id float64 1.55k 110k ⌀ | title stringlengths 1 256 ⌀ | template_id float64 0 6 ⌀ | doi stringlengths 39 49 ⌀ | url stringlengths 40 92 ⌀ | authors stringlengths 1 933 ⌀ | protocol_text stringlengths 34 1.08M | steps_list stringlengths 2 269k |
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null | null | null | dx.doi.org/10.17504/protocols.io.j89crz6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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81,616 | Tissue handling for mice, marmoset, and rhesus macaques injected with AAV | 4 | dx.doi.org/10.17504/protocols.io.5qpvormddv4o/v1 | https://www.protocols.io/view/tissue-handling-for-mice-marmoset-and-rhesus-macaq-ctxqwpmw | Miguel Chuapoco | TITLE: Tissue handling for mice, marmoset, and rhesus macaques injected with AAV
AUTHORS: Miguel Chuapoco
[DESCRIPTION]
This protocol outlines all procedures for handling of tissue of animal subjects treated with AAV.
[STEPS]
SECTION: Marmoset tissue handling (individual AAV characterization)
2. Raise and house marm... | ["[Marmoset tissue handling (individual AAV characterization)] Raise and house marmosets in compliance with your local Institutional Animal Care and Use Committee (IACUC) and ensure that all protocols and procedures have been approved by the appropriate ethical and regulatory committees.", "[Rhesus macaque tissue handl... |
59,236 | Modular generation of cortical, striatal and ventral midbrain progenitor cells | 4 | dx.doi.org/10.17504/protocols.io.b54cq8sw | https://www.protocols.io/view/modular-generation-of-cortical-striatal-and-ventra-b54cq8sw | Carles Calatayud, Esther Muñoz-Pedrazo, Sandra Fernández-Gallego, Patrik Verstreken | TITLE: Modular generation of cortical, striatal and ventral midbrain progenitor cells
AUTHORS: Carles Calatayud, Esther Muñoz-Pedrazo, Sandra Fernández-Gallego, Patrik Verstreken
[DESCRIPTION]
The present protocol describes the modular generation of cortical, striatal, and ventral midbrain human neural progen... | ["[Preparation of the hiPSC for starting the neuralization] Notes before starting:\nWe maintain hPSC in mTESR-Plus or StemFlex medium on Matrigel-coated plates and split the cells as clumps using RELESR or 0.5 mM EDTA. Accutase is used when cells need to be counted such as in the initial step of the protocol. Or for th... |
71,139 | Successes and Challenges | 1 | null | https://www.protocols.io/view/successes-and-challenges-chqbt5sn | Paul Lorenzo A Gaite, Dr Ritchie Mae T Gamot, Prof Lyre Anni E Murao | TITLE: Successes and Challenges
AUTHORS: Paul Lorenzo A Gaite, Dr Ritchie Mae T Gamot, Prof Lyre Anni E Murao
[DESCRIPTION]
This page outlines the successes and challenges encountered by PGC Mindanao during the PHA4GE subgrant.
[STEPS]
2. Successes
One of the major successes of this grant is the assistance the PHA4... | ["Successes\n\nOne of the major successes of this grant is the assistance the PHA4GE group has extended to PGC Mindanao as its sub-grantee. The PHA4GE technical working group was always available for advice and open to answer any queries and address any challenges PGC Mindanao might have had in the duration of the proj... |
15,852 | Purification of Haustoria from Arabidopsis in Response to Infection by E. cichoracearum | 1 | dx.doi.org/10.17504/protocols.io.tqkemuw | https://www.protocols.io/view/purification-of-haustoria-from-arabidopsis-in-resp-tqkemuw | Harley King | TITLE: Purification of Haustoria from Arabidopsis in Response to Infection by E. cichoracearum
AUTHORS: Harley King
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This procedure describes steps for the purification of </span><span style = "font-style:italic;">Arabidopthis thaliana</span><span... | ["[Grind Plants Containing Haustoria]\nWeigh out 5-10g frozen Arabidopsis leaves. Set aside 2-3 leaves for quantifying haustoria with a confocal microscope before purification.Grind leaves in ice-cold 1x PBS buffer pH 7.4 for 1 min in kitchen blender in cold room.Filter grindate through 100um Nylon mesh. Haustoria are... |
36,853 | child 2 protocol | null | dx.doi.org/10.17504/protocols.io.bf8vjrw6 | https://www.protocols.io/view/child-2-protocol-bf8vjrw6 | Mariia Guliakina, masha test | TITLE: child 2 protocol
AUTHORS: Mariia Guliakina, masha test
[STEPS]
?. test
?. test step 2 | ["test", "test step 2"] |
43,722 | Low-Volume Titrations for Ligand Binding Monitored by Circular Dichroism | 1 | dx.doi.org/10.17504/protocols.io.bnximfke | https://www.protocols.io/view/low-volume-titrations-for-ligand-binding-monitored-bnximfke | Rohanah Hussain, Charlotte S. Hughes, Giuliano Siligardi | TITLE: Low-Volume Titrations for Ligand Binding Monitored by Circular Dichroism
AUTHORS: Rohanah Hussain, Charlotte S. Hughes, Giuliano Siligardi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">CD spectroscopy is the essential tool to quickly ascertain in the far-UV region the global conformationa... | ["Measure the concentration of protein solution at A280. Use this value to calculate the dilution factor for the stock solution for the working solution. The concentration of the protein to be used during the experiment is in part determined with respect to the UV absorbance contribution of the ligand at each titration... |
107,208 | Stereotaxic Injection by Nanoject Protocol | 1 | dx.doi.org/10.17504/protocols.io.bp2l6nr7kgqe/v5 | https://www.protocols.io/view/stereotaxic-injection-by-nanoject-protocol-dkxg4xjw | Allen Institute for Brain Science | TITLE: Stereotaxic Injection by Nanoject Protocol
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
This protocol describes the delivery of a neuronal tracer using the Nanoject II. The surgery uses a stereotaxic system to target specific brain coordinates in the mouse.
Note: Research reported in this publicat... | [] |
102,158 | Quality control and assurance for S. Typhi amplicon sequencing | 0 | dx.doi.org/10.17504/protocols.io.6qpvr8k92lmk/v1 | https://www.protocols.io/view/quality-control-and-assurance-for-s-typhi-amplicon-dfzn3p5e | Jaspreet Mahindroo, Catherine Troman, Anton Spadar, Zoe Dyson, Kathryn Holt, Nick Grassly | TITLE: Quality control and assurance for S. Typhi amplicon sequencing
AUTHORS: Jaspreet Mahindroo, Catherine Troman, Anton Spadar, Zoe Dyson, Kathryn Holt, Nick Grassly
[DESCRIPTION]
The following quality control points should be followed alongside the amplicon sequencing protocol for genotyping Salmonella Typhi and ... | [] |
50,826 | Human Kidney, Urinary Tract, and Lung Cell Type Mapping Pipeline for the Human Biomolecular Atlas Program (HuBMAP) | 1 | dx.doi.org/10.17504/protocols.io.bvvin64e | https://www.protocols.io/view/human-kidney-urinary-tract-and-lung-cell-type-mapp-bvvin64e | Blue Lake, Elizabeth Duong, Dinh H. Diep, Xin Sun, Peter K, Jim Hagood, Gloria Pryhuber, Sanjay Jain, Kun Zhang [University Of California | TITLE: Human Kidney, Urinary Tract, and Lung Cell Type Mapping Pipeline for the Human Biomolecular Atlas Program (HuBMAP)
AUTHORS: Blue Lake, Elizabeth Duong, Dinh H. Diep, Xin Sun, Peter K, Jim Hagood, Gloria Pryhuber, Sanjay Jain, Kun Zhang [University Of California
[DESCRIPTION]
<div class = "text-blocks"><div cla... | ["Collection and processing of human tissues.Bladder, Ureter, Kidney: dx.doi.org/10.17504/protocols.io.568g9hwLung airways and parenchyma: dx.doi.org/10.17504/protocols.io.bjuxknxn and dx.doi.org/10.17504/protocols.io.bjtnknme", "Isolation of single nuclei for omic assays.Bladder, Ureter, Kidney: dx.doi.org/10.17504/pr... |
null | null | null | dx.doi.org/10.17504/protocols.io.dxq7mv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This collection presents some of the most widely used methodological approaches for isolation and purification of bacteriophages and cyanophages, the first step in detailed studies of virus–host interactions and viral genetic composition, and discusses the applications and limit... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.cdps5m | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
A set of Stellaris FISH Probes comprises up to 48 singly labeled oligonucleotides designed to selectively bind to targeted transcripts. Stellaris FISH Probes bound to target RNA produce fluorescent signals that permit detection of single RNA molecules as diffraction-limited spot... | [] |
78,210 | Compound Screening and Growth Curves | 1 | dx.doi.org/10.17504/protocols.io.6qpvr4qzzgmk/v1 | https://www.protocols.io/view/compound-screening-and-growth-curves-cqmavu2e | Carlos Goller | TITLE: Compound Screening and Growth Curves
AUTHORS: Carlos Goller
[DESCRIPTION]
Overview
The bacterial genus Delftia was named for the city of Delft in the Netherlands, where the species type was isolated and for the Delft research groups that had a critical role in the early development of bacteriology. Species of D... | ["[Plate Setup and Incubation] Read the procedure listed below. Discuss with your lab partner the key steps to program the liquid handler to successfully complete this task. Pay attention to the reagents, tube format, and equipment we have. Remember the goal: reproducibly testing compounds (with replicates) and includi... |
67,379 | What is the need NTX Nutrition Keto Gummies? | 4 | dx.doi.org/10.17504/protocols.io.q26g74eq3gwz/v1 | https://www.protocols.io/view/what-is-the-need-ntx-nutrition-keto-gummies-cd2ts8en | Vitality Hq Keto Gummies | TITLE: What is the need NTX Nutrition Keto Gummies?
AUTHORS: Vitality Hq Keto Gummies
[DESCRIPTION]
NTX Nutrition Keto Gummies
[STEPS]
1. NTX Nutrition Keto Gummies:-
After that pandemic hit the world, everyone got very lazy. Everyone stays at home and is doing desk jobs. You may even get lazy and as a result, y... | ["NTX Nutrition Keto Gummies:-\n\n\n\n\nAfter that pandemic hit the world, everyone got very lazy. Everyone stays at home and is doing desk jobs. You may even get lazy and as a result, you store fat in different body parts. All these things lead to various other health issues like depression, body pain issues, headache... |
null | null | null | dx.doi.org/10.17504/protocols.io.fmtbk6n | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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95,749 | Systematic review: Use of the Dermatology Life Quality Index (DLQI) in National and Regional Registries and Guidelines | 0 | null | https://www.protocols.io/view/systematic-review-use-of-the-dermatology-life-qual-c9rdz526 | Jeffrey Johns | TITLE: Systematic review: Use of the Dermatology Life Quality Index (DLQI) in National and Regional Registries and Guidelines
AUTHORS: Jeffrey Johns
[DESCRIPTION]
Rationale: Since its publication in 1994, the DLQI has become the most widely used patient measurement instrument in
dermatology to measure the impact of sk... | ["[Header] Review title: Use of the Dermatology Life Quality Index (DLQI) in National and Regional Registries and Guidelines", "[Header] Anticipated or actual start date. 05/12/2023", "[Header] Anticipated completion date. 31/12/2024", "[Header] Stage of review at time of this submission. The review has not yet star... |
69,048 | Optimized protocol for translatome analysis of mouse brain endothelial cells | 4 | dx.doi.org/10.17504/protocols.io.8epv59or6g1b/v2 | https://www.protocols.io/view/optimized-protocol-for-translatome-analysis-of-mou-cfnytmfw | Won-Jong OH, Namsuk Kim, Mi-Hee Jun, Jin-Young Jeong | TITLE: Optimized protocol for translatome analysis of mouse brain endothelial cells
AUTHORS: Won-Jong OH, Namsuk Kim, Mi-Hee Jun, Jin-Young Jeong
[DESCRIPTION]
Brain endothelial cells (BECs) are important conduits that deliver oxygen and nutrients, protect parenchyma cells from toxins, and drain wastes to maintain br... | ["[Vessel isolation] The whole mouse cortex of a Tie2-Cre; Rpl22HA/HA mouse is isolated in the chilled DMEM. Then, tissues are dissociated by using a glass homogenizer (WHEATON, 357542) in 10 mL of chilled DMEM.", "[Vessel isolation] 1000 x g, 10 min, 4 °C", "[Vessel isolation] After discarding the supernatants, the pe... |
29,546 | Purification of DPP8/9 from Sf9 Cells for structural and biochemical studies | 1 | dx.doi.org/10.17504/protocols.io.84ihyue | https://www.protocols.io/view/purification-of-dpp8-9-from-sf9-cells-for-structur-84ihyue | Louis Hollingsworth | TITLE: Purification of DPP8/9 from Sf9 Cells for structural and biochemical studies
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... | ["[Bacmid production]\nObtain pFastBac HTB plasmids encoding DPP of interest (DPP9 short or long isoform, WT or catalytically-inactive) from Addgene (https://www.addgene.org/Hao_Wu/). DPP8 (cDNA also on Addgene) can be subcloned into this same vector, or the insect expression construct can be obtained from Drs. Breyan ... |
79,919 | Open, non-comparative, clinical investigation to evaluate the performance and safety of the medical device H42 (collagen paste for filling) in repairing periodontal pockets due to periodontitis.protocol | 1 | dx.doi.org/10.17504/protocols.io.4r3l27rzxg1y/v1 | https://www.protocols.io/view/open-non-comparative-clinical-investigation-to-eva-csapwadn | franco.barattini | TITLE: Open, non-comparative, clinical investigation to evaluate the performance and safety of the medical device H42 (collagen paste for filling) in repairing periodontal pockets due to periodontitis.protocol
AUTHORS: franco.barattini
[DESCRIPTION]
Research protocol to evaluate safety and overall performance of a co... | ["[Tested Product] H42 a collagen paste for filling manufactured by Bioteck.", "Open, non-comparative, clinical investigation to evaluate the performance and safety of the medical device H42 (collagen paste for filling) in repairing periodontal pockets due to periodontitis.", "[Duration for each patient] Twelve (12) we... |
96,708 | Applying Spinal Cord Organoids as a quantitative approach to study the mammalian Hedgehog Signaling | 0 | dx.doi.org/10.17504/protocols.io.kxygx3r6og8j/v1 | https://www.protocols.io/view/applying-spinal-cord-organoids-as-a-quantitative-a-dapc2diw | Markus Holzner, Anton Wutz, Giulio Di Minin | TITLE: Applying Spinal Cord Organoids as a quantitative approach to study the mammalian Hedgehog Signaling
AUTHORS: Markus Holzner, Anton Wutz, Giulio Di Minin
[DESCRIPTION]
The Hedgehog (HH) pathway is crucial for embryonic development, and adult homeostasis. Its dysregulation is implicated in multiple diseases. Exis... | ["[mESC maintenance] Note: the procedure describes the necessary amounts for the expansion of mouse ESCs in a 3 cm dish. This dimension will provide enough cells to derive SCOs. Volumes can, however, easily be adapted according to the user’s needs.\n \n Pre-coat the necessary number of wells of a 3 cm dish with 1 mL of... |
104,714 | Isolation and Transfection of Nicotiana benthamiana Mesophyll Protoplasts for Fluorescent Protein Visualization | 0 | null | https://www.protocols.io/view/isolation-and-transfection-of-nicotiana-benthamian-dihi4b4e | Namitha Nayak, Sandhya Mehrotra, Rajesh Mehrotra | TITLE: Isolation and Transfection of Nicotiana benthamiana Mesophyll Protoplasts for Fluorescent Protein Visualization
AUTHORS: Namitha Nayak, Sandhya Mehrotra, Rajesh Mehrotra
[DESCRIPTION]
Protoplast transfection is routinely used to study the sub-cellular localization of fluorescent-tagged proteins. Using N. bentha... | [] |
78,464 | Quantification of synapse polarization ("the conjugate assay") | 4 | dx.doi.org/10.17504/protocols.io.5qpvordr9v4o/v1 | https://www.protocols.click/view/quantification-of-synapse-polarization-34-the-conj-cqu8vwzw | Philippa R Kennedy | TITLE: Quantification of synapse polarization ("the conjugate assay")
AUTHORS: Philippa R Kennedy
[DESCRIPTION]
NK cells form structured interfaces with tumor cells, known as immune synapses. The forces and receptor-ligand interactions at the immune synapse determine whether the NK cell kills the tumor cell or... | ["[Prepare coverglass for adherent cells] Optional: Coat coverglass with fibronectin (10μg/mL in PBS, Sigma-Aldrich, Cat. F1141) to allow tumor cells to spread across the coverglass and NK cells to migrate across the surface.\n\nOptions for coating\n30 min at 37°C\n45 min at room temperature\novernight at 4°C", "[Prepa... |
22,928 | Studying Root System Architecture changes in tomato (S.lycopersicum and S.pimpinellifolium) in response to stress | null | dx.doi.org/10.17504/protocols.io.2mqgc5w | null | Magdalena Julkowska | TITLE: Studying Root System Architecture changes in tomato (S.lycopersicum and S.pimpinellifolium) in response to stress
AUTHORS: Magdalena Julkowska
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a simple protocol, adapted from the Arabidopsis protocol (https://dx.doi.org/10.17504/protocol... | ["[Experiment preparation]\nPrepare the salt stress media Use the basic media concentration as described in Step 1 - but now add salt - make media containing 0, 75 or 100 mM NaCl (added after pH measurement - pH should be ok because of the MES buffer).Pour the plates according to the instructions above and let dry in t... |
85,066 | UV Exposure Protocol | 4 | null | https://www.protocols.io/view/uv-exposure-protocol-cxbixike | Martin O Pollard | TITLE: UV Exposure Protocol
AUTHORS: Martin O Pollard
[DESCRIPTION]
A procedure utilising a UV crosslinker to expose isolated DNA to UV radiation with the aim of inducing lesions in the DNA typical of that kind of damage induced by UV.
[STEPS]
SECTION: UV treatment
1. Pipette 2.2 µL of which has a measured concent... | ["[UV treatment] Pipette 2.2 µL of which has a measured concentration of 227 µg/ml from stock tube to sterile plastic petri dish.", "[UV treatment] Dilute material in petri dish with 22.8 µL of buffer to achieve a target of 25 µL of DNA at 20 ng/µl yielding 0.5 µg of DNA. Gently mix but do not agitate vigorously.", ... |
47,260 | The impact of the traditional male role norms on the post-traumatic stress disorder. A cross-sectional study on Polish male firefighters. | 1 | dx.doi.org/10.17504/protocols.io.bsd4na8w | https://www.protocols.io/view/the-impact-of-the-traditional-male-role-norms-on-t-bsd4na8w | Tomasz Jakubowski, Magdalena Sitko-Dominik | TITLE: The impact of the traditional male role norms on the post-traumatic stress disorder. A cross-sectional study on Polish male firefighters.
AUTHORS: Tomasz Jakubowski, Magdalena Sitko-Dominik
[DESCRIPTION]
The aim of the current study is to assess potential associations between compliance with masculinity norms... | ["[Protocol] Tomasz Jakubowski, Magdalena Sitko-Dominik\nThe impact of the traditional male role norms on the post-traumatic stress disorder. A cross-sectional study on Polish male firefighters.\n\n\nDesign Plan\nThe project will be realized as an observational cross-sectional study. It will not use any blinding nor an... |
59,181 | HisPur Purification of His-Tagged Proteins--CHEM 584 | 4 | dx.doi.org/10.17504/protocols.io.b52mq8c6 | https://www.protocols.io/view/hispur-purification-of-his-tagged-proteins-chem-58-b52mq8c6 | Ken Christensen | TITLE: HisPur Purification of His-Tagged Proteins--CHEM 584
AUTHORS: Ken Christensen
[DESCRIPTION]
The Thermo Scientific HisPur Ni-NTA Resin enables effective immobilized metal affinity chromatography (IMAC) purification of polyhistidine-tagged proteins from a soluble protein extract. This resin is composed of nicke... | ["Add 250 µL of a 50% Ni-NTA resinslurry to a 1.7 ml microcentrifuge tube. Centrifuge tube for 2 min at 700 × g and carefully remove and discard the supernatant.", "Add two resin-bed volumes of Equilibration Buffer and mix gently until the resin is fully resuspended", "Centrifuge tube for 2 min at 700 × g and carefully... |
36,040 | RNA Extraction Protocol for Aurantiochytrium limacinum | null | dx.doi.org/10.17504/protocols.io.bffgjjjw | https://www.protocols.io/view/rna-extraction-protocol-for-aurantiochytrium-limac-bffgjjjw | Michael Horowitz, Mariana Rius, Jackie Collier | TITLE: RNA Extraction Protocol for Aurantiochytrium limacinum
AUTHORS: Michael Horowitz, Mariana Rius, Jackie Collier
[STEPS]
?. [Prepare cells]
Start a preculture 4 days prior to extraction by inoculating 5 ml of 790 with a colony of Aurantiochytrium limacinum (ATCC MYA-1381). Incubate overnight at 28 C 171 rpm.Use p... | ["[Prepare cells]\nStart a preculture 4 days prior to extraction by inoculating 5 ml of 790 with a colony of Aurantiochytrium limacinum (ATCC MYA-1381). Incubate overnight at 28 C 171 rpm.Use preculture to inoculate 20 ml of 790 in a 250 ml flask. Culture for three days at 28 C, 171 rpm.", "[Prepare cells]\nDetermine v... |
101,152 | Isolation and Characterization of Tissue and Cell-Derived Extracellular Vesicles and Non-Vesicular Extracellular Particles | 0 | null | https://www.protocols.io/view/isolation-and-characterization-of-tissue-and-cell-dez83f9w | Marta Garcia Contreras, Emeli Chatterjee, Abhik Chakraborty, Michail Spanos, Kriti Bomb, Priyanka Gokulnath, Jeffery L. Franklin, Erika Duggan, John P. Nolan, Priyadarshini Pantham, Louise C. Laurent, Saumya Das | TITLE: Isolation and Characterization of Tissue and Cell-Derived Extracellular Vesicles and Non-Vesicular Extracellular Particles
AUTHORS: Marta Garcia Contreras, Emeli Chatterjee, Abhik Chakraborty, Michail Spanos, Kriti Bomb, Priyanka Gokulnath, Jeffery L. Franklin, Erika Duggan, John P. Nolan, Priyadarshini Pantham,... | ["[Processing of Conditioned Culture Media following Tissue and Cell Culture] Culture DiFi cells11 under the appropriate culture conditions as previously\npublished. BeWo cells were cultured as published earlier12,13 with the\nmodification of addition of 10% exosome-depleted FBS).", "[Processing of Conditioned Culture ... |
68,412 | FAVIS: Fast and Versatile protocol for metabarcoding of bulk Insect Samples from large-scale diversity monitoring projects | 4 | dx.doi.org/10.17504/protocols.io.kqdg36261g25/v2 | https://www.protocols.click/view/favis-fast-and-versatile-protocol-for-metabarcodin-ce24tggw | Elżbieta Iwaszkiewicz-Eggebrecht, Piotr Łukasik, Mateusz Buczek, Junchen Deng, Emily Hartop, Harald Havnås, Monika Prus-Frankowska, Carina R. Ugarph, Paulina Viteri, Anders F. Andresson, Tomas Roslin, Ayco J. M. Tack, Fredrik Ronquist, Andreia Miraldo | TITLE: FAVIS: Fast and Versatile protocol for metabarcoding of bulk Insect Samples from large-scale diversity monitoring projects
AUTHORS: Elżbieta Iwaszkiewicz-Eggebrecht, Piotr Łukasik, Mateusz Buczek, Junchen Deng, Emily Hartop, Harald Havnås, Monika Prus-Frankowska, Carina R. Ugarph, Paulina Viteri, Anders F. Andre... | ["[SECTION 1: Preparation] Set up washing stations", "[SECTION 1: Preparation] Set up a 80 L plastic container with washing liquid and water.", "[SECTION 1: Preparation] Set up a 80 L plastic container with 10% bleach solution by adding nine parts water to one part laboratory bleach (NaOCl - sodium hypochlorite soluti... |
39,998 | Procedure for Operation and Maintenance of the Illumina MiSeq for Whole Genome Sequencing | 1 | dx.doi.org/10.17504/protocols.io.bja6kihe | https://www.protocols.io/view/procedure-for-operation-and-maintenance-of-the-ill-bja6kihe | Julie Haendiges, Ruth Timme, Maria Balkey | TITLE: Procedure for Operation and Maintenance of the Illumina MiSeq for Whole Genome Sequencing
AUTHORS: Julie Haendiges, Ruth Timme, Maria Balkey
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This procedure outlines the procedures for operation and maintenance of an Illumina MiSeq Sequencer for ... | ["[Starting the Illumina MiSeq Desktop Sequencer]\nPower on the instrument using the power switch located on the back of the instrument.", "[Starting the Illumina MiSeq Desktop Sequencer]\nIf the MiSeq is networked, this is the point where the username and password would be entered.", "[Starting the Illumina MiSeq Desk... |
76,421 | Calcium chloride transformation buffer | 4 | null | https://www.protocols.io/view/calcium-chloride-transformation-buffer-cnvdve26 | Andreas Sagen | TITLE: Calcium chloride transformation buffer
AUTHORS: Andreas Sagen
[DESCRIPTION]
Calcium chloride (CaCl2) transformation is a laboratory technique in prokaryotic (bacterial) cell biology. The addition of calcium chloride to a cell suspension promotes the binding of plasmid DNA to lipopolysaccharides (LPS). Positivel... | ["[5 M Calcium chloride transformation buffer] Add 40 mL distilled water to a 50 mL tube", "[5 M Calcium chloride transformation buffer] Measure and add 36.7525 g Calcium chloride dihydrate\n\nMaterials:", "[5 M Calcium chloride transformation buffer] Adjust pH to pH 7.4 with concentrated sodium hydroxide or hydrogen c... |
102,314 | Safety and Efficacy of Sodium-Glucose Transport Protein 2 Inhibitors and Glucagon-like Peptide-1 Receptor Agonists in Kidney Transplant Recipients: Synthesis of Evidence | 0 | dx.doi.org/10.17504/protocols.io.e6nvw1eq9lmk/v1 | https://www.protocols.io/view/safety-and-efficacy-of-sodium-glucose-transport-pr-df6i3rce | Ioannis Bellos, Vassiliki Benetou | TITLE: Safety and Efficacy of Sodium-Glucose Transport Protein 2 Inhibitors and Glucagon-like Peptide-1 Receptor Agonists in Kidney Transplant Recipients: Synthesis of Evidence
AUTHORS: Ioannis Bellos, Vassiliki Benetou
[DESCRIPTION]
A systematic review and meta-analysis will be conducted aiming to investigate the eff... | ["Objective To determine the efficacy and safety of Sodium-Glucose Transport Protein 2 inhibitor (SGLT2-i) and Glucagon-like Peptide-1 Receptor Agonist (GLP1-RA) treatment in kidney transplant recipients.", "Eligibility criteria The population of the study will consist of kidney transplant recipients. The intervention ... |
77,717 | Multiplexed Iterative FISH Experimental Protocol SOP002.v3.12 | 4 | dx.doi.org/10.17504/protocols.io.yxmvmk6k6g3p/v3 | https://www.protocols.io/view/multiplexed-iterative-fish-experimental-protocol-s-cp5vvq66 | Rory Kruithoff, Lei Zhou, Douglas Shepherd | TITLE: Multiplexed Iterative FISH Experimental Protocol SOP002.v3.12
AUTHORS: Rory Kruithoff, Lei Zhou, Douglas Shepherd
[DESCRIPTION]
This document, SOP002 - Multiplexed Iterative FISH Experimental Protocol, describes the process for in-situ fluorescence labeling of RNA transcripts in cells and tissues using a layere... | ["[Part 1 - Tissue or Cell-Based Experiment Preparation] Part 1 of this protocol describes the steps to setup a multiplexed iterative FISH experiment for tissue or cell-based samples. These steps are focused on the biochemical requirements for tissue or cell preparation, probe hybridization and imaging. This protocol d... |
null | null | null | dx.doi.org/10.17504/protocols.io.eufbetn | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p>1) 10-40% linear sucrose gradient for SW27 (or SW28) rotor tubes for 6 gradients</p>
<p> </p>
<p> 96.0 mL of sucrose (600 mg/mL)</p>
<p> <u> 48.0</u> mL of 3X buffer</p>
<p> 144.0 mL total of 400 mg/mL sucrose</p>
<p> ... | [] |
94,182 | Qubit 4 Fluorometer (Common Peanut Lab) | 4 | null | https://www.protocols.io/view/qubit-4-fluorometer-common-peanut-lab-c78ezrte | Nimalka Weerasuriya | TITLE: Qubit 4 Fluorometer (Common Peanut Lab)
AUTHORS: Nimalka Weerasuriya
[DESCRIPTION]
This protocol is to guide the use of the Qubit 4 Fluorometer in the Stillwater, OK, ARS USDA facility. The complete user guide is also available for download at thermofisher.com/qubit. This guide contains some additional informat... | ["[Introduction] From the Home screen, you can: \nSelect one of the assays: dsDNA, RNA, oligo (ssDNA), protein, or Ion Sphere™.\nSelect the Fluorometer mode (the instrument behaves like a mini-fluorometer).\nAccess and export saved data.\nConfigure instrument settings.\nUse the Reagent Calculator to determine the exact... |
36,447 | Ab Lysis Buffer | null | dx.doi.org/10.17504/protocols.io.bft7jnrn | https://www.protocols.io/view/ab-lysis-buffer-bft7jnrn | Colin Daniel | TITLE: Ab Lysis Buffer
AUTHORS: Colin Daniel
[STEPS]
?. Tris NaCl Triton-X100 DOC SDS EDTA
?. On ice add protease and phosphotase inhibitors (Roche) | ["Tris NaCl Triton-X100 DOC SDS EDTA", "On ice add protease and phosphotase inhibitors (Roche)"] |
99,134 | PCR Protocol Template | 1 | null | https://www.protocols.io/view/pcr-protocol-template-dc262yhe | Andreas Novotny | TITLE: PCR Protocol Template
AUTHORS: Andreas Novotny
[DESCRIPTION]
A protocol template created through the BeBOP project for PCR.
[BEFORE_START]
Read background information, MIOP and BePOP-OBON information under the "Guidelines" tab.
[GUIDELINES]
MIOP: Minimum Information about an Omics Protocol
AUTHORS
... | ["[PREPARATION] Please specify the preparatory actions you took before you collected the samples and note what equipment was needed to do so (e.g. disinfection of work surfaces, preparations to the equipment you intend to use later on).\n\nStep", "[PCR] Please specify the actions you took to amplify the previously extr... |
29,269 | Nuclei Isolation for SNARE-seq2 | null | dx.doi.org/10.17504/protocols.io.8tvhwn6 | null | Carter Palmer, Christine Liu, Jerold Chun | TITLE: Nuclei Isolation for SNARE-seq2
AUTHORS: Carter Palmer, Christine Liu, Jerold Chun
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is intended to be used for the isolation of nuclei from fresh-frozen brain tissue in preparation for analysis by Single-Nucleus Chromatin Accessibi... | ["[Buffer Preparation]\nNuclei Extraction Buffer (NEB): ABCDE1 Final Concentration Chemical to Add Stock Concentration 2 Sucrose 320 mM 5.48g Solid 3 Magnesium Acetate 3 mM 32.16mg Solid 4 CaCl2 5 mM 50µl 5M Stock 5 EDTA 100 µM 10µl 0.5M ... |
null | null | null | dx.doi.org/10.17504/protocols.io.hnmb5c6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A method to transform the chloroplast of <em>Amphidinium carterae</em> using biolistics.</p>
<pre>orcid.org/0000-0002-2469-0611</pre>
<pre>orcid.org/0000-0002-6975-8640</pre>
<pre>orcid.org/0000-0003-4487-196X</pre>
<pre> </pre>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.... | [] |
62,293 | Superior Nutra Keto - SCAM ALERT? READ MY EXPERIENCE! | 3 | dx.doi.org/10.17504/protocols.io.ewov1n547gr2/v1 | https://www.protocols.io/view/superior-nutra-keto-scam-alert-read-my-experience-b83vryn6 | H Shi | TITLE: Superior Nutra Keto - SCAM ALERT? READ MY EXPERIENCE!
AUTHORS: H Shi
[DESCRIPTION]
That is where an enhancement like this can have a significant effect. To find out more, continue to peruse our Superior Nutra Keto audit. We'll give you the subtleties that you want!
[STEPS] | [] |
52,115 | Intact cell cross-linking | 4 | dx.doi.org/10.17504/protocols.io.bw5tpg6n | https://www.protocols.io/view/intact-cell-cross-linking-bw5tpg6n | Veerle Baekelandt | TITLE: Intact cell cross-linking
AUTHORS: Veerle Baekelandt
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Intact cell cross-linking</span></div></div>
[STEPS]
?. seed cells (SHSY-5Y) in 10 cm dishes at a density of 6 x 10^6 cells per plate.incubate for
?. wash ce... | ["seed cells (SHSY-5Y) in 10 cm dishes at a density of 6 x 10^6 cells per plate.incubate for", "wash cells 2 times with 1X PBS", "harvest cells with 1x PBS + PI cocktail (PBS + PI buffer)", "and resuspend in + PI buffer\nCentrifuge: 1000 34, 15 min\n400 µl", "divide resuspended cells over 2 vialstube 1: add 1 µM disuc... |
54,236 | Mercury Sequence and Sample Metadata Prep for Submission Workflow on the Terra Platform | 5 | null | https://www.protocols.io/view/mercury-sequence-and-sample-metadata-prep-for-subm-by74pzqw | Jill V Hagey, Kevin Libuit, Lingzi Xiaoli, Technical Outreach and Assistance for States Team | TITLE: Mercury Sequence and Sample Metadata Prep for Submission Workflow on the Terra Platform
AUTHORS: Jill V Hagey, Kevin Libuit, Lingzi Xiaoli, Technical Outreach and Assistance for States Team
[DESCRIPTION]
Public health laboratories are encouraged to submit sequencing data for SARS-CoV-2 to multiple public dat... | ["[Where to Begin] This workflow is intended for users of Titan workflows for SARS-CoV-2 strain characterization on the Terra platform and expects the following protocols have already been completed: \n\nTerra and Google Cloud Accounts\nSamples uploaded\nOutput from the Titan workflow\n\nThis protocol is intended only ... |
36,106 | Small-scale Expression and Solubility Testing of Proteins in BL21 E. coli | 1 | null | https://www.protocols.io/view/small-scale-expression-and-solubility-testing-of-p-bfhijj4e | Vincent Bielinski | TITLE: Small-scale Expression and Solubility Testing of Proteins in BL21 E. coli
AUTHORS: Vincent Bielinski
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Scaled-down solubility screen for bacterial overexpression constructs. </div></div>
[STEPS]
?. [Screening]
Grow and induce BL21cells in medium... | ["[Screening]\nGrow and induce BL21cells in medium of your choice with appropriate temperature and inducer conditions. We often use Teriffic Broth and culture cells at 30 oC, with induction carried out at 18 oC overnight (1mM IPGTG or 0.5% L-arabinose).", "[Screening]\nHarvest 10 mL overnight expression culture by cent... |
99,524 | Genome Assembly, Scaffolding, and Annotation in Sugar Beet | 5 | dx.doi.org/10.17504/protocols.io.bp2l621w5gqe/v1 | https://www.protocols.io/view/genome-assembly-scaffolding-and-annotation-in-suga-ddfc23iw | Olivia Todd, kevin.dorn | TITLE: Genome Assembly, Scaffolding, and Annotation in Sugar Beet
AUTHORS: Olivia Todd, kevin.dorn
[DESCRIPTION]
This protocol was designed for use in Beta vulgaris and Beta crop wild relatives.
It uses several types of software and the online platform, GenSAS for assembly and annotation.
Data input sequencing types... | ["[Iso-Seq data pre-processing] This protocol uses the file name \"FC309\" as the base name of the population being sequenced.", "[Installing necessary software and modules] The computational steps are completed using USDA-ARS's High Performance Computing Platform, Ceres.", "Use the following page as a guideline for th... |
36,220 | Lake biofilms sampling for both downstream DNA analysis and microscopic counts | 1 | dx.doi.org/10.17504/protocols.io.bfk4jkyw | https://www.protocols.io/view/lake-biofilms-sampling-for-both-downstream-dna-ana-bfk4jkyw | Frederic Rimet, Rainer Kurmayer, Nico Salmaso, Camilla Capelli, Cecile Chardon, Agnès Bouchez, Julie Gueguen, Marine Vautier, Isabelle Domaizon | TITLE: Lake biofilms sampling for both downstream DNA analysis and microscopic counts
AUTHORS: Frederic Rimet, Rainer Kurmayer, Nico Salmaso, Camilla Capelli, Cecile Chardon, Agnès Bouchez, Julie Gueguen, Marine Vautier, Isabelle Domaizon
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class =... | ["[When & where to sample]\nChoice of the sampling season and period- Phytobenthic communities’ composition are changing along seasons. In large lakes, the major variables explaining these temporal changes are nutrients (and phosphorus especially).- Moreover, the heterogeneity between the communities present alon... |
65,388 | It improves your skin and prevents you from acne, pimples etc | 1 | dx.doi.org/10.17504/protocols.io.5qpvob177l4o/v1 | https://www.protocols.io/view/it-improves-your-skin-and-prevents-you-from-acne-p-cb4ksquw | Condor CBD Gummies | TITLE: It improves your skin and prevents you from acne, pimples etc
AUTHORS: Condor CBD Gummies
[DESCRIPTION]
Perhaps you will put your own spin on Condor CBD Gummies after this.
[STEPS]
SECTION: It improves your skin and prevents you from acne, pimples etc
1. A majority of buddies were depressed in relation to Con... | ["[It improves your skin and prevents you from acne, pimples etc] A majority of buddies were depressed in relation to Condor CBD Gummies. If you imagine that there is an actual debate over Handles stress and tension by addressing the source of the problem. then you are misinformed. Greatly enhances the digestive proces... |
102,455 | Crystallisation of Enterovirus coxsackievirus A16 2A protease | 1 | dx.doi.org/10.17504/protocols.io.q26g715eqgwz/v1 | https://www.protocols.io/view/crystallisation-of-enterovirus-coxsackievirus-a16-dgax3sfn | ryan Lithgo, Peter Marples, Lizbé Koekemoer, Daren Fearon | TITLE: Crystallisation of Enterovirus coxsackievirus A16 2A protease
AUTHORS: ryan Lithgo, Peter Marples, Lizbé Koekemoer, Daren Fearon
[DESCRIPTION]
Picornaviridae coxsackievirus A16 is the causative agent of paediatric hand-foot-and-mouth disease, and a target for pandemic preparedness due to the risk of higher orde... | ["[Crystallisation experiment] Protein and buffer requirements:\n43.2 µL20 mg/mL \n3.36 mL \n14.4 µL seeds, dilution 1:1000", "[Crystallisation experiment] Dispense 35 µL into SwissCI 3 lens plate reservoir wells using a 100 µl multi-channel pipette.\nDispense 150 nL20 mg/mL to each lens using the SPT mosquito.\nDis... |
54,299 | How to make a cup of tea | 1 | dx.doi.org/10.17504/protocols.io.by93pz8n | https://www.protocols.io/view/how-to-make-a-cup-of-tea-by93pz8n | Shiau Haln Chen, ines.boehm | TITLE: How to make a cup of tea
AUTHORS: Shiau Haln Chen, ines.boehm
[DESCRIPTION]
This protocol is part of the Record Keeping lesson within the FAIR in (biological) practice DataCarpentry course. Here we explore the perfect protocol to brew tea.
[BEFORE_START]
Make sure the kettle is cleaned and the bottom of t... | ["[Preparation of water and tea] Fill the kettle with ~500mL of water, or until your min fill line and boil the water.", "[Preparation of water and tea] In the meantime prepare your tea bag, unpack it and place it in the cup/mug so that the tag is positioned outside of the mug.", "[Preparation of water and tea] Once th... |
20,421 | Tomato Transformation Media | null | dx.doi.org/10.17504/protocols.io.x7dfri6 | null | Alex Rajewski | TITLE: Tomato Transformation Media
AUTHORS: Alex Rajewski
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is simply the media recipes for use with my tomato transformation protocol.</div></div>
[STEPS]
?. To make 1L, for each media, dissolve the following components to ~800mL of Milli... | ["To make 1L, for each media, dissolve the following components to ~800mL of MilliQ water in a 1L beaker ABCDEFG1Component:1/2MSOMS0-2%KCMS2Z1ZRooting2MS Basal Salts2.15g4.3g4.3g------3MS Salts with Nitsch Vitamins------4.3g4.3g4.3g4Sucrose10g20g30g20g20g30g5myo-Inositol100mg100mg100mg100mg100mg--6KH2PO4----200mg-----... |
20,562 | UC Davis - Adiposity | null | dx.doi.org/10.17504/protocols.io.ybsfsne | null | Jon Ramsey | TITLE: UC Davis - Adiposity
AUTHORS: Jon Ramsey
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span><span style = "font-weight:bold;"> </span></div><div class = "text-block">The major fat pads of mice will be dissected and weighed. This approach provides ... | ["Body weight of animal is taken before anesthesia.", "The mouse is euthanized according to the methods approved in the study’s IACUC protocol.", "A midline incision is made to open the abdominal cavity.", "Forceps are used to pull up the epididymal fat pad (males). The fat pad is cut just above the epididymis and remo... |
37,138 | INSIGHT: a scalable isothermal NASBA-based platform for COVID-19 diagnosis | 1 | dx.doi.org/10.17504/protocols.io.bghsjt6e | https://www.protocols.io/view/insight-a-scalable-isothermal-nasba-based-platform-bghsjt6e | Qianxin Wu, Chenqu Suo, Tom Brown, Tengyao Wang, Sarah Teichmann, Andrew Bassett | TITLE: INSIGHT: a scalable isothermal NASBA-based platform for COVID-19 diagnosis
AUTHORS: Qianxin Wu, Chenqu Suo, Tom Brown, Tengyao Wang, Sarah Teichmann, Andrew Bassett
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We present here INSIGHT (Isothermal NASBA-Sequencing based hIGH-througput Tes... | ["Lysis of saliva samples\n\t\t\t\t\t\t\t .justify:after {\n\t\t\t\t\t\t\t content: \"\";\n\t\t\t\t\t\t\t display:inline-block;\n\t\t\t\t\t\t\t width: 100%;\n\t\t\t\t\t\t\t }\n\t\t\t\t\t\t\tMix crude saliva at 1:1 ratio with QuickExtract DNA Extraction Solution. Incubate at 95 °C for 5 min to ensure complete... |
54,979 | NAN KB Demo: Change form for Serum sample preparation and data acquisition | 3 | null | https://www.protocols.io/view/nan-kb-demo-change-form-for-serum-sample-preparati-bzxbp7in | Abby Moore | TITLE: NAN KB Demo: Change form for Serum sample preparation and data acquisition
AUTHORS: Abby Moore
[DESCRIPTION]
The purpose of this document is to track changes, approval and testing for the protocol Serum sample preparation and data acquisition.
[STEPS] | [] |
45,461 | Amino Acid Table | 4 | null | https://www.protocols.io/view/amino-acid-table-bqmvmu66 | Elizabeth Fozo | TITLE: Amino Acid Table
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Amino acid and DNA Bases table</div></div>
[STEPS]
?. [Amino Acids and DNA Bases]
Alanine0.5% (5 mg/ml)waterART/4°C40800Arginine HCI1% (10 mg/ml)waterART/4°C20200Asparagine0.5% (5 mg/ml)waterART/4°C40800... | ["[Amino Acids and DNA Bases]\nAlanine0.5% (5 mg/ml)waterART/4°C40800Arginine HCI1% (10 mg/ml)waterART/4°C20200Asparagine0.5% (5 mg/ml)waterART/4°C40800Aspartic Acid1% (10 mg/ml)0.2 N NaOHFRT1001000Cysteine0.5% (5 mg/ml)waterFRT/4°C40800Glutamine2% (20 mg/ml)waterART/4°C40200Glutamic Acid1% (10 mg/ml)0.2 N NaOHFRT10010... |
104,782 | Archival DNA extraction protocol for insect specimens from museum collections | 4 | dx.doi.org/10.17504/protocols.io.81wgbybqyvpk/v3 | https://www.protocols.io/view/archival-dna-extraction-protocol-for-insect-specim-dijn4cme | Fernando Lopes, Nicole Gunter, Conrad P. D. T. Gillett, Giulio Montanaro, Michele Rossini, Federica Losacco, Gimo M. Daniel, Nicolas Straube, Sergei Tarasov | TITLE: Archival DNA extraction protocol for insect specimens from museum collections
AUTHORS: Fernando Lopes, Nicole Gunter, Conrad P. D. T. Gillett, Giulio Montanaro, Michele Rossini, Federica Losacco, Gimo M. Daniel, Nicolas Straube, Sergei Tarasov
[DESCRIPTION]
This protocol can be used to dry specimens from natura... | ["[DNA extraction (protocol's adaptation)]", "[Filtering and washing] The next day: after 30 min lysis and UV on plastic ware:", "[Concentration and purity measurements] We advise the use of Qubit High-Sensitive reagents and 1 µL-2 µL of extract for DNA concentration measurements. In addition, Nanodrop can be used... |
54,898 | Recombinant protein expression and purification of codon-optimized Pfu-Sso7d | 4 | dx.doi.org/10.17504/protocols.io.bzusp6we | https://www.protocols.io/view/recombinant-protein-expression-and-purification-of-bzusp6we | Maira Rivera, Javiera Reyes, Paula Blazquez-Sanchez, Cesar A Ramirez-Sarmiento | TITLE: Recombinant protein expression and purification of codon-optimized Pfu-Sso7d
AUTHORS: Maira Rivera, Javiera Reyes, Paula Blazquez-Sanchez, Cesar A Ramirez-Sarmiento
[DESCRIPTION]
This protocol has been optimized for the recombinant expression of a codon-optizimed Pfu-Sso7d DNA polymerase. This is a fusion... | ["[DAY 1 – Plasmid transformation] Transform 100 ng of plasmid containing codon-optimized into E. coli C41 competent cells using either heat shock or electroporation.", "[DAY 1 – Plasmid transformation] Spread transformed cells in LB Agar plates supplemented with 0.05 mg/mLKan. Grow plate overnight at 37 °C", "[DAY 2 –... |
58,929 | Rotarod | 4 | dx.doi.org/10.17504/protocols.io.b5srq6d6 | https://www.protocols.io/view/rotarod-b5srq6d6 | Haley Geertsma | TITLE: Rotarod
AUTHORS: Haley Geertsma
[DESCRIPTION]
This protocol is used to test mice in the Rotarod behavioural test.
[STEPS]
1. Habituate mice in the testing room for 60 minutes.
2. Place each mouse on the rod and turn on the rotarod machine at 4-40rpm over 5 minutes. Record how long each mouse can stay on the ... | ["Habituate mice in the testing room for 60 minutes.", "Place each mouse on the rod and turn on the rotarod machine at 4-40rpm over 5 minutes. Record how long each mouse can stay on the pole.", "Once testing is complete, place mice back into their home cage and wait for 10 minutes.", "Repeat this for 4 trials per day t... |
64,367 | HILIC-MS analysis of central carbon metabolites in gram negative bacteria | 6 | dx.doi.org/10.17504/protocols.io.4r3l2opzxv1y/v1 | https://www.protocols.io/view/hilic-ms-analysis-of-central-carbon-metabolites-in-ca4psgvn | Bashar Amer, Ramu Kakumanu, Edward EK Baidoo | TITLE: HILIC-MS analysis of central carbon metabolites in gram negative bacteria
AUTHORS: Bashar Amer, Ramu Kakumanu, Edward EK Baidoo
[DESCRIPTION]
Central carbon metabolites are essential for energy metabolism, secondary metabolite and macromolecule biosynthesis in prokaryotes. Phosphorylated intermediates such as s... | ["[Sample preparation] Calibration curves: Pure analytical standards were dissolved in 50:50 methanol:water (v/v) to make a stock solution of 100 micromolar (µM) concentration. The stock solution was diluted 4-fold to make a standard solution of 25 micromolar (µM)(with 50:50 methanol:water, v/v). A seven-point calibrat... |
30,932 | Synthetic media (A1) for Aurantiochytrium limacinum (ATCC MYA-1381) | null | dx.doi.org/10.17504/protocols.io.bafuibnw | null | Anbarasu Karthikaichamy, Jackie Collier | TITLE: Synthetic media (A1) for Aurantiochytrium limacinum (ATCC MYA-1381)
AUTHORS: Anbarasu Karthikaichamy, Jackie Collier
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Synthetic media recipe for </span><span style = "font-style:italic;">Aurantiochytrium limacinum </span><span>(ATCC MYA-138... | ["[5x A1stock]\nMeasure and add the following components to an appropriate media bottle. Make up the solution to desired volume with water. Autoclave for at 15 PSI and AB1Componentsg/L2CaCl2·2H2O2.53Glycerol1504KCl 25KH2PO4 206maleic acid 297MgCl2 48Na2SO4 159NaCl7210Sodium-glutamate hydrat... |
18,635 | Design and PCR Synthesis of Infrared Fluorophore-Labeled Modular DNA Probes | null | dx.doi.org/10.17504/protocols.io.wfjfbkn | null | Michael Van Dyke | TITLE: Design and PCR Synthesis of Infrared Fluorophore-Labeled Modular DNA Probes
AUTHORS: Michael Van Dyke
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">IR fluorophore-modified DNAs and IR fluorescence imaging provide a safe and effective alternative for investigating ligand-DNA interactions tha... | ["[Modular DNA probe design]\nA modular DNA probe is designed to be capable of amplification by PCR. Thus, it needs to contain two flanking regions of defined sequence and a central region containing those sequences under investigation. Length and sequence of the flanking regions are dictated by their role in the annea... |
65,908 | Chiral Analysis | 4 | null | https://www.protocols.io/view/chiral-analysis-cckusuww | BOC Sciences | TITLE: Chiral Analysis
AUTHORS: BOC Sciences
[DESCRIPTION]
Chirality plays an important role in the fields of asymmetric synthesis, biology and medicine. Therefore, it is of great significance to analyze chiral compounds quickly, sensitively, and selectively. BOC Sciences can perform chiral analysis following re... | [] |
48,598 | A FAIR protocol of the Best-RAD sequencing approach | 4 | dx.doi.org/10.17504/protocols.io.rm7vz3ok4gx1/v1 | https://www.protocols.io/view/a-fair-protocol-of-the-best-rad-sequencing-approac-btpwnmpe | Laure Benoit, Sabine Nidelet, Emeline Charbonnel, Marie-Pierre Chapuis | TITLE: A FAIR protocol of the Best-RAD sequencing approach
AUTHORS: Laure Benoit, Sabine Nidelet, Emeline Charbonnel, Marie-Pierre Chapuis
[DESCRIPTION]
The protocol is based on the Best-RAD sequencing approach developed in Ali et al. (2016) that allows two main improvements of the RAD-sequencing approach developed b... | ["[Part II - Selection of fragments carrying the restriction site] Preparation of Dynabead M-280 magnetic streptavidin beads\n\nSince streptavidin beads adhere to tips, re-suspend by vortexing and not by pipetting.\n\nIncubate the streptavidin beads at room temperature for at least 30 min before using it.\n\n\nFor eac... |
9,952 | Motility Medium(Buffer) | 1 | dx.doi.org/10.17504/protocols.io.mx8c7rw | https://www.protocols.io/view/motility-medium-buffer-mx8c7rw | Erçağ Pinçe | TITLE: Motility Medium(Buffer)
AUTHORS: Erçağ Pinçe
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">MM for bacterial motility experiments</div></div>
[STEPS]
?. [Prepare Stock Solutions]
Potassium Phosphate(KPO4) Stock Buffer [1M] (100x):1-) Prepare 1M Potassium Phosphate Monobasic - 500 mL ddH2O (... | ["[Prepare Stock Solutions]\nPotassium Phosphate(KPO4) Stock Buffer [1M] (100x):1-) Prepare 1M Potassium Phosphate Monobasic - 500 mL ddH2O (milliQ)- 68.045 gr of Monobasic potassium phosphate (KH2PO4) [1M]- 87.09 gr of Dibasic potassium phosphate (K2HPO4) [1M] 2-) Adjust the pH of the solution to 7.0 3-) Filter steril... |
29,200 | Click histochemistry for whole-mount staining of brain structures | null | dx.doi.org/10.17504/protocols.io.8rqhv5w | null | Alexander Lazutkin | TITLE: Click histochemistry for whole-mount staining of brain structures
AUTHORS: Alexander Lazutkin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Labeling of the replicating DNA with synthetic thymidine analogs is commonly used for marking the dividing cells. However, until now this method has on... | ["[Tissue sample preparation]\nInject animal with a synthetic thymidine analogue 5-ethynyl-2’-deoxyuridine at a dose of 40-123 mg/kg. The time to euthanasia may vary depending on the specific research question.", "[Tissue sample preparation]\nAnesthetize animal with chloral hydrate (10 mg/kg) immediately before euthana... |
43,801 | Nuclei Isolation and Sorting from Frozen Human Temporal Cortex | 4 | dx.doi.org/10.17504/protocols.io.j8nlk4k55g5r/v1 | https://www.protocols.io/view/nuclei-isolation-and-sorting-from-frozen-human-tem-bnzzmf76 | Clemens Scherzer | TITLE: Nuclei Isolation and Sorting from Frozen Human Temporal Cortex
AUTHORS: Clemens Scherzer
[DESCRIPTION]
This protocol is about nuclei isolation and sorting from frozen human temporal cortex.
[BEFORE_START]
Prepare Buffers as described in section 'Materials'.
[STEPS]
SECTION: Method
1. Cut 100 mg - 200 mg into... | ["[Method] Cut 100 mg - 200 mg into small pieces on dry ice.", "[Method] Put cut tissue into a microcentrifuge tube (pre-cooled on dry ice), weigh in a balance.", "[Method] Transfer tissue to a glass dounce tissue grinder on regular ice.", "[Method] Add 2 mL to the tissue grinder.", "[Method] Homogenize tissue with p... |
105,082 | UDA-5'RNA-protocol | 0 | dx.doi.org/10.17504/protocols.io.6qpvr82pplmk/v1 | https://www.protocols.io/view/uda-5-39-rna-protocol-diu24eye | Yun Li | TITLE: UDA-5'RNA-protocol
AUTHORS: Yun Li
[DESCRIPTION]
Droplet microfluidics-based single-cell combinatorial indexing sequencing represents an attractive way to balance cost, scalability,
robustness, and accessibility. However, current methods need a tailored protocol for specific modality respectively, which may... | ["[GEM Generation & Barcoding.] Prepare Master Mix & Load Chromium Next GEM Chip K", "[GEM Generation & Barcoding.] A certain number of cells or nuclei were added to Master Mix (18.8ul RT Reagent B (2000165); 7.3ul 1.1ul Template Switch Oligo (3000228); 1.9ul Reducing Agent B (2000087) and 8.3ul RT Enzyme C(200... |
42,525 | Holobiont Virus Extraction Protocol (Veglia et al.) | 1 | dx.doi.org/10.17504/protocols.io.bmr5k586 | https://www.protocols.io/view/holobiont-virus-extraction-protocol-veglia-et-al-bmr5k586 | Alex Veglia | TITLE: Holobiont Virus Extraction Protocol (Veglia et al.)
AUTHORS: Alex Veglia
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The decribed holobiont virus extraction protocol contains five steps: i) Rinse and rest, ii) Tissue separation, iii) Physical cell disruption and homogenization, iv) ... | ["[Rinse and rest]\nFirst, invertebrate samples taken at reef or from aquarium must be rinsed with sterile seawater to mitigate potential contamination from ambient seawater.", "[Rinse and rest]\nBefore beginning the protocol, all bench areas should be sterilized using either 70% ethanol and/or lysol (or both)1) Remove... |
24,925 | Denver Botanic Gardens Research and Conservation Field Work Metadata Dictionary | null | dx.doi.org/10.17504/protocols.io.4j5guq6 | null | Richard A. Levy, Amy Sahud, Christina Alba, Michelle DePrenger-Levin, Rebecca Hufft | TITLE: Denver Botanic Gardens Research and Conservation Field Work Metadata Dictionary
AUTHORS: Richard A. Levy, Amy Sahud, Christina Alba, Michelle DePrenger-Levin, Rebecca Hufft
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Glossary of terms agreed upon and used by Denver Botanic Gardens Researc... | ["Introduction\n \n This booklet serves as a reference dictionary for terms used while recording data in the field relating to specimens, biological assets, surveys, monitoring, location and site descriptions, etc.\n \n Regular use and consultation of this booklet allows for researchers across projects to describe bi... |
null | null | null | dx.doi.org/10.17504/protocols.io.uk5euy6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
How to run Megahit version 1.1.3 (Li et al. 2015) through the iMicrobe plaform.
Megahit is a de-novo assembler for large and complex metagenomics NGS reads relying on succinct de Bruijn graph (SdBG) to achieve low memory assembly.
More informations about Megahit can be found... | ["[De Novo assembly of paired-end illumina dataset] {\"blocks\":[{\"key\":\"bboko\",\"text\":\"Note :This protocol uses a samples from the HMP project (SRS143565). This sample is a right cubital fossa WGS dataset from a healthy female subject.\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[{\"offset\":0,\"l... |
50,078 | SOP002 Human pluripotent stem cell HDR-mediated gene editing using CRISPR/Cas9 and PiggyBac technology | 1 | dx.doi.org/10.17504/protocols.io.bu56ny9e | https://www.protocols.io/view/sop002-human-pluripotent-stem-cell-hdr-mediated-ge-bu56ny9e | Patrick Ovando-Roche | TITLE: SOP002 Human pluripotent stem cell HDR-mediated gene editing using CRISPR/Cas9 and PiggyBac technology
AUTHORS: Patrick Ovando-Roche
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The piggyBac transposon system can be combined with CRISPR/Cas9 to efficiently perform genetic manipulations in ... | ["[Plate preparation]\nDay -1Coat each well of a 6-well plate with of Laminin-521 (Biolamina stock) diluted in of DPBS+Ca+Mg to make a final coating concentration of . Incubate at . Prepare three wells of a 6 well plate per desired gene editing per PSC cell line.\n75 µl\n1 mL\n4 °C\nNote: It is important to use the ... |
26,802 | Will CGRP Antibodies Be a Blockbuster for Migraine Treatment? I | null | dx.doi.org/10.17504/protocols.io.6eshbee | null | susan wind | TITLE: Will CGRP Antibodies Be a Blockbuster for Migraine Treatment? I
AUTHORS: susan wind
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">Pain management drugs have always been the world of small molecules, as well as migraine. On September 28, 2016... | [] |
90,574 | Combinatorial selective ER-phagy remodels the ER during neurogenesis | 2 | dx.doi.org/10.17504/protocols.io.81wgbx13nlpk/v2 | https://www.protocols.io/view/combinatorial-selective-er-phagy-remodels-the-er-d-c4pnyvme | Melissa Hoyer, Cristina Capitanio, Ian R. Smith, Julia C. Paoli, Anna Bieber, Yizhi Jiang, Joao A. Paulo, Florian Wilfling, Brenda A. Schulman, Harper JW | TITLE: Combinatorial selective ER-phagy remodels the ER during neurogenesis
AUTHORS: Melissa Hoyer, Cristina Capitanio, Ian R. Smith, Julia C. Paoli, Anna Bieber, Yizhi Jiang, Joao A. Paulo, Florian Wilfling, Brenda A. Schulman, Harper JW
[DESCRIPTION]
The endoplasmic reticulum (ER) employs a diverse proteome landscap... | [] |
24,365 | Ultracentrifugal separation of HDL alone and calculation of non-HDL | null | dx.doi.org/10.17504/protocols.io.32mgqc6 | null | Daniel Teupser, Jan Breslow | TITLE: Ultracentrifugal separation of HDL alone and calculation of non-HDL
AUTHORS: Daniel Teupser, Jan Breslow
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This protocol is used to isolate the various lipid fractio... | ["Add 60 ul of plasma to Beckman ultracentrifugation tube (7 x 20 mm; thick walled; polyallomer; cat. # 343621).", "Layer 60 ul of PBS on top of the plasma and place tubes in a TLA100 rotor.", "Spin for 3 hours Beckman Optima TL tabletop ultracentrifuge at 70,000 rpm, 4°C.", "Using a 100 μl Hamilton syringe, carefully ... |
41,548 | Integrated Virus Detection System - sample collection - prep - processing | 4 | dx.doi.org/10.17504/protocols.io.bktkkwkw | https://www.protocols.io/view/integrated-virus-detection-system-sample-collectio-bktkkwkw | mrwick | TITLE: Integrated Virus Detection System - sample collection - prep - processing
AUTHORS: mrwick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">IVDS is uniquely suited to large volume sampling.Collection from saliva or sputum are straightforward – collection in disposable pipette and transfer to a... | ["[Collection]\nSample collection:•Collect saliva in a disposable pipet by haveing the subject placing the squeezed pipet into subject's mouth and releasing pressure on the bulb, with patient directing the pipet to the pooled saliva in the mouth.This will collect to of sample.\n1 mL\n2.5 µl", "[Collection]\nSample pr... |
42,848 | Determining the total cell concentration (TCC) in drinking water with flow cytometry | 4 | null | https://www.protocols.io/view/determining-the-total-cell-concentration-tcc-in-dr-bm38k8rw | juerg.sigrist , frederik.hammes | TITLE: Determining the total cell concentration (TCC) in drinking water with flow cytometry
AUTHORS: juerg.sigrist , frederik.hammes
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to stain cells in (drinking) water samples with SYBR Green I for the purpose of total cell... | ["Transfer of the water sample into a labelled 3.5 mL sample tube. Or the corresponding volume when using other sample tubes.\n500 µl", "Add of SYBR Green I® working solution (1:100 dilution of stock solution) to the tube and vortex briefly. The final SYBR Green I® dilution in the sample is therefore 1:10'000.\n5 µl... |
37,938 | Protocol for use with NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645, E7103) | 1 | dx.doi.org/10.17504/protocols.io.3byl46jjgo5d/v2 | https://www.protocols.io/view/protocol-for-use-with-nebnext-ultra-ii-dna-library-bhasj2ee | New England Biolabs | TITLE: Protocol for use with NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645, E7103)
AUTHORS: New England Biolabs
[DESCRIPTION]
The NEBNext Ultra II DNA Library Prep Kit for Illumina contains enzymes and buffers required to convert a broad range of input amounts of DNA into high quality libraries for next-... | ["[NEBNext End Prep] Add the following components to a sterile nuclease-free tube:\n\n Component Volume NEBNext Ultra II End Prep Enzyme Mix 3 µl NEBNext Ultra II End Prep Reaction Buffer 7 µl Fragmented DNA 50 µl Total volume 60 µl", "[NEBNext End Prep] Set a 100 μl or 200 μl pipette to 50 μl and then pipet... |
90,805 | Immunofluorescence and object-based colocalization analysis | 1 | dx.doi.org/10.17504/protocols.io.8epv5xdodg1b/v1 | https://www.protocols.io/view/immunofluorescence-and-object-based-colocalization-c4wvyxe6 | Leonardo A Parra-Rivas | TITLE: Immunofluorescence and object-based colocalization analysis
AUTHORS: Leonardo A Parra-Rivas
[DESCRIPTION]
Immunofluorescence and object-based colocalization analysis
[STEPS]
SECTION: Immunofluorescence
1.
For immunostaining, DIV17-21 neurons were fixed in 100% ice-cold methanol solution
for 15 min at room ... | ["[Immunofluorescence] For immunostaining, DIV17-21 neurons were fixed in 100% ice-cold methanol solution\nfor 15 min at room temperature, followed by extraction in 0.1 % Triton X-100\nfor 10 min, blocked in 10% BSA for 1 h at room temperature, and incubated\novernight at 4°C\nwith primary antibodies. We found that the... |
37,598 | Dataset of Contrasting effects of information sharing on common-pool resource extraction behavior: experimental findings | 3 | dx.doi.org/10.17504/protocols.io.bgx6jxre | https://www.protocols.io/view/dataset-of-contrasting-effects-of-information-shar-bgx6jxre | Dimitri Dubois, Rouchier Juliette, Nguyen-Van Phu, Farolfi Stefano | TITLE: Dataset of Contrasting effects of information sharing on common-pool resource extraction behavior: experimental findings
AUTHORS: Dimitri Dubois, Rouchier Juliette, Nguyen-Van Phu, Farolfi Stefano
[STEPS] | [] |
102,548 | Fast rodent genotyping | 0 | dx.doi.org/10.17504/protocols.io.bp2l627k5gqe/v1 | https://www.protocols.io/view/fast-rodent-genotyping-dgdu3s6w | Alexandros C Kokotos, Timothy A. Ryan | TITLE: Fast rodent genotyping
AUTHORS: Alexandros C Kokotos, Timothy A. Ryan
[DESCRIPTION]
This protocol describes a very fast method (approximately 2 h) to do genotyping from rodent tail clips and other samples.
[BEFORE_START]
The current protocol describes genotyping using rodent tail clips. This protocol has been ... | ["[DNA extraction] Tail clips from mice or rats of appropriate age should be snipped using sharp operating scissors and in compliance to local protocols by national and institutional regulatory organizations and placed in sterile Eppendorf tubes.", "[DNA extraction] Note: This protocol has been tested using the smalles... |
40,174 | nCoV-2019 McGill Nextera Flex LibPrep Protocol | 1 | dx.doi.org/10.17504/protocols.io.bjgnkjve | https://www.protocols.io/view/ncov-2019-mcgill-nextera-flex-libprep-protocol-bjgnkjve | Marie-Michelle Simon, Sarah Reiling | TITLE: nCoV-2019 McGill Nextera Flex LibPrep Protocol
AUTHORS: Marie-Michelle Simon, Sarah Reiling
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">How the Nextera DNA Flex Assay Works </span></div><div class = "text-block">The Nextera DNA Flex library prep kit uses ... | ["[Amplicon Quantification and normalisation]\nUse the 30 ul with 150 ng DNA for Nextera Flex Tagmentation. Protocol can be found here:https://emea.support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_nextera/nextera_dna_flex/nextera-dna-flex-library-prep-referen... |
63,428 | Steve Harvey CBD Gummies Shark TankReviews Benefits,Ingredients,side effects and Is it legitor Does it Really Work [HOAX OR SCAM]{Update 2022}-, What To Know Before Using It?? | 1 | dx.doi.org/10.17504/protocols.io.5jyl89km7v2w/v1 | https://www.protocols.io/view/steve-harvey-cbd-gummies-shark-tankreviews-benefit-b97cr9iw | kkk | TITLE: Steve Harvey CBD Gummies Shark TankReviews Benefits,Ingredients,side effects and Is it legitor Does it Really Work [HOAX OR SCAM]{Update 2022}-, What To Know Before Using It??
AUTHORS: kkk
[DESCRIPTION]
Steve Harvey CBD Gummies
[STEPS]
1. Steve Harvey CBD Gummies
➢Product Name —Steve Harvey CBD Gummies R... | ["Steve Harvey CBD Gummies\n\n \n\n➢Product Name —Steve Harvey CBD Gummies Reviews\n➢Main Benefits—Improve Metabolism & Help in Pain Relief\n➢Composition —NaturalOrganic Compound\n➢Side-Effects—NA\n➢Rating :—⭐⭐⭐⭐⭐\n➢Availability —Online\n➢Price (for Sale) Buy Now Here —Click Here\nSteve Harvey CBD Gummies - You plan to... |
93,580 | OT-2 Counter-Selection | 5 | dx.doi.org/10.17504/protocols.io.5qpvor5xdv4o/v3 | https://www.protocols.io/view/ot-2-counter-selection-c7mkzk4w | Ana Mariya Anhel, Lorea Alejaldre, Ángel Goñi-Moreno | TITLE: OT-2 Counter-Selection
AUTHORS: Ana Mariya Anhel, Lorea Alejaldre, Ángel Goñi-Moreno
[DESCRIPTION]
This protocol is meant to select the samples from one or more source plate(s) that has 2 different selecting conditions: one condition gives higher values and the other lower values. From these selected samples th... | ["[Files Preparation] Preparing Customized Template\n\nPreparing the template (a .xlsx) with the specific variables for each experiment.\n\nHere we attach a template of the variable file with several sheets and a PDF file explaining each variable:\n\nGeneralVariables: variables related mainly to the labware that is goi... |
47,778 | Cell-based analysis of PINK1-Parkin pathway activation in primary mouse cortical neurons | 2 | dx.doi.org/10.17504/protocols.io.bswanfae | https://www.protocols.io/view/cell-based-analysis-of-pink1-parkin-pathway-activa-bswanfae | Odetta Antico, Miratul M. Muqit | TITLE: Cell-based analysis of PINK1-Parkin pathway activation in primary mouse cortical neurons
AUTHORS: Odetta Antico, Miratul M. Muqit
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Mutations in PINK1 cause early-onset Parkinson’s disease. PINK1 becomes stabilised and active upon mitochondrial d... | [] |
78,010 | iSeq Bacterial WGS Protocol using a quarter of the reagents | 1 | dx.doi.org/10.17504/protocols.io.6qpvr44rbgmk/v2 | https://www.protocols.io/view/iseq-bacterial-wgs-protocol-using-a-quarter-of-the-cqe2vtge | Sonsiray Alvarez Narvaez, Zhenyu Shen, Lifang Yan | TITLE: iSeq Bacterial WGS Protocol using a quarter of the reagents
AUTHORS: Sonsiray Alvarez Narvaez, Zhenyu Shen, Lifang Yan
[DESCRIPTION]
This is an adaptation of protocol https://dx.doi.org/10.17504/protocols.io.bij8kcrw in which initial the initial DNA concentration and library prep reagent volumes have been reduc... | ["[Bacterial propagation and DNA extraction] See \"guidelines and warnings\" for general precautions. \n\nAssemble the following materials and reagents:\n\n Kit and Reagent Components Amount for 1 sample Initials Qiagen DNeasy Blood & Tissue Kit Buffer ATL 180 μL ... |
59,741 | Detection and Quantification of Calcitonin Gene-Related Peptide in Human Blood Plasma using a Modified Enzyme-Linked Immunosorbent Assay | 1 | dx.doi.org/10.17504/protocols.io.3byl4b98jvo5/v1 | https://www.protocols.io/view/detection-and-quantification-of-calcitonin-gene-re-b6j5rcq6 | Pavan S. Krishnan, Fernando T. Zamuner, Carolyn M. Jenks, Yanjun Xie, Lisa Zhang, Mohammed Lehar, Marcos Iglesias Lozano, Neal S. Fedarko, Lauren R. DeVine, Mariana Brait, Robert N. Cole, John P. Carey | TITLE: Detection and Quantification of Calcitonin Gene-Related Peptide in Human Blood Plasma using a Modified Enzyme-Linked Immunosorbent Assay
AUTHORS: Pavan S. Krishnan, Fernando T. Zamuner, Carolyn M. Jenks, Yanjun Xie, Lisa Zhang, Mohammed Lehar, Marcos Iglesias Lozano, Neal S. Fedarko, Lauren R. DeVine, Mariana Br... | ["[Sample Collection and Preparation] Collect whole blood from antecubital vein into 6.0 mL BD Vacutainer EDTA collection tube", "[Sample Collection and Preparation] Centrifuge at 3000 rpm for 4 minutes at 4°C, within 60 minutes of blood collection", "[Sample Collection and Preparation] Take off plasma fraction with an... |
48,192 | Chimeric Protein-LG and Protein-LAG sandwich ELISA | 1 | dx.doi.org/10.17504/protocols.io.bta8nihw | https://www.protocols.io/view/chimeric-protein-lg-and-protein-lag-sandwich-elisa-bta8nihw | Angel Justiz-Vaillant | TITLE: Chimeric Protein-LG and Protein-LAG sandwich ELISA
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This ELISA is used to study the interactions between protein-LG (SpLG) and protein-LAG (PLAG) with different immunoglobulin preparations from mammals and avian sp... | ["This ELISA is used to study the interactions between protein-LG (SpLG) and protein-LAG (PLAG) with different immunoglobulin preparations from mammals and avian species. The 96 well microtiter plate was coated overnight at 4°C with 2 µg/µl per well of SpLG in carbonate-bicarbonate buffer pH 9.6.", "The plate was then ... |
28,049 | Protocol for bacterial depletion of Aiptasia anemones - Towards the generation of gnotobiotic/germ-free cnidarian host animals | null | dx.doi.org/10.17504/protocols.io.7mrhk56 | null | Rúben M Costa, Anny Cárdenas, Christian Voolstra | TITLE: Protocol for bacterial depletion of Aiptasia anemones - Towards the generation of gnotobiotic/germ-free cnidarian host animals
AUTHORS: Rúben M Costa, Anny Cárdenas, Christian Voolstra
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol aims to obtain bacteria-depleted Aiptasia poly... | ["[Rearing Protocol]\nPrepare Artificial seawater (ASW) by mixing reagents in MilliQ water and adjusting the pH of the final volume to 8.0-8.2. Filter through 0.22 µm pore size filter.", "[Rearing Protocol]\nPrepare the antibiotic solution (ABS) by mixing antibiotics with ASW and sterile filter the final solution throu... |
48,082 | Standards-Compliant General Protocol for Systematic Reviews | 1 | dx.doi.org/10.17504/protocols.io.n92ldydzxl5b/v2 | https://www.protocols.io/view/standards-compliant-general-protocol-for-systemati-bs7snhne | Paul Whaley, Stephen M Wattam | TITLE: Standards-Compliant General Protocol for Systematic Reviews
AUTHORS: Paul Whaley, Stephen M Wattam
[DESCRIPTION]
This general protocol is designed to support the planning of SRs that are concerned with the effects of environmental exposures human health outcomes, or the prevention or mitigation thereof.
It h... | ["[A. Securing capacity, competencies, and tools] [competencies] Assign team members to core systematic review competencies. \nCOSTER 1.1.1 / PRISMA-P 3b \n\nAssign a team member to each of the competencies listed below. \n\nMark the step as complete when at least one team member has been assigned to each competency.",... |
null | null | null | dx.doi.org/10.17504/protocols.io.q62dzge | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A protocol for quantification of circulating microRNA using TaqMan Low Density Array.</p>
<p>MicroRNAs are purified from platelet-poor plasma using Nucleospin columns</p>
<p>During the purification step samples are spiked with cel-miR-39 as a mean of technical normalization</... | [] |
59,852 | tetA dual selection protocols | 2 | dx.doi.org/10.17504/protocols.io.5jyl892y7v2w/v1 | https://www.protocols.io/view/teta-dual-selection-protocols-b6pkrdkw | Carolyn N Bayer, Ana Gabriela Veiga Sepulchro, Maja Rennig, Morten Norholm | TITLE: tetA dual selection protocols
AUTHORS: Carolyn N Bayer, Ana Gabriela Veiga Sepulchro, Maja Rennig, Morten Norholm
[DESCRIPTION]
Engineering of bacterial genomes is a fundamental craft in contemporary biotechnology. The ability to precisely edit bacterial chromosomes allows for the development of cells with sp... | [] |
27,379 | Evaluating the Clinical Cost-effectiveness of Two Primary Mental Health Service Frameworks in Yogyakarta, Indonesia | null | dx.doi.org/10.17504/protocols.io.6ythfwn | null | Sabrina Anjara, Chiara Bonetto, Carol Brayne, Tine Van Bortel | TITLE: Evaluating the Clinical Cost-effectiveness of Two Primary Mental Health Service Frameworks in Yogyakarta, Indonesia
AUTHORS: Sabrina Anjara, Chiara Bonetto, Carol Brayne, Tine Van Bortel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Background</span><span> ... | ["[DESIGN]\nStudy DesignThis study (“the trial”) set out to compare patient outcomes following usual care either by primary care doctors additionally trained in the Indonesian-adapted WHO mhGAP framework or clinical psychologists in the Specialist Co-location framework through a pragmatic, two-arm partially randomised,... |
63,868 | Bacterial Delivery System | 4 | dx.doi.org/10.17504/protocols.io.kqdg3pyjpl25/v1 | https://www.protocols.io/view/bacterial-delivery-system-cak4scyw | contact.microbialtec | TITLE: Bacterial Delivery System
AUTHORS: contact.microbialtec
[DESCRIPTION]
Protein synthesis can be controlled with the bacterial translation machinery. Control of invasion is necessary to carry the produced proteins into cells. Invasion requires both flagella and the type III secretion system-1 (T3SS-1). Flagella... | [] |
23,978 | (EN) Freezing Tissue in OCT using Isopentane - (FR) Congélation de tissus dans de l'OCT avec l'isopentane | null | dx.doi.org/10.17504/protocols.io.3nigmce | null | Liz Tuck, Heather Etchevers | TITLE: (EN) Freezing Tissue in OCT using Isopentane - (FR) Congélation de tissus dans de l'OCT avec l'isopentane
AUTHORS: Liz Tuck, Heather Etchevers
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><h1>Introduction</h1></div><div class = "text-block">This protocol describes how to freeze tissues in ... | ["On a downflow or fume hood: Place metal container on dry ice and half fill with isopentane (use enough iso-pentane to completely immerse the tissue pieces). Sous la hotte ou sorbonne : mettre le petit recipient sur carboglace et la remplir jusqu'à moins d'un centimère du bord avec de l'iso-pentane. Il faut que le niv... |
72,325 | Using ebFRET for Hidden Markov Modeling | 1 | null | https://www.protocols.io/view/using-ebfret-for-hidden-markov-modeling-civdue26 | Clark Fritsch | TITLE: Using ebFRET for Hidden Markov Modeling
AUTHORS: Clark Fritsch
[DESCRIPTION]
This protocol follows from the "Formatting Data for Use With ebFRET Hidden Markov Modeling Software" protocol and is the third step towards analyzing your single-molecule FRET traces using Hidden Markov Modeling. In this protocol, we t... | ["After creating your \".dat\" file for ebFRET, you need to open up MATLAB and open \"ebFRET\" by typing \"ebFRET = ebFRET()\" in the console, as shown below:\n\n \nThen click \"Enter\" and ebFRET will open. Because of the size of the program, it may take some time for it to open depending on the computer that you are... |
62,262 | The TARGET System: Rapid Identification of Direct Targets of Transcription Factors by Gene Regulation in Plant Cells | 4 | dx.doi.org/10.17504/protocols.io.rm7vz32yrgx1/v2 | https://www.protocols.io/view/the-target-system-rapid-identification-of-direct-t-b82wryfe | Matthew D. Brooks, Kelsey M. Reed, Gabriel Krouk, Gloria M. Coruzzi, Bastiaan O. R. Bargmann | TITLE: The TARGET System: Rapid Identification of Direct Targets of Transcription Factors by Gene Regulation in Plant Cells
AUTHORS: Matthew D. Brooks, Kelsey M. Reed, Gabriel Krouk, Gloria M. Coruzzi, Bastiaan O. R. Bargmann
[DESCRIPTION]
The TARGET system allows for the rapid identification of direct regulated gene ... | [] |
38,857 | nCoV-2019 sequencing protocol (RAPID barcoding, 1200bp amplicon) | 1 | null | https://www.protocols.io/view/ncov-2019-sequencing-protocol-rapid-barcoding-1200-bh7hj9j6 | Nikki Freed, Olin Silander | TITLE: nCoV-2019 sequencing protocol (RAPID barcoding, 1200bp amplicon)
AUTHORS: Nikki Freed, Olin Silander
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">To enable faster, easier sequencing of SARS-COV2 genomes with fewer steps than current methods, we use multiplexed 1200 base pair PCR amplicons ... | ["[cDNA preparation]\nMix the following components in an 0.2mL 8-strip tube;Component Volume50µM random hexamers 10mM dNTPs mix (10mM each) Template RNA Total\n1 µl\n1 µl\n11 µl\n13 µl\nViral RNA input from a clinical sample sho... |
26,315 | Growing bacteria in b-broth | null | dx.doi.org/10.17504/protocols.io.5xjg7kn | null | Cristian Riccio | TITLE: Growing bacteria in b-broth
AUTHORS: Cristian Riccio
[STEPS]
?. Find an isolated colony of bacteria on the agar plate.
?. At the Bunsen burner, touch the colony with the tip of a pipette tip and drop the pipette tip into a 100 ml bottle of b-broth.
?. Put the 100 ml bottle of b-broth with the bacteria in the in... | ["Find an isolated colony of bacteria on the agar plate.", "At the Bunsen burner, touch the colony with the tip of a pipette tip and drop the pipette tip into a 100 ml bottle of b-broth.", "Put the 100 ml bottle of b-broth with the bacteria in the incubator, 37 C for E. coli."] |
90,326 | ColabFold Protein Structure Prediction and Membrane Interaction Modeling | 1 | dx.doi.org/10.17504/protocols.io.rm7vzxod2gx1/v1 | https://www.protocols.io/view/colabfold-protein-structure-prediction-and-membran-c4fwytpe | Leonardo A Parra-Rivas | TITLE: ColabFold Protein Structure Prediction and Membrane Interaction Modeling
AUTHORS: Leonardo A Parra-Rivas
[DESCRIPTION]
ColabFold Protein Structure Prediction and Membrane Interaction Modeling
[STEPS]
1. Protein structures (WT and phospho-mutant α-syn) were predicted using ColabFold (https://colabfold.mmseqs.co... | ["Protein structures (WT and phospho-mutant α-syn) were predicted using ColabFold (https://colabfold.mmseqs.com/),which uses MMseqs2 for homology detection and multiple sequence alignment, and AlphaFold2 for simulated protein folding.", "The full-length human α-synuclein isoform 1 sequence (Uniprot, P37840-1) was inpu... |
null | null | null | dx.doi.org/10.17504/protocols.io.d5k84v | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<span style="color: #333333; font-family: helvetica, sans-serif; font-size: 14px; line-height: 21px;"><strong>Motivation:</strong> An important step of "metagenomics" analysis is the assembly of multiple genomes from mixed sequence reads of multiple species in a microbial commun... | [] |
77,543 | Protoplast Formation and Purification for Coccidioides | 4 | dx.doi.org/10.17504/protocols.io.4r3l27bbxg1y/v1 | https://www.protocols.io/view/protoplast-formation-and-purification-for-coccidio-cpyfvptn | Bridget M. Barker, Ashley Itogawa, Heather Mead, mitchellbryant, Austin Blackmon, Seth Charley | TITLE: Protoplast Formation and Purification for Coccidioides
AUTHORS: Bridget M. Barker, Ashley Itogawa, Heather Mead, mitchellbryant, Austin Blackmon, Seth Charley
[DESCRIPTION]
This protocol will allow the researcher to create protoplast of Coccidioides spp.
[BEFORE_START]
Make fresh reagents
[STEPS]
1. Place qua... | ["Place quantified Coccidioides spp. arthroconidia and other supplies needed in BSC. Inoculate 100 ml 1XGYE broth in a 250 ml filter-capped, baffled Erlenmeyer flask with up to 5 × 108 Coccidioides spp. arthroconidia and incubate at 30℃ with shaking (200RPM).", "Monitor the germination process using microscopy or cultu... |
71,386 | S1 Table. A general sample of the values of the specific activity of radionuclides in soil samples (Bq/kg), including values below MDA. | 1 | dx.doi.org/10.17504/protocols.io.e6nvwj5wzlmk/v1 | https://www.protocols.io/view/s1-table-a-general-sample-of-the-values-of-the-spe-chx2t7qe | Panitskiy | TITLE: S1 Table. A general sample of the values of the specific activity of radionuclides in soil samples (Bq/kg), including values below MDA.
AUTHORS: Panitskiy
[DESCRIPTION]
A general sample of the values of the specific activity of radionuclides in soil samples (Bq/kg), including values below MDA.
[STEPS] | [] |
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