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 |
|---|---|---|---|---|---|---|---|
44,803 | Abdominal Emitter Implantation | 4 | dx.doi.org/10.17504/protocols.io.bpzbmp2n | https://www.protocols.io/view/abdominal-emitter-implantation-bpzbmp2n | Nathan Lee | TITLE: Abdominal Emitter Implantation
AUTHORS: Nathan Lee
[STEPS]
?. [Surgery Preparation]
Preparation for implantation of Emitters has to occur at least 24 hours prior of the surgery time for proper sterilization of the Emitter.
?. [Surgery Preparation]
In your 50ml falcon tube mix 25ml Glutaraldehyde plus solution a... | ["[Surgery Preparation]\nPreparation for implantation of Emitters has to occur at least 24 hours prior of the surgery time for proper sterilization of the Emitter.", "[Surgery Preparation]\nIn your 50ml falcon tube mix 25ml Glutaraldehyde plus solution and 800ul Activator plus solution (=Glutaraldehyde Sterilization So... |
53,618 | RNA Extraction from Sterivex Filters | 4 | dx.doi.org/10.17504/protocols.io.bykspuwe | https://www.protocols.io/view/rna-extraction-from-sterivex-filters-bykspuwe | William Brazelton, H Lizethe Pendleton | TITLE: RNA Extraction from Sterivex Filters
AUTHORS: William Brazelton, H Lizethe Pendleton
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Modified 2020 by H. Lizethe Pendleton from the Brazelton Lab DNA extraction protocol.</div></div>
[STEPS]
?. [Prepare DEB]
Nucleic Acid Extraction Buffer (NEB... | ["[Prepare DEB]\nNucleic Acid Extraction Buffer (NEB):0.1M Tris-HCl (pH 8) 4.5 mL of 1.0 M0.1M Na-EDTA (pH 8) 9 mL of 0.5M0.1M KH2PO4 (pH 8) 0.54 g1.5M NaCl 13.5 mL of 5M 0.8M Guanidine HCl 3.44 g0.5% Triton-X 100 225 μL of 100%Add above ing... |
72,260 | NCBI submission protocol for SARS-CoV-2 wastewater data: SRA, BioSample, and BioProject | 1 | dx.doi.org/10.17504/protocols.io.ewov14w27vr2/v10 | https://www.protocols.io/view/ncbi-submission-protocol-for-sars-cov-2-wastewater-citcueiw | Ruth Timme, Candace.Bias, Maria Balkey | TITLE: NCBI submission protocol for SARS-CoV-2 wastewater data: SRA, BioSample, and BioProject
AUTHORS: Ruth Timme, Candace.Bias, Maria Balkey
[DESCRIPTION]
PURPOSE:
This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr Laboratories; however, this protocol was written ... | ["["Ingredients" to have in place before starting your submissions] Set up a new NCBI submission environment for your lab\n1.1: Create an NCBI user account\n1.2: Set up an NCBI submission user group for your lab\n1.3: Bookmark the link to your Submission Portal\n1.4. Identify or establish new BioProjects (det... |
52,746 | Image_processing_to_investigate_mitophagy_in_HelaM_and_neurons | 1 | dx.doi.org/10.17504/protocols.io.bxripm4e | https://www.protocols.io/view/image-processing-to-investigate-mitophagy-in-helam-bxripm4e | OLIVIA HARDING, Chantell Evans | TITLE: Image_processing_to_investigate_mitophagy_in_HelaM_and_neurons
AUTHORS: OLIVIA HARDING, Chantell Evans
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a method for imaging cells and quantifying subcellular structures in the resulting data. We developed this protocol for assessing cle... | ["[Imaging]\nCollect images of cells with a confocal microscope at 100X.", "[Imaging]\nRefer to https://svi.nl/NyquistCalculator in order to determine optimal collection parameters", "[Imaging]\nDepending on the analysis, you may collect 3D samples (XYZ or XYT)", "[Imaging]\nTry to maximize the number of cells in the f... |
79,958 | SARS-COV-2 Main Protease (Mpro) Fluorescence Dose Response | 1 | null | https://www.protocols.io/view/sars-cov-2-main-protease-mpro-fluorescence-dose-re-csbwwape | Haim Barr, Noa Lahav | TITLE: SARS-COV-2 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 SARS-COV-2 Main Protease.
Utilizing a direct enzyme activity measurement method, the experiment was perform... | ["[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... |
96,675 | Mouse sample collection for metabolomics studies | 0 | dx.doi.org/10.17504/protocols.io.14egn3pkzl5d/v1 | https://www.protocols.io/view/mouse-sample-collection-for-metabolomics-studies-danb2dan | Livia Hecke Morais | TITLE: Mouse sample collection for metabolomics studies
AUTHORS: Livia Hecke Morais
[DESCRIPTION]
Protocol used in the Mazmanian lab for collecting brain and gut tissues and plasma from mouse for metabolomics
[STEPS]
SECTION: Samples collection for metabolomics studies
1. At 4 months of age, mice were sacrificed by
d... | ["[Samples collection for metabolomics studies] At 4 months of age, mice were sacrificed by\ndecapitation", "[Samples collection for metabolomics studies] The brain was rapidly removed from the skull and placed in an ice-chilled stainless steel coronal\nmatrix", "[Samples collection for metabolomics studies] Brain tiss... |
67,156 | S-Trap™ plate digestion protocol (Protifi) of proteins for LC-MS / proteomics | 1 | dx.doi.org/10.17504/protocols.io.kxygxzd2zv8j/v1 | https://www.protocols.io/view/s-trap-plate-digestion-protocol-protifi-of-protein-cdtus6nw | ronan.ocualain, Davidknight, Staceywarwood, Jamesallsey, Emmakeevill | TITLE: S-Trap™ plate digestion protocol (Protifi) of proteins for LC-MS / proteomics
AUTHORS: ronan.ocualain, Davidknight, Staceywarwood, Jamesallsey, Emmakeevill
[DESCRIPTION]
This protocol details the in-house BioMS procedure of S-Trap™ 96-well plate protein clean-up and digestion.
It is adapted from the long proto... | ["[Sample preparation] To the 50 µLvolume of sample in S-trap lysis buffer, add 5 µL of 12 % (v/v) aqueous phosphoric acid at 1:10 for a final concentration of 1.2 % (v/v) phosphoric acid and vortex mix.", "[Sample preparation] Add 350 µL of S-Trap binding buffer to the acidified lysis buffer and mix.", "[Sample prepar... |
21,284 | Yale - Blood Albumin | null | dx.doi.org/10.17504/protocols.io.y2cfyaw | null | Gary Cline, John Stack | TITLE: Yale - Blood Albumin
AUTHORS: Gary Cline, John Stack
[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 albumin in blood, plasma, and serum. Albumin is measured as i... | ["Calibrate Cobas for Albumin analysis by running an albumin standard, assayed control serum 1 and assayed control serum 2.", "Sample handling as performed by the Cobas Mira Plus. a) Pipette 2µL of sample into a cuvette slot. b) Add 250 µL of Albumin reagent and mix. c) Mixture is incubated at 37˚C and s... |
null | null | null | dx.doi.org/10.17504/protocols.io.uy2exye | null | null | TITLE: No Title
AUTHORS:
[STEPS]
SECTION: Preparation of LBv2 medium
?.
SECTION: Preparation of glycerol stock
?.
SECTION: Preparation of glycerol stock
?.
SECTION: Preparation of glycerol stock
?.
SECTION: Preparation of glycerol stock
?.
SECTION: Preparation of glycerol stock
?. | ["[Preparation of LBv2 medium] Prepare LBv2 medium (LB medium supplemented with 204mM NaCl, 4.2mM KCl and 23.14mM MgCl2)", "[Preparation of glycerol stock] Grow overnight (ON) culture of V. natriegens.", "[Preparation of glycerol stock] Centrifuge 1 mL of ON culture at 3000 rcf, 1min.", "[Preparation of glycerol stock]... |
41,934 | Reagent Safety & PPE | 3 | null | https://www.protocols.io/view/reagent-safety-amp-ppe-bk7nkzme | TITLE: Reagent Safety & PPE
AUTHORS:
[STEPS] | [] | |
null | null | null | dx.doi.org/10.17504/protocols.io.crrv55 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
19,227 | Light sheet microscopy | 1 | dx.doi.org/10.17504/protocols.io.wz3ff8n | https://www.protocols.io/view/light-sheet-microscopy-wz3ff8n | Clara Huesing, Hayden Torres, David Burk, Heike Muenzberg | TITLE: Light sheet microscopy
AUTHORS: Clara Huesing, Hayden Torres, David Burk, Heike Muenzberg
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol documents how to operate light sheet microscope (UltraMicroscope II, LaVision BioTec)</div></div>
[STEPS]
?. [Microscope set-up]
Must turn laser ... | ["[Microscope set-up]\nMust turn laser and microscope on before starting software(Version: Imspector Pro 328)", "[Microscope set-up]\nRemove lid from cuvette", "[Microscope set-up]\nHandling only frosted portion of cuvette, place cuvette onto extended stage mounting apparatus and slowly lower into position. The two fro... |
82,786 | DART-FISH Protocol | 4 | dx.doi.org/10.17504/protocols.io.e6nvwjxnzlmk/v1 | https://www.protocols.io/view/dart-fish-protocol-cu4awyse | Chien-Ju Chen, Kian Kalhor, Kun Zhang | TITLE: DART-FISH Protocol
AUTHORS: Chien-Ju Chen, Kian Kalhor, Kun Zhang
[DESCRIPTION]
In the manuscript Mapping Human Tissues with Highly Multiplexed RNA in situ Hybridization
(https://doi.org/10.1101/2023.08.16.553610), we describe a highly multiplexed in situ hybridization technique based on in situ padlock probe c... | ["[Preparation] Wash, dry and UV the silicone isolators. UV the EasyDip jars. Move away unused stuff from the bench. Wipe the working area by 70% ethanol and RNase Zap. Set the HybEZ oven 37 °C.", "[Fixation] Prepare 80ml of 4% formaldehyde in 1x PBS. Store at 4 °C for use in the same day.", "[Fixation] Take the tissu... |
35,891 | TEV Protease | 1 | null | https://www.protocols.io/view/tev-protease-bfatjien | New England Biolabs | TITLE: TEV Protease
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">TEV Protease is a highly specific cysteine protease that recognizes the amino-acid sequence Glu-Asn-Leu-Tyr-Phe-Gln-(Gly/Ser) and cleaves between the Gln and Gly/Ser residues.</div><div class = "text-blo... | ["[Typical Reaction Conditions for TEV Protease]\nDialyze the protein against , .\n[Tris-HCl]", "[Typical Reaction Conditions for TEV Protease]\nDetermine the protein concentration.", "[Typical Reaction Conditions for TEV Protease]\nCombine (if necessary) to make a total reaction volume.\n[of protein and H20]\n45 µl"... |
23,720 | KU Leuven Exp Urology - Urodynamics in Female MInipigs | null | dx.doi.org/10.17504/protocols.io.3eggjbw | null | Yodi Soebadi, Marko Bakula, Lukman Hakim, Robert Puers, Dirk De Ridder | TITLE: KU Leuven Exp Urology - Urodynamics in Female MInipigs
AUTHORS: Yodi Soebadi, Marko Bakula, Lukman Hakim, Robert Puers, Dirk De Ridder
[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 = ... | ["Preparation: Bring machine and all consumables to room", "Fill calibration tube with saline", "Check calibration with tube", "Open charge switch AND flush baloon", "Measurement: Isolate minipig for study, bring in transport cart & administer sedation: Ketamine 15 mg/kg (Nimatek 100 mg/ml) Xylazine 2 mg/kg (Xyl-M 2%)... |
57,423 | Decontamination of tooth roots/petrous bone cores for ancient DNA extraction | 1 | dx.doi.org/10.17504/protocols.io.eq2lynp4qvx9/v1 | https://www.protocols.io/view/decontamination-of-tooth-roots-petrous-bone-cores-b4bpqsmn | Marcel Keller, Christiana L Scheib | TITLE: Decontamination of tooth roots/petrous bone cores for ancient DNA extraction
AUTHORS: Marcel Keller, Christiana L Scheib
[DESCRIPTION]
Protocol for decontamination of tooth roots and petrous bone cores from archaeological human remains for reduction of surface contaminations and increase of endogenous DNA prior... | ["[Preparation] Clean drill hood and table bench surfaces with DNA Exitus and rinse with water", "[Preparation] Set up 100 ml beaker decontamination station:\n1x NaOCl (bleach, 6% v/v)\n1x MilliQ water\n1x Ethanol", "[Preparation] Place toothbrush and tweezers in bleach.", "[Preparation] Prepare two 50 ml tubes per sam... |
null | null | null | dx.doi.org/10.17504/protocols.io.hchb2t6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A protocol to cast a polyacrylamide gel. </p>
<p>Used in for iGEM SDU 2016</p>
[GUIDELINES]
<p><span style="text-decoration: underline;"><strong>20% Separation gel-mix 15 mL</strong></span></p>
<table style="height: 198px;" width="406">
<tbody>
<tr>
<td style="width: 126.515... | [] |
59,166 | Preparing multiplexed WGS/MetaG SMRTbell libraries with the Express TPK2.0 for the PacBio Sequel2 | 4 | dx.doi.org/10.17504/protocols.io.36wgq7313vk5/v1 | https://www.protocols.io/view/preparing-multiplexed-wgs-metag-smrtbell-libraries-b5z6q79e | André M Comeau, Gina V Filloramo | TITLE: Preparing multiplexed WGS/MetaG SMRTbell libraries with the Express TPK2.0 for the PacBio Sequel2
AUTHORS: André M Comeau, Gina V Filloramo
[DESCRIPTION]
The preparation of (meta)genomic libraries using the PacBio Express Template Kit 2.0 (TPK2.0) with the Barcoded Adapter Plate 3.0 at the IMR.
Based upon PacB... | ["[gDNA Shearing with Covaris g-TUBEs] Dilute 1 µg gDNA with water into 100 µL to get a final concentration of 10 ng/µL.", "[gDNA Shearing with Covaris g-TUBEs] Transfer gDNA to the g-TUBE and centrifuge (cap up) at 860 x g, 5 min (MBI centrifuge D3024 fixed-angle rotor) to achieve a target mode size of 9-10 kb. Repeat... |
50,005 | From low cost plant HMW DNA extraction to MinION sequencing | 4 | dx.doi.org/10.17504/protocols.io.bu3vnyn6 | https://www.protocols.io/view/from-low-cost-plant-hmw-dna-extraction-to-minion-s-bu3vnyn6 | Julien Serret, marie.couderc , Cedric Mariac, Laurencealbar , Francois Sabot | TITLE: From low cost plant HMW DNA extraction to MinION sequencing
AUTHORS: Julien Serret, marie.couderc , Cedric Mariac, Laurencealbar , Francois Sabot
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This low cost protocol is efficient to extract high molecular weight DNA from several tropica... | ["[Plant materiel sampling]\nCollect up to of fresh young leaves in a 50ml clean tube.Grind sample with liquid nitrogen, mortar and pestel to a fine powder.An analytical grinder (A15, IKA, Germany) can also be used for 2x .\n5 g", "[Tissue lysis]\nAdd of freshly prepared MATAB lysis buffer (100mM Tris pH8, 1.4M NaCl... |
44,001 | Vivarium Population Spenser: Mortality protocol | 5 | dx.doi.org/10.17504/protocols.io.bn79mhr6 | https://www.protocols.io/view/vivarium-population-spenser-mortality-protocol-bn79mhr6 | Camila Rangel Smith, Kasra Hosseini | TITLE: Vivarium Population Spenser: Mortality protocol
AUTHORS: Camila Rangel Smith, Kasra Hosseini
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Description of the steps followed by Vivarium Population Spenser library when running the Mortality module. </div></div>
[STEPS]
?. Divide the annual m... | ["Divide the annual mortality rates for a given local authority by the number of time steps existing in a year.", "For each time step:", "Select all individuals in the sample that appear as \"alive\" and have an associated gender.", "For these individuals, get the mortality rate given their age, gender, ethnicity and l... |
36,750 | Shipping Paraffin Blocks to the Bodenmiller Lab for IMC Analysis | null | dx.doi.org/10.17504/protocols.io.bf5njq5e | https://www.protocols.io/view/shipping-paraffin-blocks-to-the-bodenmiller-lab-fo-bf5njq5e | Marda Jorgensen | TITLE: Shipping Paraffin Blocks to the Bodenmiller Lab for IMC Analysis
AUTHORS: Marda Jorgensen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This SOP describes the methods used to ship paraffin-embedded blocks to the University of Zurich. </div></div>
[STEPS]
?. Create a shipping label through ... | ["Create a shipping label through the FedEx website. Select Priority Overnight Shipping. Enter the address in the document box below. Print out label.\nStefanie EnglerWinterthurestrasse 190Bodenmiller Lab, Y11-J80Zurich, CH805741446356630", "In addition to the shipping label, a customs invoice must be created to ship i... |
90,660 | Stereotaxic Injections | 1 | dx.doi.org/10.17504/protocols.io.yxmvm3zy5l3p/v1 | https://www.protocols.io/view/stereotaxic-injections-c4scywaw | Lindsay Meyerdirk, Michael Henderson | TITLE: Stereotaxic Injections
AUTHORS: Lindsay Meyerdirk, Michael Henderson
[DESCRIPTION]
This protocol details stereotaxic injections for any purpose, but in this case is primarily used for the injection of misfolded proteins.
[GUIDELINES]
*All experiments involving animals must comply with federal and local law. Al... | ["[Preparing Mouse] Turn on the heating box so the pad starts warming.", "[Preparing Mouse] Make sure surgery area is sterilized then set up entire station, leaving all sterilized tools covered until ready to start procedure.", "[Preparing Mouse] Anaesthetize mouse per IACUC protocol, mouse weight and genetic backgroun... |
58,782 | Filming Daphnia Swimming in 2D Protocol | 3 | null | https://www.protocols.io/view/filming-daphnia-swimming-in-2d-protocol-b5m6q49e | Laura Lopez | TITLE: Filming Daphnia Swimming in 2D Protocol
AUTHORS: Laura Lopez
[DESCRIPTION]
This is a protocol used to record Daphnia individuals swimming (swimming speed, acceleration, time spent moving).
[STEPS] | [] |
54,214 | Co-production scoping review: protocol | 3 | dx.doi.org/10.17504/protocols.io.by7epzje | https://www.protocols.io/view/co-production-scoping-review-protocol-by7epzje | Helen J J. Smith, Luke Budworth, Chloe Grindey, Isabel Hague, Natalie Hamer, Roman Kislov, Peter van der Graaf, Joe Langley | TITLE: Co-production scoping review: protocol
AUTHORS: Helen J J. Smith, Luke Budworth, Chloe Grindey, Isabel Hague, Natalie Hamer, Roman Kislov, Peter van der Graaf, Joe Langley
[DESCRIPTION]
Background
Interest in and use of co-production in healthcare services and research is growing. Previous reviews have summar... | [] |
54,042 | Environmental DNA sampling protocols for the surveillance of marine non-indigenous species | 1 | dx.doi.org/10.17504/protocols.io.byz2px8e | https://www.protocols.io/view/environmental-dna-sampling-protocols-for-the-surve-byz2px8e | null | TITLE: Environmental DNA sampling protocols for the surveillance of marine non-indigenous species
AUTHORS:
[DESCRIPTION]
This document describes a series of protocols for the collection of environmental samples intended for the monitoring and surveillance of marine invasive species by means of eDNA metabarcoding ana... | ["[HEALTH AND SAFETY]", "[Protocol for collection of water samples (low volume water)] SAMPLING", "[Protocol for collection of water samples (low volume water)] Put on clean, single-use gloves.\n\nChange gloves if a glove has contacted anything except the sampled water body or decontaminated equipment. For example, if ... |
61,706 | Patch-Seq Internal Solution with Biocytin | 1 | dx.doi.org/10.17504/protocols.io.261geo4qol47/v4 | https://www.protocols.io/view/patch-seq-internal-solution-with-biocytin-b8hirt4e | Allen Institute for Brain Science | TITLE: Patch-Seq Internal Solution with Biocytin
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
This SOP provides instruction to prepare Internal Solution which is used for patch clamp electrophysiology, modified for cleanliness and mRNA capture and sustainability.
Note: Research reported in this publicatio... | [] |
94,708 | Viral genome analysis using CLC Genomics Workbench | 5 | dx.doi.org/10.17504/protocols.io.kxygx3dnzg8j/v1 | https://www.protocols.io/view/viral-genome-analysis-using-clc-genomics-workbench-c8quzvww | Kenichi Komabayashi | TITLE: Viral genome analysis using CLC Genomics Workbench
AUTHORS: Kenichi Komabayashi
[DESCRIPTION]
This protocol aims to determine an nearly complete viral genomic sequence from Illumina sequencing reads which include those originating from virus, host cell, and sometimes bacteria. In the primary analysis, the raw r... | ["[Preparation of data] Hereafter abbreviated as CGW.\n \nHereafter abbreviated as CMGM.\nCMGM is a plug-in for CGW, designed for the analysis of microbial genomes.\n\n \n\nHereafter abbreviated as CGFM.\nCGFM is a plug-in for CGW, designed to help finishing small genomes such as bacterial genomes.", "[Preparation of d... |
27,687 | MojoSort™ Human anti-APC Nanobeads Column Protocol | null | dx.doi.org/10.17504/protocols.io.7afhibn | null | Sam Li | TITLE: MojoSort™ Human anti-APC Nanobeads Column Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>BioLegend MojoSort™ nanobeads work in commonly used separation columns, based on our internal research as well as validation by external testing by academic labs. This simp... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes.", "In the final wash of your sample preparation, resuspend the cells in MojoSort™ Buffer by adding up to 4 mL in a 5 mL (12 x 75 mm) polypropylene tube.Note: Keep MojoSort™ Buffer on ice throughout the procedure.", "Filter the cells with... |
null | null | null | dx.doi.org/10.17504/protocols.io.fi8bkhw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Introduction to functional annotation and Integrated Microbial Genomes (IMG) at the Joint Genome Institute (JGI).</p>
<p> </p>
<p>Open this protocol inside the virtual machine (details in 'Start Instructions') for easy copy, paste of commands into the command line terminal wi... | [] |
80,191 | Untargeted IMS Tentative Identification Lipidomics | 1 | dx.doi.org/10.17504/protocols.io.4r3l27j7qg1y/v1 | https://www.protocols.io/view/untargeted-ims-tentative-identification-lipidomics-csi7wchn | Lukasz Migas, Madeline E. Colley, Katerina V Djambazova, Martin Dufresne, Angela R.S. Kruse, David Anderson, Olof Isberg, Jamie Allen, ali.zahraei, Melissa Farrow, Jeff Spraggins, Raf Van De Plas | TITLE: Untargeted IMS Tentative Identification Lipidomics
AUTHORS: Lukasz Migas, Madeline E. Colley, Katerina V Djambazova, Martin Dufresne, Angela R.S. Kruse, David Anderson, Olof Isberg, Jamie Allen, ali.zahraei, Melissa Farrow, Jeff Spraggins, Raf Van De Plas
[DESCRIPTION]
The purpose of this protocol is to... | ["Following pre-processing, tentative identification is performed using an in-house developed annotation software - annotine.", "Generate an average mass spectrum of the dataset (in profile mode).", "Scale the mass spectrum between 0 and 1, and peak-pick its profile to retrieve a list of m/z features (commonly 100s to ... |
null | null | null | dx.doi.org/10.17504/protocols.io.kahcsb6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Background</strong></p>
<p>Recently, neoadjuvant chemotherapy with docetaxel/cisplatin/5-fluorouracil (NAC-DCF) was identified as a novel strong regimen with a high rate of pathological complete response (pCR) in advanced esophageal cancer in Japan. Predicting pCR wil... | [] |
21,204 | Leaf Punch DNA Extraction | null | dx.doi.org/10.17504/protocols.io.yxufxnw | null | Alex Rajewski, Cecilia McGregor | TITLE: Leaf Punch DNA Extraction
AUTHORS: Alex Rajewski, Cecilia McGregor
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is a quick (and very cheap) genomic DNA extraction protocol for fresh leaf or seed tissue in many plant species. It should be use preferably for extractions that do no... | ["[Preparation]\nCollect young leaf (the size of a penny) into a 2 mL Eppendorf tube. Store tubes at -80°C until extraction.", "[Grind Tissue]\nSnap freeze the tubes in a dewar of liquid nitrogen (LN2).", "[Lysis]\nPrepare 750µL of 60% Edwards buffer and 40% 5M NaCl for each tube.\n[Edward's Buffer]\n[5M NaCl]", "[Lysi... |
97,114 | CRISPR/Cas9-Mediated Knockdown in LUHMES Cells: Nucleofection and Validation Protocol | 0 | dx.doi.org/10.17504/protocols.io.36wgq32d3lk5/v3 | https://www.protocols.io/view/crispr-cas9-mediated-knockdown-in-luhmes-cells-nuc-da322gqe | Mallory Wright, William J Buchser, Colin Kremitzki, Serena Elia, Graham Bachman, emanuel gerbi, Jason Waligorski, Nicholas Tu, Lina Mohammed Ali | TITLE: CRISPR/Cas9-Mediated Knockdown in LUHMES Cells: Nucleofection and Validation Protocol
AUTHORS: Mallory Wright, William J Buchser, Colin Kremitzki, Serena Elia, Graham Bachman, emanuel gerbi, Jason Waligorski, Nicholas Tu, Lina Mohammed Ali
[DESCRIPTION]
Utilizing a CRISPR RNP complex and nucleofection, this pro... | ["[Nucleofection Protocol] Maintain cell confluency between 70–85% to optimize Nucleofection efficiencies; optimal results typically occur with cells in the logarithmic growth phase.", "[Nucleofection Protocol] Coat a new 6-well plate freshly with poly-L-ornithine (50ug/mL) and fibronectin (2ug/mL) to facilitate LUHMES... |
27,230 | Flame Photometry Protocol | null | dx.doi.org/10.17504/protocols.io.6t6here | null | Mariam Awlia | TITLE: Flame Photometry Protocol
AUTHORS: Mariam Awlia
[STEPS]
?. [Preparation of 1% nitric acid]
If stock is 70% nitric acid, pour of MilliQ-water for every of nitric acid. (x 21.4 for 1.5L).If stock is 69% nitric acid, pour of MilliQ-water for every of nitric acid. (x 21.8 for 1.5L)Pour nitric acid to MilliQ-wa... | ["[Preparation of 1% nitric acid]\nIf stock is 70% nitric acid, pour of MilliQ-water for every of nitric acid. (x 21.4 for 1.5L).If stock is 69% nitric acid, pour of MilliQ-water for every of nitric acid. (x 21.8 for 1.5L)Pour nitric acid to MilliQ-water.\nWork in the fume hood.Wear lab coat, eye protection, glove... |
26,273 | Culturing C. elegans worms in liquid culture | null | dx.doi.org/10.17504/protocols.io.5v9g696 | null | Cristian Riccio, Asia Kosalka, WormBook | TITLE: Culturing C. elegans worms in liquid culture
AUTHORS: Cristian Riccio, Asia Kosalka, WormBook
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Growing C. elegans worms in liquid culture</div></div>
[STEPS]
?. Reagents
?. S Basal [5.85 g NaCl, 1 g K2 HPO4, 6 g KH2PO4, 1 ml cholesterol (5 mg/ml... | ["Reagents", "S Basal [5.85 g NaCl, 1 g K2 HPO4, 6 g KH2PO4, 1 ml cholesterol (5 mg/ml in ethanol), H2O to 1 litre. Sterilize by autoclaving.]", "1 M Potassium citrate pH 6.0 [20 g citric acid monohydrate, 293.5 g tri-potassium citrate monohydrate, H2O to 1 litre. Sterilize by autoclaving.]", "Trace metals solution [1.... |
18,871 | Trapping and blood-sampling small mammals in semi-arid environments | null | dx.doi.org/10.17504/protocols.io.wnxfdfn | null | Pedro E. Cattan, Carezza Botto-Mahan, Juana P. Correa, Antonella Bacigalupo, Berenice Cornejo-Villar | TITLE: Trapping and blood-sampling small mammals in semi-arid environments
AUTHORS: Pedro E. Cattan, Carezza Botto-Mahan, Juana P. Correa, Antonella Bacigalupo, Berenice Cornejo-Villar
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Brief guide to trapping and blood-sampling of small terrestrial mam... | ["[Trapping]\nIf the target or sympatric species are suspected to transmit infectious diseases, wear disposable gloves underneath and over the thick gloves, a whole-body disposable suit (e.g. Tyvek™), filtered mask, or even a respirator through the whole process.", "[Trapping]\nVisually inspect the areas where is inten... |
100,292 | KAPP-Sen TMC: Xenium Pancreas FFPE Tissue Preparation | 0 | dx.doi.org/10.17504/protocols.io.kqdg32x5zv25/v1 | https://www.protocols.io/view/kapp-sen-tmc-xenium-pancreas-ffpe-tissue-preparati-dd7c29iw | Emily Soja, Shruti Bhargava, Santhosh Sivajothi, William F Flynn, Elise T Courtois | TITLE: KAPP-Sen TMC: Xenium Pancreas FFPE Tissue Preparation
AUTHORS: Emily Soja, Shruti Bhargava, Santhosh Sivajothi, William F Flynn, Elise T Courtois
[DESCRIPTION]
Xenium protocol for sectioning FFPE tissue blocks.
[STEPS]
1. Xenium In Situ for FFPE - Tissue Preparation Guide CG000578 Rev C:
The optimal water b... | ["Xenium In Situ for FFPE - Tissue Preparation Guide CG000578 Rev C: \n\nThe optimal water bath temperature for pancreas tissue was determined to be 38 C (see page 22 of CG000578 Rev C)."] |
25,794 | 13 Gel filtration | null | dx.doi.org/10.17504/protocols.io.5fag3ie | null | TJUSLS China | TITLE: 13 Gel filtration
AUTHORS: TJUSLS China
[STEPS]
?. [Choice of Gel]
According to the size of the target protein, firstly select the appropriate gel to adapt to the size of protein.
?. [Column equilibrium]
Connect the proper column which adapts to target protein to AKTA high pressure tomographic system, use buffe... | ["[Choice of Gel]\nAccording to the size of the target protein, firstly select the appropriate gel to adapt to the size of protein.", "[Column equilibrium]\nConnect the proper column which adapts to target protein to AKTA high pressure tomographic system, use buffer of gel filtration chromatography (buffer: 25mMTris， 1... |
null | null | null | dx.doi.org/10.17504/protocols.io.pdadi2e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><em>The MELD Project is an international collaboration aiming to create open-access, robust and generalisable tools for FCD detection. To this end, we will train a neural network classifier on MRI features from FCD patients from multiple centres worldwide.</em></p>
<p><strong... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.haib2ce | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol (like its companion protocol for liposome suspension and extrusion) was original created by <a href=""http://www.whoi.edu/sbl/liteSite.do?litesite" target="_blank">Krista Longnecker</a> and <a href="http://jamesrco.github.io/" target="_blank">Jamie Collins<... | [] |
85,856 | Ligand docking using Patchdock for Biochemistry I | 1 | null | https://www.protocols.io/view/ligand-docking-using-patchdock-for-biochemistry-i-cx38xqrw | Chris Berndsen | TITLE: Ligand docking using Patchdock for Biochemistry I
AUTHORS: Chris Berndsen
[DESCRIPTION]
A protocol for JMU students to dock ligands to proteins using Patchdock
[BEFORE_START]
Have PDB file of protein and ligand
[STEPS]
SECTION: Docking setup
1. Navigate to Patchdock
SECTION: Docking setup
2. In Receptor mol... | ["[Docking setup] Navigate to Patchdock", "[Docking setup] In Receptor molecule: Provide your PDB file as a RCSB code OR upload a .PDB file", "[Docking setup] In Ligand molecule: Provide your PDB file as a RCSB code OR upload a .PDB file.", "[Docking setup] Under Advanced Options: You can specify a binding site if you ... |
83,554 | spotPCR: A Rapid and Efficient Approach for Indexing Individual Template Molecules using Unique Molecular Identifiers | 4 | dx.doi.org/10.17504/protocols.io.261ged66wv47/v1 | https://www.protocols.io/view/spotpcr-a-rapid-and-efficient-approach-for-indexin-cvuaw6se | Jason D Limberis | TITLE: spotPCR: A Rapid and Efficient Approach for Indexing Individual Template Molecules using Unique Molecular Identifiers
AUTHORS: Jason D Limberis
[DESCRIPTION]
Low-frequency mutations provide valuable insights in various fields, including drug resistance identification, cancer and infectious disease research. One... | ["[Stage 1 PCR] AB1COMPONENTVolume (µl)25X Q5 Reaction Buffer1035X Q5 High GC Buffer10410 mM dNTPs15Q5 High-Fidelity DNA Polymerase0.5610µM Forward primer 11710µM Reverse primer 21820 mg/ml BSA59Template DNA (~1ng/ul)510Nuclease-Free Water18.5\n \n ABCD1StepTemp (C)Time (s)Cycles2Denaturation9812013Denaturation9810... |
80,226 | In Vitro FSCV Testing of Carbon Fiber Electrodes to Characterize Functional Operation in Dopamine Detection | 1 | dx.doi.org/10.17504/protocols.io.rm7vzbdxrvx1/v1 | https://www.protocols.io/view/in-vitro-fscv-testing-of-carbon-fiber-electrodes-t-cskawcse | Helen N Schwerdt, Ann M Graybiel, Michael J Cima | TITLE: In Vitro FSCV Testing of Carbon Fiber Electrodes to Characterize Functional Operation in Dopamine Detection
AUTHORS: Helen N Schwerdt, Ann M Graybiel, Michael J Cima
[DESCRIPTION]
Methods to measure performance characteristics of carbon fiber electrodes for neurochemical recording are described.
[GUIDELINES]
A... | ["Each carbon fiber (CF) electrode was tested in vitro in a beaker containing 0.9% sodium chloride saline to determine its functional properties (i.e., background current and noise) before soldering to another circuit board.", "In vitro testing was performed in a Faraday cage to minimize electromagnetic interference (E... |
103,916 | Agrobacterium-mediated transformation of Diplodia sapinea | 0 | dx.doi.org/10.17504/protocols.io.5qpvok7ozl4o/v1 | https://www.protocols.io/view/agrobacterium-mediated-transformation-of-diplodia-dhqk35uw | Anne Geertje Oostlander, Laura Brodde, Miriam von Bargen, Bernard Slippers, Yvonne Becker, Ulrike Brandt, Frank Klawonn, Christiaan Grobler, Lucas Well, Jan Stenlid, Jonàs Oliva, Malin Elfstrand, André Fleißner | TITLE: Agrobacterium-mediated transformation of Diplodia sapinea
AUTHORS: Anne Geertje Oostlander, Laura Brodde, Miriam von Bargen, Bernard Slippers, Yvonne Becker, Ulrike Brandt, Frank Klawonn, Christiaan Grobler, Lucas Well, Jan Stenlid, Jonàs Oliva, Malin Elfstrand, André Fleißner
[DESCRIPTION]
This protocol detail... | ["[Transformation of electrocompetent Agrobacterium sp. AGL-1cells with plasmid DNA by electroporation] Thaw electrocompetent cells on ice.", "[Transformation of electrocompetent Agrobacterium sp. AGL-1cells with plasmid DNA by electroporation] Add 1 - 1.5 µl of plasmid DNA to 50 µl of cells.", "[Transformation of el... |
82,305 | Characterization of the VKORC1 and CYP2C9 genotypes | 1 | dx.doi.org/10.17504/protocols.io.kxygx9edzg8j/v6 | https://www.protocols.io/view/characterization-of-the-vkorc1-and-cyp2c9-genotype-cuk9wuz6 | Mirsada Causevic, Edin Begic | TITLE: Characterization of the VKORC1 and CYP2C9 genotypes
AUTHORS: Mirsada Causevic, Edin Begic
[DESCRIPTION]
Vitamin K antagonists (e.g. warfarin) are anticoagulants which represent widely prescribed drugs for prevention and treatment of thromboembolic disorders.
Warfarin's molecular target is vitamin K epoxide re... | ["[Genomic DNA extraction] Patients' whole blood was collected in ethylenediaminetetraacetic acid (EDTA)-containing tubes and stored at -20°C until use. Genomic DNA extraction from the human whole blood, that is, leukocytes, was carried out according to the protocol described by Subbarayan PR and colleagues (doi: 10.21... |
76,666 | RNAi Library screen | 1 | null | https://www.protocols.io/view/rnai-library-screen-cn42vgye | e.warren | TITLE: RNAi Library screen
AUTHORS: e.warren
[DESCRIPTION]
Protocol for screening a RNAi knockdown library in for behavioural and phenotypic effects in C. elegans
[STEPS]
SECTION: Perparing C. elegans
1. Prepare in advance
Prepare ten 90 mm NGM agar plates for each replicate of the screen for worm maintenance.
To ... | ["[Perparing C. elegans] Prepare in advance\nPrepare ten 90 mm NGM agar plates for each replicate of the screen for worm maintenance. \n\nTo prepare NGM follow the steps in the protocol for \"Making normal NGM\" and pour 35 ml per plate.", "[Perparing C. elegans] 11 days before tracking\nChunk worms onto ten seeded 90... |
44,830 | Cytochrome C Assay | 4 | null | https://www.protocols.io/view/cytochrome-c-assay-bpz6mp9e | Elizabeth Fozo | TITLE: Cytochrome C Assay
AUTHORS: Elizabeth Fozo
[STEPS]
?. [Steps]
Start ON cultures of a strain of interest.
?. [Steps]
The next day, measure 100 mL BHI into each flask to be used.
?. [Steps]
Measure OD600 of each overnight and calculate how much of your overnight culture you need for OD600~ 0.01in 100mL.
TKO – 20 ... | ["[Steps]\nStart ON cultures of a strain of interest.", "[Steps]\nThe next day, measure 100 mL BHI into each flask to be used.", "[Steps]\nMeasure OD600 of each overnight and calculate how much of your overnight culture you need for OD600~ 0.01in 100mL.\nTKO – 20 min – WT – 10 min – DKO", "[Steps]\nAdd supplement if do... |
40,377 | Enzyme linked immunosorbent assay for investigating the immunoglobulin-binding bacterial protein (IBBP) to avian egg yolk antibodies. | 6 | dx.doi.org/10.17504/protocols.io.bjnzkmf6 | https://www.protocols.io/view/enzyme-linked-immunosorbent-assay-for-investigatin-bjnzkmf6 | Angel Justiz-Vaillant | TITLE: Enzyme linked immunosorbent assay for investigating the immunoglobulin-binding bacterial protein (IBBP) to avian egg yolk antibodies.
AUTHORS: Angel Justiz-Vaillant
[STEPS]
?. This ELISA is used to study the interaction of proteins A, L and LA with different avian IgY preparations.
?. The 96 well microtitre pl... | ["This ELISA is used to study the interaction of proteins A, L and LA with different avian IgY preparations.", "The 96 well microtitre plate is coated overnight at 4°C with 1 µl/mg per well of unlabelled SpL, SpA or SpLA in carbonate-bicarbonate buffer pH 9.6.", "Then plate is treated with bovine serum albumin solutio... |
41,656 | Whole-mitogenome sequencing of Oncorhynchus masou masou by next-generation sequencing | 1 | dx.doi.org/10.17504/protocols.io.bkwykxfw | https://www.protocols.io/view/whole-mitogenome-sequencing-of-oncorhynchus-masou-bkwykxfw | Yoko Kato-Unoki, Kosuke Tashiro | TITLE: Whole-mitogenome sequencing of Oncorhynchus masou masou by next-generation sequencing
AUTHORS: Yoko Kato-Unoki, Kosuke Tashiro
[STEPS]
?. [Preparation of the mitogenome libraries for next-generation sequencing]
Amplify and purify the mitogenome libraries by using a QIAseq FX DNA Library Kit (QIAGEN) and Agencou... | ["[Preparation of the mitogenome libraries for next-generation sequencing]\nAmplify and purify the mitogenome libraries by using a QIAseq FX DNA Library Kit (QIAGEN) and Agencourt AMpure XP beads (Beckman Coulter), respectively. To reduce reagent use, library preparation can be performed on a quarter of the scale descr... |
53,548 | Seawater filtration and preservation for environmental DNA metabarcoding - rocky intertidal habitats | 1 | dx.doi.org/10.17504/protocols.io.bp2l6b5o1gqe/v1 | https://www.protocols.io/view/seawater-filtration-and-preservation-for-environme-byikpucw | Mary McElroy | TITLE: Seawater filtration and preservation for environmental DNA metabarcoding - rocky intertidal habitats
AUTHORS: Mary McElroy
[DESCRIPTION]
This protocol describes in-situ filtration and preservation of 1-L seawater samples from rocky intertidal habitats for environmental DNA (eDNA) metabarcoding. This protocol wa... | ["[Filtration] Wearing gloves, set up peristaltic pumps and secure Masterflex pump tubing into each pump head, leaving enough length on the 'in' side of the pump head to place the 10-cm tubing plus attached filter into the open sample. Leave enough room on the 'out' side of the pump head to make sure you can control th... |
65,083 | Fixation and imaging of HeLa cells after mitochondrial depolarization | 1 | dx.doi.org/10.17504/protocols.io.n92ldz6oxv5b/v1 | https://www.protocols.io/view/fixation-and-imaging-of-hela-cells-after-mitochond-cbs3sngn | OLIVIA HARDING, Erika L.F. Holzbaur | TITLE: Fixation and imaging of HeLa cells after mitochondrial depolarization
AUTHORS: OLIVIA HARDING, Erika L.F. Holzbaur
[DESCRIPTION]
Ectopic expression of p62/SQSTM1 often induces puncta formation and poor cell health due to p62’s proclivity to multimerize and form filaments. We used the cell fixation protocol desc... | ["[AntA/OligA treatment] Prepare working AntA/OligA solution by transferring 0.5 mL conditioned media to a 1.5 mL tube and adding 0.25 µL 10 millimolar (mM) OligA and 2 mL 45 millimolar (mM) AntA.", "[AntA/OligA treatment] Gently drop working AntA/OligA solution onto cells.", "[AntA/OligA treatment] Incubate at 37 °C, ... |
69,914 | Submission of sequence and contextual data to GISAID, INSDC repositories, or other databases | 1 | null | https://www.protocols.io/view/submission-of-sequence-and-contextual-data-to-gisa-cgh2tt8e | Paul Lorenzo A Gaite, Dr Ritchie Mae T Gamot, Dr Lyre Anni E Murao | TITLE: Submission of sequence and contextual data to GISAID, INSDC repositories, or other databases
AUTHORS: Paul Lorenzo A Gaite, Dr Ritchie Mae T Gamot, Dr Lyre Anni E Murao
[DESCRIPTION]
Timely submission of viral sequence and corresponding contextual data by public health laboratories is an essential step to SARS-... | ["PGC Mindanao workflow\n\n\nThis section outlines the PGC Mindanao workflow for the submission of sequence and contextual data to a public database. Figure 1 shows an overview of the entire workflow. The workflow ultimately deposits the sequence and contextual data to the online public database GISAID. \n \n \n\n... |
25,704 | 10 Affinity Chromatography | null | dx.doi.org/10.17504/protocols.io.5cgg2tw | null | TJUSLS China | TITLE: 10 Affinity Chromatography
AUTHORS: TJUSLS China
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Lysis of the bacteria.1. Resuspend the frozen cell paste as best you can in the Lysis Buffer using a 10 mL pipet or whatever means necessary. Let this suspension incubate for 20 minutes at room temper... | ["Lysis of the bacteria.1. Resuspend the frozen cell paste as best you can in the Lysis Buffer using a 10 mL pipet or whatever means necessary. Let this suspension incubate for 20 minutes at room temperature, or until the suspension becomes turbid and viscous due to release of the bacteria's genomic DNA.2. Smash the... |
40,807 | ELISA for quantification of IL-40 in human serum. | 6 | dx.doi.org/10.17504/protocols.io.bj4fkqtn | https://www.protocols.io/view/elisa-for-quantification-of-il-40-in-human-serum-bj4fkqtn | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-40 in human serum.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells.... | ["An anti-human IL-40 coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.", "Add 50 µl of human serum. Human IL-40 present in the serum sample binds to antibodies adsorbed into the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and... |
87,168 | Qiagen RNEasy PowerMicrobiome RNA extraction kit | 4 | dx.doi.org/10.17504/protocols.io.q26g7p181gwz/v2 | https://www.protocols.io/view/qiagen-rneasy-powermicrobiome-rna-extraction-kit-czc8x2zw | Michael Dan Siemon, Christelle Schang et al, Jessica Pardy, Richard Gibson, Dilan Joseph, Justin Donovan, christopher.degroot | TITLE: Qiagen RNEasy PowerMicrobiome RNA extraction kit
AUTHORS: Michael Dan Siemon, Christelle Schang et al, Jessica Pardy, Richard Gibson, Dilan Joseph, Justin Donovan, christopher.degroot
[DESCRIPTION]
The samples were processed using the Qiagen RNeasy PowerMicrobiome kit with the modifications described by Schang ... | ["[Qiagen RNEasy PowerMicrobiome RNA] As a substitute for vortexing described in the kit protocol, bead-beating was used. Bead-beating was conducted 4x for 30s at 4 m/s.", "[Qiagen RNEasy PowerMicrobiome RNA] Add 100 µl phenol–chloroform–isoamyl alcohol to a PowerBead Bead Tube, Glass 0.1 mm. Place 0.25 g stool or bios... |
41,675 | VPH_AUTOGENE-COVID_Diagnosis_Protocol_XPRIZE | 4 | dx.doi.org/10.17504/protocols.io.bkxjkxkn | https://www.protocols.io/view/vph-autogene-covid-diagnosis-protocol-xprize-bkxjkxkn | Dr Vikas Pandey, Dr Saurabh Singh, Shruti Ahuja, Avishek Dev, Manu Kadyan, Mukesh Pandit, Amir Khan, Sambit Dam, Tanish Garg | TITLE: VPH_AUTOGENE-COVID_Diagnosis_Protocol_XPRIZE
AUTHORS: Dr Vikas Pandey, Dr Saurabh Singh, Shruti Ahuja, Avishek Dev, Manu Kadyan, Mukesh Pandit, Amir Khan, Sambit Dam, Tanish Garg
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Valetude Primus Healthcare (VPH) is a healthcare spinoff from IIT... | ["[Sample Collection]\nCollect nasopharyngeal or oropharyngeal samples from patients at a healthcare facility using a flocked tapered nylon swab. For specimen collection of nasal swabs, follow the CDC Swab Collection Guidelines and swab manufacturers' recommendations. Tilt the patient’s head back 70 degrees. While gent... |
107,726 | X-ClickSeq: Custom-Primed Protocol with Single Indexing using ClickSeq Kit | 0 | dx.doi.org/10.17504/protocols.io.rm7vzjdm2lx1/v1 | https://www.protocols.io/view/x-clickseq-custom-primed-protocol-with-single-inde-dmfn43me | Andrew Routh, Elizabeth Jaworski | TITLE: X-ClickSeq: Custom-Primed Protocol with Single Indexing using ClickSeq Kit
AUTHORS: Andrew Routh, Elizabeth Jaworski
[DESCRIPTION]
ClickSeq is a simple, fragmentation-free method for the synthesis of Next-Generation Sequencing (NGS) libraries. ClickSeq derives its name by using ‘Click-Chemistry‘ in the place of... | ["[Reverse Transcription and RNA Removal] In a 0.2ml tube, dilute 100 ng-1 µg of input RNA to 10 µL using nuclease free water.", "[Reverse Transcription and RNA Removal] Add 1 µL of user-provided primer(s) to the diluted RNA. Mix well.", "[Reverse Transcription and RNA Removal] Incubate the mixture at 65 °C for 5 min t... |
50,864 | Ultra Expansion microscopy protocol with improved setup for upright and inverted microscopes. | 3 | dx.doi.org/10.17504/protocols.io.bvwqn7dw | https://www.protocols.io/view/ultra-expansion-microscopy-protocol-with-improved-bvwqn7dw | Elinacasas , Nicolas LANDREIN, Mélanie Bonhivers | TITLE: Ultra Expansion microscopy protocol with improved setup for upright and inverted microscopes.
AUTHORS: Elinacasas , Nicolas LANDREIN, Mélanie Bonhivers
[DESCRIPTION]
Ultra
[STEPS] | [] |
68,508 | Manual isolation of nuclei from human brain using CellRaft device and single nucleus Whole Genome Amplification | 1 | dx.doi.org/10.17504/protocols.io.kxygxzjjov8j/v1 | https://www.protocols.click/view/manual-isolation-of-nuclei-from-human-brain-using-ce54tg8w | Ester Kalef-Ezra, Diego Perez-Rodriguez, Christos Proukakis | TITLE: Manual isolation of nuclei from human brain using CellRaft device and single nucleus Whole Genome Amplification
AUTHORS: Ester Kalef-Ezra, Diego Perez-Rodriguez, Christos Proukakis
[DESCRIPTION]
Protocol for manual nuclear isolation from human brain tissue using Cell Raft device for single cell Whole Genome Amp... | ["[Nuclear extraction from human brain:] Transfer 20 mg -50 mg frozen brain tissue to microcentrifuge tube containing 500 µL of NIM. Transfer the tissue in a tube with the lid on using a pair of forceps.", "[Nuclear extraction from human brain:] Gently triturate the tissue with a cut pipette tip (1 mL tip). Repeat seve... |
87,287 | ICGRC Portal Tripal Data Generation and Setup | 5 | null | https://www.protocols.io/view/icgrc-portal-tripal-data-generation-and-setup-czgxx3xn | l.mansueto. | TITLE: ICGRC Portal Tripal Data Generation and Setup
AUTHORS: l.mansueto.
[DESCRIPTION]
The data provided by the International Cannabis Genomics Research Consortium ICGRC, web portal (https://icgrc.info) consist both results from past analyses made publicly available, and results we generated using the steps descr... | ["[Prepare RNA-Seq Sequences] NGS RNA-Seq sequences are downloaded from NCBI SRA, and trimmed to remove adapters. Three sets of RNA-Seqs are prepared for: 1) Purple Kush gene prediction, 2) Finola gene prediction, 3) transcript assembly, expression level, and variant discovery for trichomes from 21 samples", "[Gene fun... |
101,278 | Transfection of mammalian cell lines with plasmids and siRNAs | 0 | dx.doi.org/10.17504/protocols.io.261ge55byg47/v1 | https://www.protocols.io/view/transfection-of-mammalian-cell-lines-with-plasmids-de563g9e | Agnes Roczniak-Ferguson, Shawn M. Ferguson | TITLE: Transfection of mammalian cell lines with plasmids and siRNAs
AUTHORS: Agnes Roczniak-Ferguson, Shawn M. Ferguson
[DESCRIPTION]
This protocol details the transfection of mammalian cell lines with plasmids and siRNAs.
[STEPS]
SECTION: Lipofectamine 2000 (Invitrogen) or Fugene HD (Promega) or Fugene 6 (Promega) ... | ["[Lipofectamine 2000 (Invitrogen) or Fugene HD (Promega) or Fugene 6 (Promega) transfection reagents] On the day before transfection, plate 100,000 HeLa cells per well in a 6 well dish. For other cell lines, the number of cells will need to be optimized to achieve 50-75% confluency on the day of transfection.", "[Lipo... |
81,129 | Bleach extraction protocol: damaged or degraded DNA recovery from bone or tooth powder. | 4 | null | https://www.protocols.io/view/bleach-extraction-protocol-damaged-or-degraded-dna-ctghwjt6 | Valeria Mattiangeli, cassidl, Kevin Daly, mullinv | TITLE: Bleach extraction protocol: damaged or degraded DNA recovery from bone or tooth powder.
AUTHORS: Valeria Mattiangeli, cassidl, Kevin Daly, mullinv
[DESCRIPTION]
This protocol describes the steps to extraction degraded DNA molecules from ancient or historic bone and teeth powder, first washing the powder with d... | ["[Extraction Day 1: Bleach treatment] Add 990 µL of 0.5 % (v/v) sodium hypochlorite solution to each sample tube.", "[Extraction Day 1: Bleach treatment] Vortex and incubate at Room temperature for 15 min a rotator (H2020plus Incubated tube rotator from Benchmark Scientific, speed 35) or in thermomixer at .", "[Extr... |
48,586 | Histone extraction for mass spectrometry-based analysis of post-translational modifications in the fungal genus Aspergillus | 4 | dx.doi.org/10.17504/protocols.io.btpinmke | https://www.protocols.io/view/histone-extraction-for-mass-spectrometry-based-ana-btpinmke | Xin Zhang, Roberta Noberini, Tiziana Bonaldi, Michael F. Seidl, Jérȏme Collemare | TITLE: Histone extraction for mass spectrometry-based analysis of post-translational modifications in the fungal genus Aspergillus
AUTHORS: Xin Zhang, Roberta Noberini, Tiziana Bonaldi, Michael F. Seidl, Jérȏme Collemare
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Mass spectrometry i... | ["[Sample collection and disruption]\nHarvest fungal spores from 4- or 5 -day old sporulating plates with a spreader in 12.5 mL ice-cold ACES buffer", "[Sample collection and disruption]\nDiscard supernatant and resuspend spores in 25 mL ice-cold ACES buffer.", "[Sample collection and disruption]\nResuspend spores in 1... |
null | null | null | dx.doi.org/10.17504/protocols.io.mfrc3m6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes how to systemically infect fruit flies with either a bacterial or viral infection through pricking the mesopleuron of the thorax</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
20,782 | Measuring leaf carbon fractions with the ANKOM2000 Fiber Analyzer | null | dx.doi.org/10.17504/protocols.io.yinfude | null | Jocelyne Ayotte, Etienne Laliberté | TITLE: Measuring leaf carbon fractions with the ANKOM2000 Fiber Analyzer
AUTHORS: Jocelyne Ayotte, Etienne Laliberté
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Here we describe the standardized protocol used by the </span><a href="http://www.caboscience.org" style = "text-decoration:under... | ["[Sample preparation]\nUse a solvent resistant marker to label the filter bags to be used in the analysis.", "[Sample preparation]\nWeigh and record the weight of each empty filter bag to the nearest 0.0001 g (in Fulcrum). Zero the balance.\nNOTE: Do not pre-dry filter bags. Any moisture will be accounted for by the b... |
72,462 | Extraction and ONT MinION Library Preparation of uHMW gDNA | 4 | dx.doi.org/10.17504/protocols.io.j8nlkww11l5r/v2 | https://www.protocols.io/view/extraction-and-ont-minion-library-preparation-of-u-ciznuf5e | Kaylee S. Herzog, jfauver | TITLE: Extraction and ONT MinION Library Preparation of uHMW gDNA
AUTHORS: Kaylee S. Herzog, jfauver
[DESCRIPTION]
This custom protocol optimizes extraction, purification, and Oxford Nanopore Technologies (ONT) MinION library preparation for ultra-high molecular weight genomic DNA (uHMW gDNA) from parasitic nematodes.... | ["[Part 1: Ultra-HWM gDNA extraction | Zymo Quick-DNA HWM MagBead Plus Kit | ~3 hr] Set dry bath to 55 °C", "For each sample, add the following to a clean 1.5 mL microcentrifuge tube to create a master mix:\n 95 µL \n 95 µL \n 10 µL", "Vortex the master mix gently to mix, then spin down and keep ... |
86,096 | Preparing mitochondrial samples for immunoblotting | 4 | null | https://www.protocols.io/view/preparing-mitochondrial-samples-for-immunoblotting-cybqxsmw | Louise Uoselis | TITLE: Preparing mitochondrial samples for immunoblotting
AUTHORS: Louise Uoselis
[DESCRIPTION]
Protocol for preparation of mitochondrial samples for immunoblot analysis
[STEPS]
1. Thaw mitochondrial stocks on ice, and aliquot out the desired amount of mitochondria.
2. Centrifuge each aliquot for 10 min 10000 x g, 4... | ["Thaw mitochondrial stocks on ice, and aliquot out the desired amount of mitochondria.", "Centrifuge each aliquot for 10 min 10000 x g, 4 °C", "Carefully aspirate the supernatant from each sample.", "Add a volume of 1x SDS sample buffer (5% w/v SDS, 10% v/v glycerol, 100 mM DTT, 50 mM Tris-Cl pH 6.8) equal to the amo... |
69,618 | The role of sphingolipids in the pathogenesis of psoriasis | 1 | dx.doi.org/10.17504/protocols.io.36wgqjr8kvk5/v1 | https://www.protocols.io/view/the-role-of-sphingolipids-in-the-pathogenesis-of-p-cf8strwe | Mateusz Matwiejuk, Hanna Mysliwiec, Adrian Chabowski, Iwona Flisiak | TITLE: The role of sphingolipids in the pathogenesis of psoriasis
AUTHORS: Mateusz Matwiejuk, Hanna Mysliwiec, Adrian Chabowski, Iwona Flisiak
[DESCRIPTION]
Psoriasis is complexed, chronic, immunologically mediated disease, which involves skin and joints. Psoriasis is commonly connected with numerous other diseases s... | [] |
68,385 | Guidance for populating GenomeTrakr metadata templates (BioSample and SRA) | 1 | dx.doi.org/10.17504/protocols.io.dm6gpb71dlzp/v1 | https://www.protocols.io/view/guidance-for-populating-genometrakr-metadata-templ-cez9tf96 | Ruth Timme, Maria Balkey, William Wolfgang, Errol Strain | TITLE: Guidance for populating GenomeTrakr metadata templates (BioSample and SRA)
AUTHORS: Ruth Timme, Maria Balkey, William Wolfgang, Errol Strain
[DESCRIPTION]
PURPOSE: Guidance on how to populate NCBI's metadata packages, maximizing interoperability for foodborne pathogen surveillance.
SCOPE: This protocol provi... | ["[Overview] Guidance for organizing and populating the metadata templates required for direct submission to NCBI. This guidance is applicable for most enterics and/or microbial pathogens. \n\n****If your laboratory uses the BioNumerics platform for submission, please follow this protocol.****\n\nTwo metadata template... |
20,138 | Single Cell Calling Cards Library Preparation | null | dx.doi.org/10.17504/protocols.io.xwifpce | null | Arnav Moudgil, Robi D. Mitra | TITLE: Single Cell Calling Cards Library Preparation
AUTHORS: Arnav Moudgil, Robi D. Mitra
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes how to create calling card libraries from single cell RNA. We assume you have successfully transformed cells with </span><span styl... | ["[Single Cell Barcoding and Reverse Transcription]\nPrepare cells for isolation and encapsulation in gel bead emulsions (GEMs). If your experiment involves a piggyBac transposase with PB-SRT-Puro transposons, cells that have survived sleection should be dissociated and resuspended in solution. If you are using piggyBa... |
107,911 | H_QTof_PL_v1 | 0 | dx.doi.org/10.17504/protocols.io.n92ld8xr8v5b/v1 | https://www.protocols.io/view/h-qtof-pl-v1-dmmf443n | UTD Mass Spec Core, M, Fang Bian | TITLE: H_QTof_PL_v1
AUTHORS: UTD Mass Spec Core, M, Fang Bian
[DESCRIPTION]
To extract plasma lipids for LCMS analysis.
[BEFORE_START]
Use LCMS grade water and solvents.
[GUIDELINES]
Use glassware throughout this protocol.
[STEPS]
SECTION: To extract plasma lipids for LCMS study
1. Transfer plasma 50 ul (regular ... | ["[To extract plasma lipids for LCMS study] Transfer plasma 50 ul (regular pipette tips) into a 3 ml glass tube", "[To extract plasma lipids for LCMS study] Add 200 ul of LCMS grade-chloroform/methanol (2:1)", "[To extract plasma lipids for LCMS study] Stand for 5 min at room temperature.", "[To extract plasma lipids f... |
52,193 | Low cost methods for Hydra care | 4 | dx.doi.org/10.17504/protocols.io.bw79phr6 | https://www.protocols.io/view/low-cost-methods-for-hydra-care-bw79phr6 | Callen Hyland, Jennifer DeSantis | TITLE: Low cost methods for Hydra care
AUTHORS: Callen Hyland, Jennifer DeSantis
[DESCRIPTION]
Hydra, is genus of freshwater cnidarian polyp found in freshwater ponds and streams all over the world. Its remarkable ability to regenerate missing body parts, and even its whole bodies from fragments, has made Hydra a m... | ["[Brine shrimp cyst storage] Store brine shrimp cysts:\n\nBrine shrimp eggs can form thick-shelled cysts that remain dormant for many years until exposed to water. Freshly hatched nauplii (first developmental stage) of the brine shrimp Artemia franciscana are a convenient food for Hydra because they are easily stored ... |
null | null | null | dx.doi.org/10.17504/protocols.io.uy9exz6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol provides a workflow for platereader measuremtns with V. natriegens.
[STEPS]
SECTION: Sample preparation
?.
SECTION: Sample preparation
?.
SECTION: Sample preparation
?.
SECTION: Sample preparation
?.
SECTION: Preculture
?.
SECTION: Preculture
?.
SECTION: Pre... | ["[Sample preparation] Aliquot 50 µL LBv2 in 1.5 mL reaction tubes", "[Sample preparation] Transfer material from glycerol stock into these reaction tubes", "[Sample preparation] Prepare transparent 96 well plat with 190 µL LBv2", "[Sample preparation] Use 10 µL of LBv2 with cells from glycerol stock to inoculate the 9... |
98,898 | Whole blood viscosity test implementation: Community based participatory approach study protocol | 0 | dx.doi.org/10.17504/protocols.io.rm7vzj39rlx1/v1 | https://www.protocols.io/view/whole-blood-viscosity-test-implementation-communit-dcts2wne | Ezekiel U Nwose, Phillip Bwititi, Lexin Wang, Rasheda Khanam, Hayder Al-Aubaidy, San Low, Simon Tawasu, Chukwudiebube Ajaero | TITLE: Whole blood viscosity test implementation: Community based participatory approach study protocol
AUTHORS: Ezekiel U Nwose, Phillip Bwititi, Lexin Wang, Rasheda Khanam, Hayder Al-Aubaidy, San Low, Simon Tawasu, Chukwudiebube Ajaero
[DESCRIPTION]
This study would employ a Community-Based Participatory Research (C... | ["[Introduction in brief] Monitoring of whole blood viscosity (WBV) is critical in patients at risk of hyperviscosity (The\nRoyal College of Pathologies of Australia, 2019). Prothrombin Time Test (PT/INR), which is currently used is insufficient to predict bleeding risk (Cao et al., 2024). There is a test for blood vis... |
98,039 | An improved image analysis method for micropattern traction microscopy: dot tracking and traction force calculation script protocols | 0 | dx.doi.org/10.17504/protocols.io.n2bvjny65gk5/v1 | https://www.protocols.io/view/an-improved-image-analysis-method-for-micropattern-dbyx2pxn | Katie A. Bunde, Weiyuan Fan, Dimitrije Stamenovic, Paul E. Barbone, Michael L. Smith | TITLE: An improved image analysis method for micropattern traction microscopy: dot tracking and traction force calculation script protocols
AUTHORS: Katie A. Bunde, Weiyuan Fan, Dimitrije Stamenovic, Paul E. Barbone, Michael L. Smith
[DESCRIPTION]
The dot tracking script takes timelapse images of fluorescent micropatt... | ["[Dot Tracking Script] Name all timelapse images you plan to analyze in order according to the format “filename01, filename02, filename03, etc.” for as many images as you have. Our group typically has a stack of 25 images, so the number of images would go up to “filename25,” but any number of files can be used. Save t... |
null | null | null | dx.doi.org/10.17504/protocols.io.essbeee | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p><strong>Buffers and Solutions</strong></p>
<p> </p>
<p><strong>Suspension Buffer (SB):</strong></p>
<p>25 mM Tris pH 7.5</p>
<p>1 M Sorbitol</p>
<p>25 mM EDTA pH 8.0</p>
<p> </p>
<p><strong>Digestion Buffer (DB):</strong></p>
<p>250 mM EDTA pH 9.5</p>
<p>1% N-Lauroylsarcosine<... | [] |
104,183 | Infecting Cells with SeV or RSV in A549 or LLCMK2 cells | 0 | dx.doi.org/10.17504/protocols.io.dm6gpzeojlzp/v1 | https://www.protocols.io/view/infecting-cells-with-sev-or-rsv-in-a549-or-llcmk2-dhyx37xn | Carolina Lopez | TITLE: Infecting Cells with SeV or RSV in A549 or LLCMK2 cells
AUTHORS: Carolina Lopez
[DESCRIPTION]
Infection of SeV or RSV in A549 or LLCMK2 cells
[STEPS]
SECTION: Infecting Cells with SeV or RSV in A549 or LLCMK2 cells
1. Infecting cells with SeV or RSV in A549 or LLCMK2 cells
1. Prepare a virus dilution in infec... | ["[Infecting Cells with SeV or RSV in A549 or LLCMK2 cells] Infecting cells with SeV or RSV in A549 or LLCMK2 cells\n\n1. Prepare a virus dilution in infection media with the correct virus-specific media (see materials section for media composition).\nCalculate the volume of virus needed (X) using the MOI formula: \n ... |
48,556 | EPCAM Sorting Protocol | 4 | null | https://www.protocols.io/view/epcam-sorting-protocol-btnknmcw | Morrisey Lab | TITLE: EPCAM Sorting Protocol
AUTHORS: Morrisey Lab
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Epcam sorting Protocol</span></div><div class = "text-block"><div class = "justify" style = "text-align:justify"><span style = "font-weight:bold;">FACS Buffer: </span... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.paadiae | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>We found many specific steps and conditions for gram-negative bacteria while working with DNeasy Blood & Tissue Kit. These details are described in DNeasy Blood & Tissue Handbook (https://www.qiagen.com/us/resources/resourcedetail?id=6b09dfb8-6319-464d-996c-79e8c7045a... | [] |
84,049 | Automatic labeling tissue and cell of human skin | 5 | dx.doi.org/10.17504/protocols.io.j8nlko5z5v5r/v1 | https://www.protocols.click/view/automatic-labeling-tissue-and-cell-of-human-skin-cwbrxam6 | kyu sang han, peihsun.wu | TITLE: Automatic labeling tissue and cell of human skin
AUTHORS: kyu sang han, peihsun.wu
[DESCRIPTION]
This is first upload from TMC - Johns Hopkins
[STEPS]
SECTION: Tissue biopsy collection
1. After punch/excisional biopsy from a operating room (OR), place the skin tissue into a tissue container prefilled with buff... | ["[Tissue biopsy collection] After punch/excisional biopsy from a operating room (OR), place the skin tissue into a tissue container prefilled with buffered formalin for 12-24 hours at room temperature (RT)", "[Tissue biopsy collection] Discard formalin, rinse with PBS, refill PBS, and leave the tissue in PBS for 1 min... |
null | null | null | dx.doi.org/10.17504/protocols.io.me7c3hn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Sperm isolation and fixation </p>
<p> </p>
[STEPS]
?.
?.
?. | [] |
75,974 | PhageFISH | 2 | dx.doi.org/10.17504/protocols.io.rm7vzb7z2vx1/v1 | https://www.protocols.io/view/phagefish-cnfevbje | Line Jensen Ostenfeld, Saria Otani | TITLE: PhageFISH
AUTHORS: Line Jensen Ostenfeld, Saria Otani
[DESCRIPTION]
This is a collection of protocols for phageFISH.
[STEPS] | [] |
37,593 | Instructions of the Experiment - Contrasting effects of information sharing on common-pool resource extraction behavior: experimental findings | 1 | dx.doi.org/10.17504/protocols.io.bgxzjxp6 | https://www.protocols.io/view/instructions-of-the-experiment-contrasting-effects-bgxzjxp6 | Dimitri Dubois, Rouchier Juliette, Nguyen-Van Phu, Farolfi Stefano | TITLE: Instructions of the Experiment - Contrasting effects of information sharing on common-pool resource extraction behavior: experimental findings
AUTHORS: Dimitri Dubois, Rouchier Juliette, Nguyen-Van Phu, Farolfi Stefano
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Instructions of the experi... | [] |
52,173 | The blueprint and materials for building an imaging platform | 1 | dx.doi.org/10.17504/protocols.io.j8nlk4p6xg5r/v1 | https://www.protocols.io/view/the-blueprint-and-materials-for-building-an-imagin-bw7mphk6 | Wei-Ping Chan | TITLE: The blueprint and materials for building an imaging platform
AUTHORS: Wei-Ping Chan
[DESCRIPTION]
Details could be found in the Supplementary Information of "A high-throughput multispectral imaging system for museum specimens"
[STEPS]
2. Materials
3. Other accessory designs that improve workflow
2.2. Imaging p... | ["Materials", "Other accessory designs that improve workflow", "Imaging platform\nMaterials:\n \nTools:", "Blueprint", "Special clips for label removal and attachment\nHairdressing double prong pin (1.8\") link\nThis special clip can remove the labels and keep the pin holes labels aligned. It saves time for reattaching... |
54,612 | Recipe for standard BG-11 media | 1 | dx.doi.org/10.17504/protocols.io.bzjup4nw | https://www.protocols.io/view/recipe-for-standard-bg-11-media-bzjup4nw | Anna Behle, Alice Pawlowski | TITLE: Recipe for standard BG-11 media
AUTHORS: Anna Behle, Alice Pawlowski
[DESCRIPTION]
Stanier RY, Deruelles J, Rippka R, Herdman M, Waterbury JB: Generic Assignments, Strain Histories and Properties of Pure Cultures of Cyanobacteria. Microbiology 1979, 111:1–61.
Recipes for standard and alternative BG11 for cul... | ["[100 x BG11 stock:] CaCl2 2H2O (3.6 g · L-1)\nCitric acid (0.6 g · L-1)\nNaNO3 (149.58 g · L-1)\nMgSO4 · 7 H2O (7.49 g · L-1)\n0.25 M Na2-EDTA, pH 8.0 (0.56 ml · L-1)", "[Supplemental stocks for standard media:] 1000x Na2CO3: 20 mg mL-1\n100x TES-buffer, pH 8.0 (1M), adjust with KOH\n1000x K2HPO4 x 3 H2O: 30 mg · mL... |
18,578 | BioMark Single Cell Protocol (Two-Step RTSTA) | null | dx.doi.org/10.17504/protocols.io.wdsfa6e | null | Shaina Robbins, Alison Moss, Sean Nieves | TITLE: BioMark Single Cell Protocol (Two-Step RTSTA)
AUTHORS: Shaina Robbins, Alison Moss, Sean Nieves
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol utilizes Fluidigm's Biomark system which performs high-throughput real-time PCR that can assay 48 or 96 genes for 48 or 96 samples resp... | ["[LCM Extraction]\nPrepare lysis buffer as follows:Lysis enhancer (CellDirect kit)Resuspension buffer (CellDirect kit)Total lysis buffer per sample\n0.5 µl\n5 µl\n5.5 µl", "[RNA Dilution Series (Optional)]\nPrepare total RNA dilutions of 1 ng/ul, 300 pg/ul, 100 pg/ul, 30 pg/ul, 10 pg/ul, 3 pg/ul, 1 pg/ul, 300 fg/ul an... |
28,749 | First strand cDNA synthesis (ThermoScientific RevertAid) | null | dx.doi.org/10.17504/protocols.io.8bmhsk6 | null | Ben Kuipers | TITLE: First strand cDNA synthesis (ThermoScientific RevertAid)
AUTHORS: Ben Kuipers
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The following protocol is optimized to generate first-strand cDNA for use in (q)PCR</div></div>
[STEPS]
?. Add reaction components into sterile, nuclease-free tube on... | ["Add reaction components into sterile, nuclease-free tube on ice in the indicated order: AB1Template RNA100 ng ( 1pg - 5 µg)2Oligo(dT)181 µl (100 pmol)3Water, nuclease-freeto 12 µl\nAB1Template RNA100 ng ( 1pg - 5 µg)2Oligo(dT)181 µl (100 pmol)3Water, nuclease-freeto 12 µl", "Optional: If the RNA template... |
92,713 | Prognostic value of soluble suppression of tumorigenicity 2 in chronic kidney disease: a systematic review and meta-analysis | 1 | dx.doi.org/10.17504/protocols.io.dm6gp3m48vzp/v1 | https://www.protocols.io/view/prognostic-value-of-soluble-suppression-of-tumorig-c6shzeb6 | Ioannis Bellos, Vassiliki Benetou | TITLE: Prognostic value of soluble suppression of tumorigenicity 2 in chronic kidney disease: a systematic review and meta-analysis
AUTHORS: Ioannis Bellos, Vassiliki Benetou
[DESCRIPTION]
Cardiovascular disease represents the main complication of chronic kidney disease. Robust biomarkers of increased cardiovascular r... | ["Objective To determine the association of soluble suppression of tumorigenicity 2 (sST2) levels with survival, kidney disease progression and cardiovascular disease in patients with chronic kidney disease.", "Eligibility criteria The population of the study will consist of adults with diagnosed with chronic kidney di... |
null | null | null | dx.doi.org/10.17504/protocols.io.dru56v | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
1 µl 10x CutSmart buffer, 1 µl T4 DNA ligase buffer, 0.25µl U6 plasmid (about 100ng), 1µl annealed oligos, 0.3 µl T4 DNA ligase, 0.3 µl BsmBI, 0.2µl PstI (optional), 0.2 µl SalI (optional), 5µl H2O
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
28,752 | Microplate Reader Workflow | null | dx.doi.org/10.17504/protocols.io.8bqhsmw | null | NUS iGEM | TITLE: Microplate Reader Workflow
AUTHORS: NUS iGEM
[STEPS]
?. Refresh overnight cell culture in LB media at
37 °C
?. Measure OD600 of cell culture for desired OD value
?. Load of cell samples into three wells of a 96-well plate (triplicates)
200 µl
?. Induce appropriate volumes of chemical inducers (not exceeding ) ... | ["Refresh overnight cell culture in LB media at\n37 °C", "Measure OD600 of cell culture for desired OD value", "Load of cell samples into three wells of a 96-well plate (triplicates)\n200 µl", "Induce appropriate volumes of chemical inducers (not exceeding ) in each well\n6 µl", "Include LB media as blanks", "Load the... |
105,923 | Sternoclavicular joint-Targeted External jugular venipuncture Method (STEM) | 0 | dx.doi.org/10.17504/protocols.io.eq2lywqkevx9/v1 | https://www.protocols.io/view/sternoclavicular-joint-targeted-external-jugular-v-djpb4min | Suguru Yamauchi, Andrei Gurau, Kaitlyn Ecoff, Kristen P. Rodgers, Yuping Mei, Frank Bosmans, Franck Housseau, Yun Chen, John Michel, Andreas S Barth, Jinny S Ha, Takumi Iwasawa, Kazunori Kato, Ryohma Tsuchiya, Miki Yamauchi, Hajime Orita, Shinji Mine, Tetsu Fukunaga, Malcolm V Brock | TITLE: Sternoclavicular joint-Targeted External jugular venipuncture Method (STEM)
AUTHORS: Suguru Yamauchi, Andrei Gurau, Kaitlyn Ecoff, Kristen P. Rodgers, Yuping Mei, Frank Bosmans, Franck Housseau, Yun Chen, John Michel, Andreas S Barth, Jinny S Ha, Takumi Iwasawa, Kazunori Kato, Ryohma Tsuchiya, Miki Yamauchi, Haj... | ["[Procedure] A. Blood sampling\n\nThis original blood collection protocol for mice was developed for the left external jugular vein (EJV) and Fig 1 and Video 1 showing the procedure in detail is provided. \n\n \n\nWe also share a modified version of this protocol that can be adapted for procedures involving the right ... |
30,701 | Western Blotting Protocol | null | dx.doi.org/10.17504/protocols.io.98mh9u6 | null | Sam Li | TITLE: Western Blotting Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Sample Preparation:]
Place cells in a microcentrifuge tube and centrifuge to collect the cell pellet.
?. [Sample Preparation:]
Lyse the cell pellet with 100µl of lysis buffer on ice for 30 min (For 1 X 106 cel... | ["[Sample Preparation:]\nPlace cells in a microcentrifuge tube and centrifuge to collect the cell pellet.", "[Sample Preparation:]\nLyse the cell pellet with 100µl of lysis buffer on ice for 30 min (For 1 X 106 cells, lyse with 100µl of lysis buffer).", "[Sample Preparation:]\nCentrifuge at 14,000 rpm (16,000xg) for 10... |
77,745 | Whole-cell radioligand saturation binding | 1 | dx.doi.org/10.17504/protocols.io.ewov1oxe2lr2/v1 | https://www.protocols.io/view/whole-cell-radioligand-saturation-binding-cp6rvrd6 | Angus Li, Samuel Liu, Rennica Huang, Seungkirl Ahn, Robert J Lefkowitz | TITLE: Whole-cell radioligand saturation binding
AUTHORS: Angus Li, Samuel Liu, Rennica Huang, Seungkirl Ahn, Robert J Lefkowitz
[DESCRIPTION]
This protocol details an experimental procedure used to generate results described in the manuscript Li, A., Liu, S., Huang, R., Ahn, S., & Lefkowitz, R. J. (2023). Loss of bia... | ["[Day 1] Grow cells on 150 mm dish to ~70% confluency", "[Day 1] Wash twice with 10 mL PBS", "[Day 1] Detach cells with 1 mL trypsin-EDTA + 11 mL media. Trypsinize for 5 minutes and check under microscope for complete detachment; tap dish if necessary", "[Day 1] Count cells with hematocytometer and dilute collected ce... |
93,087 | Mouse Brain Heatmap - Whole brain data compilation and quality control | 1 | dx.doi.org/10.17504/protocols.io.n2bvj31jblk5/v1 | https://www.protocols.io/view/mouse-brain-heatmap-whole-brain-data-compilation-a-c657zg9n | Michael X. Henderson, Daniella DeWeerd, Kevin Kurgat | TITLE: Mouse Brain Heatmap - Whole brain data compilation and quality control
AUTHORS: Michael X. Henderson, Daniella DeWeerd, Kevin Kurgat
[DESCRIPTION]
This is a protocol for R shiny apps that accept output from the QUINT workflow (or similar mouse brain registration and segmentation data) and allows you to create g... | ["[Using N2U for the first time] Begin by hitting the browse button labeled for the ‘left side’ and select all files in the ‘left’ folder.", "[Using N2U for the first time] Hit the ‘open’ button to start loading the data.", "[Using N2U for the first time] If you have a ‘data’ folder, select all files in that folder ins... |
51,708 | Preparation of Single Cell Suspension from Human Spleen Tissue | 1 | dx.doi.org/10.17504/protocols.io.bwq4pdyw | https://www.protocols.io/view/preparation-of-single-cell-suspension-from-human-s-bwq4pdyw | Steven B. Wells, Peter A. Szabo | TITLE: Preparation of Single Cell Suspension from Human Spleen Tissue
AUTHORS: Steven B. Wells, Peter A. Szabo
[DESCRIPTION]
This protocol describes a method for the isolation of pan-lymphocytes, pan-myeloid cells, and progenitors from human spleen tissue. By providing defined media formulations, volumes at each step,... | ["[Preparing Medium and Buffer] Create the following IMDM-FBS-PSQ Media in a 500 mL bottle of IMDM by using the table below:\n \n Component Volume (mL) Starting Conc. Final Conc.* IMDM 500 - - Penicillin-Streptomycin-Glutamine 5 100X 1X FBS 50 100% 10%", "[Preparing Medium and Buffer] Creat... |
91,432 | Cyclic Heat Induced Epitope Retrieval (CHIER) | 4 | dx.doi.org/10.17504/protocols.io.kxygx3284g8j/v1 | https://www.protocols.io/view/cyclic-heat-induced-epitope-retrieval-chier-c5igy4bw | Victor Dieriks | TITLE: Cyclic Heat Induced Epitope Retrieval (CHIER)
AUTHORS: Victor Dieriks
[DESCRIPTION]
Immunolabeling is a cornerstone technique in molecular biology and pathology, providing critical insights into protein localisation and function within biological tissues. However, one of the persistent challenges in immunolabel... | ["[Paraffin-embedded formalin-fixed brain tissue] Human paraffin-embedded formalin-fixed brain tissue was utilised for this project. All brain tissues were washed using an ethanol (EtOH) series at Room temperature :\n20 min 70% EtOH\n20 min 80% EtOH\n20 min 2 x 95% EtOH \n30 min 2 x 100 % xylene \n\nOnce washed and deh... |
42,086 | Preparation of single cell suspensions from human intestinal biopsies for single cell genomics applications | 1 | dx.doi.org/10.17504/protocols.io.bmcek2te | https://www.protocols.io/view/preparation-of-single-cell-suspensions-from-human-bmcek2te | Ran Zhou, Oni Basu | TITLE: Preparation of single cell suspensions from human intestinal biopsies for single cell genomics applications
AUTHORS: Ran Zhou, Oni Basu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The protocol is adapted from Fujii's and Smillies's reports for single cell transcriptome analysis from human... | ["[Pre-Dissociation]\nChill wash media and dissociation media on ice. Samples are transfered with Advanced DMEM/F12 based media in 1.7 ml eppendorf tubes on ice. Once received in lab, samples are transfered to 35 mm dish using sharp-end forceps after the media are chilled. Alternatively, tissues can be transferred usin... |
39,757 | LEGENDplex™ Assay Setup Protocol for Cytek® Aurora and Northern Lights Flow Cytometers | 1 | dx.doi.org/10.17504/protocols.io.bi3mkgk6 | https://www.protocols.io/view/legendplex-assay-setup-protocol-for-cytek-aurora-a-bi3mkgk6 | Sam Li | TITLE: LEGENDplex™ Assay Setup Protocol for Cytek® Aurora and Northern Lights Flow Cytometers
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>To view images that accompany this protocol, click </span><a href="https://www.biolegend.com/Files/Images/BioLegend/legendplex/instructi... | ["[Setting Up LEGENDplex™ for the First Time on Your Cytek® Instrument:]\nPerform instrument start up procedure and instrument QC per manufacturer’s recommendations.", "[Setting Up LEGENDplex™ for the First Time on Your Cytek® Instrument:]\nImport the LEGENDplex™ Experiment Template into the SpectroFlo® software, or fo... |
76,526 | Cost-effective targeted nanopore sequencing of P. falciparum malaria | 1 | null | https://www.protocols.io/view/cost-effective-targeted-nanopore-sequencing-of-p-f-cnynvfve | Mariateresa de Cesare, Mulenga Mwenda, Anna E. Jeffreys, Daniel J Bridges, Jason A Hendry | TITLE: Cost-effective targeted nanopore sequencing of P. falciparum malaria
AUTHORS: Mariateresa de Cesare, Mulenga Mwenda, Anna E. Jeffreys, Daniel J Bridges, Jason A Hendry
[DESCRIPTION]
This protocol outlines a cost-effective approach for amplicon sequencing of P. falciparum malaria from dried blood spots (DBS). Th... | ["[Preparation of primer pools.] Prepare the sWGA primer pool (see Materials).", "[Preparation of primer pools.] If you have ordered the primers lyophilised, make them up to 1000uM in nuclease-free water.", "[Preparation of primer pools.] To make the 1000uM sWGA primer pool, combine equal volumes of each primer (e.g. P... |
44,502 | Qualitative Assessment of Islet Viability by Staining with Fluorescein Diacetate (FDA) and Propidium Iodide (PI) Dyes | 4 | dx.doi.org/10.17504/protocols.io.bppwmmpe | https://www.protocols.io/view/qualitative-assessment-of-islet-viability-by-stai-bppwmmpe | Human Islet Phenotyping Program (HIPP) of the IIDP | TITLE: Qualitative Assessment of Islet Viability by Staining with Fluorescein Diacetate (FDA) and Propidium Iodide (PI) Dyes
AUTHORS: Human Islet Phenotyping Program (HIPP) of the IIDP
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-style:italic;font-weight:bold;">This Standard ... | ["[Procedures]\nLimitations", "[Procedures]\nOnce the dye is added to the islets, the assessment must take place as quickly as possible. If there is a delay of more than 15 minutes, the accuracy of the assessment will be diminished as the islets lose their viability with time.", "[Procedures]\nBoth of the fluorescen... |
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