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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49,903 | Automated Protein Normalization and Tryptic Digestion on a Biomek-NX Liquid Handler System | 1 | dx.doi.org/10.17504/protocols.io.buypnxvn | https://www.protocols.io/view/automated-protein-normalization-and-tryptic-digest-buypnxvn | Yan Chen, Tad Ogorzalek, Nurgul Kaplan Lease, Jennifer Gin, Christopher J Petzold | TITLE: Automated Protein Normalization and Tryptic Digestion on a Biomek-NX Liquid Handler System
AUTHORS: Yan Chen, Tad Ogorzalek, Nurgul Kaplan Lease, Jennifer Gin, Christopher J Petzold
[DESCRIPTION]
This protocol details steps to normalize the amount of protein for tryptic digestion in quantitative proteomic w... | ["[Biomek NX-S8 input file preparation] After measuring protein concentration by the DC (detergent compatible) protein assay (Bio-Rad), export protein concentration report through MD Spectramax 250 software that controls the microplate reader. Copy the content in the exported text file and paste it into Excel, and the... |
66,606 | High-throughput papain-based DNA extraction from whole invertebrates | 4 | dx.doi.org/10.17504/protocols.io.261genb8dg47/v1 | https://www.protocols.io/view/high-throughput-papain-based-dna-extraction-from-w-cdans2de | Rosa Whittingham, James JN Kitson, Jordan P Cuff | TITLE: High-throughput papain-based DNA extraction from whole invertebrates
AUTHORS: Rosa Whittingham, James JN Kitson, Jordan P Cuff
[DESCRIPTION]
This protocol is designed for extracting DNA from individual invertebrates in 96-well plate format for downstream barcoding or metabarcoding. The reagents and methods prop... | ["[Collection of samples] Consider how systematic the study needs to be and the various constraints imposed on the data by the study design.", "[DNA extraction: purification] Protein Denaturation Buffer should be comprised of the following reagents:", "[DNA extraction: purification] Add 200 μL of the supernatant from S... |
86,116 | Bakteriel WGS - SSI | 4 | dx.doi.org/10.17504/protocols.io.5qpvo3r7bv4o/v1 | https://www.protocols.io/view/bakteriel-wgs-ssi-cyccxssw | Theis Hass THTR Thorsen, Sekventeringsenheden SB | TITLE: Bakteriel WGS - SSI
AUTHORS: Theis Hass THTR Thorsen, Sekventeringsenheden SB
[DESCRIPTION]
Method used at Sequencing Core Facility - Statens Serum Institut for sequencing of bacterial isolates.
This protocol is specified for high-throughput sequencing of 96 isolates (sometimes less depending on the number of ... | ["[Tagmentering af input-DNA] Find følgende komponenter frem.\n\nKomponenter opbevaret på frost:\n \n \n- Tø op på is. Vend de optøede rør 3-5 gange og centrifugér derefter kortvarigt.\n\n \n\n\nKomponent opbevaret ved stuetemperatur: \n \n- Tjek for bundfald. Hvis der er bundfald til stede, vortex indtil alle partik... |
null | null | null | dx.doi.org/10.17504/protocols.io.eq6bdze | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p><strong>Materials:</strong><br /><br /></p>
<p>1) 60-65°C heat block or water bath</p>
<p>2) Microfuge</p>
<p>3) 1.5 and 2.0 mL microfuge tubes (screw-cap)</p>
<p>4) 50 mM Tris-HCl, pH 7.5, 10 mM MgCl<sub>2</sub></p>
<p>5) Triton X-100<br />6) DNAse I, 2.0 mg/mL in 50 mM Tris-... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.gr5bv86 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The SpinSmart PCR purification and gel extraction technologies utilize a lysis buffer containing chaotropic salts that allow DNA to bind to a silica membrane. Binding buffer PCR 1 is added to a PCR reaction or agarose gel slice; the mixture is subsequently loaded directly ont... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.nxbdfin | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Galvanic vestibular stimulation (GVS) is a method that stimulates the vestibular afferents with a small current, triggering a motor reflex response in the posture-controlling muscles. This response can be captured by electromyography (EMG) and is called vestibular evoked myog... | [] |
81,513 | A protocol of nuclei extraction from germinating spores of the wheat stripe rust pathogen | 4 | null | https://www.protocols.io/view/a-protocol-of-nuclei-extraction-from-germinating-s-ctuhwnt6 | Ramawatar Nagar | TITLE: A protocol of nuclei extraction from germinating spores of the wheat stripe rust pathogen
AUTHORS: Ramawatar Nagar
[DESCRIPTION]
Extracting nuclei from rust fungi is important because it allows for the study of the genetic material of these pathogens, which can provide insights into their biology, evolution, an... | ["Spore germination", "Collect fresh spores ~300 mg for a Pyrex baking tray of size 33X23XX5 cm and put in a spore dispenser. The spore dispenser was made out of a 50 mL falcon tube by cutting the cap of it as shown in Figure 1.2 \n F", "Keep a Pyrex baking tray of size 33X23XX5 in a plastic container of size ?? Ad... |
69,977 | Self-perception of Physical Appearance of Adolescents and Associated Factors in Addis Ababa, Ethiopia | 1 | dx.doi.org/10.17504/protocols.io.8epv5j635l1b/v1 | https://www.protocols.io/view/self-perception-of-physical-appearance-of-adolesce-cgjztup6 | ziyadahm, ziyadahm, Semira Ahmed2, Aynye Woldekiros Negese | TITLE: Self-perception of Physical Appearance of Adolescents and Associated Factors in Addis Ababa, Ethiopia
AUTHORS: ziyadahm, ziyadahm, Semira Ahmed2, Aynye Woldekiros Negese
[DESCRIPTION]
Introduction: Establishing a positive body image is a critical factor for adolescents’ physical and mental health, as it determi... | [] |
41,677 | Pinpoint Science 30-Second Covid-19 Test Protocol | 1 | dx.doi.org/10.17504/protocols.io.bkxmkxk6 | https://www.protocols.io/view/pinpoint-science-30-second-covid-19-test-protocol-bkxmkxk6 | lisa.diamond | TITLE: Pinpoint Science 30-Second Covid-19 Test Protocol
AUTHORS: lisa.diamond
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Pinpoint's nanosensor-based platform detects SARS-CoV-2 antigen by (1) measuring baseline current through our functionalized nanosensor chip in ordinary PBS buffer; (2) mea... | ["INSTALL THE PINPOINT APPOn a smart device (smartphone or tablet), install the Pinpoint App.Scan the the 2D barcode on the test package, or download the mobile app from:- [URL for IOS]\t- [URL for Android]", "SET UP PINPOINT READER- Unbox the Pinpoint Reader from its packaging.- Plug the Reader AC adapter into an AC o... |
87,520 | Quantitative analyses of the ultrastructural features of dopaminergic axon terminals | 2 | dx.doi.org/10.17504/protocols.io.bp2l694xdlqe/v2 | https://www.protocols.io/view/quantitative-analyses-of-the-ultrastructural-featu-czp8x5rw | Natalie M Doig, Peter J Magill | TITLE: Quantitative analyses of the ultrastructural features of dopaminergic axon terminals
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 inappropriate dopamine release often correlates with changes... | [] |
56,481 | Crosslinking assay to study a specific cargo-coat interaction through a transmembrane receptor in the secretory pathway | 4 | dx.doi.org/10.17504/protocols.io.b3d9qi96 | https://www.protocols.io/view/crosslinking-assay-to-study-a-specific-cargo-coat-b3d9qi96 | Javier Manzano-Lopez†*, Sofia Rodriguez-Gallardo†, Susana Sabido-Bozo†, Alejandro Cortes-Gomez, Ana Maria Perez-Linero, Rafael Lucena, Antonio Cordones-Romero, Sergio Lopez, Auxiliadora Aguilera-Romero*, Manuel Muñiz* | TITLE: Crosslinking assay to study a specific cargo-coat interaction through a transmembrane receptor in the secretory pathway
AUTHORS: Javier Manzano-Lopez†*, Sofia Rodriguez-Gallardo†, Susana Sabido-Bozo†, Alejandro Cortes-Gomez, Ana Maria Perez-Linero, Rafael Lucena, Antonio Cordones-Romero, Sergio Lopez, Auxiliador... | ["[Yeast transformation and culture] Transform the yeast strain genomically expressing Lst1-mCherry with a centromeric plasmid expressing GFP-tagged Gas1 under control of its own promoter (pRS416-GAS1-GFP).", "[Yeast transformation and culture] Pick up a transformed colony and streak it on an SC-URA agar plate and incu... |
50,502 | Expression and purification protocol of GST-TAX1BP1 | 1 | dx.doi.org/10.17504/protocols.io.bvjen4je | https://www.protocols.io/view/expression-and-purification-protocol-of-gst-tax1bp-bvjen4je | Chunmei Chang | TITLE: Expression and purification protocol of GST-TAX1BP1
AUTHORS: Chunmei Chang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details the expression and purification protocol of GST-TAX1BP1.</div></div>
[STEPS]
?. [Protein expression]
Transform the E.Coli BL21DE3 cells with a pla... | ["[Protein expression]\nTransform the E.Coli BL21DE3 cells with a plasmid encoding for GST-TAX1BP1 and plate them on Amp plate.", "[Protein expression]\nCarry out protein expression in LB medium, induce with IPTG (isopropyl- -d-thiogalactopyranoside) to an OD600 of 0.8 and grow at .\n1.5 L\n18 °C", "[Protein express... |
null | null | null | dx.doi.org/10.17504/protocols.io.phqdj5w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The present work provides information about the distribution, quantity and nature of lipophilic substances beneath the surface in air- and kiln-dried Scots pine (<em>Pinus sylvestris</em> L.) sapwood boards. Samples were taken from knot-free sapwood surfaces and the compositi... | [] |
64,420 | Ocuprime is texted clinically and it is been used by most of the users for this | 3 | dx.doi.org/10.17504/protocols.io.kqdg3pwzpl25/v1 | https://www.protocols.io/view/ocuprime-is-texted-clinically-and-it-is-been-used-ca6cshaw | fluxactive | TITLE: Ocuprime is texted clinically and it is been used by most of the users for this
AUTHORS: fluxactive
[DESCRIPTION]
Main Benefits - Improve Eye Vision Without Any Side Effect
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.i8jchun | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol was developed in order to remove secondary compounds which inhibited restriction enzyme digestion of <em>Xanthorrhoea</em> genomic DNA. It has also been used to successfully obtain high quality, high weight DNA from other recalcitrant plant tissues, including <e... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.c3jykm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Culley Protocol (from Culley & Steward (2007), <a href="http://aem.asm.org/content/73/18/5937.full" target="_blank">New genera of RNA viruses in subtropical seawater, inferred from polymerase gene sequences</a>, Applied & Environmental Microbiology 73(18):5937-5944).
[G... | [] |
16,450 | Protocol for use with rRNA Depleted FFPE RNA and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760, E7765) | null | dx.doi.org/10.17504/protocols.io.ubaesie | null | New England Biolabs | TITLE: Protocol for use with rRNA Depleted FFPE RNA and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760, E7765)
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina contains the enzymes ... | ["[Priming of Highly Degraded RNA (FFPE) Which has a RIN ≤ 2 and Does not Require Fragmentation]\nBriefly spin down the samples in a microcentrifuge.", "[Priming of Highly Degraded RNA (FFPE) Which has a RIN ≤ 2 and Does not Require Fragmentation]\nIncubate the sample in a preheated thermocycler as follows: at , with h... |
106,983 | Nematode DNA Illumina Amplicon Sequencing using two step PCR | 1 | null | https://www.protocols.io/view/nematode-dna-illumina-amplicon-sequencing-using-tw-dkqf4vtn | Lindsay Kate Newbold, Joe Taylor, Vilma Cortes | TITLE: Nematode DNA Illumina Amplicon Sequencing using two step PCR
AUTHORS: Lindsay Kate Newbold, Joe Taylor, Vilma Cortes
[DESCRIPTION]
This document is designed to provide the researcher with all of the information required to undertake the metabarcoding of DNA from Nematodes which have already been physically sepa... | ["[Nextera index plates- Prepared prior to Step 1 PCR] Order indexing primers direct from oligo manufacturer (For example IDT, Sigma genosys or MWG) suspended in water 0.5 µM scale, Desalt purification and10 µM concentration. These indexing primers consist of: an Illumina Nextra adapter i5 (Forward primer) AATGATACGG... |
null | null | null | dx.doi.org/10.17504/protocols.io.n5idg4e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a basic protocol to make a 0.5M EDTA stock solution at pH 8.0. I have mostly copied it from CSHL's recipe.</p>
[STEPS]
?.
?.
?.
?.
?. | [] |
72,743 | Spinfection for Suspension and Adherent Cells | 4 | dx.doi.org/10.17504/protocols.io.4r3l2722xg1y/v1 | https://www.protocols.io/view/spinfection-for-suspension-and-adherent-cells-cjafuibn | Kevin Wilkins | TITLE: Spinfection for Suspension and Adherent Cells
AUTHORS: Kevin Wilkins
[DESCRIPTION]
This protocol is for infection of adherent cells (such as HEK293t) with prepackaged lentivirus.
Different cell lines will have different infection rates, and the infectivity of lentivirus stocks will also depend and vary. Optimi... | ["[Plating cells] For HEK293t cells, plate 50,000 cells/well in 0.5 mL of DMEM on 24-well plate the day prior.", "[Spinfection] 30+ min before spinfection, make sure the table-top centrifuge is at 30 °C .", "[Spinfection] Add lentivirus and polybrene to each well.", "[Spinfection] Virus amount\nVirus titer will vary, s... |
96,266 | Electrolyte Leakage Assay to Quantify Cell Death in Leaves | 0 | null | https://www.protocols.io/view/electrolyte-leakage-assay-to-quantify-cell-death-i-c99iz94e | Laura Tovar-Rosales, Kalpana Nanjareddy, Manoj-Kumar Arthikala | TITLE: Electrolyte Leakage Assay to Quantify Cell Death in Leaves
AUTHORS: Laura Tovar-Rosales, Kalpana Nanjareddy, Manoj-Kumar Arthikala
[DESCRIPTION]
The production of reactive oxygen species occurs naturally in certain cellular organelles as metabolic byproducts. However, under stress conditions, their accumulation... | ["Let the samples sit for 30 min to allow the removal of electrolytes adhered to the leaf surface and those released during the cutting process. Subsequently, replace the deionized water with fresh water after rinsing.", "[Measurement Procedure] Utilize a conductivity meter (SevenCompact, Mettler-Toledo) to measure con... |
72,217 | NCBI submission protocol for SARS-CoV-2 wastewater data: SRA, BioSample, and BioProject | 1 | dx.doi.org/10.17504/protocols.io.ewov14w27vr2/v9 | https://www.protocols.io/view/ncbi-submission-protocol-for-sars-cov-2-wastewater-cirzud76 | Ruth Timme, Candace.Bias, Maria Balkey | TITLE: NCBI submission protocol for SARS-CoV-2 wastewater data: SRA, BioSample, and BioProject
AUTHORS: Ruth Timme, Candace.Bias, Maria Balkey
[DESCRIPTION]
PURPOSE:
This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr Laboratories; however, this protocol was written ... | ["["Ingredients" to have in place before starting your submissions] Set up a new NCBI submission environment for your lab\n1.1: Create an NCBI user account\n1.2: Set up an NCBI submission user group for your lab\n1.3: Bookmark the link to your Submission Portal\n1.4. Identify or establish new BioProjects (det... |
null | null | null | dx.doi.org/10.17504/protocols.io.hqrb5v6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Chronic pain and mental health conditions after injury have an enormous impact on quality of life, placing a huge personal and financial burden on the individual, their families, as well as health and compensation systems. This observational prospective cohort study evaluated... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.pnrdmd6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><u>Goal:</u></p>
<p>This document has the objective of standardizing the protocol for Western blot<em>. </em>This technique allows the detection of specific proteins separated on polyacrylamide gel and transferred to a membrane, using antibodies.</p>
<p><u> </u></p>
<p><u>Gen... | [] |
93,828 | Concentration and nucleic acid extraction of viruses from aggregated airplane waste | 4 | dx.doi.org/10.17504/protocols.io.5jyl8poy6g2w/v1 | https://www.protocols.io/view/concentration-and-nucleic-acid-extraction-of-virus-c7vczn2w | Ari N Machtinger, Olivia S Hershey, William J Bradshaw, Daniel P Rice, Michael R McLaren | TITLE: Concentration and nucleic acid extraction of viruses from aggregated airplane waste
AUTHORS: Ari N Machtinger, Olivia S Hershey, William J Bradshaw, Daniel P Rice, Michael R McLaren
[DESCRIPTION]
This protocol details our workflow for performing concentration and total nucleic acid extraction from aggregated ai... | ["[Reagent Preparation] Prepare a 10 % volume Tween 20 stock solution. For a 40 mL stock, combine 4 mL of Tween 20 with 36 mL of 1X PBS. Filter sterilize with a 0.22 um vacuum filtration unit.", "[Part 1: Waste Handling, Dissociation, Filtration] Transfer the waste sample (within secondary container) from the refrigera... |
49,657 | LEAP100 Pin-to-Plate Device Protocol for Treating Cancer Cells | 1 | dx.doi.org/10.17504/protocols.io.buqznvx6 | https://www.protocols.io/view/leap100-pin-to-plate-device-protocol-for-treating-buqznvx6 | Almha Gilheany, Sebnem Gunes, Laurence Scally, Patrick J Cullen, Brijesh Tiwari, James Curtin, Andressa Maria Aguiar de Carvalho | TITLE: LEAP100 Pin-to-Plate Device Protocol for Treating Cancer Cells
AUTHORS: Almha Gilheany, Sebnem Gunes, Laurence Scally, Patrick J Cullen, Brijesh Tiwari, James Curtin, Andressa Maria Aguiar de Carvalho
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Plasma can be described as the fourth state ... | ["[Installation and Connection of Pin-to-Plate Device]\nInstall the Electrodes: Pin Electrodes", "[Installation and Connection of Pin-to-Plate Device]\nConnect the bottom flat electrode to the ground. The system will not work correctly without this connection.", "[Installation and Connection of Pin-to-Plate Device]\nU... |
44,545 | Purification of Cyclic GMP-AMP from Viruses and Measurement of Its Activity in Cell Culture | 4 | dx.doi.org/10.17504/protocols.io.bpq9mmz6 | https://www.protocols.io/view/purification-of-cyclic-gmp-amp-from-viruses-and-me-bpq9mmz6 | Alice Mayer, Jonathan Maelfait, Anne Bridgeman, Jan Rehwinkel | TITLE: Purification of Cyclic GMP-AMP from Viruses and Measurement of Its Activity in Cell Culture
AUTHORS: Alice Mayer, Jonathan Maelfait, Anne Bridgeman, Jan Rehwinkel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Sensing of cytoplasmic DNA by cGAS is essential for the initiation of immune respo... | ["[3.1 cGAMP Purification from Viral Particles]\nResuspend pelleted viruses in , transfer to 1.5 mL tubes, and incubate , vortex regularly.\n[X-100 lysis buffer]\non ice\nWe typically analyze pelleted virus stocks corresponding to at least 106infectious units, although this will depend on the type of virus and the amou... |
84,495 | NDB_covid19_medical_resource_usage | 1 | dx.doi.org/10.17504/protocols.io.eq2lyj34qlx9/v1 | https://www.protocols.io/view/ndb-covid19-medical-resource-usage-cwrpxd5n | Keita Fukuyama | TITLE: NDB_covid19_medical_resource_usage
AUTHORS: Keita Fukuyama
[DESCRIPTION]
Purpose: The coronavirus disease 2019 (COVID-19) pandemic
exhibited several different waves threatening global health care. During this pandemic, medical resources were depleted.
However, the kind of medical resources provided
to each wa... | ["[Approval to use NDB data.] Approval to NDB usage\nThere are two ways to conduct analysis using Japanese receipt data in NDB: either On-site Research Center, where the analysis is performed in an analysis environment, or by having the data set for the extracted analysis provided to the researcher.\nIn this study, On-... |
22,877 | Protocol for sampling and transport of nose- and thoratsamples in the Fit Futures study | null | dx.doi.org/10.17504/protocols.io.2j5gcq6 | null | Dina Stensen, Anne-Sofie Furberg, Karina Olsen, Gunnar Skov Simonsen, Johanna UE Sollid, Lars Småbrekke, Guri Grimnes, Cristopher Sievert Nielsen | TITLE: Protocol for sampling and transport of nose- and thoratsamples in the Fit Futures study
AUTHORS: Dina Stensen, Anne-Sofie Furberg, Karina Olsen, Gunnar Skov Simonsen, Johanna UE Sollid, Lars Småbrekke, Guri Grimnes, Cristopher Sievert Nielsen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><s... | ["[Nasal samples]\nMoisture the rayon-tipped swab in 2-3 drops of sterile NaCl 0,9 mg/ml. There should be two samples from the nasal cavity.", "[Nasal samples]\nLead the rayon-tipped swab carefully into the nasal cavity approximately 1-2 cm and rotate with delicate pressure 3 times in both nasal cavity. The same swab s... |
21,104 | UC Davis - Morris Water Maze | null | dx.doi.org/10.17504/protocols.io.yuqfwvw | null | Mari Golub | TITLE: UC Davis - Morris Water Maze
AUTHORS: Mari Golub
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span><span style = "font-weight:bold;"> </span></div><div class = "text-block">The Morris water maze (MWM) is a widely used tool to study spatial learni... | ["Study design and scheduling:Time of day: Time of day strongly affects performance. For any experiment, testing should take place during the same 2-3 hour period on each day. Morning or afternoon testing at least one hour prior to dark cycle onset are appropriate. Testing after “lights out” in the vivarium is not appr... |
null | null | null | dx.doi.org/10.17504/protocols.io.pngdmbw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?. | [] |
18,090 | Protocol for DNA Extraction and Quantitative PCR Detection of Verticillium dahliae from Soil | null | dx.doi.org/10.17504/protocols.io.vwie7ce | null | David Wheeler, Jeness Scott, Jeremiah Kam Sung Dung, Dennis Allen Johnson | TITLE: Protocol for DNA Extraction and Quantitative PCR Detection of Verticillium dahliae from Soil
AUTHORS: David Wheeler, Jeness Scott, Jeremiah Kam Sung Dung, Dennis Allen Johnson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the extraction of DNA from relatively large v... | ["[Pre-Extraction Sample Preparation:]\nThe soil cores are combined, air-dried and processed through a sieve (No. 10/2.0 mM). Dried soil samples are stored in a cool dark place until use. When stored in the fridge, keep them in sealed plastic bags to prevent the soil from absorbing moisture.", "[Pre-Extraction Sample P... |
40,267 | Western for Brain Punches | 4 | null | https://www.protocols.io/view/western-for-brain-punches-bjjjkkkn | Olivier George, Lieselot Carrette, Francisco Ramirez | TITLE: Western for Brain Punches
AUTHORS: Olivier George, Lieselot Carrette, Francisco Ramirez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the step-by-step procedure of a western blot; for isolating and probing for proteins from a rat brain punch. </div></div>
[STEPS]
?. ... | ["[Cell Lysis & Protein Extraction]\nMake lysis solutionAdd RIPA an 100X HALT (for end solution of 1X HALT)", "[Cell Lysis & Protein Extraction]\nAdd RIPA/HALT solution to brain punch.\n20 µl", "[Cell Lysis & Protein Extraction]\nHomogenize with micropipette (by pipetting up & down and avoiding bubbles).", "[Cell Lys... |
52,040 | Cubic Clearing and Whole Mount Imaging of Mouse Lung Lobes | 1 | dx.doi.org/10.17504/protocols.io.bw3gpgjw | https://www.protocols.io/view/cubic-clearing-and-whole-mount-imaging-of-mouse-lu-bw3gpgjw | Jamie Verheyden | TITLE: Cubic Clearing and Whole Mount Imaging of Mouse Lung Lobes
AUTHORS: Jamie Verheyden
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a protocol for cubic clearing of mouse lung tissue for whole lobe imaging using Zeiss Lightsheet Imaging.</div></div>
[STEPS]
?. See attached protocol ... | ["See attached protocol file."] |
null | null | null | dx.doi.org/10.17504/protocols.io.rqzd5x6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?. | ["Flies from each of the 4 mitotypes were placed in individual egg collection containers.", "Eggs were collected manually and added to either the 1:2 or 1:16 P:C diet with ~200 eggs per bottle with 6 bottles/mitotype/diet.", "Microbiome was added after 48 hours and flies that eclosed in a 3d window were collected, coun... |
81,587 | UMN-Mouse-rnaSeq_skeletal_muscle | 4 | dx.doi.org/10.17504/protocols.io.n2bvj87bpgk5/v1 | https://www.protocols.io/view/umn-mouse-rnaseq-skeletal-muscle-ctwtwpen | Xu Zhang | TITLE: UMN-Mouse-rnaSeq_skeletal_muscle
AUTHORS: Xu Zhang
[DESCRIPTION]
Protocol for mouse rnaSeq for skeletal muscle
[STEPS]
1. Description Source name Skeletal muscle Organism Mus musculus Characteristics stain: C57BL/6 age: 6 month Treatment protocol NA Growth protocol NA Extracted molecule total RNA
2. Process Ex... | ["Description Source name\tSkeletal muscle Organism\tMus musculus Characteristics\tstain: C57BL/6 age: 6 month Treatment protocol\tNA Growth protocol\tNA Extracted molecule\ttotal RNA", "Process Extraction protocol\tQuadriceps muscle were collected in Trizol solution (Invitrogen, Carlsbad, CA, USA) and RNA isolation wa... |
89,780 | LRRK2 cloning, plasmid construction, and mutagenesis | 1 | dx.doi.org/10.17504/protocols.io.kxygx35ddg8j/v1 | https://www.protocols.io/view/lrrk2-cloning-plasmid-construction-and-mutagenesis-c3wuypew | David Snead, Yu Xuan Lin | TITLE: LRRK2 cloning, plasmid construction, and mutagenesis
AUTHORS: David Snead, Yu Xuan Lin
[DESCRIPTION]
Protocol for Cloning, plasmid construction, and mutagenesis of LRRK2 and LRRK2-RCKW as done by Leschziner and Reck-Peterson Labs.
Original protocol by David Snead and Yu Xuan Lin.
[STEPS]
SECTION: Cloning, p... | ["[Cloning, plasmid construction, and mutagenesis] The DNA coding for LRRK2-RCKW residues 1327 to 2527 (taken from Mammalian Gene Collection) was PCR-amplified using the forward primer TACTTCCAATCCATGAAAA491AGGCTGTGCCTTATAACCGA and the reverse primer TATCCACCTTTACTGTCACTCAACAGATGTTCGTCTCATTTTTTCA. \nThe DNA coding for ... |
44,063 | Sample preparation for Illumina MiSeq Dual Index metabarcoding | 4 | dx.doi.org/10.17504/protocols.io.bn97mh9n | https://www.protocols.io/view/sample-preparation-for-illumina-miseq-dual-index-m-bn97mh9n | Xiaohuan Sun, Yuehua Hu, Zewei Song | TITLE: Sample preparation for Illumina MiSeq Dual Index metabarcoding
AUTHORS: Xiaohuan Sun, Yuehua Hu, Zewei Song
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The protocol shows amplicon sequencing samples preoared by Illumina Dual Index strategy, and sequened with Illumina MiSeq (RRID:SCR_016... | ["Perform the first PCR (duplicates of each sample) using Illumina adaptor attached primers that target the gene of your choice. Here we present the protocol using the eukaryotic primers 5.8S and ITS4. AB1The primer sequences25.8SR_NexteraTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG3TCGATGAAGAACGCAGCG4ITS4_NexteraGTCTCGTGGCTCGGA... |
19,474 | Transposon insertion sequencing (Tn-seq) library preparation protocol - includes UMI for PCR duplicate removal | null | dx.doi.org/10.17504/protocols.io.w9sfh6e | null | Nagendra palani | TITLE: Transposon insertion sequencing (Tn-seq) library preparation protocol - includes UMI for PCR duplicate removal
AUTHORS: Nagendra palani
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Transposon insertion sequencing (Tn-Seq) is an NGS method to </span><span style = "font-style:italic;">... | ["[Adaptor formation]\nUse 0.1x TE to prepare 100 μM stock of all the oligos.In a 0.2 ml PCR tube, add the following reagents, vortex well, and spin down. Place on the thermal cycler at for (heated lid). -------------------------------------------- After incubation, terminate the incubation and let the heat block... |
86,620 | Retroviral transduction of primary murine CD8 T cells | 4 | dx.doi.org/10.17504/protocols.io.kqdg3xxkpg25/v1 | https://www.protocols.io/view/retroviral-transduction-of-primary-murine-cd8-t-ce-cyt4xwqw | Tamer B Shabaneh, Andrew R Stevens | TITLE: Retroviral transduction of primary murine CD8 T cells
AUTHORS: Tamer B Shabaneh, Andrew R Stevens
[DESCRIPTION]
This protocol will guide you through the process of how our group (Riddell Lab, Fred Hutchinson Cancer Center) generates murine CD8+ CAR T cells.
We normally begin this protocol on Monday, transduce... | ["[Day 1: Plating the plat-E cells] Approximately 20 hours prior to transfection of platinum-E (plat-E) cells, generate a working stock of 0.001 % (v/v) poly-L-lysine (PLL) by diluting 0.1% PLL stock 1:100 in 1x D-PBS and coat a 6-well-plate well with 1.5 mL for 15 min.", "[Day 1: Plating the plat-E cells] Dissociate ... |
101,038 | Library Bottlenecking Protocol (Basic Microbial Culture Equipment) | 0 | dx.doi.org/10.17504/protocols.io.x54v9227pl3e/v2 | https://www.protocols.io/view/library-bottlenecking-protocol-basic-microbial-cul-dewn3fde | David Ross | TITLE: Library Bottlenecking Protocol (Basic Microbial Culture Equipment)
AUTHORS: David Ross
[DESCRIPTION]
Protocol for bottlenecking a library using a basic microbial culture equipment.
[STEPS]
SECTION: Create the first overnight culture
1. Dilute a full 1 mL vial of the library glycerol stock into 50 mL of media i... | ["[Create the first overnight culture] Dilute a full 1 mL vial of the library glycerol stock into 50 mL of media in a 250 mL baffled flask.", "[Prepare all flasks and tubes] Prepare 18 1.5 mL microcentrifuge tubes\nNumber the tubes 1.1, 1.2, 1.3, 2.1, 2.2, 2.3, …, 6.1, 6.2, 6.3\nLeave tubes 1.1, 2.1, 3.1, …, 6.1 empty\... |
34,293 | Sequence alignment for Biochemistry I | null | null | https://www.protocols.io/view/sequence-alignment-for-biochemistry-i-bdqvi5w6 | Belle Houston, Chris Berndsen | TITLE: Sequence alignment for Biochemistry I
AUTHORS: Belle Houston, Chris Berndsen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Comparing DNA or protein sequences can provide insight into the structure or function of newly discovered or characterized open reading frames or proteins. The am... | ["[Obtain Sequence from Uniprot]\nObtain sequence from Uniprot OR extract sequence from structure in YASARA (skip to step 3)\nSome things to note about the sequence you use:If you obtain sequences from Uniprot, these are full sequences of proteins where the structure may not be entirely known for all amino acids. If yo... |
87,530 | Rodent Facility Environmental Summary | 1 | dx.doi.org/10.17504/protocols.io.261ged5qov47/v1 | https://www.protocols.io/view/rodent-facility-environmental-summary-czqix5ue | Debra Dukes, Michael Elmore | TITLE: Rodent Facility Environmental Summary
AUTHORS: Debra Dukes, Michael Elmore
[DESCRIPTION]
Mice (Mus Musculus) are the most common research organisms used in biomedical research. We have
housed and maintained a variety of strains at the Stowers Institute for Medical Research since 2000.
Our environment and housi... | ["Rodent Facility Environmental Summary"] |
null | null | null | dx.doi.org/10.17504/protocols.io.h3nb8me | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol has been optimized for electroporation of natural communities in coastal surface waters. As natural communities may vary in different places, we recommend to use this protocol as a starting point and re-optimize according to the results. Guidelines are provided.... | [] |
59,846 | S1 File The Protocols for preparing the laboratory practical lessons | 4 | dx.doi.org/10.17504/protocols.io.b6perdje | https://www.protocols.io/view/s1-file-the-protocols-for-preparing-the-laboratory-b6perdje | Jessica Gasparello, Matteo Zurlo, Lucia Carmela Cosenza, Giulia Breveglieri, Cristina Zuccato, Roberto Gambari, Alessia Finotti | TITLE: S1 File The Protocols for preparing the laboratory practical lessons
AUTHORS: Jessica Gasparello, Matteo Zurlo, Lucia Carmela Cosenza, Giulia Breveglieri, Cristina Zuccato, Roberto Gambari, Alessia Finotti
[DESCRIPTION]
The protocols here described are related to the sections presented in Figure 1A (open boxes... | ["[S1 File The Protocols for preparing the laboratory practical lessons] A549 cell culture and transfection with pCMV3-Spike-GFPSpark plasmid", "[S1 File The Protocols for preparing the laboratory practical lessons] RNA extraction.", "[S1 File The Protocols for preparing the laboratory practical lessons] A549 cell c... |
101,674 | Amplicon Sequencing for Genotyping S. Typhi | 4 | dx.doi.org/10.17504/protocols.io.36wgq31dylk5/v3 | https://www.protocols.io/view/amplicon-sequencing-for-genotyping-s-typhi-dfii3kce | Jaspreet Mahindroo, Anton Spadar, Catherine Troman, Zoe Dyson, Kathryn Holt, Nick Grassly | TITLE: Amplicon Sequencing for Genotyping S. Typhi
AUTHORS: Jaspreet Mahindroo, Anton Spadar, Catherine Troman, Zoe Dyson, Kathryn Holt, Nick Grassly
[DESCRIPTION]
The following protocol is for amplifying and sequencing amplicons targeting Salmonella Typhi. It is primarily for use with samples that are already suspect... | ["[Preparation for sequencing using ONT Native barcodes] From the ONT kit (SQK-NBD114.24 or .96) thaw AMPure XP beads (AXP), mix by vortexing, then keep at room temperature.\n\nThaw the NEBnext Ultra II End Repair reagents on ice, flick or invert the tubes to mix, then spin down.", "[Preparation for sequencing using ON... |
49,246 | Moore Swab Methods for Concentrating and Detecting Salmonella Typhi and Salmonella Paratyphi A in Environmental Wastewater Samples | 4 | null | https://www.protocols.io/view/moore-swab-methods-for-concentrating-and-detecting-bub6nsre | Pengbo Liu;, Makoto Ibaraki;, Christine Moe | TITLE: Moore Swab Methods for Concentrating and Detecting Salmonella Typhi and Salmonella Paratyphi A in Environmental Wastewater Samples
AUTHORS: Pengbo Liu;, Makoto Ibaraki;, Christine Moe
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This methods describes a tool to concentrate and te... | ["[Summary of Moore Swab]\nThe Moore swab is placed into the source water for 24-72 hours. When water passes through the Moore swab, bacteria such as S. Typhi may be captured by size exclusion, on particulate matter, electrostatic interactions, or by other mechanisms. The sample is enriched in broth to recover the targ... |
38,568 | Making Freezing Solution | 4 | dx.doi.org/10.17504/protocols.io.bhwgj7bw | https://www.protocols.io/view/making-freezing-solution-bhwgj7bw | Priota Islam | TITLE: Making Freezing Solution
AUTHORS: Priota Islam
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The freezing solution can be made in advance and stored in sterile containers at room temperature till needed.</div></div>
[STEPS]
?. [Steps]
Book the autoclave beforehand
?. [Steps]
Make 0.05M K2H... | ["[Steps]\nBook the autoclave beforehand", "[Steps]\nMake 0.05M K2HPO4 by dissolving 8.71g of K2HPO4 in 1L of DIW", "[Steps]\nMake 0.05M KH2PO4 by dissolving 6.80g of KH2PO4 in 1L of DIW", "[Steps]\nMake S Buffer solution by adding the following:129 ml 0.05 M K2HPO4871 ml 0.05 M KH2PO45.85 g NaCl", "[Steps]\nMake the f... |
null | null | null | dx.doi.org/10.17504/protocols.io.uvuew6w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Genome editing using nucleases such as CRISPR-Cas induces programmable DNA damage at a target genomic site, but can also affect off-target sites. We develop a powerful assay for the unbiased identification of off-target sites that we term DISCOVER-seq. This approach takes advant... | ["[RNP editing of cells] {\"blocks\":[{\"key\":\"8v65r\",\"text\":\"Culture your cell line of interest so that you can edit 1x10^7 cells on the day of nucleofection. \",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[{\"offset\":56,\"length\":12,\"style\":\"bold\"}],\"entityRanges\":[],\"data\":[]},{\"key\":\"... |
103,742 | Protocol for Use with Standard Insert Libraries (370-420 bp) (NEB#E7120) | 1 | dx.doi.org/10.17504/protocols.io.261geo8dyl47/v2 | https://www.protocols.io/view/protocol-for-use-with-standard-insert-libraries-37-dhi634he | New England Biolabs | TITLE: Protocol for Use with Standard Insert Libraries (370-420 bp) (NEB#E7120)
AUTHORS: New England Biolabs
[DESCRIPTION]
This protocol details how to construct DNA libraries from start to finish using NEBNext reagents.
The corresponding NEB manual is here: https://www.neb.com/-/media/nebus/files/manuals/manuale71... | ["[DNA Preparation] DNA and Control DNA\nCombine genomic DNA (10–200 ng) with control DNAs specified below. Genomic DNA can be in any of the following buffers:\n10 mM Tris pH 8.0, 1X TE (10mM Tris pH 8.0, 1mM EDTA), or low TE (10 mM Tris pH 8.0, 0.1 mM EDTA).\n \nThe following table is a guide for the amount of (lilac)... |
80,979 | Working in AnVIL: A Clinical Sequencing Evidence-Generating Research (CSER) consortium perspective. | 5 | dx.doi.org/10.17504/protocols.io.q26g7ye68gwz/v1 | https://www.protocols.click/view/working-in-anvil-a-clinical-sequencing-evidence-ge-ctbtwinn | Richard Green, Kathleen Ferar, Jeffrey Ou, Michael Schatz, Stephen Mosher, David R Crosslin, Gail P Jarvik | TITLE: Working in AnVIL: A Clinical Sequencing Evidence-Generating Research (CSER) consortium perspective.
AUTHORS: Richard Green, Kathleen Ferar, Jeffrey Ou, Michael Schatz, Stephen Mosher, David R Crosslin, Gail P Jarvik
[DESCRIPTION]
Analysis, Visualization, and Informatics Lab-space (AnVIL) is a powerful new Genom... | ["[Introduction] AnVIL is a powerful data-sharing genomics platform that allows for data processing and analysis to be shared in the cloud. The goal of this protocol is to get new users that are relatively new to AnVIL up and running. The AnVIL is a cloud-centric platform that provides tools to interface with local har... |
93,400 | Irradiation and single-cell dissociation of hESCs and cortical spheroids | 4 | dx.doi.org/10.17504/protocols.io.bp2l6xwbzlqe/v1 | https://www.protocols.io/view/irradiation-and-single-cell-dissociation-of-hescs-c7fyzjpw | Annika Martin, Hanqin Li, Dirk Hockemeyer | TITLE: Irradiation and single-cell dissociation of hESCs and cortical spheroids
AUTHORS: Annika Martin, Hanqin Li, Dirk Hockemeyer
[DESCRIPTION]
This protocol describes the procedure of irradiation and single-cell dissociation of hESCs and cortical spheroids for MULTI-Seq barcoding and sequencing.
Protocol Overview
... | ["[Irradiation of hESCs] Culture hESCs with feeder-free system (dx.doi.org/10.17504/protocols.io.b4mcqu2w)", "[Irradiation of hESCs] 3 days before irradiation, passage cells and let them grow to approximately 50% confluence.", "[Irradiation of hESCs] On the day of irradiation, change media to hESC media + 10uM Rock Inh... |
68,319 | Glassware & Sample Bottle Cleaning and Sterilization | 1 | dx.doi.org/10.17504/protocols.io.4r3l2odbpv1y/v1 | https://www.protocols.io/view/glassware-amp-sample-bottle-cleaning-and-steriliza-cex7tfrn | Aaron Bivins | TITLE: Glassware & Sample Bottle Cleaning and Sterilization
AUTHORS: Aaron Bivins
[DESCRIPTION]
This protocol outlines the basic procedure for cleaning and sterilizing glassware as performed in the Bivins Lab.
[BEFORE_START]
Prior to cleaning glassware that contains culture-derived materials or sample material, ... | ["[Material Disposal] Used glassware in the lab could contain at variety of materials, chemicals or reagents at the conclusion of experimental procedures. This material must be disposed of properly prior to cleaning and sterilizing glassware. For liquid cultures and samples that DO NOT contain guanidium salts (frequent... |
23,367 | Isolation of ribosome-associated nascent chains of soluble proteins produced in Escherichia coli | null | dx.doi.org/10.17504/protocols.io.23fggjn | null | Renuka Kudva, Andreas Vogt, Kärt Denks, Gunnar von Heijne | TITLE: Isolation of ribosome-associated nascent chains of soluble proteins produced in Escherichia coli
AUTHORS: Renuka Kudva, Andreas Vogt, Kärt Denks, Gunnar von Heijne
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Isolation of ribosome-nascent chains of co-translationally folded domains. Detail... | ["Expression tests (perform after transformation of constructs into KC6 cells)Day 1Pick 5 single clones from plates and seed into 2 ml LB supplemented with antibiotic of choice. Grow overnight at 37°C by shaking at 200 rpm. Prepare a master plate seeded with each of the clones used. Day 2 Sub-culture the overnight cult... |
41,031 | NLP screening (dot blot) | 4 | dx.doi.org/10.17504/protocols.io.bkbfksjn | https://www.protocols.io/view/nlp-screening-dot-blot-bkbfksjn | Andreea S | TITLE: NLP screening (dot blot)
AUTHORS: Andreea S
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In order to determine if the His-tagged NLP is expressed and secreted by the bacteria, we plan to use the dot blot procedure with anti-His tag anti-bodies. Dot blot is an immunological technique used f... | ["On nitrocellulose membrane indicate the blotting region by drawing a grid by pencil.", "Slowly applyof sample on the nitrocellulose membrane at the center of the grid.\n2 µl", "Use purified NLP-His and apply 5 points of increasing concentration of them on the nitrocellulose membrane in order to create a standard conc... |
41,564 | INDICAID Rapid Point-of-Care Test for SARS-CoV-2 Antigen | 4 | dx.doi.org/10.17504/protocols.io.bkt4kwqw | https://www.protocols.io/view/indicaid-rapid-point-of-care-test-for-sars-cov-2-a-bkt4kwqw | Phase Diagnostics | TITLE: INDICAID Rapid Point-of-Care Test for SARS-CoV-2 Antigen
AUTHORS: Phase Diagnostics
[STEPS]
?. [Test Procedure]
The INDICAID Rapid Point-of-Care Test for SARS-CoV-2 Antigen includes swabs for nasal specimen collection.
?. [Test Procedure]
Remove the swab from the nostril and repeat on the other nostril using th... | ["[Test Procedure]\nThe INDICAID Rapid Point-of-Care Test for SARS-CoV-2 Antigen includes swabs for nasal specimen collection.", "[Test Procedure]\nRemove the swab from the nostril and repeat on the other nostril using the same swab.", "[Test Procedure]\nThe Collection Vial cap is composed of two parts. Remove the enti... |
92,489 | A protocol for the extraction of microremains from archaeological human dental calculus | 1 | dx.doi.org/10.17504/protocols.io.3byl4q6r8vo5/v1 | https://www.protocols.io/view/a-protocol-for-the-extraction-of-microremains-from-c6jhzcj6 | Elena Fiorin, Emanuela Cristiani | TITLE: A protocol for the extraction of microremains from archaeological human dental calculus
AUTHORS: Elena Fiorin, Emanuela Cristiani
[DESCRIPTION]
This revised protocol will describe the extraction and analysis of human dental calculus using polarised light microscopy. This step-by-step procedure results from year... | ["[Sampling] Select and document the DC sample\n \nThis is a critical step since DC size and texture vary from sample to sample. Calculus might be: \na) minimal and, once sampled, could break into a fine powder (powdered DC is not suitable for this protocol); \nb) medium-sized, the piece can be easily removed; \nc) lar... |
71,277 | Mouse genetic models to manipulate enterochromaffin cell activity - Murine Organoid ELISA | 1 | dx.doi.org/10.17504/protocols.io.8epv5jz54l1b/v1 | https://www.protocols.io/view/mouse-genetic-models-to-manipulate-enterochromaffi-chumt6u6 | Koki Tohara | TITLE: Mouse genetic models to manipulate enterochromaffin cell activity - Murine Organoid ELISA
AUTHORS: Koki Tohara
[DESCRIPTION]
This protocol describes how we maintain murine intestinal organoids and perform the enzyme-linked immunosorbent assay (ELISA) for serotonin (5-HT).
[STEPS]
SECTION: Preparation or basal ... | ["[Preparation or basal media] Add 5 mL of GlutaMAX, 1 M HEPES, and Penicillin-Streptomycin to 500 mL of Advanced DMEM/F-12 and filter through 0.22 um. This basal media can last up to1 month.", "[Maintenance of intestinal organoids] Put an aliquot of matrigel in fridge at 4°C. Put a 24-well plate to a 37°C incubator.",... |
null | null | null | dx.doi.org/10.17504/protocols.io.ktkcwkw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The consumption of antibiotics is a major driver for the development of antibiotic resistance in bacteria. We identified the trends and patterns of total antibiotic consumption in China’s tertiary hospitals from 2011 to 2015. We retrospectively analyzed aggregated monthly sur... | [] |
75,793 | Automatic Deposition of CHCA Matrix for MALDI Analysis of Lipids | 1 | dx.doi.org/10.17504/protocols.io.ewov1o3xylr2/v1 | https://www.protocols.io/view/automatic-deposition-of-chca-matrix-for-maldi-anal-cm9ru956 | Elizabeth Neumann, Carrie Romer, Jamie Allen, Jeff Spraggins | TITLE: Automatic Deposition of CHCA Matrix for MALDI Analysis of Lipids
AUTHORS: Elizabeth Neumann, Carrie Romer, Jamie Allen, Jeff Spraggins
[DESCRIPTION]
Scope:
To describe the procedure for spraying tissue sections with CHCA for lipids. CHCA is used as a safer matrix to ship coated slides to collaborators.
Expe... | ["[Autofluorescence Scan] Remove slides from freezer and place in desiccator for 30 min .", "[Autofluorescence Scan] Scan for autofluorescence on Zeiss Axio Scanner.", "[TM Sprayer Setup] Change nitrogen to 6 psi and turn on sprayer.", "[TM Sprayer Setup] Open software and set nozzle temperature to 85 °C", "[TM Sprayer... |
80,150 | Semi-Structured Interview Protocol, Community Perceptions and Expectations of the Gump Station in Mo'orea, French Polynesia | 1 | dx.doi.org/10.17504/protocols.io.rm7vzbd32vx1/v1 | https://www.protocols.io/view/semi-structured-interview-protocol-community-perce-cshwwb7e | Grace Sandel | TITLE: Semi-Structured Interview Protocol, Community Perceptions and Expectations of the Gump Station in Mo'orea, French Polynesia
AUTHORS: Grace Sandel
[DESCRIPTION]
This project aims to understand community perceptions and expectations of the Gump Station in Mo’orea, French Polynesia and how the Gump Station can... | ["[Interview questions] Where do you live? How long have you lived on Mo'orea for?", "[Interview questions] What do you do for a living?", "[Interview questions] Have you heard of the Gump Station?", "[Interview questions] What comes to mind when you think about science and research on Mo'orea?", "[Interview questions]... |
21,014 | UC Davis - Meal Pattern Analysis | null | dx.doi.org/10.17504/protocols.io.yrwfv7e | null | Trina Knotts | TITLE: UC Davis - Meal Pattern Analysis
AUTHORS: Trina Knotts
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Behaviorally, meals are defined as periods of intense feeding and drinking separated by periods of activity,... | ["Recommend acclimation to MBP Vivarium Room 115 for one week prior to study.a. Animals will be placed in single housing (duplex cages: one cage with clear divider) after transfer. While acclimating in the MBAL animal room the mice will be introduced to the sifted powdered version of their normal accustomed rodent cho... |
97,394 | Purification of viral RNA from cell culture isolates or FTA cards using MagMAX Viral RNA Isolation Kit | 0 | dx.doi.org/10.17504/protocols.io.x54v928mml3e/v1 | https://www.protocols.io/view/purification-of-viral-rna-from-cell-culture-isolat-dbcs2iwe | Erika Bujaki, Dimitra Klapsa, Kafayat Arowolo, Joyce Akello, Nick Grassly, Javier Martin | TITLE: Purification of viral RNA from cell culture isolates or FTA cards using MagMAX Viral RNA Isolation Kit
AUTHORS: Erika Bujaki, Dimitra Klapsa, Kafayat Arowolo, Joyce Akello, Nick Grassly, Javier Martin
[DESCRIPTION]
This protocol describes the viral nucleic acid recovery and purification from poliovirus isolates... | ["[Reagent Preparation] DTT solution (1M)\nDissolve 0.6168g of DTT in 4 ml of Nuclease Free water.\nSterilize by filtration with 0.45 µm syringe filter unit and a 5 ml syringe.\nPrepare aliquots and store at -20°C.", "[Reagent Preparation] To process samples from FTA cards, prepare all the reagents listed, to start fro... |
95,341 | Immunofluorescence staining, vibratome sections | 1 | dx.doi.org/10.17504/protocols.io.3byl4qoxrvo5/v1 | https://www.protocols.io/view/immunofluorescence-staining-vibratome-sections-c9cmz2u6 | eduard.bentea, María Sanchiz Calvo, Veerle Baekelandt | TITLE: Immunofluorescence staining, vibratome sections
AUTHORS: eduard.bentea, María Sanchiz Calvo, Veerle Baekelandt
[DESCRIPTION]
Protocol for performing immunofluorescence staining on free-floating vibratome cut brain sections from rats or mice.
[STEPS]
SECTION: Day 1
1. Transfer sections to be stained to a new 24... | ["[Day 1] Transfer sections to be stained to a new 24-well plate filled with 1X PBS. All incubations are with 500 µL solution per well unless stated otherwise.", "[Day 1] Antigen retrieval step (using oven).", "[Day 1] Incubate sections in antigen retrieval solution (10 mM citrate buffer pH 6.0 ; see recipe in Material... |
39,632 | AMOVA AND PHILOGENY IN HIV-1 PROTOCOLS | 5 | dx.doi.org/10.17504/protocols.io.bixqkfmw | https://www.protocols.io/view/amova-and-philogeny-in-hiv-1-protocols-bixqkfmw | Pierre Teodosio | TITLE: AMOVA AND PHILOGENY IN HIV-1 PROTOCOLS
AUTHORS: Pierre Teodosio
[STEPS]
?. [METHODOLOGY]
?. [METHODOLOGY]
DATABANK: The 153 gene sequences of the integrase gene of human immunodeficiency virus 1 were collected from GENBANK (https://www.ncbi.nlm.nih.gov/popset/?term=MN888087.1 and participate in a PopSet dipped ... | ["[METHODOLOGY]", "[METHODOLOGY]\nDATABANK: The 153 gene sequences of the integrase gene of human immunodeficiency virus 1 were collected from GENBANK (https://www.ncbi.nlm.nih.gov/popset/?term=MN888087.1 and participate in a PopSet dipped by Totmenin and collaborators on March 25, 2020 (Popset:1822236350).", "[METHODO... |
78,544 | Preparing Agarose Gel | 4 | dx.doi.org/10.17504/protocols.io.kqdg391q1g25/v1 | https://www.protocols.io/view/preparing-agarose-gel-cqxqvxmw | alyssa.jeng | TITLE: Preparing Agarose Gel
AUTHORS: alyssa.jeng
[DESCRIPTION]
N/A
[STEPS]
SECTION: Materials
1. 1X TAE Buffer
SYBRsafe
Agarose powder
Weigh boat
500mL Erlenmeyer flask
Gel Electrophoresis tray
Gel Electrophoresis comb
Tape
SECTION: Procedure
2. Tape up the gel electrophoresis tray and add well comb
SECTION: Procedu... | ["[Materials] 1X TAE Buffer\nSYBRsafe\nAgarose powder\nWeigh boat\n500mL Erlenmeyer flask\nGel Electrophoresis tray\nGel Electrophoresis comb\nTape", "[Procedure] Tape up the gel electrophoresis tray and add well comb", "[Procedure] Add 200mL of 1X TAE buffer to the Erlenmeyer flask", "[Procedure] Weigh the right amoun... |
16,524 | Defining critical illness – a scoping review and thematic content analysis: Protocol for a scoping review. | null | dx.doi.org/10.17504/protocols.io.udkes4w | null | Hedi Mollazadegan, Tim Baker, Helle Mölsted Alvesson, Martin Gerdin Wärnberg | TITLE: Defining critical illness – a scoping review and thematic content analysis: Protocol for a scoping review.
AUTHORS: Hedi Mollazadegan, Tim Baker, Helle Mölsted Alvesson, Martin Gerdin Wärnberg
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;"> </span><span styl... | ["[Protocol and registration]\nA protocol will be registered with protocols.io.", "[Eligibility criteria]\nThe inclusion criteria are:All documents and articles identified by the search that discuss critical illness, are written in English, are published since 2008, and involve only human subjects, will be included. We... |
49,802 | Ultrafiltration Methods for Concentrating and Detecting Salmonella Typhi and Salmonella Paratyphi A in Wastewater Samples | 4 | null | https://www.protocols.io/view/ultrafiltration-methods-for-concentrating-and-dete-buvinw4e | Pengbo Liu, Makoto Ibaraki, Christine Moe | TITLE: Ultrafiltration Methods for Concentrating and Detecting Salmonella Typhi and Salmonella Paratyphi A in Wastewater Samples
AUTHORS: Pengbo Liu, Makoto Ibaraki, Christine Moe
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Tangential flow ultrafiltration is used to concentrate large vol... | ["[Ultrafiltration Preparation]", "[Ultrafiltration Procedures]", "[Ultrafiltration Cleanup]", "[PEG Precipitation]", "[DNA Extraction]", "[Real-time PCR Detection of Salmonella Typhi and Paratyphi]"] |
82,475 | ADI IsletCore Minimal Donor Criteria | 1 | null | https://www.protocols.click/view/adi-isletcore-minimal-donor-criteria-cusjwwcn | Jocelyn E Manning Fox, James Lyon, Patrick MacDonald | TITLE: ADI IsletCore Minimal Donor Criteria
AUTHORS: Jocelyn E Manning Fox, James Lyon, Patrick MacDonald
[DESCRIPTION]
This SOP defines the pancreas donor profile acceptable for use by the Alberta Diabetes Institute IsletCore in their human islet isolation program.
ADI IsletCore receives pancreases from multiple Ca... | ["[ADI IsletCore Donor Inclusion Criteria] The following are ADI IsletCore inclusion criteria for pancreas donors for human islet isolation:\n\nA multi-organ donor or pancreas-only donor if the donor meets all the criteria for multi-organ donation\nAny type of donation (NDD, DCD, MAiD)\nDCD warm ischemia time <30 minut... |
63,347 | Thawing Cells | 4 | dx.doi.org/10.17504/protocols.io.eq2lyn1mevx9/v1 | https://www.protocols.io/view/thawing-cells-b94tr8wn | salvatore spanò | TITLE: Thawing Cells
AUTHORS: salvatore spanò
[DESCRIPTION]
Thawing cells, routine lab protocol
[STEPS]
SECTION: Thawing Cells
1. Take the cryovial from nitrogen, clean it with disinfectant, put it in the waterbath set to 37°C.
SECTION: Thawing Cells
2. In the meanwhile prepare a flask tagging it with cell line name... | ["[Thawing Cells] Take the cryovial from nitrogen, clean it with disinfectant, put it in the waterbath set to 37°C.", "[Thawing Cells] In the meanwhile prepare a flask tagging it with cell line name, passage, date and operator. Fill it with medium 10ml.\nIf coating is required, check in advance which kind of is needed.... |
36,650 | Imaging Mass Cytometry Data Acquisition | null | dx.doi.org/10.17504/protocols.io.bf2ijqce | https://www.protocols.io/view/imaging-mass-cytometry-data-acquisition-bf2ijqce | Michelle Daniel, Marda Jorgensen | TITLE: Imaging Mass Cytometry Data Acquisition
AUTHORS: Michelle Daniel, Marda Jorgensen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This SOP describes the image acquisition with an Imaging Mass Cytometer (IMC or</div><div class = "text-block">Hyperion).</div><div class = "text-block">Prior to t... | ["[Set up the flat-bed scanner]\n1. Attach the flat-bed scanner to a computer.", "[Create overview images of the slides]\n1. Use the flat-bed scanner with the custom sample holder and load up to 12 slides to be acquired.2. Scan the slides to .jpg at a resolution of 600 dpi and save the image.\nThe low resolution overvi... |
64,951 | Standard Operating Procedure for conducting larval and pupal surveys for Anopheles | 1 | dx.doi.org/10.17504/protocols.io.14egn7ro6v5d/v1 | https://www.protocols.io/view/standard-operating-procedure-for-conducting-larval-cbnxsmfn | Tanya L L Russell, Kyran Staunton, Thomas R Burkot | TITLE: Standard Operating Procedure for conducting larval and pupal surveys for Anopheles
AUTHORS: Tanya L L Russell, Kyran Staunton, Thomas R Burkot
[DESCRIPTION]
This SOP describes the materials and methods to perform larval surveys of anopheline mosquitoes.
Description: Larval sampling involves capturing immatur... | ["Gather all equipment required.", "Once a potential habitat has been identified:\nProceed slowly and step lightly to not vibrate the water or disturb the vegetation more than is necessary.\nApproach the water facing the sun to avoid casting a shadow on the water.\nIf there is a strong wind, dipping should be done on t... |
101,549 | Working with patient-derived enteroids and colonoids | 4 | dx.doi.org/10.17504/protocols.io.ewov1q7e2gr2/v2 | https://www.protocols.io/view/working-with-patient-derived-enteroids-and-colonoi-dfem3jc6 | Tatiana Karakasheva | TITLE: Working with patient-derived enteroids and colonoids
AUTHORS: Tatiana Karakasheva
[DESCRIPTION]
This is a compilations of protocols for working with patient-derived enteroids or colonoids, from recovery to cryopreservation, in expansion culture (minimal differentiation)
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.phidj4e | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
30,785 | Cell Surface Flow Cytometry Staining Protocol | null | dx.doi.org/10.17504/protocols.io.baa9iah6 | null | Sam Li | TITLE: Cell Surface Flow Cytometry Staining Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Harvest Tissue or Cells:]
Obtain desired tissue (e.g. spleen, lymph node, thymus, bone marrow) and prepare a single cell suspension in Cell Staining Buffer (BioLegend Cat. No. 420201). If u... | ["[Harvest Tissue or Cells:]\nObtain desired tissue (e.g. spleen, lymph node, thymus, bone marrow) and prepare a single cell suspension in Cell Staining Buffer (BioLegend Cat. No. 420201). If using in vitro stimulated cells, simply resuspend previously activated cultures in Cell Staining Buffer and proceed to Step 2.",... |
null | null | null | dx.doi.org/10.17504/protocols.io.ersbd6e | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p><strong>MATERIALS</strong></p>
<p> </p>
<p> 1) Overnight cultures of the bacterial recombinants to be screened</p>
<p> 2) Agarose beads</p>
<p> 3) Phenol:Chloroform (1:1)</p>
<p> 4) Microfuge tubes</p>
<p> <br /><strong>Refer... | [] |
48,784 | Isolation of mouse brain pericytes (PDGFR-B+) using magnetic sorting (MACS) | 4 | dx.doi.org/10.17504/protocols.io.yxmvmk5bbg3p/v1 | https://www.protocols.io/view/isolation-of-mouse-brain-pericytes-pdgfr-b-using-m-btvqnn5w | Daniel Manrique-Castano | TITLE: Isolation of mouse brain pericytes (PDGFR-B+) using magnetic sorting (MACS)
AUTHORS: Daniel Manrique-Castano
[DESCRIPTION]
This protocol employs a modified procedure of the Adult Brain Dissociation kit (Miltenyi Biotec) to sort PDGFR-B+ cells from mouse brains. The protocol is adapted to enhance cell recovery a... | ["[Mouse euthanasia and tissue dissection] Euthanize mice employing CO2 or decapitation according to institutional guidelines.", "[Mouse euthanasia and tissue dissection] Remove the brain following standard procedures, avoiding tissue damage. Place the brain in falcon tubes or 10-cm Petri dishes filled with 1x on ice... |
80,463 | Check the integrity of a dataset stored on Amazon S3 | 5 | dx.doi.org/10.17504/protocols.io.n92ld9qy9g5b/v2 | https://www.protocols.io/view/check-the-integrity-of-a-dataset-stored-on-amazon-cstpwemn | Sonia García-Ruiz | TITLE: Check the integrity of a dataset stored on Amazon S3
AUTHORS: Sonia García-Ruiz
[DESCRIPTION]
Background
Amazon Simple Storage Service (Amazon S3) has become a widely used and reliable platform for storing large biomedical datasets. However, unintended changes to the original data can occur during the data w... | ["[Clone GitHub repositories and tool configuration] Clone the s3md5 repo:", "[Clone GitHub repositories and tool configuration] Grant execution access to the s3md5 script file:", "[Clone GitHub repositories and tool configuration] Clone the aws-s3-integrity-check repo:", "[Clone GitHub repositories and tool configurat... |
43,690 | Analysis of Primary Cilia in Rodent Brain By Immunofluorescence Microscopy | 4 | dx.doi.org/10.17504/protocols.io.bnwimfce | https://www.protocols.io/view/analysis-of-primary-cilia-in-rodent-brain-by-immun-bnwimfce | Shahzad S. Khan, Herschel S. Dhekne, Francesca Tonelli, Suzanne R. Pfeffer | TITLE: Analysis of Primary Cilia in Rodent Brain By Immunofluorescence Microscopy
AUTHORS: Shahzad S. Khan, Herschel S. Dhekne, Francesca Tonelli, Suzanne R. Pfeffer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We describe here our method for immunostaining of primary cilia in brain sections from... | ["[Perfusion ]\nSoak the hair surrounding the ventral thorax of the mouse with .\n[ethanol]", "[Perfusion ]\nBefore making the incision, determine anesthetic depth by toe-pinch to verify absence of a withdrawal reflex.", "[Perfusion ]\nMake a midline incision through the skin over the proximal abdomen and thorax.", "[P... |
null | null | null | dx.doi.org/10.17504/protocols.io.gvrbw56 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Synthesis helps to facilitate the chemical production process. As a mature performance of synthesis technology, <a href="http://www.bocsci.com/carbohydrate-service.html" target="_blank">carbohydrate synthesis service</a> and <a href="http://www.bocsci.com/biosynthesis-of-chem... | [] |
90,887 | Cytokine profiling analysis on conditioned medium of human neurons using Luminex multiplex assay | 4 | dx.doi.org/10.17504/protocols.io.n2bvj3qm5lk5/v1 | https://www.protocols.io/view/cytokine-profiling-analysis-on-conditioned-medium-c4zfyx3n | Ching-Chieh Chou, Judith Frydman | TITLE: Cytokine profiling analysis on conditioned medium of human neurons using Luminex multiplex assay
AUTHORS: Ching-Chieh Chou, Judith Frydman
[DESCRIPTION]
This protocol is used to identify secreted inflammatory factors by cytokine profiling of the conditioned medium from human transdifferentiated neurons of healt... | ["[Sample collection] At post-induction day 35 to 38, human transdifferentiated neurons undergo the final round of medium change.", "[Sample collection] Two days after medium change, a minimum of 200 µL of cell culture medium per\nsample is collected to run duplicate wells without dilution.", "[Sample collection] Condi... |
59,065 | Testowy protokół | 4 | dx.doi.org/10.17504/protocols.io.b5wzq7f6 | https://www.protocols.io/view/testowy-protok-b5wzq7f6 | lukasz.lukjaniuk | TITLE: Testowy protokół
AUTHORS: lukasz.lukjaniuk
[DESCRIPTION]
To testowa protokół do zrobienia czegos
[STEPS]
SECTION: Section 1
9. ANB
SECTION: Section 1
9. AScdascd
9.
9.
9.
9.
9. | ["[Section 1] ANB", "[Section 1] AScdascd"] |
53,763 | Targeted ExSeq -- Probe Generation | 5 | dx.doi.org/10.17504/protocols.io.byrbpv2n | https://www.protocols.io/view/targeted-exseq-probe-generation-byrbpv2n | Anubhav Sinha, Fei Chen, Shahar Alon, Ed Boyden | TITLE: Targeted ExSeq -- Probe Generation
AUTHORS: Anubhav Sinha, Fei Chen, Shahar Alon, Ed Boyden
[DESCRIPTION]
This protocol accompanies Expansion Sequencing (ExSeq), and describes the process of generating padlock probes for targeted ExSeq. The steps detailed here are a generalization of the protoco... | ["[Preparation] Setting up BLAST with MATLAB and Building BLAST Database\n\nThe selection of appropriate homology regions for probe generation screens candidate transcript regions against the transcriptome to eliminate sequences with off-target homology. In this section, BLAST is installed locally, the files needed to ... |
53,035 | A systematic literature review into the success rate of discontinuation glucocorticoids after their use as bridging therapy in clinical trials and observational cohorts | 1 | dx.doi.org/10.17504/protocols.io.bx2jpqcn | https://www.protocols.io/view/a-systematic-literature-review-into-the-success-ra-bx2jpqcn | l.van_ouwerkerk , Sa Bergstra | TITLE: A systematic literature review into the success rate of discontinuation glucocorticoids after their use as bridging therapy in clinical trials and observational cohorts
AUTHORS: l.van_ouwerkerk , Sa Bergstra
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Obj... | ["[Methods]\nReview strategy\nThe program Rayyan will be used to keep track of the reviewing process: \nM. Ouzzani, H.Hammady, Z. Fedorowicz, A. Elmagarmid. Rayyan — a web and mobile app for systematic reviews. Systematic Reviews (2016) 5:210, DOI: 10.1186/s13643-016-0384-4.\n\nSearch results will first be screened by ... |
103,081 | Purification mCherry-ATG13 IDR | 0 | dx.doi.org/10.17504/protocols.io.81wgbz4m1gpk/v1 | https://www.protocols.io/view/purification-mcherry-atg13-idr-dgwh3xb6 | Elias Adriaenssens | TITLE: Purification mCherry-ATG13 IDR
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol details the purification of mCherry-ATG13 IDR.
[STEPS]
SECTION: Purification
1. To purify mCherry-tagged ATG13 IDR, fuse the coding sequence for ATG13 (190-517aa) or ATG13 (230-517aa) to a N-terminal 6xHis-TEV-mCherry-tag th... | ["[Purification] To purify mCherry-tagged ATG13 IDR, fuse the coding sequence for ATG13 (190-517aa) or ATG13 (230-517aa) to a N-terminal 6xHis-TEV-mCherry-tag through cloning into a pET-DUET1 vector (plasmids available from Addgene).", "[Purification] After the transformation of the pET-DUET1 vectors encoding the mCher... |
63,143 | Optogenetic Manipulation (Mouse) | 4 | dx.doi.org/10.17504/protocols.io.b9wfr7bn | https://www.protocols.io/view/optogenetic-manipulation-mouse-b9wfr7bn | Alexandra Nelson | TITLE: Optogenetic Manipulation (Mouse)
AUTHORS: Alexandra Nelson
[DESCRIPTION]
This protocol describes the steps for in vivo ontogenetic manipulation in mice, including assembly of fiber-ferrules, surgical implantation of fibers, and testing procedure.
[STEPS]
1. Fiber-ferrule implant assembly.
2. Surgery.
3. ... | ["Fiber-ferrule implant assembly.", "Surgery.", "Habituation.", "Computer and optical setup. You can send TTL pulses to the laser device via several systems (Noldus, Master8, Arduino).", "Testing. These steps are specific to the type of experiment you are running.", "Cleanup.", "To make your own optical fiber-ferrule a... |
42,798 | High resolution Nano-DESI mass spectrometry imaging of proteomics of tissue | 1 | dx.doi.org/10.17504/protocols.io.bm2nk8de | https://www.protocols.io/view/high-resolution-nano-desi-mass-spectrometry-imagin-bm2nk8de | yang1832 , Julia Laskin | TITLE: High resolution Nano-DESI mass spectrometry imaging of proteomics of tissue
AUTHORS: yang1832 , Julia Laskin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Scope:</div><div class = "text-block">Acquire imaging mass spectrometry (IMS) datasets of proteins on human kidney tissue with ~12μm spa... | ["Scanned the tissue section with PathScan Enabler IV to visuslize the morphology in optical image.", "Calibrate the instrument with Agilent tune mix.", "Set up the appropriate method for proteins.", "Place the slide on the slide holder and set up the primary capillary and secondary capillary and the solvent flow rate ... |
83,336 | A custom-made hydroponic culture system to study plant roots during root infection with Plasmodiophora brassicae | 4 | dx.doi.org/10.17504/protocols.io.8epv5z12dv1b/v2 | https://www.protocols.click/view/a-custom-made-hydroponic-culture-system-to-study-p-cvmgw43w | Susann Auer | TITLE: A custom-made hydroponic culture system to study plant roots during root infection with Plasmodiophora brassicae
AUTHORS: Susann Auer
[DESCRIPTION]
Plant roots are fascinating organs that anchor the plant in the ground, take up water and nutrients and are the interaction zone for plants with their surrounding m... | ["[Setup of the system] Place tip rack in the clean container and fill 10 ml pipette tips with sand to the top.", "[Setup of the system] Tap the tip lightly on a hard surface to make sure the sand does spread evenly in the tip. Fill tip up again to the top if necessary. You don´t want the sand to be packed too tightly ... |
41,884 | AMDx Lateral Flow Assay WIth a Cover Protocol | 3 | dx.doi.org/10.17504/protocols.io.bk54ky8w | https://www.protocols.io/view/amdx-lateral-flow-assay-with-a-cover-protocol-bk54ky8w | samz | TITLE: AMDx Lateral Flow Assay WIth a Cover Protocol
AUTHORS: samz
[STEPS] | [] |
74,683 | Unified pH measurement v2 | 6 | dx.doi.org/10.17504/protocols.io.n92ld9dj8g5b/v2 | https://www.protocols.io/view/unified-ph-measurement-v2-ck63uzgn | Agnes Heering, Ivo Leito, Markus Lahe, Martin Vilbaste, John Paulo Samin | TITLE: Unified pH measurement v2
AUTHORS: Agnes Heering, Ivo Leito, Markus Lahe, Martin Vilbaste, John Paulo Samin
[DESCRIPTION]
The purpose of this document is to present technical guidance of measuring pHabsH2O difference (ΔpHabsH2O value) between two solutions by differential potentiometry in a cell with two compar... | ["[Software] Start Quick IV Measurement Software.", "[Software] On the left hand pick Function “Source & Sampling”.", "[Software] Right hand side click on tab “Channel Communication”. Click on “Search Channels”, which opens a new window. Select USB interface and search for the channel. After the search click on the cha... |
19,354 | Embedding Rat Heart | null | dx.doi.org/10.17504/protocols.io.w52fg8e | null | Shaina Robbins | TITLE: Embedding Rat Heart
AUTHORS: Shaina Robbins
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Heart Removal]
Remove heart from rat immediately following sacrificeRinse heart in 1X PBS for to flush blood from the chambers
?. [Embedding Heart]
Place heart (still beating) in solution of 1X PBS with 25%... | ["[Heart Removal]\nRemove heart from rat immediately following sacrificeRinse heart in 1X PBS for to flush blood from the chambers", "[Embedding Heart]\nPlace heart (still beating) in solution of 1X PBS with 25% Optimal Cutting Temperature Compound (OCT) for with gentle agitationPlace heart in solution of 1X PBS with... |
51,772 | Preparation of fibrils for intracerebral injection | 1 | dx.doi.org/10.17504/protocols.io.bws4pegw | https://www.protocols.io/view/preparation-of-fibrils-for-intracerebral-injection-bws4pegw | The Michael J Fox Foundation Pff Standardization Consortium | TITLE: Preparation of fibrils for intracerebral injection
AUTHORS: The Michael J Fox Foundation Pff Standardization Consortium
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a consensus protocol developed through discussions with Laura Volpicelli-Daley, Caryl Sortwell, Kelvin Luk, Lindsey G... | ["[Preparation of fibrils for intracerebral injection. Perform ~1-2 hours prior to surgery. This takes about 30 min.]\nPerform all sonication steps in a fume hood or biosafety cabinet.\nEnsure that hood is externally ducted and does not re-circulate exhaust into the laboratory space.", "[Preparation of fibrils for intr... |
null | null | null | dx.doi.org/10.17504/protocols.io.s6yehfw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Since the 20th century, medical scientists represented by Paul Ehrlich, the father of chemotherapy, have been searching for such a "magic bullet" that distinguishes between pathogens and normal cells. Since the beginning of the new century, more and more people believe that a... | [] |
81,093 | Field sampling for drinking water | 1 | dx.doi.org/10.17504/protocols.io.ewov1o6bplr2/v1 | https://www.protocols.io/view/field-sampling-for-drinking-water-ctfdwji6 | Sneha Shrestha, Christopher LeBoa | TITLE: Field sampling for drinking water
AUTHORS: Sneha Shrestha, Christopher LeBoa
[DESCRIPTION]
The method we used for sampling drinking water for households when detecting S. Typhi and Paratyphi in Nepal
[GUIDELINES]
Sterility during water sample collection
1. Sterility of collected water sample: The primary risk... | ["All water will be collected at the point closest to the origination of that water supply prior to end-\ruser treatment to minimize the time for S. Typhi or Paratyphi DNA to degrade in \r\nwater, if present. If the only option is to sample from water that has been stored, choose the \r\nfreshest (most recently stored)... |
82,658 | Freely moving recording: Chronic recoverable Neuropixels in mice | 1 | dx.doi.org/10.17504/protocols.io.n92ldzz2ov5b/v6 | https://www.protocols.click/view/freely-moving-recording-chronic-recoverable-neurop-cuyawxse | Emily A Aery Jones | TITLE: Freely moving recording: Chronic recoverable Neuropixels in mice
AUTHORS: Emily A Aery Jones
[DESCRIPTION]
This protocol collection explains how to build a low-cost, lightweight system to implant 1 Neuropixels 1.0 probe or 2 Neuropixels 2.0 probes into mice, record during freely moving behavior, then recover th... | ["[Design the enclosure] Consider what acrylic to use (e.g. 1/4\" P95 matte black acrylic).\nUse black if you're planning to track LEDs in the dark or white if you're planning to track a Black6 mouse based on center of mass.\nUse matte finish to reduce reflections from LEDs and overhead lights.\nThicker material makes ... |
36,806 | Spatial Localization of 3D Scanned EEG Electrodes with MeshLab | 1 | dx.doi.org/10.17504/protocols.io.261geo8zjl47/v1 | https://www.protocols.io/view/spatial-localization-of-3d-scanned-eeg-electrodes-bf7ejrje | Joel P Diaz-Fong, Jordana Glouberman, Agatha Lenartowicz | TITLE: Spatial Localization of 3D Scanned EEG Electrodes with MeshLab
AUTHORS: Joel P Diaz-Fong, Jordana Glouberman, Agatha Lenartowicz
[DESCRIPTION]
This protocol outlines step-by-step instructions for utilizing Meshlab's PickPoints tool to facilitate spatial localization of electroencephalogram (EEG) electrodes from... | ["[Spatial Localization] Open the PickPoints Tool\nOnce the model is imported into the MeshLab software, you can begin to localize the fiducial and electrode coordinates with the PickPoints tool.\nTo start, find the PickPoints icon in the toolbar or select Edit > PickPoints", "[Extract Coordinates] Finally, the coordin... |
null | null | null | dx.doi.org/10.17504/protocols.io.g7zbzp6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div title="Page 2">
<p>Housekeeping proteins (HKPs) are routinely used as loading controls for Western blot normalization. Accurate normalization requires stable expression of the HKP across all experimental conditions and treatments. Because HKP normalization relies on a singl... | [] |
59,542 | Automatic Multi-functional Integration Program (AMFIP) towards All-optical Mechano-electrophysiology Interrogation | 1 | dx.doi.org/10.17504/protocols.io.b6dwra7e | https://www.protocols.io/view/automatic-multi-functional-integration-program-amf-b6dwra7e | Qin Luo, Justin Zhang, Miao Huang, Gaoming Lin, Mai Tanaka, Sharon Lepler, Juan Guan, Dietmar Siemann, Xin Tang | TITLE: Automatic Multi-functional Integration Program (AMFIP) towards All-optical Mechano-electrophysiology Interrogation
AUTHORS: Qin Luo, Justin Zhang, Miao Huang, Gaoming Lin, Mai Tanaka, Sharon Lepler, Juan Guan, Dietmar Siemann, Xin Tang
[DESCRIPTION]
Automatic operations of multi-functional and time-lap... | [] |
46,125 | The Efficacy and Safety of a Radial Approach versus a Distal Radial Approach for Diagnostic Coronary Angiography and Percutaneous Coronary Intervention: A Systematic Review and Meta-analysis (protocol) | 1 | dx.doi.org/10.17504/protocols.io.bramm2c6 | https://www.protocols.io/view/the-efficacy-and-safety-of-a-radial-approach-versu-bramm2c6 | Toshihide Izumida, Jun Watanabe, Ryo Yoshida, Kazuhiko Kotani | TITLE: The Efficacy and Safety of a Radial Approach versus a Distal Radial Approach for Diagnostic Coronary Angiography and Percutaneous Coronary Intervention: A Systematic Review and Meta-analysis (protocol)
AUTHORS: Toshihide Izumida, Jun Watanabe, Ryo Yoshida, Kazuhiko Kotani
[DESCRIPTION]
<div class = "text-blocks... | [] |
49,688 | Trauma, Social Harm and Health in Criminal Justice Involved Women: The Women's Risk Needs Assessment Validation Research Study | 1 | dx.doi.org/10.17504/protocols.io.burynv7w | https://www.protocols.io/view/trauma-social-harm-and-health-in-criminal-justice-burynv7w | Professor Simon Pemberton, Dr Susie Balderston, Dr Joanna Long | TITLE: Trauma, Social Harm and Health in Criminal Justice Involved Women: The Women's Risk Needs Assessment Validation Research Study
AUTHORS: Professor Simon Pemberton, Dr Susie Balderston, Dr Joanna Long
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Study ... | [] |
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