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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103,175 | Coimmunoprecipitation | 0 | dx.doi.org/10.17504/protocols.io.14egn6m8pl5d/v1 | https://www.protocols.io/view/coimmunoprecipitation-dgzf3x3n | Shiyi Wang | TITLE: Coimmunoprecipitation
AUTHORS: Shiyi Wang
[DESCRIPTION]
Co-Immunoprecipitation assays in HEK cells
[STEPS]
1. **Transfect HEK293T Cells** - Transfect HEK293T cells with Ezrin/Atg7 cDNA using X-tremeGENE HP (Roche) 36 hours prior to lysis. - Grow cells to 85-90% confluency.
2. **Collect Cells for Lysis** - At 3... | ["**Transfect HEK293T Cells** - Transfect HEK293T cells with Ezrin/Atg7 cDNA using X-tremeGENE HP (Roche) 36 hours prior to lysis. - Grow cells to 85-90% confluency.", "**Collect Cells for Lysis** - At 36 hours post-transfection, rinse cells with 1x PBS. - Collect cells for lysis.", "**Lysis and Protein Extraction** - ... |
27,877 | High Resolution Imaging Mass Spectrometry Analysis using Bruker Daltonics Platforms | null | dx.doi.org/10.17504/protocols.io.7gdhjs6 | null | Elizabeth Neumann, Jamie Allen, David Anderson, Danielle Gutierrez, Jeff Spraggins | TITLE: High Resolution Imaging Mass Spectrometry Analysis using Bruker Daltonics Platforms
AUTHORS: Elizabeth Neumann, Jamie Allen, David Anderson, Danielle Gutierrez, Jeff Spraggins
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Scope:</div><div class = "text-block"><span>Acquire 10 μm spatial res... | ["Scann a 3200 dpi image of the matrix coated tissue section in the MTP slide adapter 2 with sufficient contrast to visualize the tissue boundaries.", "Choose a method that has \"height correct\" initiated upon sample docking.", "While the height correct profile is being generated, open FlexImaging and follow the promp... |
41,057 | Bubble strip aqueous gas sampling | 1 | dx.doi.org/10.17504/protocols.io.bkb9ksr6 | https://www.protocols.io/view/bubble-strip-aqueous-gas-sampling-bkb9ksr6 | Daniel B Nothaft | TITLE: Bubble strip aqueous gas sampling
AUTHORS: Daniel B Nothaft
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The "bubble strip" method has been shown to be an effective means for sampling a gas phase in equilibrium with water (Kampbell et al., 1998). Here, a method optimized for sampling large... | ["[Prepping sample vials]\nPre-treat blue chlorobutyl stoppers to reduce potential contaminants by boiling in 0.1 N NaOH for 45 min followed by immersion in distilled water for ~8 hours), according to procedure of Oremland et al. (1987).Oremland R. S., Miller L. G. and Whiticar M. J. (1987) Sources and flux of natural ... |
28,713 | Protocol of HIV TDR and Subtype test in Beijing | null | dx.doi.org/10.17504/protocols.io.8ahhsb6 | null | Jingrong Ye | TITLE: Protocol of HIV TDR and Subtype test in Beijing
AUTHORS: Jingrong Ye
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We analyzed the demographic, clinical, and virological data of residents newly diagnosed with HIV in Beijing. We did population-based sequencing of the pol gene on plasma speci... | ["Ethics: Beijing CDC Ethics Committee approved the study. By law, consent was not required because these data were collected and analyzed in the course of routine public health surveillance.", "Study patients:The Beijing HIV laboratory network (BHLN), established in 1986, is a collaboration engaged in HIV diagnosis in... |
6,451 | Phage Buffer | null | dx.doi.org/10.17504/protocols.io.iitccen | null | Dr. Steven Wilhelm | TITLE: Phage Buffer
AUTHORS: Dr. Steven Wilhelm
[DESCRIPTION]
<p>Please contact Dr. Steven Wilhelm (wilhelm@utk.edu) for additional information regarding this protocol. </p>
[STEPS]
?. In a one liter bottle, add 10 ml MgSO4.
[1 Molar]
?. Add 1 ml CaCl2
[1 Molar]
?. Add 1 ml Tris-HCl (pH~7)
[1 Molar]
?. Add 1 g gelati... | ["In a one liter bottle, add 10 ml MgSO4.\n[1 Molar]", "Add 1 ml CaCl2\n[1 Molar]", "Add 1 ml Tris-HCl (pH~7)\n[1 Molar]", "Add 1 g gelatin.\n1 g", "Add Milli-Q water to a final volume of 1000 mL and autoclave sterilize."] |
77,702 | qPCR of α-synuclein, TNF and NF-κβ | 4 | dx.doi.org/10.17504/protocols.io.rm7vzb2z2vx1/v1 | https://www.protocols.io/view/qpcr-of-synuclein-tnf-and-nf-cp5evq3e | Michael J Hurley | TITLE: qPCR of α-synuclein, TNF and NF-κβ
AUTHORS: Michael J Hurley
[DESCRIPTION]
A procedure for quantitative real time reverse transcription PCR of α-synuclein, TNF and NF-κβ
[STEPS]
SECTION: qPCR
1. Extract total RNA and protein from cells or tissue using TRI Reagent® solution according to the manufacturer's ins... | ["[qPCR] Extract total RNA and protein from cells or tissue using TRI Reagent® solution according to the manufacturer's instructions. Use RNase free glycogen as a carrier for the total RNA.\nKeep protein for use in western blot.", "[qPCR] Measure the concentration of RNA with a spectrophotometer (e.g. Nanodrop 1000).",... |
39,995 | low input ChIP-sequencing of immune cells | 4 | dx.doi.org/10.17504/protocols.io.bja3kign | https://www.protocols.io/view/low-input-chip-sequencing-of-immune-cells-bja3kign | Wiebke Nahrendorf, Philip J Spence | TITLE: low input ChIP-sequencing of immune cells
AUTHORS: Wiebke Nahrendorf, Philip J Spence
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Cells can stably (and heritably) alter their gene expression profile through epigenetic modifications. Histones package DNA into chromatin and can be po... | ["[DNA-Protein crosslinking and cell sorting]\nprepare single cell suspensions and lyse erythrocytes at RECOMMENDATION: work in 15 ml sterile, RNAse/ DNAse free, non pyrogenic polypropylene conical tubes until step 11.NOTE: this protocol was optimised to isolate monocytes from mouse spleens and bone marrow - but it ca... |
null | null | null | dx.doi.org/10.17504/protocols.io.cjauid | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Blue/White Screening of Bacterial Colonies X-Gal/IPTG Plates
[BEFORE_START]
Prepare 20 mg/ml X-Gal solution in DMF (See X-Gal Stock Solution Procedure). For reduced DMF toxicity in media, you can alternatively make a 100 mg/ml X-Gal solution in DMF (this concentration is only s... | [] |
58,080 | Protocol for PPL Solid Phase Extraction for Dissolved Organic Matter (DOM) Sample Preparation for LC-MS/MS Analysis | 1 | dx.doi.org/10.17504/protocols.io.b4x8qxrw | https://www.protocols.io/view/protocol-for-ppl-solid-phase-extraction-for-dissol-b4x8qxrw | mthukral , Irina Koester, Daniel Petras, Ralph Riley Torres, Allegra Aron, Emily Gentry, Xavier Siwe-Noundou, Rosemary Dorrington, Kerry Mcphail, Aaron Hartmann, Lihini Aluwihare | TITLE: Protocol for PPL Solid Phase Extraction for Dissolved Organic Matter (DOM) Sample Preparation for LC-MS/MS Analysis
AUTHORS: mthukral , Irina Koester, Daniel Petras, Ralph Riley Torres, Allegra Aron, Emily Gentry, Xavier Siwe-Noundou, Rosemary Dorrington, Kerry Mcphail, Aaron Hartmann, Lihini Aluwiha... | ["[Preparation of Materials I] Assembly of tubing", "[Materials] General Materials", "[Materials] Cut tubing to desired length (recommended 30 inches/ 75cm) with a precise, flat cut.", "[Materials] Push tubing firmly into a glass pipette until it reaches the bottom of the pipette tip.", "[Materials] Push tubing firmly ... |
53,271 | RNA-Seq Processing Workflow | 5 | null | https://www.protocols.io/view/rna-seq-processing-workflow-bx9xpr7n | cameron_baker | TITLE: RNA-Seq Processing Workflow
AUTHORS: cameron_baker
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol contains details for running the RNA-Seq processing workflow as well as steps detailing underlying programs used and evaluation criteria for overall performance of the workflow.</... | ["[Running the workflow]\nRunning the workflow consists of a single step, kicking off the run command with the required parameters. The parameters and how to correctly set them will be described here, but the internal run commands and reasonings behind them will be explained below.We start by cloning the repository con... |
62,235 | Sarah-Blessing-CBD-Gummy-Fr | 1 | dx.doi.org/10.17504/protocols.io.n92ldz239v5b/v1 | https://www.protocols.io/view/sarah-blessing-cbd-gummy-fr-b8z3rx8n | health | TITLE: Sarah-Blessing-CBD-Gummy-Fr
AUTHORS: health
[DESCRIPTION]
Sarah Blessing CBD Gummies FranceAs Sarah Blessing CBD Gummies Fr is pretty famous and lots of critiques and reports are developing, the primary affect does appear to be good. However, most of you would possibly have queries like ‘Does Sarah Blessing C... | ["The Experts’ Guide To Sarah Blessing CBD Gummies Fr"] |
46,716 | Whole colony fixation | 4 | dx.doi.org/10.17504/protocols.io.bru4m6yw | https://www.protocols.io/view/whole-colony-fixation-bru4m6yw | Simon Blanchoud | TITLE: Whole colony fixation
AUTHORS: Simon Blanchoud
[STEPS]
?. [Anesthesia ]
Dilute 2x ASW with dH2O in a Falcon tube.
25 mL
25 mL
?. [Anesthesia ]
Transfer the colony to the filled Falcon.
?. [Anesthesia ]
Add menthol crystals to the ASW and close the container.
?. [Anesthesia ]
Leave the colony to anesthetize f... | ["[Anesthesia ]\nDilute 2x ASW with dH2O in a Falcon tube.\n25 mL\n25 mL", "[Anesthesia ]\nTransfer the colony to the filled Falcon.", "[Anesthesia ]\nAdd menthol crystals to the ASW and close the container.", "[Anesthesia ]\nLeave the colony to anesthetize for .", "[Anesthesia ]\nShake the 50x eugenol stock hard t... |
null | null | null | dx.doi.org/10.17504/protocols.io.hd8b29w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol, based on published work, demonstrates how to delivery Cas9 RNP-based gene editing reagents to cultured mamallian cells by electroporation with a Lonza 4d Nucleofector. Consider consulting some of the following papers:</p>
<p> </p>
<p>1. RNP delivery paper upon ... | [] |
26,974 | Library preparation protocol to sequence full length 16S rRNA gene in Nanopore MinION sequencer | null | dx.doi.org/10.17504/protocols.io.6j6hcre | null | Somasundhari Shanmuganandam, Yiheng Hu, Benjamin Schwessinger, Robyn Hall | TITLE: Library preparation protocol to sequence full length 16S rRNA gene in Nanopore MinION sequencer
AUTHORS: Somasundhari Shanmuganandam, Yiheng Hu, Benjamin Schwessinger, Robyn Hall
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol was optimised from an existing protocol to achieve m... | ["[PCR amplification ]\n1For a 100 µl PCR reaction, use the following setup AB1ReagentsVolume (µl) for 100 µl reaction22X Platinum SuperFi PCR Master Mix50 µl3Water, nuclease-freeupto 100 µl4Template DNA5 µl (11.5 ng)510 µM forward primer5610 µM reverse primer5 µl\nAB1ReagentsVolume (µl) for 100 µl reaction22X Platinu... |
18,067 | ChroSpin - ProteinA/G | null | dx.doi.org/10.17504/protocols.io.vvte66n | null | David Frommholz, Alexandra Ehl, Nadine Stefanczyk | TITLE: ChroSpin - ProteinA/G
AUTHORS: David Frommholz, Alexandra Ehl, Nadine Stefanczyk
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Purification Guide for the Isolation of Antibodies with ChroSpin Columns by DALEX Biotech.</span></div><div class = "text-block">E... | ["[Load and Wash]\nAdd up to 500 µl sample to the top of the column and incubate the column with end-over-end mixing or occasional inversion for 3 minutes.\nFor fast binding antibodies the incubation time can be decreased to 30 seconds. For slow binding antibodies the incubation time can be increased to 10 minutes. Lon... |
100,356 | Experiences of Adult Lung Transplant Recipients: A Qualitative Meta-Synthesis protocol | 0 | null | https://www.protocols.io/view/experiences-of-adult-lung-transplant-recipients-a-dd9c292w | Eunjin Yang, Soyoung Jang | TITLE: Experiences of Adult Lung Transplant Recipients: A Qualitative Meta-Synthesis protocol
AUTHORS: Eunjin Yang, Soyoung Jang
[DESCRIPTION]
This qualitative meta-synthesis aims to explores the comprehensive experiences of lung transplant recipients covering their pre, awaiting, and post transplantation stages. This... | ["[Experiences of Adult Lung Transplant Recipients: A Qualitative Meta-Synthesis protocol] This qualitative meta-synthesis protocol is written based on the steps of PROSPERO.", "[Experiences of Adult Lung Transplant Recipients: A Qualitative Meta-Synthesis protocol] Review title. \nExperiences of Adult Lung Transplant ... |
66,619 | Diaétoxile : mise à jour, avis, prix officiel ici | 1 | dx.doi.org/10.17504/protocols.io.4r3l2ojpjv1y/v1 | https://www.protocols.io/view/dia-toxile-mise-jour-avis-prix-officiel-ici-cda3s2gn | health | TITLE: Diaétoxile : mise à jour, avis, prix officiel ici
AUTHORS: health
[DESCRIPTION]
Diaetoxile est un produit naturel qui n'a pas d'effets secondaires. Lisez à propos des arnaques, des avis sur les prix et où trouver.
[STEPS]
1. Avis sur les Diaetoxile : Les problèmes de surpoids et d'obésité sont devenus très ... | ["Avis sur les Diaetoxile : Les problèmes de surpoids et d'obésité sont devenus très courants dans la vie de nombreuses personnes. Les gens n'ont aucun contrôle sur leurs habitudes alimentaires. Consommer de la malbouffe et de la restauration rapide peut entraîner différents types de problèmes de santé. Les personnes ... |
50,712 | Spatio-temporal modelling for future prediction of wetlands | 5 | dx.doi.org/10.17504/protocols.io.bvryn57w | https://www.protocols.io/view/spatio-temporal-modelling-for-future-prediction-of-bvryn57w | Rajashree Naik, Laxmi Kant Sharma | TITLE: Spatio-temporal modelling for future prediction of wetlands
AUTHORS: Rajashree Naik, Laxmi Kant Sharma
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is intended to help the wetland researchers willing to use remote sensing data. It is designed for conducting past, present and ... | ["[Study area]\nDecide the wetland to be studied.Collect Toposheet. Georeference and mosaic in Arc GIS. Digitize the official boundary of the wetland.Shape file is ready in .shp format (vector layer).", "[Data collection]\nCreate an account and login to USGS Earth ExplorerEnter the name of the study area, and thedata ... |
62,363 | Optimal Max Keto Reviews Shark tank pills scam or legit? | 1 | dx.doi.org/10.17504/protocols.io.n2bvj6z3plk5/v1 | https://www.protocols.io/view/optimal-max-keto-reviews-shark-tank-pills-scam-or-b853ry8n | optimalmaxetoreviews | TITLE: Optimal Max Keto Reviews Shark tank pills scam or legit?
AUTHORS: optimalmaxetoreviews
[DESCRIPTION]
Optimal Max Keto Reviews Shark tank pills scam or legit?
[STEPS]
1. Optimal Max Keto Reviews Shark tank pills scam or legit?
OPTIMAL MAX KETO REVIEWS
Optimal Max Keto is a slice- edge result that aids in t... | ["Optimal Max Keto Reviews Shark tank pills scam or legit?\nOPTIMAL MAX KETO REVIEWS \n\nOptimal Max Keto is a slice- edge result that aids in the fat- burning process. It allows you to lose weight naturally by releasing fat deposited in your body. This review will explain how it functions and how to use it. \n\nKeto s... |
88,485 | UroMOCA and StimPod Daily Testing in Pig | 1 | dx.doi.org/10.17504/protocols.io.dm6gp3d2pvzp/v1 | https://www.protocols.io/view/uromoca-and-stimpod-daily-testing-in-pig-c2ndyda6 | Dennis Bourbeau, Brett Hanzlicek | TITLE: UroMOCA and StimPod Daily Testing in Pig
AUTHORS: Dennis Bourbeau, Brett Hanzlicek
[DESCRIPTION]
This protocol is for the daily testing of StimPods implanted in a pig. Data from the StimPods and UroMOCA are recorded during these sessions.
[STEPS]
SECTION: Tolerance Testing
1. Attach BluMOCA receiver/antenna t... | ["[Tolerance Testing] Attach BluMOCA receiver/antenna to harness/jacket", "[Tolerance Testing] Charge StimPods, then confirm wireless connection to computer", "[Tolerance Testing] Wake up UroMOCA", "[Tolerance Testing] Stimulation permutations", "[Tolerance Testing] 20 Hz, 500 Hz, 10 kHz", "[Tolerance Testing] Stim0, S... |
87,107 | Virus and Prokaryote Enrichment in Coral DNA Metagenomes | 4 | dx.doi.org/10.17504/protocols.io.q26g7p1y3gwz/v1 | https://www.protocols.io/view/virus-and-prokaryote-enrichment-in-coral-dna-metag-czbbx2in | Natascha Varona, Bailey Wallace, Cynthia Silveira | TITLE: Virus and Prokaryote Enrichment in Coral DNA Metagenomes
AUTHORS: Natascha Varona, Bailey Wallace, Cynthia Silveira
[DESCRIPTION]
Tissue preparation and DNA extraction protocol for enrichment of viruses and prokaryotes in DNA metagenomes of corals.
[BEFORE_START]
Glass beads must be washed with 0.1 N HCl
Incub... | ["[Sample Preparation] Collect a coral sample of approximately 1cm3 containing coral tissue, mucus, and skeleton. Use a fresh sample if possible. If not, flash-freeze the sample and keep it at -80 °C until processing. Thaw the sample on ice before proceeding.", "[Sample Preparation] Weigh and record coral fragment wei... |
55,166 | Scanning Electron Microscopy - Focused Ion Beam Biological Sample Preparation | 1 | dx.doi.org/10.17504/protocols.io.36wgq42kyvk5/v1 | https://www.protocols.io/view/scanning-electron-microscopy-focused-ion-beam-biol-bz46p8ze | Ludovica Parisi | TITLE: Scanning Electron Microscopy - Focused Ion Beam Biological Sample Preparation
AUTHORS: Ludovica Parisi
[DESCRIPTION]
The combination of the scanning electron microscopy (SEM) with a focused ion beam (FIB), represents a pioneering and interesting tool to allow the investigation of the relationship occurring at... | ["[FIXATION] Remove culturing medium from the samples.", "[FIXATION] Gently wash the samples twice in Phosphate Buffer Saline.", "[FIXATION] Cover the surface of the samples with Gluthraldehyde 2.5% in Na-Cacodylate 0.1M buffer.", "[FIXATION] Remove the Glutaraldehyde 2.5% in Na-cacodylate 0.1M buffer from the samples ... |
18,862 | Serum soluble (s)Axl assay protocol | null | dx.doi.org/10.17504/protocols.io.wnnfdde | null | Ioannis Parodis, Huihua Ding, Chandra Mohan, Iva Gunnarsson | TITLE: Serum soluble (s)Axl assay protocol
AUTHORS: Ioannis Parodis, Huihua Ding, Chandra Mohan, Iva Gunnarsson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:center"></div></div></div>
[STEPS] | [] |
97,684 | lmmunostaining of Organoid Sections | 0 | null | https://www.protocols.io/view/lmmunostaining-of-organoid-sections-dbmu2k6w | George Chen, Daniel H. Geschwind | TITLE: lmmunostaining of Organoid Sections
AUTHORS: George Chen, Daniel H. Geschwind
[DESCRIPTION]
lmmunostaining of Organoid Sections derived from human iPS cells.
[STEPS]
1. Place organoid sections into 1ml of PBS in a 24-well plate (1 section per well)
2. Aspirate off the PBS gently
3. Add ~600ul of blocking buf... | ["Place organoid sections into 1ml of PBS in a 24-well plate (1 section per well)", "Aspirate off the PBS gently", "Add ~600ul of blocking buffer for 20mins at RT on the rocker", "Wash 3x with 500ul of PBS and aspirate off PBS", "Add primary AB at working concentration and incubate in Blocking Buffer overnight at 4°C (... |
98,296 | Paraffin embedding of tissue specimen | HuBMAP | JHU-TMC | 0 | dx.doi.org/10.17504/protocols.io.q26g71rn8gwz/v2 | https://www.protocols.io/view/paraffin-embedding-of-tissue-specimen-hubmap-jhu-t-db8y2rxw | Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Miklhail James, Sashank Reddy, Denis Wirtz | TITLE: Paraffin embedding of tissue specimen | HuBMAP | JHU-TMC
AUTHORS: Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Miklhail James, Sashank Reddy, Denis Wirtz
[DESCRIPTION]
The standard for tissue embedding is to ensure tissue samples are appropriately oriented and embedded on the “cut edge” or flattest... | ["[Orientation] The standard for tissue embedding is to ensure tissue samples are appropriately oriented and embedded on the “cut edge” or flattest edge available", "[Type of paraffin] the type of paraffin used in your laboratory should be optimal for your needs. Paraffin comes in many types. These types are differenti... |
39,485 | Olivetti PR et al 2020_Neonatal Mouse Stereotaxic Adaptor_Biotechniques Supp Protocol | 3 | dx.doi.org/10.17504/protocols.io.bis5keg6 | https://www.protocols.io/view/olivetti-pr-et-al-2020-neonatal-mouse-stereotaxic-bis5keg6 | Christoph Kellendonk, Clay O. Lacefield, Pedro Olivetti | TITLE: Olivetti PR et al 2020_Neonatal Mouse Stereotaxic Adaptor_Biotechniques Supp Protocol
AUTHORS: Christoph Kellendonk, Clay O. Lacefield, Pedro Olivetti
[STEPS] | [] |
62,204 | Kerassentials Is It a Risky Scam? Must Read Before Buying | 3 | dx.doi.org/10.17504/protocols.io.5jyl89137v2w/v1 | https://www.protocols.io/view/kerassentials-is-it-a-risky-scam-must-read-before-b8y4rxyw | officialkerassentials | TITLE: Kerassentials Is It a Risky Scam? Must Read Before Buying
AUTHORS: officialkerassentials
[DESCRIPTION]
Official Website - Click Here for Kerassentials
Availability Of Kerassentials - Online On Website
Main Benefits - Fat & Weight Loss Without Any Side Effect
VISIT THE OFFICIAL WEBSITE OF Kerassentials TO O... | [] |
96,919 | Protocol for Repix: reliable, reusable, versatile chronic Neuropixels implants using minimal components | 0 | dx.doi.org/10.17504/protocols.io.4r3l2qm2ql1y/v1 | https://www.protocols.io/view/protocol-for-repix-reliable-reusable-versatile-chr-davx2e7n | Mattias Horan, Daniel Regester, Yoh Isogai | TITLE: Protocol for Repix: reliable, reusable, versatile chronic Neuropixels implants using minimal components
AUTHORS: Mattias Horan, Daniel Regester, Yoh Isogai
[DESCRIPTION]
This is the protocol associated with Repix: reliable, reusable, versatile chronic Neuropixels implants using minimal components.
In the main ... | ["[Overview] This is the protocol associated with Repix: reliable, reusable, versatile chronic Neuropixels implants using minimal components.\n\nIn the main report, we describe the development, deployment, and evaluation of Repix, a chronic implantation system that permits the repeated re-use of the Neuropixels probes ... |
105,043 | SARS-CoV-2 nsp3 macrodomain His-tagged expression and purification protocol for assay | 1 | dx.doi.org/10.17504/protocols.io.4r3l2qb9jl1y/v1 | https://www.protocols.io/view/sars-cov-2-nsp3-macrodomain-his-tagged-expression-ditt4enn | Korvus Wang, michael fairhead, Eleanor Williams | TITLE: SARS-CoV-2 nsp3 macrodomain His-tagged expression and purification protocol for assay
AUTHORS: Korvus Wang, michael fairhead, Eleanor Williams
[DESCRIPTION]
This protocol details the expression and purification of SARS-CoV-2 nsp3 macrodomain assay construct bearing a N-terminal His tag at small scale (<6L).
[... | ["[Plasmid Transformation] CVNSP3mac1 N-terminal His-tagged assay construct was inoculated from its BL21(DE3)-RR glycerol stock.", "[Protein expression] When the OD600 approximately 4.0, lower the temperature and shaker speed to . Add IPTG to final concentration of 1 millimolar (mM) . Incubate overnight.", "[Protein P... |
52,018 | Diatom isotope sample preparation for palaeoenvironmental research | 1 | dx.doi.org/10.17504/protocols.io.36wgq4knovk5/v1 | https://www.protocols.io/view/diatom-isotope-sample-preparation-for-palaeoenviro-bw2spgee | George Swann, Andreasnelling | TITLE: Diatom isotope sample preparation for palaeoenvironmental research
AUTHORS: George Swann, Andreasnelling
[DESCRIPTION]
Diatom isotopes are increasingly used in palaeoenvironmental studies in both lacustrine and marine settings, enabling the reconstruction of a range of variables including temperature, precipita... | ["[Disaggregation of samples] This step breaks up aggregated sediment using non-alkaline chemicals so that diatoms can be successfully extracted. Full removal of external organic matter occur later in Step 6 of the protocol.", "[Disaggregation of samples] Add a further 0.5 mL of 30 % volumeH2O2 at Room temperature in a... |
62,533 | Buzzwords, De-buzzed: 10 Other Ways to Say Prima Keto Uk! | 1 | dx.doi.org/10.17504/protocols.io.81wgb62qqlpk/v1 | https://www.protocols.io/view/buzzwords-de-buzzed-10-other-ways-to-say-prima-ket-b9bdr2i6 | noxcay | TITLE: Buzzwords, De-buzzed: 10 Other Ways to Say Prima Keto Uk!
AUTHORS: noxcay
[DESCRIPTION]
Prima Keto Uk REVIEWS – Most people desire to reduce weight, but only a few take action. Many people are unable to achieve their objectives due to time limits or other factors. Their tight schedule stops them from exercisi... | ["[Prima Keto Uk]"] |
90,271 | PVA-based Rat Liver Tumor Phantom for Ultrasound Imaging | 1 | dx.doi.org/10.17504/protocols.io.eq2lyj95wlx9/v1 | https://www.protocols.io/view/pva-based-rat-liver-tumor-phantom-for-ultrasound-i-c4d7ys9n | Abhishek Kumar, Debdoot Sheet | TITLE: PVA-based Rat Liver Tumor Phantom for Ultrasound Imaging
AUTHORS: Abhishek Kumar, Debdoot Sheet
[DESCRIPTION]
The creation of a PVA-based ultrasound (US) imaging phantom involves a systematic step-by-step process. These US phantoms serve a vital role in the medical field, aiding medical professionals in various... | ["[Material required] 1. 3D printing of the organ : Polylactic Acid (PLA)\n2. Mould creation : Silicone liquid rubber with catalyst\n3. Phantom fabrication : Milli-Q water, Polyvinyl Alcohol (PVA), Silicon carbide (SiC)\n\nNote: We have used 176 ml (88%) of milli-Q water, 20 gm of PVA (... |
null | null | null | dx.doi.org/10.17504/protocols.io.hqgb5tw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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77,008 | Mouseome Cloning and PhIP-seq protocol | 3 | dx.doi.org/10.17504/protocols.io.kxygx9144g8j/v1 | https://www.protocols.io/view/mouseome-cloning-and-phip-seq-protocol-cpfqvjmw | Elze Rackaityte, Joe DeRisi | TITLE: Mouseome Cloning and PhIP-seq protocol
AUTHORS: Elze Rackaityte, Joe DeRisi
[DESCRIPTION]
Protocol used for cloning mouseome into T7 genome for PhIP-seq
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.rhmd346 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Script R for custom graphical plots used in the study of Poirier et al., Comparative analysis of 16S and gyrB amplicon sequencing of Food Microbiota</p>
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.mjac4ie | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p> ECMO inevitably increases the risk of infection over time; therefore, lowering infections acquired during ECMO should be further investigated and developed accordingly (Bizzarro, 2011). The degree of dysfunction by ECMO is evaluated using several methods, namely: ultrastru... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.c8pzvm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<strong>Purpose: </strong>This method for the enumeration of aquatic viruses is a low-cost alternative to the commonly used filter-mount method. Briefly, fluorescently-stained samples are wetmounted directly onto slides for epifluorescence microscopy after an optional chemical f... | [] |
68,860 | Scoping Review Protocol | 1 | dx.doi.org/10.17504/protocols.io.yxmvmndzng3p/v1 | https://www.protocols.io/view/scoping-review-protocol-cfg4tjyw | natalie.riblet, Sara Matsunaga, Brian Shiner, Paula P Schnurr, Bradley V Watts | TITLE: Scoping Review Protocol
AUTHORS: natalie.riblet, Sara Matsunaga, Brian Shiner, Paula P Schnurr, Bradley V Watts
[DESCRIPTION]
Clinician- and patient-administered instruments are frequently used to assess risk of death by suicide. There has been limited review of the ability of these scales to assess change in r... | ["[General Information] Title: Are suicide risk scales sensitive to change? A scoping review protocol", "[General Information] Authors: Riblet N, Matsunaga S, Shiner B, Schnurr PP, Watts BV", "[Background] Clinician- or self-administered instruments are frequently used in clinical and research settings to assist provid... |
91,044 | A Protocol to Simultaneously Examine Cardiorespiratory, Cerebrovascular and Neurophysiological Responses Inside a Hypobaric Chamber | 1 | dx.doi.org/10.17504/protocols.io.kqdg3xy47g25/v1 | https://www.protocols.io/view/a-protocol-to-simultaneously-examine-cardiorespira-c46cyzaw | Evan A. Hutcheon, Sherri Ferguson, Victoria E. Claydon, Urs Ribary, Sam M. Doesburg | TITLE: A Protocol to Simultaneously Examine Cardiorespiratory, Cerebrovascular and Neurophysiological Responses Inside a Hypobaric Chamber
AUTHORS: Evan A. Hutcheon, Sherri Ferguson, Victoria E. Claydon, Urs Ribary, Sam M. Doesburg
[DESCRIPTION]
We describe a protocol to examine neurophysiological (electroencephalogra... | ["Bring all equipment into the hypobaric chamber (Figure 1) and set it up: experimental task laptop, EEG recording computer, physiological measures recording computer, capnograph, transcranial doppler (TCD) probe, masks, analog to digital converter, oxygen saturation (SpO2) monitor, Portapres and have the EEG materials... |
101,763 | Absence of Candida africana in Ugandan Pregnant Women: Results from a Pilot Study | 0 | dx.doi.org/10.17504/protocols.io.n2bvjn9exgk5/v1 | https://www.protocols.io/view/absence-of-candida-africana-in-ugandan-pregnant-wo-dfmb3k2n | Bwambale Jonani, Ssebuliba Joshua, Atuhairwe Susan, Gerald Mboowa, Mike N Kagawa, Beatrice Achan | TITLE: Absence of Candida africana in Ugandan Pregnant Women: Results from a Pilot Study
AUTHORS: Bwambale Jonani, Ssebuliba Joshua, Atuhairwe Susan, Gerald Mboowa, Mike N Kagawa, Beatrice Achan
[DESCRIPTION]
Candida africana, an emerging variant identified since 2001 as a distinct species or variety within the Candid... | ["[Specimens collection] Explain the specimen collection procedure to study participant (Pregnant woman) and gain consent. Advise woman to pass urine if needed.", "[Specimens collection] Place the pregnant woman in a lithotomy position (lying on her back with her legs flexed and spread apart). Ensure privacy is maintai... |
36,207 | PCR with Q5® High-Fidelity 2X Master Mix (M0492) | 1 | dx.doi.org/10.17504/protocols.io.bfkpjkvn | https://www.protocols.io/view/pcr-with-q5-high-fidelity-2x-master-mix-m0492-bfkpjkvn | New England Biolabs | TITLE: PCR with Q5® High-Fidelity 2X Master Mix (M0492)
AUTHORS: New England Biolabs
[DESCRIPTION]
The Q5 High-Fidelity 2X Master Mix offers robust, high-fidelity performance in a convenient master mix format. The Q5 High- Fidelity 2X Master Mix features a high-fidelity, thermostable DNA polymerase with 3´→ 5´ exon... | ["Set up the following reaction on ice:\n Component25 µl Reaction50 µl ReactionFinal Concentration Q5 High-Fidelity 2X Master Mix 12.5 µl 25 µl 1X 10 µM Forward Primer 1.25 µl 2.5 µl 0.5 µM 10 µM Reverse Primer 1.25 µl 2.5 µl 0.5 µM Template DNA variable variable < 1,000 ng Nuclease-Free Water to 25 µl to 50 ... |
91,115 | SW-3 SWAB STORAGE | 4 | dx.doi.org/10.17504/protocols.io.n2bvj3j6plk5/v1 | https://www.protocols.io/view/sw-3-swab-storage-c48jyzun | REDI-NET Consortium | TITLE: SW-3 SWAB STORAGE
AUTHORS: REDI-NET Consortium
[DESCRIPTION]
This protocol describes swab storage.
[GUIDELINES]
OBJECTIVE
To outline steps for properly storing swab samples and nucleic acid samples purified from these samples.
SUMMARY/SCOPE
The overarching aim of the REDI-NET is to develop a collaborative l... | ["[STORAGE PROCEDURE FOR UNTREATED SAMPLE] Precool 96-well microfuge tube racks on ice.", "[STORAGE PROCEDURE FOR UNTREATED SAMPLE] Using preprinted adhesive labels or permanent markers, label 1.5 ml microfuge tubes.", "[STORAGE PROCEDURE FOR UNTREATED SAMPLE] Once the rack is full or all swab samples have been complet... |
42,314 | Chapter 8: Managing sick and injured vulture admissions | 4 | null | https://www.protocols.io/view/chapter-8-managing-sick-and-injured-vulture-admiss-bmjik4ke | Kerri Wolter | TITLE: Chapter 8: Managing sick and injured vulture admissions
AUTHORS: Kerri Wolter
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol provides guidelines for managing sick and injured vulture admissions.</div></div>
[STEPS] | [] |
91,889 | ATPase assay/ADP-glo kit | 1 | dx.doi.org/10.17504/protocols.io.3byl4q1x8vo5/v1 | https://www.protocols.io/view/atpase-assay-adp-glo-kit-c5yry7v6 | Rania Abou El Asrar, Peter Vangheluwe | TITLE: ATPase assay/ADP-glo kit
AUTHORS: Rania Abou El Asrar, Peter Vangheluwe
[DESCRIPTION]
This protocol is successfully used to assess activity of P5B-ATPases with polyamines as substrate.
[STEPS]
1. Prepare master mix on ice: 5 µg microsomes, 2.5 µg DDM (Inalco, 1758-1350), reaction buffer (50 mM MOPS-KOH, pH 7,... | ["Prepare master mix on ice: 5 µg microsomes, 2.5 µg DDM (Inalco, 1758-1350), reaction buffer (50 mM MOPS-KOH, pH 7, 100 mM KCl, 11 mM MgCl2 supplemented with 1 mM DTT and protease inhibitor (Sigmafast, Sigma, S8830-20TAB).", "Incubate master mix for 30 minutes at room temperature in overhead shaker.", "Pipet master mi... |
18,974 | Wholemount Immunolabeling for GUT Samples | null | dx.doi.org/10.17504/protocols.io.wr6fd9e | null | Marthe Howard | TITLE: Wholemount Immunolabeling for GUT Samples
AUTHORS: Marthe Howard
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Wholemount Immunolabeling-Gut</div><div class = "text-block">This protocol is used for immunostaining large blocks of tissue. The application that it was developed for is large pi... | [] |
90,662 | QuickNII Brain Atlas Registration | 4 | dx.doi.org/10.17504/protocols.io.e6nvwdme2lmk/v1 | https://www.protocols.io/view/quicknii-brain-atlas-registration-c4seywbe | Michael X. Henderson | TITLE: QuickNII Brain Atlas Registration
AUTHORS: Michael X. Henderson
[DESCRIPTION]
This protocol describes QuickNII brain atlas registration.
[STEPS]
SECTION: QuickNII Brain Atlas Registration
1. Open the QuickNII program folder.
SECTION: QuickNII Brain Atlas Registration
2. Open Filebuilder.
SECTION: QuickNII Brai... | ["[QuickNII Brain Atlas Registration] Open the QuickNII program folder.", "[QuickNII Brain Atlas Registration] Open Filebuilder.", "[QuickNII Brain Atlas Registration] Navigate to the QVN folder with the brain image exports from QuPath.", "[QuickNII Brain Atlas Registration] Click all images to be registered, and click... |
null | null | null | dx.doi.org/10.17504/protocols.io.iq4cdyw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Backgroud:</strong></p>
<p>Since sedation and analgesia are widely accepted by patients and even considered by many gastroenterologists as an integral component of the endoscopic examination, opioids are indispensible in managing pain. Nalbuphine is as effective as mo... | [] |
12,007 | ChroSpin - ProteinG | null | dx.doi.org/10.17504/protocols.io.pyfdptn | null | David Frommholz, Alexandra Ehl, Nadine Stefanczyk | TITLE: ChroSpin - ProteinG
AUTHORS: David Frommholz, Alexandra Ehl, Nadine Stefanczyk
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Purification Guide for the Isolation of Antibodies with ChroSpin Columns by DALEX Biotech.</span></div><div class = "text-block">Eas... | ["[Load and Wash]\nAdd up to 500 µl sample to the top of the column and incubate the column with end-over-end mixing or occasional inversion for 3 minutes.\nFor fast binding antibodies the incubation time can be decreased to 30 seconds. For slow binding antibodies the incubation time can be increased to 10 minutes. Lon... |
null | null | null | dx.doi.org/10.17504/protocols.io.qzhdx36 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Here is a short explanation on how to add a work in progress protocol to a private group. This protocol shows how to add a protocol editable by multiple people to edit it <strong>before</strong> its final publication on protocols.io</p>
<p> </p>
<p>This is also an example pro... | [] |
79,782 | Protocol collection - "Glucocerebrosidase is imported into mitochondria and preserves complex I integrity and energy metabolism" | 2 | dx.doi.org/10.17504/protocols.io.6qpvr4zr3gmk/v1 | https://www.protocols.io/view/protocol-collection-34-glucocerebrosidase-is-impor-cr6ev9be | michela.deleidi, María José Pérez J., Pascale Baden, Federico Bertoli, Hariam Raji | TITLE: Protocol collection - "Glucocerebrosidase is imported into mitochondria and preserves complex I integrity and energy metabolism"
AUTHORS: michela.deleidi, María José Pérez J., Pascale Baden, Federico Bertoli, Hariam Raji
[DESCRIPTION]
Collection of protocols of Deleidi Lab used in the publication: "Gl... | [] |
64,362 | @>>> https://pillsfect.com/melt-away-keto-reviews/ | 3 | dx.doi.org/10.17504/protocols.io.e6nvwkqn7vmk/v1 | https://www.protocols.io/view/gt-gt-gt-https-pillsfect-com-melt-away-keto-revie-ca4isgue | H A | TITLE: @>>> https://pillsfect.com/melt-away-keto-reviews/
AUTHORS: H A
[DESCRIPTION]
Flow Zone Pills are your hazard to discreetly repair your overall performance and wow your associate once more. Don’t omit this opportunity!
[STEPS] | [] |
40,008 | GNPS Untargeted Metabolomics Workflow | 1 | null | https://www.protocols.io/view/gnps-untargeted-metabolomics-workflow-bjbgkijw | Sierra Simpson, Olivier George | TITLE: GNPS Untargeted Metabolomics Workflow
AUTHORS: Sierra Simpson, Olivier George
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">GNPS is an open-sourced, web-based mass spectrometry ecosystem that is used for community-wide organization / sharing of raw, processed, or annotated fragmentation ma... | ["[Registration ]\nCreate a GNPS account at GNPS Signup", "[Upload Data ]\nFirst convert specific vendor formats to open format using MSConvert locally. MSConvert DownloadmsConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial ... |
null | null | null | dx.doi.org/10.17504/protocols.io.c8gztv | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
The Performance Index is calculated using the formula:<br /><br />PI=((#F5×5)+(#F4×4)+(#F3×3)+(#F2×2)+(#F1×1)+(#F0×0))/(#FT )<br /><br />where #Fn is the number of flies in the tube n (being 0 the initial tube and 5 the last tube), and&nbs... | [] |
65,463 | Imaris Coloc Protocol | 1 | dx.doi.org/10.17504/protocols.io.n2bvj61bblk5/v1 | https://www.protocols.io/view/imaris-coloc-protocol-cb6xsrfn | Hong-Yuan Chu | TITLE: Imaris Coloc Protocol
AUTHORS: Hong-Yuan Chu
[DESCRIPTION]
This protocol details the procedure of the imaris coloc protocol.
[STEPS]
SECTION: Background Subtraction
1. Open confocal files (.ND2) in ImageJ.
SECTION: Background Subtraction
2. Perform background subtraction on z-stack of images (process -> subtr... | ["[Background Subtraction] Open confocal files (.ND2) in ImageJ.", "[Background Subtraction] Perform background subtraction on z-stack of images (process -> subtract background).", "[Background Subtraction] Rolling ball radius: 50.0 pixels.", "[Background Subtraction] Save z-stack as a .TIFF file.", "[Background Subtra... |
null | null | null | dx.doi.org/10.17504/protocols.io.guubwww | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 2">
<div class="section">
<div class="layoutArea">
<div class="column">
<p>The Odyssey Fc Imager, with 600 channel capabilities, can image agarose gels stained with popular DNA stains, such as ethidium bromide and SYBR Safe DNA stain, with sub-nanog... | ["{\"blocks\":[{\"key\":\"earv8\",\"text\":\" Place gel face-up on an Odyssey Fc Imaging Tray.\\n \",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"4nt42\",\"text\":\" \",\"type\":\"atomic\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[{\"offset\"... |
22,561 | How to create a new protocol | null | dx.doi.org/10.17504/protocols.io.z99f996 | null | Anita Bröllochs, Lenny Teytelman, Alexei Stoliartchouk | TITLE: How to create a new protocol
AUTHORS: Anita Bröllochs, Lenny Teytelman, Alexei Stoliartchouk
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to create a new protocol on protocols.io.</div></div>
[STEPS]
?. [Starting new protocol ]
Click on the + icon in the upper-... | ["[Starting new protocol ]\nClick on the + icon in the upper-right corner to open the main menu, and select 'New protocol'.", "[Adding Protocol Description ]\nAdd a Title. This will be the name your protocol.", "[Adding Guidelines & Warnings ]\nNavigate to the Guidelines & Warnings tab on the top of the protocol editor... |
77,945 | Counting bats from photographs using ImageJ | 1 | dx.doi.org/10.17504/protocols.io.ewov1om9klr2/v1 | https://www.protocols.io/view/counting-bats-from-photographs-using-imagej-cqczvsx6 | Stanimira Deleva | TITLE: Counting bats from photographs using ImageJ
AUTHORS: Stanimira Deleva
[DESCRIPTION]
Counting bats from photographs is an efficient and non-invasive method for assessing the size of a colony, and it is widely used for monitoring cave-dwelling bats. This protocol describes the exact steps to count bats using the... | ["Install the ImageJ software by following the instructions at the software website.", "Open the ImageJ program.", "Open the photo for counting using the menu Open → File (Ctrl + O) (Fig. 1) or by dragging and dropping the photo into the program.", "Prepare the photo for counting. Use high-quality photos with a large s... |
40,895 | ELISA for quantification of transforming growth factor beta (TGF-β) in human serum or plasma. | 6 | dx.doi.org/10.17504/protocols.io.bj67krhn | https://www.protocols.io/view/elisa-for-quantification-of-transforming-growth-f-bj67krhn | Angel Justiz-Vaillant, Belkis Ferrer-Cosme | TITLE: ELISA for quantification of transforming growth factor beta (TGF-β) in human serum or plasma.
AUTHORS: Angel Justiz-Vaillant, Belkis Ferrer-Cosme
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Transforming growth factor beta (TGF-β) is a multifunctional cytokine belonging to the tran... | ["An anti-humanTGF-β coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.", "Add 50 µl of human serum or plasma. Human TGF-β present in the serum or plasma binds to antibodies adsorbed into the microwells.", "The microplate is blocked with 3% non-fat milk-PB... |
60,674 | Protocol for counting pathogen spores on hemocytometer | 3 | null | https://www.protocols.io/view/protocol-for-counting-pathogen-spores-on-hemocytom-b7harj2e | Meghan Duffy | TITLE: Protocol for counting pathogen spores on hemocytometer
AUTHORS: Meghan Duffy
[DESCRIPTION]
This is a protocol to quantify the number of pathogen spores you have in a sample using a hemocytometer.
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.g7rbzm6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 4">
<div class="layoutArea">
<div class="column">
<p>Infrared fluorescence detection with Odyssey Family Imaging Systems provides a quantitative two-color detection method for Western blots.</p>
<p> </p>
<p>This protocol is designed to help you achi... | [] |
63,009 | Initiating and monitoring natural infection of mice by bioluminescent Citrobacter rodentium | 2 | dx.doi.org/10.17504/protocols.io.81wgb6qnnlpk/v1 | https://www.protocols.io/view/initiating-and-monitoring-natural-infection-of-mic-b9r9r596 | Hannah Read, Priyali Patel, Siouxsie Wiles | TITLE: Initiating and monitoring natural infection of mice by bioluminescent Citrobacter rodentium
AUTHORS: Hannah Read, Priyali Patel, Siouxsie Wiles
[DESCRIPTION]
Citrobacter rodentium is a Gram-negative bacterium that infects laboratory mice in a similar way to how enteropathogenic Escherichia coli (EPEC) and ente... | [] |
92,607 | Bleaching and UV decontamination of materials | 3 | dx.doi.org/10.17504/protocols.io.q26g7pnj9gwz/v1 | https://www.protocols.io/view/bleaching-and-uv-decontamination-of-materials-c6n7zdhn | Elena Essel, Matthias Meyer, Merlin Szymanski | TITLE: Bleaching and UV decontamination of materials
AUTHORS: Elena Essel, Matthias Meyer, Merlin Szymanski
[DESCRIPTION]
Protocol for reducing DNA contamination on materials (e.g. quarz glass bottles, spatulas) used in the ancient DNA cleanroom by sodium hypochlorite (bleach) and UV treatment.
[STEPS] | [] |
64,901 | Pure Calms CBD Gummies Scam Or Legit? Does it Really Work | 3 | dx.doi.org/10.17504/protocols.io.j8nlkkyywl5r/v1 | https://www.protocols.io/view/pure-calms-cbd-gummies-scam-or-legit-does-it-reall-cbmdsk26 | alena lee | TITLE: Pure Calms CBD Gummies Scam Or Legit? Does it Really Work
AUTHORS: alena lee
[DESCRIPTION]
Pure Calms CBD Gummies United Kingdom (Scam or Legit) Read Expert Reviews!
Official Website - https://pure-calms-cbd-gmmies-uk
https://pure-calms-official-site.clubeo.com/page/pure-calms-cbd-gummies-uk-100-safe-effective-... | [] |
99,992 | Pre-Imaging Liquid Growth Medium for Methionine promoted Labeling Systems - Yeast | 0 | dx.doi.org/10.17504/protocols.io.kqdg329yqv25/v1 | https://www.protocols.io/view/pre-imaging-liquid-growth-medium-for-methionine-pr-ddvy267w | Mathias Hammer, Ammeret Rossouw, Azra Lari, Ben Montpetit, David Grunwald | TITLE: Pre-Imaging Liquid Growth Medium for Methionine promoted Labeling Systems - Yeast
AUTHORS: Mathias Hammer, Ammeret Rossouw, Azra Lari, Ben Montpetit, David Grunwald
[DESCRIPTION]
This protocol describes the steps to prepare liquid culture medium for Saccharomyces cerevisiae. This liquid medium is used to optimi... | ["[Preparation of 500ml liquid pre-imaging growth medium for Methionine promoted Labeling Systems] Compound medium for autoclave", "[Preparation of 500ml liquid pre-imaging growth medium for Methionine promoted labeling systems] Fill a 500 ml flask with 440 mLddH2O. \nAdd a magnetic stirring bar and place the flask on ... |
76,106 | Resource 6: rEV Fluorescent Detector Setting Incrementation | 4 | dx.doi.org/10.17504/protocols.io.261ge324ol47/v1 | https://www.protocols.io/view/resource-6-rev-fluorescent-detector-setting-increm-cnjivcke | Sean M Cook, Vera A. Tang, Joanne Lannigan, Jennifer Jones, Joshua A Welsh | TITLE: Resource 6: rEV Fluorescent 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 su... | ["[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 rEV 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 E... |
null | null | null | dx.doi.org/10.17504/protocols.io.iwjcfcn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?. | [] |
43,947 | Analysis of Breast Cancer Cell Invasion Using an Organotypic Culture System | 4 | dx.doi.org/10.17504/protocols.io.bn6jmhcn | https://www.protocols.io/view/analysis-of-breast-cancer-cell-invasion-using-an-o-bn6jmhcn | Romana E. Ranftl, Fernando Calvo | TITLE: Analysis of Breast Cancer Cell Invasion Using an Organotypic Culture System
AUTHORS: Romana E. Ranftl, Fernando Calvo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Metastasis is the main cause of cancer patient mortality. Local tumor invasion is a key step in metastatic dissemination wher... | ["[3.1 Gel Preparation]\nAll components of the gel mix must be kept on ice. Here we describe the protocol for 1 mL gel mix containing fibroblasts or without fibroblasts. This is the volume required for one sample in one well of a 24-well plate. The total volume of gel mix needs to be scaled up according to sample size.... |
94,248 | Protocol6_In vitro translation.pdf | 1 | dx.doi.org/10.17504/protocols.io.bp2l6x6yklqe/v1 | https://www.protocols.io/view/protocol6-in-vitro-translation-pdf-c8agzsbw | angelica.gonzalez | TITLE: Protocol6_In vitro translation.pdf
AUTHORS: angelica.gonzalez
[DESCRIPTION]
In vitro translation
[STEPS] | [] |
86,865 | Sanger Tree of Life HMW DNA Extraction: Plant Organic HMW gDNA Extraction (POE) | 4 | dx.doi.org/10.17504/protocols.io.3byl4qq4zvo5/v1 | https://www.protocols.io/view/sanger-tree-of-life-hmw-dna-extraction-plant-organ-cy3rxym6 | Benjamin Jackson, Caroline Howard | TITLE: Sanger Tree of Life HMW DNA Extraction: Plant Organic HMW gDNA Extraction (POE)
AUTHORS: Benjamin Jackson, Caroline Howard
[DESCRIPTION]
The Plant Organic HMW gDNA Extraction (POE) protocol acts as the Tree of Life's mid-throughput, reserve gDNA extraction procedure for recalcitrant, ‘routine failure’ species w... | ["[Sample lysis] Prepare an adequate volume of the ‘Direct Plant Lysis Buffer’ (recipe in Materials).\nPreheat the direct plant lysis buffer for 15–30 mins, 65 °C at 400 rpm prior to use, ensuring the total dissolution of reagents.\nAdd DTT and Proteinase K to the direct plant lysis buffer immediately prior to use, ens... |
null | null | null | dx.doi.org/10.17504/protocols.io.iztcf6n | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?. | [] |
44,062 | Sequencing at DNBSEQ-G400 platform with PE200 and SE400 modes | 4 | dx.doi.org/10.17504/protocols.io.bn96mh9e | https://www.protocols.io/view/sequencing-at-dnbseq-g400-platform-with-pe200-and-bn96mh9e | Xiaohuan Sun, Yuehua Hu, Zewei Song | TITLE: Sequencing at DNBSEQ-G400 platform with PE200 and SE400 modes
AUTHORS: Xiaohuan Sun, Yuehua Hu, Zewei Song
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used for microbial short amplicon sequencing at DNBSEQ-G400 (previously known as BGISEQ-2000, RRID:SCR_017980) sequenci... | ["Place the library on ice until use. Remove Make DNB Buffer, Low TE Buffer and Stop DNB Reaction Buffer from storage and thaw reagents at . Thaw Make DNB Enzyme Mix I for approximately on ice. After thawing, mix reagents using a vortex mixer for . Centrifuge briefly and place on ice until use.\n0 Room temperature", "... |
36,935 | Fig1 | 1 | dx.doi.org/10.17504/protocols.io.bgbfjsjn | https://www.protocols.io/view/fig1-bgbfjsjn | Runtian Zhang | TITLE: Fig1
AUTHORS: Runtian Zhang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Fig 1</div></div>
[STEPS]
?. | [] |
41,815 | Alpaca Nanobodies Rapid Ag test | 1 | dx.doi.org/10.17504/protocols.io.bk3xkypn | https://www.protocols.io/view/alpaca-nanobodies-rapid-ag-test-bk3xkypn | Anne Berking | TITLE: Alpaca Nanobodies Rapid Ag test
AUTHORS: Anne Berking
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The "Rapid Ag test based on Alpaca Nanobodies" is a test developed with single domain antibodies. This type of antibody is capable of effectively recognize the Spike protein on the surface of... | ["[Sample Collection]\nCollect saliva in the sample collection tube.", "[Sample Analyse]\nAdd Solution 1 containing the saliva to the \"Detection column\"", "[Sample Analyse]\nConnect the column to the vacuum manifold and let the full content pass through the \"Detection columns\"", "[Sample Analyse]\nAdd 20 mL of Solu... |
59,161 | Wastewater Sequencing using the EasySeq™ RC-PCR SARS CoV-2 (Nimagen) V2.0 | 4 | null | https://www.protocols.io/view/wastewater-sequencing-using-the-easyseq-rc-pcr-sar-b5zzq776 | Aaron Jeffries, Harry T Child, Steve Paterson, Matthew Loose, Ronny van Aerle | TITLE: Wastewater Sequencing using the EasySeq™ RC-PCR SARS CoV-2 (Nimagen) V2.0
AUTHORS: Aaron Jeffries, Harry T Child, Steve Paterson, Matthew Loose, Ronny van Aerle
[DESCRIPTION]
This SOP describes the procedure for generating cDNA libraries from SARS-CoV-2 viral nucleic acid extracts from wastewater samp... | ["[Cleanup of RNA extract] Aim: Reduction of any PCR inhibitors and potential concentration of RNA. Starting volume is 20 µl but this can be increased if further concentration is required (although for the latter tests on whether inhibitors are also concentrated have not been undertaken).\nNotes: Use either AMPure RNA ... |
59,955 | Phytolith extraction and counting procedure for modern plant material rich in silica skeletons | 1 | dx.doi.org/10.17504/protocols.io.q26g74mb8gwz/v1 | https://www.protocols.io/view/phytolith-extraction-and-counting-procedure-for-mo-b6streen | Francesca D’Agostini, Javier Ruiz-Pérez, Marco Madella, Vincent Vadez, Carla Lancelotti | TITLE: Phytolith extraction and counting procedure for modern plant material rich in silica skeletons
AUTHORS: Francesca D’Agostini, Javier Ruiz-Pérez, Marco Madella, Vincent Vadez, Carla Lancelotti
[DESCRIPTION]
Modern plant tissues are often processed for phytolith analysis. They represent a fundamental source of co... | ["[Drying plant material] Collect the tissues of interest from the whole plant. Store each sample in a separate paper bag and put the paper bags in a dryer. Paper bags prevent the formation of fungi and bacterial infection, allowing the evaporation of tissues’ humidity.Collect the tissues of interest from the whole pla... |
81,573 | Testing | 1 | dx.doi.org/10.17504/protocols.io.j8nlkwx2xl5r/v1 | https://www.protocols.io/view/testing-ctwdwpa6 | Sebastian Vincent | TITLE: Testing
AUTHORS: Sebastian Vincent
[DESCRIPTION]
est
[STEPS]
SECTION: Test
1.
test | ["[Test] test"] |
71,184 | Microscopy-based evaluation of Parkin translocation and mitophagy in FBXO7-/- cell linesons) | 4 | dx.doi.org/10.17504/protocols.io.yxmvm2kqog3p/v1 | https://www.protocols.io/view/microscopy-based-evaluation-of-parkin-translocatio-chrqt55w | Felix Kraus | TITLE: Microscopy-based evaluation of Parkin translocation and mitophagy in FBXO7-/- cell linesons)
AUTHORS: Felix Kraus
[DESCRIPTION]
Protocol for the microscopy-based evaluation of Parkin translocation and mitophagy in FBXO7-/- cell linesons)
[STEPS]
SECTION: Differentiation of iNeurons
23. Day 0: Treat AAVS1-TRE3G... | ["[Differentiation of iNeurons] Day 0: Treat AAVS1-TRE3G-NGN2 cells with Accutase and plate the dissociated cells in matrigel-coated 6-well plates (2x105 cells/well) in ND1 Medium supplemented with Y27632 (10 μM). \nND1 Medium: \nDMEM/F12 \nN2 (100x) 1x \nBDNF 10 ng/ml \nNT3 10 n... |
44,653 | Curva de Padrão Fosfato 16/11/20 | 1 | null | https://www.protocols.io/view/curva-de-padr-o-fosfato-16-11-20-bpummnu6 | Mariana Jacques | TITLE: Curva de Padrão Fosfato 16/11/20
AUTHORS: Mariana Jacques
[STEPS]
?. [Procedimento: ]
Em uma placa de ___ poços colocar :50 μL de H2O MiliQ
?. [Procedimento: ]
A1: 50 μL Pi 40 μM( Realizar diluições seriadas)
?. [Procedimento: ]
Adicionar 25 μL MR em cada poço da placa
?. [Procedimento: ]
Preparar Revelador 4:... | ["[Procedimento: ]\nEm uma placa de ___ poços colocar :50 μL de H2O MiliQ", "[Procedimento: ]\nA1: 50 μL Pi 40 μM( Realizar diluições seriadas)", "[Procedimento: ]\nAdicionar 25 μL MR em cada poço da placa", "[Procedimento: ]\nPreparar Revelador 4:1 Verde de Malaqueta: Molibidato de Amônioesperar 30' e filtrar", "[Pro... |
86,565 | VTEA - a tool for 3D tissue cytometry: 7-Click Analysis | 5 | dx.doi.org/10.17504/protocols.io.3byl4qqqovo5/v1 | https://www.protocols.io/view/vtea-a-tool-for-3d-tissue-cytometry-7-click-analys-cysdxwa6 | Seth Winfree, Daria Barwinska | TITLE: VTEA - a tool for 3D tissue cytometry: 7-Click Analysis
AUTHORS: Seth Winfree, Daria Barwinska
[DESCRIPTION]
VTEA is a tool for 3D tissue cytometry (3DTC) of large 3D fluorescence light microscopy image volumes ranging from 50-100s of microns thick. The objective was to unify image processing, segmentation, dat... | ["Select the VTEA menu (Click #1) and then \"VTEA 1.1.6\" (Click #2). The version number will change with ongoing updates.", "If no images are open in FIJI/ImageJ, use the open image button (Click #3). This will open up a standard FIJI open image file menu and automatically load an image into the VTEA workflow.", "If t... |
85,451 | Standardised flow cytometric protocol for the detection of immune cells subsets in breast cancer patients. | 1 | dx.doi.org/10.17504/protocols.io.14egn379ml5d/v1 | https://www.protocols.io/view/standardised-flow-cytometric-protocol-for-the-dete-cxpjxmkn | Nicole Chicken, Pieter Meyer, Ronald Anderson, Bernardo Rapoport, Catherine Worsley | TITLE: Standardised flow cytometric protocol for the detection of immune cells subsets in breast cancer patients.
AUTHORS: Nicole Chicken, Pieter Meyer, Ronald Anderson, Bernardo Rapoport, Catherine Worsley
[DESCRIPTION]
The tumour microenvironment supports tumour growth in several ways including manipulating the imm... | ["[DURAClone IM Phenotyping Treg kit test protocol for 1 sample2] Label a DURAClone IM Phenotyping Treg kit tube 1, and add 5 µL to the tube.", "[DURAClone IM Phenotyping Treg kit test protocol for 1 sample2] Add 50 µL to reagent tube 1, and vortex for 10 seconds. Incubate the tube in the dark for 15 minutes at room te... |
68,548 | Characterization of the Archaeome, Bacteriome and Eukaryome in Nasopharyngeal Swabs | 1 | dx.doi.org/10.17504/protocols.io.bp2l61ok1vqe/v1 | https://www.protocols.io/view/characterization-of-the-archaeome-bacteriome-and-e-ce7cthiw | Carolin Baehren, Anton Pembaur, Patrick P. Weil, Frank Schult, Stefan Wirth, Jan Postberg, Malik Aydin | TITLE: Characterization of the Archaeome, Bacteriome and Eukaryome in Nasopharyngeal Swabs
AUTHORS: Carolin Baehren, Anton Pembaur, Patrick P. Weil, Frank Schult, Stefan Wirth, Jan Postberg, Malik Aydin
[DESCRIPTION]
This protocol describes the Characterization of the Archaeome, Bacteriome and Eukaryome in Nasopharyn... | ["[PCR] PCR \nArchaea: Nested PCR\nEukaryotes: single PCR", "[Library preparation + sequencing:] Library Preparation + Sequencing:\n\n- 1st Purification\n- PCR preparation\n- 2nd Purification\n- Concentration measurement", "[Bioinformatics:]", "[DNA Isolation] Resuspension of pellet in 180 µL", "[DNA Isolation] Centrif... |
null | null | null | dx.doi.org/10.17504/protocols.io.c8izud | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
32,173 | One-pot native barcoding of amplicons | null | dx.doi.org/10.17504/protocols.io.bbnmimc6 | null | Josh Quick | TITLE: One-pot native barcoding of amplicons
AUTHORS: Josh Quick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a ‘one-pot ligation’ protocol for Oxford Nanopore native barcoded ligation libraries using shearing. </div></div>
[STEPS]
?. Set up the following reaction for each sample:Compone... | ["Set up the following reaction for each sample:Component VolumeDNA amplicons Nuclease-free water Ultra II End Prep Reaction Buffer Ultra II End Prep Enzyme Mix Total\n5 µl\n7.5 µl\n1.75 µl\n0.75 µl\n15 µl... |
41,209 | EPD Electronic Pathogen Detection | 1 | dx.doi.org/10.17504/protocols.io.bkgzktx6 | https://www.protocols.io/view/epd-electronic-pathogen-detection-bkgzktx6 | Ilse Pretorius | TITLE: EPD Electronic Pathogen Detection
AUTHORS: Ilse Pretorius
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Electronic pathogen detection (EPD) is a non - invasive, rapid, affordable, point- of- care test, for Covid 19 resulting from infection with SARS-CoV-2 virus.</div><div class = "text-blo... | ["[Equipment Setup]\nSwitch on EPD scan unit and PC, connect EPD scan unit to PC. Note: Make sure both PC and EPD scanner are on, and connected - indicated by a non-flashing LED indicator", "[Equipment Setup]\nOpen EPD application software on PC", "[Subject Preperation]\nEnter patient details into EPD software.Note:Mak... |
73,931 | NCBI data curation protocol - SOP for editing GenomeTrakr submissions | 1 | dx.doi.org/10.17504/protocols.io.36wgq5jb5gk5/v3 | https://www.protocols.io/view/ncbi-data-curation-protocol-sop-for-editing-genome-ckfjutkn | Ruth Timme, Candace.Bias, Errol Strain, Tina.Pfefer, Maria Balkey | TITLE: NCBI data curation protocol - SOP for editing GenomeTrakr submissions
AUTHORS: Ruth Timme, Candace.Bias, Errol Strain, Tina.Pfefer, Maria Balkey
[DESCRIPTION]
PURPOSE: After data are submitted to NCBI submitters often encounter the need to update, retract, or replace these records. This is called data curation... | ["[BioProject Curation] How to edit a BioProject", "[BioProject Curation] 1. Click on the \"Manage Data\" tab within the submission portal, or navigate directly to \"Manage Data\": https://dataview.ncbi.nlm.nih.gov to edit Title, Organism, Description, URL, or publications for your BioProject.\n\n \n\n \n2. In the men... |
63,369 | Condor CBD Gummies : Reviews, Benefits, Shark Tank, Stress Free, Reduced All Pain Relief, 100% Pure, Scam Alerts & Price Discount? | 1 | dx.doi.org/10.17504/protocols.io.ewov1nxj2gr2/v1 | https://www.protocols.io/view/condor-cbd-gummies-reviews-benefits-shark-tank-str-b95hr836 | Condor CBD Gummies | TITLE: Condor CBD Gummies : Reviews, Benefits, Shark Tank, Stress Free, Reduced All Pain Relief, 100% Pure, Scam Alerts & Price Discount?
AUTHORS: Condor CBD Gummies
[DESCRIPTION]
➢Product Name - Condor CBD Gummies
➢Main Benefits — Improve Health
➢ Composition —Natural Organic Compound
➢ Side-Effects—NA
➢... | ["[Condor CBD Gummies : Reviews, Benefits, Shark Tank, Stress Free, Reduced All Pain Relief, 100% Pure, Scam Alerts & Price Discount?] Regular utilization of Condor CBD Gummies assuages blended torment, neuropathic torment, and nociceptive agony from different pieces of the body.", "[Condor CBD Gummies : Reviews, B... |
61,474 | Top Down Proteomics Data Collection for Microdissected Kidney Tissue Functional Units | 1 | dx.doi.org/10.17504/protocols.io.rm7vzy5e5lx1/v1 | https://www.protocols.io/view/top-down-proteomics-data-collection-for-microdisse-b8aarsae | James M Fulcher, Isaac Kwame Attah, Mowei Zhou, Ljiljana.PasaTolic | TITLE: Top Down Proteomics Data Collection for Microdissected Kidney Tissue Functional Units
AUTHORS: James M Fulcher, Isaac Kwame Attah, Mowei Zhou, Ljiljana.PasaTolic
[DESCRIPTION]
The protocol describes how to use laser capture microdissection (LCM) to cut small regions of interest (~200-300 μm) from tissue section... | ["[Liquid chromatography (LC) method setup] Set up reversed-phase LC system with online trapping for desalting.\n\nDual pump configuration\nMobile phase A (MPA): 0.2% formic acid in water (LCMS grade)\nMobile phase B (MPB): 0.2% formic acid in acetonitrile (LCMS grade)", "[Mass spectrometer (MS) method setup] Calibrate... |
43,584 | Hybridization of Random-Primed DNA Probes | 4 | dx.doi.org/10.17504/protocols.io.bns8mehw | https://www.protocols.io/view/hybridization-of-random-primed-dna-probes-bns8mehw | Jonathan Houseley, Cristina Cruz | TITLE: Hybridization of Random-Primed DNA Probes
AUTHORS: Jonathan Houseley, Cristina Cruz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Over the past decade a plethora of noncoding RNAs (ncRNAs) have been identified, initiating an explosion in RNA research. Although RNA sequencing methods provide... | ["[Hybridization of Random-Primed DNA Probes]\nDNA probes lack the strand specificity of RNA or oligonucleotide probes, but are much more sensitive than oligonucleotides and are easier to strip than RNA probes.", "[Hybridization of Random-Primed DNA Probes]\nEnsure that the hybridization bottles and internal seals are ... |
72,672 | Stages of the bioeconomy of the production process sitotroga cerealella | 4 | dx.doi.org/10.17504/protocols.io.bp2l69x1klqe/v1 | https://www.protocols.io/view/stages-of-the-bioeconomy-of-the-production-process-ci78uhrw | Carlos Alberto Zuniga Gonzalez | TITLE: Stages of the bioeconomy of the production process sitotroga cerealella
AUTHORS: Carlos Alberto Zuniga Gonzalez
[DESCRIPTION]
The protocol describes the production process of Sitotroga Cerealella's bioeconomy. This process has 5 stages:
1. STAGE OF STERILIZATION OF WHEAT SUBSTRATE
a) WASHING PHASE
b) STERILI... | ["SITOTROGA SUBSTRATE STERILIZATION STAGE \n a) WASHING PHASE The duly certified raw material (wheat) of free varieties of grains other than the required is received. An inspection is carried out to verify its content and to be free of possible other varieties of grains. The bags are moved from the warehouse area in a... |
null | null | null | dx.doi.org/10.17504/protocols.io.f5gbq3w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="column">The steps for preparing the lysate are different depending on the starting material. Please ensure you follow the correct procedure for your starting material (see the section <a href="https://www.protocols.io/view/genomic-dna-removal-and-total-rna-purificati... | [] |
60,302 | RatGTEx pipeline | 5 | dx.doi.org/10.17504/protocols.io.rm7vzyk92lx1/v1 | https://www.protocols.io/view/ratgtex-pipeline-b65nrg5e | Daniel Munro, Laura M Saba, Hao Chen, Abraham Palmer, Pejman Mohammadi | TITLE: RatGTEx pipeline
AUTHORS: Daniel Munro, Laura M Saba, Hao Chen, Abraham Palmer, Pejman Mohammadi
[DESCRIPTION]
This is the pipeline used to process data for the RatGTEx Portal. It is loosely based on the GTEx eQTL mapping pipeline, though it includes some utility scripts from there in their entirety. All code... | ["[Align RNA-Seq reads] Generate the index for STAR.", "[Align RNA-Seq reads] Align RNA-Seq reads for a sample using STAR.", "[Align RNA-Seq reads] Get an individual-specific VCF file. This is used by STAR to consider the individual's variants for better alignment.", "[Identify and correct sample mixups] Get all exon r... |
48,240 | Isolation of Chlamydia from crocodile tissue samples | 1 | dx.doi.org/10.17504/protocols.io.btcqnivw | https://www.protocols.io/view/isolation-of-chlamydia-from-crocodile-tissue-sampl-btcqnivw | Somjit Chaiwattanarungruengpaisan, Metawee Thongdee, ladawan.sar | TITLE: Isolation of Chlamydia from crocodile tissue samples
AUTHORS: Somjit Chaiwattanarungruengpaisan, Metawee Thongdee, ladawan.sar
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used for isolation of Chlamydia from crocodiles</div></div>
[STEPS]
?. Dissect tissue sample (appr... | ["Dissect tissue sample (approximate 50-100 mg) into small pieces.", "Homogenize the small pieces of tissue sample with a pestle in 5 ml sucrose/phosphate/glutamate (SPG) buffer containing 500 ug/ml streptomycin, 500 ug/ml vancomycin, 50 ug/ml gentamycin, and 2.5 ug/ml fungizone and left at 4°C for 72 h.", "Centrifuge ... |
44,957 | Cell DIVE™ Platform | Ab Conjugation: Initial Conjugation & Scale up Conjugation | 1 | dx.doi.org/10.17504/protocols.io.bp55mq86 | https://www.protocols.io/view/cell-dive-platform-ab-conjugation-initial-conjugat-bp55mq86 | Anup Sood, Eric Williams, Liz McDonough | TITLE: Cell DIVE™ Platform | Ab Conjugation: Initial Conjugation & Scale up Conjugation
AUTHORS: Anup Sood, Eric Williams, Liz McDonough
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Scope</span></div><div class = "text-block">The purpose of this protocol is to co... | ["[ ]\nPlease select between the following cases:", "[Determining molar concentration of 1X Cy Dye via NanoDrop 2000c]\nNote: In case if your institution does not have NanoDrop, please use a UV spectrophotometer of your choice.For Cy2 - measure absorption at 489 nm. The Cy2 extinction coefficient is 150,000. Divide abs... |
93,286 | ssDNA2.0: Adapter/splinter mix | 3 | dx.doi.org/10.17504/protocols.io.e6nvwdnwwlmk/v1 | https://www.protocols.io/view/ssdna2-0-adapter-splinter-mix-c7cezite | Matthias Meyer, Anna Schmidt, Sarah Nagel | TITLE: ssDNA2.0: Adapter/splinter mix
AUTHORS: Matthias Meyer, Anna Schmidt, Sarah Nagel
[DESCRIPTION]
Protocol for the preparation of decontaminated (i.e., nuclease-treated) Adapter/splinter mix for the first adapter ligation in automated single-stranded DNA library preparation using the ssDNA2.0 method (Gansauge et ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.g4pbyvn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Shows how to use the BLAST.cgi on an example genetic sequence. </p>
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
26,747 | UTK Laboratory Orientation/Training | null | dx.doi.org/10.17504/protocols.io.6c3hayn | null | Gary LeCleir, Steven Wilhelm | TITLE: UTK Laboratory Orientation/Training
AUTHORS: Gary LeCleir, Steven Wilhelm
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Welcome to the Wilhelm Lab. This short training is to help orient those that are learning how to work in a laboratory environment as well as help those that are joining ou... | ["Safety - # 1 priority – we have several hazardous agents in our laboratory and your safety, and the safety of others is the most important thing here. If you notice anything unsafe or feel that the situation you have been placed in is unsafe, please immediate lab supervisor and PI know so steps can be taken to ensure... |
50,667 | Live Follicle Isolation from Human Ovarian Tissue | 4 | null | https://www.protocols.io/view/live-follicle-isolation-from-human-ovarian-tissue-bvqjn5un | Andrea Jones, Jordan Machlin, Ariella Shikanov | TITLE: Live Follicle Isolation from Human Ovarian Tissue
AUTHORS: Andrea Jones, Jordan Machlin, Ariella Shikanov
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines steps to obtain live primordial/primary follicles from fresh or cryopreserved human ovarian cortex. Here, we do no... | ["[Preparations]\nPrepare enzymes: Dilute DNase I stock (2% w/v) to 2 mg/mL by combining 10 μL stock with 90 μL DPBS +/+. Mix well and store on ice for the duration of cell isolation. Collagenase stock at 100 mg/mL should be stored on ice for the duration of cell isolation.", "[Preparations]\nPre-weigh an empty 30 mm d... |
98,608 | De - Novo Genome Protocol from only ONT reads | 0 | null | https://www.protocols.io/view/de-novo-genome-protocol-from-only-ont-reads-dciq2udw | Chase Donnelly | TITLE: De - Novo Genome Protocol from only ONT reads
AUTHORS: Chase Donnelly
[DESCRIPTION]
Draft of pipeline and code used for de novo genome assembly of non model plant specis
[STEPS]
SECTION: DNA Extraction
1. The first challenge to developing this protocol was determining a DNA extraction technique that produced ... | ["[DNA Extraction] The first challenge to developing this protocol was determining a DNA extraction technique that produced long and high-quality DNA. This protocol used a modified version of the fever tree gdna protocol available via Nanopore's community website. These modifications have since been added to or surpass... |
null | null | null | dx.doi.org/10.17504/protocols.io.vgue3ww | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Recent advances in single cell mRNA sequencing technology such as Drop-seq (Cell, 2015) have allowed the investigation of cellular composition and processes within complex tissues. Although some fresh tissue samples are available for prospective studies, there is an abundance of... | ["[Reagent Prep] For each nuclei preparation, aliquot 20 mL of EZ-Prep Lysis Buffer and prepare 7 mL NSB. Place both on ice to chill while preparing tissue.", "[Nuclei Isolation] Repeat step 5.", "[Tissue Prep] Weigh tissue to be prepared (Usable numbers of nuclei have been retrieved from 30-40 mg of heart tissue). Pri... |
79,793 | Bulk Untargeted LC-MS/MS Lipidomics | 1 | dx.doi.org/10.17504/protocols.io.ewov1ob5klr2/v1 | https://www.protocols.io/view/bulk-untargeted-lc-ms-ms-lipidomics-cr6rv9d6 | Madeline E. Colley, Jamie Allen, Katerina V Djambazova, Angela Kruse, melissa.a.farrow, Jeff Spraggins | TITLE: Bulk Untargeted LC-MS/MS Lipidomics
AUTHORS: Madeline E. Colley, Jamie Allen, Katerina V Djambazova, Angela Kruse, melissa.a.farrow, Jeff Spraggins
[DESCRIPTION]
This protocol is the detailed methodology for extracting lipids from tissue, connecting a Waters UHPLC to a timsTOF mass spectrometer via contact clo... | ["[Tissue Collection] Tissue is sectioned at 10 um width in a cryostat and (1-3) scrolls of tissue is placed into a thermo glass shell vial. \n\nKeep one empty vial with a random, known number on it without tissue inside for a sample blank.", "[Preamble] Please reference the materials section for details on materials, ... |
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