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 |
|---|---|---|---|---|---|---|---|
74,783 | Oligonucleotide-polymer conjugation for imaging mass cytometry | 4 | dx.doi.org/10.17504/protocols.io.dm6gpjz91gzp/v2 | https://www.protocols.io/view/oligonucleotide-polymer-conjugation-for-imaging-ma-ck97uz9n | Danielschulz | TITLE: Oligonucleotide-polymer conjugation for imaging mass cytometry
AUTHORS: Danielschulz
[DESCRIPTION]
This protocol describes the procedures to label 5'-thiol modified oligonucleotides with maleimide carrying polymers which are also chelated with metal-ions.
This is the basis to perform RNAscope with Imaging Mas... | ["[Oligonucleotide resuspension and reduction] Resuspend lyophilized oligos in ddH20 (RNAase and DNAse free water) to a final concentration of 250 µM in 1.5 mL eppendorf tubes", "[Oligonucleotide resuspension and reduction] Determine concentration at NanoDrop.\nNote: If there is a big discrepancy between what you measu... |
83,903 | Basic Instructions for Running Cell Cycle Analysis with Propidium Iodide on the Beckman Coulter Cytoflex S or Other Cytometers | 1 | dx.doi.org/10.17504/protocols.io.14egn3xypl5d/v1 | https://www.protocols.click/view/basic-instructions-for-running-cell-cycle-analysis-cv67w9hn | Jamie C Tijerina | TITLE: Basic Instructions for Running Cell Cycle Analysis with Propidium Iodide on the Beckman Coulter Cytoflex S or Other Cytometers
AUTHORS: Jamie C Tijerina
[DESCRIPTION]
Basic instructions for performing Cell Cycle Analysis on the Beckman Coulter Cytoflex S, or any similar flow cytometry analyzer in tube mode. Thi... | ["[Instructions] On the day of the experiment, once you are at the instrument with your negative control, PI positive control, and prepared experimental samples, set up your template in the CytoFLEX flow cytometer's CytExpert software for the appropriate filter set for the stain that you are using for Cell Cycle Analys... |
50,925 | Foulage test | 1 | dx.doi.org/10.17504/protocols.io.bvymn7u6 | https://www.protocols.io/view/foulage-test-bvymn7u6 | Tomohisa Yasuda, Toru Miwa | TITLE: Foulage test
AUTHORS: Tomohisa Yasuda, Toru Miwa
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The Foulage test is a test in which the stepping is recorded with the eyes open and closed by the ground contact method for 60 seconds in accordance with the metronome BPM120 by counting the sway... | ["1st: A step on the center of stabilometer (GP5000, Anima, Tokyo, Japan) with foot closed, lifting only the heels alternately with the metronome at a tempo of 120 BPM, for 60 seconds with eyes open.", "2nd: A step on the center of stabilometer (GP5000, Anima, Tokyo, Japan) with foot closed, lifting only the heels alte... |
36,708 | Protocol S-100B Determination in Melanoma | null | dx.doi.org/10.17504/protocols.io.bf4cjqsw | https://www.protocols.io/view/protocol-s-100b-determination-in-melanoma-bf4cjqsw | Samantha Damude, Schelto Kruijff, Harald J Hoekstra, Kevin P Wevers | TITLE: Protocol S-100B Determination in Melanoma
AUTHORS: Samantha Damude, Schelto Kruijff, Harald J Hoekstra, Kevin P Wevers
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the implementation of a dummytube system in AJCC stage III melanoma patients, to investigate whethe... | [] |
87,517 | Quantitative analyses of the ultrastructural features of dopaminergic axon terminals. Protocol #1: Tissue preparation for electron microscopy | 1 | dx.doi.org/10.17504/protocols.io.j8nlkw55wl5r/v2 | https://www.protocols.io/view/quantitative-analyses-of-the-ultrastructural-featu-czp5x5q6 | Natalie M Doig, Peter J Magill | TITLE: Quantitative analyses of the ultrastructural features of dopaminergic axon terminals. Protocol #1: Tissue preparation for electron microscopy
AUTHORS: Natalie M Doig, Peter J Magill
[DESCRIPTION]
The release of dopamine from axons is critical for normative brain function and behaviour. Impaired or otherwise in... | ["[Perfusion-Fixation] A successful perfusion is not only key to ensuring good ultrastructure of tissue when assessed in the electron microscope, but also is a requirement for successful sectioning, staining, and embedding. The following steps are written for an adult mouse but can be adapted for a rat (Lapper, S. R. &... |
92,286 | Cell culture, transfection, and imaging of K562 cells | 1 | dx.doi.org/10.17504/protocols.io.e6nvwdk4dlmk/v1 | https://www.protocols.io/view/cell-culture-transfection-and-imaging-of-k562-cell-c6c6zaze | Chase Amos, Pietro De Camilli | TITLE: Cell culture, transfection, and imaging of K562 cells
AUTHORS: Chase Amos, Pietro De Camilli
[DESCRIPTION]
This protocol details the general preparation of K562 cells for imaging.
[STEPS]
SECTION: Cell culture
1. Culture K562 cells at 37 °C and 5% CO2 in RPMI containing 10% FBS, 1 millimolar (mM) sodium pyruv... | ["[Cell culture] Culture K562 cells at 37 °C and 5% CO2 in RPMI containing 10% FBS, 1 millimolar (mM) sodium pyruvate, 100 U/mL penicillin, 100 μg/mL streptomycin, 2 millimolar (mM) L-glutamine, 1 x non-essential amino acids, (all from Gibco) and 2.5 μg/mL plasmocin (InvivoGen).", "[Transfection and imaging] For im... |
null | null | null | dx.doi.org/10.17504/protocols.io.cjmuk5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is the Sequential Double Digest Protocol with Standard Restriction Enzymes. If there is no buffer in which the two enzymes exhibit > 50% activity, this sequential digest can be performed.
[BEFORE_START]
NEB's online tools, <a href="https://www.neb.com/to... | [] |
89,265 | Mouse Stereotaxic Surgeries | 4 | dx.doi.org/10.17504/protocols.io.3byl4q5mzvo5/v1 | https://www.protocols.io/view/mouse-stereotaxic-surgeries-c3eryjd6 | Asta Zane, Nicole J Corbin-Stein, Gabrielle Childers, Jhodi Webster, Vickie Yang, Woong-Jai Won, Rajesh Gupta, Ashley Harms | TITLE: Mouse Stereotaxic Surgeries
AUTHORS: Asta Zane, Nicole J Corbin-Stein, Gabrielle Childers, Jhodi Webster, Vickie Yang, Woong-Jai Won, Rajesh Gupta, Ashley Harms
[DESCRIPTION]
This protocol allows for stereotaxic surgeries to administer unilateral or bilateral injections of small volumes of viral vectors or othe... | ["[SETUP] Sterilize all surfaces with disinfectant prior to setting up and lay out materials and utensils needed for surgery.", "[SETUP] Sterilize all utensils (including drill bit) in the glass bead sterilizer for 30 seconds. Clean the Hamilton syringe by rinsing with distilled water 10 times. Place all sterilized u... |
63,453 | Expression and purification protocol of human PI3KC3-C1 (±mCherry) | 4 | dx.doi.org/10.17504/protocols.io.8epv59mz4g1b/v1 | https://www.protocols.io/view/expression-and-purification-protocol-of-human-pi3k-b975r9q6 | Dorotea Fracchiolla | TITLE: Expression and purification protocol of human PI3KC3-C1 (±mCherry)
AUTHORS: Dorotea Fracchiolla
[DESCRIPTION]
This protocol describes the procedures for expression and purification of the active autophagy-specific human PI3KC3-C1 kinase complex.
[STEPS]
SECTION: Infection/expression/harvest
1. Infect 1 L cult... | ["[Infection/expression/harvest] Infect 1 L culture of Sf9 cells growing in Sf921 medium with antibiotics Penicillin/Streptomycin at 1-1.5 mil/ml cells/volume at 99-100% viability in log phase with Virus 1 (V1), volume according to viral titer. Baculovirus is obtained by transfection of Sf9 cells with policystronic con... |
28,684 | DNA Concentration Measurement (Protocol for Thermo Scientific NanoDrop™ 1000 Spectrophotometer) | null | dx.doi.org/10.17504/protocols.io.79khr4w | null | Alba Balletbó | TITLE: DNA Concentration Measurement (Protocol for Thermo Scientific NanoDrop™ 1000 Spectrophotometer)
AUTHORS: Alba Balletbó
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol adapted from the NanoDrop 1000 Spectrophotometer V3.8 User’s Manual. </div></div>
[STEPS]
?. Open the ND-1000 V3.8.1... | ["Open the ND-1000 V3.8.1 Program using the computer (the computer should be connected to the Nanodrop apparatus).", "Click on the corresponding application module (e.g., Nucleic acid to determine the concentration and purity of nucleic acid).", "Open the sampling arm and load a blank sample (e.g., TE Buffer, MQ Water,... |
6,246 | Methanol Precipitation of Proteins | null | dx.doi.org/10.17504/protocols.io.icecate | null | Tobias von der Haar | TITLE: Methanol Precipitation of Proteins
AUTHORS: Tobias von der Haar
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is adapted from </span><a href="https://www.ncbi.nlm.nih.gov/pubmed/6731838" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">We... | ["Select a suitable container for the precipitation. This protocol requires the addition of large amounts of additional liquid to the original sample, so the container needs to be sufficiently large as well as suitable for centrifugation. Maximal sample sizes for the following container volumes are (tube volume: maxima... |
77,323 | Frequentist, Bayesian Analysis and Complementary Statistical Tools for Geriatric and Rehabilitation Fields: Are Traditional Null-hypothesis Significance Testing Methods Sufficient? | 1 | null | https://www.protocols.io/view/frequentist-bayesian-analysis-and-complementary-st-cprjvm4n | Dahan da Cunha Nascimento | TITLE: Frequentist, Bayesian Analysis and Complementary Statistical Tools for Geriatric and Rehabilitation Fields: Are Traditional Null-hypothesis Significance Testing Methods Sufficient?
AUTHORS: Dahan da Cunha Nascimento
[DESCRIPTION]
Null hypothesis significant testing (NHST) is the dominant statistical approach in... | ["[Supplementary materials]"] |
64,588 | High-Efficiency Double-Stranded cDNA Synthesis from dsRNA Templates | 4 | dx.doi.org/10.17504/protocols.io.5qpvobdybl4o/v1 | https://www.protocols.io/view/high-efficiency-double-stranded-cdna-synthesis-fro-cbbksikw | Abdonaser Poursalavati | TITLE: High-Efficiency Double-Stranded cDNA Synthesis from dsRNA Templates
AUTHORS: Abdonaser Poursalavati
[DESCRIPTION]
High-Efficiency Double-Stranded cDNA Synthesis from dsRNA Templates
A cost-effective, custom protocol for preparing viral dsRNA for next-generation sequencing using SuperScript IV.
This protocol de... | ["[Before You Start] Thaw all reagents on ice. Briefly centrifuge all tubes before opening to collect contents at the bottom.\n\nKeep enzymes on ice or in a cold block at all times.\n\nWhen preparing master mixes, calculate the required volume for your number of samples (n) plus at least one extra reaction to account f... |
22,868 | Pig ICN recording | null | dx.doi.org/10.17504/protocols.io.2jugcnw | null | Jeffrey Ardell | TITLE: Pig ICN recording
AUTHORS: Jeffrey Ardell
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Yorshire pigs are anthesized for ICN/ neuromodulation recodings. Montior hemodynics</div><table border><tr style = "text-align:center;"><td> </td><td>A</td></tr><tr><td style = "text-align:center;">1</t... | ["Animal: Yorkshire PigSurgical Prep: Sedation Telazol (8mg/kg) Anasthesia isoflurane (1-2% inhalation),concomitant with intermittent boluses of fentanyl (1–3 μg/kg iv). Vascular Access: femoral artery (pressure), vein (fluids)Following completion of the surgery, anesthesia was changed to α-chloralose (50 mg... |
82,338 | Ezrin plasmids | 3 | dx.doi.org/10.17504/protocols.io.e6nvwjww7lmk/v1 | https://www.protocols.io/view/ezrin-plasmids-cunawvae | Shiyi Wang | TITLE: Ezrin plasmids
AUTHORS: Shiyi Wang
[DESCRIPTION]
How Ezrin plasmids were made.
[STEPS] | [] |
101,692 | Installing FIJI and SynBot (Windows Version) | 0 | dx.doi.org/10.17504/protocols.io.kqdg32qbpv25/v1 | https://www.protocols.io/view/installing-fiji-and-synbot-windows-version-dfi43kgw | Justin T Savage | TITLE: Installing FIJI and SynBot (Windows Version)
AUTHORS: Justin T Savage
[DESCRIPTION]
Video instructions for installing FIJI and SynBot and a simple SynBot run for Windows operating system.
[STEPS]
1.
SECTION: Install FIJI
2. 0:00 - 0:40 Install FIJI from https://fiji.sc .
SECTION: Install SynBot
3. 0:40 - ... | ["[Install FIJI] 0:00 - 0:40 Install FIJI from https://fiji.sc .", "[Install SynBot] 0:40 - 1:37 Download code from the SynBot GitHub repository https://github.com/Eroglu-Lab/Syn_Bot .", "[Install SynBot] 1:37 - 2:09 Move SynBot java plugins (JAR files) to the FIJI plugins folder. The ilastik4ij_Syn_Bot-1.8.2-SNAPSHO... |
80,723 | The impact of globalization on oral health in the Pacific | 1 | dx.doi.org/10.17504/protocols.io.n92ldpdbxl5b/v2 | https://www.protocols.io/view/the-impact-of-globalization-on-oral-health-in-the-cs3twgnn | Kenechi Elvis Obiorah | TITLE: The impact of globalization on oral health in the Pacific
AUTHORS: Kenechi Elvis Obiorah
[DESCRIPTION]
A literature and art review of oral health at the time of European contact and throughout written history and a survey on the oral health quality of native Pacific Islanders today to examine the effects of... | ["[Oral health quality and hygiene practices of native Pacific Islanders on Moorea, French Polynesia] Art pieces showing oral health quality (full set of teeth) will be compiled into a digital document. A literature review of journals and papers describing oral health quality from missionary/colonists/military accounts... |
null | null | null | dx.doi.org/10.17504/protocols.io.jdfci3n | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
90,746 | Generating supplement-free conditioned media for proteomic analysis following human ovarian tissue culture. | 1 | dx.doi.org/10.17504/protocols.io.x54v9pwwmg3e/v1 | https://www.protocols.io/view/generating-supplement-free-conditioned-media-for-p-c4u2ywye | hannah.anvari, francesca.e.duncan duncan | TITLE: Generating supplement-free conditioned media for proteomic analysis following human ovarian tissue culture.
AUTHORS: hannah.anvari, francesca.e.duncan duncan
[DESCRIPTION]
Purpose: This protocol is intended for use in generating supplement-free conditioned media for proteomic analysis. This protocol supplements... | ["[Wash steps to generate supplement-free conditioned media] Human ovarian tissue is processed and cultured according to an established protocol (dx.doi.org/10.17504/protocols.io.3byl4qbdjvo5/v2) upto Day 10.", "[Wash steps to generate supplement-free conditioned media] On day 10 of culture, two complete media changes ... |
75,331 | Sea Star Illness Treatment Protocol | 4 | dx.doi.org/10.17504/protocols.io.q26g7yxjkgwz/v1 | https://www.protocols.io/view/sea-star-illness-treatment-protocol-cmtbu6in | Tiffany Rudek, Evonne Mochon Collura | TITLE: Sea Star Illness Treatment Protocol
AUTHORS: Tiffany Rudek, Evonne Mochon Collura
[DESCRIPTION]
Sea Star Wasting Syndrome (SSWS) events of 2014 had a significant impact on the aquarium industry’s health management and medical treatment protocols for sick/injured sea stars. The subsequent prescription involved 3... | ["[Protocol] Step 1, Removal of external bacteria, fungus, ciliates (ex: Uronema):\nSeachem Reef Dip dosed at 10ml/gallon of sea water in the transport container for 10-15 minutes, without aeration (product may become foamy/sudsy under aeration). \nSome limb torsion is normal. However, signs of distress are reasons to ... |
93,712 | A proximity proteomics pipeline for subcellular proteome and protein interaction mapping | 4 | dx.doi.org/10.17504/protocols.io.yxmvm3jbbl3p/v1 | https://www.protocols.io/view/a-proximity-proteomics-pipeline-for-subcellular-pr-c7rqzm5w | Xiaofang Zhong, qiongyu.li, Ruth Hüttenhain | TITLE: A proximity proteomics pipeline for subcellular proteome and protein interaction mapping
AUTHORS: Xiaofang Zhong, qiongyu.li, Ruth Hüttenhain
[DESCRIPTION]
Proximity labeling (PL) coupled with mass spectrometry has emerged as a powerful technique to map proximal protein interactions in living cells. Large-scale... | ["[Cell culture] Seeding 3-4 million cells in a 10-cm dish or 500K cells in a 6-well plate on Day One. The cells will be ~70% confluent after 48 hours.", "[Cell lysis] Lyse cells in 1ml RIPA buffer supplement with protease inhibitors, antioxidants, and DTT", "[Automated enrichment protocol for biotinylated proteins in ... |
63,886 | https://www.facebook.com/DietToxilCapsule/ | 1 | dx.doi.org/10.17504/protocols.io.e6nvwk23wvmk/v1 | https://www.protocols.io/view/https-www-facebook-com-diettoxilcapsule-camnsc5e | roxyhima | TITLE: https://www.facebook.com/DietToxilCapsule/
AUTHORS: roxyhima
[DESCRIPTION]
Diaetoxil ist ein Nahrungsergänzungsmittel, das Ihrem Körper hilft, jede Diät zu bewältigen. Da die kombinierte Zufuhr von Wirkstoffen in den Bio-Kapseln extrem stark ist, fördert sie den Gewichtsverlust den ganzen Tag über.
Dies ist... | ["[DietToxil Capsule] DietToxil Austria ist ein Unternehmen, das Menschen hilft, die daran interessiert sind, ihr Fitnesswissen einzusetzen, um mehr Geld zu verdienen. Sie bieten einen Online-Blog und Videokurse an, die Hilfsmittel für Gesundheits- und Wellnessexperten bereitstellen. Sie haben diese Formel, DietToxil W... |
55,778 | VLP Extraction from Fecal Samples | 4 | dx.doi.org/10.17504/protocols.io.b2qaqdse | https://www.protocols.io/view/vlp-extraction-from-fecal-samples-b2qaqdse | Frej Larsen | TITLE: VLP Extraction from Fecal Samples
AUTHORS: Frej Larsen
[DESCRIPTION]
This protocol is for isolation of bacteriophages from fecal matter. It is based on the protocol used for the COPSAC10 cohort and was originally described by Ling Deng in doi:10.3390/v11070667. Extraction is performed using centrifugation and... | ["Thaw frozen sample in ice bucket", "Transfer up to 500 mg of sample to centrifuge tube and add SM buffer to reach a final volume of 5 mL. Place centrifuge tube back in ice box", "Homogenize samples by placing ice box on shaking board at", "Centrifuge samples at5000 rcf, 30 min, 4 °C", "Filter the supernatant through... |
51,723 | Preparation of a Single Cell Suspension from Bronchoalevolar Lavage | 1 | dx.doi.org/10.17504/protocols.io.bwrjpd4n | https://www.protocols.io/view/preparation-of-a-single-cell-suspension-from-bronc-bwrjpd4n | Steven B. Wells, Peter A. Szabo, Basak Ural | TITLE: Preparation of a Single Cell Suspension from Bronchoalevolar Lavage
AUTHORS: Steven B. Wells, Peter A. Szabo, Basak Ural
[DESCRIPTION]
This protocol describes a method for the isolation of the immune cells, structural and epithelial cells, and progenitors from lavage fluid collected from human lung. By providin... | ["[Preparing Mediums and Buffers] Create the following IMDM-FBS-PSQ Media in a 500 mL bottle of IMDM by using the table below: \n Component Volume (mL) Starting Conc. Final Conc.* IMDM 500 - - Penicillin-Streptomycin-Glutamine 5 100X 1X FBS 50 100% 10%", "[Preparing Mediums and Buffers] ... |
82,686 | Open field locomotion test | 4 | dx.doi.org/10.17504/protocols.io.e6nvwjxmdlmk/v1 | https://www.protocols.click/view/open-field-locomotion-test-cuy6wxze | Hong-Yuan Chu | TITLE: Open field locomotion test
AUTHORS: Hong-Yuan Chu
[DESCRIPTION]
This protocol describes open field locomotion test.
[STEPS]
SECTION: Set up
1. Place the open field boxes right below the camera attached to the ceiling.
SECTION: Set up
2. Connect the camera to the computer via USB.
SECTION: Set up
3. Clean the b... | ["[Set up] Place the open field boxes right below the camera attached to the ceiling.", "[Set up] Connect the camera to the computer via USB.", "[Set up] Clean the boxes with 70% ethanol.", "[Set up] Open the ANY-maze software on computer.", "[Set up] To create a new protocol, select “New Experiment”.", "[Set up] Add a... |
82,627 | DToL Taxon-specific Standard Operating Procedures for Marine Metazoa | 2 | dx.doi.org/10.17504/protocols.io.n92ldpdxnl5b/v2 | https://www.protocols.click/view/dtol-taxon-specific-standard-operating-procedures-cuxbwxin | Kesella Scott-Somme, John Bishop, Chris Fletcher, Patrick Adkins, Nova Mieszkowska , Rebekka Uhl, Freja Azzopardi, Dominic Phillips, Inez Januszczak | TITLE: DToL Taxon-specific Standard Operating Procedures for Marine Metazoa
AUTHORS: Kesella Scott-Somme, John Bishop, Chris Fletcher, Patrick Adkins, Nova Mieszkowska , Rebekka Uhl, Freja Azzopardi, Dominic Phillips, Inez Januszczak
[DESCRIPTION]
These Standard Operating Procedures (SOPs) contain guidance on how to p... | [] |
89,426 | Immunohistochemistry on free-floating cryosections | 4 | dx.doi.org/10.17504/protocols.io.rm7vzx7x8gx1/v1 | https://www.protocols.io/view/immunohistochemistry-on-free-floating-cryosections-c3jsykne | Nuriapenuelas | TITLE: Immunohistochemistry on free-floating cryosections
AUTHORS: Nuriapenuelas
[DESCRIPTION]
Immunochemistry protocol on rodent brain cryosections
[STEPS]
SECTION: 1. Section selection
1. Collect the cryosections needed for a caudo-rostral representation of each brain region (every fourth section or every sixth se... | ["[1. Section selection] Collect the cryosections needed for a caudo-rostral representation of each brain region (every fourth section or every sixth section dependeing on the section thinknes, brain region and animal species) into 24-well-plate (3-4 sections per well).", "[2. Blocking endogenous peroxidase] Incubate s... |
79,817 | Gene Expression | 1 | dx.doi.org/10.17504/protocols.io.3byl4jyr8lo5/v1 | https://www.protocols.click/view/gene-expression-cr7hv9j6 | michela.deleidi, Bianca Marchetti, Federico Bertoli, Carmela Giachino | TITLE: Gene Expression
AUTHORS: michela.deleidi, Bianca Marchetti, Federico Bertoli, Carmela Giachino
[DESCRIPTION]
RT-PCR is a technique to quantify gene expression in samples.
[STEPS]
SECTION: Gene Expression
1. Perform gene expression on tissue samples of the ventral midbrain (containing the substantia nigra pars ... | ["[Gene Expression] Perform gene expression on tissue samples of the ventral midbrain (containing the substantia nigra pars compacta, SNpc).", "[RNA Extraction] At due time points, homogenize tissue samples in 1 mL of QIAzol Lysis Reagent (Qiagen, #79306) using a rotor-stator homogenizer.", "[RNA Extraction] Isolate th... |
null | null | null | dx.doi.org/10.17504/protocols.io.ezxbf7n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a collection of BioLegend protocols for True-Nuclear™ Transcription Factor Staining Protocols. Please make sure to refer to the correct protocol, depending on whether you are using the 96-Well, U-Bottom Plate or 5 mL tubes.</p>
[STEPS]
?. | [] |
49,309 | Factors associated with admission to the intensive care unit and mortality in patients with COVID-19, Colombia | 1 | dx.doi.org/10.17504/protocols.io.bud5ns86 | https://www.protocols.io/view/factors-associated-with-admission-to-the-intensive-bud5ns86 | Jorge Enrique Machado-Alba, Luis Fernando Valladales Restrepo, Manuel E Machado Duque, Andres Gaviria Mendoza | TITLE: Factors associated with admission to the intensive care unit and mortality in patients with COVID-19, Colombia
AUTHORS: Jorge Enrique Machado-Alba, Luis Fernando Valladales Restrepo, Manuel E Machado Duque, Andres Gaviria Mendoza
[DESCRIPTION]
Introduction:Coronavirus disease 2019 (COVID-19) has affected millio... | [] |
94,941 | Populating NCBI template for submissions using BioNumerics | 1 | dx.doi.org/10.17504/protocols.io.3byl4qn4ovo5/v1 | https://www.protocols.io/view/populating-ncbi-template-for-submissions-using-bio-c8x5zxq6 | Ruth Timme, Maria Balkey, Julie Haendiges, Brian Sauders, Tina.Pfefer | TITLE: Populating NCBI template for submissions using BioNumerics
AUTHORS: Ruth Timme, Maria Balkey, Julie Haendiges, Brian Sauders, Tina.Pfefer
[DESCRIPTION]
PURPOSE: to define the standard operating procedure for collecting isolate metadata using BioNumerics for submission of food/environmental isolates to NCBI.
... | ["Metadata SampleSheet preparation \n\nBefore uploading your sequencing run or linking NCBI sequencing records at the BioNumerics platform make sure to fill out the metadata spreadsheet form. \n\nPlease download the template and guidelines included in the file \n \n\nCreate the fields NCBI_bioproject, Attribute_packa... |
44,044 | Qiagen- AllPrep DNA/RNA/protein Mini Kit for tissue | 4 | dx.doi.org/10.17504/protocols.io.bn9kmh4w | https://www.protocols.io/view/qiagen-allprep-dna-rna-protein-mini-kit-for-tissue-bn9kmh4w | Heather Robeson, Jing Jin, Mohammed S. Orloff | TITLE: Qiagen- AllPrep DNA/RNA/protein Mini Kit for tissue
AUTHORS: Heather Robeson, Jing Jin, Mohammed S. Orloff
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The protocol is based on Qiagen-AllPrep DNA/RNA/Protein Mini kit for tissue </div></div>
[STEPS]
?. [Sample disruption and homogenization... | ["[Sample disruption and homogenization]\nHomogenize the lysate in Buffer RLTDisruption using a mortar and pestle. Homogenization using a QIAshredder homogenizer.", "[Sample disruption and homogenization]\nCentrifuge the lysate for 3 min at full speed. Remove the supernatant by pipetting and transfer the homogenized ly... |
null | null | null | dx.doi.org/10.17504/protocols.io.fjabkie | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Provides a short introduction to phylogenetics and how to build a phylogenetic tree from concatenated ribosomal marker proteins. </p>
<p> </p>
<p>Open this protocol inside the virtual machine (details in 'Start Instructions') for easy copy, paste of commands into the command ... | [] |
68,254 | Salmonella detection with Kingfisher Flex/Apex extraction and 7500-FAST enrichment PCR | 1 | dx.doi.org/10.17504/protocols.io.261genyxyg47/v1 | https://www.protocols.io/view/salmonella-detection-with-kingfisher-flex-apex-ext-cev6te9e | Laura Goodman, Rebecca Franklin-Guild, Renee Anerson | TITLE: Salmonella detection with Kingfisher Flex/Apex 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 the MagMAX™ CORE Nucleic Acid Purification Kit and the M... | ["[DNA Purification] Prepare plates for Robot", "[DNA Purification] Prepare Wash Plate 1 by adding 500 μL of MagMAX™ CORE Wash Solution 1 to each well for each sample to be extracted plus controls.", "[DNA Purification] Prepare Wash Plate 2 by adding 500 μL of MagMAX™ CORE Wash Solution 2 to each well for each sample t... |
76,111 | Resource 5: rEV Scatter Detector Setting Incrementation | 4 | dx.doi.org/10.17504/protocols.io.n92ldp298l5b/v1 | https://www.protocols.io/view/resource-5-rev-scatter-detector-setting-incrementa-cnjpvcmn | Sean M Cook, Vera A. Tang, Joanne Lannigan, Jennifer Jones, Joshua A Welsh | TITLE: Resource 5: rEV Scatter Detector Setting Incrementation
AUTHORS: Sean M Cook, Vera A. Tang, Joanne Lannigan, Jennifer Jones, Joshua A Welsh
[DESCRIPTION]
Flow cytometry (FCM) is a common extracellular particles (EPs), including viruses and extracellular vesicles (EVs), characterization method. Frameworks such a... | ["[Sample Preprepation] Briefly centrifuge rEVs at 100 x g, 5 min, 4 °C before opening", "[Sample Preprepation] Add 100 µL of 4 °C deionized water to rEVs vial. Pipette up and down to mix well.", "[Sample Preprepation] Create 5 mL of a 1:2000 dilution of rEVs by pipetting 1 µL rEVs into 1999 µL DPBS in a low-binding ... |
109,060 | Measuring root system stiffness in maize or sorghum | 0 | dx.doi.org/10.17504/protocols.io.yxmvmer9ng3p/v1 | https://www.protocols.io/view/measuring-root-system-stiffness-in-maize-or-sorghu-dnrc5d2w | Ashley N. Hostetler, Jonathan W. Reneau, Erin E. Sparks | TITLE: Measuring root system stiffness in maize or sorghum
AUTHORS: Ashley N. Hostetler, Jonathan W. Reneau, Erin E. Sparks
[DESCRIPTION]
Plant mechanical failure has been evaluated with proxy measures that quantify root failure strength. However, understanding the force-displacement rate to reach that failure strengt... | ["[Before Operating the SMURF:] Open the Device Controller iPad application (Video 1).", "[Before Operating the SMURF:] Hold the SMURF horizontally and power on.", "[Before Operating the SMURF:] Click button: “Fully Retract Foot”. This will re-home the device (Video 1).", "[Before Operating the SMURF:] Click button: “S... |
68,794 | Wastewater QC workflow in GalaxyTrakr (SSQuAWK4) | 1 | dx.doi.org/10.17504/protocols.io.kxygxzk5dv8j/v8 | https://www.protocols.io/view/wastewater-qc-workflow-in-galaxytrakr-ssquawk4-cfe2tjge | Jasmine Amirzadegan, Tunc Kayikcioglu, hugh.rand, Ruth Timme, Maria Balkey | TITLE: Wastewater QC workflow in GalaxyTrakr (SSQuAWK4)
AUTHORS: Jasmine Amirzadegan, Tunc Kayikcioglu, hugh.rand, Ruth Timme, Maria Balkey
[DESCRIPTION]
PURPOSE:
Step-by-step instructions for checking sequence quality for SARS-CoV-2 wastewater samples using SSQuAWK: SARS - CoV - 2 Sequence Quality Assurance Workf... | ["[Account set up] Create a GalaxyTrakr account here: https://account.galaxytrakr.org/Account/Register", "[Account set up] Log into your GalaxyTrakr account: https://galaxytrakr.org", "[Create a new history] Create a new history. \n\nWe recommend creating a new history for each new MiSeq sequence set with details and d... |
60,678 | Single cell RNA sequencing of retrogradely labeled mouse stellate ganglion neuron | 2 | dx.doi.org/10.17504/protocols.io.261generdg47/v1 | https://www.protocols.io/view/single-cell-rna-sequencing-of-retrogradely-labeled-b7herj3e | Seoeun Lee, Daniele Neri, Lori Zeltser | TITLE: Single cell RNA sequencing of retrogradely labeled mouse stellate ganglion neuron
AUTHORS: Seoeun Lee, Daniele Neri, Lori Zeltser
[DESCRIPTION]
A collection of protocols to sequence and analyze single neurons from the stellate ganglia of mice after injection of Cholera Toxin B (CTB) in the interscapular brow... | [] |
98,091 | CODEX Antibody Conjugation Protocol | 0 | dx.doi.org/10.17504/protocols.io.4r3l2q8q4l1y/v1 | https://www.protocols.io/view/codex-antibody-conjugation-protocol-db2j2qcn | Bei Wei, Joanna Bi | TITLE: CODEX Antibody Conjugation Protocol
AUTHORS: Bei Wei, Joanna Bi
[DESCRIPTION]
Used by the Snyder Lab at Stanford University for CODEX for human intestine.
[STEPS]
1. Block non-specific absorption of antibody onto 50k MWCO spin column with PBS-tween (0.2% tween solution) by adding 500 uL into the top of each c... | ["Block non-specific absorption of antibody onto 50k MWCO spin column with PBS-tween (0.2% tween solution) by adding 500 uL into the top of each column (rinse all areas of filter) and spinning down at 12,000g for 2 minutes", "Remove all liquid from the top of the column and discard flow-through. Label each column and f... |
null | null | null | dx.doi.org/10.17504/protocols.io.qx6dxre | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is kit-free and can be used to simultanously isolate high quality genomic DNA of <em>Symbiodinium</em> and Aiptasia from symbiotic anemones which can be used e.g. as PCR template for genotyping.</p>
<p> </p>
<p> It is based on the method described in Coffroth et... | [] |
96,433 | Sequencing fungal metabarcode with PCR primer based barcoding and Nanopore | 0 | null | https://www.protocols.io/view/sequencing-fungal-metabarcode-with-pcr-primer-base-daer2bd6 | Abigail Graetz, Ashley Jones, Benjamin Schwessinger | TITLE: Sequencing fungal metabarcode with PCR primer based barcoding and Nanopore
AUTHORS: Abigail Graetz, Ashley Jones, Benjamin Schwessinger
[DESCRIPTION]
This protocols is part of the ANU Biosecurity mini-research project #1 "Plant Pathogen Diagnostics: Visuals, subcultures, and genomics".
You will be provided f... | ["[Preparation of input DNA] This first step has been performed by a demonstrator using DNA from the groups we selected in week 5. We selected three research groups so that we have three replicates per treatment group. This gives us 15 PCR reactions plus 1 negative control. We skip the extraction control for this pract... |
80,459 | Assay for determination of functional concentration of Tn5 transposase | 4 | null | https://www.protocols.io/view/assay-for-determination-of-functional-concentratio-cstjwekn | Adrian Mcnairn | TITLE: Assay for determination of functional concentration of Tn5 transposase
AUTHORS: Adrian Mcnairn
[DESCRIPTION]
Tn5 is used by multiple labs world-wide for its ability to introduce DNA oligos and barcode sequences into libraries and for genomic assays. In many instances, labs produce their own Tn5 enzyme in-ho... | ["[Transposome preparation and assembly] Prepare ME A/Rev or ME-B/rev oligos by annealing equal concentrations of primers. \nWe typically target 40uM stocks.\n Example: 40uL 100uM Tn5-ME-A +40uL 100uM Tn5-REV +20uL nuclease-free water or 0.1x TE (can be scaled as needed)\nThermocycler program: 95°C for 2min, slow cool ... |
94,792 | DNA Quality Control by Agarose Gel Electrophoresis | 4 | dx.doi.org/10.17504/protocols.io.kqdg3xzb1g25/v1 | https://www.protocols.io/view/dna-quality-control-by-agarose-gel-electrophoresis-c8tgzwjw | Benjamin Schwessinger | TITLE: DNA Quality Control by Agarose Gel Electrophoresis
AUTHORS: Benjamin Schwessinger
[DESCRIPTION]
This protocols is part of the ANU Biosecurity mini-research project #1 "Plant Pathogen Diagnostics: Visuals, subcultures, and genomics".
You will be provided four pots of 3-4 week old wheat plants that have been i... | ["[Week 5: DNA agarose gel electrophoresis] You will load all DNA and PCR samples into one lane of a 1% agarose gel each. You will share your gel with another research group as each gel has two rows.", "[Week 5: DNA agarose gel electrophoresis] You will receive your ITS PCR strip tubes of 8 with PCR reaction from last ... |
58,721 | Human Placenta Tissue Collection and Preservation Methods - UCSD Female Reproductive TMC | 1 | dx.doi.org/10.17504/protocols.io.b5j9q4r6 | https://www.protocols.io/view/human-placenta-tissue-collection-and-preservation-b5j9q4r6 | Valentina Stanley, Scott Lindsay-Hewett, Louise Laurent, Mana Parast | TITLE: Human Placenta Tissue Collection and Preservation Methods - UCSD Female Reproductive TMC
AUTHORS: Valentina Stanley, Scott Lindsay-Hewett, Louise Laurent, Mana Parast
[DESCRIPTION]
Human Placenta Tissue collection and storage protocol for HuBMAP's UCSD Female Reproductive TMC.
[STEPS]
None. d. Lower ... | ["d. Lower the mold slowly into liquid nitrogen until the whole block freezes, then store in -80C freezer", "[Preparation] Collect placenta from delivery room within 1 hour of delivery.", "[Preparation] Place placenta into bucket and photograph prior to sampling.", "[Preparation] Select 2 sites (A and B) from which... |
71,768 | DIMPLE library generation and assembly protocol v1.1 | 4 | dx.doi.org/10.17504/protocols.io.rm7vzy7k8lx1/v2 | https://www.protocols.io/view/dimple-library-generation-and-assembly-protocol-v1-cibyuapw | Christian Macdonald, David Nedrud, Patrick Rockefeller Grimes, Donovan Trinidad, James Fraser, Willow Coyote-Maestas | TITLE: DIMPLE library generation and assembly protocol v1.1
AUTHORS: Christian Macdonald, David Nedrud, Patrick Rockefeller Grimes, Donovan Trinidad, James Fraser, Willow Coyote-Maestas
[DESCRIPTION]
This is a protocol for generating and QCing mutagenic libraries using the DIMPLE protocol. This version is updated to i... | ["[Preparation] Use DIMPLE to generate mutagenic oligos and primers.", "[Preparation] Important notes: DIMPLE breaks a gene up into sub-library fragments and generates mutagenic insert oligo pools, where each oligo contains barcodes, Type IIS restriction cutsites, and a sub-region of the gene. Be sure to review your li... |
25,026 | Preparing Chemically Competent E coli for Transformation | null | dx.doi.org/10.17504/protocols.io.4pagvie | null | Stephen Floor | TITLE: Preparing Chemically Competent E coli for Transformation
AUTHORS: Stephen Floor
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol prepares chemically competent E coli for plasmid transformation. The competency is high enough for routine cloning but working with libraries may requi... | ["[Starter Culture Growth]\nStreak cell-stock on an LB agar plate, and grow o/n at .\n37 °C", "[Starter Culture Growth]\nInoculate a single colony from the plate into a LB liquid culture and grow o/n at with shaking.\n5 ml\n37 °C", "[Starter Culture Growth]\nTypically prepare TFB1/TFB2 solutions now, and store at o/... |
19,159 | Environmental DNA (eDNA) 12S metabarcoding Illumina MiSeq NGS (2-step) PCR Protocol | 1 | null | https://www.protocols.io/view/environmental-dna-edna-12s-metabarcoding-illumina-wxxffpn | Kathleen Pitz, Kristine Walz | TITLE: Environmental DNA (eDNA) 12S metabarcoding Illumina MiSeq NGS (2-step) PCR Protocol
AUTHORS: Kathleen Pitz, Kristine Walz
[DESCRIPTION]
This protocol is aimed at amplifying the 12S rRNA gene in eukaryotes. The primers (Mifish_U) utilized in this protocol are based on the primers utilized in Miya et al., 2015. T... | ["[PCR] PCR reactions for 12S were run with Fluidigm two-step amplification protocol for each sample.", "[Primary PCR] Primary PCR amplifications were carried out in triplicate 25-μl reactions using: \n1 μl DNA extract\n12.5 μl AmpliTaq Gold Fast PCR master mix (Applied Biosystems)\n1 μl each of forward and reverse pri... |
100,761 | Nuclei Isolation for HMBA FACS | 4 | dx.doi.org/10.17504/protocols.io.kxygx35ywg8j/v3 | https://www.protocols.io/view/nuclei-isolation-for-hmba-facs-demz3c76 | Lakme Caceres | TITLE: Nuclei Isolation for HMBA FACS
AUTHORS: Lakme Caceres
[DESCRIPTION]
This protocol is for purifying nuclei for downstream 10X sequencing.
[GUIDELINES]
Keep tissue/nuclei on ice as much as possible.
[STEPS]
SECTION: Prepare Fresh Solutions
4. Make 3 mL Homogenization Buffer by adding 2.892 mL Nuclear Isolation ... | ["[Prepare Fresh Solutions] Make 3 mL Homogenization Buffer by adding 2.892 mL Nuclear Isolation Media to a 5 mL eppendorf tube. Then add 60 uL protease inhibitor, 30 μL 10% Triton X-100, 15 uL RNase inhibitor, and 3 μL 100 mM DTT.", "[Prepare Stock Solutions] Make 50 mL Nuclear Isolation Media by filling a 50 mL steri... |
78,942 | Tetiaroa Sugar Water Crazy Ant Sampling | 1 | null | https://www.protocols.io/view/tetiaroa-sugar-water-crazy-ant-sampling-crb6v2re | Laura Barragan, clairewiegand, ame | TITLE: Tetiaroa Sugar Water Crazy Ant Sampling
AUTHORS: Laura Barragan, clairewiegand, ame
[DESCRIPTION]
Sugar water vial protocol for crazy ant sampling.
[BEFORE_START]
Wear long pants and long sleeve top.
[STEPS]
1. Place vial at designated point on Gaia and label the transect number on the vial
2. Take photo to ... | ["Place vial at designated point on Gaia and label the transect number on the vial", "Take photo to capture surroundings", "After 90 minutes, retrieve vials in the order you placed them", "Count ants in vial; if there are too many ants in the vial, freeze the vial and recount later", "Record the number of ants in vial ... |
null | null | null | dx.doi.org/10.17504/protocols.io.r27d8hn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes the methodology to determine the experimental values of the 12 SeDeM parameters.</p>
[GUIDELINES]
<p>Bulk density (Da): The method is described in Section 2.9.34 of Eur. Ph. (Ph Eur, 2011) Tapped density (Dc): The method is described in Section 2.9.34... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.d5288d | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This tutorial covers a full QIIME workflow using Illumina sequencing data and was adapted from a <a href="http://nbviewer.ipython.org/github/biocore/qiime/blob/1.9.1/examples/ipynb/illumina_overview_tutorial.ipynb" target="_blank">tutorial</a> on the QIIME website.. This tutoria... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.h8xb9xn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
73,401 | GC/MS Method for the Detection of Terbufos, Diazinon and Parathion in Blood | 6 | dx.doi.org/10.17504/protocols.io.j8nlkw83dl5r/v1 | https://www.protocols.io/view/gc-ms-method-for-the-detection-of-terbufos-diazino-cjwzupf6 | Christina Wilson-Frank, Michael Ewbank | TITLE: GC/MS Method for the Detection of Terbufos, Diazinon and Parathion in Blood
AUTHORS: Christina Wilson-Frank, Michael Ewbank
[DESCRIPTION]
Scope
This is a multi-residue method for the detection of the organophosphate pesticides, terbufos, diazinon and parathion in blood by gas chromatography and mass spectrometr... | ["[Extraction Solution and Standard Diluent Preparation] Preparation of acetonitrile:toluene (3:1) solution:", "[Extraction Solution and Standard Diluent Preparation] Transfer 600 mL of acetonitrile to 1L graduated cylinder.", "[Extraction Solution and Standard Diluent Preparation] Add 200 mL of toluene to the 1L gradu... |
29,300 | Plasmid: NK588 (pAct-nanoluc) | null | dx.doi.org/10.17504/protocols.io.8uuhwww | null | David Booth, Nicole King | TITLE: Plasmid: NK588 (pAct-nanoluc)
AUTHORS: David Booth, Nicole King
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The attached file is the full sequence for a plasmid that uses gene regulatory elements from </span><span style = "font-style:italic;">S. rosetta </span><span>to drive the exp... | [] |
20,769 | UC Davis - Dynamic contrast enhanced magnetic resonance imaging | null | dx.doi.org/10.17504/protocols.io.yh9ft96 | null | John Rutledge | TITLE: UC Davis - Dynamic contrast enhanced magnetic resonance imaging
AUTHORS: John Rutledge
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) is used to a... | ["Animal Preparation: 1. Prior to DCE-MRI, the animal should have been through the Femoral Vein Cannulation protocol.", "Setting Up the Microgradients and Animal stage: 1. Transport the mice to the NMR facility 2. Turn off main power source to the 7T and the water circulator. 3. Disconnect the power cables and water ci... |
25,503 | Total RNA Protocol (extraction, quantification and Illumina library preparation) | null | dx.doi.org/10.17504/protocols.io.457gy9n | null | Antonio Mondini, Morten Dencker Schcostag, Lea Ellegard-Jensen, Toke Bang-Andreasen, Muhammad Zohaib Anwar, Cristina Purcarea, Carsten Suhr Jacobsen | TITLE: Total RNA Protocol (extraction, quantification and Illumina library preparation)
AUTHORS: Antonio Mondini, Morten Dencker Schcostag, Lea Ellegard-Jensen, Toke Bang-Andreasen, Muhammad Zohaib Anwar, Cristina Purcarea, Carsten Suhr Jacobsen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div c... | ["[Water samples filtration]\nOnce completed the filtration, transfer the filters in the 15 mL tubes with beads (provided in the RNeasy®kit).\nTransfer the filters carefully folding it to fit in the 15mL tubes using two forceps and letting the surface with visible filtered particles inward the tube. Push carefully down... |
103,082 | Immunofluorescence and confocal microscopy | 0 | dx.doi.org/10.17504/protocols.io.6qpvr8p1olmk/v1 | https://www.protocols.io/view/immunofluorescence-and-confocal-microscopy-dgwi3xce | Elias Adriaenssens | TITLE: Immunofluorescence and confocal microscopy
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol details the process of immunofluorescence and confocal microscopy.
[STEPS]
SECTION: Steps
1. Seed the cells on glass coverslips (12 mm #1.5) at a concentration of 100.000 cells/well, and after treatment with Rapa... | ["[Steps] Seed the cells on glass coverslips (12 mm #1.5) at a concentration of 100.000 cells/well, and after treatment with Rapalog for the indicated time, fix in 4% paraformaldehyde (28906, Thermo Fisher Scientific) for 10 min at Room temperature.", "[Steps] After washing with PBS, permeabilize the cells with 0.1% (v... |
41,244 | ThEA Direct Swab | 4 | dx.doi.org/10.17504/protocols.io.bkh4kt8w | https://www.protocols.io/view/thea-direct-swab-bkh4kt8w | Miriam Schwartz, Nikhil Ponon, Caleb Stewart, Luke Saban, Jody Ranck | TITLE: ThEA Direct Swab
AUTHORS: Miriam Schwartz, Nikhil Ponon, Caleb Stewart, Luke Saban, Jody Ranck
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">RAM Group has developed ThEA™ - an optical, reagent free / chemical free detection system for rapid diagnosis for SARS-Cov-2. The system consists of ... | ["[Calibration]\nTake a measurement of air and save to DB, i.e. no sample in beam optical path (once per hour) – Air spectrum.", "[Calibration]\nScan the barcode and take a measurement of the calibration cartridge provided - Substrate spectrum, once per hour just after Air measurement in previous step and save to DB.",... |
67,101 | Real-time quantitative polymerase chain reaction (RT-qPCR) | 4 | dx.doi.org/10.17504/protocols.io.j8nlkkqmxl5r/v1 | https://www.protocols.io/view/real-time-quantitative-polymerase-chain-reaction-r-cdr5s586 | An.Huang, Qiaowa Gong | TITLE: Real-time quantitative polymerase chain reaction (RT-qPCR)
AUTHORS: An.Huang, Qiaowa Gong
[DESCRIPTION]
Real-time quantitative polymerase chain reaction (RT-qPCR) helps determine the expression level of a certain gene by amplifying DNA according to the target mRNA template. This protocol describes the procedure... | ["Thaw the GoTaq® Master Mix and Nuclease-Free Water. Thaw the cDNA templates and primer.", "Determine the number of reactions to be set up, including negative control reactions. Add 1 or 2 reactions to this number to compensate for pipetting error.", "Prepare the reaction mix (minus DNA template) by combining the GoTa... |
67,447 | https://www.facebook.com/ViaKetoAppleGummiesinCA/ | 1 | dx.doi.org/10.17504/protocols.io.eq2lynk3wvx9/v1 | https://www.protocols.io/view/https-www-facebook-com-viaketoapplegummiesinca-cd4xs8xn | roxyompo | TITLE: https://www.facebook.com/ViaKetoAppleGummiesinCA/
AUTHORS: roxyompo
[DESCRIPTION]
Viaketo Gummies Canada : A significant number of people worldwide are struggling with obesity, making it a widespread issue. When a person is overweight, it is usually difficult to exercise every day to shed excess pounds. Peopl... | ["[Via Keto Apple Gummies Canada] Excess glucose is stored as fat after digestion. Experts say you can only lose weight if your body burns fat. In ketosis, your body burns fat for heat and energy. This is the safest and most effective technique to lose fat permanently. Getting into ketosis isn’t easy. The ketogenic die... |
42,440 | Culture and purification of Plasmodium berghei ookinetes | 2 | dx.doi.org/10.17504/protocols.io.bmpgk5jw | https://www.protocols.io/view/culture-and-purification-of-plasmodium-berghei-ook-bmpgk5jw | Benito Recio Totoro | TITLE: Culture and purification of Plasmodium berghei ookinetes
AUTHORS: Benito Recio Totoro
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>A collection of protocols we use routinely in the lab to produce and purify ookinetes of </span><span style = "font-style:italic;">Plasmodium berghei</sp... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.tqeemte | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Electrophysiology by MEA. Electrical recording and stimulation of the cultures using MEA set-up (by Multichannel Systems).
[STEPS]
SECTION: MEA set-up preparation
?.
SECTION: MEA software preparation
?.
SECTION: MEA electrical stimulation set-up
?.
SECTION: MEA electrical st... | ["[MEA set-up preparation] For extracellular voltage recording and stimulation of cortical cultures use MEA (60MEA200/30iR-Ti-gr and 60MEA500/30iR-Ti-pr; Multichannel Systems), utilizing low noise pre-amplifier board (MEA- 1060-BC, amplifier, gain x1100; Multichannel Systems)；\nFor recording simultaneously with calciu... |
null | null | null | dx.doi.org/10.17504/protocols.io.cp7vrm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Radioactive Labeling with T4 Polynucleotide Kinase
[STEPS]
?.
?.
?. | [] |
44,340 | NEBNext Ultra End Prep Mixture E7442 | 1 | dx.doi.org/10.17504/protocols.io.bpiumkew | https://www.protocols.io/view/nebnext-ultra-end-prep-mixture-e7442-bpiumkew | Isabel Gautreau | TITLE: NEBNext Ultra End Prep Mixture E7442
AUTHORS: Isabel Gautreau
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [NEBNext End Prep]
Starting Material: 5 ng-1 μg fragmented DNAMix the following comonents in a sterile, nuclease-free tube: AB1ComponentVolume2End Prep Enzyme Mix3 µl3End Repair Reaction Bu... | ["[NEBNext End Prep]\nStarting Material: 5 ng-1 μg fragmented DNAMix the following comonents in a sterile, nuclease-free tube: AB1ComponentVolume2End Prep Enzyme Mix3 µl3End Repair Reaction Buffer (10X)6.5 µl4Fragmented DNA55.5 µl5Total Volume65 µl\nAB1ComponentVolume2End Prep Enzyme Mix3 µl3End Repair Reaction Buffer... |
52,365 | Inoculating a Liquid Bacterial Culture | 1 | dx.doi.org/10.17504/protocols.io.bxdmpi46 | https://www.protocols.io/view/inoculating-a-liquid-bacterial-culture-bxdmpi46 | Addgene The Nonprofit Plasmid Repository, Joe Kaczmarski | TITLE: Inoculating a Liquid Bacterial Culture
AUTHORS: Addgene The Nonprofit Plasmid Repository, Joe Kaczmarski
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is for inoculating a liquid bacterial culture. To see the full abstract and additional resources, visit </span><a href="... | ["If you haven't already, prepare autoclaved liquid LB. For example, to make of LB, weigh out the following into a glass bottle: NaCl Tryptone Yeast Extractadd dH2O to Loosely close the cap on the bottle (do NOT close all the way or the bottle may explode!) and then loosely cover the entire top of the bottle with alu... |
91,591 | ATAC-seq, primary human T cells overexpressing BATF3 | 4 | null | https://www.protocols.io/view/atac-seq-primary-human-t-cells-overexpressing-batf-c5pfy5jn | Andrea R Daniel | TITLE: ATAC-seq, primary human T cells overexpressing BATF3
AUTHORS: Andrea R Daniel
[DESCRIPTION]
This protocol describes methods for performing ATACseq on human HER2 targeted CAR T cells overexpressing BATF3 or GFP. Chromatin remodeling was assessed in acutely and chronically stimulated cells.
[STEPS]
SECTION: Tra... | ["[Transfections for high-titer lentiviral production] Plate 1.2 x 106 or 7 x 106 HEK293T cells in a 6 well plate or 10 cm dish in the afternoon with 2 mL or 12 mL of complete opti-MEM (Opti-MEM‱ I Reduced Serum Medium supplemented with 1x Glutamax, 5% FBS, 1 mM Sodium Pyruvate, and 1x MEM Non-Essential Amino Acids)."... |
95,567 | Sucrose Preference | 0 | dx.doi.org/10.17504/protocols.io.4r3l22wwxl1y/v1 | https://www.protocols.io/view/sucrose-preference-c9jpz4mn | daniel.dautan daniel, Per Svenningsson | TITLE: Sucrose Preference
AUTHORS: daniel.dautan daniel, Per Svenningsson
[DESCRIPTION]
Test for anhedonia-like behavior in mice.
[STEPS]
1. Individually house mice.
2. Place two bottles in random positions in each cage:
1) one bottle containing regular water
2) the second containing 1% sucrose diluted in water
3. Re... | ["Individually house mice.", "Place two bottles in random positions in each cage:\n1) one bottle containing regular water\n2) the second containing 1% sucrose diluted in water", "Record the weight of the each bottle before and after 24 hours.", "Sucrose preference index is defined as the total sucrose consumption over ... |
47,470 | LAMP/RT-LAMP COVID positive control | 4 | dx.doi.org/10.17504/protocols.io.bsknncve | https://www.protocols.io/view/lamp-rt-lamp-covid-positive-control-bsknncve | Anibal Arce Medina, Isaac Núñez, Tamara Matute, Fernan Federici | TITLE: LAMP/RT-LAMP COVID positive control
AUTHORS: Anibal Arce Medina, Isaac Núñez, Tamara Matute, Fernan Federici
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol explains how to prepare dsDNA and ssRNA target positive control for LAMP and RT-LAMP reactions. Particularly it describes ... | ["[N gene Amplification]\nAmplify SARS-Cov-2 Nucleocapsid (N) gene fragment dsDNA from ReClone or IDT positive control plasmid with the ultramers indicated in Table 1.The amplification can be carried out using any standard PCR reaction formulation (e.g. Phusion DNA polymerase with HF buffer), adding to of the plasmid... |
58,423 | High Molecular Weight DNA extraction from tunicates | 4 | dx.doi.org/10.17504/protocols.io.b5axq2fn | https://www.protocols.io/view/high-molecular-weight-dna-extraction-from-tunicate-b5axq2fn | Marta Wawrzyniak, Simon Blanchoud | TITLE: High Molecular Weight DNA extraction from tunicates
AUTHORS: Marta Wawrzyniak, Simon Blanchoud
[DESCRIPTION]
This protocol has been successfully used with Botrylloides diegensis and has been based on the following publication (with small changes):
https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/0014-... | ["Clean the slide from which you will take the colony of your interest. See Cleaning colonial ascidians.", "Isolate a cleaned colony composed of approx. 20-30 zooids.", "Incubate at 55 °C for 10 min .", "Add 4 µL of Proteinase K and mix by vortexing.", "Transfer to a 2 mL tube and spin at maximum speed for 2 min .", "H... |
39,509 | IgG expression and purification | 4 | dx.doi.org/10.17504/protocols.io.bitvken6 | https://www.protocols.io/view/igg-expression-and-purification-bitvken6 | Bei Wang, Wen-Hsin Sandy Lee, Helen Huang, Patricia Ng, Eve Ngoh, Chia Yin Lee, Hwee Ching Tan, Rabiatul Adawiyah, Mun Kuen Soh, Frannie Teo, Yvonne Yeap, Yuanyu Hu, Cheng-I Wang | TITLE: IgG expression and purification
AUTHORS: Bei Wang, Wen-Hsin Sandy Lee, Helen Huang, Patricia Ng, Eve Ngoh, Chia Yin Lee, Hwee Ching Tan, Rabiatul Adawiyah, Mun Kuen Soh, Frannie Teo, Yvonne Yeap, Yuanyu Hu, Cheng-I Wang
[STEPS]
?. [IgG Expression]
Day 0: Transfection of ExpiCHO-S cells
?. [IgG Expression]
Ster... | ["[IgG Expression]\nDay 0: Transfection of ExpiCHO-S cells", "[IgG Expression]\nSterile the plasmids by filtering through 0.22 µm spin-X column.", "[IgG Expression]\nAccording to the transfection manual of ExpiFectamine™ CHO Transfection Kit, 0.8 µg of plasmid per ml of ExpiCHO-S cells (20 µg of heavy chain plasmid and... |
53,152 | Genome editing in the choanoflagellate Salpingoeca rosetta | 1 | dx.doi.org/10.17504/protocols.io.bx58pq9w | https://www.protocols.io/view/genome-editing-in-the-choanoflagellate-salpingoeca-bx58pq9w | David Booth | TITLE: Genome editing in the choanoflagellate Salpingoeca rosetta
AUTHORS: David Booth
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol details the preparation and execution of CRISPR/Cas9 genome editing in </span><span style = "font-style:italic;">S. rosetta</span><span>. The pr... | ["[Culture Cells]\nSeed a large culture of S. rosetta.", "[Culture Cells]\nTwo days prior to transfection, inoculate of high nutrient media with a culture of S. rosetta feeding on E. pacifica to a final concentration of S. rosetta of .\n120 mL", "[Culture Cells]\nGrow the culture for in a 3-layer flask at .\n[with 6... |
97,764 | Extract dinoflagellates (Karenia brevis) RNA from filter samples. | 0 | null | https://www.protocols.io/view/extract-dinoflagellates-karenia-brevis-rna-from-fi-dbqc2msw | Cong Fei, Carly M Moreno, Shady Amin | TITLE: Extract dinoflagellates (Karenia brevis) RNA from filter samples.
AUTHORS: Cong Fei, Carly M Moreno, Shady Amin
[DESCRIPTION]
This protocol is designed for the extraction of total RNA from filter samples containing phytoplankton. It has been validated with a total of 105 cells. The entire procedure requires app... | ["Retrieve the from the -80°C freezer, and immediately transfer it to dry ice contained within an ice box for temperature preservation.", "Add 450 mL RTL buffer to a sterile 2 mL Eppendorf tube with three (ea) 2.8 mm ceramic beads.", "Using tweezers, securely hold the filter. Next, finely cut it using scissors. Car... |
52,129 | SPM Addition in cells | 4 | dx.doi.org/10.17504/protocols.io.bw59pg96 | https://www.protocols.io/view/spm-addition-in-cells-bw59pg96 | Veerle Baekelandt | TITLE: SPM Addition in cells
AUTHORS: Veerle Baekelandt
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">SPM Addition in cells for intact cell cross-linking</div></div>
[STEPS]
?. seed cells for in a 10 cm dish at a density of 6 x 106 cells per plate
?. treat cells for with 10 µM freshly prepared... | ["seed cells for in a 10 cm dish at a density of 6 x 106 cells per plate", "treat cells for with 10 µM freshly prepared SPM.SPM (Sigma-Aldrich, Saint Louis, MO, USA) was prepared to a final stock concentration of 200 mM in 0.1 M 3-(N-morpholino)propane sulfonic acid (MOPS)-KOH (pH 7.0)", "wash cells with 1X PBS and ... |
86,987 | Protocol to isolate and fix nuclei from flash frozen mouse gastrocnemius for IGVF | 4 | null | https://www.protocols.io/view/protocol-to-isolate-and-fix-nuclei-from-flash-froz-cy7jxzkn | Elisabeth Rebboah | TITLE: Protocol to isolate and fix nuclei from flash frozen mouse gastrocnemius for IGVF
AUTHORS: Elisabeth Rebboah
[DESCRIPTION]
This protocol describes isolation of nuclei from 10 week old left or right mouse gastrocnemius muscle from 8 founder strains (B6J, AJ, 129S1J, NZOJ, WSBJ, NODJ, PWKJ, and CASTJ), preparatio... | ["[Setup] Pre-chill centrifuge to 4C.", "[Setup] Prepare 2 large ice buckets.", "[Setup] Prepare lysis buffer on ice in a 50 mL conical tube. Distribute 2 mL into 8 gentleMACS C Tubes on ice.", "[Setup] Prepare NB + BSA + RNAse inhibitor in a 5 mL tube.", "[Setup] Prepare RSB on ice in a 50 mL conical tube. We keep a l... |
22,489 | The pipeline of assembly and annotation of the Scapharca broughtonii genome | null | dx.doi.org/10.17504/protocols.io.z7zf9p6 | null | Chang-Ming Bai | TITLE: The pipeline of assembly and annotation of the Scapharca broughtonii genome
AUTHORS: Chang-Ming Bai
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol include the detailed methods of assembly and annotation of the </span><span style = "font-style:italic;">Scapharca broughtoni... | ["The original data generated with PacBio and Nanopore platforms were base-called, quality controlled, combined and transferred to FASTA format for assembly.", "Run Canu (v1.5) for long reads correction, triming and assembly.\ncorrectedErrorRate=0.045, corOutCoverage=6.", "Run Wtdbg (v1.1) for further assembly of the d... |
78,858 | Utilizing the Public GenomeTrakr Database for Foodborne Pathogen Traceback | 2 | dx.doi.org/10.17504/protocols.io.eq2lyprkplx9/v3 | https://www.protocols.io/view/utilizing-the-public-genometrakr-database-for-food-cq9ivz4e | Ruth Timme, Maria Sanchez, Marc Allard | TITLE: Utilizing the Public GenomeTrakr Database for Foodborne Pathogen Traceback
AUTHORS: Ruth Timme, Maria Sanchez, Marc Allard
[DESCRIPTION]
This protocol outlines the all the steps necessary to become a GenomeTrakr data contributor. GenomeTrakr is an international genomic reference database of mostly food and envi... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.g2sbyee | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
38,940 | Total Protein Extraction from Plants | 4 | null | https://www.protocols.io/view/total-protein-extraction-from-plants-bh94j98w | May Shen | TITLE: Total Protein Extraction from Plants
AUTHORS: May Shen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Total Protein Extraction from </span><span style = "font-weight:bold;">Plants</span></div></div>
[STEPS]
?. [New Sample Preparation]
+ finely grounded.Move into 1.5 ml eppendorf.
[pla... | ["[New Sample Preparation]\n+ finely grounded.Move into 1.5 ml eppendorf.\n[plant tissue]\n[2X sample buffer]", "[New Sample Preparation]\ndry bath for\n65 °C", "[New Sample Preparation]\nCentrifuge: 12000 33, 1 min", "[Old sample thawing back]\ndry bath for\n65 °C", "[Old sample thawing back]\nCentrifuge: 12000 33, 1 ... |
90,683 | Storage & Revival of Oomycetes | 4 | dx.doi.org/10.17504/protocols.io.n92ldmqw7l5b/v1 | https://www.protocols.io/view/storage-amp-revival-of-oomycetes-c4s3ywgn | Diana Lee | TITLE: Storage & Revival of Oomycetes
AUTHORS: Diana Lee
[DESCRIPTION]
Cryopreservation of oomycetes such as Phytophthora and Pythium species is essential for the long-term maintenance of these organisms. In this method we present an improved cryopreservation protocol for oomycete cultures, using carbon filter pap... | ["[Preparation of Oomycetes for Storage] Inoculate a small agar plug of the oomycete culture into a thin film of rye broth in a petri dish.", "[Preparation of Oomycetes for Storage] Incubate at 20 °C until mycelium has grown about 4-5cm in diameter.", "[Preparation of Oomycetes for Storage] Tear the mycelium mat and p... |
43,422 | Nanosight LM10 | 1 | null | https://www.protocols.io/view/nanosight-lm10-bnm6mc9e | Joshua Welsh, Bryce Killingsworth, Jason Savage, Tim Traynor, Jennifer Jones | TITLE: Nanosight LM10
AUTHORS: Joshua Welsh, Bryce Killingsworth, Jason Savage, Tim Traynor, Jennifer Jones
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a protocol for performing nanoparticle tracking analysis measurements on the Translational Nanobiology Sections Nanosight LM10 (405 nm) ... | ["[Equipment Start Up]\nEnsure that the black power strip is turned on.\nSpecific to Translational Nanobiology Section", "[Equipment Start Up]\nTurn on the computer on the shelf, login using the password written above screen\nSpecific to Translational Nanobiology Section", "[Equipment Start Up]\nTurn on the Nanosight m... |
null | null | null | dx.doi.org/10.17504/protocols.io.ddq25v | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Protocol for preparation of short single and paired-end libraries from genomic dsDNA starting from low DNA quantity (up to 10 ng) for Illumina sequenincg. Developed by Adriana Alberti at Genoscope.
[GUIDELINES]
<strong><strong>Reagents and consumables<br /><br /></strong></stro... | [] |
19,861 | U Cinn - Phospholipids Assay | null | dx.doi.org/10.17504/protocols.io.xmvfk66 | null | Patrick Tso, Dana Lee | TITLE: U Cinn - Phospholipids Assay
AUTHORS: Patrick Tso, Dana Lee
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Determinations of phospholipids in plasma/serum/lymph will be made using the Wako Phospholipids C enzy... | ["Prepare working standards by making a serial dilution of the stock 300mg/dl standard. (See diagram below) *Stock standard included in kit.", "Prepare Working Reagent by reconstituting one vial of Color Reagent with a portion of Buffer then transferring entire contents to Buffer bottle, rinsing Color Reagent vial seve... |
28,477 | Plant Infection with Xanthomonas Campestris Campestris | null | dx.doi.org/10.17504/protocols.io.725hqg6 | null | Cleo B. | TITLE: Plant Infection with Xanthomonas Campestris Campestris
AUTHORS: Cleo B.
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Plant infection of three week old plants with </span><span style = "font-style:italic;">Xanthomonas Campestris </span><span>Campestris. </span></div></div>
[STEPS]
?... | ["[Day 1 ]\nMake at least 40 mL of overnight culture of Xanthomonas Campestris Campestris at\n28 °C", "[Day 2]\nMeasure OD600 of O/N culture", "[Day 2]\nCentrifuge culture for at\nCentrifuge: 4000 33", "[Day 2]\nRemove supernatant", "[Day 2]\nDissolve pellet in H2O until an OD600 of 1. Make sure you have at least 30 m... |
101,001 | Xenotransplantation of cortical progenitors into athymic mouse brain | 0 | dx.doi.org/10.17504/protocols.io.j8nlk889dl5r/v1 | https://www.protocols.io/view/xenotransplantation-of-cortical-progenitors-into-a-devh3e36 | courtney.wright Wright, louise.cottle, Lachlan Thompson, Clare Parish, Deniz Kirik | TITLE: Xenotransplantation of cortical progenitors into athymic mouse brain
AUTHORS: courtney.wright Wright, louise.cottle, Lachlan Thompson, Clare Parish, Deniz Kirik
[DESCRIPTION]
This protocol details the surgical procedure for xenotransplantation of cortical progenitors into the striatum of athymic mice (details o... | ["[Animal preparation] Lubricant is applied to both eyes to prevent them from drying out during anaesthesia (e.g. Lacrilube). Analgesia (Buprenorphine at a dose of 0.05mg/kg s.c.) is administered peri-operatively while the animals are maintained on heat pads.", "[Animal preparation] Heating pads on both the stereotaxic... |
91,102 | L-3 LEECH STORAGE | 4 | dx.doi.org/10.17504/protocols.io.rm7vzx234gx1/v1 | https://www.protocols.io/view/l-3-leech-storage-c476yzre | REDI-NET Consortium | TITLE: L-3 LEECH STORAGE
AUTHORS: REDI-NET Consortium
[DESCRIPTION]
This protocol describes leech storage.
[GUIDELINES]
OBJECTIVE
To outline steps for properly storing field-collected leech samples and nucleic acid samples purified from these soil.
SUMMARY/SCOPE
The overarching aim of the REDI-NET is to develop a ... | ["[STORAGE PROCEDURE FOR UNTREATED SAMPLE] Cool 96-well microfuge tube racks on ice.", "[STORAGE PROCEDURE FOR UNTREATED SAMPLE] Using clean forceps, transfer individual leech into the corresponding pre-labeled 2.0 mL microfuge tubes and put it onto the microfuge tube rack on ice sequentially.", "[STORAGE PROCEDURE FOR... |
25,981 | Frozen tissue dissociation for single-nucleus RNA-Seq | 1 | null | https://www.protocols.io/view/frozen-tissue-dissociation-for-single-nucleus-rna-5k5g4y6 | Linas Mazutis, Ignas Masilionis, Ojasvi Chaudhary | TITLE: Frozen tissue dissociation for single-nucleus RNA-Seq
AUTHORS: Linas Mazutis, Ignas Masilionis, Ojasvi Chaudhary
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The protocol described here relies on mechanical dissociation of frozen lung tissue (human or mouse), filtering and washing the nucl... | ["[Tissue grinding]\nPrepare the laminar hood and the grinding glassware:Clean the surface and glassware thoroughly with DRNAse Free Reagent Spray followed by 70% ethanol. Bring the ice bucket in the cell culture hood and spray it with DRNAse Free Reagent.Place fully assembled Dounce homogenizer on ice and to let it co... |
80,806 | Qiagen DNA PowerWater DNeasy Extraction | 1 | dx.doi.org/10.17504/protocols.io.261ge3mdyl47/v1 | https://www.protocols.io/view/qiagen-dna-powerwater-dneasy-extraction-cs6ewhbe | Christopher LeBoa, Sneha, Sneha | TITLE: Qiagen DNA PowerWater DNeasy Extraction
AUTHORS: Christopher LeBoa, Sneha, Sneha
[DESCRIPTION]
These are instructions for using the Qiagen Power Water Kit for doing Extraction from drinking water samples
[BEFORE_START]
Solution PW1 must be warmed at 55°C for 5–10 minutes to dissolve precipitates.
If Solution ... | ["Insert the filter into a 5 ml PowerWater DNA Bead Tube.", "Add 1 ml of Solution PW1 to the PowerWater DNA Bead", "Secure the tube horizontally to a Vortex and tape it extensively", "Vortex at maximum speed for 5 min. Centrifuge the tubes ≤4000 x g for 1 min at room temperature", "Transfer the supernatant to a clean 2... |
46,504 | Are false-positive, second-trimester maternal serum screens for fetal aneuploidy associated with adverse outcomes amongst singleton pregnancies globally? A protocol for a systematic review and meta-analysis. | 1 | dx.doi.org/10.17504/protocols.io.brngm5bw | https://www.protocols.io/view/are-false-positive-second-trimester-maternal-serum-brngm5bw | Christy Pylypjuk, Joel Monarrez-Espino | TITLE: Are false-positive, second-trimester maternal serum screens for fetal aneuploidy associated with adverse outcomes amongst singleton pregnancies globally? A protocol for a systematic review and meta-analysis.
AUTHORS: Christy Pylypjuk, Joel Monarrez-Espino
[DESCRIPTION]
<div class = "text-blocks"><div class = "t... | ["[TITLE]\nAre false-positive, second-trimester maternal serum screens for fetal aneuploidy associated with adverse outcomes amongst singleton pregnancies globally? A protocol for a systematic review and meta-analysis.[Prepared for LSHTM EPM500 Coursework on 01 August 2018]", "[BACKGROUND]\nINTRODUCTION Prenatal screen... |
103,180 | Quantitative Proteomic Data Analysis | 0 | dx.doi.org/10.17504/protocols.io.kxygxy5pzl8j/v1 | https://www.protocols.io/view/quantitative-proteomic-data-analysis-dgzk3x4w | Shiyi Wang | TITLE: Quantitative Proteomic Data Analysis
AUTHORS: Shiyi Wang
[DESCRIPTION]
Quantitative Proteomic Data Analysis
[STEPS]
1. **Data Import and Alignment** - Import data from 15 UPLC-MS/MS analyses into Proteome Discoverer 3.0 (Thermo Scientific Inc.). - Exclude conditioning runs but include 3 replicate SPQC samples.... | ["**Data Import and Alignment** - Import data from 15 UPLC-MS/MS analyses into Proteome Discoverer 3.0 (Thermo Scientific Inc.). - Exclude conditioning runs but include 3 replicate SPQC samples. - Align individual LCMS data files based on accurate mass and retention time of detected precursor ions using the Minora Feat... |
22,097 | Colonic epithelial cell isolation for Single Cell RNA-sequencing | null | dx.doi.org/10.17504/protocols.io.ztrf6m6 | null | David Fawkner-Corbett | TITLE: Colonic epithelial cell isolation for Single Cell RNA-sequencing
AUTHORS: David Fawkner-Corbett
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for isolation of single colonic epithelial cells from human endoscopic biopsies.</div><div class = "text-block"><span>Reference - </span><a... | ["Biopsies transported on ice in 10ml of transport medium", "Wash with 10ml of cold (4degree) wash medium, shake, remove media, repeat a total of 3 times", "Transfer biopsies to 5mL warm (water bath at 37 degree) chelation medium", "Incubate at 37C for 20mins – shake after 10mins and 20mins", "Remove supernatant, Trans... |
41,011 | Priming and loading a MinION flowcell v2 | 1 | null | https://www.protocols.io/view/priming-and-loading-a-minion-flowcell-v2-bkatksen | Josh Quick | TITLE: Priming and loading a MinION flowcell v2
AUTHORS: Josh Quick
[STEPS]
?. Thaw the following reagents at room temperature before placing on ice: Sequencing buffer (SQB)Loading beads (LB)Flush buffer (FLB)Flush tether (FLT)
?. Add FLT to the FLB tube and mix well by vortexing.
30 µl
?. If required place a new Mi... | ["Thaw the following reagents at room temperature before placing on ice: Sequencing buffer (SQB)Loading beads (LB)Flush buffer (FLB)Flush tether (FLT)", "Add FLT to the FLB tube and mix well by vortexing.\n30 µl", "If required place a new MinION flowcell onto the MinION by flipping open the lip and pushing one end of... |
77,209 | Formation of Optimal Cutting Temperature (OCT) Tissue Blocks for Cryosectioning | 4 | dx.doi.org/10.17504/protocols.io.81wgby911vpk/v1 | https://www.protocols.io/view/formation-of-optimal-cutting-temperature-oct-tissu-cpmzvk76 | Brett Laffey, Zbigniew Mikulski | TITLE: Formation of Optimal Cutting Temperature (OCT) Tissue Blocks for Cryosectioning
AUTHORS: Brett Laffey, Zbigniew Mikulski
[DESCRIPTION]
Optimal cutting temperature compound (OCT) is used to prepare frozen tissue blocks for cutting on a cryostat. This provides benefits for certain histological, immunofluorescen... | ["[Fixed Tissue Cryoprotection (Fresh tissue start at Step 2)] a. Prepare a solution of 30% weight/volume sucrose in 1X PBS by adding 30g of sucrose to 100 ml of 1X PBS. Increase this amount based on the number of fixed tissues that need to be cryoprotected. \n\nb. Prepare 1:1 PBS to OCT solution day before use, vortex... |
97,580 | Bulk preparation of agarose gel | 0 | dx.doi.org/10.17504/protocols.io.kxygxym7dl8j/v1 | https://www.protocols.io/view/bulk-preparation-of-agarose-gel-dbik2kcw | Callen Hyland | TITLE: Bulk preparation of agarose gel
AUTHORS: Callen Hyland
[DESCRIPTION]
For applications when you only need a small amount of agarose gel, it is convenient to prepare the gel in bulk ahead of time. The desired quantity of agarose can then be remelted when needed. This protocol can be modified for any agarose perce... | ["[Bulk agarose gel prep] Weigh 2 g of agarose powder and add it to a beaker or Erlenmeyer flask. Use a beaker or Erlenmeyer flask that is at least 2X the volume of the agarose you are preparing.", "[Bulk agarose gel prep] Add 200 mL of buffer to the beaker or flask and swirl to mix. For gel electrophoresis, use 1X TBE... |
61,227 | WU sn-prep Protocol for Solid Tumors - snRNA protocol v2.8 | 4 | dx.doi.org/10.17504/protocols.io.14egn7w6zv5d/v1 | https://www.protocols.io/view/wu-sn-prep-protocol-for-solid-tumors-snrna-protoco-b72jrqcn | Wagma Caravan, Reyka Jayasinghe, Nataly Naser Al Deen | TITLE: WU sn-prep Protocol for Solid Tumors - snRNA protocol v2.8
AUTHORS: Wagma Caravan, Reyka Jayasinghe, Nataly Naser Al Deen
[DESCRIPTION]
WU sn-prep Protocol for Solid Tumors -snRNA protocol v2.7
[STEPS]
SECTION: Reagents and Tools
1.
1x Lysis buffer (2mL):
10mM Tris-HCl (pH 7.4) (Thermo; 15567027), 20 uL
10... | ["[Reagents and Tools] 1x Lysis buffer (2mL):\n10mM Tris-HCl (pH 7.4) (Thermo; 15567027), 20 uL\n10mM NaCl (Thermo; AM9759), 4 uL\n3 mM MgCl2 (Thermo; AM9530G), 6 uL\nNP-40 substitute (Sigma, 74385-1L), 2 uL\n1 M DTT (Sigma, 646563), 2 uL\nNuclease Free Water (Invitrogen, AM9937), 1.966 mL", "[Reagents and Tools] Lysis... |
83,213 | DNA extraction (BOMB) | 4 | dx.doi.org/10.17504/protocols.io.n2bvj6mdnlk5/v7 | https://www.protocols.click/view/dna-extraction-bomb-cvhmw346 | Yin-Tse Huang, Tsu-Chun Hung | TITLE: DNA extraction (BOMB)
AUTHORS: Yin-Tse Huang, Tsu-Chun Hung
[DESCRIPTION]
DNA extraction (BOMB)
[STEPS]
SECTION: Sample Collection
1. Add 200 µL of 0.5 mm beads to 2mL screw tube
SECTION: Sample Collection
2. Add200 µL of 1 mm beads to 2mL screw tube
SECTION: Sample Collection
3. Add870 µL Lysis master m... | ["[Sample Collection] Add 200 µL of 0.5 mm beads to 2mL screw tube", "[Sample Collection] Add200 µL of 1 mm beads to 2mL screw tube", "[Sample Collection] Add870 µL Lysis master mix to 2mL screw tube. The final look:", "[Sample Collection] Collect 20-50 mg of sample to 2mL screw tube", "[Sample crush] Put the 2mL screw... |
94,442 | Live tracking of multiple mice in a neuromelanin-inducing PD model over several weeks | 1 | dx.doi.org/10.17504/protocols.io.36wgq3z25lk5/v1 | https://www.protocols.io/view/live-tracking-of-multiple-mice-in-a-neuromelanin-i-c8giztue | Cristian González-Cabrera, Matthias Prigge | TITLE: Live tracking of multiple mice in a neuromelanin-inducing PD model over several weeks
AUTHORS: Cristian González-Cabrera, Matthias Prigge
[DESCRIPTION]
The Live Mouse Tracker (LMT) system is engineered for long-term, automated tracking and behavioral analysis of mice, integrating machine learning, computer vis... | ["[Animal Preparation for Recordings] Anesthetizing the Mouse: Anesthetize the mouse in the isofluorane induction chamber. Monitor the mouse to ensure it is properly anesthetized and does not feel pain.\nImplantation Site Preparation: Gently clean and disinfect the area of the belly where the RFID probe will be implant... |
54,753 | Spike Detection | 4 | dx.doi.org/10.17504/protocols.io.bzp9p5r6 | https://www.protocols.io/view/spike-detection-bzp9p5r6 | Bryan Yoo, Jessica Griffiths, Sarkis Mazmanian | TITLE: Spike Detection
AUTHORS: Bryan Yoo, Jessica Griffiths, Sarkis Mazmanian
[DESCRIPTION]
Protocol for spike detection of GCaMP6F imaging data used in Yoo et al 2021
[STEPS]
1. Data sets of fluorescent values recorded at a rate of 0.206 s from GCaMP6F-expressing unstimulated neurons in the myenteric plexus of ... | ["Data sets of fluorescent values recorded at a rate of 0.206 s from GCaMP6F-expressing unstimulated neurons in the myenteric plexus of the proximal large intestine and analyzed with the MLspike software for Matlab downloaded from GitHub (https://github.com/MLspike/spikes) (Deneux et al., 2016).", "MLspike determines a... |
81,381 | 10x Protocols: Chromium Single Cell/Nuclei Gene Expression Flex Fixation -- University of Minnesota TMCs (CG000478 Rev B) | 1 | dx.doi.org/10.17504/protocols.io.81wgby3x3vpk/v1 | https://www.protocols.io/view/10x-protocols-chromium-single-cell-nuclei-gene-exp-ctqdwms6 | IOx Genomics, Laura J Niedernhofer, David A Bernlohr | TITLE: 10x Protocols: Chromium Single Cell/Nuclei Gene Expression Flex Fixation -- University of Minnesota TMCs (CG000478 Rev B)
AUTHORS: IOx Genomics, Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
DOIs for dissociation protocols and 10x Genomics fixation for Chromium Single Cell Expression flex protocols.
P... | ["https://www.10xgenomics.com/products/single-cell-gene-expression-flex\nhttps://www.10xgenomics.com/support/single-cell-gene-expression-flex", "10x Protocol CG000478, Rev B (Fixation):"] |
26,550 | UC Davis - Luminex/Multiplex | null | dx.doi.org/10.17504/protocols.io.56wg9fe | null | Lori Haapanen | TITLE: UC Davis - Luminex/Multiplex
AUTHORS: Lori Haapanen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This core will provide services for quantification and comparison in animal models for hormone measurements; ki... | ["Pre-wet the filter plate with 200 ul assay buffer, agitate, incubate for 10 minutes RT and vacuum.", "Add 25 ul of standards, controls, assay buffer, samples, matrix serum and beads to appropriate wells on the filter plate.", "Place filter plate on plate stand, seal, wrap in foil and incubate overnight while agitatin... |
43,342 | 15N2 label preparation (dissolved method) | 1 | null | https://www.protocols.io/view/15n2-label-preparation-dissolved-method-bnjnmcme | Molly Moynihan | TITLE: 15N2 label preparation (dissolved method)
AUTHORS: Molly Moynihan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A protocol for making pre-dissolved 15N2 label in sterile seawater</div></div>
[STEPS]
?. [Calculations]
The following protocol is based on the dissolved gas method described by ... | ["[Calculations]\nThe following protocol is based on the dissolved gas method described by Mohr et al. 2010 and Klawoon et al. 2015. This protocol makes 4x 500mL serum bottles of 15N2 labels enriched to ~90%. Enrichment of each serum bottle depends on the vacuum pressure used for degassing. The following calculations c... |
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