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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33,088 | Morris USF Lab protocol | null | dx.doi.org/10.17504/protocols.io.bci8iuhw | null | Lauren Segers, Kendall Morris, Donald Bolser | TITLE: Morris USF Lab protocol
AUTHORS: Lauren Segers, Kendall Morris, Donald Bolser
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Surgical Protocol]
Methods were as previously described (Morris et al., 2010; Ott et al., 2012). Data were obtained from 13 decerebrated, paralyzed, and artificially ventila... | ["[Surgical Protocol]\nMethods were as previously described (Morris et al., 2010; Ott et al., 2012). Data were obtained from 13 decerebrated, paralyzed, and artificially ventilated adult cats of either sex. Prior to initiating the surgical protocol, atropine was injected to reduce mucus secretion in the airways. Dexame... |
98,734 | A protocol for tissue clearing and three-dimensional imaging of human sigmoid mucosal biopsies | 0 | null | https://www.protocols.io/view/a-protocol-for-tissue-clearing-and-three-dimension-dcnn2vde | Pu-Qing Yuan, tao li, Yvette Taché | TITLE: A protocol for tissue clearing and three-dimensional imaging of human sigmoid mucosal biopsies
AUTHORS: Pu-Qing Yuan, tao li, Yvette Taché
[DESCRIPTION]
This protocol was developed for tissue clearing and 3D imaging of human sigmoid mucosal biopsies by adapting and modifying the original CLARITY tissue clearin... | [] |
83,652 | Single nuclei isolation from frozen human adipose tissue for 10x Genomics multiome sequencing | 4 | dx.doi.org/10.17504/protocols.io.5jyl8pnj6g2w/v1 | https://www.protocols.io/view/single-nuclei-isolation-from-frozen-human-adipose-cvxcw7iw | Lynn M Geletka, Clarissa Streider-Barboza, Robert W. O"Rourke, Carey Lumeng | TITLE: Single nuclei isolation from frozen human adipose tissue for 10x Genomics multiome sequencing
AUTHORS: Lynn M Geletka, Clarissa Streider-Barboza, Robert W. O"Rourke, Carey Lumeng
[DESCRIPTION]
Here we present a modified version of a 10x Genomics demonstrated protocol that we adapted for the isolation of nuclei ... | ["[Buffer Preparation] Prepare all the buffers listed in the tables below. Any buffers that contain RNase Inhibitor must be prepared the day of the nuclei isolation. Buffers without RNase Inhibitor may be prepared a day ahead.\n\nNP40 Lysis Buffer: (A)\n \n\nDPBS/1% BSA/1U/uL RNase Inhibitor Buffer:\n \n\nLysis Buffe... |
77,988 | Isolation of bacterial DNA with Gentra Puregene kit (modified protocol) | 4 | dx.doi.org/10.17504/protocols.io.5qpvorwo7v4o/v1 | https://www.protocols.io/view/isolation-of-bacterial-dna-with-gentra-puregene-k-cqecvtaw | o.pogoutse, Megan Frederickson | TITLE: Isolation of bacterial DNA with Gentra Puregene kit (modified protocol)
AUTHORS: o.pogoutse, Megan Frederickson
[DESCRIPTION]
The Qiagen protocol for purification of genomic DNA from gram-positive bacterial cultures using Yeast/Bact. Kit ( Gentra Puregene Handbook - QIAGEN) was modified to aid in the isolation... | ["[Cell lysis] transfer culture to 1.5ml microfuge tube", "[Cell lysis] centrifuge for 10min at 12000rpm to pellet cells", "[Cell lysis] decant or aspirate off supernatant", "[Cell lysis] add 1 ml sterile PBS to pellet and vortex briefly to resuspend cells", "[Cell lysis] resuspend pellet in 50ul PBS buffer", "[Cell ly... |
45,494 | Cell-Free Protein Synthesis | 1 | dx.doi.org/10.17504/protocols.io.bqnwmvfe | https://www.protocols.io/view/cell-free-protein-synthesis-bqnwmvfe | Anne Zemella, Theresa Richter, Lena Thoring, Stefan Kubick | TITLE: Cell-Free Protein Synthesis
AUTHORS: Anne Zemella, Theresa Richter, Lena Thoring, Stefan Kubick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">This is part 3.3 of the "A Combined Cell-Free Protein Synthesis and Fluorescence-Based Approach to Investigate GPCR... | ["[3.3 Cell-Free Protein Synthesis]\nThaw all required components for cell-free protein synthesis (see Note 8).\non ice", "[3.3 Cell-Free Protein Synthesis]\nThe cell-free protein synthesis is performed in a coupled mode where transcription and translation reaction take place in one vessel. A standard reaction is comp... |
null | null | null | dx.doi.org/10.17504/protocols.io.eq9bdz6 | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p><strong>Components:<br /></strong><br />10 mM K-MES, pH 6.2, 100 mM KCl, 45 mM MnCl<sub>2</sub><sup>.</sup>4H<sub>2</sub>O, 10 mM CaCl<sub>2</sub><sup>.</sup>2H<sub>2</sub>O, 3 mM HaCoCl<sub>3</sub>. </p>
[STEPS]
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36,371 | Subcellular localisation of newly synthesized viral RNA in coronavirus infection by EM autoradiography | 1 | dx.doi.org/10.17504/protocols.io.bfrtjm6n | https://www.protocols.io/view/subcellular-localisation-of-newly-synthesized-vira-bfrtjm6n | Ronald W.A.L. Limpens, Eric J. Snijder, Abraham J. Koster, Montserrat Bárcena | TITLE: Subcellular localisation of newly synthesized viral RNA in coronavirus infection by EM autoradiography
AUTHORS: Ronald W.A.L. Limpens, Eric J. Snijder, Abraham J. Koster, Montserrat Bárcena
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol allowed the subcellular localisation of... | ["[Metabolic labelling of newly-synthesized viral RNA and EM sample preparation]\nInfect cells with virus, preferably at a high multiplicity of infection (MOI ≥5)Control samples: It is important to include several control samples in the experiment. The first control sample does not receive radioactive label (skip step ... |
53,876 | HMA determination | 4 | dx.doi.org/10.17504/protocols.io.byuupwww | https://www.protocols.io/view/hma-determination-byuupwww | Shuning Guo | TITLE: HMA determination
AUTHORS: Shuning Guo
[DESCRIPTION]
This protocol is used to determine the yield of HMA producted by E. coli by using HPLC.
[BEFORE_START]
Wash the sample bottle with ddH2O for 3 times and absolute ethanol for 1 time by using ultrasonic cleaner.
Prepare 8 mM KH2PO4 (pH 2.4) and filter it ... | ["[Activation of the cells] Inoculate 5 ml of LB medium with 1% volume of E. coli culture and culture at 37℃ for 12h.", "[Induction of protein expression] Prepare ZYM-5052 medium (5ml) by mix ingredients below: (for detailed recipe", "[Induction of protein expression] Inoculate 5 ml of ZYM-5052 medium with 1% volume of... |
103,516 | Pooled, Growth-Based Assays | 0 | dx.doi.org/10.17504/protocols.io.5qpvokq1bl4o/v1 | https://www.protocols.io/view/pooled-growth-based-assays-dhb432qw | David Ross | TITLE: Pooled, Growth-Based Assays
AUTHORS: David Ross
[DESCRIPTION]
This protocol outlines a pooled, growth-based assay for measuring the fitness of a library of variants in E.Coli. This protocol defines paths for either:
only measuring a pool of control variants
or an entire library of variants pooled in addition to... | ["[Culture Preparation & Overnight Growth] Start a culture of the mixed calibration variants in a 15 mL snap-cap culture tube.\nTake a scraping from the glycerol stock of the mixed calibration variants and put it in 5 mL of M9 Media to start culture.", "[Culture Preparation & Overnight Growth] Incubate all cult... |
96,866 | Bone and tooth collagen extraction for stable isotope analysis and radiocarbon dating | 0 | dx.doi.org/10.17504/protocols.io.36wgqnr75gk5/v1 | https://www.protocols.io/view/bone-and-tooth-collagen-extraction-for-stable-isot-daua2ese | Prudence Robert, Mathieu Boudin, Samuel Bodé | TITLE: Bone and tooth collagen extraction for stable isotope analysis and radiocarbon dating
AUTHORS: Prudence Robert, Mathieu Boudin, Samuel Bodé
[DESCRIPTION]
Several collagen extraction protocols are described in the literature, but most lack detailed descriptions of the laboratory manipulations and the specific ma... | ["[Removal of lipids and humic acids] Remove any DI-water from the tubes with the samples. If the sample was frozen, wait for it to thaw and remove the excess of DI-water.", "[Demineralisation] In a fume hood, add approximately 10 mL of the diluted HCl solution to the reaction tube, ensuring the sample is fully submerg... |
87,471 | Gibson Assembly Cloning | 4 | dx.doi.org/10.17504/protocols.io.eq2lyjwyqlx9/v1 | https://www.protocols.io/view/gibson-assembly-cloning-cznpx5dn | Claire Y Chiang, Suzanne R Pfeffer | TITLE: Gibson Assembly Cloning
AUTHORS: Claire Y Chiang, Suzanne R Pfeffer
[DESCRIPTION]
Gibson assembly requires a vector backbone and one or more inserts that have been PCR amplified. The inserts should have 15-20 base pairs of overlap at ligation sites, so primers used to amplify the inserts should contain a tail ... | ["[Prepare Gibson master mix] Make 5 ml of 5x reaction buffer", "[Prepare Gibson master mix] Prepare master mix", "[Prepare Gibson master mix] 25% PEG-8000\t\t 1.25 g\n500 mM Tris-HCl pH 7.5\t2.5 ml\n50 mM MgCl2\t\t 0.25 ml of 1M\n50 mM DTT\t\t 0.25 ml of 1M\n1 mM each dNTPs\t ... |
68,033 | TS Spurrs - cell pellet (TM - 013, sections 5.3 & 6.6) | 4 | dx.doi.org/10.17504/protocols.io.81wgb6jpolpk/v1 | https://www.protocols.io/view/ts-spurrs-cell-pellet-tm-013-sections-5-3-amp-6-6-cen9tdh6 | sandra.crameri | TITLE: TS Spurrs - cell pellet (TM - 013, sections 5.3 & 6.6)
AUTHORS: sandra.crameri
[DESCRIPTION]
This method is used for conventional processing of cell pellets to Spurrs resin.
[GUIDELINES]
All time are minimum times, it is acceptable to go over time specified for any given step. Good place steps to leave ove... | ["[HEADER] SAN:\n\n\nSPEC No:\n\n\nOPERATOR & STEPS:\n\n\nOPERATOR & STEPS:", "[CONVENTIONAL] 2.5 % volume for at least 40 min", "[CONVENTIONAL] Wash 0.1 Molarity (M) Sorenson's Phosphate Buffer pH 07.2 (300mosmol/kg) for 15 min", "[CONVENTIONAL] 1 % volume in buffer for 60 min", "[CONVENTIONAL] 70 % volume for a... |
45,274 | COVID19 RTLAMP Assay_Nov_2020 | 4 | null | https://www.protocols.io/view/covid19-rtlamp-assay-nov-2020-bqf2mtqe | Arun Manoharan Arunprimediscoveriescom, Eugene Joseph | TITLE: COVID19 RTLAMP Assay_Nov_2020
AUTHORS: Arun Manoharan Arunprimediscoveriescom, Eugene Joseph
[STEPS]
?. [Sample Lysis / Inactivation]
Thaw the lysis Buffer on ice 1 to 3 hours before starting the experiment. It is recommended to aliquot the lysis buffer in small volumes and use it as needed to avoid excessive f... | ["[Sample Lysis / Inactivation]\nThaw the lysis Buffer on ice 1 to 3 hours before starting the experiment. It is recommended to aliquot the lysis buffer in small volumes and use it as needed to avoid excessive freeze-thawing cycles. If using the Lysis Bufferthaw the Buffer on ice 1 to 3 hours before starting the exper... |
28,860 | Restoration of euglycemia in the RCS10 mice with Metformin | null | dx.doi.org/10.17504/protocols.io.8e4htgw | null | Ian Simpson | TITLE: Restoration of euglycemia in the RCS10 mice with Metformin
AUTHORS: Ian Simpson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">In this series of studies we wished to determine whether Metformin was able to esta... | ["The Metformin was administered to the mice in their water to which 0.15% saccharin was added to ensure that mice consumed sufficient metformin/water to normalize their blood sugar (0.8-1.3 g/kg/D). The saccharin levels in the water of control mice were diluted to normalize saccharin consumption. Figure 3 describes th... |
42,422 | Working Alone in the Lab--CHEM 584 | 1 | dx.doi.org/10.17504/protocols.io.bmnwk5fe | https://www.protocols.io/view/working-alone-in-the-lab-chem-584-bmnwk5fe | Ken Christensen | TITLE: Working Alone in the Lab--CHEM 584
AUTHORS: Ken Christensen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Working alone in the laboratory should be minimized; however, CHEM 584 students can work alone in the laboratory if they adhere to the following Standard Operating Procedure (SOP).</div... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.hgxb3xn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div>
<div>
<p>This protocol is from 'Flower Ca<sup>2+</sup> channel in CME and ADBE' of Yao CK et al.</p>
<p> </p>
<p>Please see the manuscript for the full method details.</p>
</div>
</div>
[BEFORE_START]
<p>You'll need: </p>
<p> </p>
<p><strong>RIPA buffer: </strong></p>
<ul... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ppjdmkn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a protocol for cell adhesion assays using 293T cells or N-cadherin-deficient 293NC cells (Yamagata et al., 2018). HEK293T(ATCC CRL-3216) cells are easily transfectable with plasmids. The 293NC cells lack N-cadherin (Cadherin-2), but maintain the property of its pare... | [] |
33,382 | Cutting and Drilling Clear Acrylic Sheet | null | dx.doi.org/10.17504/protocols.io.bcueiwte | null | Jakub Nedbal | TITLE: Cutting and Drilling Clear Acrylic Sheet
AUTHORS: Jakub Nedbal
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A clear acrylic sheet is cut to to form a transparent platform, on which the algal cell cultures in flasks are being shaken.</div><div class = "text-block"><span style = "font-weight... | ["Measure the size and positions of mounting holes on your orbital shaker. There is a technical drawing file available for the orbital shaker KJ-201BD used in this project, available in Onshape:Orbital Shaker PlatformA technical drawing of the clear acrylic platform for the KJ-201BD orbital shaker, including the four m... |
38,298 | LucifeRace: A luminescence-based competition assay | 1 | null | https://www.protocols.io/view/luciferace-a-luminescence-based-competition-assay-bhm2j48e | Andrew Giacomelli, Hans R. Widlund, Joseph Rosenbluh, William C. Hahn | TITLE: LucifeRace: A luminescence-based competition assay
AUTHORS: Andrew Giacomelli, Hans R. Widlund, Joseph Rosenbluh, William C. Hahn
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Fluorescence-based cell competition assays have been used effectively to validate genetic dependencies predicted by... | ["[Generate stable cell lines]\nSelect an appropriate cell line using the Cancer Dependency Map portal. This protocol has been optimized for adherent cell lines that are propagated in serum-containing medium and are resilient when treated with trypsin.", "[Generate stable cell lines]\nUsing lentiviral transduction, eng... |
null | null | null | dx.doi.org/10.17504/protocols.io.tcyeixw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Abstract</strong></p>
<p><strong>Background</strong></p>
<p>This paper describes the association between workplace violence and job satisfaction among physicians and nurses in Macau. It further examines the risk factors for intrinsic and extrinsic job satisfaction amo... | [] |
44,878 | Mimulus sp. CTAB Low Salt Nucleic Acid Prep | 4 | dx.doi.org/10.17504/protocols.io.261ge43zyv47/v1 | https://www.protocols.io/view/mimulus-sp-ctab-low-salt-nucleic-acid-prep-bp3nmqme | Dylan Moxley, Mackenzie Urquhart-Cronish, Amy Angert | TITLE: Mimulus sp. CTAB Low Salt Nucleic Acid Prep
AUTHORS: Dylan Moxley, Mackenzie Urquhart-Cronish, Amy Angert
[DESCRIPTION]
This protocol is an adaptation of Xin & Chen (2012) and Arseneau et al. (2017). From the high salt suspension step, users can follow Xin & Chen (2012) protocol to completion for quick clean-u... | ["[Tissue Prep] Flash freeze in liquid nitrogen and load into tube mix mill grind plates chilled to -20 °C", "[Tissue Prep] Grind 45 s 30/sec and gently knock tissue until free in the tube. Check how well the tissue is ground (should still be frozen).", "[Tissue Prep] If needed, flash freeze again and flip the orientat... |
91,671 | Enrichment Analysis: Fundamentals and Visualization of Enrichment Analysis in Genomic Data Interpretation | 5 | dx.doi.org/10.17504/protocols.io.eq2lyjqpqlx9/v1 | https://www.protocols.io/view/enrichment-analysis-fundamentals-and-visualization-c5rxy57n | Hussain Zubair | TITLE: Enrichment Analysis: Fundamentals and Visualization of Enrichment Analysis in Genomic Data Interpretation
AUTHORS: Hussain Zubair
[DESCRIPTION]
This article encapsulates a dialogue on enrichment analysis and its applications in genomics, specifically focusing on the analytical and visualization techniques for i... | ["[Content of this article] This article will exemplify the application of KEGG enrichment analysis to elucidate: \n1) The conceptual framework of enrichment analysis; \n2) The underlying principles governing enrichment analysis; and \n3) The methodologies for visual representation of enrichment analysis findings.", "[... |
null | null | null | dx.doi.org/10.17504/protocols.io.nggdbtw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
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?.
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48,193 | Chimeric Protein-AG and Protein-LAG sandwich ELISA | 1 | dx.doi.org/10.17504/protocols.io.bta9nih6 | https://www.protocols.io/view/chimeric-protein-ag-and-protein-lag-sandwich-elisa-bta9nih6 | Angel Justiz-Vaillant | TITLE: Chimeric Protein-AG and Protein-LAG sandwich ELISA
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This ELISA is used to study the interaction between protein-AG (SpAG) and protein-LAG (PLAG) with different immunoglobulin preparations from mammalian and avian s... | ["This ELISA is used to study the interaction between protein-AG (SpAG) and protein-LAG (PLAG) with different immunoglobulin preparations from mammalian and avian species. The 96 well microtiter plate was coated overnight at 4°C with 2 µg/µl per well of SpAG in carbonate-bicarbonate buffer pH 9.6.", "The plate was then... |
102,496 | PrediKt Study Protocol | 0 | null | https://www.protocols.io/view/predikt-study-protocol-dgb83srw | Calvin Wang | TITLE: PrediKt Study Protocol
AUTHORS: Calvin Wang
[DESCRIPTION]
We strive to build a predictive model to estimate risk of postoperative knee pain in patients undergoing total knee replacement.
[STEPS]
SECTION: PrediKt Study Protocol
1. Select patients from Zuckerberg San Francisco General Hospital and Trauma Center,... | ["[PrediKt Study Protocol] Select patients from Zuckerberg San Francisco General Hospital and Trauma Center, specifically looking for patients who underwent total knee arthroplasty. Use inclusion and exclusion criteria to select the sample size of patients in our retrospective cohort.", "[PrediKt Study Protocol] Extrac... |
63,016 | Chemiluminescence-enhanced ELISA measurements for α-Synuclein fibrils | 4 | dx.doi.org/10.17504/protocols.io.5qpvob8odl4o/v1 | https://www.protocols.io/view/chemiluminescence-enhanced-elisa-measurements-for-b9sgr6bw | Arpine Sokratian | TITLE: Chemiluminescence-enhanced ELISA measurements for α-Synuclein fibrils
AUTHORS: Arpine Sokratian
[DESCRIPTION]
This protocol is optimized The BioLegend LEGEND MAX‱ α-Synuclein Aggregate ELISA Kit in a 96-well strip plate precoated with rat monoclonal anti-α-synuclein aggregate antibody. We use in-house a-syn fib... | ["[Preparation of buffers] Preparation of 1X Reagent Diluent \n\n1. Label an appropriate sized bottle as “1X Reagent Diluent”. \n\n2. Dilute 2X Reagent Diluent to 1X by adding 30mL of 2X Reagent Diluent to 30mL of lab grade water in the bottle labeled “1XReagentDiluent”. \n\n3. Mix well by vortex.", "[Preparation of st... |
30,910 | A simple ATAC-seq protocol for population epigenetics | 1 | dx.doi.org/10.17504/protocols.io.bae6ibhe | https://www.protocols.io/view/a-simple-atac-seq-protocol-for-population-epigenet-bae6ibhe | Ronaldo De Carvalho Augusto, Aki MINODA, Christoph Grunau | TITLE: A simple ATAC-seq protocol for population epigenetics
AUTHORS: Ronaldo De Carvalho Augusto, Aki MINODA, Christoph Grunau
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We describe here a step-by-step protocol for the generation of sequence-ready libraries for the Assay for Transposase Access... | ["Step 1: Daphnia/Schistosoma samplingSet Eppendorf ThermoMixer with agitation to 37°C.1. Cut a 1 mL pipette tip to create larger opening2. Catch a single daphnia with pipette3. Take a microphotograph4. Remove all water by pipetting with 100 μL tip;orPerfuse S.mansoni worms and take single worm as dry as possible with ... |
46,608 | Laser Microdissection (LMD) for Regional Proteomics | 4 | dx.doi.org/10.17504/protocols.io.brrqm55w | https://www.protocols.io/view/laser-microdissection-lmd-for-regional-proteomics-brrqm55w | Samir Parikh, John Shapiro, Brad Rovin | TITLE: Laser Microdissection (LMD) for Regional Proteomics
AUTHORS: Samir Parikh, John Shapiro, Brad Rovin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Recent advances in multi-scale interrogation of human tissue, including advanced imaging techniques and the powerful application of large dataset... | ["[Cryosectioning for Regional Proteomics]\nSections are collected and mounted to LMD slides as specified in the 'Laser microdissection for regional transcriptomics and proteomics' protocol linked below. The LMD slides are then subsequently shipped from IU to OSU for analysis.\n{\"blocks\":[{\"key\":\"bg65u\",\"text\"... |
62,946 | P2 20/05 | 1 | null | https://www.protocols.io/view/p2-20-05-b9qar5se | Maria Gul | TITLE: P2 20/05
AUTHORS: Maria Gul
[DESCRIPTION]
qa
[STEPS]
1. test
Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Nam libero tempore, cum soluta nobis est eligendi optio cumque nihil impedit quo minus id quod maxime placeat facere possimus, omni... | ["test \n\nLorem ipsum dolor sit amet, consectetuer adipiscing elit. Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Nam libero tempore, cum soluta nobis est eligendi optio cumque nihil impedit quo minus id quod maxime placeat facere possimus, omnis voluptas assumenda est, omnis dolor repellendus. Morbi imper... |
94,639 | BCCDC / ARTIC Mpox V2.3.4 2500bp amplicon generation and NGS | 1 | dx.doi.org/10.17504/protocols.io.n2bvj34nnlk5/v1 | https://www.protocols.io/view/bccdc-artic-mpox-v2-3-4-2500bp-amplicon-generation-c8npzvdn | Anthea Lam, Chris Kent, Michael Chan, Alan O'Dwyer, Jorja M Eacrett, Tracy Lee, Frankie Tsang, Tara Newman, Dan Fornika, Natalie Prystajecky, James Zlosnik, Agatha Jassem, Josh Quick, John Tyson | TITLE: BCCDC / ARTIC Mpox V2.3.4 2500bp amplicon generation and NGS
AUTHORS: Anthea Lam, Chris Kent, Michael Chan, Alan O'Dwyer, Jorja M Eacrett, Tracy Lee, Frankie Tsang, Tara Newman, Dan Fornika, Natalie Prystajecky, James Zlosnik, Agatha Jassem, Josh Quick, John Tyson
[DESCRIPTION]
This procedure provides instruc... | ["[Preparation of primer pools from individual primers]", "[Preparation of PCR Reagents] Prepare both PCR Master Mix 1 (MM1 containing Primer Pool 1) and 2 (MM2 containing Primer Pool 2) separately in a PCR Clean Room as follows:\n \nLabel two PCR Plates with the experiment code followed by “PCR Pool 1” or “PCR Pool 2.... |
45,666 | Single cell RNA sequencing library preparation (2-level sci-RNA-seq) | 4 | null | https://www.protocols.io/view/single-cell-rna-sequencing-library-preparation-2-l-bquamwse | Sanjay Srivatsan, Junyue Cao | TITLE: Single cell RNA sequencing library preparation (2-level sci-RNA-seq)
AUTHORS: Sanjay Srivatsan, Junyue Cao
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Sci-RNA-seq is a protocol developed by Junyue Cao in the Shendure Lab at the University of Washington and adapted by others in the Shendur... | ["[Preparation]\nReagents to prepare prior to beginning protocol:1. Prepare 5mL of NSBNSB - Nuclei Buffer + Superase In + BSA-------------------------------10mM Tris/HCl pH 7.410mM NaCl3mM MgCl21% (v./v) Superase-Inhibitor 1% (vol./vol.) BSASolvent: Nuclease Free Water2. Prepare 5mL of NBBNBB - Nuclei Buffer + BSA----... |
92,164 | Association between the overall inflammatory potential of diet during pregnancy and the child’s subsequent risk of type 1 diabetes | 1 | dx.doi.org/10.17504/protocols.io.5qpvo3dxbv4o/v1 | https://www.protocols.io/view/association-between-the-overall-inflammatory-poten-c59cy92w | Rohina Noorzae, anne.ahrendt.bjerregaard, tih, sfo | TITLE: Association between the overall inflammatory potential of diet during pregnancy and the child’s subsequent risk of type 1 diabetes
AUTHORS: Rohina Noorzae, anne.ahrendt.bjerregaard, tih, sfo
[DESCRIPTION]
A growing body of evidence suggests that diet is a modifiable determinant of low-grade systemic inflammatio... | [] |
22,559 | Improving Diagnosis in Cognitive Disorders | null | dx.doi.org/10.17504/protocols.io.z97f99n | null | Laura McWhirter, Craig Ritchie, Alan Carson, Jon Stone | TITLE: Improving Diagnosis in Cognitive Disorders
AUTHORS: Laura McWhirter, Craig Ritchie, Alan Carson, Jon Stone
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Functional cognitive disorders are likely to account for a significant proportion of adults presenting with cognitive (memory and thinking... | [] |
58,082 | Collecting Spleens for genotyping rats | 4 | dx.doi.org/10.17504/protocols.io.6qpvr665ovmk/v1 | https://www.protocols.io/view/collecting-spleens-for-genotyping-rats-b4yaqxse | Gabriel J Barrero, Oksana Polesskaya, Abraham Palmer | TITLE: Collecting Spleens for genotyping rats
AUTHORS: Gabriel J Barrero, Oksana Polesskaya, Abraham Palmer
[DESCRIPTION]
This protocol describes how to dissect and collect soft tissue (spleen) from rats. Collected spleen tissue is intended to be used for DNA extraction and genotyping
[STEPS]
SECTION: Materials
1.... | ["[Materials] Rats are euthanized as per IACUC guidelines\nSpray fur with ethanol. Pick up skin above the sternum, and make a cut through skin and muscle layers.\nDon’t cut the chest cavity (don’t go above the diaphragm).", "[Materials] Cut skin and muscles from the sternum down to the lower belly. Mostly you will see ... |
85,270 | Olfactory mucosa immunostaining | 1 | dx.doi.org/10.17504/protocols.io.x54v9pyeqg3e/v1 | https://www.protocols.click/view/olfactory-mucosa-immunostaining-cxhwxj7e | maria.xylaki | TITLE: Olfactory mucosa immunostaining
AUTHORS: maria.xylaki
[DESCRIPTION]
This protocol describes the immunostaining of olfactory mucosa cells after cocnentrating and depositing a monolayer of the cell suspension onto a slide. For the preparation of the olfactory mucosa suspension refer to protocol "Olfactory mucos... | ["[Preparation of OM suspension] Follow the protocol for olfactory mucosa collection and extraction of the cells from the nasal swab. Centrifuge the cell suspension at 2000 x g for 20 mins at 4 °C and resuspend the cells in 1mL 0.9% NaCl.", "[Preparation of OM suspension] Count the number of cells in the suspension and... |
24,643 | DASH Protocol v2.5 | null | dx.doi.org/10.17504/protocols.io.4bbgsin | null | Amy Lyden, Emily Crawford, Jenai Quan, Saharai Caldera, David Dynerman | TITLE: DASH Protocol v2.5
AUTHORS: Amy Lyden, Emily Crawford, Jenai Quan, Saharai Caldera, David Dynerman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is for performing Depletion of Abundant Sequences by Hybridization (DASH) after preparing sequencing libraries and pooling together.... | ["[Prepare indexed RNA-seq library]\nFollow all steps using NEB Ultra II RNA library preparation kit. Use an input RNA volume of 25ng if available, or less if not available. Perform 12-18 cycles of indexing PCR.", "[Prepare indexed RNA-seq library]\nChoose one option:a. Pooled DASH: If there are multiple samples, you m... |
98,843 | Crystallization of SARS-CoV-2 N Protein | 1 | dx.doi.org/10.17504/protocols.io.4r3l2q4b3l1y/v1 | https://www.protocols.io/view/crystallization-of-sars-cov-2-n-protein-dcr32v8n | Peter Marples, Lizbé Koekemoer, Daren Fearon | TITLE: Crystallization of SARS-CoV-2 N Protein
AUTHORS: Peter Marples, Lizbé Koekemoer, Daren Fearon
[DESCRIPTION]
The crystallization protocol and buffer conditions used to obtain reproducible SARS C0V-2 Nucelocapsid crystals suitable for XChem fragment screening.
[STEPS]
SECTION: Crystallization experiment
3. Prot... | ["[Crystallization experiment] Protein and buffer requirements:\n57.6 µL20 mg/mL \n2.88 mL \n5.76 µL seeds, dilution 1:100", "[Crystallization experiment] Dispense 30 µL into SwissCI 3 lens plate reservoir wells using a 100 µl multi-channel pipette.\nDispense 200 nL20 mg/mL to each lens using the SPT mosquito.\nD... |
21,910 | Multi-Contact 4C (MC-4C): long molecule sequencing of complex proximity ligation products to uncover local cooperative and competitive chromatin topologies | null | dx.doi.org/10.17504/protocols.io.zmwf47e | null | Carlo Vermeulen, Amin Allahyar, Britta A.M. Bouwman, Peter H.L. Krijger, Marjon J.A.M. Verstegen, Geert Geeven, Christian Valdes-Quezada, Ivo Renkens, Roy Straver, Wigard P. Kloosterman, Jeroen de Ridder, Wouter de Laat | TITLE: Multi-Contact 4C (MC-4C): long molecule sequencing of complex proximity ligation products to uncover local cooperative and competitive chromatin topologies
AUTHORS: Carlo Vermeulen, Amin Allahyar, Britta A.M. Bouwman, Peter H.L. Krijger, Marjon J.A.M. Verstegen, Geert Geeven, Christian Valdes-Quezada, Ivo Renken... | [] |
67,429 | InstaHard: Does InstaHard Reviews Work? | 3 | dx.doi.org/10.17504/protocols.io.8epv5946dg1b/v1 | https://www.protocols.io/view/instahard-does-instahard-reviews-work-cd4ds8s6 | InstaHard Reviews | TITLE: InstaHard: Does InstaHard Reviews Work?
AUTHORS: InstaHard Reviews
[DESCRIPTION]
InstaHard
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.g5zby76 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
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?. | [] |
97,070 | HuBMAP | GE HealthCare/UPitt Cell DIVE™ and scRNA Modality Overview | 1 | dx.doi.org/10.17504/protocols.io.x54v92ekzl3e/v1 | https://www.protocols.io/view/hubmap-ge-healthcare-upitt-cell-dive-and-scrna-mod-da2n2gde | Liz McDonough | TITLE: HuBMAP | GE HealthCare/UPitt Cell DIVE™ and scRNA Modality Overview
AUTHORS: Liz McDonough
[DESCRIPTION]
This is an overview of all protocols currently in use for the 2024 GE HealthCare/UPitt collaboration for the Human BioMolecular Atlas Program (HuBMAP). It includes links to each of the individual protocols t... | ["[Obtaining Donors and Tissue Blocks] Confirm donor acceptance criteria for inclusion.\n\nDonor Acceptance Criteria for GE/UPitt HuBMAP Inclusion", "[Obtaining Donors and Tissue Blocks] 5 mm skin biopsies obtained from donor subjects are divided into two parts, with one half for formalin fixed and paraffin embedded (F... |
89,557 | Blood pressure | 1 | dx.doi.org/10.17504/protocols.io.81wgbx55qlpk/v1 | https://www.protocols.io/view/blood-pressure-c3pvymn6 | Núria Peñuelas | TITLE: Blood pressure
AUTHORS: Núria Peñuelas
[DESCRIPTION]
Blood pressure measurement in mice
[STEPS]
1. Measure blood pressure using the tail-cuff method (LE-5002 Non-Invasive Blood Pressure Meter, Panlab).
2. Assess the systolic and diastolic blood pressure (in mmHg) in two independent sessions for each mouse.
3. ... | ["Measure blood pressure using the tail-cuff method (LE-5002 Non-Invasive Blood Pressure Meter, Panlab).", "Assess the systolic and diastolic blood pressure (in mmHg) in two independent sessions for each mouse.", "Calculate the mean from the valid values of 10 measurements in each session."] |
20,014 | U Mass - Body composition (organs) | null | dx.doi.org/10.17504/protocols.io.xsnfnde | null | Jason Kim | TITLE: U Mass - Body composition (organs)
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span><span style = "font-weight:bold;"> </span></div><div class = "text-block">
The EchoMRI 3-in-1 uses ¹H- magnetic resonance spectroscopy to noni... | ["Euthanize mice using intraperitoneal injection of pentobarbital.", "Quickly dissect and extract specific organs to measure their composition.", "Place specific organ into an instrument column.", "Measure composition of organ using instrument standard operating procedure."] |
29,803 | ONT DirectRNA Library preparation for poly(A) estimation | null | dx.doi.org/10.17504/protocols.io.9cjh2un | null | Maximilian Krause, Adnan M Niazi | TITLE: ONT DirectRNA Library preparation for poly(A) estimation
AUTHORS: Maximilian Krause, Adnan M Niazi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol provides a detailed explanation of of the steps necessary for successful Direct RNA Library preparation for Oxford Nanopore Sequenci... | ["[RNA extraction and quality control]\nResuspend and homogenize necessary amount of fresh sample in TRIZol reagent (1ml of TRIZol per 50mg tissue or 3x10^7 cells) in an Eppendorf Safe-Lock 1.5ml tube\nHomogenization should be kept as gentle as possible to avoid RNA molecule degradation. Reduce number of pestle strokes... |
94,701 | Quantification of glutamate released from human induced pluripotent stem cells (iPSC) derived cortical neurons (CNs) | 1 | dx.doi.org/10.17504/protocols.io.j8nlkoqdxv5r/v1 | https://www.protocols.io/view/quantification-of-glutamate-released-from-human-in-c8qmzvu6 | Humaira Noor, Richard Wade-Martins | TITLE: Quantification of glutamate released from human induced pluripotent stem cells (iPSC) derived cortical neurons (CNs)
AUTHORS: Humaira Noor, Richard Wade-Martins
[DESCRIPTION]
This protocol describes the procedure to quantify glutamate released from induced pluripotent stem cells derived cortical neurons (iPSC-C... | ["[Collection of Condition Media] Collection of conditioned media for tonic release:", "[Collection of Condition Media] Remove the cell culture media and add 60 µl of pre-warmed HBSS++ (2.4 mM KCl) media to the cells.", "[Collection of Condition Media] Collection of conditioned media for evoked release:", "[Collection ... |
27,088 | Immunofluorescence staining of paraffin embedded cell block sections | null | dx.doi.org/10.17504/protocols.io.6pqhdmw | https://www.protocols.io/view/immunofluorescence-staining-of-paraffin-embedded-c-6pqhdmw | Erez Nissim Baruch, Rona Ortenberg | TITLE: Immunofluorescence staining of paraffin embedded cell block sections
AUTHORS: Erez Nissim Baruch, Rona Ortenberg
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is designated for Immunofluorescence staining of paraffin embedded cell block sections. </div></div>
[STEPS]
?. A... | ["After the slides were cut, let them dry in room temprature over-night, or 2-3 hours on a heating plate at 37°C.Before stainig incubate the slides in oven at 55°C for 1 - 2 hours", "In a chemical hood:Wash in Xylene for 10 minutesWash in new Xylene for another 10 minutesWash in Ethanol 100% for 3 minutes", "On the ben... |
65,271 | De Novo Assembly of Sequences from Eurofins with Geneious | 1 | dx.doi.org/10.17504/protocols.io.eq2lyn5wqvx9/v1 | https://www.protocols.io/view/de-novo-assembly-of-sequences-from-eurofins-with-g-cbyxspxn | Dakota Betz | TITLE: De Novo Assembly of Sequences from Eurofins with Geneious
AUTHORS: Dakota Betz
[DESCRIPTION]
Our protocols are constantly evolving and old versions will be deleted.
The documents here are not intended to be cited in publications
[STEPS]
1. Download the results from Eurofins. You should get an email like this:
... | ["Download the results from Eurofins. You should get an email like this:\n\n \n\nClick on the underlined and blue highlighted \"Download Results\" in the second line of the email content. This will download a .zip file of the sequencing results.\n\nThen, to keep your computer organized, move that file from your downloa... |
40,343 | Protocol of preparation of horseradish peroxidase (HRP) conjugated to anti-human IgG to be used as secondary antibody in immunoassays. | 6 | dx.doi.org/10.17504/protocols.io.bjmxkk7n | https://www.protocols.io/view/protocol-of-preparation-of-horseradish-peroxidase-bjmxkk7n | Angel Justiz-Vaillant | TITLE: Protocol of preparation of horseradish peroxidase (HRP) conjugated to anti-human IgG to be used as secondary antibody in immunoassays.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Peroxidase labeled anti-human IgG is a conjugated secondary antibody that can... | ["Human IgG can be isolated from human serum or plasma by Protein-A agarose affinity chromatography. To develop the anti-human IgG a laboratory or farm animal is usually immunized and then, the anti-IgG is isolated. The Mancini test can estimate the anti-human IgG concentration.", "Horseradish peroxidase (500 µg in 50 ... |
6,367 | General proteomics FASP (Filter-Aided Sample Preparation) | 1 | dx.doi.org/10.17504/protocols.io.if7cbrn | https://www.protocols.io/view/general-proteomics-fasp-filter-aided-sample-prepar-if7cbrn | Jacob Waldbauer, Lichun Zhang | TITLE: General proteomics FASP (Filter-Aided Sample Preparation)
AUTHORS: Jacob Waldbauer, Lichun Zhang
[DESCRIPTION]
Spin-filter based protein digestion and purification for bottom-up proteomics
[BEFORE_START]
Passivate Vivacon filter unit (Satorius Vivicon 500, 30,000 MWCO) and collection tube overnight in 5% (v/... | ["[Day 1] Prepare fresh buffers in LC-MS water: \nExchange buffer: 8M urea, 0.2% (w/v) deoxycholate, 1M ammonium bicarbonate (pH 8)\nDigestion buffer: 0.2% (w/v) deoxycholate, 50 mM ammonium bicarbonate (pH 8)\nTrypsin dissolution/peptide recovery buffer: 50 mM ammonium bicarbonate (pH 8)", "[Day 1] Dispense 25-50μL (d... |
27,598 | Automated, Rapid Preparation of Tissue Sections for Proteomic Analysis | null | dx.doi.org/10.17504/protocols.io.67nhhme | null | Jamie Allen, Jeff Spraggins, Danielle Gutierrez | TITLE: Automated, Rapid Preparation of Tissue Sections for Proteomic Analysis
AUTHORS: Jamie Allen, Jeff Spraggins, Danielle Gutierrez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Scope:</div><div class = "text-block">To describe the procedure for the lysis, reduction/alkylation, trypsin digestio... | ["[Lysis/Concentration Assay]\nPlace 5-10 sections of tissue in an Eppendorf tube and keep on ice.", "Add lysis buffer to tubes and vortex for 30-60 seconds.\n200 µl", "Place tubes in dry ice for", "Defrost tubes on wet ice for and then vortex briefly.", "Add ice to water in the sonicator to make an icy slurry.", "Son... |
null | null | null | dx.doi.org/10.17504/protocols.io.e3wbgpe | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?. | [] |
48,527 | Oxycodone IV Self-Administration | 1 | null | https://www.protocols.io/view/oxycodone-iv-self-administration-btmpnk5n | Lani Tieu, McKenzie Pavlich, Brent Boomhower, Molly Brennan, Giordano De Guglielmo, Marsida Kallupi, Olivier George | TITLE: Oxycodone IV Self-Administration
AUTHORS: Lani Tieu, McKenzie Pavlich, Brent Boomhower, Molly Brennan, Giordano De Guglielmo, Marsida Kallupi, Olivier George
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the procedure of conducting intravenous oxycodone self-admini... | ["[Session Setup]\nBring animals to the experimentation room where you will run self-administration.", "[Session Setup]\nPick up the animal from its cage and place it in operant chamber.", "[Session Setup]\nWith a microchip reader, scan RFID on the chamber door then scan the rat. Animals must be scanned each test day t... |
29,359 | Planetary Dominos - How microbes drive biogeochemical cycles | null | dx.doi.org/10.17504/protocols.io.8wphxdn | null | Nadia Szeinbaum, Abbigail Johnson, Thomas Swofford | TITLE: Planetary Dominos - How microbes drive biogeochemical cycles
AUTHORS: Nadia Szeinbaum, Abbigail Johnson, Thomas Swofford
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the step to assemble your own Planetary Domino. </div><div class = "text-block"><span>We designed th... | ["Print this file into a poster, cut each piece and add an adhesive magnet. These will be the domino pieces, and they are now able to stick to any magnetic surface. The pieces here are enough for at least three different sets, as they repeat. The design was created by Image Alleviation, in collaboration with us, specif... |
39,242 | Duke - Isolation, Culture, and Maintenance of Patient-Derived Tumor Biopsy | 4 | dx.doi.org/10.17504/protocols.io.bijikcke | https://www.protocols.io/view/duke-isolation-culture-and-maintenance-of-patient-bijikcke | Xiling Shen, Marcos Negrete, Kun Xiang | TITLE: Duke - Isolation, Culture, and Maintenance of Patient-Derived Tumor Biopsy
AUTHORS: Xiling Shen, Marcos Negrete, Kun Xiang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is split into 3 sections: collecting tumor cells, passaging, and cryopreserving organoids. </div><div class ... | ["[Disassociation of Tumor Cells]\nStore tissue samples in cold transport media (). Keep samples on ice at all time and process within\n10 mL", "[Disassociation of Tumor Cells]\nTransfer the tumor biopsy sample (1-2 cm3) and transport media into a petri dish and remove remnant non-tumor tissue with sterile tweezers.\nT... |
104,136 | Detection of central and obstructive sleep apneas in mice: a new surgical and recording protocol | 0 | null | https://www.protocols.io/view/detection-of-central-and-obstructive-sleep-apneas-dhxg37jw | Gabriele Matteoli, Sara Alvente, Chiara Berteotti, Dario Coraci, Viviana Lo Martire, Martina Lops, Elena Miglioranza, Alessandro Silvani, Emilia Volino, Giovanna Zoccoli, Stefano Bastianini* | TITLE: Detection of central and obstructive sleep apneas in mice: a new surgical and recording protocol
AUTHORS: Gabriele Matteoli, Sara Alvente, Chiara Berteotti, Dario Coraci, Viviana Lo Martire, Martina Lops, Elena Miglioranza, Alessandro Silvani, Emilia Volino, Giovanna Zoccoli, Stefano Bastianini*
[DESCRIPTION]
S... | ["[Overview] Figure 1 summarizes the chronological steps of the protocol.\n\nFigure 1. Overview of the protocol\n\nThe experimental protocol involves the crafting (Day -1) and the surgical implantation (Day 0) of the electrodes for the recording of electroencephalogram (EEG), nuchal muscle electromyogram (nEMG), and di... |
85,201 | Supplementary materials for: Lower hemoglobin levels associate with higher baroreflex sensitivity and heart rate variability | 1 | dx.doi.org/10.17504/protocols.io.j8nlko4z5v5r/v1 | https://www.protocols.io/view/supplementary-materials-for-lower-hemoglobin-level-cxfrxjm6 | joona.tapio | TITLE: Supplementary materials for: Lower hemoglobin levels associate with higher baroreflex sensitivity and heart rate variability
AUTHORS: joona.tapio
[DESCRIPTION]
Supplementary materials for: Lower hemoglobin levels associate with higher baroreflex sensitivity and heart rate variability
[STEPS] | [] |
11,838 | Cell lysis and extraction of total protein from Synechocystis sp. PCC 6803 | null | dx.doi.org/10.17504/protocols.io.ps6dnhe | null | Anna Behle | TITLE: Cell lysis and extraction of total protein from Synechocystis sp. PCC 6803
AUTHORS: Anna Behle
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Cell lysis and extraction of total protein. Soluble and insoluble fractions can be further separated. Total protein can be then used for quantificatio... | ["[Before starting]\nPrepare 1x TB (thylakoid-buffer). ABC1ComponentMolecular weight (g/mol)Concentration2HEPES / NaOH, pH = 7238,350 mM3MgCl25 mM4CaCl225 mM5(optional: glycerol)10 % (v/v)To 10 mL 1x TB: Add 1 tablet protease-inhibitor (complete ULTRA Tablets, Mini, EDTA-free, EASYpack by Roche)\nABC1ComponentMolecula... |
11,347 | Home-made TOP10 competent heat-shock cells | null | dx.doi.org/10.17504/protocols.io.pbtdinn | null | Magdalena Julkowska | TITLE: Home-made TOP10 competent heat-shock cells
AUTHORS: Magdalena Julkowska
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The standard protocol to propagate TOP10 Competent cells for Heatshock transformation method</div></div>
[STEPS]
?. Grow a 5ml overnight culture of cells in LB media. In th... | ["Grow a 5ml overnight culture of cells in LB media. In the morning, dilute this culture back into 25-50ml of fresh LB media in a 200ml conical flask. You should aim to dilute the overnight culture by at least 1/100..\tGrow the diluted culture to an OD600 of 0.2 - 0.5. (You will get a very small pellet if you grow 25ml... |
22,271 | NGM Agar | 1 | dx.doi.org/10.17504/protocols.io.zy7f7zn | https://www.protocols.io/view/ngm-agar-zy7f7zn | Adrien Assie, Buck Samuel | TITLE: NGM Agar
AUTHORS: Adrien Assie, Buck Samuel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">NGM agar recipe from wormbook</div></div>
[STEPS]
?. Start with
[water]
?. NaCl
3 g
?. Peptone
2.5 g
?. Agar
17 g
?. Autoclave with stir bar
?. Cool to (faster in water bath)
55 °C
?. Then add the fo... | ["Start with\n[water]", "NaCl\n3 g", "Peptone\n2.5 g", "Agar\n17 g", "Autoclave with stir bar", "Cool to (faster in water bath)\n55 °C", "Then add the following while stirring on heat plate (DO NOT OVERHEAT)", "of CaCl2 (sterile)\n0.5 mL", "of 5 mg/mL Cholesterol (dissolved in ethanol)\n1 mL", "of MgSO4 (sterile)\n1... |
20,398 | Scholarly Certainty Survey and Analysis | null | dx.doi.org/10.17504/protocols.io.x6nfrde | null | Mark Wilkinson, Mario Prieto Godoy | TITLE: Scholarly Certainty Survey and Analysis
AUTHORS: Mark Wilkinson, Mario Prieto Godoy
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Using the TAC Biomedical Summarization Corpus </span><a style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">(Min-Yen)</span><... | ["[Survey Design]\nWe designed three surveys - S1, S2 and S3 - where respondents were asked to assign certainty based on a number of certainty categories - 4, 2, and 3 respectively for surveys S1, S2, and S3. The surveys used identical corpori of biomedically-oriented scholarly statements. To minimize the bias of pri... |
50,660 | EMb encystment medium preparation (500 mL) | 1 | dx.doi.org/10.17504/protocols.io.bvqcn5sw | https://www.protocols.io/view/emb-encystment-medium-preparation-500-ml-bvqcn5sw | Carrie A Flynn, Barbara Kazmierczak | TITLE: EMb encystment medium preparation (500 mL)
AUTHORS: Carrie A Flynn, Barbara Kazmierczak
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Recipe for EMb encystment medium, which is used to induce synchronous encystment of </span><span style = "font-style:italic;">Acanthamoeba castellanii<... | ["[Dry ingredients]\nTo 500 mL bottle, add: KCl (0.1 M) NaHCO3 (0.04 M) MgSO4 x 7H2O (8 mM) CaCl2 x 2H2O (0.4 mM) 2-Amino-2-methyl-1,3-propanediol (AMPD, 0.32 mM)-stir bar\n3.728 g\n1.68 g\n0.986 g\n0.03 g\n0.017 g\nWe have found that AMPD is a superior amine buffer to Tris for this medium and maintains a constant pH o... |
98,541 | The effect of cooking practices on charred seeds fragmentation | 0 | dx.doi.org/10.17504/protocols.io.3byl49k2ogo5/v1 | https://www.protocols.io/view/the-effect-of-cooking-practices-on-charred-seeds-f-dcgm2tu6 | Juliette Élie, Léonard Botton, Sirikanya Chantasri | TITLE: The effect of cooking practices on charred seeds fragmentation
AUTHORS: Juliette Élie, Léonard Botton, Sirikanya Chantasri
[DESCRIPTION]
Since the dawn of mankind, human beings have used a variety of plant-based economies, including culinary practices. Very often found charred in archaeological contexts, the ai... | ["[Measurement and documentation of the material before the experiment] Measurement of biometric data:\nFor each taxa, choose randomly 20 whole seeds, and for each seed, measure the width, length and thickness (mm) with a numeric microscope.\n\n\n \n\n\nYou can complete the following table with the biometric data colle... |
null | null | null | dx.doi.org/10.17504/protocols.io.c9nz5d | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Protocol for labeling bacteria with N15. The bacterial DNA was made “heavy” so that community viral and host bacterial DNA could be distinguished from each other after sorting by using density gradient centrifugation.
[STEPS]
?.
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70,945 | Transformation of Neurospora crassa conidia by electroporation | 3 | dx.doi.org/10.17504/protocols.io.ewov1o4nylr2/v1 | https://www.protocols.io/view/transformation-of-neurospora-crassa-conidia-by-ele-chh9t396 | kdcastillo | TITLE: Transformation of Neurospora crassa conidia by electroporation
AUTHORS: kdcastillo
[DESCRIPTION]
Here, we describe the transformation of Neurospora crassa conidia by electroporation. This process introduces DNA constructs such as reporter tags or genes conferring resistance to antibiotics for selection.
[STEPS... | [] |
44,839 | Gravlax | 1 | null | https://www.protocols.io/view/gravlax-bp2fmqbn | Monica Hassan | TITLE: Gravlax
AUTHORS: Monica Hassan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Gravlax is fresh salmon that’s been cured with a combination of salt, sugar, herbs and grated beetroot. </div></div>
[STEPS]
?. Peel and grate it
[beetroots]
?. Chop
[dill]
?. Put in a plastic food container and... | ["Peel and grate it\n[beetroots]", "Chop\n[dill]", "Put in a plastic food container and fully cover it with the mix from Step 5\n[fresh salmon]\nSalmon skin side should be down", "Mix with and all ingredients you've prepared above in a bowl\n[sea salt]\n[sugar]", "Ground\n[black pepper]", "Grate\n[lemon zest]", "... |
38,551 | FCMPASS - Importing fcs files | 5 | dx.doi.org/10.17504/protocols.io.bhvxj67n | https://www.protocols.io/view/fcmpass-importing-fcs-files-bhvxj67n | Joshua Welsh, Jennifer Jones | TITLE: FCMPASS - Importing fcs files
AUTHORS: Joshua Welsh, Jennifer Jones
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the steps required to import fcs files for calibration using the FCMPASS software. This is one of a number of protocols in the pipeline for performing sm... | ["Once a dataset has been created click the ‘Begin Calibration’ button.", "Import fcs files by selecting the ‘+’ icon next to the ‘Files to calibrate’ table.", "In the new window navigate to the folder containing the fcs files you wish to calibrate and select ‘OK’.", "The fcs files and related metadata will now be impo... |
null | null | null | dx.doi.org/10.17504/protocols.io.d9k94v | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Purification of viruses via CsCl gradient and ultracentrifugation</strong></p>
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.grkbv4w | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
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39,708 | Cassiopea In Situ Hybridization | 3 | dx.doi.org/10.17504/protocols.io.biz4kf8w | https://www.protocols.io/view/cassiopea-in-situ-hybridization-biz4kf8w | Bailey Steinworth | TITLE: Cassiopea In Situ Hybridization
AUTHORS: Bailey Steinworth
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is a protocol for </span><span style = "font-style:italic;">in situ </span><span>hybridization using Digoxigenin-labeled RNA probes to genes of interest. A separate protocol d... | [] |
27,784 | Genomic DNA extraction from diatom P. multistriata | null | dx.doi.org/10.17504/protocols.io.7dghi3w | null | FRANCESCO MANFELLOTTO, monia teresa russo, Rossella Annunziata, Mariella Ferrante | TITLE: Genomic DNA extraction from diatom P. multistriata
AUTHORS: FRANCESCO MANFELLOTTO, monia teresa russo, Rossella Annunziata, Mariella Ferrante
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Genomic DNA extraction from diatom P. multistriata </div></div>
[STEPS]
?. Grow cells in 250 ml
?. fil... | ["Grow cells in 250 ml", "filter coltures with 1.2 μm nitrocellulose membranes", "rinse filter with 1 ml f/2 medium in a falcon and then move cells to a 2 ml eppendorf", "Centrifuge at 6000 rpm for 5 minutes at 4 °C and remove medium", "Add: 400 mg of 0.2-0.3 mm zirconia/silica diameter beads, 500 μl phenol.", "Mix wit... |
102,632 | Immunoprecipitation | 0 | dx.doi.org/10.17504/protocols.io.kxygxynzwl8j/v1 | https://www.protocols.io/view/immunoprecipitation-dggg3ttw | Elias Adriaenssens | TITLE: Immunoprecipitation
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol details the process of immunoprecipitation.
[STEPS]
SECTION: Steps
1. Collect the HeLa cells by trypsinization and wash the cell pellet with PBS once before cells are lysed in lysis buffer (100 mM KCl, 2.5 mM MgCl2, 20 mM Tris-HCl pH 7... | ["[Steps] Collect the HeLa cells by trypsinization and wash the cell pellet with PBS once before cells are lysed in lysis buffer (100 mM KCl, 2.5 mM MgCl2, 20 mM Tris-HCl pH 7.4, 0.5% NP-40).", "[Steps] Lyse the samples for 20 min on ice before cell lysates are cleared by centrifugation at 20000 x g, 10 min, 4 °C.", "[... |
null | null | null | dx.doi.org/10.17504/protocols.io.esybefw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in <a href="https://www.protocols.io/view/CviRI-Purification-From-XZ-6E-Virus-Infected-NC64A-er4bd8w" target="_blank">CviRI Purification From XZ-6E Virus Infected NC64A Chlorella</a>.
[STEPS]
?.
?.
?. | [] |
92,398 | hsqc-tocsy_metab.nan | 5 | dx.doi.org/10.17504/protocols.io.8epv5x2rng1b/v3 | https://www.protocols.io/view/hsqc-tocsy-metab-nan-c6gnzbve | NAN KB, John Glushka, Mario Uchimiya, Saraa Al Jawad, Christopher Esselman, Leandro I Ponce, Laura Morris, Arthur Edison | TITLE: hsqc-tocsy_metab.nan
AUTHORS: NAN KB, John Glushka, Mario Uchimiya, Saraa Al Jawad, Christopher Esselman, Leandro I Ponce, Laura Morris, Arthur Edison
[DESCRIPTION]
This is a protocol for running the Bruker pulse program "hsqcdietgpsisp.2".
[BEFORE_START]
This protocol assumes:
Your sample is loaded, locked, t... | ["[Create a new dataset]", "[Create a new dataset] On the menu bar on TopSpin, click on\nStart → Create Dataset", "[Create noesypr1d experiment file] When Lock, Tune, Shim are complete proceed to the specific protocol for your desired pulseprogram(s).", "[Acquire a spectrum]", "[Acquire a spectrum] Click on\nAcquire → ... |
75,550 | Single-molecule Immunofluorescence Tissue Staining Protocol for Oligomer Imaging | 4 | dx.doi.org/10.17504/protocols.io.5qpvorp6bv4o/v2 | https://www.protocols.io/view/single-molecule-immunofluorescence-tissue-staining-cmz6u79e | Rebecca Andrews, Joanne Lachica, Steven F. Lee, Sonia Ghandi | TITLE: Single-molecule Immunofluorescence Tissue Staining Protocol for Oligomer Imaging
AUTHORS: Rebecca Andrews, Joanne Lachica, Steven F. Lee, Sonia Ghandi
[DESCRIPTION]
This protocol details background fluorescence quenching and immunofluorescence staining of human brain tissue for oligomer imaging.
[GUIDELINES]
U... | ["[Immunofluorescences staining protocol for oligomer imaging] Cut tissue sections on a microtome and load onto glass slides.", "[Immunofluorescences staining protocol for oligomer imaging] Dry slides 10 min at 37 °C – cover over the top.", "[Immunofluorescences staining protocol for oligomer imaging] Before staining... |
37,897 | UT Southwestern - Human Melanoma Metastatic Potential in Mice | 4 | null | https://www.protocols.io/view/ut-southwestern-human-melanoma-metastatic-potentia-bg9hjz36 | Arin Aurora, Sean Morrison | TITLE: UT Southwestern - Human Melanoma Metastatic Potential in Mice
AUTHORS: Arin Aurora, Sean Morrison
[STEPS]
?. [DISSOCIATION PREPARATION]
Materials: Surgical dissection toolsIce1x HBSS (w/o Ca++ or Mg++) [Gibco #14175]50 mL Falcon tubesDisposable pipettes40 μm cell strainers for Falcon tubes [Fisher #22363547] Ce... | ["[DISSOCIATION PREPARATION]\nMaterials: Surgical dissection toolsIce1x HBSS (w/o Ca++ or Mg++) [Gibco #14175]50 mL Falcon tubesDisposable pipettes40 μm cell strainers for Falcon tubes [Fisher #22363547] Cell counter Make Stock SolutionsCollagenase Type IV: 2,000 u/mL make up in HBSS, Collagenase IV powder stock (Worth... |
42,093 | Protocols for Materials | 2 | null | https://www.protocols.io/view/protocols-for-materials-bmcmk2u6 | TITLE: Protocols for Materials
AUTHORS:
[STEPS] | [] | |
102,538 | Protocol for Nuclei/ Cell Isolation and 10X Genomics Fixed RNA profiling for Human Ovary | 0 | dx.doi.org/10.17504/protocols.io.n92ld8rwxv5b/v3 | https://www.protocols.io/view/protocol-for-nuclei-cell-isolation-and-10x-genomic-dgdi3s4e | Nicolas Martin | TITLE: Protocol for Nuclei/ Cell Isolation and 10X Genomics Fixed RNA profiling for Human Ovary
AUTHORS: Nicolas Martin
[DESCRIPTION]
This is the 10X Genomics protocol to fix, dissociate, and profile RNA from human ovary tissue.
[GUIDELINES]
This protocol needs prior approval by the users' institutional review board... | ["[Cell/Nuclei Isolation Protocol for Human Ovary] The protocol CG000553 REV B was used to fix, dissociate, and isolate cells/nuclei from frozen human ovaries with the following modifications: \n\n1) 0.2 mg / mL of Liberase TH was used for dissociation at Step 2b, Page 6.\n2) Two extra \"spin only\" (i.e., steps 3 and ... |
71,072 | MIBI: MIBI staining of fresh-frozen/OCT-embedded samples | 1 | dx.doi.org/10.17504/protocols.io.bp2l69b8dlqe/v1 | https://www.protocols.io/view/mibi-mibi-staining-of-fresh-frozen-oct-embedded-sa-chm8t49w | Sven Truxa, Felix J Hartmann | TITLE: MIBI: MIBI staining of fresh-frozen/OCT-embedded samples
AUTHORS: Sven Truxa, Felix J Hartmann
[DESCRIPTION]
This protocol entails the recommended staining procedure for Multiplex Ion Beam Imaging Time of Flight instrument (MIBI_TOF) as developed in the Sean C. Bendall and Michael R. Angelo labs, and has been a... | ["[Buffer preparation] Verify stock of 1x PBS wash buffer and prepare accordingly if running low\nThis buffer does NOT contain Tween!", "[Thaw and fix, wash] Transfer the slides in the first MIBI 1x PBS wash buffer and dip shortly to remove PFA", "[Thaw and fix, wash] Transfer the slides to the second 1x PBS wash buffe... |
null | null | null | dx.doi.org/10.17504/protocols.io.se4ebgw | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
<p>Resuspend the lyophilized QIAGEN Protease in 1.4 ml of Buffer FG3 (hydration buffer) and store at 2–8°C or in aliquots at –20°C</p>
<p> </p>
<p>Frozen blood should be thawed in a 37°C water bath</p>
<p> </p>
<p>For every 1 ml of blood, mix together 500 μl Buffer FG2 (denatur... | [] |
94,576 | Sample preparation and data collection for Serial Block Face Scanning Electron Microscopy of Mammalian Cell Monolayers | 4 | dx.doi.org/10.17504/protocols.io.e6nvwdz5zlmk/v2 | https://www.protocols.io/view/sample-preparation-and-data-collection-for-serial-c8kqzuvw | Noelle Antao, Joseph Sall, Christopher Petzold, Damian C. Ekiert, Gira Bhabha, Feng-Xia Liang | TITLE: Sample preparation and data collection for Serial Block Face Scanning Electron Microscopy of Mammalian Cell Monolayers
AUTHORS: Noelle Antao, Joseph Sall, Christopher Petzold, Damian C. Ekiert, Gira Bhabha, Feng-Xia Liang
[DESCRIPTION]
Serial block face scanning electron microscopy (SBF-SEM) is a volume EM tech... | ["[Culturing mammalian cells and sample fixation] Culture adherent mammalian cells for 24 - 48 h in a 60 mm or 100 mm tissue culture dish for cell pellet samples, or 35 mm tissue culture dish with a gridded glass bottom for CLEM samples (final density 3-6 x 105 cells) according to the standard protocol for the cell lin... |
12,426 | pMOA 189F-682R | 1 | dx.doi.org/10.17504/protocols.io.rm7vzz1rvx1w/v1 | https://www.protocols.io/view/pmoa-189f-682r-qdids4e | Roey Angel, Eva Petrova | TITLE: pMOA 189F-682R
AUTHORS: Roey Angel, Eva Petrova
[DESCRIPTION]
A PCR assay targeting the alpha subunit of the particulate methane monooxygenase gene (pmoA).
This is a general assay for methane oxidising bacteria using primers 189F–682R.
Note: these primers might occasionally also amplify the amoA gene of ammoni... | ["[PCR mixture] * Buffer contains 1.5 mM MgCl2 at final concentration", "[PCR program] 1. 94◦C – 4′\n2. x 10 {\n a. 94◦C – 1′\n b. 62◦C – 1°C – 1’\n c. 68◦C – 1′\n }\n 3. x 25 {\n a. 94◦C – 1′\n b. 52◦C – 1′\n c. 68◦C – 1′\n }\n \n4. 68◦C – 10'"] |
null | null | null | dx.doi.org/10.17504/protocols.io.pjvdkn6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol to apply bisulfite conversion of methyl cytosine to the analysis of the epigenome of single cell nuclei isolated from brain tissue, as performed within the Center for Epigenomics of the Mouse Bain Atlas (CEMBA) and in coordination with the BRAIN Initiative Cell Censu... | [] |
29,628 | Lipid Annotation of MALDI IMS Datasets | null | dx.doi.org/10.17504/protocols.io.864hzgw | null | Elizabeth Neumann, Jamie Allen, Jeff Spraggins, Danielle Gutierrez | TITLE: Lipid Annotation of MALDI IMS Datasets
AUTHORS: Elizabeth Neumann, Jamie Allen, Jeff Spraggins, Danielle Gutierrez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Scope: </div><div class = "text-block">Annotate lipid species detected by MALDI IMS analysis.</div><div class = "text-block">Expec... | ["Perform a quadratic recalibration of the IMS dataset using common well-characterized lipids:m/z 734.5694, 760.5851, 782.5670, 788.6164, 798.5410, 810.6007, 832.5827, and 848.5566Software used are DataAnalysis or Mmass, and ppm error calculated in excel.", "Create mass list from the averaged, re-calibrated IMS data s... |
25,180 | Calculo área ImageJ | null | dx.doi.org/10.17504/protocols.io.4t4gwqw | null | Javiera Poblete | TITLE: Calculo área ImageJ
AUTHORS: Javiera Poblete
[STEPS]
?. Para el cálculo de área de las rocas se utilizó el programa ImageJ versión 1.8. Dentro del programa se abre la imagen deseada, se va a “seleccionar”, luego click en “Straight” y señala una medida de referencia (1 cm), luego seleccionar “Analyze” y posterio... | ["Para el cálculo de área de las rocas se utilizó el programa ImageJ versión 1.8. Dentro del programa se abre la imagen deseada, se va a “seleccionar”, luego click en “Straight” y señala una medida de referencia (1 cm), luego seleccionar “Analyze” y posteriormente “Set scale”, donde se marcó “ know distance: 1; Unit o... |
36,889 | Clinical efficacy and safety of drug interventions for primary and secondary prevention of osteoporotic fractures in postmenopausal women: network meta-analysis followed by factor and cluster analysis | null | dx.doi.org/10.17504/protocols.io.bf9zjr76 | https://www.protocols.io/view/clinical-efficacy-and-safety-of-drug-interventions-bf9zjr76 | Liangliang Ding | TITLE: Clinical efficacy and safety of drug interventions for primary and secondary prevention of osteoporotic fractures in postmenopausal women: network meta-analysis followed by factor and cluster analysis
AUTHORS: Liangliang Ding
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The protocol for t... | ["Clinical efficacy and safety of drug interventions for primary and secondary prevention of osteoporotic fractures in postmenopausal women: network meta-analysis followed by factor and cluster analysis"] |
97,519 | Piggybac-mediated stable expression of NGN2 in iPSCs for differentiation into excitatory glutamatergic neurons | 1 | dx.doi.org/10.17504/protocols.io.e6nvwj54dlmk/v2 | https://www.protocols.io/view/piggybac-mediated-stable-expression-of-ngn2-in-ips-dbgp2jvn | Dan Dou, C. Alexander Boecker, Erika L.F. Holzbaur | TITLE: Piggybac-mediated stable expression of NGN2 in iPSCs for differentiation into excitatory glutamatergic neurons
AUTHORS: Dan Dou, C. Alexander Boecker, Erika L.F. Holzbaur
[DESCRIPTION]
We adapted a previously-described method (Pantazis et al., 2022) for employing Piggybac transfection to stably express doxycycl... | ["[Piggybac-mediated stable expression of NGN2 in iPSCs for differentiation into excitatory glutamatergic neurons] Culture iPSCs in a 10 cm dish coated with Growth Factor Reduced Matrigel (Corning) and feed daily with Essential 8 media (ThermoFisher).", "[Piggybac-mediated stable expression of NGN2 in iPSCs for differe... |
68,921 | Primary culture cortical / hippocampal neurons E15-17 mouse - PFF testing | 4 | dx.doi.org/10.17504/protocols.io.ewov1nemkgr2/v1 | https://www.protocols.io/view/primary-culture-cortical-hippocampal-neurons-e15-1-cfiztkf6 | Rong Chen, Sabina Marciano, Roberta Marongiu, Ted Dawson | TITLE: Primary culture cortical / hippocampal neurons E15-17 mouse - PFF testing
AUTHORS: Rong Chen, Sabina Marciano, Roberta Marongiu, Ted Dawson
[DESCRIPTION]
This protocol is linked to the preparation of Pre Formed Fibrils by Ted Dawson's laboratory.
Tae-In Kam, Rong Chen, Ted Dawson . Production of alpha synuclei... | ["[Dissection/Culture] Dissect the cortex/hippocampus and separate and remove the soft membrane and blood vessels.", "[Dissection/Culture] Collect all the cortices/hippocampus in 30 mL PBS on ice.", "[Dissection/Culture] Transfer the cortices/hippocampus to a 15 ml tube containing 9 mL trypsin–EDTA (0.25%) and incub... |
10,499 | Calcium chloride preparation of competent cells | null | dx.doi.org/10.17504/protocols.io.nhbdb2n | null | Moriah Beck | TITLE: Calcium chloride preparation of competent cells
AUTHORS: Moriah Beck
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Day 1]
Innoculate 1-2 mls LB (no antibiotics) with single colony of cells and incubate at 37 °C overnight with shaking.
?. [Day 2]
Use 1/100 volume of overnight to start culture. i.e... | ["[Day 1]\nInnoculate 1-2 mls LB (no antibiotics) with single colony of cells and incubate at 37 °C overnight with shaking.", "[Day 2]\nUse 1/100 volume of overnight to start culture. i.e. If you are growing up 50 mls of competent cells, than add 500 μL of starter.", "[Day 2]\nGrow cells to OD600 of 0.5-0.7 at 37 °C.",... |
null | null | null | dx.doi.org/10.17504/protocols.io.hrgb53w | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?. | [] |
94,838 | Anti-condensation agent | 4 | dx.doi.org/10.17504/protocols.io.e6nvwdrq2lmk/v1 | https://www.protocols.io/view/anti-condensation-agent-c8uwzwxe | John Bergqvist | TITLE: Anti-condensation agent
AUTHORS: John Bergqvist
[DESCRIPTION]
Preventing plate lids from fogging up by applying an anti-condensation agent. This allows longer recordings of e.g. worm behaviour.
[BEFORE_START]
Make sure to treat lids that are for use at least a day after treatment.
[STEPS]
SECTION: Making an... | ["[Making anti-condensation agent] Make a mixture of 0.05% Triton X-100 and 20% ethanol in a 50 mL test tube. \n\nFor 20 mL, mix:\n4 mL \n0.1 mL\n16 mL", "[Treating plate lids] Treating lids with the anti-condensation agent should be done at least a day before using the plates to study worm behaviour.", "[Treating plat... |
24,245 | Efficacy and safety of the PRO-087 Ophthalmic solution versus systane(R) Ultra and Systane(R) Ultra Preservative-free on the tear film dysfunction syndrome from mild to moderate. | null | dx.doi.org/10.17504/protocols.io.3wvgpe6 | null | Sandra Belalcázar-Rey, Valeria Sánchez, Juan C Ochoa-Tabares, Samuel Altamirano, Abraham Soto-Gómez, Ruben Suárez-Velasco, Filiberto García-Félix., Leopoldo Baiza-Durán, Oscar Olvera-Montaño, Patricia Muñoz-Villegas. | TITLE: Efficacy and safety of the PRO-087 Ophthalmic solution versus systane(R) Ultra and Systane(R) Ultra Preservative-free on the tear film dysfunction syndrome from mild to moderate.
AUTHORS: Sandra Belalcázar-Rey, Valeria Sánchez, Juan C Ochoa-Tabares, Samuel Altamirano, Abraham Soto-Gómez, Ruben Suárez-Velasco, Fi... | [] |
94,524 | Pythium Zoospore Production Soaking Solution | 4 | null | https://www.protocols.io/view/pythium-zoospore-production-soaking-solution-c8i4zugw | Nimalka Weerasuriya | TITLE: Pythium Zoospore Production Soaking Solution
AUTHORS: Nimalka Weerasuriya
[DESCRIPTION]
Creation and test of soaking solutions to be used for large-scale zoospore production for Pythium myriotylum. This is modified from methods in:
Nyochembeng, L. M., Pacumbaba, R. P., & Beyl, C. A. (2002). Calcium Enhanced Zo... | ["[Soaking Solutions] Make Soaking Solutions 1, 2, 3, and Control.\nPrep 4 x 1 L autoclavable bottles for each Soaking Solutions (1-3) and Control.", "[Preparation] Have mature colonies of verified Pythium myriotylum growing on CMA or 1.5-2% WA 90 mm plates. Colony maturity ~7-14 days, with visible oospores.", "[Soakin... |
65,364 | Fluxactive Complete Does it really work? Review After 30 Days Use | 3 | dx.doi.org/10.17504/protocols.io.5qpvob1q7l4o/v1 | https://www.protocols.io/view/fluxactive-complete-does-it-really-work-review-aft-cb3usqnw | Fluxactive Complete | TITLE: Fluxactive Complete Does it really work? Review After 30 Days Use
AUTHORS: Fluxactive Complete
[DESCRIPTION]
Fluxactive Complete – Official Website Link – Click Here
[STEPS] | [] |
94,807 | GWAS prioritization analysis | 4 | dx.doi.org/10.17504/protocols.io.q26g7pe61gwz/v1 | https://www.protocols.io/view/gwas-prioritization-analysis-c8txzwpn | Peter Kilfeather | TITLE: GWAS prioritization analysis
AUTHORS: Peter Kilfeather
[DESCRIPTION]
GWAS prioritization analysis from Kilfeather, Khoo et al., 2024
[STEPS]
SECTION: Protocol
1. A list of 303 genes (sourced from Nalls et al., 2019 supplementary materials), containing SNPs at an r2 > 0.5 and located within ±1 Mb of 107 common... | ["[Protocol] A list of 303 genes (sourced from Nalls et al., 2019 supplementary materials), containing SNPs at an r2 > 0.5 and located within ±1 Mb of 107 common risk variants for sporadic PD was used for prioritization analysis. To convert between human and mouse gene symbols, homologene (v1.4.68.19.3.27, RRID:SCR_00... |
null | null | null | dx.doi.org/10.17504/protocols.io.gsebwbe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 1">
<div class="layoutArea">
<div class="column">
<p><strong>Developed for:</strong></p>
<p> </p>
<p>Aerius,<br /> Odyssey® Classic,</p>
<p>Odyssey CLx, and</p>
<p>Odyssey Sa<br /> Infrared Imaging Systems</p>
</div>
</div>
</div>
[GUIDELINES]
<p><... | [] |
68,077 | Protocol to secretome investigation of tumor 3D co-culture model | 1 | dx.doi.org/10.17504/protocols.io.81wgb6123lpk/v2 | https://www.protocols.io/view/protocol-to-secretome-investigation-of-tumor-3d-co-ceqmtdu6 | ANNA MARIA AP FERNANDES, Giulia Carli Mendes, Alex Rosini, Andrea Corazzi Pelosi, Leonardo Maciel, Luísa F Bueno, Lívia Maria F Silva, Rafael F Bredariol, Maycon Giovani Santana, Andreia de Melo Porcari, Denise G. Priolli | TITLE: Protocol to secretome investigation of tumor 3D co-culture model
AUTHORS: ANNA MARIA AP FERNANDES, Giulia Carli Mendes, Alex Rosini, Andrea Corazzi Pelosi, Leonardo Maciel, Luísa F Bueno, Lívia Maria F Silva, Rafael F Bredariol, Maycon Giovani Santana, Andreia de Melo Porcari, Denise G. P... | ["[2D CELL CULTURE] Use human colon carcinoma (HT-29) and pre-adipocytes cells (3T3-L1) (Banco de Células do Rio de Janeiro (BCRJ; Duque de Caxias, Brazil).", "[2D CELL CULTURE] Thaw HT-29 and 3T3-L1 cells and propagate in culture using Modified Dulbecco Eagle Medium (DMEM - Sigma D-5648, São Paulo, Brazil), supplement... |
58,135 | DNA Extract was from filter paper stored at room temperature | 1 | dx.doi.org/10.17504/protocols.io.b4zxqx7n | https://www.protocols.io/view/dna-extract-was-from-filter-paper-stored-at-room-t-b4zxqx7n | Katie Izenour, Anwar Kalalah, Fayez Salib, Sarah Zohdy | TITLE: DNA Extract was from filter paper stored at room temperature
AUTHORS: Katie Izenour, Anwar Kalalah, Fayez Salib, Sarah Zohdy
[DESCRIPTION]
Preservation of samples requiring cold-chain storage is an often unavoidable challenge especially when doing laboratory work outside the western world. Samples are a pre... | ["[Whole blood collection from animal] Using a sterile syringe and needle, collect 1-5 mL of whole blood from animal's forelimb. Immediately express the contents of the syringe into a new, clean EDTA tube and invert several times to mix.", "[Whole blood storage] IF EXTRACTING DNA ON THE SAME DAY AS BLOOD COLLECTION - ... |
51,870 | Anti-plaque efficacy of a novel Moringa oleifera dentifrice | 4 | dx.doi.org/10.17504/protocols.io.bwv6pe9e | https://www.protocols.io/view/anti-plaque-efficacy-of-a-novel-moringa-oleifera-d-bwv6pe9e | Sudhir Varma | TITLE: Anti-plaque efficacy of a novel Moringa oleifera dentifrice
AUTHORS: Sudhir Varma
[DESCRIPTION]
Objectives: The use of herbal dentifrices has grown exponentially over the years. They are categorically referred to as ethnomedicines. Various agents have been tried with contradicting findings based on phytopharmac... | ["Antiplaue efficacy of moringa", "[Abstract] Objectives: The use of herbal dentifrices has grown exponentially over the years. They are categorically referred to as ethnomedicines. Various agents have been tried with contradicting findings based on phytopharmacological analysis. Miswak is one agent which has been used... |
26,039 | Standard iGEM Cell Measurement Protocol | null | dx.doi.org/10.17504/protocols.io.5nxg5fn | null | Traci Haddock-Angelli, Jacob Beal, Natalie Farny, Chris Workman, Geoff Baldwin, Russell Buckley-Taylor, Ari Dwijayanti, Kristin Ellis, Markus Gershater, Daisuke Kiga, John Marken, Vinoo Selvarajah, Marko Storch, Richard Tennant, Paul Rutten | TITLE: Standard iGEM Cell Measurement Protocol
AUTHORS: Traci Haddock-Angelli, Jacob Beal, Natalie Farny, Chris Workman, Geoff Baldwin, Russell Buckley-Taylor, Ari Dwijayanti, Kristin Ellis, Markus Gershater, Daisuke Kiga, John Marken, Vinoo Selvarajah, Marko Storch, Richard Tennant, Paul Rutten
[DESCRIPTION]
<div cla... | ["[Day 1]\nTransform Escherichia coli DH5α with these following plasmids (all in pSB1C3) ABCD1DevicePart NumberPlateLocation2Negative controlBBa_R0040Kit Plate 7Well 2D3Positive control BBa_I20270Kit Plate 7Well 2B4Test Device 1BBa_J364000Kit Plate 7Well 2F5Test Device 2BBa_J364001Kit Plate 7Well 2H6Test Device 3BBa... |
null | null | null | dx.doi.org/10.17504/protocols.io.ddg23v | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
<strong>What you need before you start:</strong><br />1. Zobell plates<br />2. Top agar – 3.5 ml per plate<br /> a. MSM<br /> b. 6g LMP agarose/liter<br />3. Your host growing somewhere in exponential phase – 0.3 m... | [] |
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