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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97,191 | Plate Scale Tn5 based tagmentation library prep protocol | 1 | dx.doi.org/10.17504/protocols.io.4r3l2qmzpl1y/v1 | https://www.protocols.io/view/plate-scale-tn5-based-tagmentation-library-prep-pr-da6f2hbn | Cade Mirchandani, max genetti, Pingting Wang, Evan Pepper-Tunick, Shelbi Russell, Russell Corbett-Detig | TITLE: Plate Scale Tn5 based tagmentation library prep protocol
AUTHORS: Cade Mirchandani, max genetti, Pingting Wang, Evan Pepper-Tunick, Shelbi Russell, Russell Corbett-Detig
[DESCRIPTION]
This protocol is a fork of (dx.doi.org/10.17504/protocols.io.bv5gn83w), which a demonstrated efficient and high-throughput tagme... | ["[Transposon Assembly] Remove oligos Tn5ME-A, Tn5ME-B, Tn5ME-R, and Tn5 enzyme mix from freezer. Thaw primers, mix by vortexing and spin. Keep Tn5 enzyme on ice. Turn on 95 °C thermocycler.", "[Transposon Assembly] In separate PCR tubes combine:\n7 µL Tn5ME-A + 7 µL Tn5ME-R = AR oligo (14 µL)\n7 µL Tn5ME-B + 7 µL Tn5M... |
28,601 | Disruption of Synechocystis cells | null | dx.doi.org/10.17504/protocols.io.76zhrf6 | null | iGEM Dusseldorf | TITLE: Disruption of Synechocystis cells
AUTHORS: iGEM Dusseldorf
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for disrupting Synechocystis cells to get soluble and non-soluble protein in different fractions</div><div class = "text-block"><ul style = "list-style-type:disc;"><li style = "... | [] |
25,834 | Calibration Protocol - OD600 Inter-equipment Conversion with LUDOX | null | dx.doi.org/10.17504/protocols.io.5gig3ue | null | Paul Rutten, Richard Tennant, Jacob Beal, Traci Haddock-Angelli, Natalie Farny, Geoffrey Baldwin, Marko Storch, Ari Dwijayanti | TITLE: Calibration Protocol - OD600 Inter-equipment Conversion with LUDOX
AUTHORS: Paul Rutten, Richard Tennant, Jacob Beal, Traci Haddock-Angelli, Natalie Farny, Geoffrey Baldwin, Marko Storch, Ari Dwijayanti
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align... | ["[Data collection: OD 600 Reference point - LUDOX Protocol]\nAdd 100 μl LUDOX CL-X into wells A1, B1, C1, D1", "[Data collection: OD 600 Reference point - LUDOX Protocol]\nAdd 100 μl of ddH20 into wells A2, B2, C2, D2", "[Data collection: OD 600 Reference point - LUDOX Protocol]\nMeasure absorbance at 600 nm of all sa... |
81,462 | 10x Protocols: Visium v2 CytAssist FFPE Library Construction -- University of Minnesota TMCs (CG000495 Rev C) | 1 | dx.doi.org/10.17504/protocols.io.e6nvwj3zdlmk/v1 | https://www.protocols.io/view/10x-protocols-visium-v2-cytassist-ffpe-library-con-ctswwnfe | IOx Genomics, Laura J Niedernhofer, David A Bernlohr | TITLE: 10x Protocols: Visium v2 CytAssist FFPE Library Construction -- University of Minnesota TMCs (CG000495 Rev C)
AUTHORS: IOx Genomics, Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
Protocols from 10x Genomics for Visium Spatial Gene Expression v2 chemistry on FPPE samples with the CytAssist component.
Pro... | ["10x protocol CG000495, Revision C (Library construction with CytAssist)", "Additional Protocols/Resources\nhttps://www.10xgenomics.com/support/spatial-gene-expression-ffpe"] |
null | null | null | dx.doi.org/10.17504/protocols.io.cqavsd | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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47,622 | Expression and purification of Tribolium castaneum orthologue of PINK1 | 1 | dx.doi.org/10.17504/protocols.io.bsrend3e | https://www.protocols.io/view/expression-and-purification-of-tribolium-castaneum-bsrend3e | Olawale G. Raimi, Miratul M. K. Muqit | TITLE: Expression and purification of Tribolium castaneum orthologue of PINK1
AUTHORS: Olawale G. Raimi, Miratul M. K. Muqit
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Mutations in PINK1 (protein kinase) and Parkin (ubiquitin E3 ligase) have been linked to familial early-onset Parkinson’s disea... | ["[Transformation of competent bacteria]\nMix of pET 6His sumo codon optimised TcPINK1 150-end ΔI261-L270 S205E E527A K528A plasmid () with of the competent BL21(DE3) cells.\n1 µl\n50 µl", "[Transformation of competent bacteria]\nIncubate for .\non ice", "[Transformation of competent bacteria]\nHeat shock the cells i... |
92,308 | Protocol for performing PINK1 siRNA knockdown in mouse embryonic fibroblasts (MEFs) | 1 | dx.doi.org/10.17504/protocols.io.kxygx343zg8j/v1 | https://www.protocols.io/view/protocol-for-performing-pink1-sirna-knockdown-in-m-c6duza6w | Enrico Bagnoli, Miratul Muqit | TITLE: Protocol for performing PINK1 siRNA knockdown in mouse embryonic fibroblasts (MEFs)
AUTHORS: Enrico Bagnoli, Miratul Muqit
[DESCRIPTION]
This protocol details the siRNA knockdown in mouse embryonic fibroblasts (MEFs) for PINK1, but applicable for any other target.
[GUIDELINES]
72-Hr siRNA knockdown in MEFs in ... | ["[Day 1 - Cell Seeding and siRNA preparation] For Primary MEFs seed 200,000 cells per well in a 6-well plate at a total volume of 2 mL.", "[Day 1 - Cell Seeding and siRNA preparation] Add 400 µL of RNA-free water.", "[Day 1 - Cell Seeding and siRNA preparation] Incubate in hood for 5 min, vortex vigorously and store a... |
71,512 | Total RNA and DNA from Microalgae (12 samples per microplate) | 1 | dx.doi.org/10.17504/protocols.io.6qpvro85bvmk/v11 | https://www.protocols.io/view/total-rna-and-dna-from-microalgae-12-samples-per-m-ch3yt8pw | Ying-Yu Hu, Zoe V. Finkel | TITLE: Total RNA and DNA from Microalgae (12 samples per microplate)
AUTHORS: Ying-Yu Hu, Zoe V. Finkel
[DESCRIPTION]
Here we describe a protocol for extracting and quantifying bulk RNA and DNA from microalgae, which is adapted from Berdalet E. et al. (2005).
RNA and DNA are extracted from microalgae samples and the... | ["[Day 1: Freeze-dry samples] Freeze dry samples and blank filters. Freeze at -80 °C until processed.", "[Day 1: Prepare primary solutions] Turn on UV light in biosafety cabinet for 15 min", "[Day 1: Prepare primary solutions] Prepare Tris buffer 5 mM pH 8.0", "[Day 1: Prepare primary solutions] Pour 1 M pH 8.0 Tris ... |
70,629 | SOP for Spatial N-glycomics | 1 | null | https://www.protocols.io/view/sop-for-spatial-n-glycomics-cg8dtzs6 | Chris Anderton | TITLE: SOP for Spatial N-glycomics
AUTHORS: Chris Anderton
[DESCRIPTION]
This protocol describes the procedure to obtain high quality MALDI mass spectrometry images of N-linked glycans from formalin-fixed paraffin embedded tissue.
[STEPS]
SECTION: Scope
1. This protocol describes the procedure to obtain high quality ... | ["[Scope] This protocol describes the procedure to obtain high quality MALDI mass spectrometry images of N-linked glycans from formalin-fixed paraffin embedded tissue.", "[Health and Safety] Wear nitrile gloves and safety glasses. Follow standard laboratory safety procedures.", "[Procedure] Formalin fixed tissue should... |
106,703 | Miniscope calcium imaging data acquisition of cortical activity in non-human primates (NHPs) | 0 | dx.doi.org/10.17504/protocols.io.14egn612pl5d/v1 | https://www.protocols.io/view/miniscope-calcium-imaging-data-acquisition-of-cort-dkfp4tmn | Adriana Galvan, Thomas Wichmann | TITLE: Miniscope calcium imaging data acquisition of cortical activity in non-human primates (NHPs)
AUTHORS: Adriana Galvan, Thomas Wichmann
[DESCRIPTION]
The protocol describes head-mounted miniscope calcium imaging data acquisition for NHPs.
[GUIDELINES]
Introduction:
In recent years, calcium imaging has become a ... | ["[Procedure] The ability to image calcium transients requires prior placement of a GRIN lens assembly (as detailed in a separate protocol dx.doi.org/10.17504/protocols.io.e6nvw15w2lmk/v1).", "[Procedure] Calcium imaging starts several weeks after the cortical implantation of the GRIN lens assembly and injection of a v... |
28,216 | Making and running an acrylamide protein gel | null | dx.doi.org/10.17504/protocols.io.7syhnfw | null | Robert Hooftman | TITLE: Making and running an acrylamide protein gel
AUTHORS: Robert Hooftman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In this protocol, the preparation and running an acrylamide gel is explained. Using this gel, proteins with a size of >15 kDa can be visualized. For the visualization of prote... | ["Make the separation gel. In the separation gel, the proteins are separated by size. The following is needed for 10 ml of separation gel (add in the following order): ABC1Ingredients10% acrylamide gel12% acrylamide gel2dH2O 4.1 ml 3.4 ml 3Acrylamide (30%, 37.5:1; Bio-Rad) 3.3 ml 4 ml 4Tris-HCl (1.5 M, pH 8.8) 2.5 ml ... |
19,440 | Mindfulness and Empathy University of Burgos | null | dx.doi.org/10.17504/protocols.io.w8qfhvw | null | Juan Pablo Pizarro, Raquel De la Fuente Anuncibay, Ángela González Barbadillo, González-Bernal, Esther Cubo | TITLE: Mindfulness and Empathy University of Burgos
AUTHORS: Juan Pablo Pizarro, Raquel De la Fuente Anuncibay, Ángela González Barbadillo, González-Bernal, Esther Cubo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Mediating effect of mindfulness cognition on the development of empathy in a univer... | [] |
94,793 | Wheat disease symptoms observation, capture, description, and evaluation | 4 | dx.doi.org/10.17504/protocols.io.ewov1q67kgr2/v1 | https://www.protocols.io/view/wheat-disease-symptoms-observation-capture-descrip-c8thzwj6 | Erin H Hill, Benjamin Schwessinger | TITLE: Wheat disease symptoms observation, capture, description, and evaluation
AUTHORS: Erin H Hill, Benjamin Schwessinger
[DESCRIPTION]
This protocols is part of the ANU Biosecurity mini-research project #1 "Plant Pathogen Diagnostics: Visuals, subcultures, and genomics".
You will be provided four pots of 3-4 week... | ["[Disease symptom capture] You will receive five pots with wheat plants as detailed in the \"Description\" section. Please label each pot with your research group name, the date, and the treatment group.", "[Disease symptom capture] Carefully, study the plants in each pot. Select four to five leaves for each treatment... |
62,878 | Protocol: MHC class I and dengue hemorrhagic fever: a systematic review of HLA-A*24 and HLA-B*44 | 4 | dx.doi.org/10.17504/protocols.io.b9m6r49e | https://www.protocols.io/view/protocol-mhc-class-i-and-dengue-hemorrhagic-fever-b9m6r49e | Andrew C Cook, Dylan Thibaut | TITLE: Protocol: MHC class I and dengue hemorrhagic fever: a systematic review of HLA-A*24 and HLA-B*44
AUTHORS: Andrew C Cook, Dylan Thibaut
[DESCRIPTION]
This project will examine the effect of two MHC class I alleles, HLA-A*24 and HLA-B*44 on dengue hemorrhagic fever susceptibility. A systematic review will be con... | ["[Title] MHC class I and dengue hemorrhagic fever: a systematic review of HLA-A*24 and HLA-B*44", "[Introduction]", "[Methods]", "[Introduction] The association of HLA alleles with dengue fever and dengue hemorrhagic fever is a topic of research interest. Dengue fever has been evaluated for associations with HLA allel... |
null | null | null | dx.doi.org/10.17504/protocols.io.rtfd6jn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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?. | ["For inhibitors, freshly prepared aldose reductase (polyol pathway) inhibitor (Epalrestat, Sigma SML0527) and carnitine palmitoyltransferase-1 inhibitor (Etomoxir, Sigma E1905) were solubilised in water to prepare a 5 mM stock.", "Glycolysis inhibitor (2-Deoxy-D-Glucose, Sigma D8375) was solubilised in water to prepar... |
90,729 | Confocal-based bead-binding | 4 | dx.doi.org/10.17504/protocols.io.8epv5xdbng1b/v1 | https://www.protocols.io/view/confocal-based-bead-binding-c4uhywt6 | Dan Tudorica | TITLE: Confocal-based bead-binding
AUTHORS: Dan Tudorica
[DESCRIPTION]
Method of quantifying in vitro binding.
[STEPS]
SECTION: Protein preparation
1. In order to prepare proteins for a fluorescent bead-binding experiment, you need one protein that can bind a resin (in my case MBP-Rubicon RH domain, which can bind ... | ["[Protein preparation] In order to prepare proteins for a fluorescent bead-binding experiment, you need one protein that can bind a resin (in my case MBP-Rubicon RH domain, which can bind amylose resin) and a fluorescently labelled bait protein (in my case, Rab7-AlexaFluor 647).\n\nTo prepare my AlexaFluor 647, used a... |
8,041 | Carbonic Anhydrase Activity Assay | null | dx.doi.org/10.17504/protocols.io.j4hcqt6 | null | Jack Koch, Virginia Weis | TITLE: Carbonic Anhydrase Activity Assay
AUTHORS: Jack Koch, Virginia Weis
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Carbonic anhydrase (CA) is an enzyme which catalyzes the interconversion of bicarbonate ions (HCO</span><span style = "vertical-align:sub;vertical-align:super;">3</span><s... | ["[Mixing Carbonic Anhydrase (CA) Buffers]\nStock 50mM barbital buffer", "[Mixing Carbonic Anhydrase (CA) Buffers]\n25 mM Veronal buffer (Buffer A)Mix 250mL of 50mM barbital buffer with 250mL of deionized waterAdjust pH of Buffer A to 8.2 with 1M HCl", "[Mixing Carbonic Anhydrase (CA) Buffers]\nExtraction bufferMix 250... |
18,667 | Cleaning up a biohazardous spill outside of a biosafety cabinet | null | dx.doi.org/10.17504/protocols.io.wgjfbun | null | Steven Wilhelm, Gary LeCleir, Ashley Humphrey | TITLE: Cleaning up a biohazardous spill outside of a biosafety cabinet
AUTHORS: Steven Wilhelm, Gary LeCleir, Ashley Humphrey
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">BIOLOGICAL SPILL RESPONSE </span><span>method to be used in the event of a biosafety inciden... | ["Close off the area and allow aerosols to settle.", "Notify others including supervisor.", "Assemble all spill cleanup materials and review procedure.", "Don appropriate PPE: laboratory coat, safety glasses or chemical splash goggles (depending on risk of splashes), Nitrile gloves.", "Cover spill with paper towels.", ... |
40,289 | Purification of anti-anti-SpA antibody (Ab-2) using SpA-bearing Staphylococcus aureus cells. | 6 | dx.doi.org/10.17504/protocols.io.bjj9kkr6 | https://www.protocols.io/view/purification-of-anti-anti-spa-antibody-ab-2-using-bjj9kkr6 | Angel Justiz-Vaillant | TITLE: Purification of anti-anti-SpA antibody (Ab-2) using SpA-bearing Staphylococcus aureus cells.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">A novel method was designed for the purification of Ab-2 from undiluted WSF of hyperim... | ["Mix in an Eppendorf microtube 0.9 ml of undiluted WSF from immunized birds with 25 μl of SpA-bearing Staphylococcus aureus cells (Sigma-Aldrich).", "Incubate the microtube at 37oC for 30 min.", "After the incubation period, centrifuge the microtube in an Eppendorf 5424 centrifuge for 5 min.", "Observe the microtube t... |
null | null | null | dx.doi.org/10.17504/protocols.io.jk7ckzn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol can be used for mapping transcriptional start site(s) (TSS) of a specific gene of interest in bacteria.</p>
<p>By slightly modifying this protocol, whole transcriptome TSS could also potentially be mapped.</p>
[BEFORE_START]
<p>Oligos used:</p>
<table style="wi... | [] |
58,494 | Pharmacokinetics and bioequivalence of two imidocarb formulations in cattle after subcutaneous injection | 1 | dx.doi.org/10.17504/protocols.io.b5c6q2ze | https://www.protocols.io/view/pharmacokinetics-and-bioequivalence-of-two-imidoca-b5c6q2ze | Anonymous , Chen Chen, Maolin Liu, Xiaojie Chen, Chunshuang Liu, Yanyan Feng, Xinbo Yan, Yiming Liu, Xiubo Li, Honglei Wang | TITLE: Pharmacokinetics and bioequivalence of two imidocarb formulations in cattle after subcutaneous injection
AUTHORS: Anonymous , Chen Chen, Maolin Liu, Xiaojie Chen, Chunshuang Liu, Yanyan Feng, Xinbo Yan, Yiming Liu, Xiubo Li, Honglei Wang
[DESCRIPTION]
Imidocarb (IMD) is commonly used for treatment of eperythro... | ["Sample collection \nBlood samples (10–15 mL) were collected from the jugular vein at 0 h before administration and 10 min, 30 min, 1, 2, 4, 6, 8, 10, 12, 24, 48, 72 and 96 h after subcutaneous administration, and were drawn in vacutainers containing disodium EDTA as anticoagulant. The samples were immediately centrif... |
74,738 | Recombinant protein expression and purification of fuGFP | 4 | dx.doi.org/10.17504/protocols.io.e6nvwje79lmk/v1 | https://www.protocols.io/view/recombinant-protein-expression-and-purification-of-ck8suzwe | Javiera A Avilés, Tamara Matute, Isaac Núñez, Maira Rivera, Javiera Reyes, Anibal Arce Medina, Cesar A Ramirez-Sarmiento, Fernan Federici | TITLE: Recombinant protein expression and purification of fuGFP
AUTHORS: Javiera A Avilés, Tamara Matute, Isaac Núñez, Maira Rivera, Javiera Reyes, Anibal Arce Medina, Cesar A Ramirez-Sarmiento, Fernan Federici
[DESCRIPTION]
This protocol has been optimized for the recombinant expression of fuGFP encoded in an open ... | ["[DAY 1 – Plasmid transformation] Transform 100 ngof the open pTi plasmid containing fuGFP into E. coli BL21 (DE3) 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.",... |
58,696 | Biolistic transformation of Pseudo-nitzschia multistriata | 4 | dx.doi.org/10.17504/protocols.io.b5jgq4jw | https://www.protocols.io/view/biolistic-transformation-of-pseudo-nitzschia-multi-b5jgq4jw | Anna Santin, Monia Teresa Russo, Pina Marotta, Francesco Manfellotto, Antonella Ruggiero, Mariella Ferrante | TITLE: Biolistic transformation of Pseudo-nitzschia multistriata
AUTHORS: Anna Santin, Monia Teresa Russo, Pina Marotta, Francesco Manfellotto, Antonella Ruggiero, Mariella Ferrante
[DESCRIPTION]
Optimized protol to transform the pennate diatom Pseuodo-nitzschia multistriata.
[STEPS]
SECTION: First day: Cells... | ["[First day: Cells plating] Plate 5 x 106 cells of P. multistriata culture in exponential phase (1.5-2 x 105 cells/ml) on 0.4% agarose in F/2 plates. Make a circular cell mat of diameter 4 cm.", "Sterilize rapture disks and macrocarriers by soaking for 15 min in 70% EtOH, then allow them to dry in sterile hood.", "[Be... |
70,383 | OT-2 PCR sample preparation protocol | 5 | dx.doi.org/10.17504/protocols.io.n92ldpyznl5b/v1 | https://www.protocols.io/view/ot-2-pcr-sample-preparation-protocol-cgyptxvn | Ana Mariya Anhel, Lorea Alejaldre, Manuel Gimenez, Ángel Goñi-Moreno | TITLE: OT-2 PCR sample preparation protocol
AUTHORS: Ana Mariya Anhel, Lorea Alejaldre, Manuel Gimenez, Ángel Goñi-Moreno
[DESCRIPTION]
This protocol is meant to perform samples preparation of PCR plates for several primer sets to the same samples, i.e, we will have for all the selected samples (we can set the initi... | ["[Files Preparation] Preparing Customized Template\n\nPreparing the template (a .csv) with the specific variables for each experiment.\n\nHere we attach one excel with several sheets:\nTemplate to use in protocol\nExplanation of each variable\nSeveral examples", "[Running Protocol] Setting Labware", "[After-running] R... |
63,843 | Quant-IT DNA Quantification (Assay) | 4 | null | https://www.protocols.io/view/quant-it-dna-quantification-assay-cakbscsn | Allyson Hirsch, George Testo | TITLE: Quant-IT DNA Quantification (Assay)
AUTHORS: Allyson Hirsch, George Testo
[DESCRIPTION]
Perform dsDNA quantification easily and quickly with Quant-iT dsDNA assay kits. Both the Quant-iT High-Sensitivity dsDNA Assay Kit and the Quant-iT Broad-Range dsDNA Assay Kit provide concentrated assay reagent, dilution bu... | ["[Making Working Solution] Make working solution (number of samples + 24 standards + 10% = total volume).", "[Making Working Solution] 200uL Buffer (per sample) + 1uL Reagent (per sample)", "[Making Working Solution] Cover conical with a foil seal to prevent light exposure.", "[Making Working Solution] Vortex working ... |
89,686 | Protocol for Facially Guided Digital Diagnosis in Orthodontics | 1 | dx.doi.org/10.17504/protocols.io.8epv5x9q6g1b/v2 | https://www.protocols.io/view/protocol-for-facially-guided-digital-diagnosis-in-c3twynpe | Rupert HG Kelley, Álvaro Ferrando Cascales, Raúl Ferrando Cascales | TITLE: Protocol for Facially Guided Digital Diagnosis in Orthodontics
AUTHORS: Rupert HG Kelley, Álvaro Ferrando Cascales, Raúl Ferrando Cascales
[DESCRIPTION]
As the digital age of dentistry continues to flourish, it has never been more important to have protocols to guide dentists through the planning and performan... | ["[Treatment Planning] Records: NHP pictures, STL and DICOM files", "[Treatment Planning] Orientation and alignment of STL and DICOM files with photographs\n\nOnce all the records have been obtained, the digital impressions (STLs) can be superimposed onto the natural head position photographs using a software package s... |
60,003 | Shipping wastewater samples to FDA-CFSAN | 1 | dx.doi.org/10.17504/protocols.io.14egn797zv5d/v1 | https://www.protocols.io/view/shipping-wastewater-samples-to-fda-cfsan-b6ubresn | Maria Balkey | TITLE: Shipping wastewater samples to FDA-CFSAN
AUTHORS: Maria Balkey
[DESCRIPTION]
This SOP provides guidance for shipping wastewater samples to the US FDA Center for Food Safety and Applied Nutrition (CFSAN), covering specific steps for registering samples with CFSAN and for the preparation of shipments (documenta... | ["[Submission of metadata] Fill out the BioSample custom wastewater template (extension of NCBI's Generic SARS-CoV-2: wastewater surveillance, v1.0 ) according to the NCBI submission protocol for SARS-Cov-2 protocol, once completed, send it to covidtrakr@fda.hhs.gov for registration. Successful registrations will re... |
73,191 | Staining of Gfap, Iba1,and NeuN on PFA-fixed mouse brain sections | 1 | dx.doi.org/10.17504/protocols.io.4r3l27q5pg1y/v1 | https://www.protocols.io/view/staining-of-gfap-iba1-and-neun-on-pfa-fixed-mouse-cjqfumtn | Daniel Manrique-Castano | TITLE: Staining of Gfap, Iba1,and NeuN on PFA-fixed mouse brain sections
AUTHORS: Daniel Manrique-Castano
[DESCRIPTION]
Staining protocol for Gfap, Iba1, and NeuN on PFA-fixed mouse brain sections.
[GUIDELINES]
Read the full protocol before starting the procedure.
Note that this protocol uses 3 hours (room temperat... | ["[Tissue preparation and blocking] Take out sections from -80 and place them in an incubator/plate for 20 min at 37 °C. This step is performed to ensure tissue attachment to the crystal slides.", "[Tissue preparation and blocking] 2. Draw a hydrophobic barrier on each slide using ImmEdge®Hydrophobic Barrier PAP Pen a... |
60,419 | Activation Induced Marker (AIM) Staining Protocol | 4 | dx.doi.org/10.17504/protocols.io.4r3l2o9w3v1y/v1 | https://www.protocols.io/view/activation-induced-marker-aim-staining-protocol-b69brh2n | Gregory P. Williams, cecilia | TITLE: Activation Induced Marker (AIM) Staining Protocol
AUTHORS: Gregory P. Williams, cecilia
[DESCRIPTION]
This protocol details about activation induced marker staining.
[STEPS]
SECTION: Peptide Stimulation Solution
1. Label U-bottom plate with donor, stimulation solution, name and date.
SECTION: Peptide Stimulati... | ["[Peptide Stimulation Solution] Label U-bottom plate with donor, stimulation solution, name and date.", "[Peptide Stimulation Solution] Prepare PHA and DMSO mix separately", "[Peptide Stimulation Solution] Prepare and arrange the remaining stimulation solution. Mix thoroughly by pipetting up and down before adding to ... |
41,198 | HTAPP_Dissociation of primary neuroblastoma core needle biopsy to a single-cell suspension for single-cell RNA-seq (using papain, density gradient, and optionally ACK) | 1 | dx.doi.org/10.17504/protocols.io.bkgnktve | https://www.protocols.io/view/htapp-dissociation-of-primary-neuroblastoma-core-n-bkgnktve | Sara Napolitano, Jingyi Wu, Michal Slyper, Sébastien Vigneau, Asaf Rotem, Bruce Johnson, Orit Rozenblatt-Rosen, Aviv Regev | TITLE: HTAPP_Dissociation of primary neuroblastoma core needle biopsy to a single-cell suspension for single-cell RNA-seq (using papain, density gradient, and optionally ACK)
AUTHORS: Sara Napolitano, Jingyi Wu, Michal Slyper, Sébastien Vigneau, Asaf Rotem, Bruce Johnson, Orit Rozenblatt-Rosen, Aviv Regev
[DESCRIPTIO... | ["[Tissue Description]\nReport sample processing information.\nSample ID:Date:Time Received:Anatomical Site of the Biopsy:Number of Biopsy Cores:Core(s) Priority Number:Media Used for Transportation:Person Processing:", "[Tissue Description]\nTransfer sample to a Petri dish with cold PBS kept on ice to better visualize... |
94,958 | Assessing Growth Parameters in amphipod, Parhyale hawaiensis: Weighing and Measuring Length | 4 | dx.doi.org/10.17504/protocols.io.6qpvr3552vmk/v1 | https://www.protocols.io/view/assessing-growth-parameters-in-amphipod-parhyale-h-c8ynzxve | Ibrahim Lawan | TITLE: Assessing Growth Parameters in amphipod, Parhyale hawaiensis: Weighing and Measuring Length
AUTHORS: Ibrahim Lawan
[DESCRIPTION]
The developed protocol provides a standardised method for precisely determining the weight and length of Parhyale hawaiensis, a crucial model organism in ecotoxicology and ecophysiolo... | ["[Introduction] Parhyale hawaiensis is a circumtropical marine amphipod crucial for epibenthic communities in tropical marine ecosystems (Poovachiranon et al., 1986). This amphipod has gained recognition for its sensitivity to environmental stressors and ecological significance, making it a promising model organism fo... |
null | null | null | dx.doi.org/10.17504/protocols.io.im6cc9e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Southeast (SE) Asia is one of the most biodiverse regions in the world and it holds approximately 20% of all mammal species. Despite this, the majority of SE Asia’s genetic diversity is still poorly characterized. The growing interest in using environmental DNA (eDNA) to asse... | [] |
86,796 | The Anniversary Study – 20 years of Clavien-Dindo Classification & 10 years of Comprehensive Complication Index® | 1 | dx.doi.org/10.17504/protocols.io.bp2l6xxzrlqe/v1 | https://www.protocols.io/view/the-anniversary-study-20-years-of-clavien-dindo-cl-cyzkxx4w | Fariba Abbassi, Matthias Pfister, Anja Domenghino, Milo A Puhan, Pierre-A. Clavien | TITLE: The Anniversary Study – 20 years of Clavien-Dindo Classification & 10 years of Comprehensive Complication Index®
AUTHORS: Fariba Abbassi, Matthias Pfister, Anja Domenghino, Milo A Puhan, Pierre-A. Clavien
[DESCRIPTION]
Outcome reporting of surgical procedures was revolutionized in 2004 with the introducti... | ["[Background] Outcome reporting of surgical procedures was revolutionized in 2004 with the introduction of the Clavien-Dindo (CD) classification.1 This 5-scale grading system offers an objective, simple, reliable, and reproducible way of recording complications, and has gained wide acceptance among the international s... |
63,327 | Trim Clinical Keto Review | 3 | dx.doi.org/10.17504/protocols.io.14egn7n5yv5d/v1 | https://www.protocols.io/view/trim-clinical-keto-review-b937r8rn | JeffDlton | TITLE: Trim Clinical Keto Review
AUTHORS: JeffDlton
[DESCRIPTION]
Trim Clinical Keto is a fat burner formula to get you a slim & trim figure Safe For You Buy Now On The Official Website
[STEPS] | [] |
71,490 | Protocols from Kilfeather, Khoo et al., 2024 | 2 | dx.doi.org/10.17504/protocols.io.36wgqj75kvk5/v1 | https://www.protocols.io/view/protocols-from-kilfeather-khoo-et-al-2024-ch3at8ie | Peter Kilfeather, Maria Claudia Caiazza | TITLE: Protocols from Kilfeather, Khoo et al., 2024
AUTHORS: Peter Kilfeather, Maria Claudia Caiazza
[DESCRIPTION]
This protocol collection includes immunohisto/chemical staining methods, DAT-TRAP methods and the protocol for the Fura-2 assay in Kilfeather, Khoo et al., 2024.
[STEPS] | [] |
38,319 | fatty acid analysis sponges | 6 | dx.doi.org/10.17504/protocols.io.bhnpj5dn | https://www.protocols.io/view/fatty-acid-analysis-sponges-bhnpj5dn | Anna de Kluijver | TITLE: fatty acid analysis sponges
AUTHORS: Anna de Kluijver
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol has been used to analyse fatty acid composition of sponges (Porifera). The original protocol has been developed at NIOZ Yerseke, former NIOO-CEME (Netherlands) (Boschker and Mi... | ["[Total lipid extraction]\nAdd Blight and Dyer mix, close with lid and shake/vortex\n28.5 mL", "[Total lipid extraction]\nWeight 30-50 mg dried sponge sample in extraction tubes (Kimax®centrifuge tube). This amount is enough to do either lipid-class or total lipid analysis, if you want to do both, weight a double a... |
54,355 | Bacterial isolation and genomic DNA extraction of Mycobacterium avium from pig lymph nodes | 2 | dx.doi.org/10.17504/protocols.io.bzbtp2nn | https://www.protocols.io/view/bacterial-isolation-and-genomic-dna-extraction-of-bzbtp2nn | Tetsuya Komatsu, Kenji Ohya, Justice Opare Odoi, Shota Suganuma, Kotaro Sawai, Takayuki Wada, Tomotada Iwamoto, Fumito Maruyama | TITLE: Bacterial isolation and genomic DNA extraction of Mycobacterium avium from pig lymph nodes
AUTHORS: Tetsuya Komatsu, Kenji Ohya, Justice Opare Odoi, Shota Suganuma, Kotaro Sawai, Takayuki Wada, Tomotada Iwamoto, Fumito Maruyama
[DESCRIPTION]
Mycobacterium avium subsp. hominissuis (MAH) is one of the most impor... | [] |
38,236 | SEM Metal Sputter Coater User Guide | 1 | dx.doi.org/10.17504/protocols.io.yxmvmxjynl3p/v1 | https://www.protocols.io/view/sem-metal-sputter-coater-user-guide-bhj4j4qw | Dakota Betz | TITLE: SEM Metal Sputter Coater User Guide
AUTHORS: Dakota Betz
[DESCRIPTION]
How to use the SEM Metal Sputter Coater at SIO.
[STEPS]
3. Turn on the Argon (gas cylinder in the corner of the room, the first one (check that it doesn't say nitrogen), turn the knob to the left just until you feel it give way and Ar start... | ["Turn on the Argon (gas cylinder in the corner of the room, the first one (check that it doesn't say nitrogen), turn the knob to the left just until you feel it give way and Ar starts to flow).", "To put specimens in the sputter coater, WITH GLOVES, carefully open the canister lid and with your non-dominant hand pick ... |
46,953 | qPCR Primer Design | 1 | dx.doi.org/10.17504/protocols.io.br4hm8t6 | https://www.protocols.io/view/qpcr-primer-design-br4hm8t6 | Steven Burgess | TITLE: qPCR Primer Design
AUTHORS: Steven Burgess
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for designing qPCR primers for analysis of transcript abundance using SYBR Green chemistry.</div><div class = "text-block"><span>There are many good guides about how to do this online such as <... | ["[Identify target sequence]\nDecide on a gene of interest, download the transcript sequence in .gb format and upload to a new folder on Benchling for analysis.\nIf analyzing an endogenous (as compared to transgene), gene sequences can be obtained from public databases such as NCBI. For many plant genes, my preference ... |
26,070 | EASY AND INEXPENSIVE NUCLEIC ACID EXTRACTION PROTOCOL FOR RECALCITRANT SPECIES | null | dx.doi.org/10.17504/protocols.io.5pwg5pe | null | Lilian Matallana, Yusuf Kurt, William Kohlway, John Frampton, Ross Whetten | TITLE: EASY AND INEXPENSIVE NUCLEIC ACID EXTRACTION PROTOCOL FOR RECALCITRANT SPECIES
AUTHORS: Lilian Matallana, Yusuf Kurt, William Kohlway, John Frampton, Ross Whetten
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Background</span><span>: Some of the major co... | ["[Prepare lysate]\nThis section provides guidelines and instructions to isolate DNA and RNA from different types of tissues and plant species. A general protocol is described but users need to read carefully for specific instructions to improve the quality and yield of the isolated genomic material. We have tested bot... |
19,744 | U Mass - STZ-induced type 1 diabetes model | null | dx.doi.org/10.17504/protocols.io.xh8fj9w | null | Jason Kim | TITLE: U Mass - STZ-induced type 1 diabetes model
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span><span style = "font-weight:bold;"> </span></div><div class = "text-block">Streptozotocin can selectively destroy the pancreatic β-cell... | ["Administer an intraperitoneal injection of streptozotocin (50 mg/kg body weight) daily for 5 days.", "Monitor glucose level for onset of hyperglycemia."] |
41,765 | Aegea Biotechnologies rapid PCR SARS-CoV-2 test (high sensitivity & specificity; able to detect different strain types) | 4 | dx.doi.org/10.17504/protocols.io.bk2dkya6 | https://www.protocols.io/view/aegea-biotechnologies-rapid-pcr-sars-cov-2-test-hi-bk2dkya6 | Lyle J. Arnold Ph.D., Stella M. Sung Ph.D. | TITLE: Aegea Biotechnologies rapid PCR SARS-CoV-2 test (high sensitivity & specificity; able to detect different strain types)
AUTHORS: Lyle J. Arnold Ph.D., Stella M. Sung Ph.D.
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is for the Aegea Biotechnologies rapid PCR-based SARS-CoV-2... | ["Prepare Reaction Mix10ul of the isolated total RNA will be used in a 20ul reaction with TaqPath™ 1-Step RT-qPCR Master Mix (5ul TaqPath Mastermix and 5ul of an oligo mix containing a. 0.5uM AEGEASwitch-Blocker (FAM),b. 0.5uM AEGEA COVID Forward Primer C, c. 2uM AEGEA COVID Reverse Primer, d. 0.8uM AEGEA L-Strain ... |
36,739 | Zooarchaeology by Mass Spectrometry (ZooMS) for bone material - Acid soluble protocol | 1 | dx.doi.org/10.17504/protocols.io.bf5bjq2n | https://www.protocols.io/view/zooarchaeology-by-mass-spectrometry-zooms-for-bone-bf5bjq2n | Samantha Brown, Sandra Hebestreit, Naihui Wang, Nicole Boivin, Katerina Douka, Kristine Richter | TITLE: Zooarchaeology by Mass Spectrometry (ZooMS) for bone material - Acid soluble protocol
AUTHORS: Samantha Brown, Sandra Hebestreit, Naihui Wang, Nicole Boivin, Katerina Douka, Kristine Richter
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This collection details the different established prot... | ["[Reagent preparation]\nGeneral Information:We recommend to use glassware for buffers and solutions and no long-term storage in plastic containers and/or tubes.TFA, HCl and ACN stock solutions should be handled under a fume hood only.Always label all chemicals with the compound name, concentraion and the date.Chemical... |
81,531 | An affordable solution for investigating zebra finch intracranial EEG signals | 1 | dx.doi.org/10.17504/protocols.io.q26g7y2w8gwz/v1 | https://www.protocols.io/view/an-affordable-solution-for-investigating-zebra-fin-ctu3wnyn | Mohammad-Mahdi Abolghasemi, Shahrar Rezghi Shirsavar, Milad Yekani | TITLE: An affordable solution for investigating zebra finch intracranial EEG signals
AUTHORS: Mohammad-Mahdi Abolghasemi, Shahrar Rezghi Shirsavar, Milad Yekani
[DESCRIPTION]
The Zebra finch is a well-studied model animal for neural mechanisms of speech, and Electrophysiology is the primary technique for understandi... | ["[Hardware preparation] Electrode preparation:\nFor recording electrodes, we used 2.5 cm of stainless steel wire and uncoat two ends of it with a scalpel blade. \nmake a loop in one end about 1 or 2mm in diameter. use a surgical clamp to bend it. \nDo not make a bigger loop, it may not fit into the hole in the sk... |
47,326 | Immunofluorescence staining of PFA or fresh frozen mouse brain section | 4 | null | https://www.protocols.io/view/immunofluorescence-staining-of-pfa-or-fresh-frozen-bsf6nbre | Daniel Manrique-Castano | TITLE: Immunofluorescence staining of PFA or fresh frozen mouse brain section
AUTHORS: Daniel Manrique-Castano
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is suitable for immunofluorescence staining of PFA fixed or Fresh Frozen mouse brain sections.</div></div>
[STEPS]
?. [Rehydra... | ["[Rehydration and permeabilization]\nIf fixed sections are kept in , rehydrate them before starting the staining procedure by incubating themin PBS for .\n-80 °C\nFor fresh frozen sections kept at , incubate with PFA during followed by 3 washes in PBS, each.", "[Rehydration and permeabilization]\nTo permeabi... |
63,378 | Where Can I Buy Ikaria Lean Belly Juice: Does It Work?? Must Know !! | 3 | dx.doi.org/10.17504/protocols.io.261genjp7g47/v1 | https://www.protocols.io/view/where-can-i-buy-ikaria-lean-belly-juice-does-it-wo-b95sr86e | healthodiet | TITLE: Where Can I Buy Ikaria Lean Belly Juice: Does It Work?? Must Know !!
AUTHORS: healthodiet
[DESCRIPTION]
Where Can I Buy Ikaria Lean Belly Juice: Does It Work?? Must Know !!
[STEPS] | [] |
61,564 | Getting started with Micro-Meta App Tutorial | 5 | null | https://www.protocols.io/view/getting-started-with-micro-meta-app-tutorial-b8c4rsyw | Alessandro Rigano, Mathias Hammer, Joel Ryan, Claire M. Brown, David Grunwald, Caterina Strambio De Castillia | TITLE: Getting started with Micro-Meta App Tutorial
AUTHORS: Alessandro Rigano, Mathias Hammer, Joel Ryan, Claire M. Brown, David Grunwald, Caterina Strambio De Castillia
[DESCRIPTION]
For quality, interpretation, reproducibility, and sharing value, microscopy images should be accompanied by detailed descripti... | ["[Before the tutorial] Video introduction", "[Tutorial - 1 - Download and Install Micro-Meta App] Download Micro-Meta App\n\nFollow the instructions in this step and in Video 3 of the tutorial series to download and install the stand-alone version of the Micro-Meta App.", "[Tutorial - 1 - Download and Install Micro-Me... |
61,921 | Custom Peptide Design | 6 | dx.doi.org/10.17504/protocols.io.ewov1n35ygr2/v1 | https://www.protocols.io/view/custom-peptide-design-b8p9rvr6 | Cathy Miller | TITLE: Custom Peptide Design
AUTHORS: Cathy Miller
[DESCRIPTION]
Interested in the use of biologically active proteins and peptides as potential therapeutic agents has grown dramatically in recent years. Although many meaningful studies can be performed, it is important to consider several factors such as the length ... | [] |
44,232 | Stable transfection of unicellular relative of animals, Corallochytrium limacisporum, using Lonza Nucleofector | 1 | null | https://www.protocols.io/view/stable-transfection-of-unicellular-relative-of-ani-bpfgmjjw | Aleksandra Kozyczkowska, Sebastian Najle, Eduard Ocaña-Pallarès, Cristina Aresté, Iñaki Ruiz-Trillo, Elena Casacuberta | TITLE: Stable transfection of unicellular relative of animals, Corallochytrium limacisporum, using Lonza Nucleofector
AUTHORS: Aleksandra Kozyczkowska, Sebastian Najle, Eduard Ocaña-Pallarès, Cristina Aresté, Iñaki Ruiz-Trillo, Elena Casacuberta
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span... | ["[Cell Culture preparation ]\nInoculate 100 μl of C. limacisporum culture in 5ml of Marine Broth in 25cm2 flask. Keep at 23°C air incubator for two days.", "[Cell count]\nScrape gently and count cells to reach 1.5E6 cells / condition using hemocytometerIf there are more conditions, it is recommended to pull the cells ... |
37,930 | Perceptions, knowledge and attitudes of the adult populations towards COVID-19 : A scoping review protocol | 1 | dx.doi.org/10.17504/protocols.io.bhaij2ce | https://www.protocols.io/view/perceptions-knowledge-and-attitudes-of-the-adult-p-bhaij2ce | Nathalie Clavel, Mathieu Seppey, Lara Gautier, Mélanie Lavoie-Tremblay | TITLE: Perceptions, knowledge and attitudes of the adult populations towards COVID-19 : A scoping review protocol
AUTHORS: Nathalie Clavel, Mathieu Seppey, Lara Gautier, Mélanie Lavoie-Tremblay
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Perceptions, knowledge and attitudes of the adult populati... | ["[Title and author identification]\nPerceptions, knowledge and attitudes of the adult populations towards COVID-19 : A scoping review protocol Nathalie Clavel1, Mathieu Seppey2, Lara Gautier2,3, Mélanie Lavoie-Tremblay11 Ingram School of Nursing, McGill University2 School of Public Health, University of Montreal 3 Dep... |
54,816 | Diagnostic accuracy of home sleep apnea testing using peripheral arterial tonometry for sleep apnea syndrome: protocol for a systematic review and meta-analysis | 1 | dx.doi.org/10.17504/protocols.io.bzr8p59w | https://www.protocols.io/view/diagnostic-accuracy-of-home-sleep-apnea-testing-us-bzr8p59w | Masahiro Ichikawa, Tomoaki Akiyama, Yasushi Tsujimoto, Keisuke Anan, Tadashi Yamakawa, Yasuo Terauchi | TITLE: Diagnostic accuracy of home sleep apnea testing using peripheral arterial tonometry for sleep apnea syndrome: protocol for a systematic review and meta-analysis
AUTHORS: Masahiro Ichikawa, Tomoaki Akiyama, Yasushi Tsujimoto, Keisuke Anan, Tadashi Yamakawa, Yasuo Terauchi
[DESCRIPTION]
INTRODUCTION
Ratio... | [] |
75,908 | Protocol: Neutrophil/lymphocyte ratio and overall survival in patients with breast cancer: a cohort study in a Latin-American hospital | 1 | dx.doi.org/10.17504/protocols.io.kxygx95xdg8j/v1 | https://www.protocols.io/view/protocol-neutrophil-lymphocyte-ratio-and-overall-s-cndcva2w | Martha Sofia Cervera-Ocaña, Jhony A. De La Cruz-Vargas, Dante Manuel Quiñones-Laveriano, Nataly Briyit Huamán Córdova | TITLE: Protocol: Neutrophil/lymphocyte ratio and overall survival in patients with breast cancer: a cohort study in a Latin-American hospital
AUTHORS: Martha Sofia Cervera-Ocaña, Jhony A. De La Cruz-Vargas, Dante Manuel Quiñones-Laveriano, Nataly Briyit Huamán Córdova
[DESCRIPTION]
PURPOSE OF STUDY
The primary objecti... | ["[Neutrophil/lymphocyte ratio and overall survival in patients with breast cancer: a cohort study in a Latin-American hospital]"] |
106,575 | MRI_preprocessing_protocol | 0 | dx.doi.org/10.17504/protocols.io.14egn61byl5d/v1 | https://www.protocols.io/view/mri-preprocessing-protocol-dkbp4smn | Miguel López-Aguirre, José A. Pineda-Pardo, Jose Obeso | TITLE: MRI_preprocessing_protocol
AUTHORS: Miguel López-Aguirre, José A. Pineda-Pardo, Jose Obeso
[DESCRIPTION]
Preprocessing protocol for structural, DWI and T2* MRI acquisitions
[STEPS]
SECTION: Structural T1w (MP-RAGE acquisition)
1. Data transformation from DICOM to NIFTI standard (software: dcm2niix)
SECTION: S... | ["[Structural T1w (MP-RAGE acquisition)] Data transformation from DICOM to NIFTI standard (software: dcm2niix)", "[Structural T1w (MP-RAGE acquisition)] Field of view optimization (command: fslreorient2std; software: FSL)", "[Structural T1w (MP-RAGE acquisition)] Bias field correction (command: N4BiasFieldCorrection; s... |
41,075 | TMA-TNP Section Map and Slide Processing - Phase 1 | 1 | dx.doi.org/10.17504/protocols.io.bkctkswn | https://www.protocols.io/view/tma-tnp-section-map-and-slide-processing-phase-1-bkctkswn | Heidi Feiler, Koei Chin | TITLE: TMA-TNP Section Map and Slide Processing - Phase 1
AUTHORS: Heidi Feiler, Koei Chin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Human Tumor Atlas Tissue MicroArrary TNP (TMA-TNP)</div><br/><div class = "text-block">The Tissue MicroArray (TMA) TNP will extend the SARDANA-TNP characteriz... | ["[Preparation]\nVerify the identity of the FFPE block to be cut against written request for sectioning. The FFPE block (TMA1) will be utilized for TMA-TNP Phase 1.", "[Preparation]\nEach slide was labeled with a unique OHSU Slide ID corresponding to the FFPE section map (below). ABCDE1 Slide ID &nbs... |
63,348 | Production: 10x TBE Buffer Powder Sachets | 4 | null | https://www.protocols.io/view/production-10x-tbe-buffer-powder-sachets-b94ur8ww | Jenny Molloy, Nadine Mowoh, Stephane Fadanka | TITLE: Production: 10x TBE Buffer Powder Sachets
AUTHORS: Jenny Molloy, Nadine Mowoh, Stephane Fadanka
[DESCRIPTION]
Desired concentrations of Components in the 10x buffer
Boric acid-0.89M
Tris-0.89M
Na2EDTA-0.02M
Concentration of 1x TBE buffer
Tris-Borate-0.089M
Na2EDTA-0.002M
[BEFORE_START]
Ensure all powder... | ["Weigh about 35 g of Boric acid into a weighing boat and place the weighing boat in a vacuum tupperware half-filled with silica gel beads.", "Close the tupperware and use the vacuum pump to create a vacuum until you are not able to hand pump any more air out or the pump shuts off.", "Allow it to stay overnight at room... |
95,960 | Western blot for tissue extract | 0 | dx.doi.org/10.17504/protocols.io.yxmvm38q9l3p/v1 | https://www.protocols.io/view/western-blot-for-tissue-extract-c9xyz7pw | María Sanchiz Calvo, eduard.bentea, Veerle Baekelandt | TITLE: Western blot for tissue extract
AUTHORS: María Sanchiz Calvo, eduard.bentea, Veerle Baekelandt
[DESCRIPTION]
Protocol for the detection of proteins by Western blot from tissue extract
[BEFORE_START]
Perform protein extraction from snap-frozen brain tissue:
- weigh tissue
- add RIPA buffer (see Materials) : 1... | ["[Day 1] Prepare sample for western blot\n15 µg of protein in 12 µL \nAdd 4 µL \nBoil at 98 °C for 10 min", "[Day 1] Load samples, together with 7 µL of mass marker (PageRuler‱ Plus Prestained Protein Ladder) on a on 4–15% Criterion‱ Tris-HCl Protein Gel.", "[Day 1] Run the gel for 10 min at 80V", "[Day 1] Run the g... |
86,602 | U54 SCENT Intracellular Staining (ICS) Senescence Flow Cytometry Panel | 1 | dx.doi.org/10.17504/protocols.io.rm7vzxxk5gx1/v1 | https://www.protocols.io/view/u54-scent-intracellular-staining-ics-senescence-fl-cytixwke | Zachary R Healy, David Murdoch, Alicia Cooper-Volkheimer | TITLE: U54 SCENT Intracellular Staining (ICS) Senescence Flow Cytometry Panel
AUTHORS: Zachary R Healy, David Murdoch, Alicia Cooper-Volkheimer
[DESCRIPTION]
This protocol describes the Intracellular Staining (ICS) Senescence Flow Cytometry Panel
[STEPS]
SECTION: FBS Aliquot Prep
1. FBS (hiFBS): Gemini Bio Products ... | ["[FBS Aliquot Prep] FBS (hiFBS): Gemini Bio Products Cat #100-106 1L\nPrepare FBS Aliquots:", "[FBS Aliquot Prep] Thaw heat-inactivated FBS (hiFBS):\nThaw a 500mL Bottle of FBS at 4°C. This may require more than overnight so the 500mL Bottle may be removed 2 or 3 days prior to use. Do not leave the FBS at room tempera... |
67,728 | Visualization of a low concentration and molecular weight DNA (DNA gel stain) | 4 | dx.doi.org/10.17504/protocols.io.5jyl89x46v2w/v2 | https://www.protocols.io/view/visualization-of-a-low-concentration-and-molecular-cedqta5w | Nadine Mowoh, Stephane Fadanka, Shalo Minette | TITLE: Visualization of a low concentration and molecular weight DNA (DNA gel stain)
AUTHORS: Nadine Mowoh, Stephane Fadanka, Shalo Minette
[DESCRIPTION]
After PCR amplification of DNA, agarose gel electrophoresis is run to separate the DNA based on their size.
The agarose gel consists of microscopic pores ... | ["[Visualization of a low concentration and molecular weight DNA]", "[Visualization of a low concentration and molecular weight DNA] To confirm visualization of a low molecular weight DNA\n\n\nFollow the steps in preparing a 2% agarose gel as described in this protocol, \n \n\nLoad the gel (made from the test gel stain... |
30,052 | PROTOCOL FOR LARVICIDE BIOASSAYS | null | dx.doi.org/10.17504/protocols.io.9kch4sw | null | Dr. Wanderli Pedro Tadei, Rochelly da Silva Mesquita | TITLE: PROTOCOL FOR LARVICIDE BIOASSAYS
AUTHORS: Dr. Wanderli Pedro Tadei, Rochelly da Silva Mesquita
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is designed for the evaluation of the larvicidal activity of perspective insecticides on Anopheles larvae. The tests are performed accor... | ["Preparation of the stock solutionsDissolve accurately weighed quantity of the test substance in an appropriate volume of dimethylsulfoxide (DMSO) and/or distilled water (depends on the sample solubility) to obtain the concentration of .Final volume suggestion: to , depending on the amount of the material available ... |
11,024 | Thigmotaxis_Detection_2018 | null | dx.doi.org/10.17504/protocols.io.nzqdf5w | null | Akinori Higaki, Masaki Mogi, Jitsuo Higaki, Masatsugu Horiuchi | TITLE: Thigmotaxis_Detection_2018
AUTHORS: Akinori Higaki, Masaki Mogi, Jitsuo Higaki, Masatsugu Horiuchi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We share the minimal dataset for our study "Recognition for Early Stage Thigmotaxis in Morris Water Maze Test with Convolutional Neural Network" h... | [] |
35,809 | HuBMAP UF TMC - 10x Genomics scRNAseq Modality Overview | null | dx.doi.org/10.17504/protocols.io.be79jhr6 | https://www.protocols.io/view/hubmap-uf-tmc-10x-genomics-scrnaseq-modality-overv-be79jhr6 | Marda Jorgensen, Maigan Brusko | TITLE: HuBMAP UF TMC - 10x Genomics scRNAseq Modality Overview
AUTHORS: Marda Jorgensen, Maigan Brusko
[STEPS]
?. Specimen/Organ Prep:Spleen: dx.doi.org/10.17504/protocols.io.bc3kiykwLymph Node: dx.doi.org/10.17504/protocols.io.bbgnijveThymus: dx.doi.org/10.17504/protocols.io.bbgmiju6
?. Single Cell Isolation/Storage... | ["Specimen/Organ Prep:Spleen: dx.doi.org/10.17504/protocols.io.bc3kiykwLymph Node: dx.doi.org/10.17504/protocols.io.bbgnijveThymus: dx.doi.org/10.17504/protocols.io.bbgmiju6", "Single Cell Isolation/Storage: dx.doi.org/10.17504/protocols.io.bd9vi966", "10x Library Construction and Sequencing: dx.doi.org/10.17504/protoc... |
68,197 | CompetentCell | 4 | dx.doi.org/10.17504/protocols.io.j8nlkkzd6l5r/v1 | https://www.protocols.io/view/competentcell-ceudtes6 | Ana Belem García González, Georgina Diego, Irán Alessandra Chaparro Rodríguez, Jair Alexis Gardea Sáenz | TITLE: CompetentCell
AUTHORS: Ana Belem García González, Georgina Diego, Irán Alessandra Chaparro Rodríguez, Jair Alexis Gardea Sáenz
[DESCRIPTION]
A protocol for making chemically competent cells is shown.
[STEPS]
SECTION: Competent cells protocol with CaCl2
1. Inoculate 100 µL of E. coli in10 mL of antibiotic-free... | ["[Competent cells protocol with CaCl2] Inoculate 100 µL of E. coli in10 mL of antibiotic-free starter LB culture medium. Incubate during at 37 °C and", "[Competent cells protocol with CaCl2] Heat the LB media in the water bath at37 °C", "[Competent cells protocol with CaCl2] Inoculate 40 mL of LB media with 1 mL of c... |
58,991 | 623.1.HTC_Precision_Cut_Lung_Slices | 1 | dx.doi.org/10.17504/protocols.io.4r3l2o26xv1y/v1 | https://www.protocols.io/view/623-1-htc-precision-cut-lung-slices-b5upq6vn | Cory Poole, Lisa Rogers, Gloria S Pryhuber | TITLE: 623.1.HTC_Precision_Cut_Lung_Slices
AUTHORS: Cory Poole, Lisa Rogers, Gloria S Pryhuber
[DESCRIPTION]
Purpose and Scope of the Procedure or Laboratory Assay
Provide high quality, viable, 500 µm sections of human lung for culture and other in vitro assays
Current preparation has limited ability to produce qualit... | ["[Inflation of the Lung] Before dissections begin, place new sterile HBSS in a clean water bath set between 37°C and 40°C. This way the HBSS will be up to temperature by the time inflations begin. Pour more HBSS into another clean container, that is places within another larger container filled with wet ice, that will... |
null | null | null | dx.doi.org/10.17504/protocols.io.cjvun5 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
99,144 | Wake Forest University Health Sciences Manual of Procedures Biospecimen Collection and Processing V3 | 1 | dx.doi.org/10.17504/protocols.io.kqdg32p6ev25/v1 | https://www.protocols.io/view/wake-forest-university-health-sciences-manual-of-p-dc3g2yjw | Kim Kennedy, Heather Gregory | TITLE: Wake Forest University Health Sciences Manual of Procedures Biospecimen Collection and Processing V3
AUTHORS: Kim Kennedy, Heather Gregory
[DESCRIPTION]
This includes the methods associated with obtaining muscle, blood, and urine along with demographic, clinical, health, and functional data from younger and old... | [] |
97,923 | cosy_metab.nan | 5 | dx.doi.org/10.17504/protocols.io.eq2lyw3zpvx9/v1 | https://www.protocols.io/view/cosy-metab-nan-dbvb2n2n | NAN KB, John Glushka, Mario Uchimiya, Saraa Al Jawad, Christopher Esselman, Leandro I Ponce, Laura Morris, Arthur Edison | TITLE: cosy_metab.nan
AUTHORS: NAN KB, John Glushka, Mario Uchimiya, Saraa Al Jawad, Christopher Esselman, Leandro I Ponce, Laura Morris, Arthur Edison
[DESCRIPTION]
This is a protocol for running the Bruker pulse program "cosygpprqf" for metabolomics samples.
[BEFORE_START]
This protocol assumes:
Your sample is load... | ["[Create a new dataset]", "[Create noesypr1d experiment file] When Lock, Tune, Shim are complete proceed to the specific protocol for your desired pulseprogram(s).", "[Create a new dataset] On the menu bar on TopSpin, click on\nStart → Create Dataset", "[Create a new dataset] Enter\nNAME: Name of a set of datasets (e.... |
91,406 | Preparation of cells for live-cell imaging of a FOXO-based AKT kinase translocation reporter by widefield microscopy | 4 | dx.doi.org/10.17504/protocols.io.261gedjkjv47/v1 | https://www.protocols.io/view/preparation-of-cells-for-live-cell-imaging-of-a-fo-c5hny35e | Ralitsa R Madsen | TITLE: Preparation of cells for live-cell imaging of a FOXO-based AKT kinase translocation reporter by widefield microscopy
AUTHORS: Ralitsa R Madsen
[DESCRIPTION]
This protocol provides detailed instructions for imaging of cells with stable expression of a kinase translocation reporter, alongside a nuclear marker for... | ["[Dish assembly and coating] Take the required number of Ibidi dishes that will be needed for the experiment, along with the equivalent number of inserts. (NB: you can reuse inserts once provided that they have been sterilised in 70% ethanol and dried since the last use; we do this by passing them through PBS once, th... |
91,885 | Human iPSCs culture and cardiomyocyte subtype differentiation in fully chemically defined conditions | 4 | null | https://www.protocols.io/view/human-ipscs-culture-and-cardiomyocyte-subtype-diff-c5ymy7u6 | Joanna Delimata-Raczek, Natalia Koralewska, Marek Figlerowicz, Ireneusz Stolarek | TITLE: Human iPSCs culture and cardiomyocyte subtype differentiation in fully chemically defined conditions
AUTHORS: Joanna Delimata-Raczek, Natalia Koralewska, Marek Figlerowicz, Ireneusz Stolarek
[DESCRIPTION]
Cardiomyocyte in vitro differentiation represents a pivotal avenue in stem cell research, offering unprece... | ["[iPSC culture and maintenance] iPSC culture", "[Subtype differentiation of hiPSCs into cardiomyocytes] Standard iPSC culture before differentiation.", "[iPSC culture and maintenance] iPSC passage", "[iPSC culture and maintenance] iPSC cryopresevation", "[iPSC culture and maintenance] The optimal time for harvest or p... |
50,463 | Making normal NGM | 1 | dx.doi.org/10.17504/protocols.io.bvh7n39n | https://www.protocols.io/view/making-normal-ngm-bvh7n39n | Bonnie Evans | TITLE: Making normal NGM
AUTHORS: Bonnie Evans
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">C. elegans is maintained in the laboratory on Nematode Growth Medium (NGM) agar which has been aseptically poured into petri plates using a peristaltic pump. NGM (rather than no peptone NGM) may also be us... | ["[Pouring multi-well plates]\nFor pouring multi-well imaging plates:\n{\"blocks\":[{\"key\":\"fmd1o\",\"text\":\"Protocol for pouring agar into 96 well plates using Integra VIAFILL dispenser. Agar should be prepared in advance, and kept in 60oC waterbath until ready to dispense, and whilst dispensing. The X, Y, Z posi... |
107,129 | Single_Stranded_Library_Workflow_Gut_Virome | 0 | dx.doi.org/10.17504/protocols.io.8epv5r5w5g1b/v1 | https://www.protocols.io/view/single-stranded-library-workflow-gut-virome-dkuz4wx6 | Xichuan Zhai | TITLE: Single_Stranded_Library_Workflow_Gut_Virome
AUTHORS: Xichuan Zhai
[DESCRIPTION]
Protocol of single-stranded library (SSLR) preparation for virome study
[BEFORE_START]
Fill bucket with crushed ice.
[GUIDELINES]
This protocol is designed for virome library preparation with our lab-customed single-stranded libra... | ["[Step1: Virome isolation and extraction] Checklist before starting", "[Step2: Heat treatment] Checklist before starting", "[Step3: Reverse transcription (RT)] Checklist before starting", "[Step4: Fragmentation] Checklist before starting", "[Step5: Ligation] Checklist before starting", "[Step6: Index PCR] Checklist be... |
41,923 | Acute toxicity of injected drugs and substances in fish | 4 | dx.doi.org/10.17504/protocols.io.bk7bkzin | https://www.protocols.io/view/acute-toxicity-of-injected-drugs-and-substances-in-bk7bkzin | Bruna Patrícia D.c., Sabrina Alana Gomes Pinto, Layana Aquino Moura, Diógenes Silva, Kelly Christina Ferreira Castro, Caio Maximino | TITLE: Acute toxicity of injected drugs and substances in fish
AUTHORS: Bruna Patrícia D.c., Sabrina Alana Gomes Pinto, Layana Aquino Moura, Diógenes Silva, Kelly Christina Ferreira Castro, Caio Maximino
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol, modified from OECD 203 (Acute to... | ["[Anesthesia and injection procedures]\nAnesthesize fish in ice-cold water (12-14 ºC). Remove animal from water as soon as movements stop.\non ice", "[Anesthesia and injection procedures]\nTransfer animal to surgical bed (water-soaked sponge with a cut to fixate the fish), kept in a vessel with ice-cold water.\non ice... |
23,874 | BGISEQ-500 10X library construction | null | dx.doi.org/10.17504/protocols.io.3jagkie | null | ziqiang chen | TITLE: BGISEQ-500 10X library construction
AUTHORS: ziqiang chen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">BGISEQ-500 is a desktop sequencer developed by BGI. This protocol adjusts the process in order to apply the 10X contruction to the BGISEQ-500 rather than illumina.</div></div>
[STEPS]
?.... | ["Input HMW gDNA Quantification", "Quantitate 3 μl of extracted gDNA solution (with a minimum of 2 replicates).", "If the gDNA stock is >20 ng/μl, prepare an intermediate dilution of the extracted gDNA solution at", "Quantitate 3 μl of the", "According to the table below, dilute gDNA with bufferEB concentration less th... |
35,379 | Opentrons COVID-19 testing (Zymo, station B, 48 samples) | null | dx.doi.org/10.17504/protocols.io.bestjeen | null | Max Marrone | TITLE: Opentrons COVID-19 testing (Zymo, station B, 48 samples)
AUTHORS: Max Marrone
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Station B: Initial OT-2 setup]
Clean the OT-2.
?. [Station B: Initial OT-2 setup]
Place the following labware on the OT-2's deck:Slot 1: An Opentrons Temperature Module wit... | ["[Station B: Initial OT-2 setup]\nClean the OT-2.", "[Station B: Initial OT-2 setup]\nPlace the following labware on the OT-2's deck:Slot 1: An Opentrons Temperature Module with an Opentrons 96 well aluminum block and an empty, sterile NEST 100 µL PCR plate.Slots 3, 6, 7, 9, and 10: A full, sterile rack of Opentrons 2... |
57,737 | Ultra-high field, multi-echo MRI acquisition for resting-state functional connectivity | 1 | dx.doi.org/10.17504/protocols.io.dm6gpbbj1lzp/v1 | https://www.protocols.io/view/ultra-high-field-multi-echo-mri-acquisition-for-re-b4mhqu36 | Elizabeth Rizor, Dr. Scott Grafton | TITLE: Ultra-high field, multi-echo MRI acquisition for resting-state functional connectivity
AUTHORS: Elizabeth Rizor, Dr. Scott Grafton
[DESCRIPTION]
This is an MRI acquisition sequence used to examine resting-state functional connectivity of open and closed loop motor circuits in healthy controls and those with Par... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.jqjcmun | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ekwbcxe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Stellaris® RNA FISH Cells in Suspension Protocol is specifically optimized to allow to visualization of single RNA transcripts in suspended, fixed cells.
[BEFORE_START]
<p align="LEFT">Reagents and Equipment</p>
<p align="LEFT">Reagents and Consumables:</p>
<p align="LEFT">a) T... | [] |
18,493 | Water Sampling and Plating Generations (Antimicrobial Group) | 1 | dx.doi.org/10.17504/protocols.io.ewov1yd87vr2/v1 | https://www.protocols.click/view/water-sampling-and-plating-generations-antimicrobi-wa5fag6 | Melissa B Duhaime, Aubrey Reed, Nicole Sunshine, Renae Lyons | TITLE: Water Sampling and Plating Generations (Antimicrobial Group)
AUTHORS: Melissa B Duhaime, Aubrey Reed, Nicole Sunshine, Renae Lyons
[DESCRIPTION]
Protocol developed by the Antimicrobial Group class project. The goal was to isolate microbes from freshwater lakes that produce antimicrobial compounds in order to st... | ["Collect whole water at six sites using a Van Dorn water collector for deep (~122.5-123.7 m) samples and 2 L containers for surface samples (~15 cm below the surface).", "Set site names and classifications\n \n3. Prefilter whole water using 20μm mesh. \n4. Set up peristaltic pump with 3 µm filter\n5. Filter approxima... |
91,600 | The relationship between chronic skin conditions and depression and how successful dermatologic treatment could improve patients’ mental health: An evidence-based systematic review protocol | 1 | null | https://www.protocols.io/view/the-relationship-between-chronic-skin-conditions-a-c5pqy5mw | Aime Lee, Nami Watanabe, Emma Gregory, Cobi Desilva, Jenina Joyce Pali, Lindsey Leonhard, Samia Valeria Ozorio Dutra | TITLE: The relationship between chronic skin conditions and depression and how successful dermatologic treatment could improve patients’ mental health: An evidence-based systematic review protocol
AUTHORS: Aime Lee, Nami Watanabe, Emma Gregory, Cobi Desilva, Jenina Joyce Pali, Lindsey Leonhard, Samia Valeria Ozorio Dut... | [] |
94,688 | Rotarod test in rats | 1 | dx.doi.org/10.17504/protocols.io.5qpvo3zo9v4o/v1 | https://www.protocols.io/view/rotarod-test-in-rats-c8p8zvrw | eduard.bentea, María Sanchiz Calvo, Veerle Baekelandt | TITLE: Rotarod test in rats
AUTHORS: eduard.bentea, María Sanchiz Calvo, Veerle Baekelandt
[DESCRIPTION]
Protocol for performing the rotarod test in rats. This test evaluated motor coordination and balance, and can be used in rat models with motor deficits, such as models of Parkison's disease. Rats with impaired moto... | ["[Training] Bring cages to the behavioral room for at least 60 min prior to the test for habituation", "[Training] Habituate rats on the rotarod for 5 min at 5 rpm, place back in case they fall", "[Training] 5 min rest", "[Training] Test rats for 1 min at 5 rpm", "[Training] 5 min rest", "[Training] Test rats for 1 mi... |
94,117 | Immunohistochemistry free-floating rat brain cryosections | 4 | dx.doi.org/10.17504/protocols.io.3byl4q4zrvo5/v1 | https://www.protocols.io/view/immunohistochemistry-free-floating-rat-brain-cryos-c76dzra6 | mariangela.massarocenere | TITLE: Immunohistochemistry free-floating rat brain cryosections
AUTHORS: mariangela.massarocenere
[DESCRIPTION]
Protocol for immunohistochemistry on rat brain cryosections
[STEPS]
SECTION: 1. Sections selection
1. Collect the cryosections needed for a caudo-rostral representation of each brain region (every fift... | ["[1. Sections selection] Collect the cryosections needed for a caudo-rostral representation of each brain region (every fifth or sith sections depending on the section's thickness, brain region, and animal species) into a 24-well-plate (3-4 sections per well)", "[2. Inactivation of endogenous peroxidase] Incubate sec... |
102,750 | In vitro co-culture system using a fiber-supported liquid approach | 0 | dx.doi.org/10.17504/protocols.io.rm7vzj56xlx1/v1 | https://www.protocols.io/view/in-vitro-co-culture-system-using-a-fiber-supported-dgj63ure | Alejandro Calle, Jeffrey Adelberg, Guido Schnabel, Jacqueline Naylor-Adelberg, Jhulia Gelain, Yeter Karakoc, Jared Weaver, Christopher Saski, Ksenija Gasic | TITLE: In vitro co-culture system using a fiber-supported liquid approach
AUTHORS: Alejandro Calle, Jeffrey Adelberg, Guido Schnabel, Jacqueline Naylor-Adelberg, Jhulia Gelain, Yeter Karakoc, Jared Weaver, Christopher Saski, Ksenija Gasic
[DESCRIPTION]
In vitro co-culture techniques that allow the growth of plants and... | ["[Establishment of Plant Cultures] Establishment of plant cultures from dormant shoots", "[Establishment of Plant Cultures] Collect dormant shoots, cut them (3 cm in length),and cleanse them by submerging in 70% ethanol for 1 minute, followed by rinsing with sterile deionized water. Then, immerse the shoots in a 10% b... |
24,178 | Podocyte Count and Density Analysis | null | dx.doi.org/10.17504/protocols.io.3usgnwe | null | Frank Brosius | TITLE: Podocyte Count and Density Analysis
AUTHORS: Frank Brosius
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This protocol describes the procedures for quantifying the podocyte count and density in the glomerulus.... | ["[Procedure:]\n1) Stain the Perfusion-fixed paraffin embedded sections (3.9 and 10.2 microns thick) with WT-1 antibody and immunoperoxidase and then take photograph at 40x by using Spot Advanced Software Camera.\n2) Photograph 50 consecutive glomerular cross-sections moving systematically from outer cortex to inner ... |
51,934 | TEA-seq | 4 | dx.doi.org/10.17504/protocols.io.bwx6pfre | https://www.protocols.io/view/tea-seq-bwx6pfre | Elliott Swanson, Lucas Graybuck, Peter Skene | TITLE: TEA-seq
AUTHORS: Elliott Swanson, Lucas Graybuck, Peter Skene
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">TEA-seq is a method for Transcriptomic, Epitope, and Accessibility measurement from thousands of single cells on the 10x Genomics Multiome platform. It generates scRNA-seq, scATAC-seq... | ["[Buffer preparation]\nStain Buffer Dulbecco's phosphate-buffered saline (DPBS) supplemented with 2% w/v bovine serum albumin.Wash Buffer Final composition of 20 mM Tris HCl (Tris(hydroxymethyl)aminomethane hydrochloride) pH 7.4, 150 mM NaCl, 3 mM MgCl2.Perm Buffer Wash Buffer (above) with the addition of digitonin t... |
90,854 | DNA barcoding SOPs for the Darwin Tree of Life Project | 2 | dx.doi.org/10.17504/protocols.io.261ged91jv47/v1 | https://www.protocols.io/view/dna-barcoding-sops-for-the-darwin-tree-of-life-pro-c4yeyxte | Jordan Beasley, Rebekka Uhl, Laura L Forrest, David Bell, Michelle Hart, Rebecca Yahr, Estelle Kilias | TITLE: DNA barcoding SOPs for the Darwin Tree of Life Project
AUTHORS: Jordan Beasley, Rebekka Uhl, Laura L Forrest, David Bell, Michelle Hart, Rebecca Yahr, Estelle Kilias
[DESCRIPTION]
This collection of protocols describe the standard operating procedures for DNA barcoding in the Darwin Tree of Life project.
The SO... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.rbsd2ne | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol outlines the steps taken to support sexual reproduction in Aiptasia lab cultures. It also provides steps for handling embryos and larvae, and basic husbandry to keep them alive.</p>
<p>Spawning protocol based on the methods from Grawunder et al. 2015.</p>
[STEP... | [] |
101,615 | Single-step assembly of double guide plasmid (pCas9-Duo) for gene-editing in Plasmodium | 0 | dx.doi.org/10.17504/protocols.io.n2bvjn9d5gk5/v1 | https://www.protocols.io/view/single-step-assembly-of-double-guide-plasmid-pcas9-dfgp3jvn | Abhinay Ramaprasad | TITLE: Single-step assembly of double guide plasmid (pCas9-Duo) for gene-editing in Plasmodium
AUTHORS: Abhinay Ramaprasad
[DESCRIPTION]
This protocol describes a one-pot GoldenGate assembly of a new dual-guide targeting plasmid (pCas9-Duo) expressing two distinct guide RNAs in order to enhance the chances of a succe... | ["[gRNA oligo design] Add the overhangs \"ATTG\" and \"AAAC\" to forward and reverse oligos of gRNA1, and \"TTGG\" and \"TAAA\" to gRNA2 respectively.", "[Anneal gRNA oligos] Set up annealing reactions. \n \n1.0 µL gRNA.F 100 micromolar (µM) \n1.0 µL gRNA.R 100 micromolar (µM) \n1.0 µL \n0.5 µL \n6.5 µL", "[An... |
86,286 | Live Imaging of Primary Mouse Neuron Cultures | 4 | dx.doi.org/10.17504/protocols.io.e6nvwdjydlmk/v1 | https://www.protocols.io/view/live-imaging-of-primary-mouse-neuron-cultures-cyhnxt5e | Robert Edwards, Shweta Jain | TITLE: Live Imaging of Primary Mouse Neuron Cultures
AUTHORS: Robert Edwards, Shweta Jain
[DESCRIPTION]
This protocol describes live imaging of primary neuron cultures. Included are methods for preparing hippocampal or dopamine neuronal cultures from neonatal mouse brain tissue. The imaging described involves labeling... | ["[Preparation of Hippocampal Cultures] Collect mouse pups at postnatal day 0", "[Preparation of Hippocampal Cultures] Decapitate and remove brain, dissect out hippocampi from each hemisphere into Hank's balanced salt solution (HBSS) containing 10 mM HEPES and 20 mM glucose", "[Preparation of Hippocampal Cultures] Dige... |
64,888 | PLATERO - Green Fluorescence Calibration in Plate Readers | 1 | null | https://www.protocols.io/view/platero-green-fluorescence-calibration-in-plate-re-cbkyskxw | Alejandro Vignoni, Yadira Boada | TITLE: PLATERO - Green Fluorescence Calibration in Plate Readers
AUTHORS: Alejandro Vignoni, Yadira Boada
[DESCRIPTION]
One of the most common sources of information in Synthetic Biology is the data coming from plate reader fluorescence measurements. These experiments provide a measure of the light emitted by certa... | ["[Stock Reference Fluorescein solution] Start from at least 1 mL of 10 micromolar (µM) solution in .", "[Prepare the serial dilutions of Fluorescein] Accurate pipetting is essential. Serial dilutions will be performed in 5 tubes. There will be a sixth tube that must contain PBS buffer only. Initially, you will s... |
null | null | null | dx.doi.org/10.17504/protocols.io.h7bb9in | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><img id="s-mce-img" class="s-mce-img" src="https://s3.amazonaws.com/pr-journal/j4gdmie.png" data-src="https://s3.amazonaws.com/pr-journal/j4fdmie.png" data-ofn="cpib_root_analysis.png" /></p>
[STEPS]
?.
?.
?.
?.
?.
?.
?. | [] |
66,128 | Protocol: A Systematic Review of Graves' Disease and its Interconnection with MHC Class II | 1 | dx.doi.org/10.17504/protocols.io.cctqswmw | https://www.protocols.io/view/protocol-a-systematic-review-of-graves-39-disease-cctqswmw | Dylan Thibaut, Connor Sweeney, Shannon South, Mohamed Hussein | TITLE: Protocol: A Systematic Review of Graves' Disease and its Interconnection with MHC Class II
AUTHORS: Dylan Thibaut, Connor Sweeney, Shannon South, Mohamed Hussein
[DESCRIPTION]
Graves’ disease continues to be a problematic autoimmune thyroid condition debilitating patients with hyperthyroidism. HLAs play ... | ["[Administrative Information] Title\n\"A Systematic Review of Graves' Disease and its Interconnection with MHC Class II\"\n\nRegistration \nprotocols.io", "[Introduction] Rationale\n Through meta-analysis, data from research can be extracted and evaluated to find specific HLA-DRB1 and HLA-DQ molecules associated w... |
46,675 | Flow Cytometer Fluorescence Voltration for FCMPASS | 1 | dx.doi.org/10.17504/protocols.io.brttm6nn | https://www.protocols.io/view/flow-cytometer-fluorescence-voltration-for-fcmpass-brttm6nn | Joshua A Welsh, Sean M Cook, Jennifer Jones | TITLE: Flow Cytometer Fluorescence Voltration for FCMPASS
AUTHORS: Joshua A Welsh, Sean M Cook, Jennifer Jones
[DESCRIPTION]
Protocol to perform flow cytometer voltration to identify optimal detector settings for small particle analysis. Data acquired from this protocol are compatible with semi-automated analysis too... | ["[Sample preparation] Vortex bottle on a high setting for 5 s.", "[Sample preparation] Pipette 500 µL of to two . Label one tube 'DPBS\" and the second tube 'Beads'.", "[Sample preparation] Add 3 drops of to the 'Beads' and vortex for r 5 s.", "[Cytometer Setup] Ensure cytometer is clean and that -Height and... |
54,748 | Quantitative PCR of Viral Abundance | 4 | dx.doi.org/10.17504/protocols.io.bzp4p5qw | https://www.protocols.io/view/quantitative-pcr-of-viral-abundance-bzp4p5qw | Bryan Yoo, Jessica Griffiths, Sarkis Mazmanian | TITLE: Quantitative PCR of Viral Abundance
AUTHORS: Bryan Yoo, Jessica Griffiths, Sarkis Mazmanian
[DESCRIPTION]
Protocol for quantifying viral abundance by PCR used in Yoo et al 2021
[STEPS]
1. AAV-PHP.S:hSYN1-mNeonGreen was delivered systemically to wildtype mice at 6-8 weeks of age.
2. 3-4 weeks following viral... | ["AAV-PHP.S:hSYN1-mNeonGreen was delivered systemically to wildtype mice at 6-8 weeks of age.", "3-4 weeks following viral infection, 1cm of proximal, medial, and distal small intestine (SI) and colon were harvested and flash frozen in TRIzol (ThermoFisher Scientific, Waltham, MA-Cat. No. 15596018) and RNA was extracte... |
27,204 | Distribution of aerophilous diatom communities associated with terrestrial green macroalgae in the South Shetland Islands, Maritime Antarctica - PROTOCOL | null | dx.doi.org/10.17504/protocols.io.6tcheiw | null | Juliana Ferreira da Silva, Maria Angélica Oliveira, Raylane Ribeiro Anunciação, Eduardo Pereira da Silva, Rodrigo Paidano Alves, Adriano Luis Schunemann, Filipe de Carvalho Victoria, Margéli Pereira de Albuquerque, Antonio Batista Pereira | TITLE: Distribution of aerophilous diatom communities associated with terrestrial green macroalgae in the South Shetland Islands, Maritime Antarctica - PROTOCOL
AUTHORS: Juliana Ferreira da Silva, Maria Angélica Oliveira, Raylane Ribeiro Anunciação, Eduardo Pereira da Silva, Rodrigo Paidano Alves, Adriano Luis Schunem... | [] |
76,894 | Ambrecht et al. 2020: An optimized method for the extraction of ancient eukaryote DNA from marine sediments | 4 | dx.doi.org/10.17504/protocols.io.x54v9dw3qg3e/v1 | https://www.protocols.io/view/ambrecht-et-al-2020-an-optimized-method-for-the-ex-cpb6vire | Linda Armbrecht | TITLE: Ambrecht et al. 2020: An optimized method for the extraction of ancient eukaryote DNA from marine sediments
AUTHORS: Linda Armbrecht
[DESCRIPTION]
Four combinations of sedaDNA extraction treatments using marine sediments collected at a water depth of 104 m off Maria Island in Tasmania are compared. These metho... | ["[Method 1: Bead-beating + spin column (DNeasy PowerLyzer PowerSoil Kit, Qiagen; “Kit”)] This technique was applied to 0.25 g of sediment subsamples stored at 4 °C, following the manufacturer's protocol with the some modifications:", "[Shotgun sequencing library preparation] We prepared four libraries as described in ... |
37,028 | Western blot analysis and immunoprecipitation assay | null | dx.doi.org/10.17504/protocols.io.bgecjtaw | https://www.protocols.io/view/western-blot-analysis-and-immunoprecipitation-assa-bgecjtaw | Marzia Ognibene | TITLE: Western blot analysis and immunoprecipitation assay
AUTHORS: Marzia Ognibene
[STEPS]
?. Cells are washed in cold PBS and lysed on ice in a buffer containing 1.6 mM NaH2PO4, 8.6 mM Na2HPO4, 1% Triton X-100, 0.1% SDS; 0.1% NaCl, 0.5% NaDoc, 2 mM AEBSF, 20 mg/mL each of aprotinin and leupeptin.
?. Cell lysates are... | ["Cells are washed in cold PBS and lysed on ice in a buffer containing 1.6 mM NaH2PO4, 8.6 mM Na2HPO4, 1% Triton X-100, 0.1% SDS; 0.1% NaCl, 0.5% NaDoc, 2 mM AEBSF, 20 mg/mL each of aprotinin and leupeptin.", "Cell lysates are centrifuged in a microfuge at maximum speed for 10 min to eliminate debris.", "Protein conten... |
28,743 | Removal of gDNA from totalRNA | null | dx.doi.org/10.17504/protocols.io.8bfhsjn | null | iGEM Dusseldorf | TITLE: Removal of gDNA from totalRNA
AUTHORS: iGEM Dusseldorf
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Removal of genomic DNA from RNA preparations</div></div>
[STEPS]
?. [Digestion of DNA]
pipet components into a RNase-free 1.5 ml tube (following order: H2O, buffer, total RNA, DNaseI)
?. [D... | ["[Digestion of DNA]\npipet components into a RNase-free 1.5 ml tube (following order: H2O, buffer, total RNA, DNaseI)", "[Digestion of DNA]\nincubate reaction at 37°C", "[Extraction of DNaseI-digested RNA]\nadd 1 µl 50 mM EDTA and incubate at 65°C", "[Extraction of DNaseI-digested RNA]\nadd 1/10 Volume NaOAc and 3 Vol... |
12,937 | Electroporation of the protist Cafeteria roenbergensis cells using the Neon Transfection System | null | dx.doi.org/10.17504/protocols.io.qvhdw36 | null | Sarah Duponchel, Monica Berjon-Otero, Matthias Fischer | TITLE: Electroporation of the protist Cafeteria roenbergensis cells using the Neon Transfection System
AUTHORS: Sarah Duponchel, Monica Berjon-Otero, Matthias Fischer
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Cell preparation]
Before the experiment (it can be the day before without affecting too muc... | ["[Cell preparation]\nBefore the experiment (it can be the day before without affecting too much the cell viability)\n{\"blocks\":[{\"data\":[],\"depth\":0,\"entityRanges\":[],\"inlineStyleRanges\":[{\"length\":24,\"offset\":165,\"style\":\"italic\"}],\"key\":\"1ovn6\",\"text\":\"Heterotrophic flagellates require co-cu... |
null | null | null | dx.doi.org/10.17504/protocols.io.k6tczen | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p>Overall Notes:</p>
<ul>
<li>Measure all regions twice (on separate days)
<ul>
<li>Use Pearson coefficient to determine how similar they are</li>
<li>If Pearson coefficient is 0.9, then average them together</li>
<li>If not, measure regions again and re-calculate the Pearson’s ... | [] |
97,729 | Open-source tools for Spatial Tissue Exploration Program (STEP) PhenoCycler-Fusion image analysis. | 0 | null | https://www.protocols.io/view/open-source-tools-for-spatial-tissue-exploration-p-dbn92mh6 | Daniel H Geschwind, George Chen | TITLE: Open-source tools for Spatial Tissue Exploration Program (STEP) PhenoCycler-Fusion image analysis.
AUTHORS: Daniel H Geschwind, George Chen
[DESCRIPTION]
Link to PhenoCycler User Guide to allow for multi-plex spatial proteomic detection on fresh frozen and FFPE tissue sections plus image analysis.
[STEPS]
SEC... | ["[PhenoCycler Imaging Analysis protocol] Imaging Analysis protocol can be found here:\nThis protocol is working for us.", "[STEP protocol for PhenoCycler coverslip preparation] STEP protocol for PhenoCycler coverslip preparation can be found here: \nThis protocol is working for us."] |
68,546 | Hamster infestation with cercariae | 4 | null | https://www.protocols.io/view/hamster-infestation-with-cercariae-ce7athie | Frédéric D. Chevalier | TITLE: Hamster infestation with cercariae
AUTHORS: Frédéric D. Chevalier
[DESCRIPTION]
This protocol describes the steps, materials and precautions needed for infecting hamsters with schistosome cercariae. Note that the use of vertebrates for research needs to be approved by the Institutional Animal Care and Use Commi... | ["Shed cercariae from snails during 2h under light in TBRI water", "Discard the shedding water in a new beaker", "Shed cercariae from snails again during 2h under light in new TBRI water", "Transfer the water in a new dish", "Get the hamster", "Wet the hamster in jar containing hot water (~30°C). BE CAREFUL to keep alw... |
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