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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30,794 | PBMC Isolation | 1 | null | https://www.protocols.io/view/pbmc-isolation-babiiake | Sierra Simpson, Olivier George | TITLE: PBMC Isolation
AUTHORS: Sierra Simpson, Olivier George
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Isolation of peripheral blood monocytes (PBMC) for later expansion and differentiation </div></div>
[STEPS]
?. [Solution Preparation ]
Prepare Tricine Stock ( Fresh ) 0.895g Tricine ... | ["[Solution Preparation ]\nPrepare Tricine Stock ( Fresh ) 0.895g Tricine 50ml Water", "[Blood Collection]\nCollect blood by cardiac puncture into a 10ml syringe with 18g needle by slowly allowing blood to enter the syringe. Remove needle and drop blood into a purple top EDTA Tube (no vacuum – this increases hem... |
null | null | null | dx.doi.org/10.17504/protocols.io.ixmcfk6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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66,364 | Via Keto Gummies Australia This May Change Your Body Forever” ! Buy Now! | 1 | dx.doi.org/10.17504/protocols.io.5qpvob6rbl4o/v1 | https://www.protocols.io/view/via-keto-gummies-australia-this-may-change-your-bo-cc24sygw | ViaKeto Gummies | TITLE: Via Keto Gummies Australia This May Change Your Body Forever” ! Buy Now!
AUTHORS: ViaKeto Gummies
[DESCRIPTION]
Via Keto Apple Gummies Australia Reviews, Chemist Warehouse and Keto BHB Formula 2022
===>(OFFICIAL WEBSITE) Click Here To Order Via Keto Gummies In Australia (AU)
Via Keto Apple Gummies Survey: Many... | [] |
79,541 | Sequencing of construct | 4 | dx.doi.org/10.17504/protocols.io.3byl4jy7jlo5/v1 | https://www.protocols.io/view/sequencing-of-construct-crwvv7e6 | Pascale Baden, michela.deleidi | TITLE: Sequencing of construct
AUTHORS: Pascale Baden, michela.deleidi
[DESCRIPTION]
This protocol describes sequencing of construct.
[STEPS]
SECTION: PCR to amplify region of interest
1.
Master mix 1x H2O 13,3 5x Colorless Reaction Buffer (Promega, #M3005) 4 10mM dNTPs (ThermoFisher, #R0182) ... | ["[PCR to amplify region of interest] Master mix 1x H2O 13,3 5x Colorless Reaction Buffer (Promega, #M3005) 4 10mM dNTPs (ThermoFisher, #R0182) 0,4 Fw primer (CMV FW) 0,6 Rv primer (BGH RV) 0,6 GoTaq Polymerase (Promega, #M3005) 0,1 Σ 19µl \n Mix 19 µL MM with 1 µL DNA (50 ng).",... |
null | null | null | dx.doi.org/10.17504/protocols.io.mqic5ue | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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84,096 | DNA extraction from whole blood and buffy coat using the QIAamp DNA mini kit | 4 | null | https://www.protocols.click/view/dna-extraction-from-whole-blood-and-buffy-coat-usi-cwc8xazw | Annika Fendler | TITLE: DNA extraction from whole blood and buffy coat using the QIAamp DNA mini kit
AUTHORS: Annika Fendler
[DESCRIPTION]
This protocol is for extraction of total RNA from whole blood, or buffy coat or PBMCs using the QIAamp DNA mini kit.
[BEFORE_START]
Prepare:
AW1: Add 25ml EtOH to new bottle
AW2: Add 30 ml EtOH t... | ["[DNA Isolation] Transfer 200 µL buffy coat or 400 µL whole blood in 1.5 ml collection tubes", "[DNA Isolation] Add 20 µL 40 µL Proteinase K and mix by pipetting up or down", "[DNA Isolation] Add 4 µL 8 µL vortex for 15 s", "[DNA Isolation] Add 200 µL 400 µL buffer AL, vortex for 15 s", "[DNA Isolation] transfer t... |
67,831 | Preparation of PBS Solution | 1 | dx.doi.org/10.17504/protocols.io.3byl4bxjrvo5/v2 | https://www.protocols.io/view/preparation-of-pbs-solution-cegxtbxn | Stephane Fadanka, Shalo Minette, Nadine Mowoh | TITLE: Preparation of PBS Solution
AUTHORS: Stephane Fadanka, Shalo Minette, Nadine Mowoh
[DESCRIPTION]
Phosphate buffered Saline ( PBS) is a buffer solution commonly used in biological research. It is a salty solution containing sodium chloride, sodium phosphate, and (in some formulations) potassium chlori... | ["[Preparing reagents and workspace] Before beginning the procedure, put on Personal Protective Equipment (Lab Gown, Gloves, shoes, masks and goggles).\n\nClean up work surfaces and environment using disinfection solution (Bleach and after 70% alcohol).\n\nEnsure that all reagents and equipment needed for the procedure... |
81,781 | Efficient insect DNA extraction protocol. | 4 | dx.doi.org/10.17504/protocols.io.81wgby3mqvpk/v1 | https://www.protocols.io/view/efficient-insect-dna-extraction-protocol-ct4vwqw6 | Angelo José Rinaldi | TITLE: Efficient insect DNA extraction protocol.
AUTHORS: Angelo José Rinaldi
[DESCRIPTION]
Extracting DNA from insects can be a difficult process due to a number of factors. Some of these factors include the size and quantity of the insect, the presence of enzymes that degrade DNA, as well as the presence of chemical... | ["[Buffer preparation.] Lysis buffer solution CTAB 2% (4 g of 2% CTAB, 20 mL of 1M Tris-HCl pH 8.0, 16,4 g of 1,4 M NaCl, 8 mL of 20 mM EDTA, 400 mL of 0,2 % Beta mercapethanol for 200 mL water).\n\n\nNote: Betamercaptoethanol (BME), added on day of use.\nBME helps remove polyphenolic compounds, tannins, and proteins.\... |
72,253 | Evaluating endocytic rate in cells. | 1 | dx.doi.org/10.17504/protocols.io.8epv5jjedl1b/v1 | https://www.protocols.io/view/evaluating-endocytic-rate-in-cells-cis5ueg6 | Marine Houdou, Peter Vangheluwe, Nathalie Jacobs | TITLE: Evaluating endocytic rate in cells.
AUTHORS: Marine Houdou, Peter Vangheluwe, Nathalie Jacobs
[DESCRIPTION]
Assess endocytic rate in cells using tagged transferrin (Alexa647) and flow cytometry readout.
[BEFORE_START]
Prepare cell culture medium without FBS and keep it at 37°C.
Prepare Flow Cytometry (FC) buf... | ["Seed cells in 12 wellplate that they reach 70-80% confluency the day of the experiment.", "The day of the experiment, remove cell culture medium and pre-treat the cells in medium without FBS in a final volume of500 µL, for 30 min. The different conditions to consider are:", "After pre-treatment, keep the plate on ice... |
44,736 | Removal of FRT flanked antibiotic resistance gene | 4 | null | https://www.protocols.io/view/removal-of-frt-flanked-antibiotic-resistance-gene-bpw8mphw | Elizabeth Fozo | TITLE: Removal of FRT flanked antibiotic resistance gene
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol: Removal of antibiotic resistance marker with FRT sites using pCP20 plasmids</div></div>
[STEPS]
?. [Protocol based on Datsenko 2000]
Transform with pCP20 follow... | ["[Protocol based on Datsenko 2000]\nTransform with pCP20 following transformation protocol. Rescue at and spread cells on Amp plates.\n30 °C", "[Protocol based on Datsenko 2000]\nIncubate overnight at .(While cells are growing at the flippase should be in action and should flip out the resistance marker at FRT ... |
43,741 | CUT&Tag with Drosophila tissues | 1 | dx.doi.org/10.17504/protocols.io.bnx5mfq6 | https://www.protocols.io/view/cut-tag-with-drosophila-tissues-bnx5mfq6 | Kami Ahmad, Steven Henikoff | TITLE: CUT&Tag with Drosophila tissues
AUTHORS: Kami Ahmad, Steven Henikoff
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is a modification of the Benchtop CUT&Tag method (</span><a href="https://dx.doi.org/10.17504/protocols.io.bcuhiwt6" style = "text-decoration:underline;color:blue;cu... | ["[Prepare solutions and beads]\nPrepare Wash+ Buffer (50 mL):Add 50 mL of Wash $ buffer solution to a 50 mL conical tube Add 1 large Roche cOmplete EDTA-free tabletsAdd 12.5 µL 2 M Spermidine final 0.5 mMKeep on ice or store overnight at 4˚C.", "[Dissect larvae]\nWork with a dissecting microscope with tang... |
51,939 | Supporting protocol for use-case 1: Dimensionality reduction in "M2aia - Interactive, fast and memory efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data" | 5 | dx.doi.org/10.17504/protocols.io.bwybpfsn | https://www.protocols.io/view/supporting-protocol-for-use-case-1-dimensionality-bwybpfsn | Jonas Cordes | TITLE: Supporting protocol for use-case 1: Dimensionality reduction in "M2aia - Interactive, fast and memory efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data"
AUTHORS: Jonas Cordes
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><a href="https://jtfcordes.github.io/M2aia" s... | ["[Load Data into M²aia]\nOpen the Data view and define the signal processing:set your normalization strategy (e.g. TIC)set your smoothing strategy (e.g. Gaussian)set your baseline correction strategy (e.g. Median)Load at least one continuous profile *.imzML image file into M²aia: File > Open File or Ctrl + O.Ensure, ... |
73,435 | Catalogación Publicaciones Seriadas Biblioteca UCAM | 1 | dx.doi.org/10.17504/protocols.io.n92ldp87xl5b/v1 | https://www.protocols.io/view/catalogaci-n-publicaciones-seriadas-biblioteca-uca-cjx3upqn | Antonio Rex Alegria | TITLE: Catalogación Publicaciones Seriadas Biblioteca UCAM
AUTHORS: Antonio Rex Alegria
[DESCRIPTION]
Una Publicación Seriada es una publicación impresa o no, editada en partes sucesivas con designaciones numéricas o cronológicas y que pretende continuarse indefinidamente.
La catalogación es el proceso de selección y... | ["La clasificación de revistas está adaptada a las titulaciones de la UCAM.\n\nEn la Hemeroteca podemos encontrar:\n\n-Publicaciones Periódicas: revistas y prensa\n-Publicaciones Oficiales.\n\nAdemás de esta clasificación por titulaciones hay Publicaciones Periódicas relativas a materias generales como: UCAM, Religión,... |
48,424 | Oxford Nanopore sequencing and library construction | 4 | dx.doi.org/10.17504/protocols.io.btignkbw | https://www.protocols.io/view/oxford-nanopore-sequencing-and-library-constructio-btignkbw | Rui Zhang | TITLE: Oxford Nanopore sequencing and library construction
AUTHORS: Rui Zhang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a protocol for Oxford Nanopore sequencing and library construction, which was used in the humpback puffer genome sequence.</div></div>
[STEPS]
?. ONT Library prepara... | ["ONT Library preparation and Quality Control", "After obtaining the qualified DNA, the large size fraction was selected by automated gel electrophoresis (BluePippin).", "Next, the DNA was treated with the end-repair/dA tailing module.", "After purification, adapter ligation was performed using ligation sequencing kit ... |
95,951 | Freshwater mussel eDNA: water sampling and filtration through Sterivex filter unit | 4 | dx.doi.org/10.17504/protocols.io.14egn35npl5d/v1 | https://www.protocols.io/view/freshwater-mussel-edna-water-sampling-and-filtrati-c9xpz7mn | Marine Vautier | TITLE: Freshwater mussel eDNA: water sampling and filtration through Sterivex filter unit
AUTHORS: Marine Vautier
[DESCRIPTION]
The objective of this protocol is the sampling and the filtration of water samples through 0.45 µm Sterivex™ filter units. This protocol is used upstream to molecular biology analysis (e.g.... | ["[WATER SAMPLING] Wear gloves and open the bottle without touching the inside of the cap or the neck of the bottle.\n\nSeveral options are available:\n\n-Surface sampling :Collect by hand sub-surface water (10-20 cm below the water surface) and close the bottle carefully. \n\n-Depth sampling : If water is collected d... |
37,741 | NaCl | 3 | null | https://www.protocols.io/view/nacl-bg4mjyu6 | Marco Cosentino, Elisa Storelli, Alessandra Luini, Emanuela Rasini, Massimiliano Legnaro, Marco Ferrari, Franca Marino | TITLE: NaCl
AUTHORS: Marco Cosentino, Elisa Storelli, Alessandra Luini, Emanuela Rasini, Massimiliano Legnaro, Marco Ferrari, Franca Marino
[STEPS] | [] |
106,089 | Fiber Photometry on Noradrenergic/Dopaminergic Neurons (Open Field) | 0 | dx.doi.org/10.17504/protocols.io.3byl496bzgo5/v1 | https://www.protocols.io/view/fiber-photometry-on-noradrenergic-dopaminergic-neu-djuh4nt6 | Cristian González-Cabrera, Matthias Prigge | TITLE: Fiber Photometry on Noradrenergic/Dopaminergic Neurons (Open Field)
AUTHORS: Cristian González-Cabrera, Matthias Prigge
[DESCRIPTION]
The goal is to monitor in vivo calcium activity in noradrenergic and dopaminergic neurons within the hindbrain and midbrain of mice using fiber photometry during an open-field se... | ["[Pre-Experiment Preparation:] Animal Preparation:", "[Pre-Experiment Preparation:] Ensure that the mice have undergone appropriate surgical procedures for fiber implantation and calcium indicator expression in the relevant brain region targeting catecholaminergic neurons. Allow for recovery and acclimatization.", "[P... |
78,911 | Manual extraction of High Molecular Weight DNA from single mosquitoes using the Qiagen MagAttract HMW DNA kit | 4 | dx.doi.org/10.17504/protocols.io.n92ldp6ool5b/v1 | https://www.protocols.io/view/manual-extraction-of-high-molecular-weight-dna-fro-cra7v2hn | Fiona Teltscher, Harriet Johnson, Mara Lawniczak | TITLE: Manual extraction of High Molecular Weight DNA from single mosquitoes using the Qiagen MagAttract HMW DNA kit
AUTHORS: Fiona Teltscher, Harriet Johnson, Mara Lawniczak
[DESCRIPTION]
This is a protocol for the manual extraction of high molecular weight (HMW) DNA from insects. It uses the Qiagen MagAttract kit an... | ["[Procedure] Prepare an open insulated box of dry ice to store sample tubes on whilst working through steps 2-4.", "[Procedure] Make mastermix of reagents for lysis.\n \nCalculate the mastermix volumes for the number of samples plus 1 for spare pipetting volume. Volumes per sample are: 100 µL ; 10 µL (Mix by invert... |
57,724 | Coating plates | 4 | dx.doi.org/10.17504/protocols.io.b4k4quyw | https://www.protocols.io/view/coating-plates-b4k4quyw | Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner | TITLE: Coating plates
AUTHORS: Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner
[DESCRIPTION]
This protocol describes the process of coating plates using either VTN, Matrigel or Geltrex for use in culturing of feeder-free human pluripotent stem cells (hPSCs)
Protocol overview
Coating plates
... | ["[A. VTN] Thaw aliquoted VTN on ice. Each 6-well plate needs 60 µl VTN.", "[A. VTN] Incubate in a 37 °C incubator for 60 min", "[A. VTN] Add the diluted VTN to each well, shake and tilt the plate so the VTN solution covers the entire well.", "[A. VTN] For each well of 6-well plate, dilute 10 µl VTN in 1 ml pre-chille... |
17,152 | Microplastic SEM Sample Prep | null | dx.doi.org/10.17504/protocols.io.uy8exzw | null | Melissa B. Duhaime, Rachel Cable | TITLE: Microplastic SEM Sample Prep
AUTHORS: Melissa B. Duhaime, Rachel Cable
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Sample Dehydration]
Fill a petri dish with enough PBS to submerge your microplastic sample. Rinse the plastic in the PBS bath to remove loosely associated debris.
?. [Drying]
Air-d... | ["[Sample Dehydration]\nFill a petri dish with enough PBS to submerge your microplastic sample. Rinse the plastic in the PBS bath to remove loosely associated debris.", "[Drying]\nAir-dry the dehydrated samples overnight in desiccator underneath a fume hood.\n[overnight]", "[Affix]\nAffix plastic to double-side carbon ... |
47,249 | TaqMan Genotyping Assay for Detection of B.1.1.7 SARS-CoV-2 | 4 | null | https://www.protocols.io/view/taqman-genotyping-assay-for-detection-of-b-1-1-7-s-bsdrna56 | isaac.bell , Mark Adams | TITLE: TaqMan Genotyping Assay for Detection of B.1.1.7 SARS-CoV-2
AUTHORS: isaac.bell , Mark Adams
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">At the end of 2020, several new lineages of SARS-CoV-2 were reported that may be more transmissible, less responsive to antibody therapy, or able to “es... | ["[Assay Preparation]\nGather Supplies Needed for the Assay as listed in the Materials tab and:384-Well PCR PlateOptical Grade PCR plate adhesive film seal384-Well cold blockIce Bucket (ice)Pipettes and Tips for p20 and p200 pipettes", "[Sample Preparation]\nLocate and thaw on ice the extracted RNA samples to be tested... |
87,154 | Cell Culture Reagents and Sources – 2023-08-30 | 1 | dx.doi.org/10.17504/protocols.io.261ged55wv47/v1 | https://www.protocols.io/view/cell-culture-reagents-and-sources-2023-08-30-czcsx2we | Vipasha Dwivedi, David J Riese II | TITLE: Cell Culture Reagents and Sources – 2023-08-30
AUTHORS: Vipasha Dwivedi, David J Riese II
[DESCRIPTION]
The COVID-19 pandemic and its aftermath have created additional challenges in maintaining the supply chain to support biomedical research laboratory operations. A related challenge is recording and sharing c... | ["The COVID-19 pandemic and its aftermath have created additional challenges in maintaining the supply chain to support biomedical research laboratory operations. A related challenge is recording and sharing cell culture conditions and reagents among laboratory members. Through this protocols.io publication, we attem... |
61,862 | Electroporation of fluorescent antisense molecules into Bodo saltans and live imaging | 4 | dx.doi.org/10.17504/protocols.io.e6nvwk8e2vmk/v1 | https://www.protocols.io/view/electroporation-of-fluorescent-antisense-molecules-b8nervbe | Mastaneh Ahrar, g.hurst , Ewa Chrostek | TITLE: Electroporation of fluorescent antisense molecules into Bodo saltans and live imaging
AUTHORS: Mastaneh Ahrar, g.hurst , Ewa Chrostek
[DESCRIPTION]
This is the protocol used in our Laboratory at the University of Liverpool to electroporate molecules into Bodo saltans.
[STEPS]
SECTION: Overview
1. Antisense... | ["[Overview] Antisense peptide nucleic acids (PNAs, synthetised by Panagene, South Korea) were electroporated into Bodo slatans cells using Neon® Transfection System MPK1025 (Invitrogen).", "[Bodo culture conditions] Bodo saltans was cultured in a cerophyl-based medium enriched with 3.5 mM sodium phosphate dibasic (Na2... |
50,192 | Preparing Microbiome Samples for Cryo Shipment | 4 | null | https://www.protocols.io/view/preparing-microbiome-samples-for-cryo-shipment-bu9qnz5w | Alicia Rich | TITLE: Preparing Microbiome Samples for Cryo Shipment
AUTHORS: Alicia Rich
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a generic protocol written for any collaborators or contributing institutions sending samples to the Rich Lab at Otterbein University for microbiome or other genetic ana... | ["Keep all samples on cooling blocks or ice during these procedures.\non ice", "Label sterile, RNase/DNase-free tubes for each sample that you will be transferring. You should label them using a thin-tip permanent marker, and copy the information on the previous tube. If that information is not visible, add your initia... |
null | null | null | dx.doi.org/10.17504/protocols.io.euebete | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<strong>Materials:</strong><br /><br />
<ol>
<li>Glass petri plates of NC64A chlorella lawns with virus plaques (use plates that have been incubating for 3-4 days)</li>
<li>Nitrocellulose circles</li>
<li>Tris buffered saline + Tween 20 (TBST, 1X): 10 mM Tris-HCl, pH 8.0, 150 mM ... | [] |
98,985 | Calibration Protocol - Conversion of OD600 to Colony Forming Units (CFUs) | 1 | null | https://www.protocols.io/view/calibration-protocol-conversion-of-od600-to-colony-dcwh2xb6 | Paul Rutten, Richard Tennant, Jacob Beal, Christopher Workman, Traci Haddock-Angelli, Natalie Farny, Vinoo Selvarajah | TITLE: Calibration Protocol - Conversion of OD600 to Colony Forming Units (CFUs)
AUTHORS: Paul Rutten, Richard Tennant, Jacob Beal, Christopher Workman, Traci Haddock-Angelli, Natalie Farny, Vinoo Selvarajah
[DESCRIPTION]
This procedure can be used to calibrate OD600 to colony forming unit (CFU) counts, which are dire... | ["[Sample Preparation] This protocol will result in CFU/mL for 0.1 OD600. Your overnight cultures will have a much higher OD600 and so this section of the protocol, called “Sample Preparation”, will give you the “Starting Sample” with a 0.1 OD600 measurement.", "[Sample Preparation] Measure the OD600 of your cell cultu... |
47,646 | PROCEDURE TO ISOLATE AND CULTURE NEURONS FROM EMBRYONIC MOUSE CORTEX | 1 | dx.doi.org/10.17504/protocols.io.bsr6nd9e | https://www.protocols.io/view/procedure-to-isolate-and-culture-neurons-from-embr-bsr6nd9e | Odetta Antico, Miratul M. Muqit | TITLE: PROCEDURE TO ISOLATE AND CULTURE NEURONS FROM EMBRYONIC MOUSE CORTEX
AUTHORS: Odetta Antico, Miratul M. Muqit
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Mutations in PINK1 cause early-onset Parkinson’s disease. PINK1 becomes stabilised and</div><div class = "text-block">active upon mito... | ["[Coating of multiwell dishes with poly-L-lysine]\nIn a sterile laminar hood, prepare poly-L-lysine in sterile from stock solution.\n◊TIMING , 1 d before culture in this section.", "[Coating of multiwell dishes with poly-L-lysine]\nAdd enough poly-L-lysine solution to cover the bottom of the well, ensure that the vo... |
68,672 | Salmonella detection with spin column extraction and 7500-FAST enrichment PCR | 1 | dx.doi.org/10.17504/protocols.io.261genyxyg47/v2 | https://www.protocols.io/view/salmonella-detection-with-spin-column-extraction-a-cfa8tihw | Laura Goodman, Rebecca Franklin-Guild, Renee Anerson | TITLE: Salmonella detection with spin column extraction and 7500-FAST enrichment PCR
AUTHORS: Laura Goodman, Rebecca Franklin-Guild, Renee Anerson
[DESCRIPTION]
This procedure is used to test enrichment broth from environmental or animal specimens using Qiagen spin columns and the MicroSEQ Salmonella spp. Detection Ki... | ["[Preparation of RVS broth and Quality Check] This broth is used for the enrichment of specimens for Salmonella spp. isolation. The Rappaport Vassiliadis (RVS) media has an expiration date of 6 months from the preparation date.\n\nDetermine batch size:\n \n RO water 0.5 L 1 L 2 L 3 L 4 ... |
28,425 | Virus titration | null | dx.doi.org/10.17504/protocols.io.7zhhp36 | null | Norfitriah Mohamed Sohaimi, Mohd Hair Bejo, Abdul Rahman Omar, Aini Ideris, Nurulfiza Mat Isa | TITLE: Virus titration
AUTHORS: Norfitriah Mohamed Sohaimi, Mohd Hair Bejo, Abdul Rahman Omar, Aini Ideris, Nurulfiza Mat Isa
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.urzev76 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
SECTION: Prepare individual amino acid stock solutions
?.
SECTION: Prepare amino acid mix solution (∼17 nM each)
?.
SECTION: Prepare maltodextrin-based energy solution
?.
SECTION: Prepare maltodextrin-based energy solution
?.
SECTION: Prepare amino acid mix solution (∼14 mM each)
... | ["[Prepare individual amino acid stock solutions] {\"blocks\":[{\"key\":\"7lvbc\",\"text\":\" \",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"bsv38\",\"text\":\"Dissolve the given amount of each amino acid with 1 ml of 5M KOH in a 3 ml screw-cap tube according\\... |
90,744 | IHC analysis of brain regions from PCB exposed rats | 4 | dx.doi.org/10.17504/protocols.io.kqdg3xbbeg25/v1 | https://www.protocols.io/view/ihc-analysis-of-brain-regions-from-pcb-exposed-rat-c4uyywxw | Amanda Bullert, Morgan Linahon, Michael Dailey, Hansjoachim Lehmler | TITLE: IHC analysis of brain regions from PCB exposed rats
AUTHORS: Amanda Bullert, Morgan Linahon, Michael Dailey, Hansjoachim Lehmler
[DESCRIPTION]
This protocol describes a method to analyze the effect of PCB52 inhalation on brain cells in adolescent rats. PCB52 (2,2’,5,5’-tetrachlorobiphenyl) was administered to a... | ["[Extraction and preparation of cerebellum brain region] Using a rat brain matrix, the brain is cut into roughly 12 sections, each 2 mm thick", "[Extraction and preparation of cerebellum brain region] Drop fix the individual sections in 2 mL of 4% formalin per well for 24 hours at 4°C", "[Extraction and preparation of... |
85,473 | KAPP-Sen TMC: Pancreas Donor Acceptance Criteria | 1 | dx.doi.org/10.17504/protocols.io.j8nlkokddv5r/v1 | https://www.protocols.click/view/kapp-sen-tmc-pancreas-donor-acceptance-criteria-cxp9xmr6 | Cristina Aguayo-Mazzucato, Kanako Iwasaki | TITLE: KAPP-Sen TMC: Pancreas Donor Acceptance Criteria
AUTHORS: Cristina Aguayo-Mazzucato, Kanako Iwasaki
[DESCRIPTION]
Pancreas Donor Acceptance Criteria
[STEPS]
SECTION: Inclusion Criteria
1. Age groups:
5 donors of age under 35
10 donors of age at least 35 and under 60
10 donors of age at least 60
SECTION: Exclus... | ["[Inclusion Criteria] Age groups:\n5 donors of age under 35\n10 donors of age at least 35 and under 60\n10 donors of age at least 60", "[Exclusion Criteria] Diabetes mellitus\nBMI > 30\nPancreatitis\nPancreatic cancer or metastasis"] |
82,907 | Quantifying Synaptic Colocalizations with SynBot (ilastik Thresholding) | 5 | dx.doi.org/10.17504/protocols.io.q26g7yqo3gwz/v1 | https://www.protocols.click/view/quantifying-synaptic-colocalizations-with-synbot-i-cu73wzqn | Justin T Savage, Juan Ramirez, Dolores Irala, Cagla Eroglu | TITLE: Quantifying Synaptic Colocalizations with SynBot (ilastik Thresholding)
AUTHORS: Justin T Savage, Juan Ramirez, Dolores Irala, Cagla Eroglu
[DESCRIPTION]
Protocol for quantifying synapse numbers using the ilastik thresholding method in SynBot.
[STEPS]
SECTION: Installation
1. Install/Update FIJI. The newest ve... | ["[Installation] Install/Update FIJI. The newest version of Fiji can be found at https://fiji.sc/ Some features may not function properly if your Fiji is not up to date.", "[Installation] Visit the Syn_Bot GitHub repository (https://github.com/Eroglu-Lab/Syn_Bot) and download the ilastik4ij_Syn_Bot-1.8.2-SNAPSHOT.jar f... |
85,790 | KAPP-Sen TMC: Dissociation of Pancreatic Islets (recovered) Protocol | 1 | null | https://www.protocols.io/view/kapp-sen-tmc-dissociation-of-pancreatic-islets-rec-cxz6xp9e | Juliana Alcoforado Diniz, Dylan Baker, Jessica Garofalo, Paul Robson | TITLE: KAPP-Sen TMC: Dissociation of Pancreatic Islets (recovered) Protocol
AUTHORS: Juliana Alcoforado Diniz, Dylan Baker, Jessica Garofalo, Paul Robson
[DESCRIPTION]
The dispersed samples were shipped cold from PRODOLABS. Prior to scRNA-seq dispersed samples from brain dead donor’s pancreatic islets were recovered a... | ["[Abstract] The dispersed samples were shipped from PRODOLABS. Prior to scRNA-seq dispersed samples from brain dead donor's pancreatic islets were recovered and dissociated as follows.", "[Cell Dissociation with Accutase] NOTE: Before beginning cell dissociation coat all the materials (pipettes, tubes, etc.) with PIM-... |
88,119 | Akoya Phenocycler-Fusion Tissue Staining and Imaging Protocol for Formalin-Fixed Paraffin-Embedded Samples adapted from Indiana University | 1 | dx.doi.org/10.17504/protocols.io.4r3l229xpl1y/v1 | https://www.protocols.io/view/akoya-phenocycler-fusion-tissue-staining-and-imagi-c2axyafn | Archibald Enninful, negin.farzad, yao.lu.yl, Rong Fan | TITLE: Akoya Phenocycler-Fusion Tissue Staining and Imaging Protocol for Formalin-Fixed Paraffin-Embedded Samples adapted from Indiana University
AUTHORS: Archibald Enninful, negin.farzad, yao.lu.yl, Rong Fan
[DESCRIPTION]
This protocol presents the Yale University TMC Akoya Phenocycler-Fusion Tissue Staining & Imagin... | ["[Tissue Baking - Day 1] Bake tissue slides in a 60°C drying oven overnight for optimal tissue adherence to the glass slide. For some tissue samples, baking at 60°C for 1 hour will be sufficient to stick to the glass slide.\n\n For optimal use of reagents, 2-3 tissue slides are prepared in one batch.", "[Tissue depara... |
40,610 | Vezina Lab Silastic Capsule Implantation | 1 | null | https://www.protocols.io/view/vezina-lab-silastic-capsule-implantation-bjwakpae | Chad Vezina | TITLE: Vezina Lab Silastic Capsule Implantation
AUTHORS: Chad Vezina
[STEPS]
?. [2 weeks prior to experiment ]
Call RARC and reserve: (1) Isoflurane vaporizer and (2) glass bead sterilizer.Also, ensure that a sufficient amount of control and steroid pellets are available.Make more if needed.
?. [2. 2 days prior to e... | ["[2 weeks prior to experiment ]\nCall RARC and reserve: (1) Isoflurane vaporizer and (2) glass bead sterilizer.Also, ensure that a sufficient amount of control and steroid pellets are available.Make more if needed.", "[2.\t 2 days prior to experiment]\nCollect necessary supplies and ensure that isoflurane and buprenor... |
null | null | null | dx.doi.org/10.17504/protocols.io.pthdnj6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?. | [] |
19,966 | MICROALGAE ENCAPSULATION‐VITRIFICATION | null | dx.doi.org/10.17504/protocols.io.xq6fmze | null | Estefania Paredes | TITLE: MICROALGAE ENCAPSULATION‐VITRIFICATION
AUTHORS: Estefania Paredes
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">MICROALGAE ENCAPSULATION‐VITRIFICATION</div></div>
[STEPS] | [] |
96,585 | DESEq2 for time series | 0 | null | https://www.protocols.io/view/deseq2-for-time-series-dajh2cj6 | Karina Jhingan | TITLE: DESEq2 for time series
AUTHORS: Karina Jhingan
[DESCRIPTION]
This is a differential analysis for a time series experiment using DESeq2.
[STEPS]
SECTION: Introduction
1. This protocol is heavily based off of the protocol provided by https://alexslemonade.github.io/refinebio-examples/03-rnaseq/differential-expre... | ["[Introduction] This protocol is heavily based off of the protocol provided by https://alexslemonade.github.io/refinebio-examples/03-rnaseq/differential-expression_rnaseq_01.html.\n\nNote that DESeq and any other differential analysis requires replicates.", "[Imports/Libraries] Citation: “ashr” for LFC shrinkage\nStep... |
22,349 | SYSB3036 W11: Transcriptomic Analyses | null | dx.doi.org/10.17504/protocols.io.z3mf8k6 | null | Frank O. . Aylward | TITLE: SYSB3036 W11: Transcriptomic Analyses
AUTHORS: Frank O. . Aylward
[STEPS]
?. First let's get the data from GitHub and move inside the new folder we download:git clone https://github.com/faylward/transcriptomics_tutorialcd transcriptomics_tutoriallsYou should see two files: "homework_rnaseq_data.txt" and counts
... | ["First let's get the data from GitHub and move inside the new folder we download:git clone https://github.com/faylward/transcriptomics_tutorialcd transcriptomics_tutoriallsYou should see two files: \"homework_rnaseq_data.txt\" and counts", "For the rest of the tutorial we will be working in the R console, so move to t... |
101,423 | Total RNA extraction protocol for marine ostracods (bioluminescent and non-bioluminescent ostracods) | 0 | dx.doi.org/10.17504/protocols.io.eq2lyw6dmvx9/v1 | https://www.protocols.io/view/total-rna-extraction-protocol-for-marine-ostracods-dfap3idn | Lisa Mesrop | TITLE: Total RNA extraction protocol for marine ostracods (bioluminescent and non-bioluminescent ostracods)
AUTHORS: Lisa Mesrop
[DESCRIPTION]
Marine ostracods are tiny crustaceans, just 1-2 millimeters in size, with important ecological roles in marine ecosystems. However, extracting RNA from single individuals and ... | ["[Prep] Remove the RNA AMPure XP magnetic beads from the fridge and allow the beads to reach room temperature for 30 minutes.", "[Prep] (Optional) Remove the Proteinase K aliquot (stock 20 mg/ml) from the freezer and allow the aliquot to reach room temperature.", "[Prep] Remove RNA samples from the -80°C freezer and l... |
null | null | null | dx.doi.org/10.17504/protocols.io.nfkdbkw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>High-quality, highly enriched mitochondrial DNA (mtDNA) sample enables detection of extremely low-frequency mtDNA variants. When mtDNA is carefully enriched, fragmented in the presence of EDTA and sequenced with unique dual indices by Illumina HiSeq in paired-end mode, it is ... | [] |
65,453 | Standard Operating Procedure: Vibratomes | 1 | dx.doi.org/10.17504/protocols.io.8epv595ojg1b/v1 | https://www.protocols.io/view/standard-operating-procedure-vibratomes-cb6msrc6 | Hong-Yuan Chu | TITLE: Standard Operating Procedure: Vibratomes
AUTHORS: Hong-Yuan Chu
[DESCRIPTION]
This protocol details the procedure of the standard operating procedure (SOP) describes the safe use of vibratomes in the Chu lab.
[GUIDELINES]
Type of SOP: Hazardous equipment.
Purpose and scope: This Standard Operating Procedure (... | ["[Tissue sectioning procedure] Remove the blade from manufacturer package and wash it with ethanol and distilled water.", "[Tissue sectioning procedure] Install the blade carefully in the vibratome according to the procedure describes in the manual for the specific vibratome used.", "[Tissue sectioning procedure] Moun... |
31,303 | Next of Kin Participation in Care | null | dx.doi.org/10.17504/protocols.io.batfiejn | null | Albert Westergren | TITLE: Next of Kin Participation in Care
AUTHORS: Albert Westergren
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Excel database. Next of Kin Participation In care.</span></div><div class = "text-block">Sex (female = 0; male = 1)</div><div class = "text-block">Age... | [] |
108,571 | The "Material and Methods" section of the manuscript entitled "The prognostic value of H3K27me3 implies potential therapeutic targets in sinonasal soft tissue sarcoma: evidence gained from a single-arm, prospective, observational trial interim | 0 | dx.doi.org/10.17504/protocols.io.yxmvmeq5bg3p/v3 | https://www.protocols.io/view/the-34-material-and-methods-34-section-of-the-manu-dm93498n | Chengle Zhou, Jingyi Yang, Hongmeng Yu | TITLE: The "Material and Methods" section of the manuscript entitled "The prognostic value of H3K27me3 implies potential therapeutic targets in sinonasal soft tissue sarcoma: evidence gained from a single-arm, prospective, observational trial interim
AUTHORS: Chengle Zhou, Jingyi Yang, Hongmeng Yu
[DESCRI... | ["[7. Construction of Tissue microarrays] Whole slides staining of 27 formalin-fixed, paraffin-embedded (FFPE) tumor samples was firstly conducted utilizing available surgical specimen obtained from the observational trial cohort for primitive discovery. For subsequent validation, remaining FFPE specimens of the previo... |
96,041 | TNF ELISA Protocol | 0 | dx.doi.org/10.17504/protocols.io.3byl4qp88vo5/v1 | https://www.protocols.io/view/tnf-elisa-protocol-c92hz8b6 | caitlynhenry | TITLE: TNF ELISA Protocol
AUTHORS: caitlynhenry
[DESCRIPTION]
The purpose of this experiment is to investigate the effects of forskolin-mediated cAMP activation on TNF-ɑ secretion by LPS-treated Schwann cells. The immortalized rat RT4-D6P2T cell line (ATCC #CRL-2768) was cultured and received one of the following trea... | ["[To prepare RT4-D6P2T cell media samples (for three 6-well plates):] Aseptically culture immortalized rat RT4-D6P2T Schwann cells (ATCC, Cat #CRL-2768, Manassas, VA) in Dulbecco's Modified Eagle Medium (DMEM) (ATCC, Cat #30-2002, Manassas, VA) supplemented with 10% fetal bovine serum (FBS) (Thermo Fisher, Cat #160000... |
32,872 | Digestion with NEBNext dsDNA Fragmentase (M0348) | 1 | dx.doi.org/10.17504/protocols.io.bccgistw | https://www.protocols.io/view/digestion-with-nebnext-dsdna-fragmentase-m0348-bccgistw | New England Biolabs | TITLE: Digestion with NEBNext dsDNA Fragmentase (M0348)
AUTHORS: New England Biolabs
[DESCRIPTION]
NEBNext dsDNA Fragmentase is an enzyme-based reagent that shears DNA to produce fragments of the desired sizes in a time-dependent manner, for next generation sequencing library preparation protocols
dsDNA Fragmentase... | ["Combine the following components in a sterile PCR tube and vortex: \n component amount DNA (5 ng–3 μg) 1–16 μl 10X Fragmentase Reaction Buffer v2 2 μl Sterile Water variable", "Add 2 µL and vortex mixture for 3 s.", "Incubate at 37 °C for the recommended times below to generate the desired fragment size:\n \... |
64,541 | Beetle rearing media | 1 | dx.doi.org/10.17504/protocols.io.3byl4b62jvo5/v1 | https://www.protocols.io/view/beetle-rearing-media-ca95sh86 | Yin-Tse Huang, Tina | TITLE: Beetle rearing media
AUTHORS: Yin-Tse Huang, Tina
[DESCRIPTION]
ambrosia beetle rearing
[STEPS]
1. The recipe produces enough medium to fill approximately 18 culture tubes.(12cm)
First, add powder or solid
3. All ingredients were mixed thoroughly, then put cotton plugs into the mouth of the filled tubes... | ["The recipe produces enough medium to fill approximately 18 culture tubes.(12cm)\nFirst, add powder or solid", "All ingredients were mixed thoroughly, then put cotton plugs into the mouth of the filled tubes.", "The culture tubes was autoclaved at 121 °C for 30 min.", "Put culture tubes to dry 2 days in oven at 55°C.\... |
46,884 | EXTRACTS PRODUCTION AND FRACTIONATION | 4 | dx.doi.org/10.17504/protocols.io.br2cm8aw | https://www.protocols.io/view/extracts-production-and-fractionation-br2cm8aw | Rene Flores Clavo, Cristian Daniel Asmat Ortega, Nataly Ruiz Quinones | TITLE: EXTRACTS PRODUCTION AND FRACTIONATION
AUTHORS: Rene Flores Clavo, Cristian Daniel Asmat Ortega, Nataly Ruiz Quinones
[STEPS]
?. [Pre-inoculum]
Put three to four colonies of the bacteria in 5.0 mL of R2A broth supplemented with ASW with NaCl 7%, pH 7.0, and incubated at 28 °C for 5 to 7 days
?. [Inoculum]
After... | ["[Pre-inoculum]\nPut three to four colonies of the bacteria in 5.0 mL of R2A broth supplemented with ASW with NaCl 7%, pH 7.0, and incubated at 28 °C for 5 to 7 days", "[Inoculum]\nAfter cultures grow, transfer the total volume to an Erlenmeyer of 500.0 mL containing the same culture broth and incubated for 7 days at... |
76,858 | Pipetting | 1 | dx.doi.org/10.17504/protocols.io.n2bvj8x35gk5/v2 | https://www.protocols.io/view/pipetting-cpa2vige | Carlos Goller, Carly Sjogren | TITLE: Pipetting
AUTHORS: Carlos Goller, Carly Sjogren
[DESCRIPTION]
Overview and Goals
Lab micropipettes allow us to accurately transfer small volumes of liquids. Units to measure small volumes with micropipettes are: microliter (uL) and milliliter (mL). There are 1000 uL in 1 mL). Effectively using lab micropipette... | ["[Using a pipette] To draw up liquid", "[Using a pipette] Set volume using the volume adjustment wheel", "[Using a pipette] Press a new tip onto the shaft", "[Using a pipette] Press plunger TO the FIRST STOP", "[Using a pipette] Dip tip into liquid", "[Using a pipette] Slowly release the plunger to collect liquid into... |
95,981 | Candida auris sequencing by Illumina miSeq using Illumina DNA Prep | 0 | null | https://www.protocols.io/view/candida-auris-sequencing-by-illumina-miseq-using-i-c9ymz7u6 | Brenna M McGruder Rawson | TITLE: Candida auris sequencing by Illumina miSeq using Illumina DNA Prep
AUTHORS: Brenna M McGruder Rawson
[DESCRIPTION]
Candida auris sequencing is becoming more important for public health and surveillance. This protocol is designed to guide individuals experienced in sequencing in setting up a SOP for sequencing... | ["[Sample and Library preparation] Quantitate samples", "[Sample and Library preparation] For each sample determine the volume of sample to add that will be equal to or less than 100ng of DNA (volume must be less than 30 uL)", "[Sample and Library preparation] Add molecular grade water to a total volume of 30 uL", "[Sa... |
22,487 | Sample Preparation for Western Blot | null | dx.doi.org/10.17504/protocols.io.z7xf9pn | null | Qi Y | TITLE: Sample Preparation for Western Blot
AUTHORS: Qi Y
[STEPS]
?. For cultured cells, choose one of the following methods
?. Trypson digestion methods
?. Trypson digested not | ["For cultured cells, choose one of the following methods", "Trypson digestion methods", "Trypson digested not"] |
68,018 | Preparation of Bacteria Glycerol Stocks | 1 | dx.doi.org/10.17504/protocols.io.x54v9ykd4g3e/v2 | https://www.protocols.io/view/preparation-of-bacteria-glycerol-stocks-censtdee | Stephane Fadanka, Shalo Minette, Nadine Mowoh | TITLE: Preparation of Bacteria Glycerol Stocks
AUTHORS: Stephane Fadanka, Shalo Minette, Nadine Mowoh
[DESCRIPTION]
This protocol is meant to provide researchers with a step by step procedure on how to prepare glycerol stocks in order to preserve and store bacteria for long term.
Bacterial glycerol stoc... | ["[Preparing liquid culture of the bacteria to be stored] Prepare LB following this protocol depending on the desired amount of LB and subsequent number of glycerol stock tubes needed.\n\nUsing an inoculating wire loop, pick up some bacteria colonies from a culture plate and inoculate in an Erlenmeyer flask containing ... |
43,393 | Cell subculture | 4 | null | https://www.protocols.io/view/cell-subculture-bnk9mcz6 | PMAT0001 | TITLE: Cell subculture
AUTHORS: PMAT0001
[STEPS]
?. Pre-warm reagents to in water bath for about .
37 °C
?. Aspirate spent culture media from cell culture vessel.
?. Wash cells once with PBS ( is enough to wash T25 flasks and maybe for T75 flasks).
2 mL
5 mL
?. Aspirate PBS (from the side of the plate that does ... | ["Pre-warm reagents to in water bath for about .\n37 °C", "Aspirate spent culture media from cell culture vessel.", "Wash cells once with PBS ( is enough to wash T25 flasks and maybe for T75 flasks).\n2 mL\n5 mL", "Aspirate PBS (from the side of the plate that does not have any cells, so as to avoid disturbing the... |
84,238 | Cells electroporation for cell transfection with NEON system | 4 | dx.doi.org/10.17504/protocols.io.e6nvwd9jwlmk/v1 | https://www.protocols.click/view/cells-electroporation-for-cell-transfection-with-n-cwhnxb5e | Juan.Gonzalez | TITLE: Cells electroporation for cell transfection with NEON system
AUTHORS: Juan.Gonzalez
[DESCRIPTION]
Protocol for cell electroporation with the NEON transfection system
[STEPS]
1. Warm the resuspension buffer and the E2 buffer in the water bath out of the water at 37 °C
2. Put the electrode part inside the left... | ["Warm the resuspension buffer and the E2 buffer in the water bath out of the water at 37 °C", "Put the electrode part inside the left hand side hood in 419", "Put a NEON glass tube matching the electrode position", "Add 3 mL of E2 buffer in the glass tube.", "Switch on the NEON equipment", "Load the saved settings.", ... |
55,148 | Mouse Pancreatic Islet Isolation | 4 | dx.doi.org/10.17504/protocols.io.bz4kp8uw | https://www.protocols.io/view/mouse-pancreatic-islet-isolation-bz4kp8uw | Islet and Pancreas Analysis Core | TITLE: Mouse Pancreatic Islet Isolation
AUTHORS: Islet and Pancreas Analysis Core
[DESCRIPTION]
This SOP defines the methods used by the Vanderbilt Diabetes Center Islet and Pancreas Analysis (IPA) Core for isolation of pancreatic islets from wild type and transgenic mice.
[STEPS]
SECTION: Reagent preparation
1. 0.6... | ["[Reagent preparation] 0.6 mg/mL collagenase P solution – Weigh out between 20-30 mg of collagenase P into a 50 mL conical tube. Divide the precise mg mass by 0.6 to determine volume (mL) of HBSS to add to the tube. Once HBSS is added, vortex for about 30 seconds until collagenase goes into solution. Once prepared, ke... |
103,581 | Standard Operating Procedure: Mouse Spinal Cord Injection Surgery | 0 | dx.doi.org/10.17504/protocols.io.81wgbz5e3gpk/v1 | https://www.protocols.io/view/standard-operating-procedure-mouse-spinal-cord-inj-dhd53286 | Chu | TITLE: Standard Operating Procedure: Mouse Spinal Cord Injection Surgery
AUTHORS: Chu
[DESCRIPTION]
The intent of this Standard Operating Procedure (SOP) is to describe procedures for mouse spinal cord injection surgery.
[GUIDELINES]
RESPONSIBILITY
Principal investigator (PI), their staff, or any individual performi... | ["[Surgical and Station Preparation:] Print and prepare spinal cord surgery forms from Chu Lab SharePoint.", "[Surgical and Station Preparation:] Prepare solutions (e.g., PBS, AAV virus, and retrograde beads) needed for spinal cord surgery following Chu Lab inventory and SOPs.", "[Surgical and Station Preparation:] Ste... |
47,288 | Modified Zhen et al. SARS-CoV-2 Spike-Gene qRT-PCR assay for highly sensitive detection of the HV69/70 deletion | 1 | null | https://www.protocols.io/view/modified-zhen-et-al-sars-cov-2-spike-gene-qrt-pcr-bseynbfw | d.noerz | TITLE: Modified Zhen et al. SARS-CoV-2 Spike-Gene qRT-PCR assay for highly sensitive detection of the HV69/70 deletion
AUTHORS: d.noerz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The SARS-CoV-2 B.1.1.7 lineage (British variant) features a number of hallmark mutations, which can be used for scr... | ["Modified Primer/Probe set based on Zhen et al., (J Mol Diagn, 2020): (5' - 3')S-gene fwdTCAACTCAGGACTTGTTCTTACS-gene revTGGTAGGACAGGGTTATCAAACS-gene P-1FAM-TGGTCCCAGAGACATGTATAGCAT-BHQ1S-gene P-2 (new)Yak-TGGTCCCAG(+A)(+G)AT(+A)GC(+A)T-BHQ1\nS-gene fwdTCAACTCAGGACTTGTTCTTACS-gene revTGGTAGGACAGGGTTATCAAACS-gene P-1FA... |
52,330 | Guidance for populating GenomeTrakr metadata templates (BioSample and SRA) | 1 | dx.doi.org/10.17504/protocols.io.bxcipiue | https://www.protocols.io/view/guidance-for-populating-genometrakr-metadata-templ-bxcipiue | 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]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">PURPOSE: </span><span>Guidance on how to populate NCBI's metadata pack... | ["[Overview]\nGuidance for organizing and populating the metadata templates required for direct submission to NCBI. This guidance is applicable for most enterics and/or microbial pathogens. ****If your laboratory uses the BioNumerics platform for submission, please follow this protocol.****Two metadata templates are r... |
95,918 | LENTIVIRAL TITRATION FOR HUMAN PLURIPOTENT STEM CELLS | 0 | null | https://www.protocols.io/view/lentiviral-titration-for-human-pluripotent-stem-ce-c9wnz7de | Renuka Ravi Gupta, Nona Farbehi, hendersa, Vikram Khurana, Gist Croft, Lorenz Studer, Joseph Powell | TITLE: LENTIVIRAL TITRATION FOR HUMAN PLURIPOTENT STEM CELLS
AUTHORS: Renuka Ravi Gupta, Nona Farbehi, hendersa, Vikram Khurana, Gist Croft, Lorenz Studer, Joseph Powell
[DESCRIPTION]
We have developed a protocol for lentiviral titration of human pluripotent stem cells (hPSCs), including induced pluripotent stem cells... | ["[Day 0: Coating wells with VTN-N and seeding hPSCs] Coat 100 ul per well in a 48-well plate.", "[Day 0: Coating wells with VTN-N and seeding hPSCs] Incubate the plate at room temperature for an hour and the plate is ready to be used.", "[Day 0: Coating wells with VTN-N and seeding hPSCs] Seed 3x104 cells/cm2 in a 48 ... |
35,750 | Blunting ends by 3’ overhang removal and 3’ recessed (5’ overhang) end fill-in using T4 DNA Polymerase (M0203) | 1 | dx.doi.org/10.17504/protocols.io.be6ejhbe | https://www.protocols.io/view/blunting-ends-by-3-overhang-removal-and-3-recessed-be6ejhbe | New England Biolabs | TITLE: Blunting ends by 3’ overhang removal and 3’ recessed (5’ overhang) end fill-in using T4 DNA Polymerase (M0203)
AUTHORS: New England Biolabs
[DESCRIPTION]
Protocol for blunting ends by 3' overhang removal and fill-in of 3' recessed (5' overhang) ends using T4 DNA Polymerase.
[GUIDELINES]
CAUTION: Elevated te... | ["Dissolve DNA in any 1 X supplemented with 100 Micromolar (µM) .", "Add 1 unit of T4 DNA Polymerase per microgram DNA.", "Incubate 15 min at 12 °C.", "Stop reaction by adding EDTA to a final concentration of 10 Milimolar (mM).", "Heat for 20 min at 75 °C."] |
null | null | null | dx.doi.org/10.17504/protocols.io.i9sch6e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The six-minute walk test (6MWT) is a safe, simple, inexpensive tool for evaluating the functional exercise capacity of patients with chronic respiratory disease. However, there is a lack of standard reference equations for the six-minute walk distance (6MWD) in the healthy Ch... | [] |
87,763 | sciPlex-ATAC3 | 1 | null | https://www.protocols.io/view/sciplex-atac3-czxtx7nn | Gregory T Booth | TITLE: sciPlex-ATAC3
AUTHORS: Gregory T Booth
[DESCRIPTION]
Single-cell chromatin accessibility has emerged as a powerful means of understanding the epigenetic landscape of diverse tissues and cell types, but profiling cells from many independent specimens is challenging and costly. Here we describe a novel approach, ... | ["[Hash capture oligo annealing ~ 15 Minutes] Distribute 50,000 nuclei/well (10 uL of 5x10e6/ml) to desired number of wells.\nNote: Typically we will load 24 wells (1.2x10e6 cells) for 96x96x96 well barcoding experiments. For 384x384x384 experiments we will load 96 wells (4.2x10e6 cells) \nAdd 2 uL of 25uM PolyDT (LNA)... |
20,631 | Cassava Root Sampling for Cyanide Analysis | null | dx.doi.org/10.17504/protocols.io.ydxfs7n | null | Matema Imakumbili | TITLE: Cassava Root Sampling for Cyanide Analysis
AUTHORS: Matema Imakumbili
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to collect cassava root samples from a field or experimental plot for total cyanide (HCN) determination. </div></div>
[STEPS]
?. [Plant selection]... | ["[Plant selection]\nRandomly select four (4) plants from which cassava roots shall be sampled. The plants can be harvested from a field or an experimental plot. Select cassava plants that are representative of most plants on the plot. Also ensure that you sample plants of relatively the same age when sampling a farmer... |
98,313 | Investing In Paradise Protocol | 0 | dx.doi.org/10.17504/protocols.io.dm6gpzrmdlzp/v1 | https://www.protocols.io/view/investing-in-paradise-protocol-db9h2r36 | Gobind Thind | TITLE: Investing In Paradise Protocol
AUTHORS: Gobind Thind
[DESCRIPTION]
This research employs a mixed-methods approach to investigate the long-term socio-economic benefits of investing in sustainable tourism infrastructure and practices in Moorea. Data collection methods include structured surveys distributed to loc... | ["[Survey] A structured questionnaire will be developed to gather quantitative data on various aspects related to sustainable tourism, such as economic impacts, environmental considerations, and community well-being.", "[Survey] Before full-scale distribution, the survey will be pilot-tested with a small group of local... |
null | null | null | dx.doi.org/10.17504/protocols.io.ss3eegn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>From this protocol, we can know detail methods of assembly and annotation of the L. maculatus genome.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
39,627 | AMOVA AND PHILOGENY IN SARS-COV- 2 PROTOCOLS | 5 | dx.doi.org/10.17504/protocols.io.bixjkfkn | https://www.protocols.io/view/amova-and-philogeny-in-sars-cov-2-protocols-bixjkfkn | Pierre Teodosio | TITLE: AMOVA AND PHILOGENY IN SARS-COV- 2 PROTOCOLS
AUTHORS: Pierre Teodosio
[STEPS]
?. [METHODOLOGY]
1.METHODOLOGY
?. [METHODOLOGY]
DATABANK
?. [METHODOLOGY]
0pt;line-height:150%;font-family:"Arial",sans-serif;mso-ansi-language:EN-US'>: The 153 gene sequences of theintegrase gene of human immunodeficiency virus 1 wer... | ["[METHODOLOGY]\n1.METHODOLOGY", "[METHODOLOGY]\nDATABANK", "[METHODOLOGY]\n0pt;line-height:150%;font-family:\"Arial\",sans-serif;mso-ansi-language:EN-US'>: The 153 gene sequences of theintegrase gene of human immunodeficiency virus 1 were collected from GENBANK (https://www.ncbi.nlm.nih.gov/popset/?term=MN888087.1 and... |
28,131 | The image processing protocol of “Comparison of an algorithm quantitatively estimating epifascial fibrosis in three-dimensional computed tomography images to other clinical lymphedema grading methods” | null | dx.doi.org/10.17504/protocols.io.7qbhmsn | https://www.protocols.io/view/the-image-processing-protocol-of-comparison-of-an-7qbhmsn | Kyo-In Koo, Myung-hwan Ko, Yongkwan Lee, Son Hyewon, Suwon Lee, Chang Ho Hwang | TITLE: The image processing protocol of “Comparison of an algorithm quantitatively estimating epifascial fibrosis in three-dimensional computed tomography images to other clinical lymphedema grading methods”
AUTHORS: Kyo-In Koo, Myung-hwan Ko, Yongkwan Lee, Son Hyewon, Suwon Lee, Chang Ho Hwang
[DESCRIPTION]
<div clas... | [] |
73,497 | Expression and purification protocol of the Human (Homo sapiens) LC3B Ubiquitin-like modifier | 4 | dx.doi.org/10.17504/protocols.io.j8nlkw82dl5r/v1 | https://www.protocols.io/view/expression-and-purification-protocol-of-the-human-cjzzup76 | Dorotea Fracchiolla, Liv Jensen | TITLE: Expression and purification protocol of the Human (Homo sapiens) LC3B Ubiquitin-like modifier
AUTHORS: Dorotea Fracchiolla, Liv Jensen
[DESCRIPTION]
This protocol describes expression and purification procedures for obtaining mCherry-tagged human recombinant Ubiquitin-like modifier LC3B (MAP1LC3B, Microtubule-... | ["[Protein Expression] Transform plasmid DNA (Addgene_190237) into E.Coli Rosetta pLyss cells and plate on Ampicillin LB agar plate for at 37 °C.", "[Protein Expression] The following day, inoculate a 5 mL with 1-2 colonies and grow at 37 °C shaking.", "[Protein Expression] The following day, use 5 mL to inoculate... |
35,374 | Brain Dissection of Post-natal Mice | null | dx.doi.org/10.17504/protocols.io.besnjede | null | Allen Institute for Brain Science | TITLE: Brain Dissection of Post-natal Mice
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the procedure for removal and embedding of the post-natal mouse brain.</div><div class = "text-block"><span style = "font-weight:bold;">Note</... | [] |
44,188 | Introduction to CRISPR | 3 | null | https://www.protocols.io/view/introduction-to-crispr-bpd4mi8w | TITLE: Introduction to CRISPR
AUTHORS:
[STEPS] | [] | |
90,739 | 605CefTB - Resting Medium (basta selection) | 4 | null | https://www.protocols.io/view/605ceftb-resting-medium-basta-selection-c4utywwn | leiboffs | TITLE: 605CefTB - Resting Medium (basta selection)
AUTHORS: leiboffs
[DESCRIPTION]
This is part of the Leiboff Lab maize transformation protocol for somatic embryogenesis of B104 immature embryos. This protocol is a combination of Chen et al. 2022 and Kang et al. 2022 with some modifications based on material availabi... | ["[Planning] Estimate the volume of 605CefTB you will need based on the following:\n\n \n\nMake sure to round up! Check the table below to plan your media", "[Mixing Heat-Stable Ingredients] Retrieve the following heat-stable ingredients:\n605 Medium - Stored in Main Lab, 4C Refrigerator, Top Shelf\nCasin Hydrolysate ... |
48,959 | NRTDP Top Down Standard SOP: Orbitrap Eclipse and Exploris | 1 | dx.doi.org/10.17504/protocols.io.bt27nqhn | https://www.protocols.io/view/nrtdp-top-down-standard-sop-orbitrap-eclipse-and-e-bt27nqhn | Rafael Melani, Paul Thomas, Bryon Drown | TITLE: NRTDP Top Down Standard SOP: Orbitrap Eclipse and Exploris
AUTHORS: Rafael Melani, Paul Thomas, Bryon Drown
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This standard protocol details how to make a standard mix of proteins for tracking LC-MS performance and illustrates how to configure an ... | ["[Prepare Standard Mix]\nPrepare stocks of each protein standard in Optima water. (Aliquots can be stored at )\n-80 °C", "[Prepare Standard Mix]\nPrepare the following mixture (volumes shown from respective stock solutions):ProteinVolume (uL)Stock Concentration (pmol/uL)Amount Loaded on Column (pmol, 1X)Carbonic An... |
null | null | null | dx.doi.org/10.17504/protocols.io.c4ryv5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Adapted from Steripak protocol, with addition of RNase.
[GUIDELINES]
Required volumes: for ½ plate 20 mls is plenty - split into 15 mls plus 5 mls; for a whole plate 35 mls is good - split into 30 mls plus 5 mls.
[STEPS]
?.
?.
?.
?. | [] |
66,620 | Prodentim Reviews- Pills Price in Canada, UK, NZ, Australia or Ireland | 1 | dx.doi.org/10.17504/protocols.io.kqdg3powzl25/v1 | https://www.protocols.io/view/prodentim-reviews-pills-price-in-canada-uk-nz-aust-cda4s2gw | health | TITLE: Prodentim Reviews- Pills Price in Canada, UK, NZ, Australia or Ireland
AUTHORS: health
[DESCRIPTION]
Don't buy before read Prodentim Reviews scam, price, review, results, side effects, benefits and much more.
[STEPS]
1. Prodentim Reviews there are plenty of alternatives you can do at the drugstore to get whi... | ["Prodentim Reviews there are plenty of alternatives you can do at the drugstore to get whiter teeth less than HR. See Compliance with Actions for even more information. Use the cost of baking salt. This is because baking soft drinks is easy to grungy that aids in removing stains from teeth. To start saturating your Mo... |
98,292 | Tissue H&E Staining | HuBMAP | JHU-TMC | 0 | dx.doi.org/10.17504/protocols.io.kqdg3242qv25/v2 | https://www.protocols.io/view/tissue-h-amp-e-staining-hubmap-jhu-tmc-db8u2rww | Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Miklhail James, Sashank Reddy, Denis Wirtz | TITLE: Tissue H&E Staining | HuBMAP | JHU-TMC
AUTHORS: Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Miklhail James, Sashank Reddy, Denis Wirtz
[DESCRIPTION]
The following are guidelines that will have an effective staining window of 2 to 5 minutes. Developed as progressive stains, the intensity of nucl... | ["[H&E staining] Final Step: Mount and Coverslip with Covermount", "Set 2 stations with 100% ethanol. Submerge the slide for a minute in each station.", "[H&E staining] Wash the slide in running warm water for a minute", "[H&E staining] Submerge the slide in Optik Hematoxylin for 3 minutes", "[H&E stain... |
53,753 | Plasmid DNA extraction | 4 | dx.doi.org/10.17504/protocols.io.byqzpvx6 | https://www.protocols.io/view/plasmid-dna-extraction-byqzpvx6 | Shuning Guo | TITLE: Plasmid DNA extraction
AUTHORS: Shuning Guo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to extract plasmid DNA from E. coli.</div></div>
[STEPS]
?. Solate a single colony from a freshly streaked selective plate, and inoculate a culture of 1- 5 mL LB medium contain... | ["Solate a single colony from a freshly streaked selective plate, and inoculate a culture of 1- 5 mL LB medium containing the appropriate selective antibiotic. Incubate for ~12-16 hours at 37°C with vigorous shaking (~ 300 rpm). Use a 10-20 mL culture tube or a flask with a volume of at least 4 times the volume of t... |
null | null | null | dx.doi.org/10.17504/protocols.io.etubenw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Protocol to prepare <em>E. coli</em> supercompetent cells to transform with plasmid/ligation. This protocol is originally derived from <a href="http://www.ncbi.nlm.nih.gov/pubmed/6345791" target="_blank">Hanahan, D. (1983) J. Mol. Biol. 166:557-580</a> with some changes. This ve... | [] |
97,005 | Populating NCBI template for submissions using BioNumerics | 1 | dx.doi.org/10.17504/protocols.io.36wgq3ejylk5/v3 | https://www.protocols.io/view/populating-ncbi-template-for-submissions-using-bio-daym2fu6 | Ruth Timme, Maria Balkey, Julie Haendiges, Brian Sauders, Tina Lusk Pfefer | TITLE: Populating NCBI template for submissions using BioNumerics
AUTHORS: Ruth Timme, Maria Balkey, Julie Haendiges, Brian Sauders, Tina Lusk Pfefer
[DESCRIPTION]
PURPOSE: to define the standard operating procedure for collecting isolate metadata using BioNumerics for submission of food/environmental isolates to N... | ["[New Version for this protocol] Visit the new version of this protocol by clicking the following link: https://www.protocols.io/view/populating-ncbi-template-for-submissions-using-bio-3byl4qn4ovo5/v1"] |
20,519 | PCL:PEG Electrospinning | null | dx.doi.org/10.17504/protocols.io.yaffsbn | null | Kenneth Schackart, Kattika Kaarj | TITLE: PCL:PEG Electrospinning
AUTHORS: Kenneth Schackart, Kattika Kaarj
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details how to electrospin a PCL:PEG copolymer onto glass cover slip.</div></div>
[STEPS]
?. [Make polymer solution]
In 50 mL tube, add chloroform and acetone. This... | ["[Make polymer solution]\nIn 50 mL tube, add chloroform and acetone. This is your solvent solution.\n14 ml\n6 ml\nThe solvent solution should be 70% chloroform and 30% acetone. You can adjust volumes accordingly.\nAlways work with these solvents in chemical fume hood.", "[Make polymer solution]\nIn 15 mL tube dissolve... |
70,831 | Transfer of plasmid DNA to Rhodobacter sphaeroides via Conjugal mating | 4 | dx.doi.org/10.17504/protocols.io.ewov1oydolr2/v2 | https://www.protocols.io/view/transfer-of-plasmid-dna-to-rhodobacter-sphaeroides-chept3dn | Jaya K Yakha, laible, Deborah K Hanson, Rosemarie Wilton | TITLE: Transfer of plasmid DNA to Rhodobacter sphaeroides via Conjugal mating
AUTHORS: Jaya K Yakha, laible, Deborah K Hanson, Rosemarie Wilton
[DESCRIPTION]
Rhodobacter is not capable of being transformed with pure, double-stranded DNA containing sites for endogenous restriction enzymes. The most efficient way of tr... | ["Two days prior to the conjugation, inoculate 25 ml of GYCC with desired host strain and grow at 33 °C with shaking at 125 rpm. If culture becomes too turbid prior to the conjugation, sub culturing may be necessary.", "The night before the conjugation, inoculate the donor strain of S17-1 (pXYZ) in 3 mL of growth mediu... |
37,637 | Automated 96-well PCR Purification | 1 | dx.doi.org/10.17504/protocols.io.dm6gpr19jvzp/v1 | https://www.protocols.io/view/automated-96-well-pcr-purification-bgzdjx26 | Ariel Rabines, Rob Lampe, Andrew E Allen | TITLE: Automated 96-well PCR Purification
AUTHORS: Ariel Rabines, Rob Lampe, Andrew E Allen
[DESCRIPTION]
This protocol describes a fully-automated PCR cleanup in a 96-well PCR plate format with AMPure XP beads on an Eppendorf epMotion. Multichannel pipetting with the 300 uL and 50 uL pipettes is used. It is designed ... | ["Take aliquot of beads out of refrigerator and allow to warm to room temperature.", "Prepare fresh 70% EtOH. \n\nFrom the Agencourt XP beads manual: \"Fresh 70% ethanol should be prepared for optimal results. There is also miscibility involved with ethanol and water. For example, measuring out 70 mL of ethanol and top... |
30,492 | Consistency between anticholinergic burden scales in the elderly with fractures | null | dx.doi.org/10.17504/protocols.io.9z4h78w | null | Luis Fernando Valladales Restrepo, Marlene Duran Lengua, Edgar Castro, Jorge Machado Alba | TITLE: Consistency between anticholinergic burden scales in the elderly with fractures
AUTHORS: Luis Fernando Valladales Restrepo, Marlene Duran Lengua, Edgar Castro, Jorge Machado Alba
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Consistency between anticholiner... | [] |
72,920 | Parallel detection of multiple effector functions in live T cells using a short coculture assay | 1 | dx.doi.org/10.17504/protocols.io.kqdg39xyqg25/v1 | https://www.protocols.io/view/parallel-detection-of-multiple-effector-functions-cjfyujpw | Zaki Molvi | TITLE: Parallel detection of multiple effector functions in live T cells using a short coculture assay
AUTHORS: Zaki Molvi
[DESCRIPTION]
Assays measuring T cell effector function are powerful tools for determining the antigenic specificity of T cells. Conventional flow cytometric detection of cytokine production by T ... | ["[Introduction] Assays measuring T cell effector function are powerful tools for determining the antigen-specificity of T cells. Conventional methods for measuring effector cytokine production of T cells in response to antigen include ELISPOT, ELISA, and intracellular cytokine staining (ICS). ICS enables parallel dete... |
63,207 | Immunocytochemistry (ICC) | 4 | dx.doi.org/10.17504/protocols.io.q26g74w79gwz/v1 | https://www.protocols.io/view/immunocytochemistry-icc-b9yfr7tn | mineechoi | TITLE: Immunocytochemistry (ICC)
AUTHORS: mineechoi
[DESCRIPTION]
This protocol describes how to do immunocytostochemistry for primary and hiPSC-derived cells.
[STEPS]
SECTION: Cell fixation
1. Cells are fixed in 4 % volume paraformaldehyde (PFA) and stored in phosphate-buffered saline (PBS) until use.
SECTION... | ["[Cell fixation] Cells are fixed in 4 % volume paraformaldehyde (PFA) and stored in phosphate-buffered saline (PBS) until use.", "[Permeabilizing and blocking cells] Wash cells with PBS twice.", "[Permeabilizing and blocking cells] Incubate the cells in 0.2 % volume Triton X-100, 5 % volume bovine serum albumin (BSA)... |
null | null | null | dx.doi.org/10.17504/protocols.io.idvca66 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Please contact Dr. Steven Wilhelm (wilhelm@utk.edu) for additional information regarding this protocol.</p>
<p> </p>
<p>Modified from <span style="font-family: 'Segoe UI', sans-serif; font-size: small;">Schwyn, B. & Neilands, J. B. Universal chemical assay for the detecti... | [] |
41,065 | BG11 hypersaline agar plates | 1 | dx.doi.org/10.17504/protocols.io.bkchkst6 | https://www.protocols.io/view/bg11-hypersaline-agar-plates-bkchkst6 | Bosak Lab Protocols | TITLE: BG11 hypersaline agar plates
AUTHORS: Bosak Lab Protocols
[STEPS]
?. Add the following to a beaker and dissolve using a stir bar on a magnetic stir plate. ABC1BG11 hypersaline agar plate mediumamountunit2initial Milli-Q water968ml3NaCl49.8g 4NaNO31.5g5Na2CO30.02g6KCl1.3867g7MgCl2*6H2O8.569g8MgSO4*7H2O6.4998g9... | ["Add the following to a beaker and dissolve using a stir bar on a magnetic stir plate. ABC1BG11 hypersaline agar plate mediumamountunit2initial Milli-Q water968ml3NaCl49.8g 4NaNO31.5g5Na2CO30.02g6KCl1.3867g7MgCl2*6H2O8.569g8MgSO4*7H2O6.4998g9CaCl2*2H2O2.042g10Stock A10ml11Stock B10ml12Stock C10ml13Stock 5 (trace\n ... |
40,531 | 611.2 URMC HTC Formalin-Inflated, Paraffin-Embedded Human Lung Tissue | 4 | dx.doi.org/10.17504/protocols.io.bjttknnn | https://www.protocols.io/view/611-2-urmc-htc-formalin-inflated-paraffin-embedded-bjttknnn | Gloria S Pryhuber, Heidie Huyck, Daria Krenitsky | TITLE: 611.2 URMC HTC Formalin-Inflated, Paraffin-Embedded Human Lung Tissue
AUTHORS: Gloria S Pryhuber, Heidie Huyck, Daria Krenitsky
[DESCRIPTION]
Processing of Formalin Fixed Lung and Non-Lung Tissue for the LungMAP HTC
[STEPS]
SECTION: Record Process
1. Record details of procedure in Worksheet or Directly in In... | ["[Record Process] Record details of procedure in Worksheet or Directly in Inventory or ELN", "[Record Process] Keep photographic recording of inflation and blocking of lung lobe and tissue", "[Inflation Fixed (Formalin) Lung Lobe] Inflation fixation procedure should be accomplished in a grossing station or biological ... |
61,944 | Chiral resolution process | 1 | null | https://www.protocols.io/view/chiral-resolution-process-b8qyrvxw | BOC Sciences | TITLE: Chiral resolution process
AUTHORS: BOC Sciences
[DESCRIPTION]
The separation of a racemic mixture into two optically active forms (+ or −) is known as chiral resolution. Since diastereomers have different chemical and physical properties, they can be separated into corresponding enantiomers by chiral resol... | [] |
35,862 | Basic protocol for elimination of bacteria from microalgal culture using antibiotics | null | dx.doi.org/10.17504/protocols.io.be9wjh7e | https://www.protocols.io/view/basic-protocol-for-elimination-of-bacteria-from-mi-be9wjh7e | Adriana Lopes Dos Santos, Claude Lemieux, Monique Turmel | TITLE: Basic protocol for elimination of bacteria from microalgal culture using antibiotics
AUTHORS: Adriana Lopes Dos Santos, Claude Lemieux, Monique Turmel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Method used to eliminate bacterial contamination of a marine micro-algal culture. Note, this m... | ["Using appropriate protective clothing, prepare 20ml of an antibiotic solution mixture 10X in pure water as follows: \n• Cefotaxime (5g/L)\n• Carbenicillin (5g/L)\n• Kanamycin (2g/L)\n• Augmentin (2g/L)", "Sterilize through a 0.1 or 0.22 µm filter into a sterile bottle. Keep refrigerate for up to weeks, or store at -2... |
87,305 | Sanger Tree of Life HMW DNA Extraction: Automated Plant MagAttract v.4 | 4 | dx.doi.org/10.17504/protocols.io.8epv5xrd5g1b/v1 | https://www.protocols.io/view/sanger-tree-of-life-hmw-dna-extraction-automated-p-czhhx336 | Benjamin Jackson, Caroline Howard | TITLE: Sanger Tree of Life HMW DNA Extraction: Automated Plant MagAttract v.4
AUTHORS: Benjamin Jackson, Caroline Howard
[DESCRIPTION]
This protocol describes the automated extraction and SPRI of HMW DNA from cryogenically homogenised or bead-beaten tissue samples from plants and fungi intended for long-read sequencin... | ["[Sample lysis] Set one heat block with a 50 mL SmartBlock to 65 °C and another heat block with a 2 mL SmartBlock to 55 °C.\n \n ReagentVolume per samplePhosphate buffered solution (PBS)200 µLBuffer AL150 µL", "[Sample lysis] Prepare a lysis buffer master mix in a 50 mL centrifuge tube:", "[Sample lysis] Place the l... |
35,384 | PCR Preparation & Gel Electrophoresis | 1 | dx.doi.org/10.17504/protocols.io.yxmvmxzp9l3p/v1 | https://www.protocols.io/view/pcr-preparation-amp-gel-electrophoresis-besyjefw | Dakota Betz | TITLE: PCR Preparation & Gel Electrophoresis
AUTHORS: Dakota Betz
[DESCRIPTION]
How to set up a PCR reaction (Sanger sequencing only).
[BEFORE_START]
Use 75% Ethanol to clean the lab bench, tube racks, and pipettes before taking out any reagents and starting the protocol.
[GUIDELINES]
If you need to prepare prim... | ["[Tube and Master Mix Prep] Prepare your PCR tubes. To do this, use an ethanol resistant pen to label the top of each tube (use a short, 1-2 letter or number code) and the sides of each tube (repeat the short code or use a slightly longer one; also add the gene or primers that you used if there is space). Don't forget... |
35,494 | Test-serology-protocol | null | dx.doi.org/10.17504/protocols.io.bewejfbe | null | Dr. John Smith | TITLE: Test-serology-protocol
AUTHORS: Dr. John Smith
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is an assay describing indirect sandwich ELISA for RDP Ag of SARS-CoV-2. </div><div class = "text-block">Yadda, yadda, yadda, Yadda, yadda, yadda, Yadda, yadda, yadda, Yadda, yadda, yadda, Yadd... | ["[B. Preperation of Samples]\nIf the concentration of antigen in the sample potentially exceeds the highest point of the standard curve (i.e. > 1,000 pg/ml) prepare one or more dilutions of the sample using the standard diluent.", "[A.Preparation of Standards]\nTypically a standard curve may span concentrations from 0... |
null | null | null | dx.doi.org/10.17504/protocols.io.hf6b3re | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
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?.
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?.
?. | [] |
20,565 | UC Davis - Aspartate Aminotransferase | null | dx.doi.org/10.17504/protocols.io.ybvfsn6 | null | Peter Havel | TITLE: UC Davis - Aspartate Aminotransferase
AUTHORS: Peter Havel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">
Aspartate transaminase (AST) also known as aspartate aminotransferase or (sGOT) is a metabolic enzyme ex... | ["Add 5 μl of each sample or standard (in duplicate) to the microplate wells.IMPORTANT: Make sure not to add any bubbles to the wells when dispensing reagents, this will interfere with reading in the platereader.", "Add 50 μl of AST Reagent Solution to the wells. Cover wells with the adhesive film and incubate at 37°C ... |
104,759 | Brain Clarification for Neuromelanin visualisation by OPT | 0 | dx.doi.org/10.17504/protocols.io.n92ld8qdov5b/v1 | https://www.protocols.io/view/brain-clarification-for-neuromelanin-visualisation-diix4cfn | Ariadna Laguna, Miquel Vila | TITLE: Brain Clarification for Neuromelanin visualisation by OPT
AUTHORS: Ariadna Laguna, Miquel Vila
[DESCRIPTION]
Protocol for the clarification of whole mouse brains to allow neuromelanin visualisation by Optical Projection Tomography
[STEPS]
SECTION: Brain processing
1. Mice are transcardially perfused in 4% PFA ... | ["[Brain processing] Mice are transcardially perfused in 4% PFA and postfixed in the same fixative overnight", "[Brain processing] After rinsing several times in PBS, brains are embedded in 1% low melting point agarose in water", "[Brain processing] Once dehydrated the brains are incubated during 4 hours shaking in 66%... |
45,159 | Measuring the Action of Oligonucleotide Therapeutics in the Lung at the Cell Type-Specific Level by Tissue Disruption and Cell Sorting (TDCS) | 2 | dx.doi.org/10.17504/protocols.io.bqcfmstn | https://www.protocols.io/view/measuring-the-action-of-oligonucleotide-therapeuti-bqcfmstn | Helen Graves, Steven Evans, Michael Fauler, Manfred Frick, Sterghios A. Moschos | TITLE: Measuring the Action of Oligonucleotide Therapeutics in the Lung at the Cell Type-Specific Level by Tissue Disruption and Cell Sorting (TDCS)
AUTHORS: Helen Graves, Steven Evans, Michael Fauler, Manfred Frick, Sterghios A. Moschos
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The clin... | [] |
28,857 | Vascular perfusion of mice | null | dx.doi.org/10.17504/protocols.io.8ezhtf6 | null | Peter Mundel | TITLE: Vascular perfusion of mice
AUTHORS: Peter Mundel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This protocol describes the procedure for perfusion of mice prior to organ or tissue harvesting .</div><div class ... | ["Preparation (see figure below for setup)♦ Fix tubing (small diameter tubes, below 1 cm) to the bottles: 1 bottle for PFA, 1 bottle for sucrose\n♦ Fill perfusion solutions in the bottles: solutions must be freshly prepared and filtered (using 0.22 μm filter)♦ Adjust perfusion pressure to 150-160 mm Hg\n♦ Fix needle at... |
null | null | null | dx.doi.org/10.17504/protocols.io.is4cegw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
75,967 | PhageFISH detailed protocol | 4 | dx.doi.org/10.17504/protocols.io.4r3l273wqg1y/v1 | https://www.protocols.io/view/phagefish-detailed-protocol-cne7vbhn | Line Jensen Ostenfeld, Saria Otani | TITLE: PhageFISH detailed protocol
AUTHORS: Line Jensen Ostenfeld, Saria Otani
[DESCRIPTION]
This protocol details about PhageFISh protocol.
[BEFORE_START]
Prepare buffers (see Preparation of Buffers for PhageFISH protocol).
[GUIDELINES]
Controls to consider:
Faecal sample with no target for the phage probe
Time... | ["[Fix faecal samples to glass slides] Mix a loopful faecal sample with 10-20 µL PBS (1X) and vortex thoroughly.", "[Fix faecal samples to glass slides] Allow suspension to settle for 5 min to avoid large debris.", "[Fix faecal samples to glass slides] Take 10 µL of the supernatant and place on coated glass slide.", "[... |
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