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 |
|---|---|---|---|---|---|---|---|
64,380 | https://facebook.com/Kell-Clarkson-CBD-Gummies-105983145436466/ | 3 | dx.doi.org/10.17504/protocols.io.kxygxzqxov8j/v1 | https://www.protocols.io/view/https-facebook-com-kell-clarkson-cbd-gummies-10598-ca44sgyw | kellyclaarkson | TITLE: https://facebook.com/Kell-Clarkson-CBD-Gummies-105983145436466/
AUTHORS: kellyclaarkson
[DESCRIPTION]
Cannabidiol is one of the sound cannabinoids that settle pressure and uneasiness issues.
[STEPS] | [] |
79,703 | Canine Influenza A Subtype Identification Assay | 1 | dx.doi.org/10.17504/protocols.io.14egn2o9pg5d/v1 | https://www.protocols.io/view/canine-influenza-a-subtype-identification-assay-cr3xv8pn | Come J Thieulent, Mariano Carossino, Laura Peak, Udeni B. R. Balasuriya | TITLE: Canine Influenza A Subtype Identification Assay
AUTHORS: Come J Thieulent, Mariano Carossino, Laura Peak, Udeni B. R. Balasuriya
[DESCRIPTION]
The Canine Influenza A Subtype Identification Assay is intended as an in vitro veterinary reagent set, based on Reverse Transcription quantitative PCR (RT-qPCR), for the... | ["[Reaction Setup] Thaw all reagents on ice.", "[Reaction Setup] Centrifuge all reagents on a benchtop centrifuge to ensure no liquid is in the cap and keep on ice", "[Reaction Setup] Setup the Master Mix according to the following table 1:", "[Programming the Thermocycler] The following fluorescence channels should be... |
22,161 | Fecal DNA extraction by bead beating | null | dx.doi.org/10.17504/protocols.io.zvrf656 | null | Chin Yee Tan | TITLE: Fecal DNA extraction by bead beating
AUTHORS: Chin Yee Tan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">From Surana Lab protocols</div><div class = "text-block">This protocol is suitable for extracting DNA from either human or mouse feces. Best results will be obtained with 10-60 mg of sta... | ["For each 2ml screw cap tube, Add Add Add Add .\n[beads]\n[Phenol/chloroform]\n[SDS]\n[PB buffer]", "Bead beat on Precellys, setting 2.", "Spin down the tubes for at 4000 RPM in microcentrifuge.", "Proceed to PCR purification kit – for the purification of up to 10 ug PCR products.", "Label & Place a QIAquick column ... |
null | null | null | dx.doi.org/10.17504/protocols.io.r63d9gn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This includes portions of the methods section from:</p>
<p> </p>
<p>Teytelman L, Özaydın B, Zill O, Lefrançois P, Snyder M, Rine J, et al. (2009) <a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0006700" target="_blank" rel="noopener noreferrer">Impac... | [] |
82,824 | Biolayer Interferometry for DNA-Protein Interactions | 1 | dx.doi.org/10.17504/protocols.io.36wgq48movk5/v2 | https://www.protocols.click/view/biolayer-interferometry-for-dna-protein-interactio-cu5gwy3w | John K Barrows, Michael Van Dyke | TITLE: Biolayer Interferometry for DNA-Protein Interactions
AUTHORS: John K Barrows, Michael Van Dyke
[DESCRIPTION]
Biolayer interferometry (BLI) is a widely utilized technique for determining the interaction dynamics between macromolecules. Most BLI instruments, such as the Octet RED96e used throughout this protocol,... | ["[PCR synthesis of biotinylated DNA probes] Our laboratory uses DNA probes derived from the ST2R24 selection template (sequence details can be found at: https://doi.org/10.1371/journal.pone.0159408) to identify the preferred binding sequence of thermophilic transcription factors. The design of related fluorophore-labe... |
53,888 | Construction of mutant library | 4 | dx.doi.org/10.17504/protocols.io.byu8pwzw | https://www.protocols.io/view/construction-of-mutant-library-byu8pwzw | Shuning Guo | TITLE: Construction of mutant library
AUTHORS: Shuning Guo
[DESCRIPTION]
This protocol is used to construct mutant library of target gene with high efficiency and low false positives/negatives rate after subsequent functional screening.
[BEFORE_START]
Make sure that the template of MEGAWHOP PCR is fresh to improve... | ["[Error-prone PCR] Add the following reagent to a PCR tube (50μl) (Random Mutagenesis Kit by Solarbio).", "[Error-prone PCR] Program the thermocycler as follows:", "[Error-prone PCR] Use the palm centrifuge to mix the solution in PCR tube.", "[Error-prone PCR] Put the PCR tube into the thermocycler and Run the program... |
36,001 | Cleavage of the Fusion Protein (TEV Protease) | null | dx.doi.org/10.17504/protocols.io.bfd9ji96 | https://www.protocols.io/view/cleavage-of-the-fusion-protein-tev-protease-bfd9ji96 | New England Biolabs | TITLE: Cleavage of the Fusion Protein (TEV Protease)
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">TEV Protease, also known as Tobacco Etch Virus (TEV) Protease, is a highly specific cysteine protease that recognizes the amino-acid sequence Glu-Asn-Leu-Tyr-Phe-Gln-(Gl... | ["If necessary, concentrate the fusion protein to at least .", "Perform a pilot experiment with a small portion of your protein. For example:", "Scale up the pilot experiment linearly for the amount of the fusion protein to be cleaved. Save at least a small sample of the uncut fusion as a negative control.", "Check for... |
22,434 | Siblings Neighbourhood Effects | null | dx.doi.org/10.17504/protocols.io.z6af9ae | null | Lina Hedman | TITLE: Siblings Neighbourhood Effects
AUTHORS: Lina Hedman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify">This Stata code was generated for a study using a sibling design to disentangle family and neighbourhood effects on income, with contextual s... | [] |
27,903 | 18GEZG & 18GZG Plasmid Maps | null | dx.doi.org/10.17504/protocols.io.7g7hjzn | null | Mariana Rius | TITLE: 18GEZG & 18GZG Plasmid Maps
AUTHORS: Mariana Rius
[STEPS]
?.
?. | [] |
66,015 | Functionality test (DNA loading dye) | 4 | null | https://www.protocols.io/view/functionality-test-dna-loading-dye-ccp7svrn | Nadine Mowoh, Stephane Fadanka | TITLE: Functionality test (DNA loading dye)
AUTHORS: Nadine Mowoh, Stephane Fadanka
[DESCRIPTION]
Beneficial Bio 6X DNA Loading Dye is a premixed loading buffer used to prepare samples for loading onto agarose and polyacrylamide gels. It contains bromophenol blue and Xylene cyanol dyes for visual tracking of DNA du... | ["[Functionality test of BenBio 6x DNA loading dye] Casting and loading the Electrophoresis gel\n\nPour the molten agar into the gel casting tray with the well combs in place. (Pour slowly to avoid bubbles which will disrupt the gel), allow to solidify for about 15 to 20 minutes.\nAfter the gel is solidified, remove t... |
16,928 | DNA Extraction using FastDNA Spinkit for Soil with PolyA Modifictaion | null | dx.doi.org/10.17504/protocols.io.ur8ev9w | null | Tim D'Angelo | TITLE: DNA Extraction using FastDNA Spinkit for Soil with PolyA Modifictaion
AUTHORS: Tim D'Angelo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes a modification to the MP Biomedicals FastDNA SpinKit for Soil. It has been changed to use a Retsch MM400 Mixer Mill instead of t... | ["[Prep PolyA dilution]\nFollowing the manufacturers protocol, create a stock solution of polyA in filter sterilized molecular grade water. We have used 4 ug/ul this may be modified depending on the circumstances.", "[FastDNA Spinkit Protocol with modifications]\nthaw out samples and polyA solution (4 ug/ul), get reag... |
80,335 | Immunohistochemistry for Carbon Fiber Thread Electrodes | 1 | dx.doi.org/10.17504/protocols.io.n92ldpx78l5b/v1 | https://www.protocols.io/view/immunohistochemistry-for-carbon-fiber-thread-elect-csppwdmn | Helen N Schwerdt, Tomoko Yoshida, Ann M Graybiel | TITLE: Immunohistochemistry for Carbon Fiber Thread Electrodes
AUTHORS: Helen N Schwerdt, Tomoko Yoshida, Ann M Graybiel
[DESCRIPTION]
Methods for immunofluorescent staining of brain tissue with indwelling electrodes are described.
[STEPS]
1. Free floating 25-μm sections from rat A were rinsed three times for 5 min e... | ["Free floating 25-μm sections from rat A were rinsed three times for 5 min each with 0.01 M phosphate buffered saline with 0.2% Triton X-100 (PBS-Tx), and then blocked for 60 min in TSA Blocking reagent (Akoya science FP1012) diluted in PBS-Tx (TSA block) on a shaker.", "Sections were left shaking for one night at 4°C... |
45,837 | Rapid Quantitative Evaluation of CRISPR Genome Editing by TIDE and TIDER | 4 | dx.doi.org/10.17504/protocols.io.bqzmmx46 | https://www.protocols.io/view/rapid-quantitative-evaluation-of-crispr-genome-edi-bqzmmx46 | Eva Karina Brinkman, Bas van Steensel | TITLE: Rapid Quantitative Evaluation of CRISPR Genome Editing by TIDE and TIDER
AUTHORS: Eva Karina Brinkman, Bas van Steensel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Current genome editing tools enable targeted mutagenesis of selected DNA sequences in many species. However, the effici... | ["[3.1 Control and Experimental Sample Generation]\nFor both methods genomic DNA is isolated from the cell pool that was transfected with the nuclease or guide RNA alone (control) and from cells exposed to both Cas9 and guide RNA (experimental sample). For TIDER the experimental sample is also co-transfected with the d... |
90,237 | FTIR | 1 | dx.doi.org/10.17504/protocols.io.dm6gp3xqpvzp/v1 | https://www.protocols.io/view/ftir-c4c5ysy6 | Alexander Röntgen | TITLE: FTIR
AUTHORS: Alexander Röntgen
[DESCRIPTION]
Protein FTIR protocol.
[STEPS]
7.
6.1.
SECTION: Background scan
1. Spot 5 µL of buffer on prism
Acquire background scan
7.
SECTION: Sample scan
2. Spot 5 µL of protein solution on prism
Acquire sample scan | ["[Background scan] Spot 5 µL of buffer on prism\n Acquire background scan", "[Sample scan] Spot 5 µL of protein solution on prism\n Acquire sample scan"] |
27,688 | MojoSort™ Human anti-PE Nanobeads Column Protocol | null | dx.doi.org/10.17504/protocols.io.7aghibw | null | Sam Li | TITLE: MojoSort™ Human anti-PE Nanobeads Column Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>BioLegend MojoSort™ nanobeads work in commonly used separation columns, based on our internal research as well as validation by external testing by academic labs. This simpl... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes.", "In the final wash of your sample preparation, resuspend the cells in MojoSort™ Buffer by adding up to 4 mL in a 5 mL (12 x 75 mm) polypropylene tube.Note: Keep MojoSort™ Buffer on ice throughout the procedure.", "Filter the cells with... |
68,967 | Citizen scientists Guides(Chinese) | 1 | dx.doi.org/10.17504/protocols.io.4r3l2oxzpv1y/v1 | https://www.protocols.io/view/citizen-scientists-guides-chinese-cfkftktn | Hsin-Mao Wu | TITLE: Citizen scientists Guides(Chinese)
AUTHORS: Hsin-Mao Wu
[DESCRIPTION]
Soil sample, citizen scientist
[STEPS]
SECTION: 採土
5. 移除表土，取距離土表5~7公分之處的土，裝入塑膠夾鏈袋中
[示意圖片待補]
SECTION: 採土
6. 將塑膠袋中的土均勻混合，倒入HDPE塑膠罐之中
SECTION: 採土
8. 最後拍兩張照片
SECTION: 如何加入專案
1. 開啟Line app，將頁面切換成「聊天」，並按下頂部的掃描圖示(紅框處)
SECTION... | ["[採土] 移除表土，取距離土表5~7公分之處的土，裝入塑膠夾鏈袋中\n[示意圖片待補]", "[採土] 將塑膠袋中的土均勻混合，倒入HDPE塑膠罐之中", "[採土] 最後拍兩張照片", "[如何加入專案] 開啟Line app，將頁面切換成「聊天」，並按下頂部的掃描圖示(紅框處)", "[如何加入專案] 掃描以下QR code或點選此連結微生物公民科學", "[如何加入專案] 加入成功後會顯示以下畫面", "[如何加入專案] 接著等待採集工具包寄送即可開始採集！", "[採土] 在採集紀錄紙上勾選採樣地點、採樣種類，以及填寫日期、城市、鄉鎮、地點、採集者等資訊", "[採土] 打開iNaturalist app，上傳剛剛拍攝的... |
86,701 | Motor behavioral assessment | 4 | dx.doi.org/10.17504/protocols.io.j8nlkoon6v5r/v1 | https://www.protocols.io/view/motor-behavioral-assessment-cywmxxc6 | Beatriz E Nielsen | TITLE: Motor behavioral assessment
AUTHORS: Beatriz E Nielsen
[DESCRIPTION]
This protocol describes motor behavioral assays used to assess motor function in a 6-OHDA mouse model of Parkinson's disease. These assays include open field, rotarod, cylinder, and balance beam tests.
Prior to each behavioral test, mice were ... | ["[Cylinder test: forelimb use asymmetry] Required materials:\nClear plastic cylinder: 10.5 cm diameter, 14.5 cm height.\nMirror.\nCamera.\nVideo player software (e.g. VLC).\n70% ethanol.", "[Cylinder test: forelimb use asymmetry] Set up behavior room:\nClean cylinder with 70% ethanol.\nPlace the camera in front of the... |
88,266 | PCR Protocol Template | 1 | null | https://www.protocols.io/view/pcr-protocol-template-c2fiybke | Kathleen Pitz, Raissa.meyer | TITLE: PCR Protocol Template
AUTHORS: Kathleen Pitz, Raissa.meyer
[DESCRIPTION]
A protocol template created through the BeBOP project for PCR.
[STEPS]
SECTION: Protocol Template
1. Minimum Information about an Omics Protocol (MIOP)
See https://github.com/BeBOP-OBON/miop/blob/main/model/schema/terms.yaml for list... | ["[Protocol Template] Minimum Information about an Omics Protocol (MIOP)\n\nSee https://github.com/BeBOP-OBON/miop/blob/main/model/schema/terms.yaml for list and definitions.\n\n\n\n \nMIOP Term\nValue\n \nmethodology category\n\n \nproject\n\n \npurpose\n\n \nanalyses\n\n \ngeographic location\n\n \nbroad-scale env... |
null | null | null | dx.doi.org/10.17504/protocols.io.kytcxwn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Use of geographic profiling for finding first introduction point of a biological invasion</p>
[STEPS]
?.
?.
?. | [] |
37,803 | Think Layer Chromatography (TLC) Bioautography | 1 | dx.doi.org/10.17504/protocols.io.bg6jjzcn | https://www.protocols.io/view/think-layer-chromatography-tlc-bioautography-bg6jjzcn | Dane Lyddiard | TITLE: Think Layer Chromatography (TLC) Bioautography
AUTHORS: Dane Lyddiard
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A TLC bioautography protocol to test the constituents of plant extracts and essential oils for antibacterial activity was adapted and optimised from the methods described in S... | ["Grow Bacteria (Overnight)Prepare streak plates of bacteria on appropriate solid agar media (e.g., nutrient or Mueller-Hinton agars). Incubate overnight (aerobically) at 35°C ±1°C", "Select TLC Solvent SystemCut TLC plates (handle with gloves) to 9 x 9 cm (or smaller for testing solvent systems). Using a TLC spotter o... |
98,212 | BAF_Protocol_008 Metabolomics: Soluble Metabolite Extraction | 0 | dx.doi.org/10.17504/protocols.io.yxmvmex5ng3p/v1 | https://www.protocols.io/view/baf-protocol-008-metabolomics-soluble-metabolite-e-db6c2raw | Nicholas Sherman | TITLE: BAF_Protocol_008 Metabolomics: Soluble Metabolite Extraction
AUTHORS: Nicholas Sherman
[DESCRIPTION]
This is a standard metabolite sample prep using chloroform/methanol and keeping the soluble (aqueous) phase. This method will produce a clean sample free of most lipids and very hydrophobic molecules. The sample... | ["[Liquid Samples: Urine, Plasma, Cell Media] To each sample containing 100 uL add 750 µL of -20°C cold Chloroform:methanol (2:1) mixture and vortex", "[Liquid Samples: Urine, Plasma, Cell Media] Shake tubes vigorously for 30 min at 4°C in temperature temperature-controlled thermal shaker", "[Liquid Samples: Urine, Pla... |
null | null | null | dx.doi.org/10.17504/protocols.io.m86c9ze | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Nucleosomes organize the eukaryotic genome into chromatin. In cells, nucleosome assembly relies on the activity of histone chaperones, proteins with high binding affinity to histones. At least a subset of histone chaperones promotes histone deposition <em>in vivo</em>. Howeve... | [] |
38,746 | Dissociation of neuronal culture to single cells for scRNA-seq (10x Genomics) | 4 | dx.doi.org/10.17504/protocols.io.bh32j8qe | https://www.protocols.io/view/dissociation-of-neuronal-culture-to-single-cells-f-bh32j8qe | Julie Jerber, James Haldane, Juliette Steer, Daniel Pearce, Minal Patel | TITLE: Dissociation of neuronal culture to single cells for scRNA-seq (10x Genomics)
AUTHORS: Julie Jerber, James Haldane, Juliette Steer, Daniel Pearce, Minal Patel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines a method for dissociating a human pluripotent stem cell-deriv... | ["[Buffer Preparation]\nPrepare Wash Buffer 2 by adding 10% BSA solution (100 μg/mL) to DPBS (-/-) to a final concentration of 400 μg/mL. i.e. add 60 μL 10% BSA solution to 15 mL of DPBS (-/-).", "[Dissociation]\nAspirate the media from the well(s) of the neuronal culture and gently add of DPBS (-/-) without disturbin... |
85,785 | In-vitro GCase Activity Assay | 4 | dx.doi.org/10.17504/protocols.io.dm6gp3b7dvzp/v1 | https://www.protocols.io/view/in-vitro-gcase-activity-assay-cxzzxp76 | Tae-Un Han, sidranse | TITLE: In-vitro GCase Activity Assay
AUTHORS: Tae-Un Han, sidranse
[DESCRIPTION]
This is version 2 of in-vitro GCase activity assay.
We optimized the assay condition to enhance sensitivity and specificity.
Both cell lysates and protein lysates prepared in M-buffer containing protease inhibitor and 0.25% TritonX can us... | ["Mix 20 mL (0.852 g in 30 mL) with 14 mL (0.576 g in 30 mL) to make M-buffer (pH 5.4, no additional pH adjustment required).", "Dissolve one protease inhibitor tablet (Roche cOmplet mini) in 10 mL, then add Triton X-100 solution to 0.25 % (v/v) (e.g. 25 µL in 10 mL) and0.2 Mass / % volume of sodium taurocholate to mak... |
null | null | null | dx.doi.org/10.17504/protocols.io.eiebcbe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
A simple protocol for RNA extraction from various types of samples (protists, fungi, bacteria, organelles, subcellular fractions, ribosomes, etc.). Compared to the commercial Trizol® procedure, it makes use of generally available chemicals without the need for columns, thus allo... | [] |
104,038 | An improved whole-mount immunofluorescence protocol for juvenile Amphimedon queenslandica | 0 | dx.doi.org/10.17504/protocols.io.e6nvw1o2wlmk/v1 | https://www.protocols.io/view/an-improved-whole-mount-immunofluorescence-protoco-dhue36te | Bin Yang, Bernard M. Degnan, Sandie M Degnan | TITLE: An improved whole-mount immunofluorescence protocol for juvenile Amphimedon queenslandica
AUTHORS: Bin Yang, Bernard M. Degnan, Sandie M Degnan
[DESCRIPTION]
Sponges offer a unique perspective on animal evolution because of their simple body plan and phylogenetic position in the animal kingdom (Renard et al. 20... | ["[Initial fixation] Remove all filtered artificial seawater from a 6-well plate containing juveniles reared on coverslips (Sogabe et al. 2016) and add 0.5 mL of PFA+GA fixative into each well. Note: other fixatives trialled under the same conditions are less effective in preserving A. queenslandica juvenile morphology... |
21,346 | Yale - Total Protein | null | dx.doi.org/10.17504/protocols.io.y4afyse | null | John Stack, Gary Cline | TITLE: Yale - Total Protein
AUTHORS: John Stack, Gary Cline
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Procedure to determine the total protein concentration in blood, serum, and plasma. Total Protein is determine... | ["Calibrate Cobas for Total Protein analysis by running a multi-analyte calibrator and two control serum.", "Sample handling as performed by Cobas Mira Plus a) Pipette 5µL of sample into cuvette. b) Add 150 µL of Total Protein Reagent. c) Incubate at 37ºC for 10 minutes d) Absorbance is measured at 550n... |
18,145 | Fluorescence aggregation imaging | 1 | dx.doi.org/10.17504/protocols.io.vx9e7r6 | https://www.protocols.io/view/fluorescence-aggregation-imaging-vx9e7r6 | Serena Ding | TITLE: Fluorescence aggregation imaging
AUTHORS: Serena Ding
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">For imaging aggregation behaviour of 40 young adult C. elegans on agar using the Twinnie TwinCam system. Worms are synchronised by bleaching and refeeding for 72 hours, and then 40 young adul... | ["[Imaging plate preparation (Day -7)]\nA separate batch of imaging plates is poured exactly seven days before each imaging day and stored at 4°C.\nImaging plates are 35 mm Petri dishes containing 3.5 mL low peptone (0.013% Difco Bacto) NGMagar (2% Bio/Agar, BioGene) to limit bacteria growth.", "[Imaging plate preparat... |
50,023 | Splinkerette Assay | 1 | dx.doi.org/10.17504/protocols.io.bu4fnytn | https://www.protocols.io/view/splinkerette-assay-bu4fnytn | Aazam Vahdatshoar | TITLE: Splinkerette Assay
AUTHORS: Aazam Vahdatshoar
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol used to find the exact location of the integrated piggybac construct in the genome of stably transfected cell line. This assay determines the copy number of an exogenous gene in the est... | ["[Harvest cells]\nPassage and harvest the cells following the cell culture protocol.\n100,000 cells would give enough genomic DNA.", "[Harvest cells]\nPellet the cells, aspirate the supernatant, and transfer the pellet to a Eppendorf tube.\n1.5 mL", "[Harvest cells]\nAdd PBS and centrifuge at for .\n1 mL\nCentrifug... |
98,583 | Intensive education intervention using network of involved diabetes patients to improve glycaemic control of type 2 diabetes patients in Delta State Nigeria: study protocol for a randomised controlled trial | 0 | dx.doi.org/10.17504/protocols.io.n92ld899nv5b/v1 | https://www.protocols.io/view/intensive-education-intervention-using-network-of-dchx2t7n | Victor M Oguoma, Ezekiel U Nwose, Eunice O Igumbor, Charles C Ofili, Phillip T Bwititi, Adeseye A Akintunde, Ifeoma I Ulasi, Echinei J Oshionwu, John Okuzor, Alex Odufu, Kennedy Aninze, Emmanuel Olu-Ero, Timothy C Skinner | TITLE: Intensive education intervention using network of involved diabetes patients to improve glycaemic control of type 2 diabetes patients in Delta State Nigeria: study protocol for a randomised controlled trial
AUTHORS: Victor M Oguoma, Ezekiel U Nwose, Eunice O Igumbor, Charles C Ofili, Phillip T Bwititi, Adeseye A... | ["STUDY OBJECTIVES\nThe primary objective of the trial is to evaluate whether T2D patients that undergo intensive lifestyle education within a network of T2D patients as peer-educators compared to usual lifestyle education will have better blood glycated haemoglobin (HbA1c) at 12 months of intervention.\nThe four secon... |
100,192 | HTTM : gDNA extraction | 4 | dx.doi.org/10.17504/protocols.io.q26g7yzz3gwz/v3 | https://www.protocols.io/view/httm-gdna-extraction-dd3828rw | Antoine Champie, Amélie De Grandmaison, Sebastien Rodrigue | TITLE: HTTM : gDNA extraction
AUTHORS: Antoine Champie, Amélie De Grandmaison, Sebastien Rodrigue
[DESCRIPTION]
Part of the HTTM protocol dedicated to the extraction of gDNA from transposon mutated cell pellets.
[STEPS]
SECTION: DNA extraction
2. Add 600 µLof lysis solution to each well of the deep-well plate and re... | ["[DNA extraction] Add 600 µLof lysis solution to each well of the deep-well plate and resuspend the pellet.", "[DNA extraction] Prepare the lysis solution by adding 165 µL of proteinase K to 66 mL of homemade lysis buffer and mix well.", "[DNA extraction] Cover with an adhesive aluminum foil and incubate at 55 °C for ... |
97,888 | Climate Resiliency Architecture in Mo'orea | 0 | null | https://www.protocols.io/view/climate-resiliency-architecture-in-mo-39-orea-dbt82nrw | Eva Louise Gibbs-Zehnder | TITLE: Climate Resiliency Architecture in Mo'orea
AUTHORS: Eva Louise Gibbs-Zehnder
[DESCRIPTION]
This project aims to measure the resilience to climate of traditional building techniques using place-based materials in Mo’orea. By working with the community, we hope to produce several culturally-relevant structure... | ["[Promoting Project and Community Awareness] Create flyers and social media posts informing public of project several months before desired start of project.", "[Community Workshops] Workshop 1: Identify Culturally Appropriate Materials\nInformal circle format in which community members are encouraged to share their k... |
79,530 | In vitro GCase activity assay (total cell lysate) | 1 | dx.doi.org/10.17504/protocols.io.261ge3767l47/v1 | https://www.protocols.io/view/in-vitro-gcase-activity-assay-total-cell-lysate-crwiv7ce | Federico Bertoli, Michela Deleidi | TITLE: In vitro GCase activity assay (total cell lysate)
AUTHORS: Federico Bertoli, Michela Deleidi
[DESCRIPTION]
Glucocerebrosidase is a lysosomal enzyme that catalyzes the hydrolysis of glucosylceramide (GlcCer), a membrane glyco-sphingolipid, to ceramide and glucose. This assay detects GBA activity by using a flu... | ["[Sample Lysis] Suspend samples in 50 µL of 1% Triton extraction buffer.", "[Sample Lysis] Homogenize with a Dounce homogenizer for 25 strokes.", "[Sample Lysis] Rotate samples for 30 min at 4 °C.", "[Sample Lysis] Centrifuge at 13500 x g, 4 °C for 15 min.", "[Sample Lysis] Collect supernatants.", "[Substrate prepara... |
69,783 | Soil pH 1:1 Soil Water Ratio | 1 | dx.doi.org/10.17504/protocols.io.n92ldp39nl5b/v1 | https://www.protocols.io/view/soil-ph-1-1-soil-water-ratio-cgdxts7n | maggie.bowman | TITLE: Soil pH 1:1 Soil Water Ratio
AUTHORS: maggie.bowman
[DESCRIPTION]
Soil pH can be measured at either a 1:1 or 1:2 soil to water ratio. Because of the use of the log scale, the two ratios typically provide similar results. A soil with high clay or organic matter may require a 1:2 or even 1:5 ratio to allow for e... | ["Measure 20 g dry weight soil into the Falcon tube (this should be done in the core processing step)", "Add 20 mL", "Place on reciprocating shaker for 15 min at 1000 RPM", "Rinse the pH probe well with DI water and gently pat dry with a kimwipe", "Check the calibration of the pH meter using the ph 4.01 and 7 standard.... |
84,801 | Periplasmic Bacterial Expression and Purification of Elastin-like Polymers | 1 | dx.doi.org/10.17504/protocols.io.5jyl8npw6l2w/v2 | https://www.protocols.click/view/periplasmic-bacterial-expression-and-purification-cw29xgh6 | Eva Rose Balog | TITLE: Periplasmic Bacterial Expression and Purification of Elastin-like Polymers
AUTHORS: Eva Rose Balog
[DESCRIPTION]
This protocol describes the expression and purification procedures used in the Balog lab at the University of New England for producing recombinant elastin-like polymers (ELPs) in E. coli. It has bee... | ["[Transformation] In a pre-chilled Eppendorf tube, mix 10-100 ng plasmid (typically 1-2 μL of mini-prep DNA) with 50-100 μL BL21(DE3) competent cells on ice. Let sit on ice for 30 min.", "[Transformation] Heat shock at 42 ºC in a water bath for 1 min.", "[Transformation] Allow cells to recover on ice for 2-3 min.", "[... |
91,569 | Inhibitor-free DNA extraction from soil and sediment samples | 1 | dx.doi.org/10.17504/protocols.io.bp2l6957zlqe/v2 | https://www.protocols.io/view/inhibitor-free-dna-extraction-from-soil-and-sedime-c5nry5d6 | Dominik Buchner | TITLE: Inhibitor-free DNA extraction from soil and sediment samples
AUTHORS: Dominik Buchner
[DESCRIPTION]
This protocol describes how to extract inhibitor-free DNA from soil and sediment samples. 5 g of soil or up to 10 g of sediment can be processed in one extraction, but there is also a miniaturized version for 250... | ["[Protocol for up to 10 g of input material] Prepare one 50 mL centrifuge tube per sample with 15 g of garnet beads.", "[Protocol for up to 10 g of input material] Add up to 10 g of soil to the tube.", "[Protocol for up to 10 g of input material] Add 15 mL and 1.2 mL. Vortex shortly.", "[Protocol for up to 10 g of in... |
41,038 | Purification of avian egg yolk immunoglobulins using the water dilution method, precipitation with isopropanol and using HiTrap™ Columns. | 6 | dx.doi.org/10.17504/protocols.io.bkbnksme | https://www.protocols.io/view/purification-of-avian-egg-yolk-immunoglobulins-usi-bkbnksme | Angel Justiz-Vaillant | TITLE: Purification of avian egg yolk immunoglobulins using the water dilution method, precipitation with isopropanol and using HiTrap™ Columns.
AUTHORS: Angel Justiz-Vaillant
[STEPS]
?. Separate egg yolk from the egg white.
?. Add nine parts of distilled water to one part egg yolk.
?. Mix and stir slowly for 6.30 h ... | ["Separate egg yolk from the egg white.", "Add nine parts of distilled water to one part egg yolk.", "Mix and stir slowly for 6.30 h at 4°C.", "Centrifuge at 10 000 × g, at 4°C for 25 min to precipitate the lipids.", "Collect the supernatant containing the IgY (water soluble fraction).", "Slowly add 5 ml of cold isopro... |
28,934 | Pichia pastoris transformation through electroporation | null | dx.doi.org/10.17504/protocols.io.8heht3e | null | iGEM Dusseldorf | TITLE: Pichia pastoris transformation through electroporation
AUTHORS: iGEM Dusseldorf
[STEPS]
?. [Prior]
Prior to transformation plasmid DNA containing the gene(s) of interest was linearized in restriction digests using an enzyme that only cuts once following the manufacturers manual !
?. [Transformation]
Mix approx.... | ["[Prior]\nPrior to transformation plasmid DNA containing the gene(s) of interest was linearized in restriction digests using an enzyme that only cuts once following the manufacturers manual !", "[Transformation]\nMix approx. 150 ng of linearized vector DNA with electrocompetent Pichia cells", "[Transformation]\nTranfe... |
null | null | null | dx.doi.org/10.17504/protocols.io.rigd4bw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol, which was developed in 2006 by Santiago Perez while in the Weis lab, provides a way to temporarily immobilize small Aiptasia for live imaging on a confocal microscope. As written, the protocol is used for inverted confocal microscopes, but the glass-bottom dish... | [] |
100,817 | Simple and easy method for long-term storage of human tissue for molecular analysis at room temperature | 0 | dx.doi.org/10.17504/protocols.io.3byl499e8go5/v1 | https://www.protocols.io/view/simple-and-easy-method-for-long-term-storage-of-hu-depr3dm6 | Sudhir Bhatia, Gudrun Baersch | TITLE: Simple and easy method for long-term storage of human tissue for molecular analysis at room temperature
AUTHORS: Sudhir Bhatia, Gudrun Baersch
[DESCRIPTION]
The storage of human tissue at room temperature is one of challenging areas. In the literature, there is hardly any reliable method available to achieve th... | ["Calculate the required volume of Genekam Tissue Storage Solution (GTSS) for the sample. 15ml GTSS per 5g tissue. It is also possible to store smaller tissue, e.g. 1g or less.", "Put on the gloves as for molecular analysis.", "Label the storage tube so that it cannot fade during storage.", "Take sterile scissors and p... |
35,751 | In vitro digestion of DNA with Cas9 Nuclease, S. pyogenes (M0386) | 1 | dx.doi.org/10.17504/protocols.io.be6fjhbn | https://www.protocols.io/view/in-vitro-digestion-of-dna-with-cas9-nuclease-s-pyo-be6fjhbn | New England Biolabs | TITLE: In vitro digestion of DNA with Cas9 Nuclease, S. pyogenes (M0386)
AUTHORS: New England Biolabs
[DESCRIPTION]
Cas9 Nuclease, S. pyogenes, (Cas9) is a double-stranded DNA endonuclease that is guided to its target by sequence complementarity of a small RNA loaded into the protein. This protocol describes how to... | ["Assemble the reaction at 37 Room temperature in the following order:", "Pre-incubate for 10 min at 25 °C.", "Add 3 µL (3 nM final).", "Mix thoroughly and pulse-spin in a microfuge.", "Incubate at 37 °C for 15 min.", "Add 1 µL to each sample. Mix thoroughly and pulse-spin in a microfuge.", "Incubate at 37 Room tempera... |
null | null | null | dx.doi.org/10.17504/protocols.io.jwccpaw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Let's start to download the fastq files for your project.</p>
[STEPS] | [] |
82,273 | RECC Corpus Stimulus set and protocol | 1 | dx.doi.org/10.17504/protocols.io.j8nlkwzq5l5r/v1 | https://www.protocols.io/view/recc-corpus-stimulus-set-and-protocol-cuj9wur6 | Federica Cavicchio | TITLE: RECC Corpus Stimulus set and protocol
AUTHORS: Federica Cavicchio
[DESCRIPTION]
The Rovereto Emotion and Cooperation Corpus (RECC) is a new resource collected to investigate the relationship between cooperation and emotions in an interactive setting. Previous attempts at collecting corpora to study emotions hav... | ["SET UP\nRECC consists of 21 interactions, 14 with a confederate, for a total of 280 min audiovisual and psycho-physiological recordings (heart rate and skin conductance). The psycho-physiological response was recorded and synchronized with video and audio recordings. The psycho-physiological data were recorded with a... |
37,132 | Antibiotic concentrations for LB agar plates | null | dx.doi.org/10.17504/protocols.io.bghkjt4w | https://www.protocols.io/view/antibiotic-concentrations-for-lb-agar-plates-bghkjt4w | Yoan Coudert | TITLE: Antibiotic concentrations for LB agar plates
AUTHORS: Yoan Coudert
[STEPS]
?. | [] |
94,550 | Genotyping of a candidate variant by PCR and Sanger sequencing | 4 | dx.doi.org/10.17504/protocols.io.rm7vzxp32gx1/v1 | https://www.protocols.io/view/genotyping-of-a-candidate-variant-by-pcr-and-sange-c8jwzupe | Cecile Grohs | TITLE: Genotyping of a candidate variant by PCR and Sanger sequencing
AUTHORS: Cecile Grohs
[DESCRIPTION]
This procedure describes a classic process for genotyping a simple SNP or small INDEL by PCR followed by Sanger sequencing, which can be easily analysed. It is used for the validation or invalidation of a candidat... | ["[Recover complete sequence of the gene of interest in the species of interest] First select the genome assembly of the species you wish to genotype in a genome browser (e.g. https://genome-euro.ucsc.edu/cgi-bin/hgGateway). Then, select the gene whose DNA you want to retrieve.", "[Recover complete sequence of the gene... |
106,627 | Stable integration of piggyBac plasmids into U2OS cells | 0 | dx.doi.org/10.17504/protocols.io.14egn618ql5d/v1 | https://www.protocols.io/view/stable-integration-of-piggybac-plasmids-into-u2os-dkdb4s2n | Isabel Lam, Alain Ndayisaba, Vikram Khurana | TITLE: Stable integration of piggyBac plasmids into U2OS cells
AUTHORS: Isabel Lam, Alain Ndayisaba, Vikram Khurana
[DESCRIPTION]
Stable integration of piggyBac plasmids into U2OS cells
[STEPS] | [] |
90,635 | Ultra low input library preparation of single soil invertebrate specimens for Hifi PacBio sequencing | 4 | dx.doi.org/10.17504/protocols.io.n92ldmqr7l5b/v1 | https://www.protocols.io/view/ultra-low-input-library-preparation-of-single-soil-c4rjyv4n | Leonie Schardt, Miklós Bálint | TITLE: Ultra low input library preparation of single soil invertebrate specimens for Hifi PacBio sequencing
AUTHORS: Leonie Schardt, Miklós Bálint
[DESCRIPTION]
This protocol is a modification of the Pacific Biosciences Ultra Low Input workflow for HiFi SMRTbell® Libraries. The modified workflow has been successfully ... | ["[Optional: Pre-processing of DNA] For high molecular weight (HMW) DNA extracts, fragmentation of the input material might be required. Additionally, if the whole extract is to be used for library preparation, concentrating the volume down might be necessary.", "[Optional: Pre-processing of DNA] Optional: shearing of ... |
59,496 | JAX - EZ Lysis Nuclei Isolation for 10x Genomics Assays | 1 | dx.doi.org/10.17504/protocols.io.ewov1n9npgr2/v2 | https://www.protocols.io/view/jax-ez-lysis-nuclei-isolation-for-10x-genomics-ass-b6cgratw | William F F F. Flynn, Elise Courtois, Greg Greg Perry, sandy.daigle , Paul.gabriel , Diane Luo, Jessica Grassmann | TITLE: JAX - EZ Lysis Nuclei Isolation for 10x Genomics Assays
AUTHORS: William F F F. Flynn, Elise Courtois, Greg Greg Perry, sandy.daigle , Paul.gabriel , Diane Luo, Jessica Grassmann
[DESCRIPTION]
The purpose of this protocol is to produce single nuclei from frozen human tissues for downstream assaying with t... | ["[Sample Prep] Slightly thaw sample out on ice and place onto pre chilled Petri dish on ice.", "[Sample Prep] Cut tissue into small pieces and add to a microcentrifuge tube.", "[Cell lysis] In micro centrifuge tube containing the tissue add 100 µL of lysis buffer.", "[Cell lysis] Using a plastic pestle to grind tissue... |
18,006 | Corchea: paper-based microfluidic device | null | dx.doi.org/10.17504/protocols.io.vtwe6pe | null | Gonzalo Vidal, Tim Rudge | TITLE: Corchea: paper-based microfluidic device
AUTHORS: Gonzalo Vidal, Tim Rudge
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Corchea is a paper-based microfluidic system for culture and comunicate bacteria on flow. Its has a hardware that you can make with a 3D printer and laser cut. The syste... | ["[Paper design]\nDraw the borders of your device and the future channels in your paper (#1 Whatman)", "[Paper design]\nCut the borders", "[Paper design]\nFill with wax crayons all the parts that you dont want the fluid pass", "[Channel Formation]\nMelt the wax, we use a regular oven at 100 °C for 140s. Remove it from ... |
48,627 | Isolation of SARS-CoV-2 RNA from Wastewater: Maxwell® RSC Environmental TNA Kit | 1 | dx.doi.org/10.17504/protocols.io.btqtnmwn | https://www.protocols.io/view/isolation-of-sars-cov-2-rna-from-wastewater-maxwel-btqtnmwn | subhanjan.mondal , Subhanjan Mondal, Nathan Feirer | TITLE: Isolation of SARS-CoV-2 RNA from Wastewater: Maxwell® RSC Environmental TNA Kit
AUTHORS: subhanjan.mondal , Subhanjan Mondal, Nathan Feirer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Early in the COVID-19 pandemic, scientific studies demonstrated that the genetic material of SARS-CoV-2,... | ["[Direct Capture Concentration]\nDispense 40ml of wastewater into a 50ml conical tube. You may pasteurize wastewater by incubation at 60°C for 1 hour. Please follow your institution biosafety guidelines.", "[Direct Capture Concentration]\nAdd 0.5 ml of Protease Solution, mix well by inversion and incubate for 30 minut... |
56,690 | Bogus Data Acquisition Protocol IV | 1 | dx.doi.org/10.17504/protocols.io.b3ksqkwe | https://www.protocols.io/view/bogus-data-acquisition-protocol-iv-b3ksqkwe | Abby Moore | TITLE: Bogus Data Acquisition Protocol IV
AUTHORS: Abby Moore
[DESCRIPTION]
The purpose of this protocol is to demo protocol development.
[BEFORE_START]
Before you start .....
[GUIDELINES]
Guidelines ....
[STEPS]
1. In this step, I'll refer to the software that you need to use. I used the Software compone... | ["In this step, I'll refer to the software that you need to use. I used the Software component to do this.", "In this step, I'll refer to an image using embed code from Box.", "In this step, I need to direct to to execute one of the following protocols depending on your context. Then you need to return to this protocol... |
49,306 | High-Molecular-Weight gDNA extraction protocol from moss gametophytes | 1 | dx.doi.org/10.17504/protocols.io.bud2ns8e | https://www.protocols.io/view/high-molecular-weight-gdna-extraction-protocol-fro-bud2ns8e | Lei Zhu | TITLE: High-Molecular-Weight gDNA extraction protocol from moss gametophytes
AUTHORS: Lei Zhu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The purpose of this protocol is to extract high-molecular-weight genomic DNA from gametophyte tissue of the moss </span><span style = "font-style:itali... | ["[Harvest Plant Materials]\nHarvest 3-week-old moss gametophyte tissue.", "[Harvest Plant Materials]\nCarefully remove rhizoids from leafy gametophytes.\nIMPORTANT: Rhizoids mixed in the green leafy tissue will cause pigment co-precipitated with DNA. Be careful to remove rhizoids from leafy gametophytes.", "[Harvest P... |
60,463 | Knee Cartilage Grading Protocol | 4 | dx.doi.org/10.17504/protocols.io.n2bvj695nlk5/v1 | https://www.protocols.io/view/knee-cartilage-grading-protocol-b7apridn | molmer , Martin Lotz | TITLE: Knee Cartilage Grading Protocol
AUTHORS: molmer , Martin Lotz
[DESCRIPTION]
The attached document shows the Gross Morphological Assessment Sheet we use to score and grade knee cartilage.
[STEPS]
SECTION: Gross Morphological Assessment Sheet
1. Macroscopic scores (1-4) are assigned to cartilage surfaces duri... | ["[Gross Morphological Assessment Sheet] Macroscopic scores (1-4) are assigned to cartilage surfaces during tissue harvesting and recorded on the Gross Morphological Assessment Sheet (See Description). These scores use a modified Outerbridge classification grading system.\n\nScore of 1 = normal, intact surface\nScore o... |
58,050 | Insect Cell Protocol for LRRK1 and LRRK2 Expression | 4 | dx.doi.org/10.17504/protocols.io.rm7vzyyrrlx1/v1 | https://www.protocols.io/view/insect-cell-protocol-for-lrrk1-and-lrrk2-expressio-b4xaqxie | Yu Xuan Lin, Mariusz Matyszewski | TITLE: Insect Cell Protocol for LRRK1 and LRRK2 Expression
AUTHORS: Yu Xuan Lin, Mariusz Matyszewski
[DESCRIPTION]
Protocol for expressing LRRK1 and LRRK2 in insect cells.
As used in Snead, Matyszewski, Dickey et al. 2022.
[STEPS]
SECTION: Starting Insect Cell Culture from frozen stock
1.
Pre‐chill centrifuge to... | ["[Starting Insect Cell Culture from frozen stock] Pre‐chill centrifuge to 4 °C.", "[Starting Insect Cell Culture from frozen stock] Retrieve 1 vials containing 1 mL of ~2x107 SF9 cells from liquid N2 storage.", "[Starting Insect Cell Culture from frozen stock] Thaw vial in hands until ice pellet just disappears, then ... |
89,690 | Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) Acquisition by Data-Independent Acquisition (DIA) on an Orbitrap Eclipse Tribrid Mass Spectrometer | 4 | dx.doi.org/10.17504/protocols.io.36wgq3m15lk5/v1 | https://www.protocols.io/view/liquid-chromatography-tandem-mass-spectrometry-lc-c3t2ynqe | J Bons, J P Rose, M A Watson, B Schilling | TITLE: Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) Acquisition by Data-Independent Acquisition (DIA) on an Orbitrap Eclipse Tribrid Mass Spectrometer
AUTHORS: J Bons, J P Rose, M A Watson, B Schilling
[DESCRIPTION]
Proteolytic peptide measurement using Liquid Chromatography-Tandem Mass Spectrometry (LC-M... | ["Dilute the peptide sample with solvent A (2% ACN, 0.1% FA) to the desired concentration. Transfer the samples to an autosampler vial and add iRT peptides to the sample according to the manufacturer’s instructions.", "Inject the sample onto a Dionex UltiMate 3000 liquid chromatographic system coupled to an Orbitrap Ec... |
102,917 | Immunohistochemistry for brain sections | 0 | dx.doi.org/10.17504/protocols.io.3byl4956jgo5/v1 | https://www.protocols.io/view/immunohistochemistry-for-brain-sections-dgrd3v26 | Santiago Unda, Roberta Marongiu, Michael G. Kaplitt | TITLE: Immunohistochemistry for brain sections
AUTHORS: Santiago Unda, Roberta Marongiu, Michael G. Kaplitt
[DESCRIPTION]
Protocol for processing 30um mouse brain sections for immunolabeling.
[STEPS]
SECTION: Tissue Preparation
1. Sections at cryostat:
Thickness 30 µm
Sections picked up with a wet brush (not too wet)... | ["[Tissue Preparation] Sections at cryostat:\nThickness 30 µm\nSections picked up with a wet brush (not too wet) and moved to the TBS-T wells (usually serial sections). Store section in anti-freeze solution in -20 °C if not immediately staining.", "[Day 1: Primary Antibody Incubation] Washes: 3-step wash, 10 min each, ... |
73,881 | Synthesis of double-strand cDNA (ds-cDNA) from viral dsRNA by using Random primers | 4 | dx.doi.org/10.17504/protocols.io.81wgbyrxnvpk/v1 | https://www.protocols.io/view/synthesis-of-double-strand-cdna-ds-cdna-from-viral-ckdzus76 | Vahid Jalali Javaran | TITLE: Synthesis of double-strand cDNA (ds-cDNA) from viral dsRNA by using Random primers
AUTHORS: Vahid Jalali Javaran
[DESCRIPTION]
Double-stranded cDNA synthesis from viral dsRNAs:
For dsRNA sequencing by nanopore sequencing, this protocol was used. Before treating samples with RNase T1, you should measure the tota... | ["[Synthesis of the first strand of cDNA] Mix well below components by pipetting and centrifuge or spin briefly. \nTreated dsRNA5 µlRandom primers (60 µM)2µldNTP (10 mM)1 µlH2O 6 µlTotal14 µl", "[RNase T1 and DNase I digestion] Add 10X DNase Buffer with MgCl2 (final concentration should be 1X). \nAdd 50 units RNase T1 ... |
53,449 | Nuclear RNA purification | 4 | null | https://www.protocols.io/view/nuclear-rna-purification-byfhptj6 | Michael Tellier | TITLE: Nuclear RNA purification
AUTHORS: Michael Tellier
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for purifying nuclear RNA for qRT-PCR or next generation sequencing analysis.</div></div>
[STEPS]
?. [Day 1]
?. [Day 2]
RNA extractionWash the cells twice with ice-cold PBS.Scrap the ce... | ["[Day 1]", "[Day 2]\nRNA extractionWash the cells twice with ice-cold PBS.Scrap the cells in 1.2 ml of ice-cold PBS.Centrifuge at 1,000 rpm for 5 minutes at 4°C.Resuspend the pellet with slow pipetting in 1 ml of Lysis Buffer B (10 mM Tris-HCl pH 8, 140 mM NaCl, 1.5 mM MgCl2, 0.5 % NP-40).Centrifuge at 1,000 g for 3 m... |
60,813 | Human Pregnant Fallopian Tube Tissue Collection and Preservation Methods - UCSD Female Reproductive TMC | 1 | dx.doi.org/10.17504/protocols.io.dm6gpbd5plzp/v1 | https://www.protocols.io/view/human-pregnant-fallopian-tube-tissue-collection-an-b7mmrk46 | Valentina Stanley, Scott Lindsay-Hewett, Mana Parast, Louise Laurent | TITLE: Human Pregnant Fallopian Tube Tissue Collection and Preservation Methods - UCSD Female Reproductive TMC
AUTHORS: Valentina Stanley, Scott Lindsay-Hewett, Mana Parast, Louise Laurent
[DESCRIPTION]
Human pregnant fallopian tube tissue collection and storage protocol for HuBMAP's UCSD Female Reproductive TMC... | ["[Preparation] Fallopian tubes should be collected into empty sterile cups right after sterilization (salpingectomy or tubal ligation). Keep left and right tubes separate.", "[Preparation] Take a photo of the tubes prior to sampling. If pieces of the tissue were collected for clinical pathological examination, maintai... |
94,908 | Procedure for EEG surgery | 4 | null | https://www.protocols.io/view/procedure-for-eeg-surgery-c8w4zxgw | daniel.dautan, Per Svenningsson | TITLE: Procedure for EEG surgery
AUTHORS: daniel.dautan, Per Svenningsson
[DESCRIPTION]
Standard Operating Procedure for EEG surgery
[STEPS]
SECTION: Preparation of EEG transponder (DSI)
1. The transponder has four wires, two of which will be used for EEG (by convention the orange and the orange-white wires). Cut off... | ["[Preparation of EEG transponder (DSI)] The transponder has four wires, two of which will be used for EEG (by convention the orange and the orange-white wires). Cut off a few millimeters of the plastic coating on the end of the wires and solder a M4-threaded screw (agntho’s MCS1X2) onto the exposed metal wire.", "[Sub... |
70,901 | S2_Capture ELISA to detect for IgM antibodies against 2019-nCoV protein | 1 | dx.doi.org/10.17504/protocols.io.j8nlkw4ewl5r/v1 | https://www.protocols.io/view/s2-capture-elisa-to-detect-for-igm-antibodies-agai-chgvt3w6 | jeabchanida Ruchisrisarod | TITLE: S2_Capture ELISA to detect for IgM antibodies against 2019-nCoV protein
AUTHORS: jeabchanida Ruchisrisarod
[DESCRIPTION]
ABSTRACT
Antibody assays of IgM, IgG and surrogate isotype independent virus neutralizing antibody (sVNT) targeting receptor binding domain of Severe Acute Respiratory Syndrome Coronavirus 2... | ["Coat the 96 well plate with 10ug/ml of goat anti-human IgM antibody diluted in bicarbonate buffer (for 1 full plate, add 50ul of antibody to 5ml of coating buffer) at 50ul/well in 4oC overnight.", "The next day, remove the coating solution as biohazard waste. Wash the plate 5x by filling each well with 150ul of PBST ... |
30,796 | GWAS Fecal Collection and DNA Extraction for Downstream Sequencing Applications | 1 | null | https://www.protocols.io/view/gwas-fecal-collection-and-dna-extraction-for-downs-babkiakw | Sierra Simpson, Olivier George | TITLE: GWAS Fecal Collection and DNA Extraction for Downstream Sequencing Applications
AUTHORS: Sierra Simpson, Olivier George
[STEPS]
?. [Feces Collection]
Collect fresh feces – this must be directly from the animal. Dried feces from the night before, or in the cage will not yield good DNA for sequencing.Make sure th... | ["[Feces Collection]\nCollect fresh feces – this must be directly from the animal. Dried feces from the night before, or in the cage will not yield good DNA for sequencing.Make sure the tube is labeled with an \"A\" for BSL, a \"B\" for Post-ShA, \"C\" for Post-LgA", "[Feces Collection]\nPlace the fresh feces into a ma... |
71,005 | High-throughput DNA barcoding library construction and sequencing protocol for BIOSCAN using unpurified non-destructively extracted DNA from arthropods | 1 | dx.doi.org/10.17504/protocols.io.8epv5jzxdl1b/v1 | https://www.protocols.io/view/high-throughput-dna-barcoding-library-construction-chj5t4q6 | Naomi Park, Emma Betteridge, Scott Thurston, Abdulrahman Tuameh, Marco Mosca, Lyndall Pereira da Conceicoa, Ian Johnston, Mara Lawniczak | TITLE: High-throughput DNA barcoding library construction and sequencing protocol for BIOSCAN using unpurified non-destructively extracted DNA from arthropods
AUTHORS: Naomi Park, Emma Betteridge, Scott Thurston, Abdulrahman Tuameh, Marco Mosca, Lyndall Pereira da Conceicoa, Ian Johnston, Mara Lawniczak
[DESCRIPTION... | ["[COI amplification (PCR1)] Prepare the following COI PCR master mix and mix thoroughly by vortexing on full power. Keep on ice whilst preparing for subsequent steps.\n \n \n PCR Primer Pool 1 Master Mix Vol/PCR RXN (µl) Vol/96 plate (µl) inc. excess Q5 Hotstart 2X Master Mix 12.5 14... |
97,458 | LifeWatch Belgium: FlowCam sampling and lab protocol for imaging microphytoplankton in the Belgian part of the North Sea. | 0 | dx.doi.org/10.17504/protocols.io.6qpvr8e6zlmk/v1 | https://www.protocols.io/view/lifewatch-belgium-flowcam-sampling-and-lab-protoco-dbes2jee | Rune Lagaisse | TITLE: LifeWatch Belgium: FlowCam sampling and lab protocol for imaging microphytoplankton in the Belgian part of the North Sea.
AUTHORS: Rune Lagaisse
[DESCRIPTION]
In the framework of the Belgian Lifewatch RI, a number of fixed stations in the Belgian Part of the North Sea (BPNS) are visited during mulitdisciplinary... | ["[Sample collection] 9 onshore stations are visited on a monthly frequency and 8 offshore stations are visited on a seasonal frequency during the LifeWatch muldisisciplinary campaigns in the Belgian part of the Nort Sea.", "[Presample run] For each sample we perform a small presample run to determine particle load and... |
34,853 | Effects of Whole-Body Vibrations on Neuromuscular Fatigue | 1 | dx.doi.org/10.17504/protocols.io.beadjaa6 | https://www.protocols.io/view/effects-of-whole-body-vibrations-on-neuromuscular-beadjaa6 | Milos Kalc, Ramona Ritzmann, Vojko Strojnik | TITLE: Effects of Whole-Body Vibrations on Neuromuscular Fatigue
AUTHORS: Milos Kalc, Ramona Ritzmann, Vojko Strojnik
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Purpose: </span><span>The aim of the study was to investigate the origin and magnitude of neuromuscu... | ["[Warm-up]\nwarm-up routine consisting of bench stepping ( high) at a frequency of , with a leg exchange each minute\n20\n0.5 Hz", "[Warm-up]\nrest", "[Equipment calibration]\nWe calibrated the prior to each measuring session.The signal of the dynamometer was connected torunning The same machine has been used in seve... |
69,436 | Paramecium bursaria immunofluorescence protocol | 4 | dx.doi.org/10.17504/protocols.io.yxmvm2ozng3p/v1 | https://www.protocols.io/view/paramecium-bursaria-immunofluorescence-protocol-cf24tqgw | David S Milner, Estelle Kilias, Thomas A. Richards | TITLE: Paramecium bursaria immunofluorescence protocol
AUTHORS: David S Milner, Estelle Kilias, Thomas A. Richards
[DESCRIPTION]
This protocol has been developed for immunofluorescent localisation of host proteins in Paramecium bursaria 186b.
[BEFORE_START]
Prepare 200 mL of PBS
[STEPS]
SECTION: Fixation
1. Ta... | ["[Fixation] Take 6 mL of P. bursaria culture per treatment. Centrifuge 800 x g, 10 min and remove 5 mL (i.e. concentrate sample 6-fold). Aliquot 1 mL of concentrated culture into a 1.5 mL micro-centrifuge tube per treatment for downstream steps.", "[Fixation] Centrifuge 800 x g, 10 min to pellet the cells. Remove supe... |
22,574 | Electroporation of Euplotes crassus: conditions that allow for the uptake of DAPI. | null | dx.doi.org/10.17504/protocols.io.2angade | null | Lawrence A. Klobutcher, Larry Klobutcher | TITLE: Electroporation of Euplotes crassus: conditions that allow for the uptake of DAPI.
AUTHORS: Lawrence A. Klobutcher, Larry Klobutcher
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The electroporation procedure and conditions described allow for the entry of DAPI into the cell, resultin... | ["Collect and concentrate cells down to ~40 ml by pouring the culture through a 20 um Nitex membrane.Photo of 20um Nitex membrane and a frame constructed by cutting out the top and bottom of a Tupperware container.", "Transfer the concentrated Euplotes cells to a 50 ml screw cap centrifuge tube and pellet cells by cent... |
92,204 | Cas9 enrichment for DiMeLo-sequencing | 4 | dx.doi.org/10.17504/protocols.io.5jyl8p8n7g2w/v1 | https://www.protocols.io/view/cas9-enrichment-for-dimelo-sequencing-c6akzacw | Pragya Sidhwani, Aaron Straight | TITLE: Cas9 enrichment for DiMeLo-sequencing
AUTHORS: Pragya Sidhwani, Aaron Straight
[DESCRIPTION]
This protocol builds upon two previously published protocols: this DiMeLo-seq protocol to map protein-DNA interactions at a single molecule level using long-read sequencing and this Cas9 enrichment protocol for Nanopore... | ["[Isolating pA-Hia5-treated DNA from human K562 cells] Extract DNA that has been methylated in situ by pA-Hia5 at sites of protein-DNA interactions", "[Cas9-based enrichment of pA-Hia5 methylated DNA] Dephosphorylate DNA isolated in step 3", "[Introduction] This protocol builds upon two previously published protocols:... |
29,531 | Purification of the NLRP1-DPP9 Complex from Expi293F Cells | 1 | dx.doi.org/10.17504/protocols.io.833hyqn | https://www.protocols.io/view/purification-of-the-nlrp1-dpp9-complex-from-expi29-833hyqn | Louis Hollingsworth | TITLE: Purification of the NLRP1-DPP9 Complex from Expi293F Cells
AUTHORS: Louis Hollingsworth
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol associated with "DPP9 sequesters the NLRP1 C-terminus to repress inflammasome activation" by Hollingsworth*, Sharif*, Griswold* et al., Bachovchin, ... | ["[Protein Expression]\nGrow Expi293F cells (ThermoFisher, A14527) in Expi293™ Expression Medium (ThermoFisher, A1435101) to 2-3 million cells/mL at the desired culture volume, such as 1L. Choose the appropriate flask for the desired volume of cell culture to ensure appropriate gas exchange--I use a 2L Fernbach flask f... |
75,635 | Illunina library preparation and dual hybridization protocol of ERC GLOBAL | 4 | dx.doi.org/10.17504/protocols.io.n92ldp787l5b/v1 | https://www.protocols.io/view/illunina-library-preparation-and-dual-hybridizatio-cm4tu8wn | Vincent R C Soulé, Cedric Mariac, Thomas LP Couvreur | TITLE: Illunina library preparation and dual hybridization protocol of ERC GLOBAL
AUTHORS: Vincent R C Soulé, Cedric Mariac, Thomas LP Couvreur
[DESCRIPTION]
Step by step protocol for library preparation of Annonaceae species within the ERC GLOBAL project. This protocol was followed for all libraries prepared within ... | ["[Part 1: library preparation , DNA preparation and shearing] Depending on concentration of each sample, dilute the DNA in 0.2 mL microtubes Diagenode suitable for shearing with ultrasound. Target amount of DNA should, if possible, be 3-4 µg in 50 µL (to be supplemented with water). The number of shearing cycles and ... |
55,655 | Static Incubation of Pancreatic Islets | 4 | dx.doi.org/10.17504/protocols.io.b2kfqctn | https://www.protocols.io/view/static-incubation-of-pancreatic-islets-b2kfqctn | Islet and Pancreas Analysis Core | TITLE: Static Incubation of Pancreatic Islets
AUTHORS: Islet and Pancreas Analysis Core
[DESCRIPTION]
This SOP defines the methods used by the Vanderbilt Diabetes Center Islet and Pancreas Analysis (IPA) Core for static incubation of pancreatic islets isolated from mouse or human tissue. See also our islet isolation ... | ["[Reagent preparation] RPMI with 5.6 mM glucose (cell culture media):\n\nRemove 5 mL from a 500 mL bottle of RPMI, and add 5 mL penicillin/streptomycin. Close bottle and invert to mix.\nAdd 0.505 g glucose to RPMI, invert to mix, and incubate at room temperature for 60 min to allow glucose to go into solution.\nIn a B... |
18,733 | Phylogenetic analyses of Ophiothrix (Echinodermata: Ophiuroidea) | null | dx.doi.org/10.17504/protocols.io.wimfcc6 | null | Renata Alitto, Michela Borges, Letícia Dias de Oliveira, Karin Regina Seger, Luciana Bolsoni Lourenço | TITLE: Phylogenetic analyses of Ophiothrix (Echinodermata: Ophiuroidea)
AUTHORS: Renata Alitto, Michela Borges, Letícia Dias de Oliveira, Karin Regina Seger, Luciana Bolsoni Lourenço
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Using 16S and COI fragmens in Bayesian Inference, Maximum Parsimony, ... | ["[Align Sequences]\nAll 16S and COI sequences were aligned with the MUSCLE algorithm, providing a unified matrix. All the sequences from Ophiothrix angulata (16S) and additional sequences from others Ophiotrichidae (16S, COI) available on GenBank were added to the matrix for comparison. Amphipholis squamata (Amphiurid... |
94,762 | Adolf & Du et al., 2024 | 2 | dx.doi.org/10.17504/protocols.io.e6nvwdrozlmk/v1 | https://www.protocols.io/view/adolf-amp-du-et-al-2024-c8sizwce | Frank Adolf | TITLE: Adolf & Du et al., 2024
AUTHORS: Frank Adolf
[DESCRIPTION]
These protocols details methods for cloning, expression, purification and structural determination by transmission electron cryo-microscopy of 20S CPs and assembly intermediates.
[GUIDELINES]
Please familiarise yourself with the laboratory safety ... | [] |
40,873 | Detection of total and faecal coliforms in the oysters | 4 | dx.doi.org/10.17504/protocols.io.bj6hkrb6 | https://www.protocols.io/view/detection-of-total-and-faecal-coliforms-in-the-oys-bj6hkrb6 | Sade Aisha Folashade John, Patrick E. Akpaka, Chandrashekhar Unakal, Arvind Kurhade, Angel Justiz-Vaillant | TITLE: Detection of total and faecal coliforms in the oysters
AUTHORS: Sade Aisha Folashade John, Patrick E. Akpaka, Chandrashekhar Unakal, Arvind Kurhade, Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Enterobacteriaceae the leading cause of gastroenteritis. These gram- negat... | ["The meat (10 oysters per cup) of the unprepared oysters was blended with 25ml of sterile distilled water and 25ml of sterile peptone water using a sterilized blender (the blender was washed with antibacterial soap as well as bleach and rinsed with sterile distilled water along with 70% ethanol before autoclaving prio... |
40,964 | Western Blot Detection using Licor NIR Fluorescence - CHEM 584 | 4 | dx.doi.org/10.17504/protocols.io.bj9ckr2w | https://www.protocols.io/view/western-blot-detection-using-licor-nir-fluorescenc-bj9ckr2w | Ken Christensen | TITLE: Western Blot Detection using Licor NIR Fluorescence - CHEM 584
AUTHORS: Ken Christensen
[STEPS]
?. [After the transfer, complete the following steps]
Wet in 1x PBS or TBS for , or until fully hydrated (using the appropriate buffer system).
?. [After the transfer, complete the following steps]
Place membrane in... | ["[After the transfer, complete the following steps]\nWet in 1x PBS or TBS for , or until fully hydrated (using the appropriate buffer system).", "[After the transfer, complete the following steps]\nPlace membrane in incubation box and block the membrane in 5% milk (PBS or TBS +0.2% v/v Tween® 20) for with gentle shak... |
null | null | null | dx.doi.org/10.17504/protocols.io.iy9cfz6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?. | [] |
27,718 | MojoSort™ Isolation Kits Column Protocol - 3 | null | dx.doi.org/10.17504/protocols.io.7behije | null | Sam Li | TITLE: MojoSort™ Isolation Kits Column Protocol - 3
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>BioLegend MojoSort™ nanobeads work in commonly used separation columns, based on our internal research as well as validation by external testing by academic labs. This simple pro... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes. Kits for human samples have been optimized for PBMCs, please prepare the cells using a suitable method.", "In the final wash of your sample preparation, resuspend the cells in MojoSort™ Buffer by adding up to 4 mL in a 5 mL (12 x 75 mm) ... |
51,062 | The efficacy of telemedicine using videoconferencing system in outpatient care for cancer patients: a systematic review and meta-analysis protocol | 1 | dx.doi.org/10.17504/protocols.io.bv4wn8xe | https://www.protocols.io/view/the-efficacy-of-telemedicine-using-videoconferenci-bv4wn8xe | Yasuaki Uemoto, Taro Yamanaka, Yuki Kataoka, Yoshitaka Wada, Yosuke Aoyama, Rika Kizawa, Yu Yamaguchi, Yuichiro Kikawa, Naruto Taira | TITLE: The efficacy of telemedicine using videoconferencing system in outpatient care for cancer patients: a systematic review and meta-analysis protocol
AUTHORS: Yasuaki Uemoto, Taro Yamanaka, Yuki Kataoka, Yoshitaka Wada, Yosuke Aoyama, Rika Kizawa, Yu Yamaguchi, Yuichiro Kikawa, Naruto Taira
[DESCRIPTION]
<div cla... | [] |
40,797 | ELISA for quantification of IL-32 in human serum. | 6 | dx.doi.org/10.17504/protocols.io.bj35kqq6 | https://www.protocols.io/view/elisa-for-quantification-of-il-32-in-human-serum-bj35kqq6 | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-32 in human serum.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells.... | ["An anti-human IL-32 coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.", "Add 50 µl of human serum. Human IL-32 present in the serum sample binds to antibodies adsorbed into the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and... |
20,081 | Mammalian Calling Cards Quick Start Guide | null | dx.doi.org/10.17504/protocols.io.xurfnv6 | null | Arnav Moudgil, Michael N. Wilkinson, Xuhua Chen, Robi D. Mitra | TITLE: Mammalian Calling Cards Quick Start Guide
AUTHORS: Arnav Moudgil, Michael N. Wilkinson, Xuhua Chen, Robi D. Mitra
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify"><span>Transposon calling cards can identify transcription factor (TF) binding s... | ["[Cloning and Sequence Validation of YFTF-HyPBase Fusions]\nMake C- and N- terminal fusions of your favorite transcription factor (YFTF) with HyPBase. It is important to include a linker sequence between these genes. We strongly recommend the following amino acid linker sequence: KLGGGAPAVGGGPKAADK. We have tested man... |
43,115 | 2 Methods for DNA Adsorption on a Mica Substrate for AFM Imaging in Fluid | 1 | dx.doi.org/10.17504/protocols.io.bncjmaun | https://www.protocols.io/view/2-methods-for-dna-adsorption-on-a-mica-substrate-f-bncjmaun | Philip J. Haynes, Kavit H. S. Main, Alice Pyne | TITLE: 2 Methods for DNA Adsorption on a Mica Substrate for AFM Imaging in Fluid
AUTHORS: Philip J. Haynes, Kavit H. S. Main, Alice Pyne
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is part 2 of the "Atomic Force Microscopy of DNA and DNA-Protein Interactions" collection of protocols.</div><... | ["The three Methods for DNA Adsorption on a Mica Substrate for AFM Imaging in Fluid are outlined below:", "[2.1 DNA Adsorption Using Divalent Cations]\nDivalent cations (in this case Ni2+) can be used to overcome the electrostatic repulsion between DNA and mica, thus facilitating DNA adhesion to the mica, which can als... |
72,732 | Botanical Microfossil Extraction from Paleontological Sediments - 'Bot-MEPS' Protocol | 1 | dx.doi.org/10.17504/protocols.io.bp2l69kz5lqe/v2 | https://www.protocols.io/view/botanical-microfossil-extraction-from-paleontologi-ci94uh8w | Megan C. O'Toole, Yoel E. Stuart, Jacopo Niccolo Cerasoni | TITLE: Botanical Microfossil Extraction from Paleontological Sediments - 'Bot-MEPS' Protocol
AUTHORS: Megan C. O'Toole, Yoel E. Stuart, Jacopo Niccolo Cerasoni
[DESCRIPTION]
Palaeobotanical microfossil analyses are often used to reconstruct palaeoecological histories and past environmental change. To do so, ma... | ["[Sediment Preparation] Place the bag into a mortar and use a pestle to crush the samples (as finely as possible).", "[Sediment Preparation] Pour the ground powder through a funnel into sealable falcon test tubes for storage.", "[Sediment Preparation] Transfer sample to a centrifuge tube, filling to 1/3 of the height ... |
84,047 | Immunocytochemistry of primary neurons | 1 | dx.doi.org/10.17504/protocols.io.eq2lyjdkmlx9/v1 | https://www.protocols.click/view/immunocytochemistry-of-primary-neurons-cwbpxamn | giulia.tombesi | TITLE: Immunocytochemistry of primary neurons
AUTHORS: giulia.tombesi
[DESCRIPTION]
This protocol describes the steps to obtain a great staining of primary neurons.
[STEPS]
SECTION: Cells Fixation
1. Wash cells with PBS1X/HBSS
2. Fix cells with paraformaldehyde (PFA) 4% for 30 min at room temperature
SECTION: Cel... | ["[Cells Fixation] Wash cells with PBS1X/HBSS", "Fix cells with paraformaldehyde (PFA) 4% for 30 min at room temperature", "[Cells permeabilization and saturation] Permeabilize cells with 0.3% Triton X-100 (in PBS1X) for 5 min at room temperature", "[Cells permeabilization and saturation] Wash cells with PBS1X for 5 m... |
88,975 | Golden Gate Assembly | 4 | dx.doi.org/10.17504/protocols.io.kqdg3xknqg25/v2 | https://www.protocols.io/view/golden-gate-assembly-c25pyg5n | NUS iGEM | TITLE: Golden Gate Assembly
AUTHORS: NUS iGEM
[DESCRIPTION]
2023 NUS-Singapore iGEM team followed this protocol to assemble DNA oligos containing Golden Gate restriction sites with a plasmid backbone that contains the same restriction sites. The restriction enzymes utilised in this protocol are the Type IIS restrictio... | ["[Golden Gate Assembly] Add the following reagents into a PCR tube:", "[Golden Gate Assembly] Prepare an ice box.", "[Golden Gate Assembly] Put the sample into the Thermal Cycler and run it with the following conditions: \n\n*Set \"Lid Temperature\" to 105 °C and set \"Volume\" to 20 µL", "[Golden Gate Assembly] Place... |
40,307 | nCoV-2019 McGill Nanopore LibPrep Protocol, 10 ng NB | 1 | dx.doi.org/10.17504/protocols.io.bjktkkwn | https://www.protocols.io/view/ncov-2019-mcgill-nanopore-libprep-protocol-10-ng-n-bjktkkwn | Sarah Reiling, Anne-Marie Roy, Shu-Huang Chen, Ioannis Ragoussis | TITLE: nCoV-2019 McGill Nanopore LibPrep Protocol, 10 ng NB
AUTHORS: Sarah Reiling, Anne-Marie Roy, Shu-Huang Chen, Ioannis Ragoussis
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol works for 12 native barcodes, 24 native barcodes, and 96 native barcodes.</div></div>
[STEPS]
?. [Nativ... | ["[Native barcoding]\nBarcode the amplicon pools using native barcodes.\nThis is a ‘one-pot ligation’ protocol for native barcoded ligation libraries. We have seen no reduction in performance compared to standard libraries, and is made faster by using the Ultra II® ligation module which is compatible with the Ultra II®... |
27,247 | First steps using a jupyter notebook | null | dx.doi.org/10.17504/protocols.io.6uphevn | null | Alise J. Ponsero | TITLE: First steps using a jupyter notebook
AUTHORS: Alise J. Ponsero
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Install and start using awesome jupyter ! </div></div>
[STEPS]
?. [Install Anaconda]
Open your favorite web browser and go to https://www.anaconda.com/distribution/Select the distri... | ["[Install Anaconda]\nOpen your favorite web browser and go to https://www.anaconda.com/distribution/Select the distribution that fits your personal computer (Linux, Windows or MacOS)", "[Install Anaconda]\nFor Windows users :Download the executable file and open it. This should start the installation wizard. Follow th... |
83,665 | General Media Recipes: WA, PDA, LB, CMA, V8 | 4 | null | https://www.protocols.click/view/general-media-recipes-wa-pda-lb-cma-v8-cvxrw7m6 | rebecca.bennett, Nimalka M Weerasuriya | TITLE: General Media Recipes: WA, PDA, LB, CMA, V8
AUTHORS: rebecca.bennett, Nimalka M Weerasuriya
[DESCRIPTION]
These are current general media recipes for (acidified) water agar, (acidified) potato dextrose agar, LB broth, cornmeal agar, P5ARP/P10ARP, and clarified V8 juice agar.
[BEFORE_START]
Prepare the followi... | ["[Making Media] Select media types from below:", "[Preparation] Autoclave liquid setting for 20 minutes to sterilize.", "[Preparation] Add stir bar and stir contents well. \nPlace a loose orange cap. Label cap with autoclave tape (1.5% WA) and date.", "[Preparation] Water Agar preparation:\n \n500 mL ~ 1.5 sleeves of ... |
83,456 | 2-step PCR mixture and conditions (Barcoded-head primers for seqs pooling) | 4 | dx.doi.org/10.17504/protocols.io.kxygx3k6wg8j/v1 | https://www.protocols.click/view/2-step-pcr-mixture-and-conditions-barcoded-head-pr-cvq8w5zw | Yin-Tse Huang, Tsu-Chun Hung | TITLE: 2-step PCR mixture and conditions (Barcoded-head primers for seqs pooling)
AUTHORS: Yin-Tse Huang, Tsu-Chun Hung
[DESCRIPTION]
PCR mixture and condition (2X SUPERGREEN PCR MASTER MIX)
[STEPS]
1. Wear glove, clean up the working bench w. 1% bleach
SECTION: For 1' PCR head-primers
2. Prepare 1' PCR master m... | ["Wear glove, clean up the working bench w. 1% bleach", "[For 1' PCR head-primers] Prepare 1' PCR master mixutre for head-primers (prepare 1.2X of solutions for pipetting error if needed)\n \nPCR mixture for head-primers for each reaction", "[For 1' PCR head-primers] Mix the 1' PCR master mixture gently by pi... |
78,802 | Skin Biopsy Protocol (Mammals): Non-lethal Sampling | 1 | dx.doi.org/10.17504/protocols.io.n2bvj64nxlk5/v4 | https://www.protocols.io/view/skin-biopsy-protocol-mammals-non-lethal-sampling-cq7svzne | sanaz.arenivas, justin_bohling, comizzolip, mhouck, Rachel A Johnston, Jacquelyn Mountcastle, Budhan Pukazhenthi, phil.purdy, brian_small, seth_willey | TITLE: Skin Biopsy Protocol (Mammals): Non-lethal Sampling
AUTHORS: sanaz.arenivas, justin_bohling, comizzolip, mhouck, Rachel A Johnston, Jacquelyn Mountcastle, Budhan Pukazhenthi, phil.purdy, brian_small, seth_willey
[DESCRIPTION]
Version date: April 2023
The following protocol illustrates how to collect and ship l... | ["[Preparation] Pre-chill icepacks in the freezer the day before planning to collect and ship samples.", "[Preparation] Record all information indicated in the biopsy form, including a picture of the animal for identification and GPS location where the animal was found.", "[Preparation] For general sedation, anesthetiz... |
20,680 | Supplement Figure S3 | null | dx.doi.org/10.17504/protocols.io.yfgftjw | null | Lijun Zhang | TITLE: Supplement Figure S3
AUTHORS: Lijun Zhang
[DESCRIPTION]
<div class = "text-blocks"><div style = "text-align :; float : ;"><img style = "" src = "https://s3.amazonaws.com/pr-journal/bdkfa.png" /></div></div>
[STEPS] | [] |
38,569 | Pseudomonas syringae seed infections | 4 | dx.doi.org/10.17504/protocols.io.bhwhj7b6 | https://www.protocols.io/view/pseudomonas-syringae-seed-infections-bhwhj7b6 | William Rooney, Janet Laird (University of Glasgow), Mechna Chowdhury (University of Glasgow), Catriona MacIntosh (University of Glasgow), Xiaoyi Deng (University of Glasgow), Phoebe McBride (University of Glasgow), Joel Milner (University of Glasgow) | TITLE: Pseudomonas syringae seed infections
AUTHORS: William Rooney, Janet Laird (University of Glasgow), Mechna Chowdhury (University of Glasgow), Catriona MacIntosh (University of Glasgow), Xiaoyi Deng (University of Glasgow), Phoebe McBride (University of Glasgow), Joel Milner (University of Glasgow)
[DESCRIPTION]
... | ["[Sterlising seeds]\nTransfer seeds to a sterile tube. For cucumber seeds used in this protocol, a 50 mL conical centrifuge tube will suffice. This protocol can be adapted for bigger and smaller seeds.", "[Sterlising seeds]\nAdd the sterilisation solution (50% bleach (v/v water), 0.002% tween 20) and mix by inversion ... |
32,038 | Preparing bryophyte specimens for DNA extractions for Sanger sequencing | 1 | dx.doi.org/10.17504/protocols.io.bbieikbe | https://www.protocols.io/view/preparing-bryophyte-specimens-for-dna-extractions-bbieikbe | Laura L Forrest, Michelle Hart, David G. Long | TITLE: Preparing bryophyte specimens for DNA extractions for Sanger sequencing
AUTHORS: Laura L Forrest, Michelle Hart, David G. Long
[DESCRIPTION]
This protocol describes part of the pipeline employed at the Royal Botanic Garden, Edinburgh to generate DNA barcode reference libraries for bryophytes using Sanger seque... | ["Plant Material. In contrast to most other land plants, where DNA extractions are usually made from a single individual, bryophyte extractions are frequently from multiple stems or thalli, which can potentially represent several individuals. Thus, single bryophyte DNA extractions can contain DNA from multiple genotype... |
18,597 | Cambridge Fetal Thymus Dissociation | null | dx.doi.org/10.17504/protocols.io.wedfba6 | null | JONGEUN PARK | TITLE: Cambridge Fetal Thymus Dissociation
AUTHORS: JONGEUN PARK
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is protocol for fetal thymus dissociation. (Can be applied to other fetal tissues)</div><div class = "text-block">Can be also adapted to adult thymus or lymphoid organs. (Volume of s... | [] |
80,147 | Cell viability assessment | 1 | dx.doi.org/10.17504/protocols.io.eq2ly7rpelx9/v1 | https://www.protocols.io/view/cell-viability-assessment-cshtwb6n | Qing Wang | TITLE: Cell viability assessment
AUTHORS: Qing Wang
[DESCRIPTION]
This is the protocol for assessing cell viability using a MTS cell proliferation assay kit.
[STEPS]
1. 1. Cells are seeded and differentiated for 4 days; assess cell viability using an MTS cell proliferation assay kit (ab197010, Abcam).
2. 2. Treat the... | ["1. Cells are seeded and differentiated for 4 days; assess cell viability using an MTS cell proliferation assay kit (ab197010, Abcam).", "2. Treat the differentiated cells with synthetic DOPA pheomelanin or synthetic DOPA eumelanin or vehicle PBS to determine the time and dose responses of the cells to the treatment."... |
null | null | null | dx.doi.org/10.17504/protocols.io.kgrctv6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This method is modified from that described by Nakatani Y, Ogryzko V. Immunoaffinity purification of mammalian protein complexes. Methods Enzymol. 2003;370:430-44. Epub 2004/01/10. doi: 10.1016/S0076-6879(03)70037-8 S0076687903700378 [pii]. PubMed PMID: 14712665. It can be us... | [] |
39,353 | Neurolucida 360: Tree Segmentation | 1 | null | https://www.protocols.io/view/neurolucida-360-tree-segmentation-binzkdf6 | Maci Heal | TITLE: Neurolucida 360: Tree Segmentation
AUTHORS: Maci Heal
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">3D neuron reconstruction using Neurolucida 360 software from MBF Bioscience.</div></div>
[STEPS]
?. [Set-up]
Download and install Neurolucida 360 application (RRID:SCR_016788).
?. [Set-up]
L... | ["[Set-up]\nDownload and install Neurolucida 360 application (RRID:SCR_016788).", "[Set-up]\nLaunch the application and set-up SciCrunch connection.", "[Set-up]\nSelect the \"SPARC Vocabulary Services\" icon from the Trace ribbon.", "[Set-up]\nGo to https://scicrunch.org/ and click REGISTER in the top menu. Fill out th... |
92,344 | Isolation of Trophoblast Cells from Placenta | 1 | null | https://www.protocols.io/view/isolation-of-trophoblast-cells-from-placenta-c6eyzbfw | vfarmer | TITLE: Isolation of Trophoblast Cells from Placenta
AUTHORS: vfarmer
[DESCRIPTION]
Protocol to derive trophoblast stem cells from placenta and culture them to form trophoblast organoids
[STEPS]
SECTION: Preparations
1. °C the following items (and preferably have extras on had if needed):
- 2 100mL bottles
- 2 small s... | ["[Preparations] °C the following items (and preferably have extras on had if needed):\n- 2 100mL bottles\n- 2 small stir bars\n- 1 large funnel\n- cheese cloth cut into squares that are large enough to sit in the funnel\n- dissection scissors", "[Preparations] Prepare the following Solutions and place all at 37 °C \n\... |
82,342 | Collecting supernatant from C. elegans culture and lyophilizing supernatant | 4 | dx.doi.org/10.17504/protocols.io.36wgqjxxxvk5/v1 | https://www.protocols.io/view/collecting-supernatant-from-c-elegans-culture-and-cunewvbe | Muhammad Zaka Asif, Man Shah, Yosef Smadi | TITLE: Collecting supernatant from C. elegans culture and lyophilizing supernatant
AUTHORS: Muhammad Zaka Asif, Man Shah, Yosef Smadi
[DESCRIPTION]
This protocol describes day 5 of our workflow to grow worms in liquid culture to induce the production of natural products (in this case, 1-HP derivatives). In this protoc... | ["Remove the flasks from the shaker and estimate their population by aliquoting onto glass slides as before.", "Centrifuge at 525 RCF for 1 minute and collect the supernatant in multiple 2 mL microcentrifuge tubes.", "Save the worm pellet at -80˚C if desired for future studies.", "Centrifuge the microcentrifuge tubes a... |
17,503 | Fuhrman Lab 515F-926R 16S and 18S rRNA Gene Sequencing Protocol | null | dx.doi.org/10.17504/protocols.io.vb7e2rn | null | David Needham, Erin Fichot, Alma Parada, Yi-Chun Yeh, Jed Fuhrman | TITLE: Fuhrman Lab 515F-926R 16S and 18S rRNA Gene Sequencing Protocol
AUTHORS: David Needham, Erin Fichot, Alma Parada, Yi-Chun Yeh, Jed Fuhrman
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [PCR]
Use UV-Crosslinker to treat consumables. Press “Time”, then “10.0” to run for 10 minutesPCR strip tubes (ca... | ["[PCR]\nUse UV-Crosslinker to treat consumables. Press “Time”, then “10.0” to run for 10 minutesPCR strip tubes (cat# )PCR waterAny tubes needed to make a master mix", "[Assess Amplification]\nPreparing gel1.0 g agarose100 mL TAE buffer (or TBE)Swirl to mix agarose and buffer", "[Assess Amplification]\nMicrowave 1 min... |
null | null | null | dx.doi.org/10.17504/protocols.io.e7hbhj6 | null | null | TITLE: No Title
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