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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26,937 | Anthoceros agrestis (hornwort) transformation v01 | 1 | dx.doi.org/10.17504/protocols.io.6izhcf6 | https://www.protocols.io/view/anthoceros-agrestis-hornwort-transformation-v01-6izhcf6 | Eftychis Frangedakis | TITLE: Anthoceros agrestis (hornwort) transformation v01
AUTHORS: Eftychis Frangedakis
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-style:italic;">Anthoceros agrestis</span><span> (hornwort) transformation</span></div><div class = "text-block">pre-print:</div><div class = "t... | ["Tissue preparation: Collect approximately 2 g of thallus tissue grown for 4 weeks under low light intensity (approximately 0.1 g of tissue per petri dish - 20 petri dishes in total) - Figure 4.1Split tissue into three parts, transfer each part into a 50 mL falcon tubes containing 15 mL of sterile water and homogenize... |
null | null | null | dx.doi.org/10.17504/protocols.io.ksacwae | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>I and my team used this assay between 2008-2015; we dubbed it the "Harvala assay". It produces an amplicon that includes the 3' end of VP3 and the 5' end of VP1, spanning the junction.</p>
<p><em>In silico </em>sequence alignments indicated the highly degenerate olignucleotid... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.e5gbg3w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The UPPA-PROTEIN Concentrate™ kit is used to quantitatively concentrate dilute protein samples as low as 1ng/ml into a small volume. Protein precipitation and concentration are not affected by the presence of detergents, chaotropics, or other common laboratory agents.</p>
<p>... | [] |
46,040 | Isolation of fungi associated with ambrosia beetles with pre-oral mycangia | 3 | dx.doi.org/10.17504/protocols.io.bq7ymzpw | https://www.protocols.io/view/isolation-of-fungi-associated-with-ambrosia-beetle-bq7ymzpw | Kyra Lynn, Irene Barnes | TITLE: Isolation of fungi associated with ambrosia beetles with pre-oral mycangia
AUTHORS: Kyra Lynn, Irene Barnes
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to extract fungi from ambrosia beetles that have pre-oral mycangia.</div><div class = "text-block">Note: This... | [] |
72,452 | Assembly: Chronic recoverable Neuropixels in mice | 1 | null | https://www.protocols.io/view/assembly-chronic-recoverable-neuropixels-in-mice-cizcuf2w | Emily A Aery Jones | TITLE: Assembly: 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 Neuropixels 1.0 probes into mice, record during freely moving behavior, then recover the probe for future use. This protocol explai... | ["[3D print components] Build a print file for the following pieces per mouse: 1 each of body piece, back and front flex cable holders, and dome, plus 2 wings. Print 1 headstage holder per recording rig. To re-use explanted probes, print everything except for the body piece, which is permanently affixed to the probe. F... |
null | null | null | dx.doi.org/10.17504/protocols.io.rxad7ie | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | ["48 third instar female larvae from each mitotype were placed in 0.5% agar in petri dishes.", "Individual larvae were then placed in quadrants of separate petri dishes.", "Larvae were observed for 60 seconds and larvae trails were immediately traced onto the lid of each dish. The distance moved by each larva was measu... |
15,981 | Protocol for use with FFPE RNA, NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (NEB #E6310) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760, E7765) | null | dx.doi.org/10.17504/protocols.io.tumenu6 | null | New England Biolabs | TITLE: Protocol for use with FFPE RNA, NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (NEB #E6310) 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 Librar... | ["[Probe Hybridization to RNA]\nAdd of the above mix to total RNA (from Step 1), resulting in a total volume of\n3 µl\n12 µl\n15 µl", "[Probe Hybridization to RNA]\nMix by pipetting up and down at least 10 times.", "[Probe Hybridization to RNA]\nSpin down briefly in a microcentrifuge.", "[Probe Hybridization to RNA]\... |
73,084 | Pre-Operative Ultrasound Mapping Before Arteriovenous Fistula creation: An updated Systematic Review and Meta-Analysis | 1 | null | https://www.protocols.io/view/pre-operative-ultrasound-mapping-before-arterioven-cjk4ukyw | David Dimitris Chlorogiannis, Ioannis Bellos | TITLE: Pre-Operative Ultrasound Mapping Before Arteriovenous Fistula creation: An updated Systematic Review and Meta-Analysis
AUTHORS: David Dimitris Chlorogiannis, Ioannis Bellos
[DESCRIPTION]
Arteriovenous fistulas remain the gold standard of vascular accesses in haemodialysis; however, the routine use of pre-opera... | ["[Abstract] Background \nArteriovenous fistulas remain the gold standard of vascular accesses in haemodialysis; however, the routine use of pre-operative ultrasound for vascular mapping still remains controversial. This meta analysis aims to shed some light into the reliability of routine preoperative Doppler ultrasou... |
73,247 | Creating pooled CRISPR-Cas9 knock-outs in NIH-3T3 cells | 4 | dx.doi.org/10.17504/protocols.io.eq2ly7wpmlx9/v1 | https://www.protocols.io/view/creating-pooled-crispr-cas9-knock-outs-in-nih-3t3-cjr7um9n | Herschel Dhekne, Ebsy Jaimon, Suzanne R Pfeffer | TITLE: Creating pooled CRISPR-Cas9 knock-outs in NIH-3T3 cells
AUTHORS: Herschel Dhekne, Ebsy Jaimon, Suzanne R Pfeffer
[DESCRIPTION]
To validate a genome wide CRISPR screen, we select the top hits and create lentiviruses to validate the hits. Rather than screening each virus from single cell clones, we analyze the i... | ["[Create 3T3-Cas9 cells and Clone the CRISPR guides] Generate 3T3-Cas9 cells\n Infect NIH3T3-flpin cells with Cas9-containing lentivirus to generate cells constitutively expressing Cas9 as follows:\nPlate NIH-3T3 cells into a 6 well cell dish at 1x105 cells / well\nAfter cells attach, add lentivirus made from Lenti-Ca... |
null | null | null | dx.doi.org/10.17504/protocols.io.jvccn2w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Modified from Harrison et al., 1980. A broad spectrum artifical seawater medium for coastal and open ocean phytoplankton. The final salt concentration is ~34 ppt.</p>
<p> </p>
[BEFORE_START]
<p>Acid washed all glassware with 10% HCl and rinse well (3-5 times with deionized o... | [] |
34,322 | AF-16 in peritonitis induced sepsis | 1 | dx.doi.org/10.17504/protocols.io.bdrsi56e | https://www.protocols.io/view/af-16-in-peritonitis-induced-sepsis-bdrsi56e | Annelie Tenhunen | TITLE: AF-16 in peritonitis induced sepsis
AUTHORS: Annelie Tenhunen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify">Sepsis is a life-threatening condition due to a dysregulated immunological response to infection. Apart from source control and bro... | ["The animal is weighed. Premedication with Zoletil Forte (Tiletamin/Zolazepam) 6 mg/kg + Rompun (Xylazinklorid) 2.2 mg/kg i.m in neck muscle. Establishment of a peripheral venous line in ear vein. Infusion Ringers' Acetate 30 ml/kg/h first hour, second hour until induction of peritonitis infusion with Ringers' Acetate... |
28,687 | Double Digestion and Dephosphorylation of Plasmid | null | dx.doi.org/10.17504/protocols.io.79phr5n | null | iGEM Dusseldorf | TITLE: Double Digestion and Dephosphorylation of Plasmid
AUTHORS: iGEM Dusseldorf
[STEPS]
?. Mix the following components gently: AB1Componentsng/µL2Plasmid DNA Tube X3ComponentVolume (µL)4Sterile MilliQ WaterFill up to 30.0 µl510x FastDigest Buffer3.06Plasmid DNATotal ng of DNA/Plasmid DNA concentration ng/µl7FastDi... | ["Mix the following components gently: AB1Componentsng/µL2Plasmid DNA Tube X3ComponentVolume (µL)4Sterile MilliQ WaterFill up to 30.0 µl510x FastDigest Buffer3.06Plasmid DNATotal ng of DNA/Plasmid DNA concentration ng/µl7FastDigest Enzyme 11.08FastDigest Enzyme 21.09FastAP Alkaline Phosphatase1.010Total Volume30.011... |
85,868 | Mission, vision, and principles of the protocols.io company | 1 | dx.doi.org/10.17504/protocols.io.dm6gprbnjvzp/v2 | https://www.protocols.io/view/mission-vision-and-principles-of-the-protocols-io-cx4kxquw | Lenny Teytelman | TITLE: Mission, vision, and principles of the protocols.io company
AUTHORS: Lenny Teytelman
[DESCRIPTION]
This is an internal document outlining our company culture and expectations for everyone who joins the team.
[STEPS]
SECTION: Mission
1. The broad mission of protocols.io is to accelerate research by:
increasing ... | ["[Mission] The broad mission of protocols.io is to accelerate research by:\nincreasing collaboration and sharing among researchers\nimproving efficiency of researchers by reducing mistakes and re-discovery", "[Mission] The protocol-specific mission is to make it easy to share method details before, during and after pu... |
20,515 | U Michigan - Retinal Microstructure Imaging OCT | null | dx.doi.org/10.17504/protocols.io.yabfsan | null | David A. Antonetti | TITLE: U Michigan - Retinal Microstructure Imaging OCT
AUTHORS: David A. Antonetti
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">A spectral domain ophthalmic imaging system based on the technology of optical coherenc... | ["The eyes of conscious animals are dilated by first applying a small drops (~10 µl) of tropicamide (1%) followed by a small drop of phenylephrine (2.5%) 2 to 3 minutes later", "Animal is then sedated with ketamine and xylazine", "After sedation, the corneas are kept moist with the wetting agents (Systane)", "Animal is... |
30,943 | Quick & Dirty DNA Extraction | null | dx.doi.org/10.17504/protocols.io.baf7ibrn | null | Sam Mantel, Andrea Sweigart | TITLE: Quick & Dirty DNA Extraction
AUTHORS: Sam Mantel, Andrea Sweigart
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Modified from Cheung et al., 1993 </div></div>
[STEPS]
?. [Prep]
Pre-heat Quick & Dirty extraction buffer with detergent in a incubator.
60 °C
?. [Prep]
Place one steel ball bea... | ["[Prep]\nPre-heat Quick & Dirty extraction buffer with detergent in a incubator.\n60 °C", "[Prep]\nPlace one steel ball bearing into each sample tube.", "[Extract and Wash DNA]\nWhen tissue is ground to a fine powder centrifuge briefly to remove powder from the inside of caps.", "[Make Quick & Dirty extraction buffer... |
53,493 | RNA Extraction from Wastewater Concentrates Using RNeasy and Zymo Kits | 4 | dx.doi.org/10.17504/protocols.io.bygvptw6 | https://www.protocols.io/view/rna-extraction-from-wastewater-concentrates-using-bygvptw6 | Jacquelina.Woods , rachel.rodriguez | TITLE: RNA Extraction from Wastewater Concentrates Using RNeasy and Zymo Kits
AUTHORS: Jacquelina.Woods , rachel.rodriguez
[DESCRIPTION]
This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wastewater. Pr... | ["[RNeasy Mini] Obtain one virus concentrate (if concentrate is frozen, allow thawing) from Virus Concentration from Wastewater Using PEG Precipitation and Ultracentrifugation (protocols.io)", "[RNeasy Mini] Add 500 µL 6M GITC.\n \n.", "[RNeasy Mini] Vortex 75 s to dissolve concentrate.", "[RNeasy Mini] Add 700 µL of 5... |
null | null | null | dx.doi.org/10.17504/protocols.io.ssbeean | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
<p>Clean the benches and all the material that will be used with alcohol 70. </p>
<p>Use tips with filter. </p>
<p>Add 4 volumes of 100% ethanol to the RPE buffer.</p>
<p>To lyse the cells, you can use β-mercaptoethanol or 2 M dithiothreitol. For each 1ml of the RLT buffer, add... | [] |
22,678 | Safety of intravitreal ziv-aflibercept in patients with diabetic macular edema, macular edema following retinal vein occlusion and neovascular age related macular degeneration in a Ghanaian population: A phase I randomized interventional study | null | dx.doi.org/10.17504/protocols.io.2dwga7e | null | Imoro Zeba Braimah, Ernest Kenu, Kwesi N. Amissah-Arthur, Akafo Stephen, Kwaku Oppong Kwarteng, Winfried M. Amoaku | TITLE: Safety of intravitreal ziv-aflibercept in patients with diabetic macular edema, macular edema following retinal vein occlusion and neovascular age related macular degeneration in a Ghanaian population: A phase I randomized interventional study
AUTHORS: Imoro Zeba Braimah, Ernest Kenu, Kwesi N. Amissah-Arthur, Ak... | ["[Randomisation process and Procedures]\nComprehensive ocular examination will be repeated at day 1 and 7 after the initial anti-VEGF injection and in all subsequent visits. All patients will undergo fundus photography (ZEISS 450 FUNDUS CAMERA, ZEISS INC. JENA, GERMANY), Fluorescein angiography (ZEISS 450 FUNDUS CAMER... |
null | null | null | dx.doi.org/10.17504/protocols.io.kmtcu6n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A real-time PCR method for the detection of Molluscum contagiosum virus from human samples. This assay targets the MC021L gene and detects both subtype 1 and 2 of the virus.</p>
[BEFORE_START]
<ul>
<li>If using a different brand or model of real-time thermocycler, check the ... | [] |
98,242 | Light Sheet Fluorescence Microscopy of Human Kidney Using Clearing with CUBIC | 4 | dx.doi.org/10.17504/protocols.io.36wgqn5eogk5/v1 | https://www.protocols.io/view/light-sheet-fluorescence-microscopy-of-human-kidne-db7a2rie | Liam Mclaughlin, Bo Zhang, Amanda Knoten, Praveen Krishnamoorthy, Sanjay Jain | TITLE: Light Sheet Fluorescence Microscopy of Human Kidney Using Clearing with CUBIC
AUTHORS: Liam Mclaughlin, Bo Zhang, Amanda Knoten, Praveen Krishnamoorthy, Sanjay Jain
[DESCRIPTION]
Light sheet fluorescence microscopy (LSFM) is a method to cover micro-mesoscale (µm-cm) areas of tissue while achieving depth of se... | ["[Tips] Tips:\n\n•\tClearing with CUBIC (Matsumoto, K., Mitani, T.T., Horiguchi, S.A. et al. Advanced CUBIC tissue clearing for whole-organ cell profiling. Nat Protoc 14, 3506–3537 (2019). https://doi.org/10.1038/s41596-019-0240-9) -infiltrated samples takes around fourteen days to complete.\n\n•\tCUBIC clearing is a ... |
40,212 | Conjugation of peptide fragment 579-601 of HIV-gp41 or fragments 308-331 or 421-438 of the HIV-gp120 with keyhole limpet hemocyanin (KLH). | 6 | dx.doi.org/10.17504/protocols.io.bjhukj6w | https://www.protocols.io/view/conjugation-of-peptide-fragment-579-601-of-hiv-gp4-bjhukj6w | Angel Justiz-Vaillant | TITLE: Conjugation of peptide fragment 579-601 of HIV-gp41 or fragments 308-331 or 421-438 of the HIV-gp120 with keyhole limpet hemocyanin (KLH).
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Chemical synthesis facilitates the generation of peptides which are very d... | ["These peptide fragment (579-601 from HIV-gp41) is dimerized by cysteine oxidation with dimethyl-sulfoxide. The HIV peptide is dissolved in 5% acetic acid to a final concentration of 5.1 mg/ml.", "The pH of the medium is adjusted to 6 with 1 M (NH4)2CO3.", "Dimethyl-sulfoxide is added to 20% of the final volume, and... |
68,738 | Reduced Representation Bisulfite Sequencing (RRBS) with NEB Reagents | 4 | dx.doi.org/10.17504/protocols.io.e6nvwkxb9vmk/v1 | https://www.protocols.io/view/reduced-representation-bisulfite-sequencing-rrbs-w-cfdati2e | Noah Noah Snyder-Mackler | TITLE: Reduced Representation Bisulfite Sequencing (RRBS) with NEB Reagents
AUTHORS: Noah Noah Snyder-Mackler
[DESCRIPTION]
This protocol is for generating Reduced Representation Bisulfite Sequencing (RRBS) libraries. We recommend using 200ng input, but the protocol has worked with inputs as low as 50ng.
We recommen... | ["[Fragment DNA] Prepare fragment master mix (fragment MM) in a 1.5 mL tube for n+1 samples.\n\nPer sample, prepare 4 µL mixture containing:\n(Thaw) : 3 µL \n(On ice) : 1 µL \n\nInvert to mix. DO NOT VORTEX.", "[Fragment DNA] Spin down samples before adding fragment MM. Add 4 µL of fragment MM to the template DNA.\n ... |
43,262 | Calibrating a pH meter | 1 | null | https://www.protocols.io/view/calibrating-a-ph-meter-bng6mbze | PMAT0001 | TITLE: Calibrating a pH meter
AUTHORS: PMAT0001
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Step-by-step instructions on calibrating a pH meter</div></div>
[STEPS]
?. [Main steps]
Press “Cal”
?. [Main steps]
Press “✔️”
?. [Main steps]
Dip in pH 4
?. [Main steps]
Press “✔️”
?. [Main steps]
Rins... | ["[Main steps]\nPress “Cal”", "[Main steps]\nPress “✔️”", "[Main steps]\nDip in pH 4", "[Main steps]\nPress “✔️”", "[Main steps]\nRinse pH meter", "[Main steps]\nDip in pH 7", "[Main steps]\nPress “✔️”", "[Main steps]\nDip into sample; Note percentage purity as well", "[Important notes]\n- When liquid level falls way b... |
55,719 | Assessment of Human Islet Composition and Acinar Cell Component by Immunofluorescence Staining | 4 | dx.doi.org/10.17504/protocols.io.b2nfqdbn | https://www.protocols.io/view/assessment-of-human-islet-composition-and-acinar-c-b2nfqdbn | IIDP-HIPP | TITLE: Assessment of Human Islet Composition and Acinar Cell Component by Immunofluorescence Staining
AUTHORS: IIDP-HIPP
[DESCRIPTION]
This Standard Operating Procedure (SOP) is based on the Human Islet Phenotyping Program of the IIDP Immunofluorescence Staining Procedure. This SOP provides the HIPP procedure for im... | ["[Preparation of Reagents] Preparation of Reagents for Immunofluorescence Staining of Islet Cryosections", "[Preparation of Reagents] 10% Triton X-100 stock (30 mL) – combine 3 mL Triton-X-100 and 27 mL 1X PBS. Mix on shaker for 30 min or until Triton X-100 is completely dissolved and store at 4 °Cfor up to 1 month.",... |
61,606 | Western blot (NuPAGE and MES buffer) | 4 | dx.doi.org/10.17504/protocols.io.261genwyyg47/v1 | https://www.protocols.io/view/western-blot-nupage-and-mes-buffer-b8eertbe | Laura Smith | TITLE: Western blot (NuPAGE and MES buffer)
AUTHORS: Laura Smith
[DESCRIPTION]
Cells were lysed in 1% Triton X 100 lysis buffer with protease and phosphatase inhibitors. Cell lysates were electrophoresed with NuPage™ Bis-Tris protein gels. Proteins were transferred to a PVDF membrane, blocked in 10% milk and treated ... | ["[Gel Electrophoresis] Make loading dye using NuPAGE Sample Buffer (4X) and Reducing agent (10X). For 18 µL of sample, add 6 µL sample buffer and 1 µL reducing agent.", "[Gel Electrophoresis] Combine sample and loading dye and heat at 70 °C for 10 minutes .", "[Gel Electrophoresis] Prepare precast gel (NuPAGE) by re... |
84,273 | Explant Surgery: Chronic recoverable Neuropixels in mice | 1 | dx.doi.org/10.17504/protocols.io.bp2l6113dvqe/v5 | https://www.protocols.io/view/explant-surgery-chronic-recoverable-neuropixels-in-cwirxcd6 | Emily A Aery Jones | TITLE: Explant Surgery: 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 the probes... | ["[Prepare mouse] Set O2 flow rate to 1-1.5L/min and isoflurane to 3%. Place mouse in anesthetic chamber.", "[Prepare mouse] When breathing has slowed to 1Hz, move animal to the toothbar. Switch isoflurane from chamber to nosecone. Wait until unresponsive to pedal reflex test, then lower to 1.5% isoflurane.", "[Prepare... |
91,275 | Chronic intermittent hypoxia remodels catecholaminergic innervation in mouse atria | 4 | dx.doi.org/10.17504/protocols.io.14egn3jmzl5d/v1 | https://www.protocols.io/view/chronic-intermittent-hypoxia-remodels-catecholamin-c5djy24n | Ariege Bizanti, Yuanyuan Zhang, Zulema Toledo, Kohlton Bendowski, Scott W. Harden, Anas Mistareehi, Jin Chen, David Gozal, Maci Heal, Richard Christie, Peter J. Hunter, Julian F.R. Paton, Zixi Jack Cheng | TITLE: Chronic intermittent hypoxia remodels catecholaminergic innervation in mouse atria
AUTHORS: Ariege Bizanti, Yuanyuan Zhang, Zulema Toledo, Kohlton Bendowski, Scott W. Harden, Anas Mistareehi, Jin Chen, David Gozal, Maci Heal, Richard Christie, Peter J. Hunter, Julian F.R. Paton, Zixi Jack Cheng
[DESCRIPTION]
Ch... | ["[Hypoxia exposure] Mice were placed in cages (2 per cage) inside identical chambers with oxygen levels controlled by computerized environmental chambers (30 × 20 × 20 inches; Oxycycler A44XO, BioSpherix, Redfield, NY) for automatic delivery of intermittent hypoxia.", "[Heart dissection and flat-mount preparation] Mic... |
null | null | null | dx.doi.org/10.17504/protocols.io.igdcbs6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The following protocols is submitted as part of the Cikapundung Research 2017, as can be divided in to 3 submissions:</p>
<p> </p>
<p>1. Identifying landuse and calculating its alteration in time</p>
<p>2. Vegetation and zoobentos observation</p>
<p>3. Water sampling</p>
<... | [] |
52,981 | Plasmid Sequence Analysis from Long Reads | 1 | dx.doi.org/10.17504/protocols.io.bxyvppw6 | https://www.protocols.io/view/plasmid-sequence-analysis-from-long-reads-bxyvppw6 | David Eccles | TITLE: Plasmid Sequence Analysis from Long Reads
AUTHORS: David Eccles
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol demonstrates how to assemble reads from plasmid DNA, and generate a circularised and non-repetitive consensus sequence</div><br/><div class = "text-block">At the momen... | ["[Read file preparation]\nDemultiplex reads as per protocol Demultiplexing Nanopore reads with LAST.If this has been done, then the following command should produce output without errors:for bc in $(awk '{print $2}' barcode_counts.txt); do ls demultiplexed/reads_${bc}.fq.gz;doneExample output:demultiplexed/reads_BC02... |
33,842 | Virus IgM antibody detection | 1 | dx.doi.org/10.17504/protocols.io.bdasi2ee | https://www.protocols.io/view/virus-igm-antibody-detection-bdasi2ee | Wenjing Liu, Shihong Fu | TITLE: Virus IgM antibody detection
AUTHORS: Wenjing Liu, Shihong Fu
[DESCRIPTION]
Two JEV IgM antibody detection kits were used to test serum and CSF samples.the Beixi Capture ELISA 24 Test ELISA kit (REVI-001M,LOT:1807-1;Shanghai B&C ,China)andthe JE Detect IgM Antibody Capture ELISA Kit(JEMS-1,LOT:XC1285,InBios In... | ["[Beixi kit] 1. \t After the kit has equilibrated to room temperature, unpack the microplates and remove the required amount of strips and place them in the holder. The remaining strips should be re-placed in the packaging bag for sealing and stored at 2-8℃.", "[Beixi kit] 2. \t Cerebrospinal fluid samples were dilute... |
77,536 | Modular Reconstruction and Co-registration of Imaging from Implanted ECoG and SEEG Electrodes | 5 | dx.doi.org/10.17504/protocols.io.5qpvornedv4o/v2 | https://www.protocols.io/view/modular-reconstruction-and-co-registration-of-imag-cpx8vprw | Daniel J Soper, Alex Ross, Dustine Reich, Sydney S. Cash, Ishita Basu, Noam Peled, Angelique C. Paulk | TITLE: Modular Reconstruction and Co-registration of Imaging from Implanted ECoG and SEEG Electrodes
AUTHORS: Daniel J Soper, Alex Ross, Dustine Reich, Sydney S. Cash, Ishita Basu, Noam Peled, Angelique C. Paulk
[DESCRIPTION]
This pipeline involves taking pre- and post-operative images to localized and visualize elect... | ["[Retrieving Images and Saving Files] Retrieve Images\n \nWhen retrieving imaging as DICOMs, you can download the entire imaging series or just the sequence of interest, whichever is easiest for your setup. If there is not a T1 MRI with high enough resolution, a T2/FLAIR image with good resolution can supplement (but ... |
79,012 | HV-CTAB-PCI DNA Extraction Protocol | 1 | null | https://www.protocols.io/view/hv-ctab-pci-dna-extraction-protocol-crecv3aw | Vicky Ooi, Lee McMichael, Margaret E. Hunter, Aristide Takoukam Kamla, Janet M. Lanyon | TITLE: HV-CTAB-PCI DNA Extraction Protocol
AUTHORS: Vicky Ooi, Lee McMichael, Margaret E. Hunter, Aristide Takoukam Kamla, Janet M. Lanyon
[DESCRIPTION]
A ‘High Volume- Cetyltrimethyl Ammonium Bromide- Phenol-Chloroform-Isoamyl Alcohol ’ (HV-CTAB-PCI) method was developed.
[STEPS]
1. Clean the working bench with Tr... | ["Clean the working bench with TriGene.", "Scrape 1 g of faecal material from the outer surface of a faeces and put it into a 15 mL centrifuge tube.", "Transfer the faecal material into a mortar and grind the faeces into powder with liquid nitrogen.", "Add 1 mL of Lysis Buffer 1 (LB1: CTAB 2%, Tris– HCL 100 mM, EDTA 20... |
null | null | null | dx.doi.org/10.17504/protocols.io.gwgbxbw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>!!! ~~~~~ IN DEVELOPMENT ~~~~~ !!!</p>
<p>This approach uses in-vitro transcription to generate a dinoflagellate-type mRNA (i.e. capped with the dino-SL leader), which is introduced into cells using an RNA transformation reagent. Screening for expression of the protein encode... | [] |
30,784 | pL0R-LacZ | null | dx.doi.org/10.17504/protocols.io.baa8iahw | null | Bernardo Pollak | TITLE: pL0R-LacZ
AUTHORS: Bernardo Pollak
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Name</span><span>: pL0R-LacZ</span></div><div class = "text-block"><span style = "font-weight:bold;">Description</span><span>: a L0 receiver vector which can be used for domest... | [] |
36,630 | SPARC Cat - Sham Control Chronic Cat 2 Day 30 | 1 | dx.doi.org/10.17504/protocols.io.bfzwjp7e | https://www.protocols.io/view/sparc-cat-sham-control-chronic-cat-2-day-30-bfzwjp7e | Brett Hanzlicek, Anna Rietsch, Margot Damaser | TITLE: SPARC Cat - Sham Control Chronic Cat 2 Day 30
AUTHORS: Brett Hanzlicek, Anna Rietsch, Margot Damaser
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a procedure for a sham control chronic cat experiment (Day 30-terminal) for cystotomy (bladder surgery). The cystotomy is performe... | ["[Transport Cat]\nTransport cat from housing site to surgery site.", "[Animal Prep and catheter placement]\nAnimal is anesthetized and abdomen is shaved by the vet team. The cat is then moved into the surgery room and attached to monitors by the vet team.", "[Animal Prep and catheter placement]\nDrape animal and perf... |
66,318 | https://www.facebook.com/Detoxil600mg/ | 1 | dx.doi.org/10.17504/protocols.io.36wgq7z43vk5/v1 | https://www.protocols.io/view/https-www-facebook-com-detoxil600mg-ccznsx5e | cristianoballor | TITLE: https://www.facebook.com/Detoxil600mg/
AUTHORS: cristianoballor
[DESCRIPTION]
Diaetoxil 600mg: Contrairement à d'autres helpers à l'amincissement, ces cases ont un effet polyvalent sur l'organisme, de sorte qu'une réduction de poids souhaitée peut être soutenue de manière sturdy et surtout permanente. Positiv... | ["[https://www.facebook.com/Detoxil600mg/]"] |
65,068 | Addition of Antibiotic Supplement to Media | 4 | null | https://www.protocols.io/view/addition-of-antibiotic-supplement-to-media-cbsksncw | Mariam Alkattan | TITLE: Addition of Antibiotic Supplement to Media
AUTHORS: Mariam Alkattan
[DESCRIPTION]
The following protocol is for the addition of antibiotic stock solution to molten media.
[STEPS]
7. Cefotaxime stock solution preparation
0.1. Retrieve molten media from autoclave using heat resistant gloves. Place media in l... | ["Cefotaxime stock solution preparation", "Retrieve molten media from autoclave using heat resistant gloves. Place media in laminar flow hood if one is available. If laminar flow hood is not available, place media next to open flame on lab bench.", "Wait for media to cool to50 °C. Measure temperature using laser infrar... |
32,051 | Method for creating a tissue microarray-capable, slide-scanning acquisition device from any motorized microscope | null | dx.doi.org/10.17504/protocols.io.bbitiken | null | Steven P. Nilsen, M. Lora D. L. M. Ong, Jeremy Muhlich, Jay Copeland, Neal Gliksman, Jerrold R. Turner | TITLE: Method for creating a tissue microarray-capable, slide-scanning acquisition device from any motorized microscope
AUTHORS: Steven P. Nilsen, M. Lora D. L. M. Ong, Jeremy Muhlich, Jay Copeland, Neal Gliksman, Jerrold R. Turner
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>High-throughp... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.cphvj5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
The BioBrick® Assembly Kit was developed in partnership with Ginkgo BioWorks. What follows is an abbreviated set of protocols for the use of the BioBrick® Assembly Kit (to assemble an Upstream Part with a Downstream Part into a Destination Plasmid). For more details and ... | [] |
56,683 | Bogus Data Acquisition Protocol I | 1 | dx.doi.org/10.17504/protocols.io.b3kjqkun | https://www.protocols.io/view/bogus-data-acquisition-protocol-i-b3kjqkun | Abby Moore | TITLE: Bogus Data Acquisition Protocol I
AUTHORS: Abby Moore
[DESCRIPTION]
The purpose of this protocol is to demo protocol development.
The real version of this protocol might be developed with respect to existing publications. Here, I'll refer to publications using the Citation component.
[BEFORE_START]
... | ["[This is my first section] In the first step, I'll refer to an image of software by using embed code retrieved from Box.", "[This is my first section] In this step, I'll use the Command component to tell the user to run a command.", "[This is my first section] In this step, I'll refer to some software by using the So... |
null | null | null | dx.doi.org/10.17504/protocols.io.kuycwxw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Often used in Western Blots. Kept on the bottom shelf of the fridge. </p>
[STEPS]
?.
?.
?.
?. | [] |
29,522 | High molecular weight DNA extraction from plant nuclei isolation optimised for long-read sequencing | 1 | dx.doi.org/10.17504/protocols.io.83shyne | https://www.protocols.io/view/high-molecular-weight-dna-extraction-from-plant-nu-83shyne | Cedric Mariac | TITLE: High molecular weight DNA extraction from plant nuclei isolation optimised for long-read sequencing
AUTHORS: Cedric Mariac
[DESCRIPTION]
High molecular weight DNA was extracted from isolated plant nuclei and used to prepare RAD004 and LSK109 libraries for Nanopore sequencing. Typically, flow cells yielded 3-15... | ["Plant material sampling \nCollect 0.7 g to 1 g of fresh tissue in a 50 ml tube containing liquid nitrogen. \nGrind in a frozen mortar (stored at -80 °C) using a pestle. (Try to avoid mixing tissues with different developmental stages since it might affect DNA yield and quality)", "Homogenization of fresh tissue \n\nT... |
90,742 | Human Ovarian Tissue Procurement and Processing for Ovarian Explant Cultures (Static and Fluidic conditions) | 1 | dx.doi.org/10.17504/protocols.io.36wgq3ebxlk5/v1 | https://www.protocols.io/view/human-ovarian-tissue-procurement-and-processing-fo-c4uwywxe | hannah.anvari, pooja.devrukhkar, hannes.campo, francesca.e.duncan duncan | TITLE: Human Ovarian Tissue Procurement and Processing for Ovarian Explant Cultures (Static and Fluidic conditions)
AUTHORS: hannah.anvari, pooja.devrukhkar, hannes.campo, francesca.e.duncan duncan
[DESCRIPTION]
The Cellular Senescence Network (SenNet) was recently established to map senescent cells in the human body.... | ["[Processing human ovarian tissue for ovarian explant cultures]", "[Processing human ovarian tissue for ovarian explant cultures] Ovarian tissue samples are collected from the Northwestern Pathology Department and placed immediately on ice following collection. The research coordinator will bring research specimens to... |
34,478 | Bench top CUT&RUN with antibodies-online™ CUT&RUN Sets | null | dx.doi.org/10.17504/protocols.io.bdwni7de | null | Antibodies Online Gmbh | TITLE: Bench top CUT&RUN with antibodies-online™ CUT&RUN Sets
AUTHORS: Antibodies Online Gmbh
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">CUT&RUN (Cleavage Under Targets and Release Using Nuclease) offers a novel approach </div><div class = "text-block">to pursue epigenetics. The method is desig... | ["[ REAGENT SETUP (for 8 samples)]\n» Wash buffer (110 mL) ABC1ComponentVolumeFinal concentration2ddH2O103 mL-31 M HEPES pH 7.5 2.2 mL20 mM45 M NaCl 3.3 mL150 mM52 M Spermidine 27.5 µL 0.5 mM» Binding Buffer (30 mL) ABC1ComponentVolumeFinal concentration2ddH2O29 mL-31 M HEPES pH 7.5600 µL20 mM41 M KCl300 µL10 mM51 M ... |
92,822 | Immunofluorescence on Fresh Frozen Kidney Tissue - Validation of Antibodies | 1 | dx.doi.org/10.17504/protocols.io.5jyl8pwwdg2w/v1 | https://www.protocols.io/view/immunofluorescence-on-fresh-frozen-kidney-tissue-v-c6vwze7e | Maya Brewer, Yuantee Zhu, Kelly Clothier, Jeff Spraggins, Mark De Caestecker | TITLE: Immunofluorescence on Fresh Frozen Kidney Tissue - Validation of Antibodies
AUTHORS: Maya Brewer, Yuantee Zhu, Kelly Clothier, Jeff Spraggins, Mark De Caestecker
[DESCRIPTION]
We describe the procedure for immunofluorescence on human kidney tissue embedded in carboxymethylcellulose or low melting point gelatin,... | ["[Immunofluorescence] Using a hydrophobic pen, draw a large barrier around each section. Do not allow pen to touch section.", "[Immunofluorescence] Place frozen slides from the -80˚C freezer directly into the formalin, and post-fix for 5 minutes.", "[Immunofluorescence] To remove solutions from sections that are in th... |
19,719 | SYSB 3036 W01: Introduction to Unix | null | dx.doi.org/10.17504/protocols.io.xhffj3n | null | Frank Aylward | TITLE: SYSB 3036 W01: Introduction to Unix
AUTHORS: Frank Aylward
[STEPS]
?. [start]
A Unix or Unix-like operating system generally has a wide variety of build-in functions that are extremely useful for navigating between folders, exploring the contents of files, and getting various summary statistics that are useful ... | ["[start]\nA Unix or Unix-like operating system generally has a wide variety of build-in functions that are extremely useful for navigating between folders, exploring the contents of files, and getting various summary statistics that are useful before undertaking a bioinformatic analysis. Here we will explore some of t... |
91,803 | Exploring Microbial Diversity with QIIME2 | 5 | dx.doi.org/10.17504/protocols.io.14egn3y4zl5d/v1 | https://www.protocols.io/view/exploring-microbial-diversity-with-qiime2-c5v3y68n | Jialin Hu | TITLE: Exploring Microbial Diversity with QIIME2
AUTHORS: Jialin Hu
[DESCRIPTION]
This tutorial introduces Qiime2 for non-phylogenetic diversity
analysis, covering core metrics calculation, emphasizing standardized sampling
depth, and using pre-processed feature tables and metadata. It then explores
beta group signifi... | ["[Title] Title: Exploring Microbial\nDiversity with QIIME 2", "[What is qiime2?] Qiime2 (Quantitative Insights Into Microbial Ecology 2) is a\npowerful bioinformatics platform designed for the analysis of microbial\ncommunities, particularly from high-throughput sequencing data. Developed by\nthe Knight Lab, Qiime2 pr... |
null | null | null | dx.doi.org/10.17504/protocols.io.rfbd3in | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This gene encodes a member of the DNase family. The protein hydrolyzes DNA, is not inhibited by actin, and mediates the breakdown of DNA during apoptosis. Alternate transcriptional splice variants of this gene have been observed but have not been thoroughly characterized.</p>... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.uyzexx6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Following this protocol, V. Natriegens cells can be transformed with linear fragments and plasmids based on natural transformation as described in Multiplex Genome Editing by Natural Transformation (MuGENT) for Synthetic Biology in Vibrio natriegens Dalia et. al, 2017. ACS Synt... | ["[PRE CULTURE] {\"blocks\":[{\"key\":\"73i20\",\"text\":\"Of a strain containing tfoX regulated by an inducible promoter (in this case an IPTG inducible promoter).\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"2gcg1\",\"text\":\"\",\"type\":\"unstyled\",\"dept... |
33,577 | Sterivex DNA extraction | null | dx.doi.org/10.17504/protocols.io.bc2hiyb6 | null | Ariel Rabines, Rob Lampe, Andrew Allen | TITLE: Sterivex DNA extraction
AUTHORS: Ariel Rabines, Rob Lampe, Andrew Allen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A mostly automated protocol for extraction of genomic DNA from seawater filtered onto a Sterivex filter (Cat. No. SVGP0150). Reagents come from the Macherey-Nagel NucleoMag ... | ["[Lysis]\nPrepare DNA lysis buffer (N = number of samples plus extra for pipetting)", "[Lysis]\nIn sterile container, add x N of Lysis Buffer MC1\n800 µl", "[Lysis]\nAdd x N RNase A\n10 µl", "[Lysis]\n(optional) Add x N of each internal standard\n1 µl", "[Lysis]\nMix well.", "[Lysis]\nKeep sterivex on dry ice. In ... |
58,332 | NCT04556981 Safety and Immunogenicity of M72/AS01E in Participants With Well-controlled HIV (MESA-TB) | 1 | dx.doi.org/10.17504/protocols.io.b474qzqw | https://www.protocols.io/view/nct04556981-safety-and-immunogenicity-of-m72-as01e-b474qzqw | Alexander Schmidt; Gates Medical Research Institute | TITLE: NCT04556981 Safety and Immunogenicity of M72/AS01E in Participants With Well-controlled HIV (MESA-TB)
AUTHORS: Alexander Schmidt; Gates Medical Research Institute
[DESCRIPTION]
Protocol Title: A randomized, placebo-controlled, observer-blind, phase 2 study to evaluate
safety and immunogenicity of the investiga... | [] |
87,717 | Extraction of high molecular weight DNA from nasal lining fluid | 4 | null | https://www.protocols.io/view/extraction-of-high-molecular-weight-dna-from-nasal-czwdx7a6 | Samuel Montgomery | TITLE: Extraction of high molecular weight DNA from nasal lining fluid
AUTHORS: Samuel Montgomery
[DESCRIPTION]
Assessing the microbiome in respiratory samples is often difficult due to the low biomass of microbes often present in these samples. While there are published methods for efficient extraction of DNA from sa... | ["[Preparation of reagents] MetaPolyzyme is recieved as a lypholysed powder. Reconstitute following manufacturers instructions to a final concentration of 5 mg/mL, aliquot into 0.6mL microtubes, and store at -20ºC until use", "[Preparation of reagents] Create a 70 % (v/v) solution of molecular grade ethanol with UltraP... |
null | null | null | dx.doi.org/10.17504/protocols.io.mhcc32w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The methods used for re-sequencing the full <em>LPL</em> gene in Kuwaiti Arabs and to analyse the sequence variation and identify variants that could attribute to variation in plasma lipid levels for further genetic association is described in details. Samples (n=100) of an A... | [] |
27,653 | MojoSort™ Nanobeads Column Protocol - 1 | null | dx.doi.org/10.17504/protocols.io.69dhh26 | null | Sam Li | TITLE: MojoSort™ Nanobeads Column Protocol - 1
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>BioLegend MojoSort™ nanobeads work in commonly used separation columns, based on our internal research as well as validation by external testing by academic labs. This simple protocol... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes.", "In the final wash of your sample preparation, resuspend the cells in MojoSort™ Buffer by adding up to 4 mL in a 5 mL (12 x 75 mm) polypropylene tube.Note: Keep MojoSort™ Buffer on ice throughout the procedure.", "Filter the cells with... |
48,769 | In vitro alpha-glucosidase enzyme activity | 4 | dx.doi.org/10.17504/protocols.io.btu9nnz6 | https://www.protocols.io/view/in-vitro-alpha-glucosidase-enzyme-activity-btu9nnz6 | huseyin akşit | TITLE: In vitro alpha-glucosidase enzyme activity
AUTHORS: huseyin akşit
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">alpha-glucosidase enzyme hydrolyses p-NPG to p-nitro phenol and glucoside. p-nitro phenol have max absorbonce at 405 nm.</span></div></div>
[STE... | ["Add 50 µl pH=6.8 0.1 M phosphate buffer each well\n50 µl", "Add 10 µl 1U/ml enzyme solution\n10 µl", "Add 20µl sample solution containing 10, 7.5, 5, 2.5, 1, 0.75, 0.5, 0.25, 0.125 mg/ml perapared in max %20 DMSO:buffer solution\n20 µl\n37 °C", "Add 20 µl 0.5 mM p-NPG\n20 µl\n0 Room temperature", "Read absorbance a... |
null | null | null | dx.doi.org/10.17504/protocols.io.szyef7w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Degenerated PCR to test Y-linkage of genes in several Drosophila species. The reactions are made separately for males and females of 400 species and subspecies of Drosophila and related genera.</p>
[STEPS]
SECTION: Pre-Mix Preparation
?.
SECTION: Final Degenerated PCR prepa... | ["[Pre-Mix Preparation] {\"blocks\":[{\"key\":\"226ka\",\"text\":\"Usually, we performing PCR tests in large-scale, testing several DNA samples from different species at once. We prepared a pre-mix stock to economy time in PCR experiments.\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[]... |
82,433 | iPSC differentiation into Macrophages | 4 | dx.doi.org/10.17504/protocols.io.81wgbympovpk/v1 | https://www.protocols.click/view/ipsc-differentiation-into-macrophages-cuq9wvz6 | Narayana Yadavalli, Shawn M. Ferguson | TITLE: iPSC differentiation into Macrophages
AUTHORS: Narayana Yadavalli, Shawn M. Ferguson
[DESCRIPTION]
This protocol describes iPSC differentiation into macrophages.
[GUIDELINES]
This protocol is slight modification from the original protocol published.
Shi J, Xue C, Liu W, Zhang H. Differentiation of Human-Induc... | ["[iPSC differentiation into Macrophages] Day-2:\nCoat 3 wells of a 6 well pates with Matrigel. (1 hour coating also works).", "[iPSC differentiation into Macrophages] Day-1:", "[iPSC differentiation into Macrophages] Bring iPSC maintenance to plate cell culture hood, remove the media and rinse once with PBS.", "[iPSC ... |
41,247 | nf-vcf-novel-dataset-builder | 5 | dx.doi.org/10.17504/protocols.io.bkh7kt9n | https://www.protocols.io/view/nf-vcf-novel-dataset-builder-bkh7kt9n | Israel Aguilar Ordoñez | TITLE: nf-vcf-novel-dataset-builder
AUTHORS: Israel Aguilar Ordoñez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Nextflow pipeline used to build the novel variants dataset for the 100GMX project.</div><div class = "text-block">'nf-vcf-novel-dataset-builder' is a pipeline tool that builds a VCF fi... | ["[Pre-processing]\nRemove singletons and privateRemove singletons and private variants.Dependencies:\na) Filter positions where AC >= '3' to eliminate singletons and private.* AC could be modified.", "[Core-processing]\nSelect novelSelect novel SNPs, indels variants and concatenate both type variants.Dependencies:\na)... |
64,762 | An optimized and High Yielding Protocol for Isolation and Amplification of Bacteriophages Against Methicillin-resistant Staphylococcus aureus (MRSA) | 4 | dx.doi.org/10.17504/protocols.io.e6nvwk4zzvmk/v1 | https://www.protocols.io/view/an-optimized-and-high-yielding-protocol-for-isolat-cbg2sjye | Atif Khan | TITLE: An optimized and High Yielding Protocol for Isolation and Amplification of Bacteriophages Against Methicillin-resistant Staphylococcus aureus (MRSA)
AUTHORS: Atif Khan
[DESCRIPTION]
Bacteriophages are bacteria-specific viruses having great potential as therapeutic agents against multidrug-resistant strains/bac... | ["[STEP 1: PREPARATION OF WATER SAMPLE FILTRATE FOR ISOLATION OF BACTERIOPHAGES (CRITICAL STEP)*] Collect untreated sewage water samples from the domestic sewage treatment plant and hospital wastewater treatment plant.", "[STEP 1: PREPARATION OF WATER SAMPLE FILTRATE FOR ISOLATION OF BACTERIOPHAGES (CRITICAL STEP)*] Co... |
null | null | null | dx.doi.org/10.17504/protocols.io.nnsddee | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Static chamber method for field sampling of greenhouse gases. Prepared on behalf of the Sierra Mountain Meadow Restoration Research Partnership</p>
<p>July 15<sup>th</sup>, 2015</p>
[STEPS] | [] |
101,531 | Assessing Pyrene Impact on Precopulatory Behaviour: A Cost-effective Time-to-Event Experiment with Parhyale hawaiensis | 0 | dx.doi.org/10.17504/protocols.io.q26g71mp3gwz/v1 | https://www.protocols.io/view/assessing-pyrene-impact-on-precopulatory-behaviour-dfd33i8n | Ibrahim Lawan | TITLE: Assessing Pyrene Impact on Precopulatory Behaviour: A Cost-effective Time-to-Event Experiment with Parhyale hawaiensis
AUTHORS: Ibrahim Lawan
[DESCRIPTION]
Understanding the impact of environmental contaminants on chemosensation is crucial for assessing the ecological fitness of aquatic organisms. Here, we pres... | ["[Introduction] Chemosensation plays a crucial role in the survival and ecological interactions of aquatic organisms, enabling them to detect and respond to chemical cues in their environment. This chemical communication is used by crustaceans, including amphipods, for various behaviours such as food location, predato... |
null | null | null | dx.doi.org/10.17504/protocols.io.rhsd36e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>R script used for the phyloseq analysis of the Poirier et al., food microbiota dataset and comparative analysis between 16S and gyrB amplicon sequencing. </p>
[STEPS] | [] |
80,395 | MERS Main Protease (Mpro) Fluorescence Dose Response | 1 | null | https://www.protocols.io/view/mers-main-protease-mpro-fluorescence-dose-response-csrjwd4n | Haim Barr, Noa Lahav | TITLE: MERS Main Protease (Mpro) Fluorescence Dose Response
AUTHORS: Haim Barr, Noa Lahav
[DESCRIPTION]
This is a functional, biochemical assay used to identify treatments for viral infectious disease in MERS 3C-like protease.
Utilizing a direct enzyme activity measurement method, the experiment was performed in a 3... | ["[Prepare 384 Well Plate] PRIME with Assay Buffer by Multi-Drop Combi Tube Dispensing Cassette by selecting the PRIME button on the Combi Dispenser until the tubes are filled completely.", "[Prepare 384 Well Plate] DISPENSE 10 µL to Columns 1 and 23 of assay plate\nNote: These will represent the inhibitor control colu... |
null | null | null | dx.doi.org/10.17504/protocols.io.fi6bkhe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Provides a short introduction to MEGAHIT, IDBA-UD, and SPAdes assemblers, a demo on Prodigal Gene Caller, and determining % of reads and contig coverage using Bowtie2 short read aligner.</p>
<p> </p>
<p>Open this protocol inside the virtual machine (details in 'Start Instruct... | [] |
29,577 | Bench top CUT&Tag with antibodies-online™ CUT&RUN Sets | null | dx.doi.org/10.17504/protocols.io.85hhy36 | null | antibodies online GmbH | TITLE: Bench top CUT&Tag with antibodies-online™ CUT&RUN Sets
AUTHORS: antibodies online GmbH
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">CUT&RUN (Cleavage Under Targets and Release Using Nuclease) offers a novel approach </div><div class = "text-block">to pursue epigenetics. The method is desig... | ["[ REAGENT SETUP (for 16 samples)]\n» Wash buffer (100 mL) ABC1ComponentVolumeFinal concentration2ddH2O94 mL-31 M HEPES pH 7.5 2 mL20 mM45 M NaCl 3 mL 150 mM52 M Spermidine 25 µL 0.5 mM» Binding Buffer (40 mL) ABC1ComponentVolumeFinal concentration2ddH2O39 mL -31 M HEPES pH 7.5 800 µL 20 mM41 M KCl 400 µL 10 mM51 ... |
36,081 | SP3 (Single-Pot, Solid-Phase, Sample-Preperation) Protein Extraction for Dental Calculus | 1 | dx.doi.org/10.17504/protocols.io.bfgrjjv6 | https://www.protocols.io/view/sp3-single-pot-solid-phase-sample-preperation-prot-bfgrjjv6 | Shevan Wilkin, Richard Hagan, Sandra Hebestreit, Madeleine Bleasdale, Ayushi Nayak, Li Tang, Traci N Billings, Nicole Boivin, Kristine Richter | TITLE: SP3 (Single-Pot, Solid-Phase, Sample-Preperation) Protein Extraction for Dental Calculus
AUTHORS: Shevan Wilkin, Richard Hagan, Sandra Hebestreit, Madeleine Bleasdale, Ayushi Nayak, Li Tang, Traci N Billings, Nicole Boivin, Kristine Richter
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Dent... | ["[Reagent Preparation]\nGeneral InformationWe recommend to use combusted glassware for buffers and solutions. Solutions should be prepared under a dedicated dead air hood for reagent preparation.TFA should be handled only under a fume hood.Prepare the Guanidine Hydrochloride solution last! All bottle and tubes contain... |
95,346 | Sample preparation protocol for proteomic analysis of isolated lysosomes and whole cell extracts | 1 | dx.doi.org/10.17504/protocols.io.q26g7p2d8gwz/v1 | https://www.protocols.io/view/sample-preparation-protocol-for-proteomic-analysis-c9csz2we | Daniel Saarela, Raja S. Nirujogi, Dario R Alessi | TITLE: Sample preparation protocol for proteomic analysis of isolated lysosomes and whole cell extracts
AUTHORS: Daniel Saarela, Raja S. Nirujogi, Dario R Alessi
[DESCRIPTION]
Mass spectrometry-based proteomics has emerged as fundamental technique to study functional changes of proteome including post translational mo... | ["[Sample lysis and elution of lysosomal material - For immunoprecipitates:] Resuspend your dry bead slurry of LysoTag or MockTag IP in 100 µL of HEPES lysis buffer, making sure to disperse any clumps.", "[Sample lysis and elution of lysosomal material - For immunoprecipitates:] Incubate on Room temperature for 15 min ... |
30,684 | The detection of freshwater pearl mussel | null | dx.doi.org/10.17504/protocols.io.974h9qw | null | Omneya Ahmed Osman, Alexander Eiler, Mats Töpel, Tomas larsson | TITLE: The detection of freshwater pearl mussel
AUTHORS: Omneya Ahmed Osman, Alexander Eiler, Mats Töpel, Tomas larsson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>qPCR assay to detect freshwater pearl mussels </span><span style = "font-style:italic;">Margaritifera margaritifera</span><sp... | ["[Primers]\nStoeckle et al., 2016 designed primers targeting 16S rRNA gene of Margartifera margaritifera.The sequence of the primer set is:MarMa_16S2.1: 5’- GCAACACGGAAAACCCC TG -3’MarMa_16S1.2: 5’- GGCT GCGCTCATGTGAATTA -3’.", "[PCR reaction]\nA master mix was prepared and calculated according to the number of standa... |
null | null | null | dx.doi.org/10.17504/protocols.io.d9i94d | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<strong>This general protocol can be used for assessing eukaryotic populations with various diagnostic stains (SYTOX for live/dead cells; DAF-FM for nitric oxide producing cells; DCFDA for reactive oxygen species; others). It is geared for samples that are ~5-10 µm in size, usin... | [] |
57,730 | Passaging of feeder-free hPSCs | 4 | dx.doi.org/10.17504/protocols.io.b4maqu2e | https://www.protocols.io/view/passaging-of-feeder-free-hpscs-b4maqu2e | Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner | TITLE: Passaging of feeder-free hPSCs
AUTHORS: Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner
[DESCRIPTION]
This protocol describes the process of passaging human pluripotent stem cells (hPSCs) for feeder-free culturing of hPSCs using Accutase or ReLeSF
Protocol overview
A. Accutase
B. ReLeS... | ["[A. Accutase] Wash hPSCs with DPBS", "[A. Accutase] Add 1 ml Accutase/well to the 6-well plate.", "[A. Accutase] Incubate 5 min 37 °C", "[A. Accutase] Add 2 ml DMEM/F12 to each well.", "[A. Accutase] Collect all cells into 15 ml conical tube.", "[A. Accutase] Add 7 ml DMEM/F12.", "[A. Accutase] Centrifuge at 200-30... |
62,609 | Titan XL Male Enhancement You can able to reach peak sexual performance. | 3 | dx.doi.org/10.17504/protocols.io.81wgb62wolpk/v1 | https://www.protocols.io/view/titan-xl-male-enhancement-you-can-able-to-reach-pe-b9drr256 | Alpha State Male Enhancement | TITLE: Titan XL Male Enhancement You can able to reach peak sexual performance.
AUTHORS: Alpha State Male Enhancement
[DESCRIPTION]
https://www.24x7nutra.com/Order-titan-xl-male-enhancement/
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ssgeebw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes the steps to prepare and embed biological tissue into Lowicryl HM20® resin and subsequent whole brain imaging via fluorescence micro-optical sectioning tomography (fMOST). </p>
[STEPS] | [] |
98,152 | PROTOCOLO DE AVALIAÇÃO ELETROFISIOLÓGICA DIRECIONADO A CRIANÇA COM TRANSTORNO DO PROCESSAMENTO AUDITIVO CENTRAL | 0 | dx.doi.org/10.17504/protocols.io.5jyl82me8l2w/v1 | https://www.protocols.io/view/protocolo-de-avalia-o-eletrofisiol-gica-direcionad-db4g2qtw | Mariana Heloiza Ribeiro Carvalho, Pedro L Menezes, LUCAS DANIEL SOUZA DE VASCONCELOS, NATÁLIA DE LIMA BARBOSA DA SILVA, Aline Tenório Lins Carnaúba | TITLE: PROTOCOLO DE AVALIAÇÃO ELETROFISIOLÓGICA DIRECIONADO A CRIANÇA COM TRANSTORNO DO PROCESSAMENTO AUDITIVO CENTRAL
AUTHORS: Mariana Heloiza Ribeiro Carvalho, Pedro L Menezes, LUCAS DANIEL SOUZA DE VASCONCELOS, NATÁLIA DE LIMA BARBOSA DA SILVA, Aline Tenório Lins Carnaúba
[DESCRIPTION]
The assessment of Central Aud... | ["[PROTOCOLO DE AVALIAÇÃO ELETROFISIOLÓGICA DIRECIONADO A CRIANÇA COM TRANSTORNO DO PROCESSAMENTO AUDITIVO CENTRAL] IDENTIFICAÇÃO\nNome do participante: _____________________________________________________________________Idade:_____ \nEscolaridade:_______________________________________________________________________... |
50,130 | ARTIC NEB Tagmentation protocol - high throughput whole genome sequencing of SARS-CoV-2 | 1 | null | https://www.protocols.io/view/artic-neb-tagmentation-protocol-high-throughput-wh-bu7snzne | Karan Bhatt, Amy Kistler, Angela Detweiler, Ashley Byrne, Gabrielle Lee, G Renuka Kumar, Lienna Chan, Lusajo Mwakibete, Michael B, Michelle Tan, Norma Neff, Sabrina Mann, Sharon Fong | TITLE: ARTIC NEB Tagmentation protocol - high throughput whole genome sequencing of SARS-CoV-2
AUTHORS: Karan Bhatt, Amy Kistler, Angela Detweiler, Ashley Byrne, Gabrielle Lee, G Renuka Kumar, Lienna Chan, Lusajo Mwakibete, Michael B, Michelle Tan, Norma Neff, Sabrina Mann, Sharon Fong
[DESCRIPTION]
<div class = "text... | ["[Input RNA prep - Dilution and plating]\nHigh titer SARS-CoV-2 samples can exhaust-free ARTIC primers and form aberrant multimers during multiplex PCR (refer fig. 2). These larger amplicons can cause issues during downstream sequencing that impact genome sequence recovery. Hence, RNA samples need to be diluted by the... |
62,288 | Analysis of sugars, small organic acids, and alcohols by HPLC-RID | 6 | dx.doi.org/10.17504/protocols.io.5qpvob7y9l4o/v1 | https://www.protocols.io/view/analysis-of-sugars-small-organic-acids-and-alcohol-b83qrymw | Hannah M. Alt, Alexander F. Benson, Stefan J. Haugen, Morgan A. Ingraham, William E. Michener, Sean P. Woodworth, Kelsey J. Ramirez, Gregg T. Beckham | TITLE: Analysis of sugars, small organic acids, and alcohols by HPLC-RID
AUTHORS: Hannah M. Alt, Alexander F. Benson, Stefan J. Haugen, Morgan A. Ingraham, William E. Michener, Sean P. Woodworth, Kelsey J. Ramirez, Gregg T. Beckham
[DESCRIPTION]
An analytical method was developed using high performance liquid chromato... | ["[Preparation of standards] Standards\n\nAllow standard level ampules (listed in 'Materials' section) to come to room temperature, vortex, and transfer contents of ampules into 2 mL amber HPLC vials.\nTo create lower concentration calibration levels than provided in the kit, dilute the lowest concentration ampule to y... |
51,243 | Coleta de dados actigráficos - ActTrust - V.1 | 2 | dx.doi.org/10.17504/protocols.io.bwajpacn | https://www.protocols.io/view/coleta-de-dados-actigr-ficos-acttrust-v-1-bwajpacn | Daniel Vartanian | TITLE: Coleta de dados actigráficos - ActTrust - V.1
AUTHORS: Daniel Vartanian
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Esta coleção reúne os protocolos do processo de coleta de dados actigráficos do Grupo Interdisciplinar de Pesquisa em Sono (GIPSO). O processo foi desenhado para os ac... | [] |
45,215 | (Non-UDG treated) double-stranded modern dental calculus DNA library preparation for Illumina sequencing | 1 | dx.doi.org/10.17504/protocols.io.bqd7ms9n | https://www.protocols.io/view/non-udg-treated-double-stranded-modern-dental-cal-bqd7ms9n | Franziska Aron, Irina Velsko, Gunnar Neumann, Christina Warinner, Guido Brandt | TITLE: (Non-UDG treated) double-stranded modern dental calculus DNA library preparation for Illumina sequencing
AUTHORS: Franziska Aron, Irina Velsko, Gunnar Neumann, Christina Warinner, Guido Brandt
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for the preparation of double-stranded geno... | ["[Blunt End Repair (aDNA library preparation room)]\nPrepare a mastermix for the blunt end repair calculating . Use a new 1.5 ml LoBind tube to set up the mastermix. ABCD1ReagentStock concentrationFinal concentration1x Volume [µl]2NEB Buffer 210 x1 x53ATP10 mM1 mM54BSA20 mg/ml0.8 mg/ml25dNTPs25 mM each0.25 mM0.56T4 ... |
51,602 | Structure-from-Motion, Capturing Geological Samples | 1 | dx.doi.org/10.17504/protocols.io.bwmspc6e | https://www.protocols.io/view/structure-from-motion-capturing-geological-samples-bwmspc6e | Madalyn Massey | TITLE: Structure-from-Motion, Capturing Geological Samples
AUTHORS: Madalyn Massey
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Structure-from-Motion (SfM) is a photogrammetry process that creates 3D models from overlapping 2D images. This protocol focuses on its application related to geological... | ["[Introduction]\nWhat is it?Structure-from-Motion (SfM) and photogrammetry is a recent application in the earth science community. SfM is the representation of physical samples as a 3D model produced from a series of overlapping 2D images collected from multiple angles about the sample or subject of interest. Research... |
94,397 | Mouse brain hemisphere organotypic cultures on glass coverslips | 4 | dx.doi.org/10.17504/protocols.io.j8nlkojxwv5r/v1 | https://www.protocols.io/view/mouse-brain-hemisphere-organotypic-cultures-on-gla-c8e5ztg6 | Jan Tonnesen | TITLE: Mouse brain hemisphere organotypic cultures on glass coverslips
AUTHORS: Jan Tonnesen
[DESCRIPTION]
This protocol describes preparation of organotypic hemisphere cultures prepared from mouse brain and cultured as rollerdrum cultures on glass coverslips. Having the cultures directly attached to glass coverslips ... | ["[Preparatory steps] Thaw chicken plasma at 4°C, prepare thrombin working solution and keep at 4°C.", "[Preparatory steps] Disinfect surgical tools and utensils in pure ethanol and rinse off in dH2O.", "[Preparatory steps] Turn on vibratome and set to 250 μm interval slicing.", "[Brain dissections] Decapitate mouse pu... |
null | null | null | dx.doi.org/10.17504/protocols.io.rczd2x6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a protocol from the <a href="http://doudnalab.org/" target="_blank" rel="noopener noreferrer">Doudna Lab</a> for preparation of Cas9 protein. </p>
[BEFORE_START]
<div title="Page 1">
<p><strong>Materials</strong></p>
<p> </p>
<table style="height: 112px; width: 301px... | [] |
63,053 | Beetle rearing media | 1 | dx.doi.org/10.17504/protocols.io.8epv59d3jg1b/v1 | https://www.protocols.io/view/beetle-rearing-media-b9tmr6k6 | Yin-Tse Huang, Tina | TITLE: Beetle rearing media
AUTHORS: Yin-Tse Huang, Tina
[DESCRIPTION]
ambrosia beetle rearing
[STEPS]
1. The recipe produces enough medium to fill approximately 36 culture tubes.(12cm)
First, add powder or solid, then add liquid
2. All ingredients were mixed thoroughly, then put cotton plugs into the mouth of... | ["The recipe produces enough medium to fill approximately 36 culture tubes.(12cm)\nFirst, add powder or solid, then add liquid", "All ingredients were mixed thoroughly, then put cotton plugs into the mouth of the filled tubes.", "The culture tubes was autoclaved at 121 °C for 30 min.", "Put culture tubes to dry 2 night... |
93,071 | Crystallization of Zika virus NS2B-NS3 protease | 1 | dx.doi.org/10.17504/protocols.io.eq2lyj51mlx9/v1 | https://www.protocols.io/view/crystallization-of-zika-virus-ns2b-ns3-protease-c65pzg5n | xiaomin.ni Ni, Peter Marples, Daren Fearon, Lizbé Koekemoer | TITLE: Crystallization of Zika virus NS2B-NS3 protease
AUTHORS: xiaomin.ni Ni, Peter Marples, Daren Fearon, Lizbé Koekemoer
[DESCRIPTION]
Zika virus (ZIKV) infections causes microcephaly in new-borns and Guillain-Barre syndrome in adults raising a global public health concern, yet no vaccines or antiviral drugs are av... | ["[Crystallization experiment] Protein and buffer requirements:\n43.2 µL15 mg/mL \n2.88 mL", "[Crystallization experiment] Dispense 30 µL into SwissCI 3 lens plate reservoir wells using a 100 µl multi-channel pipette.\nDispense 150 nL15 mg/mL to each lens using the SPT mosquito.\nDispense 150 nL to each lens using th... |
89,327 | Waveform characteristics in thoracic paravertebral space: a prospective observational study | 1 | dx.doi.org/10.17504/protocols.io.14egn3mxpl5d/v1 | https://www.protocols.io/view/waveform-characteristics-in-thoracic-paravertebral-c3gpyjvn | Amorn Vijitpavan, Sivaporn Termpornlert, Pattika Subsoontorn, Lalinthip Vareesunthorn | TITLE: Waveform characteristics in thoracic paravertebral space: a prospective observational study
AUTHORS: Amorn Vijitpavan, Sivaporn Termpornlert, Pattika Subsoontorn, Lalinthip Vareesunthorn
[DESCRIPTION]
Background: With increased use of thoracic paravertebral block (TPVB) in thoracic surgery, many faced the chall... | ["[Protocol for the study: Waveform characteristics in thoracic paravertebral space: a prospective observational study] Anesthesiology residents or fellows at Ramathibodi Hospital obtained\npreoperative information and provided informed consent. The inclusion criteria\nwere an age of 18 to 80 years and an American Soci... |
69,886 | Rat brain processing for histological analyses | 4 | dx.doi.org/10.17504/protocols.io.e6nvwj61wlmk/v1 | https://www.protocols.io/view/rat-brain-processing-for-histological-analyses-cgg6ttze | miquel.vila | TITLE: Rat brain processing for histological analyses
AUTHORS: miquel.vila
[DESCRIPTION]
Protocol for rat brain processing in order to perform histological analyses
[STEPS]
SECTION: Rat perfusion
1. Deeply anesthetize animals with sodium pentobarbital (50 mg/kg, i.p.)
SECTION: Rat perfusion
2. Perfuse through the lef... | ["[Rat perfusion] Deeply anesthetize animals with sodium pentobarbital (50 mg/kg, i.p.)", "[Rat perfusion] Perfuse through the left ventricle with saline [0.9% (wt/vol)] at room temperature (RT)", "[Rat perfusion] Perfuse again with ice-cold formaldehyde solution 4% in PBS buffered for histology", "[Processing for micr... |
66,371 | Condor CBD Gummies Reviews (Updated 2022 Shark Tank Episode) Real Trusted Exposed! | 3 | dx.doi.org/10.17504/protocols.io.eq2lynr7evx9/v1 | https://www.protocols.io/view/condor-cbd-gummies-reviews-updated-2022-shark-tank-cc3bsyin | Condor CBD Gummies | TITLE: Condor CBD Gummies Reviews (Updated 2022 Shark Tank Episode) Real Trusted Exposed!
AUTHORS: Condor CBD Gummies
[DESCRIPTION]
Health
[STEPS] | [] |
41,493 | Differentiation of iPSC into Microglia-Like Cells (iMGL) | 1 | dx.doi.org/10.17504/protocols.io.bkrvkv66 | https://www.protocols.io/view/differentiation-of-ipsc-into-microglia-like-cells-bkrvkv66 | Fabia Filipello, Jacob Marsh, Rj Martinez, Celeste Karch | TITLE: Differentiation of iPSC into Microglia-Like Cells (iMGL)
AUTHORS: Fabia Filipello, Jacob Marsh, Rj Martinez, Celeste Karch
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the derivation of Hematopoietic Progenitor Cells and differentiation of iMGLs using iPSC cultures. ... | ["[iPSCs Culture]\nThaw and culture iPSC line per the following protocol:\n{\"blocks\":[{\"data\":[],\"depth\":0,\"entityRanges\":[],\"inlineStyleRanges\":[],\"key\":\"95clo\",\"text\":\"This protocol is about Maintenance and Expansion of induced pluripotent stem cells.\",\"type\":\"unstyled\"}],\"entityMap\":[]}", "[i... |
106,727 | Nanopore Sequencing of poliovirus isolates | 0 | dx.doi.org/10.17504/protocols.io.14egn6beql5d/v2 | https://www.protocols.io/view/nanopore-sequencing-of-poliovirus-isolates-dkgf4ttn | Catherine Troman, Erika Bujaki, Joyce Akello, Shannon Fitz, Alex Shaw, Javier Martin, Nick Grassly | TITLE: Nanopore Sequencing of poliovirus isolates
AUTHORS: Catherine Troman, Erika Bujaki, Joyce Akello, Shannon Fitz, Alex Shaw, Javier Martin, Nick Grassly
[DESCRIPTION]
This protocol is adapted from "Direct Detection of poliovirus and Nanopore Sequencing (DDNS) - Stool" to make it suitable for use with cell culture... | ["[Sample Organisation] Pairs of samples (with the same EPID) can have consecutive barcodes but try not to group samples from the same geographic area together. This helps detect any potential cross-contamination because identical sequences are then unlikely to be detected in samples with consecutive barcodes that are ... |
85,308 | HEK293 cell culture for co-immunoprecipitation experiments | 4 | dx.doi.org/10.17504/protocols.io.kxygx3zeog8j/v1 | https://www.protocols.click/view/hek293-cell-culture-for-co-immunoprecipitation-exp-cxi4xkgw | Dan Dou, Erika Holzbaur | TITLE: HEK293 cell culture for co-immunoprecipitation experiments
AUTHORS: Dan Dou, Erika Holzbaur
[DESCRIPTION]
Here, we describe HEK293 cell culture for the purpose of co-immunoprecipitation experiments
[BEFORE_START]
Cells should be routinely tested for mycoplasma contamination using MycoAlert detection kit (Lonza... | ["Culture HEK293 cells in DMEM (Corning) supplemented with 10% fetal bovine serum (HyClone)", "Maintain cells at 37 degrees Celsius with 5% CO2", "In preparation for co-immunoprecipitation experiments, passage HEK cells with Trypsin onto three 10 cm tissue culture dishes per experimental condition, at a density of 1:10... |
39,314 | Acute Kidney Injury In corona virus infection disease (COVID-19) in Derby, United Kingdom | 3 | dx.doi.org/10.17504/protocols.io.bimskc6e | https://www.protocols.io/view/acute-kidney-injury-in-corona-virus-infection-dise-bimskc6e | Nitin Kolhe, Richard J Fluck, Nicholas M Selby, Maarten W Taal | TITLE: Acute Kidney Injury In corona virus infection disease (COVID-19) in Derby, United Kingdom
AUTHORS: Nitin Kolhe, Richard J Fluck, Nicholas M Selby, Maarten W Taal
[STEPS] | [] |
51,580 | Wisecaver Lab CTAB-based extraction of high molecular weight DNA from photosynthetic sea slugs | 1 | dx.doi.org/10.17504/protocols.io.kxygxp81zl8j/v1 | https://www.protocols.io/view/wisecaver-lab-ctab-based-extraction-of-high-molecu-bwk4pcyw | Jennifer H Wisecaver, Raeya Ogas, Pax Tomko, Gregory Gavelis | TITLE: Wisecaver Lab CTAB-based extraction of high molecular weight DNA from photosynthetic sea slugs
AUTHORS: Jennifer H Wisecaver, Raeya Ogas, Pax Tomko, Gregory Gavelis
[DESCRIPTION]
Protocol for CTAB-based extraction of high molecular weight DNA from photosynthetic sea slugs. This protocol is optimized for sampl... | ["[Prepare CTAB DNA extraction buffer] Prepare 100 mL CTAB buffer:\n100 mL Ultrapure distilled water\n1.576 g TrisHCL ph 8 (100 mM)\n0.584 g EDTA (20 mM)\n8.82 g NaCl (1.4 M)\n10 mg Proteinase K (0.1 mg/mL)\n\nNote: This stock buffer is sufficient for 9-10 extractions.", "[Prepare equipment and reagents] On the day of ... |
70,847 | Guanidine-based DNA extraction with silica-coated beads or silica spin columns | 4 | dx.doi.org/10.17504/protocols.io.eq2ly73mmlx9/v1 | https://www.protocols.io/view/guanidine-based-dna-extraction-with-silica-coated-che7t3hn | Dominik Buchner | TITLE: Guanidine-based DNA extraction with silica-coated beads or silica spin columns
AUTHORS: Dominik Buchner
[DESCRIPTION]
This protocol describes how to extract DNA from samples lysed as described in
using guanidine hydrochloride and ethanol-based buffer combined with silica-coated magnetic beads or silica spin ... | ["[Bead-based protocol]", "To clear the lysates 11.000 x g, 3 min, 20 °C", "[Bead-based protocol] Place the plate on a magnet to pellet the beads for 2 min", "[Bead-based protocol] Discard the supernatant by pipetting", "[Bead-based protocol] Add 100 µL to each sample", "[Bead-based protocol]", "[Bead-based protocol] P... |
47,283 | PacBio Iso-Seq Preparation for Sequel II Systems | 4 | dx.doi.org/10.17504/protocols.io.n92ld9wy9g5b/v1 | https://www.protocols.io/view/pacbio-iso-seq-preparation-for-sequel-ii-systems-bsetnben | e.gustavsson | TITLE: PacBio Iso-Seq Preparation for Sequel II Systems
AUTHORS: e.gustavsson
[DESCRIPTION]
The Sequel Systems generate long reads that are well-suited for characterizing fulllength transcripts produced from high-quality RNA samples. This document describes a method to construct Iso-Seq SMRTbell® libraries for sequenc... | ["[cDNA synthesis using SMARTer™ PCR cDNA Synthesis Kit First-Strand cDNA Synthesis]", "[cDNA synthesis using SMARTer™ PCR cDNA Synthesis Kit First-Strand cDNA Synthesis] For each sample and Control Mouse Liver Total RNA, combine the following reagents in separate 0.5 ml reaction tubes:", "[cDNA synthesis using SMARTer... |
56,561 | Automated Protein Quantification with the Biomek-FX Liquid Handler System | 4 | dx.doi.org/10.17504/protocols.io.b3grqjv6 | https://www.protocols.io/view/automated-protein-quantification-with-the-biomek-f-b3grqjv6 | Yan Chen, Nurgul Kaplan Lease, Tad Ogorzalek, Jennifer Gin, Christopher J Petzold | TITLE: Automated Protein Quantification with the Biomek-FX Liquid Handler System
AUTHORS: Yan Chen, Nurgul Kaplan Lease, Tad Ogorzalek, Jennifer Gin, Christopher J Petzold
[DESCRIPTION]
This protocol details steps to perform the protein quantification (Lowry-based) assay by using a Biomek FX liquid handler system.... | ["[Deck Setup] Open Biomek Software that controls Biomek-FX liquid handler system. Under \"File\" drop-down menu, click \"Open\" to select the automation method \"Modular Protein Quantitation method.\"", "[Deck Setup] Click on \"Instrument Setup\" under the \"Setup\" group node to get visual instruction on how to set u... |
null | null | null | dx.doi.org/10.17504/protocols.io.rdxd27n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>CAR-T therapy has shown significant efficacy in the treatment of leukemia, lymphoma and other blood cancers. Novartis and Gilead Sciences have already received FDA approval for CAR-T therapy targeting the B cell antigen <a href="https://www.creative-biolabs.com/car-t/anti-cd1... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.nzkdf4w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Method used to derive single cell suspension from P1 mouse kidneys on ice, generating a cell suspension with greatly reduced artifact gene expresion changes and suitable for downstream analysis using 10x Chromium or DropSeq. </p>
[GUIDELINES]
<div>
<p><strong>Storage Conditi... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.sa2eage | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Zebrafish are an increasingly popular model system to better understand vertebrate physiology. Physical challenge by exercise has become popular to assess physical fitness of genetically manipulated animals or to identify gene regulatory networks that prepare the organism for... | [] |
93,646 | Gewebesammlung Frischgewebe Prostatektomie | 1 | null | https://www.protocols.io/view/gewebesammlung-frischgewebe-prostatektomie-c7pnzmme | Annika Fendler, Bettina Ergün | TITLE: Gewebesammlung Frischgewebe Prostatektomie
AUTHORS: Annika Fendler, Bettina Ergün
[DESCRIPTION]
Dieses Protokoll beschreibt die Schritte für die Sammlung von Frischgewebe, Gefriergewebe (Fresh-frozen), und Blut von Patienten mit Prostatakarzinom bei Prostatektomie.
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Protokoll zur Blutaufa... | ["[Aufarbeitung im Labor] weiter mit Protokoll:", "[Gewebesammlung im OP]", "[Gewebesammlung im OP] Nach Rückmeldung des OPs geht eine Person zur Gewebeentnahme.\nKiste Prostata und Stickstoffbehälter mitnehmen.\nArbeitsanleitung (siehe Abbildung) beachten.", "[Gewebesammlung im OP] 1x 15 ml Falcons mit 10,2 ml Transpo... |
52,750 | Assessing enrichment of proteins in the mitochondrial fraction in HEK cells | 1 | dx.doi.org/10.17504/protocols.io.bxrnpm5e | https://www.protocols.io/view/assessing-enrichment-of-proteins-in-the-mitochondr-bxrnpm5e | OLIVIA HARDING | TITLE: Assessing enrichment of proteins in the mitochondrial fraction in HEK cells
AUTHORS: OLIVIA HARDING
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a method for measuring protein enrichment on mitochondria in various conditions. In the resulting Western blot, one can assess the leve... | ["[Cell Lysis and Mitochondrial Enrichment]\nPlace dish of cells on ice and gently aspirate media.", "[Cell Lysis and Mitochondrial Enrichment]\nAdd 800 uL cold PBS and scrape cells into a 2 mL tube", "[Cell Lysis and Mitochondrial Enrichment]\nIf using multiple plates per condition, combine all cells into 800 uL PBS."... |
83,647 | Fungal Culture Long-term Storage (Dry Filter Paper Technique) | 4 | null | https://www.protocols.click/view/fungal-culture-long-term-storage-dry-filter-paper-cvw7w7hn | Anuar Morales | TITLE: Fungal Culture Long-term Storage (Dry Filter Paper Technique)
AUTHORS: Anuar Morales
[DESCRIPTION]
Culture collections are expensive to support, as they require special equipment and continuous attention in order to maintain fungal cultures without losing their pathogenicity or virulence. Two examples of the... | ["[Initial Isolation] A pinch of pure fungal culture is taken from insect or plant host and added to culture medium in a Petri dish.\nSelective media PARP5 can be used or general PDA. Additives include chloramphenicol, lactic acid, ampicillin, streptomycin, etc.", "[Initial Isolation] Filter papers (1 x 1 cm) cut and s... |
29,515 | Pulse Field Gel Electrophoresis for Long Read Sequencing | null | dx.doi.org/10.17504/protocols.io.83jhykn | null | Benjamin Schwessinger, David Stanley, Ming-Dao Chia | TITLE: Pulse Field Gel Electrophoresis for Long Read Sequencing
AUTHORS: Benjamin Schwessinger, David Stanley, Ming-Dao Chia
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Pulsefield gel electrophoresis is an easy and affordable method of quality control for high molecular weight DNA extractions, p... | ["[Reagent setup]\nPrepare 2 L of 0.5x TBE buffer, along with 100 ml of 0.5x TBE buffer in a separate container.", "[Reagent setup]\nAdd 1g of Agarose (I/Ultrapure) to the 100 ml 0.5x TBE, to make a 1% agarose gel. Heat and mix until homogenous. Add 10 µl SYBR safe dye and mix again.", "[Reagent setup]\nTransfer 200 ul... |
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