHORS: Eftychis Frangedakis, Kasey Markel
[STEPS]
?. DNAdelTM nanoparticles are supplied as a 50 mg/mL suspension in binding buffer. To dissociate any aggregates prior to use, agitate the suspension, sonicate briefly for 30 s using an ultrasonic water-bath sonicator, vort... | ["DNAdelTM nanoparticles are supplied as a 50 mg/mL suspension in binding buffer. To dissociate any aggregates prior to use, agitate the suspension, sonicate briefly for 30 s using an ultrasonic water-bath sonicator, vortex for 5 s and repeat.", "Use 0.5 mg of nanoparticles per transformation.", "Dilute DNAdelTM nanopa... |
45,452 | test publish protocol | 1 | null | https://www.protocols.io/view/test-publish-protocol-bqmkmu4w | Maria Guliakina | TITLE: test publish protocol
AUTHORS: Maria Guliakina
[STEPS]
?. Village did removed enjoyed explain nor ham saw calling talking. Securing as informed declared or margaret. Joy horrible moreover man feelings own shy. Request norland neither mistake for yet. Between the for morning assured country believe. On even f... | ["Village did removed enjoyed explain nor ham saw calling talking. Securing as informed declared or margaret. Joy horrible moreover man feelings own shy. Request norland neither mistake for yet. Between the for morning assured country believe. On even feet time have an no at. Relation so in confined smallest children... |
null | null | null | dx.doi.org/10.17504/protocols.io.ka8cshw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol tells how to fix the computer</p>
[STEPS]
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.pjrdkm6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>This is a short tutorial on how to get started with gene prediciton in Prokaryotic genomes via the command line.</strong></p>
<p> </p>
<p>Code is intended for use on an Ubuntu 16.04 LTS OS.</p>
<p> </p>
<p>The tools we will use here are:</p>
<p>Prodigal. https://githu... | [] |
108,579 | Custom Indexing for Nanopore Sequencing Platform | 0 | dx.doi.org/10.17504/protocols.io.q26g71ed8gwz/v1 | https://www.protocols.io/view/custom-indexing-for-nanopore-sequencing-platform-dnab5aan | Mrinalini Watsa, Kristina Vsevolodova, P. Sánchez-Vendizú, Gideon Erkenswick | TITLE: Custom Indexing for Nanopore Sequencing Platform
AUTHORS: Mrinalini Watsa, Kristina Vsevolodova, P. Sánchez-Vendizú, Gideon Erkenswick
[DESCRIPTION]
This indexing protocol details how to index greater than 96 samples using a combination of custom indices and the Native Barcoding Kit from Oxford Nanopore Technol... | ["[PCR 1 - Amplification PCR] PCR 1 can be any PCR reaction targeting any genetic DNA marker, but with primers that have been modified to include an overhang on the 5' end of the gene-specific priming site, which will be used subsequently for sample indexing.\n\nOverhang that is compatible with Illumina sequencing chem... |
59,118 | Stereology | 4 | dx.doi.org/10.17504/protocols.io.b5ynq7ve | https://www.protocols.io/view/stereology-b5ynq7ve | Haley Geertsma | TITLE: Stereology
AUTHORS: Haley Geertsma
[DESCRIPTION]
This protocol is used to quantify the number of TH+ cells in the substantia nigra pars compacta.
[STEPS]
1. Take 8 cryosections cut at 40μm to equally sample the substantia nigra, pars compacta (SNc) and perform diaminobenzidine staining with a tyrosine hydrox... | ["Take 8 cryosections cut at 40μm to equally sample the substantia nigra, pars compacta (SNc) and perform diaminobenzidine staining with a tyrosine hydroxylase antibody.\nNote: I take every 6th section from Bregma -2.54mm to -3.88mm", "Use StereoInvestigator software to count all TH+ cells. For this, randomly sample th... |
105,615 | Co-crystallisation protocol for SARS-CoV-2 nsp3 macrodomain in P1 21 1 with ligands | 1 | dx.doi.org/10.17504/protocols.io.n2bvjnb9bgk5/v1 | https://www.protocols.io/view/co-crystallisation-protocol-for-sars-cov-2-nsp3-ma-djdp4i5n | Jasmin Aschenbrenner, Peter Marples, Daren Fearon | TITLE: Co-crystallisation protocol for SARS-CoV-2 nsp3 macrodomain in P1 21 1 with ligands
AUTHORS: Jasmin Aschenbrenner, Peter Marples, Daren Fearon
[DESCRIPTION]
The COVID-19 pandemic has demonstrated the need for novel therapeutic interventions and improved pandemic preparedness strategies against severe acute resp... | ["[Crystallization experiment] Protein, compounds and buffer requirements:\n115.2 µL21.6 mg/mL \n2.88 mL \n28.8 µL seeds, dilution 1:2\n12 µL100 millimolar (mM) ligand in DMSO", "[Crystallization experiment] Dispense 30 µL into SwissCI 3 lens plate reservoir wells using a 100 µl multi-channel pipette.\nDispense 40... |
99,472 | Cyclic Voltammetry analysis of laser-inscribed graphene electrodes: Ruthenium(III) chloride trihydrate redox couple | 6 | null | https://www.protocols.io/view/cyclic-voltammetry-analysis-of-laser-inscribed-gra-dddq225w | Nick Cavallaro, Carmen Gomes, Eric S McLamore | TITLE: Cyclic Voltammetry analysis of laser-inscribed graphene electrodes: Ruthenium(III) chloride trihydrate redox couple
AUTHORS: Nick Cavallaro, Carmen Gomes, Eric S McLamore
[DESCRIPTION]
This protocol describes use of the cyclic voltammetry (CV) method for electrochemical analysis of laser-inscribed graphene (LIG... | ["[Preparation] Prepare LIG electrodes \nUse protocol for LIG fabrication to prepare a batch of electrodes (link here).\n \n\nExpected results from step 1:\nFig 1 shows photographs of the instrument and the expected results from a batch fabrication of six replicate electrodes based on the LIG fabrication protocol here ... |
76,100 | Resource 1: Scatter Detector Setting Incrementation for FCMPASS | 1 | dx.doi.org/10.17504/protocols.io.bp2l69rn5lqe/v1 | https://www.protocols.io/view/resource-1-scatter-detector-setting-incrementation-cnjcvciw | Sean M Cook, Jennifer Jones, Joshua A Welsh | TITLE: Resource 1: Scatter Detector Setting Incrementation for FCMPASS
AUTHORS: Sean M Cook, Jennifer Jones, Joshua A Welsh
[DESCRIPTION]
Flow cytometry (FCM) is a common extracellular particles (EPs), including viruses and extracellular vesicles (EVs), characterization method. Frameworks such as MIFlowCyt-EV exist t... | ["[Sample preparation] Vortex FluoSpheres bottle on a high setting for 5 s.", "[Sample preparation] Pipette 500 µL of DPBS into a FACS tube. Label this tube 'DPBS'.", "[Cytometer Setup] Ensure cytometer is clean and that -Height and -Area statistics are set to be collected on all parameters and that all parameters are ... |
79,098 | Deleidi Lab | Protocols | Glucocerebrosidase is imported into mitochondria and preserves complex I integrity and energy metabolism | 2 | dx.doi.org/10.17504/protocols.io.rm7vzbejrvx1/v1 | https://www.protocols.io/view/deleidi-lab-protocols-glucocerebrosidase-is-import-crg2v3ye | michela.deleidi, María José Pérez J., Hariam Raji, Federico Bertoli, Pascale Baden | TITLE: Deleidi Lab | Protocols | Glucocerebrosidase is imported into mitochondria and preserves complex I integrity and energy metabolism
AUTHORS: michela.deleidi, María José Pérez J., Hariam Raji, Federico Bertoli, Pascale Baden
[DESCRIPTION]
Collection of protocols of Team Deleidi used in the publication: "Glucoce... | [] |
46,645 | Human heart tissue harvesting | 1 | dx.doi.org/10.17504/protocols.io.brsvm6e6 | https://www.protocols.io/view/human-heart-tissue-harvesting-brsvm6e6 | Marc Halushka | TITLE: Human heart tissue harvesting
AUTHORS: Marc Halushka
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This method describes harvesting of human heart tissues for spatial transcriptomics.</div></div>
[STEPS]
?. [Prepare to dissect a heart]
Identify an acceptable human heart from autopsy, organ... | ["[Prepare to dissect a heart]\nIdentify an acceptable human heart from autopsy, organ procurement, or transplantation. The heart may be fresh or may have previously been placed in formalin.", "[Prepare to dissect a heart]\nPrepare / obtain materials to dissect the heart. Razor blades, knives, forceps, and scissors ar... |
null | null | null | dx.doi.org/10.17504/protocols.io.gzgbx3w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol to extract the inner membranes from yeast cells</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
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?. | [] |
92,735 | Preparation of Holding ACSF (artificial cerebrospinal fluid) for slice electrophysiology | 4 | dx.doi.org/10.17504/protocols.io.n92ldm6ool5b/v1 | https://www.protocols.io/view/preparation-of-holding-acsf-artificial-cerebrospin-c6s7zehn | Sarthak M. Singhal, thnasko | TITLE: Preparation of Holding ACSF (artificial cerebrospinal fluid) for slice electrophysiology
AUTHORS: Sarthak M. Singhal, thnasko
[DESCRIPTION]
Hnasko lab- preparation of Holding ACSF
Holding ACSF is used for incubating brain slices prior to cell-attached or whole-cell electrophysiological recordings of neurons.
[... | ["Prepare 10X stock solution.", "Composition of 1 L of 10X Holding ACSF (in mM): 1150 NaCl, 25 KCl, 12.3 NaH2PO4, 100 d-glucose, 20 CaCl2 and 20 MgSO4.", "Composition of 1 L of 10X Holding ACSF (in g): 67.2 NaCl, 1.86 KCl, 1.47 NaH2PO4, 18.02 d-glucose, 2.94 CaCl2 and 4.93 MgSO4.", "Dissolve all salts in 1 L of ddH2O t... |
70,061 | APEX2 labelling and screening for biotinylated proteins by proteomics | 4 | dx.doi.org/10.17504/protocols.io.dm6gpj8qjgzp/v1 | https://www.protocols.io/view/apex2-labelling-and-screening-for-biotinylated-pro-cgnmtvc6 | Chuyu Chen, Ciarra Smith, Loukia Parisiadou | TITLE: APEX2 labelling and screening for biotinylated proteins by proteomics
AUTHORS: Chuyu Chen, Ciarra Smith, Loukia Parisiadou
[DESCRIPTION]
Enzyme-catalyzed proximity labeling (PL) combined with mass spectrometry (MS) has emerged as a revolutionary approach to reveal the subcellular proteomes. APEX (engineered asc... | ["[APEX2 Labelling] Construct: AAV5-CAG-DIO-APEX2NES is injected into the ventral midbrain (VM) of DATIRES-Cre mice", "[APEX2 Labelling] Confirmation of cellular specificity: Representative slices of SN and Str stained for TH, V5 and merged", "[APEX2 Labelling] Brains perfused with aCSF by trascardial perfusion with 10... |
98,230 | In vivo Ephys: Analysis Protocol | 0 | dx.doi.org/10.17504/protocols.io.261ge5o2yg47/v1 | https://www.protocols.io/view/in-vivo-ephys-analysis-protocol-db6w2rfe | Sasha Burwell | TITLE: In vivo Ephys: Analysis Protocol
AUTHORS: Sasha Burwell
[DESCRIPTION]
This protocol details the analysis procedures performed on the in vivo electrophysiology data post-spike sorting.
[STEPS]
SECTION: Analysis Protocol
1. To plot the waveforms from one electrode of interest in the raw data (ex, Fig. 1c), run t... | ["[Analysis Protocol] To plot the waveforms from one electrode of interest in the raw data (ex, Fig. 1c), run the Matlab code \n \n on the raw continuous data.", "[Analysis Protocol] To analyze the sorted templates extracted from Spyking Circus,", "[Analysis Protocol] From the resulting Templates_data structure, save e... |
null | null | null | dx.doi.org/10.17504/protocols.io.crcv2v | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
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105,355 | Poly-ornithine/laminin substrate for neural cell culture | 0 | dx.doi.org/10.17504/protocols.io.dm6gpz2mplzp/v2 | https://www.protocols.io/view/poly-ornithine-laminin-substrate-for-neural-cell-c-di5j4g4n | Gist Croft, Regine Tipon | TITLE: Poly-ornithine/laminin substrate for neural cell culture
AUTHORS: Gist Croft, Regine Tipon
[DESCRIPTION]
This protocol is used to create adhesive and bioactive substrate for neural cell types, low to high density nuerons, astrocytes, or organoids. It is based on standard methods but includes several optimizat... | ["[Preparing Reagents] Filter sterilize and store at 4 degrees for 3 months", "[Preparing Reagents] Dissolve unopened vial of Poly-Ornithine in Borate Buffer at 1mg/ml (P-Orn)", "[Preparing Reagents] Pretreatment for coverslips:", "Add Laminin in L15+ NaBicarbonate solution: final 10ug laminin/ml, same volume and incub... |
80,276 | Tension Between Polynesians and French of Tahiti and Mo'orea Protocols | 1 | dx.doi.org/10.17504/protocols.io.5jyl8jzd7g2w/v1 | https://www.protocols.io/view/tension-between-polynesians-and-french-of-tahiti-a-csmuwc6w | Sage Moloney | TITLE: Tension Between Polynesians and French of Tahiti and Mo'orea Protocols
AUTHORS: Sage Moloney
[DESCRIPTION]
This research project will seek to answer the question: What are the sources of tension between native Polynesians and individuals from France on Tahiti and Moorea? In order to answer this question, I ... | ["[Preparing the Questionnaire] Develop questions that will reveal the perceptions of tension between Polynesians and the French from the perspective of the respondent.", "[Preparing the Questionnaire] Prior to entering the field, this questionnaire should be revised and reviewed for potential sources of bias and overa... |
27,514 | HMW DNA extraction from Caenorhabditis pellets for long read sequencing | null | dx.doi.org/10.17504/protocols.io.642hgye | null | bionano genomics | TITLE: HMW DNA extraction from Caenorhabditis pellets for long read sequencing
AUTHORS: bionano genomics
[STEPS]
?.
?. | [] |
40,442 | Universal sandwich ELISA for investigating the binding of Protein-LA (SpLA) to avian immunoglobulins using a peroxidase-labeled -anti-IgY conjugate. | 6 | dx.doi.org/10.17504/protocols.io.bjq2kmye | https://www.protocols.io/view/universal-sandwich-elisa-for-investigating-the-bi-bjq2kmye | Angel Justiz-Vaillant, Monica F. Smikle | TITLE: Universal sandwich ELISA for investigating the binding of Protein-LA (SpLA) to avian immunoglobulins using a peroxidase-labeled -anti-IgY conjugate.
AUTHORS: Angel Justiz-Vaillant, Monica F. Smikle
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. This ELISA is used to study the interaction of prot... | ["This ELISA is used to study the interaction of protein-LA (SpLA) with diverse avian immunoglobulins.", "The 96 well microtitre plate is coated overnight at 4°C with 2 µg/µl per well of recombinant SpLA or a mixture of SpA with SpL in carbonate-bicarbonate buffer pH 9.6.", "Then plate is treated with bovine serum albu... |
38,990 | Coil Resistance Testing Apparatus for VUSE ALTO | 1 | dx.doi.org/10.17504/protocols.io.bibnkame | https://www.protocols.io/view/coil-resistance-testing-apparatus-for-vuse-alto-bibnkame | Qutaiba Saleh, Edward Hensel, Risa Robinson | TITLE: Coil Resistance Testing Apparatus for VUSE ALTO
AUTHORS: Qutaiba Saleh, Edward Hensel, Risa Robinson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Measuring coil resistance of Electronic Nicotine Delivery Systems (ENDS) accurately is critical in any research studying the characteristics of ... | ["[Preparation]\nDischarge ENDS batteryThis step is critical for the safety of the operator and the lab facility. The battery can be discharged by using the ENDS until the battery is out of energy. The LED on the device flashes 10 times when the battery needs to be charged. This is a good indication that the battery is... |
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