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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72,494 | Monoclonal Culture (Limiting Dilution) | 1 | null | https://www.protocols.io/view/monoclonal-culture-limiting-dilution-ci2nugde | Binghua Darren Zhang | TITLE: Monoclonal Culture (Limiting Dilution)
AUTHORS: Binghua Darren Zhang
[DESCRIPTION]
This protocol gives a step-by-step guidance on how to generate the homogenised gene-knockout (KO) monoclonal cell line from a polyclonal "KO" cells pool.
[BEFORE_START]
Generate and prepare the stable polyclonal cell pool;
... | ["[Prep Conditioned Medium] Collect the used growth medium into a 50 mL Falcon tube.", "[Prep Conditioned Medium] Pipette the used growth medium through a 0.2 µm syringe filter to remove the waste product and dead cells.", "[Prep Conditioned Medium] Add fresh growth medium up to 30 mL (if there are three 96-well cell c... |
21,333 | Yale - LDL Cholesterol | null | dx.doi.org/10.17504/protocols.io.y3vfyn6 | null | John Stack, Gary Cline | TITLE: Yale - LDL Cholesterol
AUTHORS: John Stack, Gary Cline
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Procedure used to determine the concentration of LDL cholesterol in blood, serum, and plasma. LDL-cholestero... | ["Calibrate Cobas for LDL by running dilutions of the lipid calibrator and the addition of the two direct reagents.", "Sample handling as performed by the Cobas Mira Plus. a) Pipette 3 µL of sample into a cuvette slot. b) Add 225 µL of LDL Direct Reagent 1. c) Add 75 µL of LDL Direct Reagent 2. d) Mixture ... |
66,319 | Prima Weight Loss Dragons Den UK : Prima Weight Loss : PrimaDietPills Uk | 1 | dx.doi.org/10.17504/protocols.io.4r3l2oj4qv1y/v1 | https://www.protocols.io/view/prima-weight-loss-dragons-den-uk-prima-weight-loss-cczpsx5n | roxytinb | TITLE: Prima Weight Loss Dragons Den UK : Prima Weight Loss : PrimaDietPills Uk
AUTHORS: roxytinb
[DESCRIPTION]
Are you not satisfied with your Keto diet feature?
Not receiving actual weight loss results after spending too much time in the gym?
Looking for Advance weight loss supplement pills?
Prima Weight Los... | ["[Prima Weight Loss] Prima Weight Loss Dragons Den UK If yes then you are right place. It’s true that almost every three out of ten persons are facing the obesity issue worldwide. This unnatural weight gain not causes only physical side effects but also gives you mental illness.", "[Prima Weight Loss] Prima Weight Los... |
null | null | null | dx.doi.org/10.17504/protocols.io.nzfdf3n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol was based on a 2010 paper by Meng and Feldman for extraction of RNA from arabidopsis siliques. While the protocol remains unchanged, I have made some slight edits to streamline it in the lab and also added some notes regarding my results applying this protocol t... | [] |
48,933 | publication 2 7.4 doi | 1 | dx.doi.org/10.17504/protocols.io.bt2dnqa6 | https://www.protocols.io/view/publication-2-7-4-doi-bt2dnqa6 | Mariia Guliakina | TITLE: publication 2 7.4 doi
AUTHORS: Mariia Guliakina
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">test </div></div>
[STEPS]
?. test
?. test | ["test", "test"] |
24,217 | Transient transcriptome sequencing: experimental protocol to monitor genome-wide RNA synthesis including enhancer transcription | null | dx.doi.org/10.17504/protocols.io.3vzgn76 | null | Saskia Gressel, Katja Lidschreiber, Patrick Cramer | TITLE: Transient transcriptome sequencing: experimental protocol to monitor genome-wide RNA synthesis including enhancer transcription
AUTHORS: Saskia Gressel, Katja Lidschreiber, Patrick Cramer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify">Trans... | ["[Spike-in Pool Preparation (based on Schwalb et al. 2016)]\nPerform first strand cDNA synthesis using the Transcriptor First Strand cDNA Synthesis Kit with Anchored-oligo (dT) primers. Follow manufacturer’s instructions, use ERCC RNA Spike-in Mix.\n1 µl", "[Spike-in Pool Preparation (based on Schwalb et al. 2016)]\n... |
90,724 | Homology Modelling of Pacer RH domain in SWISS-MODEL | 1 | dx.doi.org/10.17504/protocols.io.bp2l6xmr1lqe/v1 | https://www.protocols.io/view/homology-modelling-of-pacer-rh-domain-in-swiss-mod-c4ucywsw | Dan Tudorica | TITLE: Homology Modelling of Pacer RH domain in SWISS-MODEL
AUTHORS: Dan Tudorica
[DESCRIPTION]
Using the Rubicon RH - Rab7 crystal structure as a template (6wcw)
[STEPS]
SECTION: Swiss-M
1. In Swiss Model,
> start new modelling project
> upload target sequence. Here, used the human Pacer (RUBCNL) sequence acquired ... | ["[Swiss-M] In Swiss Model,\n\n> start new modelling project\n> upload target sequence. Here, used the human Pacer (RUBCNL) sequence acquired from uniprot:\n\n>sp|Q9H714|PACER_HUMAN Protein associated with UVRAG as autophagy enhancer OS=Homo sapiens OX=9606 GN=RUBCNL PE=1 SV=3\nMVSQSTVRQDSPVEPWEGISDHSGIIDGSPRLLNTDHPPCQ... |
23,979 | Neuropathy Phentoyping Protocols - Streptozotocin Treatment For Rats | null | dx.doi.org/10.17504/protocols.io.3njgmcn | null | Eva Feldman | TITLE: Neuropathy Phentoyping Protocols - Streptozotocin Treatment For Rats
AUTHORS: Eva Feldman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block"><span style = "font-weight:bold;">Phenotyping of Rodents for the Presence ... | ["Order animals to arrive several days before the planned injection date. This allows them to acclimatize to their new surroundings.", "The day before STZ injection, remove the food from the feeders. Leave a clear note saying, \"Do Not Feed\" (specify appropriate rats) from (time, date) to (time, date). INFORM ULAM; be... |
null | null | null | dx.doi.org/10.17504/protocols.io.cf7trm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is the reaction for the "Ligation Protocol with T4 DNA Ligase"
[STEPS]
?.
?.
?.
?.
?. | [] |
50,447 | International Shipping Documentation | 1 | dx.doi.org/10.17504/protocols.io.eq2lypq1mlx9/v1 | https://www.protocols.io/view/international-shipping-documentation-bvhpn35n | Integrated Islet Distribution Program | TITLE: International Shipping Documentation
AUTHORS: Integrated Islet Distribution Program
[DESCRIPTION]
This SOP defines the completion of International Documentation necessary for the shipment of human islets and biospecimens to investigators outside of the United States for use in the National Institute of Diabetes... | ["[Materials] The IIDP will provide each center with the supplies necessary for shipments as listed in the materials section. Standard lab supplies will be provided by the IIDP Centers as listed below.\n\nThe following SOPs may be implemented for these shipments. This protocol is written to assist the participating is... |
31,137 | HuBMAP: Paraffin Embedding Tissue Samples | null | dx.doi.org/10.17504/protocols.io.bam9ic96 | null | Marda Jorgensen, Jerelyn Nick | TITLE: HuBMAP: Paraffin Embedding Tissue Samples
AUTHORS: Marda Jorgensen, Jerelyn Nick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpose of this Standard Operating Procedure (SOP) is to outline procedures for the paraffin embedding of HuBMAP specimens.</div></div>
[STEPS]
?. [Post-Proce... | ["[Post-Processing Tissue Acquisition]\nPlace processed cassettes in wax holding chamber of embedding center.Stock station with embedding utensils, gauze, and disposable embedding molds.", "[Post-Processing Tissue Acquisition]\nView the tissue sample and select an appropriately sized disposable embedding mold.", "[Post... |
62,122 | Ketosium ACV Gummies Reviews & Shark Tank, Where To Buy | 1 | dx.doi.org/10.17504/protocols.io.x54v9y3x1g3e/v1 | https://www.protocols.io/view/ketosium-acv-gummies-reviews-amp-shark-tank-where-b8wirxce | Ketosium Reviews | TITLE: Ketosium ACV Gummies Reviews & Shark Tank, Where To Buy
AUTHORS: Ketosium Reviews
[DESCRIPTION]
Ketosium ACV Gummies Reviews & Shark Tank, Where To Buy
[STEPS]
SECTION: Ketosium ACV Gummies Reviews & Shark Tank, Where To Buy Keeping one’s body in tip-top shape can be grueling, and numerous people can ... | ["[Ketosium ACV Gummies Reviews & Shark Tank, Where To Buy Keeping one’s body in tip-top shape can be grueling, and numerous people can not do so. It's getting decreasingly delicate to maintain a healthy life in the current world. There are numerous reasons why someone might not be in peak physical condition. ... |
94,459 | Fontana-Masson staining | 4 | dx.doi.org/10.17504/protocols.io.n92ldmxoxl5b/v1 | https://www.protocols.io/view/fontana-masson-staining-c8g3ztyn | Cristian González-Cabrera, Csilla Novák, Andrés Mauricio Jaramillo Flautero, Celine Winter, Matthias Prigge | TITLE: Fontana-Masson staining
AUTHORS: Cristian González-Cabrera, Csilla Novák, Andrés Mauricio Jaramillo Flautero, Celine Winter, Matthias Prigge
[DESCRIPTION]
The Fontana-Masson Staining Protocol is a detailed method for staining free-floating sections (20-50 microns) to detect melanin and other pigments in tissue ... | ["[Fontana-Masson staining] Use free floating sections between 20-50 microns.", "[Fontana-Masson staining] Silver Nitrate working solution:\n- Prepare a 1:3 solution of silver nitrate solution in distilled water. Prepare enough solution for the amount of sections you want to stain.\n- Add drop by drop concentrated ammo... |
77,818 | Extraction and PCR for animal samples using the Thermofisher Scientific TaqPath COVID-19 Combo Kit | 4 | dx.doi.org/10.17504/protocols.io.36wgqjq5ovk5/v1 | https://www.protocols.io/view/extraction-and-pcr-for-animal-samples-using-the-th-cp82vrye | Brianna Stenger | TITLE: Extraction and PCR for animal samples using the Thermofisher Scientific TaqPath COVID-19 Combo Kit
AUTHORS: Brianna Stenger
[DESCRIPTION]
To describe the steps and materials needed to perform a multiplex real-time reverse transcriptase PCR test intended for the qualitative detection of nucleic acid from SARS-Co... | ["[SARS-CoV-2 RNA Extraction] Prepare working areas by cleaning with ~10% bleach or ~70% alcohol, followed by a rinse and use of another solution to reduce the presence of RNases such as RNaseZAP or Eliminase.", "[SARS-CoV-2 RNA Extraction] Start the run and load prepared plates in positions when prompted by the instru... |
102,011 | Application of ALFA-tag and tyramide-based fluorescence signal amplification to expand the CRISPR-based DNA imaging toolkit | 0 | dx.doi.org/10.17504/protocols.io.n92ld85y7v5b/v1 | https://www.protocols.io/view/application-of-alfa-tag-and-tyramide-based-fluores-dfu33nyn | Bhanu Prakash Potlapalli, Joerg Fuchs, Twan Rutten, Armin Meister, Andreas Houben | TITLE: Application of ALFA-tag and tyramide-based fluorescence signal amplification to expand the CRISPR-based DNA imaging toolkit
AUTHORS: Bhanu Prakash Potlapalli, Joerg Fuchs, Twan Rutten, Armin Meister, Andreas Houben
[DESCRIPTION]
Understanding the spatial organization of genomes within chromatin is crucial for d... | ["[Construction of ALFA-Tagged dCas9 Vectors] (a) Cloning of ALFA-Tag Sequences:\nClone the ALFA-tag sequences either at the N- or C-terminus of the dCas9 protein present in the pET22b-dCas9-6xHis vector using restriction-based cloning (see Note 1). \n(b) Transformation and Cultivation:\nTransform plasmids into Esch... |
21,131 | DNA extraction and Nested PCR | null | dx.doi.org/10.17504/protocols.io.yvjfw4n | null | Baiyan Gong1 ¶, Yaming Yang2 ¶, Xiaohua Liu, Jianping Cao, Meng Xu, Ning Xu, Fengkun Yang, Fangwei Wu, Benfu Li, Aiqin Liu *, Yujuan Shen * | TITLE: DNA extraction and Nested PCR
AUTHORS: Baiyan Gong1 ¶, Yaming Yang2 ¶, Xiaohua Liu, Jianping Cao, Meng Xu, Ning Xu, Fengkun Yang, Fangwei Wu, Benfu Li, Aiqin Liu *, Yujuan Shen *
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is the protocol for the Nested PCR assay</div></div>
[STEPS]... | ["DNA extraction", "PCR amplificationAmplification was accomplished in final volume of 25 μL, containing 17 μL of DNase/RNase-Free Deionized Water, 0.5 μL of each primer, 0.5 μL of TaKaRa Taq DNA Polymerase (TaKaRa Bio Inc., Tokyo, Japan), 2.5 μL of 10 × PCR Buffer, 2 μL of 10 mmol dNTP and 2 μL of DNA .", "The target ... |
null | null | null | dx.doi.org/10.17504/protocols.io.e4dbgs6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A Fluorescent, Continuous Enzyme Assay.</p>
[GUIDELINES]
<p><strong>INTRODUCTION</strong></p>
<p>Methylation of key biological molecules and proteins plays important roles in numerous biological systems, including signal transduction, biosynthesis, protein repair, gene silen... | [] |
59,832 | Yeast Transformation Protocol | 4 | dx.doi.org/10.17504/protocols.io.kxygxzy6kv8j/v1 | https://www.protocols.io/view/yeast-transformation-protocol-b6nyrdfw | Sudhir Nayak | TITLE: Yeast Transformation Protocol
AUTHORS: Sudhir Nayak
[DESCRIPTION]
This protocol is based on Gietz, R.D. and R.A. Woods. (2002) TRANSFORMATION OF YEAST BY THE Liac/SS CARRIER DNA/PEG METHOD. Methods in Enzymology 350: 87-96. Some steps of this protocol are based on information obtained from:
http://www.umanitob... | ["[Preparation:] Streak or patch yeast on YAPD for 24-48hrs. Can also use yeast from older plates (3 months? at 4 deg) if efficiency is not an issue and the strain cooperates.", "[Preparation:] Inoculate 2 x 3-5ml cultures in 2xYAPD or SC media (15ml snap cap tubes) from the fresh streak and incubate O/N 30 deg, 200rp... |
106,677 | Preparation, storage and use of the positive and negative controls for DDNS | 0 | dx.doi.org/10.17504/protocols.io.8epv5r594g1b/v1 | https://www.protocols.io/view/preparation-storage-and-use-of-the-positive-and-ne-dkev4te6 | Joyce Akello, Manasi Majumdar, Alex Shaw, Catherine Troman, Erika Bujaki, Javier Martin, Nick Grassly | TITLE: Preparation, storage and use of the positive and negative controls for DDNS
AUTHORS: Joyce Akello, Manasi Majumdar, Alex Shaw, Catherine Troman, Erika Bujaki, Javier Martin, Nick Grassly
[DESCRIPTION]
This protocol describes the laboratory process for the use of run controls (positive and negative controls)
for... | ["[CVA20 positive control reconstitution] Reconstitution of the positive control", "[CVA20 positive control reconstitution] Working in the MSCII, reconstitute the vial containing the lyophilised CVA20 (freeze dried material) by adding 1mL of nuclease free water (NFW)", "[CVA20 positive control reconstitution] Vortex br... |
81,088 | Workflow for beta-range forest plots, bootstrap ridgeline plots, and bootstrap violin plots | 5 | null | https://www.protocols.io/view/workflow-for-beta-range-forest-plots-bootstrap-rid-cte8wjhw | Jonathan Fries, Sandra Oberleiter, Jakob Pietschnig | TITLE: Workflow for beta-range forest plots, bootstrap ridgeline plots, and bootstrap violin plots
AUTHORS: Jonathan Fries, Sandra Oberleiter, Jakob Pietschnig
[DESCRIPTION]
Regression is a widely used statistical method in various research areas, such as educational psychology, and it is common to display regression ... | ["[Packages] The following workflow requires the statistical programming environment R (at least version 4.2.2). Before running any command prompts, some packages need to be installed. To this end, we create a vector that contains the respective package names and run a for loop that only installs packages that are not ... |
30,386 | Miniprep (Ethanol Lysis) | null | dx.doi.org/10.17504/protocols.io.9wsh7ee | null | Nicholas Coleman, Alex Kelly | TITLE: Miniprep (Ethanol Lysis)
AUTHORS: Nicholas Coleman, Alex Kelly
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">For the purification of Plasmid DNA from E. coli or similar Gram-Negative E. Coli</div></div>
[STEPS]
?. [Day 1]
Inoculate a 10-15ml tube of LB-Antibiotic media with your plasmid-co... | ["[Day 1]\nInoculate a 10-15ml tube of LB-Antibiotic media with your plasmid-containing bacteria. Place in a 37°C incubator or water bath (ideally shaking) and grow overnight.", "[Day 2]\nPellet cells in 15mL Falcon tube by centrifuging at max speed for 5 minutes. Pour off supernatant into liquid waste.", "[Day 2]\nRes... |
45,712 | Highfield Diagnostics COVID19 LFA Protocol v.2 | 2 | dx.doi.org/10.17504/protocols.io.bqvqmw5w | https://www.protocols.io/view/highfield-diagnostics-covid19-lfa-protocol-v-2-bqvqmw5w | peijun he | TITLE: Highfield Diagnostics COVID19 LFA Protocol v.2
AUTHORS: peijun he
[STEPS] | [] |
85,937 | Proximity biotinylation of ATG8 proteins and selective autophagy receptors V2 | 4 | dx.doi.org/10.17504/protocols.io.dm6gp3jb1vzp/v1 | https://www.protocols.io/view/proximity-biotinylation-of-atg8-proteins-and-selec-cx6rxrd6 | Harper JW, Kelsey Hickey, sharan_swarup | TITLE: Proximity biotinylation of ATG8 proteins and selective autophagy receptors V2
AUTHORS: Harper JW, Kelsey Hickey, sharan_swarup
[DESCRIPTION]
Autophagy involves the formation of an autophagosome around a cellular cargo, and once encapsulated in this double membrane structure, the autophagosome fuses with the lys... | ["[Workflow for proximity biotinylation of autophagy proteins with nutrient stress] The choice of cells to employ for proximity biotinylation depends on the experimental design. Here HeLa (ATCC CCL-2, RRID: CVCL_0030) cells gene edited to lack either MAP1LC3B or GABARAPL2 (made in Vaites LP et al Mol Cell Biol. 2017, 3... |
55,730 | Total Soluble Sugar Quantification from Ethanolic Plant Extracts | 6 | dx.doi.org/10.17504/protocols.io.b2nsqdee | https://www.protocols.io/view/total-soluble-sugar-quantification-from-ethanolic-b2nsqdee | Lynn Doran, Amanda P. De Souza | TITLE: Total Soluble Sugar Quantification from Ethanolic Plant Extracts
AUTHORS: Lynn Doran, Amanda P. De Souza
[DESCRIPTION]
Quantification of total soluble sugars (as glucose) in plant tissue extracts via the sulfuric phenol method adapted for 96 well plates.
[BEFORE_START]
Extract and purify total solu... | ["[Glucose standard preparation] Prepare glucose standards in microcentrifuge by pipetting the appropriate amounts of 1 mg/mL Glucose standard and distilled water into each labeled tube.", "[Glucose standard preparation] Pipette 50 ul of each prepared glucose standard in triplicate into the assigned wells.", "Pipette 1... |
29,002 | Tissue Preparation for CLARITY | null | dx.doi.org/10.17504/protocols.io.8jihuke | null | Seth Currlin, Marda Jorgensen, Jerelyn Nick | TITLE: Tissue Preparation for CLARITY
AUTHORS: Seth Currlin, Marda Jorgensen, Jerelyn Nick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Tissue preparation for CLARITY includes fixation in 4% PFA, infusion with monomers in Hydrogel Solution, and clearing of lipids in Electrophoretic Tissue Clearin... | ["1.\tPFA Incubation: Trimmed tissues are placed fixed in 4% PFA for 20-24 hours at room temperature on a slow platform rocker.", "2.\tHydrogel Incubation: Tissues are transferred to Hydrogel Solution in for approximately 5 days at 4˚C. Tubes are kept on a 2-axis rocker for the duration.", "3.\tHydrogel Polymerization:... |
20,077 | U Mass - Creatine Kinase | null | dx.doi.org/10.17504/protocols.io.xumfnu6 | null | Jason Kim | TITLE: U Mass - Creatine Kinase
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This experiment involves a spectrophotometric measurement using Roche Cobas Clinical Chemistry Analyzer.</div></div>
[... | ["Perform daily quality control assessment of instrumentation before analysis.", "Load each sample into a specialized micro-sample cup for the clinical chemistry analyzer.", "Select Creatine Kinase test on display and run the analysis.", "Collect and analyze the data."] |
26,178 | Collection of Mammalian Embryonic Palate Tissue | null | dx.doi.org/10.17504/protocols.io.5tag6ie | null | Matthew Fox | TITLE: Collection of Mammalian Embryonic Palate Tissue
AUTHORS: Matthew Fox
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol will guide you through the process of extracting embryos from adult mice and the manipulation of embryos in order to obtain palatal tissue.</div></div>
[STEPS]
?... | ["[Preparation]\nEuthanize pregnant mouse via primary and secondary modes of IACUC approved euthanasiaCO2 gas at 2L/min until 1 minute after last gasp.Cervical separation", "[Embryo Collection]\nUsing scissors, create an abdominal incision from the genitalia to the rib cage.", "[Embryo Collection]\nLocate and lift both... |
103,174 | Protein extraction and Western blotting | 0 | dx.doi.org/10.17504/protocols.io.rm7vzj784lx1/v1 | https://www.protocols.io/view/protein-extraction-and-western-blotting-dgze3x3e | Shiyi Wang | TITLE: Protein extraction and Western blotting
AUTHORS: Shiyi Wang
[DESCRIPTION]
Protein extraction and Western blotting
[STEPS]
1. **Prepare Membrane Solubilization Buffer** - 25 mM Tris (pH 7.4) - 150 mM NaCl - 1 mM CaCl2 - 1 mM MgCl2 - 0.5% NP-40 - Protease inhibitors
2. **Wash Cultured Astrocytes** - Wash culture... | ["**Prepare Membrane Solubilization Buffer** - 25 mM Tris (pH 7.4) - 150 mM NaCl - 1 mM CaCl2 - 1 mM MgCl2 - 0.5% NP-40 - Protease inhibitors", "**Wash Cultured Astrocytes** - Wash cultured rat astrocytes twice with ice-cold TBS containing 1 mM CaCl2 and 1 mM MgCl2.", "**Extract Protein** - Incubate astrocytes on ice i... |
73,870 | Colorimetric in situ hybridisation | 4 | null | https://www.protocols.click/view/colorimetric-in-situ-hybridisation-ckdnus5e | Stephen Carter | TITLE: Colorimetric in situ hybridisation
AUTHORS: Stephen Carter
[DESCRIPTION]
The protocol for performing colorimetric in situ hybridisation in zebrafish embryos and larvae in the Wilson lab.
[STEPS]
SECTION: Probe synthesis
2. If the template DNA is a plasmid, it must first be linearised by restriction enzyme dig... | ["[Probe synthesis] If the template DNA is a plasmid, it must first be linearised by restriction enzyme digestion. If it is a PCR product, it can be used directly. \n\nPrepare probe synthesis reaction mix\n\nTemplate DNA (PCR product or plasmid) -0.5-1 µg\n10x DIG RNA mix (Roche) - 2 µL\n10x transcription buffer - 2 µL... |
50,136 | An Optimized Protocol for the Generation of Midbrain Dopamine Neurons from human iPSCs under Defined Conditions | 1 | dx.doi.org/10.17504/protocols.io.bu7ynzpw | https://www.protocols.io/view/an-optimized-protocol-for-the-generation-of-midbra-bu7ynzpw | Carlos W. Gantner, Agustín Cota-Coronado, Lachlan H. Thompson, Clare L Parish | TITLE: An Optimized Protocol for the Generation of Midbrain Dopamine Neurons from human iPSCs under Defined Conditions
AUTHORS: Carlos W. Gantner, Agustín Cota-Coronado, Lachlan H. Thompson, Clare L Parish
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:ce... | ["[BEFORE YOU BEGIN: Pluripotent Stem Cell Thawing ]\nCoat a T25 flask with – and leave in the incubator for ≥ (see Tables 1 and 2 for laminin-521 dilution).\n[Laminin-521]\nNote: is sufficient for cell lines that have been adapted to Laminin-521. For non-adapted lines (i.e. hPSC lines maintained on substrates other ... |
54,182 | Experiment 5 | 1 | null | https://www.protocols.io/view/experiment-5-by6epzbe | Dikla Perez , Yael Steinhart , Amir Grinstein , Meike Morren | TITLE: Experiment 5
AUTHORS: Dikla Perez , Yael Steinhart , Amir Grinstein , Meike Morren
[DESCRIPTION]
This experiment provides evidence for consistency in identity related actual choices in a lab setting.
This experiment also aimed to extend the results of prior experiments by showing that the effect of expected v... | ["Experimental design:\n\nWe have employed a 2 × 2 between-subjects design: identity expressed by the product involved in the first decision (expressed identity: personal or social) × visibility of the consumed product involved in the first decision (the expected visibility of the consumed product: high or low).", "Sam... |
null | null | null | dx.doi.org/10.17504/protocols.io.hfyb3pw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>E-mail: binny@paru.cas.cz</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
53,963 | Uploading Data Files to Terra | 1 | dx.doi.org/10.17504/protocols.io.byxjpxkn | https://www.protocols.io/view/uploading-data-files-to-terra-byxjpxkn | Francis J Ambrosio | TITLE: Uploading Data Files to Terra
AUTHORS: Francis J Ambrosio
[DESCRIPTION]
Uploading data to Terra.bio is an essential step in the protocol for analyzing locally stored genomic sequencing data. The Terra.bio uploads page allows users to easily organize their data files using an associated metadata file via a brow... | ["[Upload Data Files] Navigate to the Terra.bio uploads page.", "[Upload Data Files] Select an existing workspace or create the workspace where the data will be uploaded. If there are no workspaces created under the billing project associated with this account please reach out to support@theiagen.com and we will facili... |
81,170 | DAB-quant | 5 | dx.doi.org/10.17504/protocols.io.dm6gpb578lzp/v2 | https://www.protocols.io/view/dab-quant-cthswj6e | Sneh Patel, Sara Fridovich-Keil, Shauna Rasmussen, and Judith L Fridovich-Keil | TITLE: DAB-quant
AUTHORS: Sneh Patel, Sara Fridovich-Keil, Shauna Rasmussen, and Judith L Fridovich-Keil
[DESCRIPTION]
Here we describe DAB-quant, a new system that facilitates quantitation of large numbers of scanned tissue slides stained via immunohistochemistry with 3,3′-Diaminobenzidine (DAB). The python code, ins... | ["[Protocol] Here we provide DAB-quant, a new system that facilitates quantitation of large numbers of scanned tissue slides stained via immunohistochemistry with 3,3′-Diaminobenzidine (DAB). The python code, instructions, license, and a link to example scans for analysis are all available at:\n https://github.com/sara... |
57,782 | Preparing samples for NGS | 4 | dx.doi.org/10.17504/protocols.io.b4nwqvfe | https://www.protocols.io/view/preparing-samples-for-ngs-b4nwqvfe | Hanqin Li, Yogendra Verma, Dirk Hockemeyer, Frank Soldner | TITLE: Preparing samples for NGS
AUTHORS: Hanqin Li, Yogendra Verma, Dirk Hockemeyer, Frank Soldner
[DESCRIPTION]
This protocol describes a standard procedure used to prepare PCR samples for Next Generation Sequencing (NGS)
[STEPS]
2. Purify the rest of the PCR product using column based or SPRI-beads based method... | ["Purify the rest of the PCR product using column based or SPRI-beads based method, like Wizard SV Gel and PCR clean-up system or AMPure XP beads", "Following the instruction of the NGS facility, dilute the purified amplicon to a proper concentration, usually 10 ng/µl", "Send the purified samples to a NGS facility for ... |
null | null | null | dx.doi.org/10.17504/protocols.io.jinckde | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
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63,788 | TX-100 FRACTIONATION PROTOCOL | 4 | dx.doi.org/10.17504/protocols.io.5qpvob21zl4o/v1 | https://www.protocols.io/view/tx-100-fractionation-protocol-caiksccw | Svermily | TITLE: TX-100 FRACTIONATION PROTOCOL
AUTHORS: Svermily
[DESCRIPTION]
To isolate insoluble and soluble proteins from dissected brain regions frozen for biochemical analysis.
[STEPS]
SECTION: Thaw Tissue
1. If tissue stored at -80 °C, place in -20 °C for at least 240 min or 240 min to thaw prior to homogenization.
S... | ["[Thaw Tissue] If tissue stored at -80 °C, place in -20 °C for at least 240 min or 240 min to thaw prior to homogenization.", "[Prepare 1X TNE] Prepare 1X TNE with phosphatase and protease inhibitors.", "[Homogenize Tissue] Weigh tissue out in mg.", "[Homogenize Tissue] Add in 10 volumes of 1X TNE.\n10 µL of TNE per 1... |
99,993 | SMARTerV4 (0.5x) Amplification for single-cell or single-nuclei RNASeq Protocol | 1 | dx.doi.org/10.17504/protocols.io.8epv517xdl1b/v4 | https://www.protocols.io/view/smarterv4-0-5x-amplification-for-single-cell-or-si-ddvz2676 | Allen Institute | TITLE: SMARTerV4 (0.5x) Amplification for single-cell or single-nuclei RNASeq Protocol
AUTHORS: Allen Institute
[DESCRIPTION]
Protocol to generate full-length cDNA from single cells, or nuclei, using Takara SMARTer V4.
Note: Research reported in this publication was supported by the National Institute Of Mental Healt... | [] |
66,613 | FIP200-eGFP expression and purification | 4 | dx.doi.org/10.17504/protocols.io.dm6gpbkq5lzp/v1 | https://www.protocols.io/view/fip200-egfp-expression-and-purification-cdavs2e6 | Eleonora Turco, Justyna Sawa-Makarska | TITLE: FIP200-eGFP expression and purification
AUTHORS: Eleonora Turco, Justyna Sawa-Makarska
[DESCRIPTION]
This protocol describes how to express and purify human FIP200 tagged C-terminally with eGFP.
[STEPS]
SECTION: Expression
1. To generate FIP200-GFP constructs the insect codon optimized FIP200 gene was purchas... | ["[Expression] To generate FIP200-GFP constructs the insect codon optimized FIP200 gene was purchased from GenScript and cloned with respective tags into pGB-02-03 (pGB-GST-3C-FIP200-GFP - Addgene ID: 187830). Generated construct was used for expression in Sf9 insect cells using the Bac-to-Bac system (ThermoFischer Sci... |
81,848 | PRESAT_bio.nan | 5 | dx.doi.org/10.17504/protocols.io.bp2l69jndlqe/v1 | https://www.protocols.io/view/presat-bio-nan-ct6ywrfw | NAN KB, John Glushka, Alex Eletsky | TITLE: PRESAT_bio.nan
AUTHORS: NAN KB, John Glushka, Alex Eletsky
[DESCRIPTION]
This is a protocol for running the standard Bruker pulseprogram 'zggppr', a 1D proton experiment with water signal suppression by presaturation for biomolecular samples in 90%H2O/10%D2O. Alternative water suppression sequences (e.g. 'wate... | ["[Create noesypr1d experiment file] When Lock, Tune, Shim are complete proceed to the specific protocol for your desired pulseprogram(s).", "[Inspect parameters] Although routine parameters are correct at this stage, it is recommended to inspect them for errors, apply changes if needed.\n\nSelect the 'Acqpars' tab and... |
null | null | null | dx.doi.org/10.17504/protocols.io.rejd3cn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol was used to measure sealer penetration into dentinal tubules of the root canal and sealer penetration into the perimeter of the root canal walls, by mean of ImageJ program (version 1.51j8) in image samples obtained by means of confocal microscopy.</p>
[STEPS]
?... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.gx8bxrw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol is a group of the following 5 methods from the NEB website:<br />1. <a href="https://www.neb.com/protocols/2012/11/15/nebnext-end-prep-e7370" target="_blank">NEBNext End Prep </a> <br />2. <a href="https://www.neb.com/protocols/2012/11/15/adaptor-ligation-e737... | [] |
100,134 | Sanger Tree of Life HMW DNA Extraction: Automated Nucleated Blood Nanobind® | 0 | dx.doi.org/10.17504/protocols.io.6qpvr8453lmk/v1 | https://www.protocols.io/view/sanger-tree-of-life-hmw-dna-extraction-automated-n-dd2e28be | Pacific Biosciences, Adam Bates, Amy Denton, Caroline Howard | TITLE: Sanger Tree of Life HMW DNA Extraction: Automated Nucleated Blood Nanobind®
AUTHORS: Pacific Biosciences, Adam Bates, Amy Denton, Caroline Howard
[DESCRIPTION]
This protocol describes the automated extraction of HMW DNA from nucleated blood samples intended for long-read sequencing using the Nanobind® tissue ki... | ["[Laboratory Protocol] In one Thermo Fisher KingFisher™ 1 mL 96-well deep-well plate, labelled Lysis Plate, add the following reagents into each well for the number of samples being processed:", "[Laboratory Protocol] Set up the six remaining Thermo Fisher KingFisher™ 1 mL 96-well deep-well plates required for the pro... |
71,303 | Whole-cell proteomics and Analysis by Tandem Mass Tagging-based proteomics | 4 | dx.doi.org/10.17504/protocols.io.14egn2zopg5d/v1 | https://www.protocols.io/view/whole-cell-proteomics-and-analysis-by-tandem-mass-chvft63n | Felix Kraus, Sharan Swarup, Vinay V. Eapen, J. Wade Harper wade_harper@hms.harvard.edu | TITLE: Whole-cell proteomics and Analysis by Tandem Mass Tagging-based proteomics
AUTHORS: Felix Kraus, Sharan Swarup, Vinay V. Eapen, J. Wade Harper wade_harper@hms.harvard.edu
[DESCRIPTION]
The analysis of relative protein abundance has emerged as an important tool in cell biology. Typically, it is possible to quant... | ["[Harvest, precipitation and digestion] For whole proteome analysis, 50 µg is required for each replicate. Lyse cells in lysis buffer and pass them through a 21G needle 10 times. Alternatively, lyse cells by\nsonication as per manufactures instructions.", "[Harvest, precipitation and digestion] Centrifugate suspensio... |
55,235 | Analysis of Islet Function by Insulin Enzyme-linked Immunosorbent Assay (ELISA) | 4 | dx.doi.org/10.17504/protocols.io.bz7bp9in | https://www.protocols.io/view/analysis-of-islet-function-by-insulin-enzyme-linke-bz7bp9in | IIDP-HIPP | TITLE: Analysis of Islet Function by Insulin Enzyme-linked Immunosorbent Assay (ELISA)
AUTHORS: IIDP-HIPP
[DESCRIPTION]
This Standard Operating Procedure (SOP) is based on the Vanderbilt University Medical Center Human Islet Phenotyping Program (HIPP) Islet Functional Analysis. This SOP provides the HIPP procedure... | ["[Procedures] Preparation of Samples, Standards, and internal Quality Controls", "[Procedures] Thaw archived samples intended for analysis in room temperature water. Once thawed, invert capped samples ten times to thoroughly mix.", "[Procedures] Retrieve the islet hormone extracts and keep on ice.", "[Procedures] Prep... |
66,305 | Protocol: A Systematic Review of HLA-B and its Role in Congenital Adrenal Hyperplasia | 1 | dx.doi.org/10.17504/protocols.io.ccy9sxz6 | https://www.protocols.io/view/protocol-a-systematic-review-of-hla-b-and-its-role-ccy9sxz6 | Dylan Thibaut, Madison R Walter, Courtney McGonegal, Ryan C Daniel, Jerry Goodman | TITLE: Protocol: A Systematic Review of HLA-B and its Role in Congenital Adrenal Hyperplasia
AUTHORS: Dylan Thibaut, Madison R Walter, Courtney McGonegal, Ryan C Daniel, Jerry Goodman
[DESCRIPTION]
The link between specific HLA-B genes and congenital adrenal hyperplasia has been a subject of interest. This study in... | ["[Administrative Information] Title:\n\n\"A Systematic Review of HLA-B and its Role in Congenital Adrenal Hyperplasia\"\n\n\nRegistration:\n\nProtocols.io", "[Administrative Information] Authors\n\nDylan Thibaut: Lake Erie College of Osteopathic Medicine- Bradenton; AdventHealth- Sebring; University of Central Florida... |
97,936 | LD-HD Pigmentation Oscillator Model | 0 | dx.doi.org/10.17504/protocols.io.yxmvmexobg3p/v1 | https://www.protocols.io/view/ld-hd-pigmentation-oscillator-model-dbvq2n5w | Vivek T Natarajan | TITLE: LD-HD Pigmentation Oscillator Model
AUTHORS: Vivek T Natarajan
[DESCRIPTION]
LD-HD pigmentation oscillator model uses B16 mouse melanoma cells which are seeded at a very low seeding density of 100 cells/cm2 and are left without change in media. Cells under such conditions gradually starts pigmenting, beginning ... | ["[FOR LD (Low Density) CYCLE OF PIGMENTATION] Take a confluent B16 mouse melanoma cell culture maintained in DMEM+10%FBS media.\nConfluency can be checked under a microscope and by change in color of media from pink to yellow-orange.", "[FOR LD (Low Density) CYCLE OF PIGMENTATION] Discard media using a steri-pipette."... |
null | null | null | dx.doi.org/10.17504/protocols.io.i9wch7e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>We have available several plasmids designed for expression of Cas9, guide RNA, chloramphenicol acetyl-transferase, GFP, and beta-lactamase in Micromonas CCMP1545. For protein expression we used the promotor and 3' end elements from the endogenous RPS9 gene, and codon optimize... | [] |
83,344 | Workflow for SNP genotyping using the Hi-Plex method | 4 | dx.doi.org/10.17504/protocols.io.8epv5jnnnl1b/v2 | https://www.protocols.click/view/workflow-for-snp-genotyping-using-the-hi-plex-meth-cvmqw45w | Anne-Laure Besnard, Daniel J. Park, Bernard J. Pope, Fleur Hammet, Sophie Michon-Coudouel, Marine Biget, Stacy A. Krueger-Hadfield, Stéphane Mauger, Eric J. Petit | TITLE: Workflow for SNP genotyping using the Hi-Plex method
AUTHORS: Anne-Laure Besnard, Daniel J. Park, Bernard J. Pope, Fleur Hammet, Sophie Michon-Coudouel, Marine Biget, Stacy A. Krueger-Hadfield, Stéphane Mauger, Eric J. Petit
[DESCRIPTION]
Many research questions in ecology and evolution require balancing sampli... | ["[Gene Specific Primers (GSPs) and adaptator (TSITs) preparation] Gene Specific Primers (GSP) preparation\n\nGSP synthesis\n\nPrepare a fasta file with 145bp sequences that will be used to design GSPs. Sequence names should contain the position and polymorphism of the targeted SNP.\nAn example of one such sequence is:... |
null | null | null | dx.doi.org/10.17504/protocols.io.gj2buqe | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
<div class="page" title="Page 2">
<div class="section">
<div class="layoutArea">
<div class="column">
<p>Make sure that the desired protein has the correct restriction sites and is in frame with the intein in the purification vector.</p>
<ol>
<li>
<p>If that is not the case nat... | [] |
85,683 | Bueno Sopaipillas | 1 | null | https://www.protocols.click/view/bueno-sopaipillas-cxwtxpen | Chasz Griego | TITLE: Bueno Sopaipillas
AUTHORS: Chasz Griego
[DESCRIPTION]
Sopaipillas are delicious, oily dough pockets. A New Mexican staple. Eat them as a dessert with honey, or as an entree, stuffing the sopaipilla with meat, beans, cheese, rice, etc. The options are near limitless! This protocol describes the steps to make so... | ["[Ingredients] YOU WILL NEED\n1 Box of Bueno Sopaipilla Mix\n1 Tbsp vegetable oil \n3/4 cup warm water\n3 cups vegetable oil (for frying)", "[Make Dough] EMPTY entire contents of sopaipilla mix into a large bowl.", "[Make Dough] ADD 1 Tbsp. oil. Gradually add water.", "[Make Dough] KNEAD the dough on a lightly floured... |
102,012 | Transgenic mouse colony maintenance | 0 | dx.doi.org/10.17504/protocols.io.yxmvmeyx5g3p/v1 | https://www.protocols.io/view/transgenic-mouse-colony-maintenance-dfu43nyw | Ariadna Laguna, Iria Carballo-Carbajal, Miquel Vila | TITLE: Transgenic mouse colony maintenance
AUTHORS: Ariadna Laguna, Iria Carballo-Carbajal, Miquel Vila
[DESCRIPTION]
Methods for the generation and maintenance of transgenic tyrosinase mice
[STEPS]
1. Pronuclear microinjection of the human
tyrosinase complementary DNA fused to the rat tyrosine hydroxylase promoter i... | ["Pronuclear microinjection of the human\ntyrosinase complementary DNA fused to the rat tyrosine hydroxylase promoter into C57Bl6-SJL (RRID:MGI:5656718) mouse zygotes", "Selection of positive lines and backcrossing for 8-10 generations using\nC57BL/6J mice (Charles River; RRID:MGI:3028467)", "Maintainance in heterozygo... |
null | null | null | dx.doi.org/10.17504/protocols.io.c2gybv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol is used for those that do not have a ≥20,000 x g capable centrifuge.
[BEFORE_START]
Add RNase A solution to Buffer P1, mix, and store at 2–8°C.<br />Optional: Add LyseBlue® reagent to Buffer P1 at a ratio of 1:1000.<br />Prechill Buffer P3 at... | [] |
62,917 | Systematic review and meta-analysis of incidence and outcomes of hip and vertebral fractures hip fracture in patients with end-stage kidney disease | 1 | dx.doi.org/10.17504/protocols.io.3byl4brjrvo5/v1 | https://www.protocols.io/view/systematic-review-and-meta-analysis-of-incidence-a-b9pdr5i6 | Yoshinosuke Shimamura, Yasutaka Kuniyoshi, Yasushi Tsujimoto | TITLE: Systematic review and meta-analysis of incidence and outcomes of hip and vertebral fractures hip fracture in patients with end-stage kidney disease
AUTHORS: Yoshinosuke Shimamura, Yasutaka Kuniyoshi, Yasushi Tsujimoto
[DESCRIPTION]
This is the protocol for a systematic review and meta-analysis to systematic... | ["[Authors' Information] Last update: May 17, 2022.\n\nAuthors: Yoshinosuke Shimamura MD, MPH1, 2; Yasutaka Kuniyoshi MD, PhD2,3; Yasushi Tsujimoto MD, MPH2, 4.\n\n1 Department of Nephrology, Teine Keijinkai Medical Center, Sapporo, Hokkaido, Japan.\n2 Scientific Review WorkshopS Peer Support Group (SRWS-PSG), Osa... |
54,690 | Engineering brain assembloids to interrogate human neural circuits | 4 | dx.doi.org/10.17504/protocols.io.36wgq4xxkvk5/v1 | https://www.protocols.io/view/engineering-brain-assembloids-to-interrogate-human-bznap5ae | Yuki Miura, Min-Yin Li, Omer Revah, Se-Jin Yoon, Genta Narazaki, Sergiu Pasca | TITLE: Engineering brain assembloids to interrogate human neural circuits
AUTHORS: Yuki Miura, Min-Yin Li, Omer Revah, Se-Jin Yoon, Genta Narazaki, Sergiu Pasca
[DESCRIPTION]
The development of neural circuits involves wiring of neurons locally following their generation and migration, as well as establishing long-d... | ["[Maintenance of hPS cells in feeder-free conditions Timing 4–6 d] Culture hPS cells on human recombinant vitronectin with Essential 8 medium. When hPS cell cultures reach ~80% confluency, passage hPS cultures by using0.5 millimolar (mM) EDTA in PBS.", "[Maintenance of hPS cells in feeder-free conditions Timing 4–6 d] ... |
69,401 | The leading role of evidence-based practices in the treatment of patients with substance use disorders: A systematic review | 1 | null | https://www.protocols.io/view/the-leading-role-of-evidence-based-practices-in-th-cfzztp76 | qasirabbas | TITLE: The leading role of evidence-based practices in the treatment of patients with substance use disorders: A systematic review
AUTHORS: qasirabbas
[DESCRIPTION]
Objectives: This study aims to explore the effectiveness of motivational interviewing (MI), motivational enhancement therapy (MET), and cognitive behaviou... | ["[The leading role of evidence-based practices in the treatment of patients with substance use disorders: A systematic review]"] |
62,899 | An on-site adaptable test for rapid and sensitive detection of Potato mop-top virus, a soil-borne virus of potato (Solanum tuberosum) | 4 | dx.doi.org/10.17504/protocols.io.b9ntr5en | https://www.protocols.io/view/an-on-site-adaptable-test-for-rapid-and-sensitive-b9ntr5en | Ying Zhai, Bryant Davenport, Keith Schuetz, Hanu R Pappu | TITLE: An on-site adaptable test for rapid and sensitive detection of Potato mop-top virus, a soil-borne virus of potato (Solanum tuberosum)
AUTHORS: Ying Zhai, Bryant Davenport, Keith Schuetz, Hanu R Pappu
[DESCRIPTION]
Potato mop-top virus(PMTV) is considered an emerging threat to potato production in the United ... | ["Cut core tubers with blade. Take 3 - 4 cores per tuber.", "Extract with GEB extraction buffer at a ratio of 1:2 (w:v) in a mesh extraction bag (0.3 g/3 mL). Let rest for 5 minutes at room temperature.", "Remove one colored PD1 filled tube for each sample being tested. Individual tubes may be cut from the strip of tub... |
50,241 | Artificial saliva | 6 | null | https://www.protocols.io/view/artificial-saliva-bva9n2h6 | Bjorn Bartholdy, a.g.henry | TITLE: Artificial saliva
AUTHORS: Bjorn Bartholdy, a.g.henry
[DESCRIPTION]
Creating an artificial saliva solution for oral biofilm growth.
This is a modified version of Sissons et al. 1991.
[BEFORE_START]
Mix the solution under a fumehood. It can smell pretty bad.
Also have the incubator under a fumehood, if poss... | ["Add 300 mL distilled (or deionized) dH2O to a 1000 mL beaker, with stirring and heat 60 °C .", "Add:\n\n- 2.5 g \n- 5 g \n- 10 g \n- 5 g \n\nLet the reagents completely dissolve before continuing to the next step", "Add:\n\n- 2.5 g \n- 0.35 g \n- 0.2 g \n- 0.74 g \n- 0.54 g \n- 2.5 mg", "Adjust t... |
null | null | null | dx.doi.org/10.17504/protocols.io.k5pcy5n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>For convenience and for PCR products that are challenging to purify with high efficiency (<em>e.g</em>., chemically modified DNAs), it is often desirable to quantitate synthesized DNA directly from a PCR reaction. Here we describe the use of a high-sensitivity Quant-iT™ PicoG... | [] |
91,219 | Quarantine and heat treatment for Hymenochirus boettgeri infected with Bd | 1 | dx.doi.org/10.17504/protocols.io.4r3l22b9jl1y/v1 | https://www.protocols.io/view/quarantine-and-heat-treatment-for-hymenochirus-boe-c5bty2nn | Tamilie Carvalho, Catherine Si, Rebecca A. Clemons, Evelyn Faust, Timothy Y. James | TITLE: Quarantine and heat treatment for Hymenochirus boettgeri infected with Bd
AUTHORS: Tamilie Carvalho, Catherine Si, Rebecca A. Clemons, Evelyn Faust, Timothy Y. James
[DESCRIPTION]
This protocol outlines the procedures for conducting heat treatment for clearing Batrachochytrium dendrobatidis (Bd) infection of H.... | ["[Quarantine setup] Place Bd-positive frogs in 38 L standard system glass tanks, condition the water, feed the animals, and conduct water changes as described in “Housing and Care for Hymenochirus boettgeri” protocol.", "[Heat Treatment] Gradually increase the water temperature in the quarantine standard system tanks ... |
20,656 | Case - Measurement of Food Consumption and Body Weight | null | dx.doi.org/10.17504/protocols.io.yeqftdw | null | Henri Brunengraber | TITLE: Case - Measurement of Food Consumption and Body Weight
AUTHORS: Henri Brunengraber
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">During the course of development or during a diet study the amount of food and b... | ["Mice are marked by ear notches. They are weighed and the weight is recorded.", "At 9:00AM, mice are placed in a clean cage (2-3 mice/cage because singly housed mice are stressed). The amount of food is weighed and recorded.", "The next day at 9:00AM the food and mice are weighed and measurements are recorded.", "To c... |
54,356 | DMSO stock preparation | 4 | dx.doi.org/10.17504/protocols.io.bzbup2nw | https://www.protocols.io/view/dmso-stock-preparation-bzbup2nw | Akashdutta | TITLE: DMSO stock preparation
AUTHORS: Akashdutta
[DESCRIPTION]
Bacterial cultures in the form of agar plates or liquid cultures are not suitable for long term storage at low temperatures such as 4oC. Long-term storage of bacteria is best at temperatures around -80oC. However, agar plates and liquid cultures cannot ... | ["From the streaked plate of the bacteria, pick one colony and inoculate into a 250 mL flask containing 100 mL culture.", "Grow the culture till it reaches OD∼ 0.6-0.8", "Take the 100 mL culture and transfer 40 mL each into two falcon tubes.", "Leave the remaining 20 mL culture in the flask. To that, add 80 mL of mic... |
null | null | null | dx.doi.org/10.17504/protocols.io.mdyc27w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Original dataset of the study entitled "<strong>A retrospective analysis on the relationship between intraoperative hypothermia and postoperative ileus after laparoscopic colorectal surgery</strong></p>
[STEPS]
?. | [] |
82,635 | MERS-CoV Mpro fluorescence dose response for antiviral testing | 1 | dx.doi.org/10.17504/protocols.io.eq2ly7r1rlx9/v5 | https://www.protocols.io/view/mers-cov-mpro-fluorescence-dose-response-for-antiv-cuxjwxkn | Haim Barr, Noa Lahav | TITLE: MERS-CoV Mpro fluorescence dose response for antiviral testing
AUTHORS: Haim Barr, Noa Lahav
[DESCRIPTION]
This is a functional, biochemical assay used to identify treatments for viral infectious disease in MERS-CoV 3C-like protease.
Utilizing a direct enzyme activity measurement method, the experiment was p... | ["[Prepare 384 Well Plate] PRIME the dispenser with Assay Buffer by selecting the PRIME button until the tubes are filled completely.", "[Prepare 384 Well Plate] DISPENSE 10 µL to Columns 1 and 23 of assay plate \nNote: These will represent the inhibitor control columns (Contain: Substrate, Assay Buffer, DMSO, no exper... |
63,108 | DNA extraction (Zymo kit) | 4 | dx.doi.org/10.17504/protocols.io.kxygxz11ov8j/v1 | https://www.protocols.io/view/dna-extraction-zymo-kit-b9vcr62w | Tsu-Chun Hung | TITLE: DNA extraction (Zymo kit)
AUTHORS: Tsu-Chun Hung
[DESCRIPTION]
DNA extraction (Zymo kit)
[STEPS]
SECTION: Sample Collection
1. Add 200 µL of 1mm beads to 1.5ml enppendorf tube
SECTION: DNA purification
2.
SECTION: DNA purification
1.
SECTION: Sample Collection
1.
SECTION: Sample Collection
3. Add 600 µL o... | ["[Sample Collection] Add 200 µL of 1mm beads to 1.5ml enppendorf tube", "[DNA purification]", "[DNA purification]", "[Sample Collection]", "[Sample Collection] Add 600 µL of lysis solution to 1.5ml enppendorf tube", "[Sample Collection] Add 200 µL of 0.5mm beads to 1.5ml enppendorf tube", "[Sample Collection] Collect ... |
55,351 | Protocol 3D Gait Analysis using Overground Approach - MUMC+ | 1 | dx.doi.org/10.17504/protocols.io.b2axqafn | https://www.protocols.io/view/protocol-3d-gait-analysis-using-overground-approac-b2axqafn | Rachel Senden, Rik Marcellis, Paul Willems, Jeroen Vermeulen, Adhiambo Witlox, Kenneth Meijer | TITLE: Protocol 3D Gait Analysis using Overground Approach - MUMC+
AUTHORS: Rachel Senden, Rik Marcellis, Paul Willems, Jeroen Vermeulen, Adhiambo Witlox, Kenneth Meijer
[DESCRIPTION]
This protocol describes the steps that are conducted for an overground based 3D gait analaysis at the MUMC+.
[STEPS]
SECTION:... | ["[Description Set-up] The overground approach for 3D gait analysis consists of overground walking over a 9-m walkway with an instrumented force plate (1000 Hz, AMTI Biomechanics Force Platform model OR6-7) surrounded by 10 infrared cameras (100 Hz, Vicon T10S Motion System, Nexus 1.0, Oxford, UK) and two 2D cameras. \... |
58,445 | Ampicillin 100 mg/mL Stock Solution | 1 | dx.doi.org/10.17504/protocols.io.ewov1no3ogr2/v1 | https://www.protocols.io/view/ampicillin-100-mg-ml-stock-solution-b5bmq2k6 | Bailey Clark | TITLE: Ampicillin 100 mg/mL Stock Solution
AUTHORS: Bailey Clark
[DESCRIPTION]
The abstract will be added later.
[STEPS]
SECTION: Stock Solution Preparation
1. Weigh 100 mg (0.1 g ) of Ampicillin.
SECTION: Stock Solution Preparation
2. Add the Ampicillin to a 1.5 mL tube.
SECTION: Stock Solution Preparation
3. A... | ["[Stock Solution Preparation] Weigh 100 mg (0.1 g ) of Ampicillin.", "[Stock Solution Preparation] Add the Ampicillin to a 1.5 mL tube.", "[Stock Solution Preparation] Add deionized water to the 1 mL level on the tube.", "[Stock Solution Preparation] Vortex the tube for 5 s , repeat 3 times.", "[Stock Solution Prepa... |
40,763 | ELISA for quantification of IL-3 in human serum. | 6 | dx.doi.org/10.17504/protocols.io.bj23kqgn | https://www.protocols.io/view/elisa-for-quantification-of-il-3-in-human-serum-bj23kqgn | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-3 in human serum.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells... | ["An anti-human IL-3 coating antibody is adsorbed onto microwells by incubation overnight at 4°C.", "Add 50 µl of human serum. Human IL-3 present in the serum sample binds to antibodies adsorbed to the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and later wasth o remove unbound proteins.",... |
89,268 | Brain Single Cell Isolation for Flow Cytometry | 4 | dx.doi.org/10.17504/protocols.io.kqdg3x8r7g25/v1 | https://www.protocols.io/view/brain-single-cell-isolation-for-flow-cytometry-c3euyjew | Jhodi Webster, Ashley Harms, Vickie Yang, Aidan Miller | TITLE: Brain Single Cell Isolation for Flow Cytometry
AUTHORS: Jhodi Webster, Ashley Harms, Vickie Yang, Aidan Miller
[DESCRIPTION]
This protocol is used to isolate single cells from mouse brains and process these samples for flow cytometry analysis. The protocol can be optimized/altered to account for staining of int... | ["[SETUP] Make reagents needed:\nFlow media: RPMI 1640 + 10%FBS + 1% Penicillin/Streptomycin + 1% L-Glutamine\n10X Stock Enzyme: 1g Collagenase IV in 100mL serum-free media (RPMI 1640). Aliquot into 5mL and store at -20 °C until use. To use (working concentration) thaw on ice, QS to 38mL using serum-free media. Final c... |
51,886 | Processing and symmetry expansion of LRRK2RCKW on microtubules | 5 | dx.doi.org/10.17504/protocols.io.bwwnpfde | https://www.protocols.io/view/processing-and-symmetry-expansion-of-lrrk2rckw-on-bwwnpfde | Mariusz Matyszewski | TITLE: Processing and symmetry expansion of LRRK2RCKW on microtubules
AUTHORS: Mariusz Matyszewski
[DESCRIPTION]
Protocol for symmetry expansion of LRRK2RCKW filaments bound to microtubules. This protocol covers everything from preprocessing to creating a new set of symmetry expanded particles that can be used by any... | ["[Preprocessing data] Align frames and do CTF fitting\nUse your preferred software. The original publication used MotionCor 2 and CTFFIND4, but other programs should work just as long as CTF information can be imported into Relion.\nAs a note, all of the data processed was collected on lacey carbon grids rather than C... |
null | null | null | dx.doi.org/10.17504/protocols.io.c6bzam | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
To reverse the crosslinking of DNA that results from the PFA fixative, PFA fixed samples were prepared by incubating the cell lysate in 0.5M NaCl for 18 hours at 65°C.
[STEPS] | [] |
37,867 | Purification of synaptic vesicles from rodent brains, troubleshooting and column cleaning/regenerating | 4 | dx.doi.org/10.17504/protocols.io.4r3l28zzjl1y/v1 | https://www.protocols.io/view/purification-of-synaptic-vesicles-from-rodent-brai-bg8jjzun | Amberley Stephens | TITLE: Purification of synaptic vesicles from rodent brains, troubleshooting and column cleaning/regenerating
AUTHORS: Amberley Stephens
[DESCRIPTION]
Purification of synaptic vesicles from tissue samples is initially performed using sucrose gradients and ultracentrifugation. To obtain highly pure synaptic vesicle sa... | ["We follow the protocol provided by Ahmed, et al 'Small-scale isolation of synaptic vesicles from mammalian brain (2013)', which has proved to be a reproducible and well-designed protocol. We will only mention adaptations we made as we follow most of the protocol step by step.", "We use the brains of two Sprague Dawle... |
null | null | null | dx.doi.org/10.17504/protocols.io.i3jcgkn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A non-destructive DNA extraction method suitable for robust herbarium specimens and potentially useful for specimens with high levels of secondary compounds.</p>
[GUIDELINES]
<p>Perform DNA extractions and PCR set-ups in a dedicated ancient DNA laboratory.</p>
[STEPS]
?.
?... | [] |
47,618 | MBF Bioscience: FAIR Segmentation and Annotation | 1 | null | https://www.protocols.io/view/mbf-bioscience-fair-segmentation-and-annotation-bsrand2e | Maci Heal | TITLE: MBF Bioscience: FAIR Segmentation and Annotation
AUTHORS: Maci Heal
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Segmenting and annotating microscopy image data with MBF Bioscience software using built-in SciCrunch API for up-to-date anatomical terms curated by the SPARC Anatomy Working Gr... | ["[Adding Metadata and Accessing SPARC Vocabularies from SciCrunch]\nLaunch one of the following MBF Bioscience software with SPARC-mode enabled.", "[Adding Metadata and Accessing SPARC Vocabularies from SciCrunch]\nOpen a microscopy image via the Open icon, File>Open, or dragging and dropping into the program window.N... |
50,123 | Biofilm growth with starch treatment | 1 | null | https://www.protocols.io/view/biofilm-growth-with-starch-treatment-bu7jnzkn | Bjorn Bartholdy, a.g.henry | TITLE: Biofilm growth with starch treatment
AUTHORS: Bjorn Bartholdy, a.g.henry
[DESCRIPTION]
Protocol to grow mature, mineralised oral biofilm with starches.
Modified from protocol by Sissons et al.:
Sissons, C. H., Cutress, T. W., Hoffman, M. P., & Wakefield, J. S. J. (1991). A Multi-station Dental Plaque Microc... | ["[Saliva collection] Collect the saliva by spitting into 50 ml plastic centrifuge tubes.", "[Saliva collection] Make a 2-fold dilution of saliva in sterile 20 % (v/v) and vortex the solution.", "[Saliva collection] Saliva donors rinse their mouth with water for 30 seconds.", "[Saliva collection] Stimulate saliva produ... |
61,887 | JAX - EZ Lysis Nuclei Isolation for 10x Genomics Assays | 1 | dx.doi.org/10.17504/protocols.io.ewov1n9npgr2/v3 | https://www.protocols.io/view/jax-ez-lysis-nuclei-isolation-for-10x-genomics-ass-b8n7rvhn | Shannon Bessonett, Greggory A Perry, Sandra L Daigle, Paul.gabriel , Diane Luo, Jessica Grassmann, William F F Flynn, Elise Courtois, Paul Robson | TITLE: JAX - EZ Lysis Nuclei Isolation for 10x Genomics Assays
AUTHORS: Shannon Bessonett, Greggory A Perry, Sandra L Daigle, Paul.gabriel , Diane Luo, Jessica Grassmann, William F F Flynn, Elise Courtois, Paul Robson
[DESCRIPTION]
The purpose of this protocol is to produce single nuclei from frozen human tissue... | ["[Sample Prep] Slightly thaw sample out on ice and place onto pre chilled Petri dish on ice.", "[Sample Prep] Cut tissue into small pieces and add to a microcentrifuge tube.", "[Cell lysis] In micro centrifuge tube containing the tissue add 100 µL of lysis buffer.", "[Cell lysis] Using a plastic pestle to grind tissue... |
49,900 | 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-buyknxuw | 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... | ["[Running the Mercury Prep Workflow] To run the Mercury workflow, click on the 'Workflows' panel within your workspace. It should bring you to the following page:\n\n \nClick on the 'Mercury_PE_Prep' tile and it will take you to a new page. Double check that you are using the latest version of the workflow. Or if you... |
49,163 | High throughput quantification of CRISPR gRNA efficiency based on surrogate lentivirus libraries | 4 | dx.doi.org/10.17504/protocols.io.bt9jnr4n | https://www.protocols.io/view/high-throughput-quantification-of-crispr-grna-effi-bt9jnr4n | Xi Xiang, Yonglun Luo | TITLE: High throughput quantification of CRISPR gRNA efficiency based on surrogate lentivirus libraries
AUTHORS: Xi Xiang, Yonglun Luo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is developed for massively capture CRISPR gRNA efficiency in cells. The protocol is based on lentivirus... | ["[Design of surrogate oligonucleotides ]\nEach oligo (170 bp) consists of the BsmBI recognition site “cgtctc” with 4 bp specific nucleotides “acca” upstream, following the GGA cloning linker “aCACC”, one bp “g” for initiating transcription from U6 promoter, 20 bp gRNA sequences of “gN20”, 82bp gRNA scaffold sequence, ... |
93,205 | MYH9 intron 3 saturation mutagenesis screening | 4 | dx.doi.org/10.17504/protocols.io.8epv5x5qdg1b/v1 | https://www.protocols.io/view/myh9-intron-3-saturation-mutagenesis-screening-c69vzh66 | Brian D. Cosgrove, Lexi Bounds, Carson Key Taylor, Alan L. Su, Anthony J. Rizzo, Alejandro Barrera, Andrea R Daniel, Gregory E. Crawford, Brenton D. Hoffman, Charles A. Gersbach | TITLE: MYH9 intron 3 saturation mutagenesis screening
AUTHORS: Brian D. Cosgrove, Lexi Bounds, Carson Key Taylor, Alan L. Su, Anthony J. Rizzo, Alejandro Barrera, Andrea R Daniel, Gregory E. Crawford, Brenton D. Hoffman, Charles A. Gersbach
[DESCRIPTION]
This protocol describes methods for a CRISPR screen to identify ... | ["[Library design and cloning] For the MYH9 intron 3 pRE saturation mutagenesis library, we include any gRNA that are within the hit pRE from the MYH9 locus library (from our previous CRISPRi stiffness-responsive screen), which resulted in 64 gRNA across the library.", "[Library design and cloning] Include 25 non-targe... |
38,550 | FCMPASS - Creating a cytometer database and datasets | 5 | dx.doi.org/10.17504/protocols.io.bhvwj67e | https://www.protocols.io/view/fcmpass-creating-a-cytometer-database-and-datasets-bhvwj67e | Joshua Welsh, Jennifer Jones | TITLE: FCMPASS - Creating a cytometer database and datasets
AUTHORS: Joshua Welsh, Jennifer Jones
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the steps required to create flow cytometer databases and datasets using the FCMPASS software. This is one of a number of protocols... | ["Open FCMPASS.", "Click the ‘+’ icon next to ‘Cytometer IDs’ list and enter a unique name to identify a instrument.", "Select the relevant cytometer ID to add the dataset to", "Click the ‘+’ icon next to the ‘Datasets’ list.", "In the window enter the acquisition date of the calibration data and the dataset/experiment... |
56,033 | S1: Step-by-step-guide using image J in the work flow. | 5 | dx.doi.org/10.17504/protocols.io.b2x9qfr6 | https://www.protocols.io/view/s1-step-by-step-guide-using-image-j-in-the-work-fl-b2x9qfr6 | Paul Kalke, Conrad Helm | TITLE: S1: Step-by-step-guide using image J in the work flow.
AUTHORS: Paul Kalke, Conrad Helm
[DESCRIPTION]
How to use ImageJ in our 3D-workflow from data manipulation, import, segmentation and export as OBJ-file.
[STEPS]
2.
•Make sure your Image Sequence starts with 1 and choose Use virtual stack to save RAM
•Y... | ["•Make sure your Image Sequence starts with 1 and choose Use virtual stack to save RAM\n•You can scale your data set down too", "•Open Image J and import your Image Sequence\n•It is possible in Image J to transform stacks into Images Sequences and vice versa", "•Import your binned data set by right click in blank (bla... |
57,841 | Immunohistochemistry of porcine enteric neurons | 1 | dx.doi.org/10.17504/protocols.io.b4qrqvv6 | https://www.protocols.io/view/immunohistochemistry-of-porcine-enteric-neurons-b4qrqvv6 | Gemma Mazzuoli-Weber, Michael Schemann, Kristin Elfers, Birgit Kuch, Susanne Hoppe | TITLE: Immunohistochemistry of porcine enteric neurons
AUTHORS: Gemma Mazzuoli-Weber, Michael Schemann, Kristin Elfers, Birgit Kuch, Susanne Hoppe
[DESCRIPTION]
This protocol is to investigate the presence and localization of neurochemical markers in the submucosal and myenteric plexus of the porcine colon using imm... | ["Samples of colon were taken from apparently healthy pigs, placed in ice-cold oxygenated Krebs solution for preparation and immediately transferred to the laboratory. Tissues were then dissected in the ice-cold oxygenated Krebs solution for preparation to obtain whole-mount inner submucosal plexus or myenteric plexus ... |
74,863 | Lysogeny Broth (LB) medium | 4 | dx.doi.org/10.17504/protocols.io.ewov1o262lr2/v2 | https://www.protocols.io/view/lysogeny-broth-lb-medium-cmcpu2vn | Andreas Sagen | TITLE: Lysogeny Broth (LB) medium
AUTHORS: Andreas Sagen
[DESCRIPTION]
Lysogeny broth (LB) is a nutritionally rich medium which is primarily used for the growth of bacteria[1]. The initialism is also commonly, albeit incorrectly, taken to mean Luria broth, Lennox broth, or Luria-Bertani medium. According to its creato... | ["[500 mL LB-Lennox (broth) medium] All compounds are measured using a high precision analytical scale from powdered compounds. Each compound is measured to within 1% of the target weight. All compounds are mixed in a Duran bottle", "[500 mL LB-Lennox (broth) medium] Fill the bottle with 400 mL double-distilled water",... |
73,759 | Use of the waxworm Galleria mellonella larvae as an infection model to study Acinetobacter baumannii | 4 | dx.doi.org/10.17504/protocols.io.n92ldpr38l5b/v1 | https://www.protocols.io/view/use-of-the-waxworm-galleria-mellonella-larvae-as-a-cj97ur9n | Kah Ern Ten, Nazmul Hasan Muzahid, Sadequr Rahman, tan.hocksiew | TITLE: Use of the waxworm Galleria mellonella larvae as an infection model to study Acinetobacter baumannii
AUTHORS: Kah Ern Ten, Nazmul Hasan Muzahid, Sadequr Rahman, tan.hocksiew
[DESCRIPTION]
Galleria mellonella larvae have been increasingly used in various scientific research, including microbial infection studie... | ["[Galleria mellonella rearing and maintenance] Research-grade Galleria mellonella larvae were ordered in bulk from Carolina Biological (US).", "[Galleria mellonella rearing and maintenance] Set up Galleria mellonella housing according to Figure 2.", "[Galleria mellonella rearing and maintenance] Fill 2/3 of the larvae... |
null | null | null | dx.doi.org/10.17504/protocols.io.dde23d | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<strong>Purpose:</strong> This protocol describes how to analyze a natural aquatic virus sample using transmission electron microscopy (TEM). The purpose is to obtain the capsid diameter distributions of the viral assemblage, tail length distributions of the viral assemblage, an... | [] |
37,869 | Mouse transcardial perfusion | 1 | dx.doi.org/10.17504/protocols.io.ewov18kkpgr2/v1 | https://www.protocols.io/view/mouse-transcardial-perfusion-bg8mjzu6 | Randall J Kimple | TITLE: Mouse transcardial perfusion
AUTHORS: Randall J Kimple
[DESCRIPTION]
Protocol for performing pump-free transcardial perfusion in mice.
[STEPS]
SECTION: Preparation
1. Make sure there are enough sterile surgical instruments and other materials required to carry out the procedure (See list of supplies listed be... | ["[Preparation] Make sure there are enough sterile surgical instruments and other materials required to carry out the procedure (See list of supplies listed below).", "[Preparation] Prepare work area for transcardial perfusion. Clean the workspace with 70% ethanol or any other available cleaner.", "[Preparation] Set ou... |
null | null | null | dx.doi.org/10.17504/protocols.io.rw9d7h6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | ["72 early third instar wandering female larvae were collected from each mitotype and placed in lots of 12 into 6 vials", "6 x 3 cm pieces of filter paper were wetted with ddH2O and placed in each vial, and had water added twice daily to maintain humidity", "Larvae were observed 5 times daily by gentle prodding to dete... |
80,649 | MERS Main Protease (Mpro) Fluorescence Dose Response | 1 | null | https://www.protocols.io/view/mers-main-protease-mpro-fluorescence-dose-response-cszhwf36 | Haim Barr, Noa Lahav | TITLE: MERS Main Protease (Mpro) Fluorescence Dose Response
AUTHORS: Haim Barr, Noa Lahav
[DESCRIPTION]
This is a functional, biochemical assay used to identify treatments for viral infectious disease in MERS 3C-like protease.
Utilizing a direct enzyme activity measurement method, the experiment was performed in a 3... | ["[Prepare 384 Well Plate] PRIME with Assay Buffer by Multi-Drop Combi Tube Dispensing Cassette by selecting the PRIME button on the Combi Dispenser until the tubes are filled completely.", "[Prepare 384 Well Plate] DISPENSE 10 µL to Columns 1 and 23 of assay plate\nNote: These will represent the inhibitor control colu... |
69,780 | Gravimetric Water Content (GWC) | 1 | dx.doi.org/10.17504/protocols.io.kxygx9mpog8j/v1 | https://www.protocols.io/view/gravimetric-water-content-gwc-cgduts6w | maggie.bowman | TITLE: Gravimetric Water Content (GWC)
AUTHORS: maggie.bowman
[DESCRIPTION]
The method is the mass of water per mass of dry soil.
[STEPS]
1. Record the mass of the empty labeled tin in the Core processing file. Add 10 g and record the mass of the tin and soil (this should be completed in the core processing step.
... | ["Record the mass of the empty labeled tin in the Core processing file. Add 10 g and record the mass of the tin and soil (this should be completed in the core processing step.", "Place the soils in the drying oven for 1440 min at100 °C.", "After 1440 min remove samples from drying oven and allow to cool. Record the mas... |
44,008 | LR Clonase Reaction for Multisite Gateway Cloning | 4 | dx.doi.org/10.17504/protocols.io.bn8gmhtw | https://www.protocols.io/view/lr-clonase-reaction-for-multisite-gateway-cloning-bn8gmhtw | Ken Christensen | TITLE: LR Clonase Reaction for Multisite Gateway Cloning
AUTHORS: Ken Christensen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Gateway® LR Clonase™ II Plus</span><span></span></div><div class = "text-block"><div class = "justify" style = "text-align:justify">Gate... | ["[Reaction Setup]\nFor multi-fragment (i.e. 2-, 3-, or 4-fragment recombination) reactions, use an equimolar amount of each entry clone. We recommend 10 fmol of each entry clone and 10 fmol of DEST vector per 5 μl reaction.Plasmid mixture:Add the following components to a 1.5-ml microcentrifuge tube at room temperatur... |
45,792 | Effective Identification of Protein-Protein Interaction using RIME-IP | 4 | dx.doi.org/10.17504/protocols.io.bqx8mxrw | https://www.protocols.io/view/effective-identification-of-protein-protein-intera-bqx8mxrw | George Laliotis | TITLE: Effective Identification of Protein-Protein Interaction using RIME-IP
AUTHORS: George Laliotis
[STEPS]
?. [Immunoprecipitation]
Prepare the following buffers (usually prepare 25ml of each, store at And make fresh every month) at the final concentration listed :•1M Tris pH=7.5for 100mL add 12.114g baseAdjust p... | ["[Immunoprecipitation]\nPrepare the following buffers (usually prepare 25ml of each, store at And make fresh every month) at the final concentration listed :•1M Tris pH=7.5for 100mL add 12.114g baseAdjust pH to 7.5•1M NaCl For 100mL add 5.844g•50mM EDTAFor 100mL add 1.4612g•5mM EGTAFor 100mL add 0.19g•50mM DTTFor 1,... |
null | null | null | dx.doi.org/10.17504/protocols.io.t8uerww | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
GoTaq® qPCR Master Mix(a,b) is a reagent system for quantitative PCR (qPCR). The system contains a new fluorescent DNA-binding dye that often exhibits greater fluorescence enhancement upon binding to double-stranded DNA (dsDNA) than SYBR. Green I.
GoTaq® qPCR Master Mix is pro... | ["Prepare the standard DNA dilution series and experimental samples in nuclease-free water. Store on ice until use.", "{\"blocks\":[{\"key\":\"fkksp\",\"text\":\"Carefully add 10\\u03bcl of\\u00a0template\\u00a0(or water for no-template control reactions) to the appropriate wells of the reaction plate. Store plate at r... |
78,288 | HuBMAP | VU TMC Kidney | Human Kidney Processing | 1 | dx.doi.org/10.17504/protocols.io.5qpvorwexv4o/v1 | https://www.protocols.io/view/hubmap-vu-tmc-kidney-human-kidney-processing-cqpqvvmw | Olof Isberg, haichun.yang, Jamie Allen, Melissa Farrow, Audramjudd, Ray Harris, Agnes Fogo, Marc P. De Caestecker, Jeff Spraggins | TITLE: HuBMAP | VU TMC Kidney | Human Kidney Processing
AUTHORS: Olof Isberg, haichun.yang, Jamie Allen, Melissa Farrow, Audramjudd, Ray Harris, Agnes Fogo, Marc P. De Caestecker, Jeff Spraggins
[DESCRIPTION]
This protocol describes the workflow for collecting human kidney samples for multimodal downstream assays, in ... | ["[Organ dissection] Remove kidney from shipping container and place on cold dissection tray. Remove as much outer fat as possible.\n\nDissect the kidney by carefully cutting it in half and remove any visible fat. Work on one half of the kidney while the other half is left on an ice tray to keep cool.", "[Flash freez... |
46,670 | Human iPSC culture and directed differentiation to Midbrain Dopaminergic neurons. | 4 | dx.doi.org/10.17504/protocols.io.x54v9j7ezg3e/v1 | https://www.protocols.io/view/human-ipsc-culture-and-directed-differentiation-to-brtnm6me | gurvir.virdi | TITLE: Human iPSC culture and directed differentiation to Midbrain Dopaminergic neurons.
AUTHORS: gurvir.virdi
[DESCRIPTION]
Generation of hiPSC derived midbrain dopaminergic neurons.
[STEPS]
SECTION: iPSC culture and maintenance
1. Human induced pluripotent stem cells (hiPSCs) were maintained in feeder-free monolaye... | ["[iPSC culture and maintenance] Human induced pluripotent stem cells (hiPSCs) were maintained in feeder-free monolayers on Geltrex (ThermoFisherScientific) and fed daily with Essential 8 medium (Life Technologies). \nGrow cells on 6-well tissue culture plates.\nWhen confluent, hiPSCs were passaged using 0.5 μM EDTA (L... |
null | null | null | dx.doi.org/10.17504/protocols.io.gptbvnn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="column">The steps for preparing the lysate are different depending on the starting material. Please ensure you follow the correct procedure for your starting material (see the section <a href="https://www.protocols.io/view/genomic-dna-removal-and-total-rna-purificati... | [] |
87,542 | Buck Institute Morphology H & E staining protocol | 1 | null | https://www.protocols.io/view/buck-institute-morphology-h-amp-e-staining-protoco-czqwx5xe | sbreslin | TITLE: Buck Institute Morphology H & E staining protocol
AUTHORS: sbreslin
[DESCRIPTION]
Histological Stain for FFPE slides
RESULTS: Nuclei-blue; Cytoplasm, red blood cells and connective tissue-shades of pink
[STEPS]
SECTION: Hematoxylin and Eosin Staining
1. Deparaffinization and rehydration: 2 x xylene 7 min... | ["[Hematoxylin and Eosin Staining] Deparaffinization and rehydration: 2 x xylene 7 min, 100% ethanol 4 min, 95% 4 min, 80% 4 min, 70% 4 min, bring to water.", "[Hematoxylin and Eosin Staining] Hematoxylin staining for 30 seconds - 4 min. using filtered dye (usually 2 mins) - Modified Mayes’s Hematoxylin HXMMHPT StatLab... |
36,771 | LC-MS3 Proteomics Data Acquisition | 1 | dx.doi.org/10.17504/protocols.io.bf6bjran | https://www.protocols.io/view/lc-ms3-proteomics-data-acquisition-bf6bjran | Ruiqi Jian, Joanne Chan, lihua jiang | TITLE: LC-MS3 Proteomics Data Acquisition
AUTHORS: Ruiqi Jian, Joanne Chan, lihua jiang
[DESCRIPTION]
This protocol described the LC, Mass spectrometry and database search methods used to acquire quantitative proteomic data. For peptides separation, we used a high-low pH 2D LC methods set up for 12 fractions. A MS3 ma... | ["Proteomic samples were analyzed on a Thermo Scientific Orbitrap Fusion Lumos mass spectrometer coupled online with a Waters 2D liquid chromatography (Waters MClass 2DnLC).", "[Liquid Chromatography Sepration] Peptides were separated by reverse phase chromatography at high pH in the first dimension, followed by an or... |
60,288 | 2022 GenomeTrakr Proficiency Testing exercise (PulseNet Harmonized) | 1 | dx.doi.org/10.17504/protocols.io.e6nvw5m9dvmk/v3 | https://www.protocols.io/view/2022-genometrakr-proficiency-testing-exercise-puls-b648rgzw | Maria Balkey, Ruth Timme, Julie Haendiges | TITLE: 2022 GenomeTrakr Proficiency Testing exercise (PulseNet Harmonized)
AUTHORS: Maria Balkey, Ruth Timme, Julie Haendiges
[DESCRIPTION]
This SOP outlines guidelines on how to process the isolates for the 2022 GenomeTrakr (GT) Proficiency Testing exercise.
This SOP is applicable to all GenomeTrakr labs partici... | ["[Culture Preparation] Salmonella and Escherichia/Shigella Lyophilized cultures:\n\nDay 1\n\nDocument the isolate number(s) and the lyophilized date(s) for your records. Wipe the aluminum cover and outside of the vial with isopropyl alcohol. Using sturdy forceps, aseptically remove the aluminum cover and rubber stoppe... |
63,328 | Condor CBD Gummies: *Provide Rapid Relief* Formulated With Nutritious Herbal Ingredients, Vitamins, Proteins! | 3 | dx.doi.org/10.17504/protocols.io.5jyl89w48v2w/v1 | https://www.protocols.io/view/condor-cbd-gummies-provide-rapid-relief-formulated-b938r8rw | serkanpaqtus | TITLE: Condor CBD Gummies: *Provide Rapid Relief* Formulated With Nutritious Herbal Ingredients, Vitamins, Proteins!
AUTHORS: serkanpaqtus
[DESCRIPTION]
Condor CBD Gummies Reviews CBD Infused Gummies Relaxes Your Body!
[STEPS] | [] |
66,333 | Testo Edge X (Shocking!) Does Testo Edge X Really Works? | 3 | dx.doi.org/10.17504/protocols.io.81wgb6e73lpk/v1 | https://www.protocols.io/view/testo-edge-x-shocking-does-testo-edge-x-really-wor-ccz5sx86 | Testo Edge X | TITLE: Testo Edge X (Shocking!) Does Testo Edge X Really Works?
AUTHORS: Testo Edge X
[DESCRIPTION]
>>Visit Testo Edge X (Testo Alpha X) Male Enhancement UK (United Kingdom) Official Website And Order
[STEPS] | [] |
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