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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23,783 | Test protocol | null | dx.doi.org/10.17504/protocols.io.3gfgjtn | null | Alex Andre | TITLE: Test protocol
AUTHORS: Alex Andre
[STEPS]
?. Je suis l'etape 1
?. Je sius l'etape 2 | ["Je suis l'etape 1", "Je sius l'etape 2"] |
95,888 | eRNA extraction from water samples filtered through 47 mm diameter filters (NucleoMag DNA/RNA Water Kit - MACHEREY NAGEL). | 4 | dx.doi.org/10.17504/protocols.io.5qpvo3eq9v4o/v1 | https://www.protocols.io/view/erna-extraction-from-water-samples-filtered-throug-c9vqz65w | Marine Vautier, Cecile Chardon, Cyrielle Galiegue, Isabelle Domaizon | TITLE: eRNA extraction from water samples filtered through 47 mm diameter filters (NucleoMag DNA/RNA Water Kit - MACHEREY NAGEL).
AUTHORS: Marine Vautier, Cecile Chardon, Cyrielle Galiegue, Isabelle Domaizon
[DESCRIPTION]
The objective of this protocol is the environmental RNA (eRNA) extraction from water samples fil... | ["[Material and rDNase preparation] Material preparation\n\nTo limit contamination of the kit buffers, it is recommended to aliquote them:\n- Into 50 mL tubes for MWA1, MWA2, MWA3 and MWA4\n- Into 2 mL tubes for NucleoMag B-Beads solution and RNase-free H2O\n\nTubes annotation \n- one 2 mL tube per sample for lysate c... |
81,615 | Cloning individual AAV capsid variants | 4 | dx.doi.org/10.17504/protocols.io.n2bvj87ebgk5/v1 | https://www.protocols.io/view/cloning-individual-aav-capsid-variants-ctxpwpmn | Sripriya Ravindra Kumar, Timothy F. Shay, Xinhong Chen, David Brown, Tatyana Dobreva, Qin Huang, Xiaozhe Ding, Yicheng Luo, Pétur H. Einarsson, Alon Greenbaum, Min J. Jang, Benjamin E. Deverman, Viviana Gradinaru | TITLE: Cloning individual AAV capsid variants
AUTHORS: Sripriya Ravindra Kumar, Timothy F. Shay, Xinhong Chen, David Brown, Tatyana Dobreva, Qin Huang, Xiaozhe Ding, Yicheng Luo, Pétur H. Einarsson, Alon Greenbaum, Min J. Jang, Benjamin E. Deverman, Viviana Gradinaru
[DESCRIPTION]
This protocol describes the procedure... | ["Digest with and", "Design 100 bp primers for the desired plasmid variant that cover the insertion region with ~20 bp overlap of the backbone", "To synthesize the double-stranded DNA fragment, anneal the primers by PCR with 20 cycles of 98 °C for10 s, 60 °C for 30 s and 72 °C for 10 s using", "Assemble the variant... |
71,315 | Non-Volant Mammal Measurements - ISL Peru | 1 | dx.doi.org/10.17504/protocols.io.n2bvj8xwpgk5/v1 | https://www.protocols.io/view/non-volant-mammal-measurements-isl-peru-chvtt66n | Cristian Tirapelle, Gideon Erkenswick, Mrinalini Watsa, Pamela Sánchez-Vendizú | TITLE: Non-Volant Mammal Measurements - ISL Peru
AUTHORS: Cristian Tirapelle, Gideon Erkenswick, Mrinalini Watsa, Pamela Sánchez-Vendizú
[DESCRIPTION]
This protocol describes the external morphological measurements taken on mammals prior to release and is actively used by Field Projects International at the Estación B... | ["[Lenghts] Head length: Distance from the tip of the nose until the occipital bone.", "[Lenghts] Head width: it is measured on the widest part of the cranium. As a reference, we measure the distance in between the base of the pinnae.", "[Lenghts] Body length: is intended as the length of the truck of the body. It is m... |
84,912 | Design and Fabrication of CFET Arrays | 1 | dx.doi.org/10.17504/protocols.io.yxmvm3kpol3p/v1 | https://www.protocols.io/view/design-and-fabrication-of-cfet-arrays-cw6qxhdw | Helen N Schwerdt | TITLE: Design and Fabrication of CFET Arrays
AUTHORS: Helen N Schwerdt
[DESCRIPTION]
The fabrication of carbon fiber electrode threat (CFET) arrays is described here.
[STEPS]
SECTION: Design and Fabrication of CFET Arrays
1. We fabricated CFET arrays of up to 16 patterned CFETs (overall bundle diameter of 40 µm) co... | ["[Design and Fabrication of CFET Arrays] We fabricated CFET arrays of up to 16 patterned CFETs (overall bundle diameter of 40 µm) connected to a flexible printed circuit board (PCB) (flex-PCB) for interfacing with external FSCV recording instrumentation. CFETs and flex-PCBs were constructed separately. Fabrication of ... |
52,513 | Step 2: RNA extraction and RT-qPCR | 4 | null | https://www.protocols.io/view/step-2-rna-extraction-and-rt-qpcr-bxh9pj96 | Peter H L Krijger, Tim A Hoek, Sanne Boersma, Lieke I P M Donders, Maaike M C Broeders, Mark Pieterse, Pim W Toonen, Ive Logister, Bram M P Verhagen, Marjon J A M Verstegen, Thomas W van Ravesteyn, Rene J T M Roymans, Francesca Mattiroli, Jo Vandesompele, Monique Nijhuis, Stefan Meijer, Anton van Weert, Edwin Dekker, F... | TITLE: Step 2: RNA extraction and RT-qPCR
AUTHORS: Peter H L Krijger, Tim A Hoek, Sanne Boersma, Lieke I P M Donders, Maaike M C Broeders, Mark Pieterse, Pim W Toonen, Ive Logister, Bram M P Verhagen, Marjon J A M Verstegen, Thomas W van Ravesteyn, Rene J T M Roymans, Francesca Mattiroli, Jo Vandesompele, Monique Nijhu... | ["[RNA extraction and qPCR setup]\nCombine in 1 micronic tube rack: 1 micronic tube with the positive extraction control (position A1)1 micronic tube carrying the negative extraction control (position B1)1 micronic tube carrying the negative amplification control (position C1)93 micronic tubes carrying swab specimens",... |
55,939 | Test protocol II | 1 | null | https://www.protocols.io/view/test-protocol-ii-b2vbqe2n | Abby Moore | TITLE: Test protocol II
AUTHORS: Abby Moore
[DESCRIPTION]
This is a test protocol
Here's an protocol reference:
Here's a citation:
[BEFORE_START]
This is what you should know before you start
[GUIDELINES]
Responsibilities....
[STEPS]
1. Use 80:20 MeOH:H2O for this step. This is not easy to access... | ["Use 80:20 MeOH:H2O for this step. This is not easy to access by machine.", "If you haven't already, make a solution with the following components:\n\n80 % volume \n20 % volume", "If you haven't already, make a solution with the following components:\n\n80 % volume \n20 % volume", "Use this piece of equipment:"] |
80,768 | MERS-CoV Main Protease (Mpro) Fluorescence Dose Response | 1 | null | https://www.protocols.io/view/mers-cov-main-protease-mpro-fluorescence-dose-resp-cs48wgzw | Haim Barr, Noa Lahav | TITLE: MERS-CoV Main Protease (Mpro) Fluorescence Dose Response
AUTHORS: Haim Barr, Noa Lahav
[DESCRIPTION]
This is a functional, biochemical assay used to identify treatments for viral infectious disease in MERS-CoV 3C-like protease.
Utilizing a direct enzyme activity measurement method, the experiment was performe... | ["[Prepare 384 Well Plate] PRIME with Assay Buffer by Multi-Drop Combi Tube Dispensing Cassette by selecting the PRIME button on the Combi Dispenser until the tubes are filled completely.", "[Prepare 384 Well Plate] DISPENSE 10 µL to Columns 1 and 23 of assay plate\nNote: These will represent the inhibitor control colu... |
28,619 | Growth curve analysis | null | dx.doi.org/10.17504/protocols.io.77jhrkn | null | Sebastiaan Kuiper | TITLE: Growth curve analysis
AUTHORS: Sebastiaan Kuiper
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>To observe the potential of defense mechanisms of either native or synthetic systems in </span><span style = "font-style:italic;">Escherichia coli </span><span>(and more) when incubated wit... | ["[Preparations]\nMedia and bacteriophage stock solutions :1L Luria-Bertani (LB) media (with antibiotics)Desired Bacteriophage stock solution in LB media (with known Plaque Forming Units (PFU) ml-1)", "[Preparations]\nFill in plate reader protocol as follows:Set temperature: 37°C preheat before moving to next stepSt... |
63,427 | Shark TankReviews Benefits,Ingredients,side effects and Is it legitor Does it Really Work [HOAX OR SCAM]{Update 2022}-, What To Know Before Using It?? | 1 | dx.doi.org/10.17504/protocols.io.14egn7j8qv5d/v1 | https://www.protocols.io/view/shark-tankreviews-benefits-ingredients-side-effect-b97br9in | kkk | TITLE: Shark TankReviews Benefits,Ingredients,side effects and Is it legitor Does it Really Work [HOAX OR SCAM]{Update 2022}-, What To Know Before Using It??
AUTHORS: kkk
[DESCRIPTION]
Steve Harvey CBD Gummies
[STEPS]
1. Steve Harvey CBD Gummies
➢Product Name —Steve Harvey CBD Gummies Reviews
➢Main Benefits—Im... | ["Steve Harvey CBD Gummies\n\n \n\n\n➢Product Name —Steve Harvey CBD Gummies Reviews\n➢Main Benefits—Improve Metabolism & Help in Pain Relief\n➢Composition —NaturalOrganic Compound\n➢Side-Effects—NA\n➢Rating :—⭐⭐⭐⭐⭐\n➢Availability —Online\n➢Price (for Sale) Buy Now Here —Click Here\nSteve Harvey CBD Gummies - You plan ... |
27,932 | Organization for Lab Data using Bash | null | dx.doi.org/10.17504/protocols.io.7h4hj8w | null | Courtney Comrie | TITLE: Organization for Lab Data using Bash
AUTHORS: Courtney Comrie
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Organization is important in the IPA and MSBIL</div></div>
[STEPS]
?. [Introduction]
Organization is crucial in Bash and in our lab. Bash operates through directories, therefore we m... | ["[Introduction]\nOrganization is crucial in Bash and in our lab. Bash operates through directories, therefore we must be precise when storing raw data, intermediate steps, and finished images. *NOTE: Never process data in the raw data directory. Copy the raw data to a new directory in case issues occur. Always keep th... |
27,121 | Phylogenetic tree and ancestral sequence reconstruction | null | dx.doi.org/10.17504/protocols.io.6qrhdv6 | null | Matthew Kellom | TITLE: Phylogenetic tree and ancestral sequence reconstruction
AUTHORS: Matthew Kellom
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for the alignment, tree building, and ancestral sequence reconstruction of metagenomic protein coding sequences.</div></div>
[STEPS]
?. Obtain protein-codi... | ["Obtain protein-coding metagenome FASTA files.", "Obtain a set of amino acid sequences that are known/trusted target homologs (Uniprot works well for this).", "Use DIAMOND (blastx can also be used but will be slower for large datasets) to search for target hits from within the metagenome sequences. Recommend an e-valu... |
19,616 | Murashige and Skoog (MS) agar | null | dx.doi.org/10.17504/protocols.io.xd8fi9w | null | Steven Burgess | TITLE: Murashige and Skoog (MS) agar
AUTHORS: Steven Burgess
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Murashige and Skoog medium</span><span> (or </span><span style = "font-weight:bold;font-style:italic;">MSO</span><span> or </span><span style = "font-weight:... | ["Add Murashige and Skoog Basal Salt medium to a 1L flask\n4 g", "Add dH2O\n800 ml", "Add of Bacto Agar to flask and autoclave\n7 g", "Add dH2O up to 1L", "Adjust the pH to 5.7 using 2 N Potassium hydroxide KOH"] |
51,059 | Construction of individual ddRAD libraries | 1 | dx.doi.org/10.17504/protocols.io.bv4tn8wn | https://www.protocols.io/view/construction-of-individual-ddrad-libraries-bv4tn8wn | Claire Daguin Thiebaut, Stephanie Ruault, Charlotte Roby, Thomas Broquet, Frédérique Viard, Alan Brelsford | TITLE: Construction of individual ddRAD libraries
AUTHORS: Claire Daguin Thiebaut, Stephanie Ruault, Charlotte Roby, Thomas Broquet, Frédérique Viard, Alan Brelsford
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes a double digested restriction-site associated DNA (ddRAD... | ["[Preparation of double-stranded barcoded P1 adaptors 1µM]\nIn a PCR plate wells, combine each oligo 1.1 with its complementary oligo 1.2 : adaptor P1-1 10µM adaptor P1-2 10µM annealing buffer 10X (100 mM Tris-HCl, pH 8, 500 mM NaCl, 10 mM EDTA Na2) nuclease free waterSeal the plate with a thermoseal film and inc... |
75,600 | Topographical mapping of sympathetic postganglionic innervation of mouse heart | 1 | dx.doi.org/10.17504/protocols.io.n92ldzbmxv5b/v2 | https://www.protocols.io/view/topographical-mapping-of-sympathetic-postganglioni-cm3qu8mw | Ariege Bizanti, Yuanyuan Zhang, Kohlton Bendowski, Jin Chen, Mahyar Osanlouy, Maci Heal, Zixi Jack Cheng | TITLE: Topographical mapping of sympathetic postganglionic innervation of mouse heart
AUTHORS: Ariege Bizanti, Yuanyuan Zhang, Kohlton Bendowski, Jin Chen, Mahyar Osanlouy, Maci Heal, Zixi Jack Cheng
[DESCRIPTION]
This protocol describes the process of mapping the topographical organization of tyrosine hydroxylase imm... | ["Animals \nMale C57BL/6J mice (Jackson laboratory), n=6 were used. Animals were kept in the animal room with dark/light cycle set to 12/12 hours and water and food were supplied ad libitum. All procedures were carried out under the ethical guidelines of University of Central Florida and approved by the Animal Care an... |
null | null | null | dx.doi.org/10.17504/protocols.io.jz3cp8n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Background: </strong>Selective reporting distorts the aggregate body of scientific evidence, wastes resources and can harm patients’ health and the credibility of science. Selective reporting may result from a focus on preferred findings by researchers and others stak... | [] |
78,573 | Kegel exercise and Psychosexual counselling for ED in SCI | 1 | dx.doi.org/10.17504/protocols.io.j8nlkwydxl5r/v1 | https://www.protocols.io/view/kegel-exercise-and-psychosexual-counselling-for-ed-cqymvxu6 | K M Amran Hossain, Ahamadullah Hil Galeb, Md. Abu Khayer Hasnat | TITLE: Kegel exercise and Psychosexual counselling for ED in SCI
AUTHORS: K M Amran Hossain, Ahamadullah Hil Galeb, Md. Abu Khayer Hasnat
[DESCRIPTION]
The protocol describes the intervention provided in both "Kegel exercise and psychosexual counselling", and "usual counselling" for the study titled "Effectiveness of ... | ["[Study process] Screening", "[Study process] Randomization", "[Study process] Baseline assessment", "[Study process] Intervention", "[Study process] Usual counselling\nThe counselling department follows the PLISSIT MODEL developed by Annon, in 1976. \nP = Permission (verbal)\nLI= Limited Information\nSS= Specific Sug... |
63,692 | SPRI Bead Cleanup | 1 | null | https://www.protocols.io/view/spri-bead-cleanup-cafksbkw | George Testo | TITLE: SPRI Bead Cleanup
AUTHORS: George Testo
[DESCRIPTION]
SPRIselect is a SPRI-based chemistry that speeds and simplifies nucleic acid size selection for fragment library preparation for Next Generation sequencing. In this process, size selection is required to produce a uniform distribution of fragments around an... | ["[Preparing for Bead Cleanup] Make 300 µL 80% Ethanol (200-proof) (make fresh each time). Gently shake the SPRI beads bottle to resuspend any magnetic particles that may have settled. Take aliquot into a tube for working solution.", "[Preparing for Bead Cleanup] Pipette PCR product (single or pooled) and transfer to s... |
null | null | null | dx.doi.org/10.17504/protocols.io.c35yq5 | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
This protocol comes from a group of other protocols. This protocol is (4) of (4): <br />1. <a href="https://www.protocols.io/view/Large-Volume-Marine-Cyanophage-Phage-Protocols-c3iykd" target="_blank">'Large Volume Marine Cyanophage Phage Protocols'</a><br />2. <a href="https://w... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.vrxe57n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Questionnaire on eye movements complaints
Can be used for descriptive purposes only
[STEPS]
?. | ["null"] |
96,907 | Colocalisation imaging of endogenous TMEM192 with lysosomal and mitochondria markers | 0 | dx.doi.org/10.17504/protocols.io.q26g71zykgwz/v1 | https://www.protocols.io/view/colocalisation-imaging-of-endogenous-tmem192-with-davj2e4n | Rotimi Y. Fasimoye, Dario R. Alessi | TITLE: Colocalisation imaging of endogenous TMEM192 with lysosomal and mitochondria markers
AUTHORS: Rotimi Y. Fasimoye, Dario R. Alessi
[DESCRIPTION]
Immunofluorescent (IF) microscopy is a powerful tool used in cellular and molecular biology to monitor the subcellular localisation of proteins. By combining the advant... | ["[Seeding cells for immunofluorescence microscopy] Coat coverslips (sterilised in 100% ethanol prior to use) with poly-L-lysine by immersing the coverslips in poly-L-lysine solution for 60 min.", "[Seeding cells for immunofluorescence microscopy] Rinse the coated coverslips in media and place in a 6-well plate (one co... |
88,114 | Generation of induced neurons from human induced pluripotent stem cells. | 1 | dx.doi.org/10.17504/protocols.io.e6nvwdbxzlmk/v1 | https://www.protocols.io/view/generation-of-induced-neurons-from-human-induced-p-c2asyaee | Prarthana Gowda, Zhiping Pang, Mahmoud ElAchwah, Sol Diaz de Leon Guerrero | TITLE: Generation of induced neurons from human induced pluripotent stem cells.
AUTHORS: Prarthana Gowda, Zhiping Pang, Mahmoud ElAchwah, Sol Diaz de Leon Guerrero
[DESCRIPTION]
Protocol for the generation of Ngn2 (Excitatory) and Ascl1/Dlx2 (Inhibitory) induced neurons from human induced pluripotent stem cell... | ["[Infection of iPSCs - day 0] Follow the below protocols for excitatory and inhibitory neuron generation.", "[Day 13, Day18, Day23, Day28, Day 33....] Discard half of the old media, replace with 100 µL or 750 µL media every 5 days (make sure outside wells are not evaporating media faster) per well of a 96well plate a... |
82,917 | Strep pull down assay | 1 | dx.doi.org/10.17504/protocols.io.3byl4jmpolo5/v1 | https://www.protocols.io/view/strep-pull-down-assay-cu8dwzs6 | Minghao Chen, Xuefeng Ren | TITLE: Strep pull down assay
AUTHORS: Minghao Chen, Xuefeng Ren
[DESCRIPTION]
Strep pull down assay for FIP200(NTD)-TSF WT or mutants were co-transfected with GST-ATG13(363-517) and/or ULK1(MIT)-MBP
[STEPS]
SECTION: Expression
1. Transfect 10 ml HEK GNTi cells at concentration of 2 × 10^6 cells/ml
SECTION: Expres... | ["[Expression] Transfect 10 ml HEK GNTi cells at concentration of 2 × 10^6 cells/ml", "[Expression] Dilute PEI with Warm Hybridoma-SFM(1X)", "[Expression] In a separate tube, dilute DNA with Hybridoma-SFM(1X)", "[Expression] Add PEI to DNA dilution. Incubate mixture for 30 min at 37 °C", "[Expression] Add mixture to c... |
9,893 | (E)-α-bisabolene GC sample preparation | null | dx.doi.org/10.17504/protocols.io.mwdc7a6 | null | Dennis Dienst, Pia Lindberg, João Rodrigues | TITLE: (E)-α-bisabolene GC sample preparation
AUTHORS: Dennis Dienst, Pia Lindberg, João Rodrigues
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is a quick guide for the preparation of (</span><span style = "font-style:italic;">E</span><span>)-α-bisabolene samples and external standards... | ["[Preparation of BCP (β-caryophyllene) internal standard (IS) stocks]\nABCD1 BCP Standard 2Stock A1: 10 Dilution\nfrom Original BCP Stock\n(⇒ 89 mg *mL-1)\n 3 ⇓ 4Stock B ... |
28,700 | T Cell Activation with anti-CD3 Antibodies Protocol - Mouse | null | dx.doi.org/10.17504/protocols.io.794hr8w | null | Sam Li | TITLE: T Cell Activation with anti-CD3 Antibodies Protocol - Mouse
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Prepare a 5µg/ml solution of anti-CD3ε (clone 145-2C11) in sterile PBS.
?. Dispense 50µl of the antibody solution to each microwell of the 96-well assay plate. For the unstimul... | ["Prepare a 5µg/ml solution of anti-CD3ε (clone 145-2C11) in sterile PBS.", "Dispense 50µl of the antibody solution to each microwell of the 96-well assay plate. For the unstimulated control wells, add 50µl of sterile PBS.", "Seal plate. Incubate at 37°C for 2 hours or 4°C overnight.", "Aseptically decant antibody solu... |
107,786 | FUNDIS DNA Extraction | 0 | null | https://www.protocols.io/view/fundis-dna-extraction-dmhi434e | Harte Singer | TITLE: FUNDIS DNA Extraction
AUTHORS: Harte Singer
[DESCRIPTION]
A quick and easy DNA extraction protocol for fungal tissue.
[STEPS]
SECTION: Adding Extraction Buffer
6. Using a 5-50 µL 8-channel pipettor equipped with 100 µLpipette tips, add 15-30 µL of ES extraction buffer to each tube by carefully holding the pipe... | ["[Adding Extraction Buffer] Using a 5-50 µL 8-channel pipettor equipped with 100 µLpipette tips, add 15-30 µL of ES extraction buffer to each tube by carefully holding the pipette tips above the tube openings so that the tips do not make contact with the sample. This way we can use the same row of tips for many sample... |
69,413 | Guidance for populating GenomeTrakr metadata templates (BioSample and SRA) | 1 | dx.doi.org/10.17504/protocols.io.eq2ly3x1pgx9/v8 | https://www.protocols.io/view/guidance-for-populating-genometrakr-metadata-templ-cf2dtqa6 | Ruth Timme, Maria Balkey, William Wolfgang, Errol Strain | TITLE: Guidance for populating GenomeTrakr metadata templates (BioSample and SRA)
AUTHORS: Ruth Timme, Maria Balkey, William Wolfgang, Errol Strain
[DESCRIPTION]
PURPOSE: Guidance on how to populate NCBI's metadata packages, maximizing interoperability for foodborne pathogen surveillance.
SCOPE: This protocol provi... | ["[Overview] Guidance for organizing and populating the metadata templates required for direct submission to NCBI. This guidance is applicable for most enterics and/or microbial pathogens. \n\n****If your laboratory uses the BioNumerics platform for submission, please follow this protocol.****\n\nTwo metadata template... |
32,907 | iGEM Calibration Protocol - Red Fluorescent Proteins in Plate Readers | null | dx.doi.org/10.17504/protocols.io.bcdjis4n | null | Paul Rutten, Cheryl Telmer, Geoff Baldwin, Dennis Mishler, Traci Haddock-Angelli, Jacob Beal, Ari Dwijayanti, Marko Storch, Natalie Farny, Alejandro Vignoni, Richard Tennant | TITLE: iGEM Calibration Protocol - Red Fluorescent Proteins in Plate Readers
AUTHORS: Paul Rutten, Cheryl Telmer, Geoff Baldwin, Dennis Mishler, Traci Haddock-Angelli, Jacob Beal, Ari Dwijayanti, Marko Storch, Natalie Farny, Alejandro Vignoni, Richard Tennant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text... | ["[Prepare the Texas Red stock solution]\nSpin down Texas Red kit tube to make sure pellet is at the bottom of tube", "[Prepare the Texas Red stock solution]\nDilute the 10X reference stock solution with 1X PBS to make a 1X reference working solution with a concentration of 10 μM. E.g. dilute 100 μL of 10X Texas Red re... |
12,441 | RNase One Ribonuclease digestion | 1 | null | https://www.protocols.io/view/rnase-one-ribonuclease-digestion-qdzds76 | Roey Angel, Eva Petrova | TITLE: RNase One Ribonuclease digestion
AUTHORS: Roey Angel, Eva Petrova
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Modified from: http://www.promega.com/paguide/chap6.htm#RNaseAmount</div><div class = "text-block">This protocol was used to remove RNA from DNA preparations.</div><div class = "t... | ["Incubate 5–10μg of total NA 85°C for 5 minutes to denature the NAs.\n[total NA]\n85 °C", "Add 300μl of RNase digestion buffer and the appropriate amount of RNase ONE™ Ribonuclease (1-10u per 10μg of total RNA). Incubate the samples for 30–60 minutes at 20–37°C.\n[RNase digestion buffer]\n20 °C", "Stop the reaction as... |
29,524 | Transient transformation of Ostreococcus species (OTTH595, RCC809 and RCC802) and Bathycoccus | null | dx.doi.org/10.17504/protocols.io.83uhynw | null | francois-yves bouget, Francois-Yves Bouget | TITLE: Transient transformation of Ostreococcus species (OTTH595, RCC809 and RCC802) and Bathycoccus
AUTHORS: francois-yves bouget, Francois-Yves Bouget
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the preparation of cells and introduction of DNA into the cells by electr... | ["[Cell preparation]\n1) Starting from a culture of Ostreococcus tauri, RCC809 or Bathycoccus in stationary phase, innoculate cultures at 1 million cells/ml as determined by flow cytometry (Accuri C6 BD) in 200 ml plastic flasks in Artificial Seawater supplemented with Keller medium supplement (trace metals, vitamins,... |
52,923 | Utilizing the Public GenomeTrakr Database for Foodborne Pathogen Traceback | 2 | dx.doi.org/10.17504/protocols.io.bxw3ppgn | https://www.protocols.io/view/utilizing-the-public-genometrakr-database-for-food-bxw3ppgn | Ruth Timme, Maria Sanchez, Marc Allard | TITLE: Utilizing the Public GenomeTrakr Database for Foodborne Pathogen Traceback
AUTHORS: Ruth Timme, Maria Sanchez, Marc Allard
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the all the steps necessary to become a GenomeTrakr data contributor. GenomeTrakr is an internation... | [] |
62,266 | Sonuvita (SCAM or HOAX) #1 Weight Loss Supplement? | 3 | dx.doi.org/10.17504/protocols.io.36wgq7b5ovk5/v1 | https://www.protocols.io/view/sonuvita-scam-or-hoax-1-weight-loss-supplement-b822ryge | G G | TITLE: Sonuvita (SCAM or HOAX) #1 Weight Loss Supplement?
AUTHORS: G G
[DESCRIPTION]
California health insurance premiums continue to skyrocket making it hard for Californians to afford health care coverage.
[STEPS] | [] |
33,935 | Midbrain dopaminergic differentiation of human pluripotent stem cells | null | dx.doi.org/10.17504/protocols.io.bddpi25n | https://www.protocols.io/view/midbrain-dopaminergic-differentiation-of-human-plu-bddpi25n | Tilo Kunath, Szuping Chiu, Sophie Glendinning, Yixi Chen, Nicola Drummond, Maurice Canham | TITLE: Midbrain dopaminergic differentiation of human pluripotent stem cells
AUTHORS: Tilo Kunath, Szuping Chiu, Sophie Glendinning, Yixi Chen, Nicola Drummond, Maurice Canham
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Differentiation of human embryonic stem cells (hESCs) and human induced plur... | ["[Preparing reagents for mDA differentiation]\nPrepare a 10 mM SB431542 solution.", "[Preparing reagents for mDA differentiation]\nTo prepare 1190 µl of 10 mM SB431542:Add (2 x ) of DMSO (Sigma Aldrich, cat no. D2650) directly to vial containing of SB431542 (Merck Millipore, cat no. 616461-5MG) and mix by pipettin... |
20,517 | PDMS Fabrication | null | dx.doi.org/10.17504/protocols.io.yadfsa6 | null | Kenneth Schackart, Kattika Kaarj | TITLE: PDMS Fabrication
AUTHORS: Kenneth Schackart, Kattika Kaarj
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details how to make a small piece of polydimethylsiloxane (PDMS)</div></div>
[STEPS]
?. [Prepare surface]
Wipe the inside of the petri dish lid with 70% ethanol solution u... | ["[Prepare surface]\nWipe the inside of the petri dish lid with 70% ethanol solution using a Kimwipe® to rid the surface of debris.", "[Prepare surface]\nPlace petri dish lid(s) and a 10 cm × 10 cm piece of foil in the dessicator, in the fume hood.", "[Prepare surface]\nAdd Tridecafluoro-1,1,2,2-tetrahydrooctyl trichlo... |
36,770 | IHC staining | 1 | dx.doi.org/10.17504/protocols.io.bf6ajrae | https://www.protocols.io/view/ihc-staining-bf6ajrae | Marc Bosse, Sean Bendall, Mike Angelo | TITLE: IHC staining
AUTHORS: Marc Bosse, Sean Bendall, Mike Angelo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is standard immunohistochemistry (IHC) procedure recommended in the Bendall and Angelo lab.</div></div>
[STEPS]
?. [Slide baking and PT module preparation ]
Bake the sections at ... | ["[Slide baking and PT module preparation ]\nBake the sections at for in an dry incubator Optional : ; last 10 min place the slide vertical with the label side up to allow the paraffin to drip down\n70 °C\nNote: Some tissues or section size may need longer baking time. Recommended to bake at least 1 hour for ... |
40,388 | Lessons learned from the resilience of Chinese public health systems, hospitals and personnel to the COVID-19 pandemic: a scoping review protocol. | 1 | null | https://www.protocols.io/view/lessons-learned-from-the-resilience-of-chinese-pub-bjpckmiw | Jack Stennett | TITLE: Lessons learned from the resilience of Chinese public health systems, hospitals and personnel to the COVID-19 pandemic: a scoping review protocol.
AUTHORS: Jack Stennett
[DESCRIPTION]
Background: The SARS-CoV-2 pandemic has brought huge strain on hospitals worldwide; however, while the success of China’s COVID... | ["Lessons learned from the resilience of Chinese hospitals to the COVID-19 pandemic: a scoping review of empirical literature.\n\nValéry Ridde1 , Fanny Chabrol1 , Lola Traverson1 , Hou Renyou1, Jack Stennett1 \n\n1. CEPED, Institute for Research on Sustainable Development, IRD-Université de Paris, ERL INSERM SAGESUD, P... |
45,465 | (Epstein, Kim, Schanke) Trial K+ Minimal Media Recipe | 4 | null | https://www.protocols.io/view/epstein-kim-schanke-trial-k-minimal-media-recipe-bqmzmu76 | Elizabeth Fozo | TITLE: (Epstein, Kim, Schanke) Trial K+ Minimal Media Recipe
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Trial K</span><span style = "vertical-align:super;">+</span><span> Minimal Media Recipe</span></div></div>
[STEPS]
?. [1L recipe]
Rinse the beaker with DI H2OFi... | ["[1L recipe]\nRinse the beaker with DI H2OFill to ~900mL MiliQ waterSet to mix, no heat.Choose between:In media room/dry goodsAbove lab benchesIn the fridgeFill to 1L with MiliQ and mix till dissolved (can be on low heat)Check pH (should be ~7), [K+] (normally ~8 ppm), and filter", "[250mL recipe]\nRinse the beaker wi... |
108,806 | JGI/LBNL Metabolomics - Standard LC-MS/MS ESI Method - Nonpolar C18 | 1 | dx.doi.org/10.17504/protocols.io.261ge5mzjg47/v1 | https://www.protocols.io/view/jgi-lbnl-metabolomics-standard-lc-ms-ms-esi-method-dnhe5b3e | Katherine B. Louie, Suzanne Kosina, Thomas Harwood, Meghana Faltane, Marie Lynde, Benjamin P. Bowen, Trent Northen | TITLE: JGI/LBNL Metabolomics - Standard LC-MS/MS ESI Method - Nonpolar C18
AUTHORS: Katherine B. Louie, Suzanne Kosina, Thomas Harwood, Meghana Faltane, Marie Lynde, Benjamin P. Bowen, Trent Northen
[DESCRIPTION]
This protocol describes the standard LC-MS/MS ESI method developed at Lawrence Berkeley National Laborator... | ["[Mass Spectrometer Preparation] Prior to data acquisition, the mass spectrometer is calibrated using standard calibration procedures available in the Thermo XCalibur operating software. ESI needle position is optimized relative to the source to achieve stable and acceptable ion intensity levels.\n\nCalibration proce... |
27,348 | Opomba protocol | null | dx.doi.org/10.17504/protocols.io.6xuhfnw | null | Matt H | TITLE: Opomba protocol
AUTHORS: Matt H
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Hi there</span><a href="#" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;"> </span></a><span style = ":;"> </span></div></div>
[STEPS]
?. [Pre-work things]
Warm-upGet reage... | ["[Pre-work things]\nWarm-upGet reagents from the fridge", "[Pre-work things]", "[Pre-work things]"] |
76,699 | Run Clearmap 1 docker | 5 | null | https://www.protocols.io/view/run-clearmap-1-docker-cn53vg8n | Moritz Negwer | TITLE: Run Clearmap 1 docker
AUTHORS: Moritz Negwer
[DESCRIPTION]
This protocol is a supplement to our upcoming publication "FriendlyClearMap: An optimized toolkit for mouse brain mapping and analysis".
In this protocol, we describe in detail how to run Clearmap1 in a Docker container.
[STEPS]
SECTION: Docker Se... | ["[Docker Setup] On Windows: \nIf you haven't already, download and set up Docker Desktop for Windows. This requires administrator privileges and will also install the Windows Subsystem for Linux (WSL2). \n\nDownload: \nhttps://www.docker.com/products/docker-desktop \n\nAlternatively, use our install script via powersh... |
38,260 | Transfection of Cas9 RNP (ribonucleoprotein) into adherent cells using the Lipofectamine® RNAiMAX | 1 | dx.doi.org/10.17504/protocols.io.bhkuj4ww | https://www.protocols.io/view/transfection-of-cas9-rnp-ribonucleoprotein-into-ad-bhkuj4ww | New England Biolabs | TITLE: Transfection of Cas9 RNP (ribonucleoprotein) into adherent cells using the Lipofectamine® RNAiMAX
AUTHORS: New England Biolabs
[DESCRIPTION]
Cas9 nuclease may be used in vivo to create targeted genome modifications. There are several ways in which to introduce Cas9-guide RNA complexes into cells. Here we p... | ["[RNP Complex Formation] Make a 3 Micromolar (µM) by diluting the stock with nuclease-free water.", "[RNP Complex Formation] Make a 3 Micromolar (µM) by diluting with 1 X or Optimem.", "[RNP Complex Formation] Form the RNP complexes as follows below:\n Component Single Reaction x3.3 (triplicates) sgRNA (3 uM) 0.5 ... |
33,432 | Plant DNA extraction and preparation for ONT sequencing | null | dx.doi.org/10.17504/protocols.io.bcvyiw7w | null | Boas Pucker | TITLE: Plant DNA extraction and preparation for ONT sequencing
AUTHORS: Boas Pucker
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Plant DNA extraction and preparation for ONT sequencing</span></div><div class = "text-block">This CTAB-based protocol is suitable for... | ["[CTAB-based DNA extraction]\nPreheat 5 ml CTAB1 + 300 µL ß-ME in 50 ml tube to 75 C(The amount of ß-ME is working, but was not optimized)", "[CTAB-based DNA extraction]\nHomogenize fresh material with morta and pestle in liquid N2(It is important to use fresh material which was not frozen previously. Less than 1g of ... |
41,016 | Fermentor Growth of Streptococcus sanguinis | 4 | dx.doi.org/10.17504/protocols.io.bkayksfw | https://www.protocols.io/view/fermentor-growth-of-streptococcus-sanguinis-bkayksfw | Tanya Puccio, Todd Kitten | TITLE: Fermentor Growth of Streptococcus sanguinis
AUTHORS: Tanya Puccio, Todd Kitten
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-style:italic;">Streptococcus sanguinis</span><span> is a lactic acid-forming bacterium that can be cultured in both aerobic and anaerobic conditio... | ["[Inoculation]\nSet up fermentor to experiment specifications: pO2 set to 5% with 0.03 lpm max air flow; nitrogen set at 0.08 lpm; stirrer set at 250 rpm;\n37 °C\n800 mL", "[Inoculation]\nRemove media from vessel to incubate as a check for contamination.\n15 mL\n37 °C", "[Inoculation]\nCentrifuge remaining volume ... |
19,144 | Tau Thioflavin T Assay | null | dx.doi.org/10.17504/protocols.io.wxgffjw | null | Alexandra Netter-Glangeaud | TITLE: Tau Thioflavin T Assay
AUTHORS: Alexandra Netter-Glangeaud
[STEPS]
?. A 1mM stock solution of Thioflavin T was prepared in dH2O (prepared fresh and filtered through a 0.2 µm syringe filter).
?. The thioflavin T was diluted in PBS pH 7.4 so that the final Thioflavin T concentration in each well was 25 µM (volume... | ["A 1mM stock solution of Thioflavin T was prepared in dH2O (prepared fresh and filtered through a 0.2 µm syringe filter).", "The thioflavin T was diluted in PBS pH 7.4 so that the final Thioflavin T concentration in each well was 25 µM (volume per well = 100 µL).", "10 uM Heparin was added to each well.", "Tau aliquot... |
41,736 | COVIRAP testing protocol | 4 | dx.doi.org/10.17504/protocols.io.bkzgkx3w | https://www.protocols.io/view/covirap-testing-protocol-bkzgkx3w | Suman Chakraborty, Arindam Mondal, Aditya Bandopadhyay, Sujay Kumar Biswas, Saptarshi Banerjee, Nandita Kedia, Subhamoy Chatterjee, Aratrika de, Indranath Banerjee | TITLE: COVIRAP testing protocol
AUTHORS: Suman Chakraborty, Arindam Mondal, Aditya Bandopadhyay, Sujay Kumar Biswas, Saptarshi Banerjee, Nandita Kedia, Subhamoy Chatterjee, Aratrika de, Indranath Banerjee
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-alig... | ["[DNA/RNA amplification]\nAliquot RT-LAMP master mix into PCR tubes considering the total number of reactions. For one RNA sample, three reactions need to be carried out; one corresponding to RNaseP (internal control) and two corresponding to viral gene targets (N gene and ORF 1b).\n10 µl", "[DNA/RNA amplification]\... |
66,144 | Rapid, effective and low-cost purification of dideoxy-sequencing reactions by home-made magnetic beads suspension and magnetic separator | 4 | dx.doi.org/10.17504/protocols.io.kqdg3pdzel25/v1 | https://www.protocols.io/view/rapid-effective-and-low-cost-purification-of-dideo-cct8swrw | Hidenori Sassa | TITLE: Rapid, effective and low-cost purification of dideoxy-sequencing reactions by home-made magnetic beads suspension and magnetic separator
AUTHORS: Hidenori Sassa
[DESCRIPTION]
Removal of excess dideoxy terminators from the sequencing mix after the enzymatic reaction is a key process affecting the dideoxy/Sanger ... | ["[MagNA suspension]", "[MagNA suspension] Prepare 50 ml buffer without magnet beads as follow. Final concentration of each chemical is indicated in parenthesis. \nDissolve 9 g PEG 8,000 (18 %), 2.92 g NaCl (1 M), 5 ml 10x TE (1x), 25 µl Tween-20 (0.05 %) and 50 µl ProClin 300 (0.1 %) in DW to prepare 50 ml PEG-NaCl bu... |
91,906 | Microbial DNA enrichment of rectal mucosa tissue samples using NEBNext Microbiome DNA Enrichment Kit | 1 | dx.doi.org/10.17504/protocols.io.261ged89wv47/v1 | https://www.protocols.io/view/microbial-dna-enrichment-of-rectal-mucosa-tissue-s-c5zay72e | Lee Murphy, Audrey AC Coutts, Louise Evenden | TITLE: Microbial DNA enrichment of rectal mucosa tissue samples using NEBNext Microbiome DNA Enrichment Kit
AUTHORS: Lee Murphy, Audrey AC Coutts, Louise Evenden
[DESCRIPTION]
ABSTRACT
This protocol outlines the procedure for microbial DNA enrichment of rectal mucosa tissue samples using NEBNext Microbiome DNA Enrichm... | ["[DNA preparation and quantification] Samples were extracted using the protocol \"DNA extraction from rectal mucosa biopsies and matched faecal samples taken from surgery for microbiome analysis”. https://dx.doi.org/10.17504/protocols.io.eq2lyj15wlx9/v1", "[Bind MBD2-Fc protein to magnetic beads] For every 6.25ng of i... |
63,835 | To test fork notification | 1 | dx.doi.org/10.17504/protocols.io.n92ldzjxxv5b/v1 | https://www.protocols.io/view/to-test-fork-notification-caj3scqn | Gabriel Gasque | TITLE: To test fork notification
AUTHORS: Gabriel Gasque
[DESCRIPTION]
Test for Fork notifications
[STEPS]
1. Step 1
2. Step 2
3. Step 3
4. Step 4 | ["Step 1", "Step 2", "Step 3", "Step 4"] |
28,610 | NucleoSpin® Gel and PCR Clean-up | null | dx.doi.org/10.17504/protocols.io.77ahrie | null | iGEM Dusseldorf | TITLE: NucleoSpin® Gel and PCR Clean-up
AUTHORS: iGEM Dusseldorf
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><ul style = "list-style-type:disc;"><li style = "counter-reset:ol0;list-style-type:disc;">Buffer NTI</li><li style = "counter-reset:ol0;list-style-type:disc;">NucleoSpin® Gel and PCR Clea... | [] |
78,271 | ACTION Biomarker Study | 1 | dx.doi.org/10.17504/protocols.io.eq2ly7qkwlx9/v1 | https://www.protocols.io/view/action-biomarker-study-cqn7vvhn | Fiona A. Hagenbeek, Jenny van Dongen, Peter J. Roetman, Erik A. Ehli, Meike Bartels, Robert R. J. M. Vermeiren, Dorret I. Boomsma, ACTION Consortium | TITLE: ACTION Biomarker Study
AUTHORS: Fiona A. Hagenbeek, Jenny van Dongen, Peter J. Roetman, Erik A. Ehli, Meike Bartels, Robert R. J. M. Vermeiren, Dorret I. Boomsma, ACTION Consortium
[DESCRIPTION]
The goal of ACTION project (Aggression in Children: Unraveling gene-environment interplay to inform Treatment and Int... | [] |
61,490 | Complex I activity assay | 4 | dx.doi.org/10.17504/protocols.io.36wgq7ok5vk5/v1 | https://www.protocols.io/view/complex-i-activity-assay-b8asrsee | María José Pérez J., michela.deleidi | TITLE: Complex I activity assay
AUTHORS: María José Pérez J., michela.deleidi
[DESCRIPTION]
This protocol describes the complex I activity assay.
[BEFORE_START]
All assays are carried out at 25 °C.
After mitochondrial isolation (Qproteome Mitochondria Isolation Kit. QIAGEN Cat. No. / ID: 37612), resuspend the final p... | ["[Protocol] Distribute the contents of tube A and B in strips suitable for multichannel use.", "[Protocol] In a Half Volume 96-well clear plate add 50 µL of the contents of tube A to each well.", "[Protocol] Add 20 µL of sample to each well.", "[Protocol] Place plate in plate reader and add 30 µL of B to each well.", ... |
97,439 | The Bcc qPCR NAD assay for the specific rapid quantitative detection of all Bcc species | 1 | dx.doi.org/10.17504/protocols.io.4r3l223wql1y/v2 | https://www.protocols.io/view/the-bcc-qpcr-nad-assay-for-the-specific-rapid-quan-dbd72i9n | Huong Thu Duong, Shannon Fullbrook, Kate Reddington, Elizabeth Minogue, Thomas Barry | TITLE: The Bcc qPCR NAD assay for the specific rapid quantitative detection of all Bcc species
AUTHORS: Huong Thu Duong, Shannon Fullbrook, Kate Reddington, Elizabeth Minogue, Thomas Barry
[DESCRIPTION]
The Bcc qPCR NAD assay presented is an internally controlled duplex assay (incorporating an IAC), targeting a region... | ["[Prepare a qPCR master mix (in a DNA-free preparation hood)] Thaw qPCR reagents and samples on the bench, flick to mix and briefly spin down on a tabletop centrifuge.", "[The Bcc qPCR NAD assay] Transfer the plate into the thermal cycler after setting it up appropriately and carry out qPCR reaction at the following c... |
30,206 | Salmonella blood culture surveillance: work-up and pathogen identification | null | dx.doi.org/10.17504/protocols.io.9q6h5ze | null | Barbara Barbé, Sien Ombelet | TITLE: Salmonella blood culture surveillance: work-up and pathogen identification
AUTHORS: Barbara Barbé, Sien Ombelet
[STEPS] | [] |
102,856 | Protein Aggregation Capture | 0 | null | https://www.protocols.io/view/protein-aggregation-capture-dgpg3vjw | Mark Kinnin | TITLE: Protein Aggregation Capture
AUTHORS: Mark Kinnin
[DESCRIPTION]
PAC Adapted from Batth et al., 2019
[STEPS]
SECTION: Equilibration
1. Add 5 µL of to 1.5mL LoBind Eppendorf tube
SECTION: Equilibration
1.1. Place tube on magnet and allow Microparticles to clear 10 s
SECTION: Equilibration
1.2. Remove stora... | ["[Equilibration] Add 5 µL of to 1.5mL LoBind Eppendorf tube", "[Equilibration] Place tube on magnet and allow Microparticles to clear 10 s", "[Equilibration] Remove storage solution and discard", "[Equilibration] Equilibrate Microparticles by adding 100 µL and mix by gentle agitation", "[Equilibration] Place tube... |
45,105 | Sensor Protocol updated | 4 | dx.doi.org/10.17504/protocols.io.bqarmsd6 | https://www.protocols.io/view/sensor-protocol-updated-bqarmsd6 | s.yao | TITLE: Sensor Protocol updated
AUTHORS: s.yao
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The CoV-SARS-2 Antigen Diagnostic kit is a test intended for the qualitative detection of intact SARS-CoV-2 virions (SARS-CoV-2 is abbreviated as SARS-2 herein) in upper and lower respiratory specimens (su... | ["[Results and data interpretation]\nFor testing the sensor and fluorometer using negative control and positive controlCalculate an average for the five values collected per run at 30sec and 10mRecord the difference in the average fluorescence reading at 10m from 30sec for negative sample this is the Vneg value.Record ... |
55,600 | Assembly, Annotation, Quantification, and Differential Expression Analysis of Shorea sp. Transcriptome | 5 | dx.doi.org/10.17504/protocols.io.b2iqqcdw | https://www.protocols.io/view/assembly-annotation-quantification-and-differentia-b2iqqcdw | Ahmad Husaini AHS Suhaimi | TITLE: Assembly, Annotation, Quantification, and Differential Expression Analysis of Shorea sp. Transcriptome
AUTHORS: Ahmad Husaini AHS Suhaimi
[DESCRIPTION]
Assembly, annotation, and quantification of transcripts from RNA-seq reads of Shorea sp. transcriptome followed by differential expression analysis using open s... | ["[Transcript Assembly] Assemble the reads using Trinity assembler", "[Transcript Assembly] Obtain the assembly statistics", "[Transcript Annotation] Query the nonredundant nucleotide sequences against A. thaliana proteome", "[Transcript Annotation] Query the nonredundant protein sequences against Pfam, PANTHER, GO, an... |
72,700 | HCR of fixed mouse brain tissue sections | 1 | dx.doi.org/10.17504/protocols.io.8epv59725g1b/v2 | https://www.protocols.io/view/hcr-of-fixed-mouse-brain-tissue-sections-ci84uhyw | Alex Buckley | TITLE: HCR of fixed mouse brain tissue sections
AUTHORS: Alex Buckley
[DESCRIPTION]
This is an RNA fluorescent in-situ hybridization (FISH) protocol that utilizes hybridization chain reaction technology from Molecular Instruments. The protocol fluorescently labels different mRNAs (up to 4 different mRNAs) such that t... | ["[Notes] -Beginning from after fixed sections mounted on superfrost plus slides have been washed with PBS (1x5min)\n-Protocol adapted from Molecular Instruments https://files.molecularinstruments.com/MI-Protocol-RNAFISH-FrozenTissue-Rev2.pdf\n-All buffers, probes, and hairpins to be ordered from Molecular Instruments ... |
47,244 | Abeoforma whisleri_culture method | 1 | null | https://www.protocols.io/view/abeoforma-whisleri-culture-method-bsdkna4w | Meritxell Antó | TITLE: Abeoforma whisleri_culture method
AUTHORS: Meritxell Antó
[STEPS]
?. [Growing medium]
BD Difco Marine Broth 2216 • Marine Agar 2216 https://legacy.bd.com/europe/regulatory/Assets/IFU/Difco_BBL/212185.pdf
?. [Growth conditions]
Temperature 17ºC
?. [Cryopreservation and recovery (from liquid cultures)]
Cryoprese... | ["[Growing medium]\nBD Difco Marine Broth 2216 • Marine Agar 2216 https://legacy.bd.com/europe/regulatory/Assets/IFU/Difco_BBL/212185.pdf", "[Growth conditions]\nTemperature 17ºC", "[Cryopreservation and recovery (from liquid cultures)]\nCryopreservation (10%DMSO in 1M sorbitol or 10%(glycerol 60%) in sorbitol 1M)1. P... |
44,020 | Indirect ELISA protocol (abcam) | 4 | dx.doi.org/10.17504/protocols.io.bn8umhww | https://www.protocols.io/view/indirect-elisa-protocol-abcam-bn8umhww | Heather Robeson, Jing Jin, Mohammed S. Orloff | TITLE: Indirect ELISA protocol (abcam)
AUTHORS: Heather Robeson, Jing Jin, Mohammed S. Orloff
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The protocol is based on the abcam Indirect ELISA protocol.</div></div>
[STEPS]
?. [Reagent Preparation]
PARP1 Standard: A seven point standard curve using 2... | ["[Reagent Preparation]\nPARP1 Standard: A seven point standard curve using 2-fold serial dilution in Plate Coating Buffer or 1X PBS is recommended. Prepare 500 uL of high standard (1000 ng/mL) per plate assayed from stock solution.", "[Reagent Preparation]\nSample Dilutions: Using proteins extracted from tissue via Qi... |
null | null | null | dx.doi.org/10.17504/protocols.io.dsb6am | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
The traditional phenol extraction procedure, based on early work by Kirby (1957) and elaborated in most modern protocol compendia, yields very clean nucleic acids suitable for a variety of downstream applications. This extraction method is coupled with a routine alcohol precipit... | [] |
71,692 | Lectin C's gene analysis | 1 | dx.doi.org/10.17504/protocols.io.kqdg39p3pg25/v1 | https://www.protocols.io/view/lectin-c-39-s-gene-analysis-ch9kt94w | Tran Vinh Phuong, Nguyen Ngoc Phuoc, Nguyen Quang Quang Linh | TITLE: Lectin C's gene analysis
AUTHORS: Tran Vinh Phuong, Nguyen Ngoc Phuoc, Nguyen Quang Quang Linh
[DESCRIPTION]
Mammalian Tissue Total RNA Purification Protocol by GeneJET RNA Purification Kit (Thermo Scientific, USA)
Before starting:
• Supplement the required amount of Lysis Buffer with β-mercaptoethanol or ... | [] |
52,744 | GUV preparation and assay | 1 | dx.doi.org/10.17504/protocols.io.bxrgpm3w | https://www.protocols.io/view/guv-preparation-and-assay-bxrgpm3w | Chunmei Chang | TITLE: GUV preparation and assay
AUTHORS: Chunmei Chang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">LC3 lipidation on GUVs</div></div>
[STEPS]
?. GUV Preparation
?. Clean the coverslips of 25 mm diameter.
?. Coat cleaned coverslips with 60 μL 5% (w/w) polyvinyl alcohol (PVA) with a molecular... | ["GUV Preparation", "Clean the coverslips of 25 mm diameter.", "Coat cleaned coverslips with 60 μL 5% (w/w) polyvinyl alcohol (PVA) with a molecular weight of 145,000 (Millipore).", "Place the coated coverslip in a heating incubator at 60 °C to dry the PVA film for 30 min.", "Spread a lipid mixture with a molar composi... |
85,928 | Endogenous tagging of the YIPF4 gene with mNEON Green and imaging of these cells by microscopy v2 | 4 | dx.doi.org/10.17504/protocols.io.5jyl8pj9dg2w/v1 | https://www.protocols.io/view/endogenous-tagging-of-the-yipf4-gene-with-mneon-gr-cx6gxrbw | Harper JW, Kelsey Hickey, sharan_swarup | TITLE: Endogenous tagging of the YIPF4 gene with mNEON Green and imaging of these cells by microscopy v2
AUTHORS: Harper JW, Kelsey Hickey, sharan_swarup
[DESCRIPTION]
This protocol describes a method to create cells in which the YIPF4 gene has been endogenously tagged with mNEON fluorescent protein. CRISPR-based gene... | ["[Cell Culture] HEK293 (human embryonic kidney, fetus, ATCC CRL-1573, RRID: CVCL_0045) cells were grown in Dulbecco’s modified Eagle’s medium (DMEM, high glucose and pyruvate) supplemented with 10% fetal calf serum and maintained in a 5% CO2 incubator at 37oC. Cells were maintained at <80% confluency throughout the co... |
93,716 | Leica SP8 Confocal | 1 | null | https://www.protocols.io/view/leica-sp8-confocal-c7ruzm6w | Condon ND | TITLE: Leica SP8 Confocal
AUTHORS: Condon ND
[DESCRIPTION]
This is a training guide for the Leica SP8 Confocal Microscope at the Insitute for Molecular Bioscience at The University of Queensland, Brisbane, Australia.
More information about the system is available here: https://imb.uq.edu.au/microscopy-confocal-1
[ST... | ["[System Start Up] Using the Microscope Power Switches, turn on the system in the following order\nTurn on the PC by the power button on the top right of the tower.\nTurn on the PC Microscope Switch, wait until the PC is powered on and you have logged in with your AD credentials\nTurn on the Scanner power, wait 10 sec... |
70,107 | Stereotaxic injection of viral vectors | 4 | dx.doi.org/10.17504/protocols.io.q26g7yr78gwz/v1 | https://www.protocols.io/view/stereotaxic-injection-of-viral-vectors-cgp3tvqn | Maia Datunashvili | TITLE: Stereotaxic injection of viral vectors
AUTHORS: Maia Datunashvili
[DESCRIPTION]
Stereotaxic injection of viral vectors
[STEPS]
SECTION: Sterotaxic surgery steps
1. Clean the Hamilton Syringe with 70% and then with distilled water.
SECTION: Sterotaxic surgery steps
2. Calibrate Kopf frame according to the inst... | ["[Sterotaxic surgery steps] Clean the Hamilton Syringe with 70% and then with distilled water.", "[Sterotaxic surgery steps] Calibrate Kopf frame according to the instructions.", "[Sterotaxic surgery steps] Anesthetize the animal with 3-4% Isoflurane.", "[Sterotaxic surgery steps] Position the heat pad covered with th... |
54,538 | DNA extraction from mouthwash samples | 1 | null | https://www.protocols.io/view/dna-extraction-from-mouthwash-samples-bzhip34e | Ahmed A Shibl, Anique Ahmad, Tsedenia Denekew, Mamon Abd AlBaqi, Aashish Jha | TITLE: DNA extraction from mouthwash samples
AUTHORS: Ahmed A Shibl, Anique Ahmad, Tsedenia Denekew, Mamon Abd AlBaqi, Aashish Jha
[DESCRIPTION]
DNA extraction
[BEFORE_START]
Set centrifuge to 4ºC
Keep CD2 solution on ice
Prepare and label collection tubes, microcentrifuge tubes, and MB spin columns
[STEPS]
1. Thaw... | ["Thaw mouthwash samples on ice for 30 min", "Transfer desired volume into 1.5 mL or 2 mL eppendorfs\n1-2 mL", "Centrifuge transferred samples at maximum speed at 4 ºC for 10 min", "Discard the supernatant carefully without disturbing the pellet", "Add 800 µL CD1 and vortex to resuspend pellet", "Transfer entire eppend... |
25,551 | Cryopreservation of Mammalian Cells (Suspension) | null | dx.doi.org/10.17504/protocols.io.47pgzmn | null | Andrew Crowley | TITLE: Cryopreservation of Mammalian Cells (Suspension)
AUTHORS: Andrew Crowley
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A protocol for the preservation of suspension-type cells by freezing.</div><div class = "text-block">The protocol has been sucessfully used on:</div><div class = "text-bloc... | ["Measure the density and viability of the cells", "Gently pellet the cells via centrifugation", "While centrifuging, use the live cell counts from step 1 to calculate the total volume required to resuspend the cells @", "Gently aspirate the culture media from the pellet", "Gently reuspend the cell pellet in cryopreser... |
null | null | null | dx.doi.org/10.17504/protocols.io.khuct6w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Double digested Restriction-site Associated DNA (ddRAD) sequencing is a powerful approach for identifying and analyzing genome-wide SNP variation. Many studies have now used ddRAD protocols for population genetic studies. Here we have adapted the protocol from Peterson (2012)... | [] |
28,728 | Energy solution preparation for OnePot PURE cell-free system | null | dx.doi.org/10.17504/protocols.io.8ayhsfw | null | Konstantinos Ragios | TITLE: Energy solution preparation 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 to create the Energy solution used for protein expression in OnePot PURE cell-free system. </div></div>
[STEPS]
... | ["For a 2.5x Energy Solution add the materials needed tho a tube. The final concentration of the components is presented in Table 1.\nBefore adding each component make sure it is totally melted and then vortex for a few seconds", "ABC1CompoundConcentrationUnits2Amino Acids0.75mM3Magnesium acetate29.5mM4Potassium gluta... |
58,550 | SOP024: Preparing 10000x DNA gel stain | 5 | null | https://www.protocols.io/view/sop024-preparing-10000x-dna-gel-stain-b5ewq3fe | Shalo Minette, Stephane Fadanka, Nadine Mowoh | TITLE: SOP024: Preparing 10000x DNA gel stain
AUTHORS: Shalo Minette, Stephane Fadanka, Nadine Mowoh
[DESCRIPTION]
DNA dyes stain deoxyribonucleic acid for laboratory purposes such as detection and quantification. Many DNA dyes also bind to RNA and could be more broadly described as nucleic acid stains. Common dy... | ["[Preparing a 13mg/ml stock of DNA gel stain (1ml)] Use a weighing balance to carefully measure0.013 g of Thiazole Orange powder (Cas # 107091-89-4) into a 1.5ml Eppendorf tube or opaque screw cap tube.", "[Preparing a 13mg/ml stock of DNA gel stain (1ml)] Use a micropipette to pipette 1000 µL of DMSO (Cas # 67-68-5) ... |
91,667 | BBB permeability and NDP-MSH PK study | 1 | dx.doi.org/10.17504/protocols.io.4r3l22p43l1y/v1 | https://www.protocols.io/view/bbb-permeability-and-ndp-msh-pk-study-c5rty56n | Pranay Srivastava | TITLE: BBB permeability and NDP-MSH PK study
AUTHORS: Pranay Srivastava
[DESCRIPTION]
This protocol is to measure the integrity of BBB and assess NDP-MSH concentrations in plasma and brain
[STEPS]
SECTION: BBB permeability
1. The integrity of BBB was measured through FITC-albumin (Millipore Sigma, Cat# A9771) leakage... | ["[BBB permeability] The integrity of BBB was measured through FITC-albumin (Millipore Sigma, Cat# A9771) leakage from vasculature into brain parenchyma as described previously (Chen et al. 2008). Mice were treated with MPTP+LPS and sacrificed after 6 h and 24 h after the last dose.", "[BBB permeability] Mice were anae... |
50,384 | Collection of Protocols and Guidelines for Safety and Efficacy of Imatinib for Preserving Beta-cell Function in New-onset Type 1 Diabetes Mellitus | 2 | dx.doi.org/10.17504/protocols.io.bvfqn3mw | https://www.protocols.io/view/collection-of-protocols-and-guidelines-for-safety-bvfqn3mw | Stephen.Gitelman , Jeffrey A. Bluestone | TITLE: Collection of Protocols and Guidelines for Safety and Efficacy of Imatinib for Preserving Beta-cell Function in New-onset Type 1 Diabetes Mellitus
AUTHORS: Stephen.Gitelman , Jeffrey A. Bluestone
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a collection of protocols for: "Safety an... | [] |
41,747 | BW SARS-CoV-2 Laboratory Test | 4 | dx.doi.org/10.17504/protocols.io.bkztkx6n | https://www.protocols.io/view/bw-sars-cov-2-laboratory-test-bkztkx6n | ivan , peter.marx | TITLE: BW SARS-CoV-2 Laboratory Test
AUTHORS: ivan , peter.marx
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is the laboratory-based equivalent of the LAMP assay used for detecting SARS-CoV-2. A similar protocol is performed automatically within the Biology Works LLC at-home device... | ["[Assay]\nThaw reagents to room temperature\n0 Room temperature", "[Assay]\nVortex reagents\n33", "[Assay]\nBriefly spin down components in a microcentrifuge", "[Assay]\nPrepare master mix in a 1.5mL tube with the following sub-steps", "[Assay]\nAdd to tube\n12.5 µl", "[Assay]\nVortex\n33", "[Assay]\nBriefly spin dow... |
76,193 | RNA extraction protocol for the Bungarus multicinctus by using TRlZOL reagent（Invitrogen） | 4 | dx.doi.org/10.17504/protocols.io.ewov1o5qklr2/v1 | https://www.protocols.io/view/rna-extraction-protocol-for-the-bungarus-multicinc-cnm9vc96 | Boyang Liu, Liangyu Cui, Yue Ma, Diancheng Yang, Yanan Gong, Yanchun Xu, Shuhui Yang, Song Huang | TITLE: RNA extraction protocol for the Bungarus multicinctus by using TRlZOL reagent（Invitrogen）
AUTHORS: Boyang Liu, Liangyu Cui, Yue Ma, Diancheng Yang, Yanan Gong, Yanchun Xu, Shuhui Yang, Song Huang
[DESCRIPTION]
RNA was extracted from the muscle of a Bungarus multicinctus using the TRlzol reagent (Invitrogen, USA... | ["[RNA extraction] The laboratory and test bench for RNA extraction were sterilized by alcohol and ultraviolet for 30 minutes. \n30 min \n\nAll the equipment used in the experiment, such as mortar and pestle, were sterilized at high temperature one day before the experiment and dried in an oven. \n\nMasks and gloves sh... |
91,813 | A universal protocol for high-quality DNA and RNA isolation from diverse plant species | 4 | dx.doi.org/10.17504/protocols.io.8epv5xj86g1b/v2 | https://www.protocols.io/view/a-universal-protocol-for-high-quality-dna-and-rna-c5wdy7a6 | Farhad Masoomi-Aladizgeh, Leila Jabbari, Reza Khayam Nekouei, Ali Aalami, Brian J Atwell, Paul A Haynes | TITLE: A universal protocol for high-quality DNA and RNA isolation from diverse plant species
AUTHORS: Farhad Masoomi-Aladizgeh, Leila Jabbari, Reza Khayam Nekouei, Ali Aalami, Brian J Atwell, Paul A Haynes
[DESCRIPTION]
Next-generation sequencing demands high-quality nucleic acid, yet isolating DNA and RNA from plant... | ["[Lysis Buffer for DNA and RNA Isolation] The lysis buffer contains 0.5% CTAB, 1% EDTA, 2.5% Tris base and 5% NaCl. These are the four main components of the lysis buffer for DNA and RNA isolation from plant tissues. \n\nExample: Add CTAB (125 mg), EDTA (250 mg), Tris base (625 mg), and NaCl (1250 mg) to 25 ml nucleas... |
66,230 | Measuring fungal anti-E. coli activity using the zone of inhibition (ZOI) assay | 4 | dx.doi.org/10.17504/protocols.io.261gen7qjg47/v1 | https://www.protocols.io/view/measuring-fungal-anti-e-coli-activity-using-the-zo-ccwwsxfe | Shara Van De Pas, Siouxsie Wiles | TITLE: Measuring fungal anti-E. coli activity using the zone of inhibition (ZOI) assay
AUTHORS: Shara Van De Pas, Siouxsie Wiles
[DESCRIPTION]
In this protocol, we describe our use of the zone of inhibition assay to assess the anti-E. coli activity of fungi grown on different media, including Czapek Solution Agar (CSA... | ["[Setting up E. coli 25922 lux and ZOI plates] Measure the optical density of the overnight bacterial culture at 600nm (OD600). To do this dilute overnight cultures 1:10 in a 1.5 mL cuvette with Mueller Hinton Broth (MHB) ( 720 µL broth + 80 µL bacteria). Dilute the bacterial culture with MHB to give a final OD600 o... |
83,837 | Striatal Cannula Window Implantation | 1 | dx.doi.org/10.17504/protocols.io.dm6gp385jvzp/v1 | https://www.protocols.click/view/striatal-cannula-window-implantation-cv45w8y6 | Shivathmihai Nagappan | TITLE: Striatal Cannula Window Implantation
AUTHORS: Shivathmihai Nagappan
[DESCRIPTION]
This protocol describes how to implant a cannula window over the dorsolateral striatum in mice to enable two-photon imaging of dopamine axons in the dorsal striatum.
[STEPS]
1. Prepare and administer appropriate pre-operative ana... | ["Prepare and administer appropriate pre-operative analgesics.", "Anesthetize the mouse with isoflurane (5% in oxygen for induction and 1-2% in oxygen for maintenance) and secure in stereotaxic frame. Remove fur over the head and clean skin surface with Betadine solution. Then, make an incision over the midline, exposi... |
44,451 | Lab 5 Notebook | 3 | dx.doi.org/10.17504/protocols.io.bpnbmman | https://www.protocols.io/view/lab-5-notebook-bpnbmman | TITLE: Lab 5 Notebook
AUTHORS:
[STEPS] | [] | |
38,553 | FCMPASS - Light scatter calibration | 5 | dx.doi.org/10.17504/protocols.io.bhvzj676 | https://www.protocols.io/view/fcmpass-light-scatter-calibration-bhvzj676 | Joshua Welsh, Jennifer Jones | TITLE: FCMPASS - Light scatter calibration
AUTHORS: Joshua Welsh, Jennifer Jones
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the steps required to input light scatter calibration parameters using the FCMPASS software. This is one of a number of protocols in the pipeline fo... | ["If light scatter calibration is being performed click the '+' button to add a calibration parameter to the table. If light scatter calibration is not required, click 'Next'.", "If you have not yet defined the light scatter bead sets in Catalogue', click 'Catalogue' and complete as outlined in the protocol.", "Double ... |
30,638 | Phonological Short Term Memory tasks for Italian-English comparison | null | dx.doi.org/10.17504/protocols.io.96nh9de | null | Chiara Valeria Marinelli, Pierluigi Zoccolotti, Cristina Romani | TITLE: Phonological Short Term Memory tasks for Italian-English comparison
AUTHORS: Chiara Valeria Marinelli, Pierluigi Zoccolotti, Cristina Romani
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:center"><span style = "font-weight:bold;">Phonological Short ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.dkt4wm | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
Example of two PCR'd gDNA extracts, one from a nucleofected cell and one from an unzapped control, saw heteroduplexing in the edited sample and tried to get rid of it by reconditioning and/or adding more polymerase.<br /><img id="s-mce-img" class="s-mce-img" src="https://s3.amazo... | [] |
63,896 | Scam Alert:- Clinical CBD Gummies "Shark Tank" Full Data | 3 | dx.doi.org/10.17504/protocols.io.bp2l61pjdvqe/v1 | https://www.protocols.io/view/scam-alert-clinical-cbd-gummies-34-shark-tank-34-f-camysc7w | jimmyrobert | TITLE: Scam Alert:- Clinical CBD Gummies "Shark Tank" Full Data
AUTHORS: jimmyrobert
[DESCRIPTION]
At this point you need just to avoid searching and confusing your mind. Just focus using one product, rely on it, and then step into the planet of healing and painless fun. From the comfort of home so you will ... | [] |
26,564 | LAMP in situ complete | null | dx.doi.org/10.17504/protocols.io.57cg9iw | null | Nicholas W. West | TITLE: LAMP in situ complete
AUTHORS: Nicholas W. West
[STEPS]
?. [Tissue Fixiation]
Harvest tissue and submerge in an excess of FAA solution, pull a vacuum for ~2 min and agitate samples gently. Hold under vacuum for 2-3 min before slowly releasing vacuum. Once the vacuum is released the samples should sink, if tiss... | ["[Tissue Fixiation]\nHarvest tissue and submerge in an excess of FAA solution, pull a vacuum for ~2 min and agitate samples gently. Hold under vacuum for 2-3 min before slowly releasing vacuum. Once the vacuum is released the samples should sink, if tissue samples float to the surface, agitate gently and repeat vacuu... |
104,254 | Fiji-based quantification of glial parameters from IHC-stained mouse brain sections | 0 | null | https://www.protocols.io/view/fiji-based-quantification-of-glial-parameters-from-dh2638he | Karim Zahr Eddin | TITLE: Fiji-based quantification of glial parameters from IHC-stained mouse brain sections
AUTHORS: Karim Zahr Eddin
[DESCRIPTION]
This protocol provides step-by-step instructions for the quantification of glia phenotypic parameters from mouse brain sections stained by immunohistochemistry using Fiji (Image J2, versio... | ["[Protocol:] Using the Bio-Formats plugin in Fiji (Image J2, version 2.14.0), choose the file to be quantified and pick the right “Series” to access the scan. The Bio-Formats plugin will load the selected file in an import window with multiple options for viewing, to which “view stack with: Hyperstack” is selected alo... |
81,135 | Methodology for Inputs-Oriented VRS DEA in dairy farms | 1 | dx.doi.org/10.17504/protocols.io.n92ldpddnl5b/v1 | https://www.protocols.click/view/methodology-for-inputs-oriented-vrs-dea-in-dairy-f-ctgpwjvn | C A Zuniga-Gonzalez, José Luis Jaramillo-Villanueva | TITLE: Methodology for Inputs-Oriented VRS DEA in dairy farms
AUTHORS: C A Zuniga-Gonzalez, José Luis Jaramillo-Villanueva
[DESCRIPTION]
The methodology protocol for Inputs-Oriented VRS DEA in dairy farms describes the steps and procedures for data collection with the verbal consent of the producers according to the d... | ["[Protocol for the collection and processing of data with the verbal consent of the producers] The data collection procedure was as follows: a) identification of the regions of the republic with the highest volume of milk production. A questionnaire was designed to collect information from the selected producers. Dur... |
107,565 | LRRK2 PhosphoSens Assay | 0 | dx.doi.org/10.17504/protocols.io.81wgbz8qngpk/v2 | https://www.protocols.io/view/lrrk2-phosphosens-assay-dmam42c6 | Nicolai D. Raig, Stefan Knapp | TITLE: LRRK2 PhosphoSens Assay
AUTHORS: Nicolai D. Raig, Stefan Knapp
[DESCRIPTION]
With this enzymatic activity assay we were able to determine IC50 values of published inhibitors aswell as newly synthesized compounds that inhibit LRRK2. The assay is based on the in vitro phosphorylation reaction between the enzymati... | ["Pipett a dilution series of eleven concentrations between 15µM and 0.4nM (calculated with an assay volume of 10µL) of the compounds into white 384-well plates (Greiner 781207) as duplicates with an ECHO acoustic dispenser (Labcyte). Pipett a equivalent of DMSO in two wells per compound as 0% (without protein and comp... |
38,382 | Enzymatic Assay of Protease Using Azocasein as Substrate | 1 | dx.doi.org/10.17504/protocols.io.bhqnj5ve | https://www.protocols.io/view/enzymatic-assay-of-protease-using-azocasein-as-sub-bhqnj5ve | Neilier Junior | TITLE: Enzymatic Assay of Protease Using Azocasein as Substrate
AUTHORS: Neilier Junior
[STEPS]
?. [Reagent Preparation]
100 mM Tris-HCl buffer, pH 8.0, 20 mM CaCl2, at 37 °C.2.0% (w/v) Azocasein SolutionHeat gently (do not boil) to 50 - 60 °C for 10 min with stirring.Adjust the pH to 8.0 at 37 °C, if necessary, with ... | ["[Reagent Preparation]\n100 mM Tris-HCl buffer, pH 8.0, 20 mM CaCl2, at 37 °C.2.0% (w/v) Azocasein SolutionHeat gently (do not boil) to 50 - 60 °C for 10 min with stirring.Adjust the pH to 8.0 at 37 °C, if necessary, with either 1.0 M NaOH or 1.0 M HCl.110 mM Trichloroacetic Acid Reagent (TCA). Dilute with deionized w... |
60,466 | Dilution-to-Extinction Experiment Protocol_DNA Extraction Pipeline | 4 | dx.doi.org/10.17504/protocols.io.36wgq7d2ovk5/v1 | https://www.protocols.click/view/dilution-to-extinction-experiment-protocol-dna-ext-b7asriee | Shelby J Barnes, Cameron Thrash | TITLE: Dilution-to-Extinction Experiment Protocol_DNA Extraction Pipeline
AUTHORS: Shelby J Barnes, Cameron Thrash
[DESCRIPTION]
Dilution-to-Extinction Experiment Protocol_DNA Extraction Pipeline
[STEPS]
SECTION: Collection and Filtration
2. Culturing Hardware Preparation
SECTION: Inoculum Sample Enumeration
5. Sam... | ["[Collection and Filtration] Culturing Hardware Preparation", "[Inoculum Sample Enumeration] Sample Preparation", "[Medium Inoculation] All steps except incubation are performed inside a biosafety cabinet or laminar flow hood.", "[Collection and Filtration] Collect samples at any source of interest with sterile, acid-... |
57,036 | Inorganic polyphosphate from microalgae: A DAPI-based estimation in microtiter plate | 1 | dx.doi.org/10.17504/protocols.io.b3xkqpkw | https://www.protocols.io/view/inorganic-polyphosphate-from-microalgae-a-dapi-bas-b3xkqpkw | Yingyu Hu, Zoe V Finkel | TITLE: Inorganic polyphosphate from microalgae: A DAPI-based estimation in microtiter plate
AUTHORS: Yingyu Hu, Zoe V Finkel
[DESCRIPTION]
The DAPI-based fluorometric estimation of polyphosphate from microalgae has been widely used in field samples since the method was published by Martin P. et al., where fluoresce... | ["[Sample collection] Filter microalgae in liquid media onto precombusted GFF filters, using gentle vacuum pressure (5 inches Hg).", "[Sample collection] Rinse sample with filtered seawater", "[Sample collection] Place sample filters in cryogenic vials", "[Sample collection] Filter blank media (without cells) through p... |
55,202 | Lemnaceae (Duckweed) culturing protocol | 1 | null | https://www.protocols.io/view/lemnaceae-duckweed-culturing-protocol-bz6ap9ae | o.pogoutse, Jason Laurich, Chris Carlson | TITLE: Lemnaceae (Duckweed) culturing protocol
AUTHORS: o.pogoutse, Jason Laurich, Chris Carlson
[DESCRIPTION]
Protocol for culturing duckweed.
[STEPS]
SECTION: YMA Media Preparation
2. To prepare 500ml of 1x YMA media in the biosafety cabinet pour 100 ml of sterile
5x YMA media into sterile cylinder.
SECTION: Ster... | ["[YMA Media Preparation] To prepare 500ml of 1x YMA media in the biosafety cabinet pour 100 ml of sterile\n5x YMA media into sterile cylinder.", "[Sterilisation and Setup] Spray down inside of biosafety cabinet with ethanol, including materials\n to be used.", "[YMA Media Preparation] Next add sterile H2O till the be... |
46,220 | Tris Buffered Saline (TNT) | 1 | dx.doi.org/10.17504/protocols.io.brdkm24w | https://www.protocols.io/view/tris-buffered-saline-tnt-brdkm24w | Allen Institute for Brain Science | TITLE: Tris Buffered Saline (TNT)
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to prepare Tris Buffered Saline (TNT). 10X TNT is the stock solution used to prepare 1X TNT, which equilibrates tissue and maintains pH in physiological ... | [] |
49,779 | How to make a cup of tea DOI Forked | 1 | null | https://www.protocols.io/view/how-to-make-a-cup-of-tea-doi-forked-buutnwwn | ines.boehm | TITLE: How to make a cup of tea DOI Forked
AUTHORS: ines.boehm
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is part of the </span><a href="https://carpentries-incubator.github.io/fair-bio-practice/06-record-keeping/index.html" style = "text-decoration:underline;color:blue;cur... | ["[Preparation of water and tea]\nFill the kettle with ~250mL of water, or until your min fill line and boil the water.", "[Preparation of water and tea]\nIn the meantime prepare your tea bag, unpack it and place it in the cup/mug so that the tag is positioned outside of the mug.", "[Preparation of water and tea]\nOnce... |
69,866 | RNAseH-based ribodepletion | 4 | dx.doi.org/10.17504/protocols.io.36wgqj9n5vk5/v1 | https://www.protocols.click/view/rnaseh-based-ribodepletion-cggittue | Nicole Schonrock, Helaine Graziele Santos Vieira, Oguzhan Begik, Eva Maria Novoa | TITLE: RNAseH-based ribodepletion
AUTHORS: Nicole Schonrock, Helaine Graziele Santos Vieira, Oguzhan Begik, Eva Maria Novoa
[DESCRIPTION]
Goal: Method to ribodeplete samples from rRNAs using RNAseH nuclease.
Summary: DNA oligos are complementary to human rRNAs. They will anneal to the rRNA molecules. RNAseH will degr... | [] |
31,293 | Vegan Latkes | null | dx.doi.org/10.17504/protocols.io.bas5ieg6 | null | Lenny Teytelman, Hannah Gershik | TITLE: Vegan Latkes
AUTHORS: Lenny Teytelman, Hannah Gershik
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This recipe is a traditional Eastern-European Jewish latkes (potato pancakes). It is finely grated, unlike coarse in American latkes. Also, egg turns out to be completely unnecessary, so thi... | ["Peel and wash 6 Russet potatoes.", "Add 1 teaspoon of salt.", "Add \\frac{1}{4} cup of flour to the potatoes", "Cut up the potatoes and grate in a food processor.", "Cover bottom of a frying pan with oil and heat to medium-high.", "Use a spoon to remove the water; keep doing this as you fry.Put the spoon onto the sur... |
82,789 | Protocol for coarse grained simulation of protein ligand system using GROMACS | 5 | dx.doi.org/10.17504/protocols.io.3byl4jm8rlo5/v1 | https://www.protocols.click/view/protocol-for-coarse-grained-simulation-of-protein-cu4dwys6 | M Purushotham Rao, Akshay Uttarkar, Vidya Niranjan | TITLE: Protocol for coarse grained simulation of protein ligand system using GROMACS
AUTHORS: M Purushotham Rao, Akshay Uttarkar, Vidya Niranjan
[DESCRIPTION]
Coarse-grained (CG) simulations are a powerful tool for studying the behavior of biomolecular systems. They are becoming increasingly important tools for drug d... | ["Preprocessing of protein \nRemoval of Heteroatoms and if required removing other chains \ngrep \"^ATOM\" 1m4i.pdb > 1m4i_clean.pdb | grep \" A \" 1m4i_clean.pdb > 1m4i_singlechain.pdb", "Finding secondary structure of 1m4i (AAC2)\nmkdssp -i 1m4i.pdb -o 1m4i.dssp\npython dssp2ssd.py -i 1m4i.dssp -o 1m4i.ssd\nSecond li... |
null | null | null | dx.doi.org/10.17504/protocols.io.grdbv26 | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
<p>Prepare Edwards buffer</p>
<table style="width: 50px;">
<tbody>
<tr>
<td style="width: 10.0167px;"> </td>
<td style="width: 33.9833px;">
<table style="height: 148px; width: 416px;">
<tbody>
<tr>
<td style="width: 76px;">Reagent</td>
<td style="width: 76px;">Final conc. </td>... | [] |
38,856 | Minipump Subcutaneous Implantation for Rats | 1 | null | https://www.protocols.io/view/minipump-subcutaneous-implantation-for-rats-bh7gj9jw | Lani Tieu, Lauren Smith, Olivier George | TITLE: Minipump Subcutaneous Implantation for Rats
AUTHORS: Lani Tieu, Lauren Smith, Olivier George
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the step-by-step procedure for performing subcutaneous implantation of osmotic minipumps on rats. </div></div>
[STEPS]
?. [Proce... | ["[Procedure]\nAnesthetize rat in induction chamber with isoflurane vaporizer dial on 5.", "[Procedure]\nShave the rat’s back starting from above the hind legs to the shoulders.", "[Procedure]\nWeigh the rat and record weight on the surgery sheet.", "[Procedure]\nPlace the rat on surgery table and put its nose in the n... |
25,468 | Plant Chromatin Immunoprecipitation | null | dx.doi.org/10.17504/protocols.io.444gyyw | null | Laura Poza-Viejo, Ivan del Olmo, Pedro Crevillén | TITLE: Plant Chromatin Immunoprecipitation
AUTHORS: Laura Poza-Viejo, Ivan del Olmo, Pedro Crevillén
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify"><span>Chromatin Immunoprecipitation (ChIP) is a crucial technique to study chromatin regulation, ep... | ["[Harvest and crosslinking]\nHarvest 1-2 g of Arabidopsis or Brassica seedlings/leaf tissue/inflorescence in a 50ml conical centrifuge tube.", "[Harvest and crosslinking]\nAdd Phosphate-buffered saline buffer (PBS) with 1% formaldehyde (FAA)1.To detect histone modifications this is enough, but for protein binding we p... |
87,408 | Protocol Collection: Perfusing, Sectioning, IHC, Mounting and Coverslipping Mouse Brain Specimens | 6 | dx.doi.org/10.17504/protocols.io.kxygx3yxkg8j/v1 | https://www.protocols.io/view/protocol-collection-perfusing-sectioning-ihc-mount-czkqx4vw | Naveen Ouellette, daphne.toglia, Holly Myers | TITLE: Protocol Collection: Perfusing, Sectioning, IHC, Mounting and Coverslipping Mouse Brain Specimens
AUTHORS: Naveen Ouellette, daphne.toglia, Holly Myers
[DESCRIPTION]
This protocol collection details the steps for a whole mouse brain specimen to be perfused, sliced, stained with antibodies, DAPI, or both, and ma... | ["[Sectioning Mouse Brain with Sliding Microtome] Reference the Sectioning Mouse Brain with Sliding Microtome protocol.", "[Immunohistochemistry (IHC) Staining Mouse Brain Sections] If antibody staining or both antibody and DAPI staining is needed, reference the Immunohistochemistry (IHC) Staining Mouse Brain Sections ... |
72,068 | 0.01M Phosphate buffered saline (1L) | 1 | null | https://www.protocols.io/view/0-01m-phosphate-buffered-saline-1l-cimcuc2w | Thomas R Clarke | TITLE: 0.01M Phosphate buffered saline (1L)
AUTHORS: Thomas R Clarke
[DESCRIPTION]
Guide for making 0.01M PBS.
Used as the solution for slicing brains in the vibratome, and for transcardial perfusionsTHIS IS A DRAFT PROTOCOL - PLEASE EXERCISE CAUTION
[STEPS]
1. Measure ~900mL distilled water
2. Add 5 phosphate buffe... | ["Measure ~900mL distilled water", "Add 5 phosphate buffered saline tablets (Sigma) and stir with magnetic flea", "Fill up to 1000ml with distilled water", "Measure pH and adjust to 7.4"] |
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