Datasets:
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... |
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