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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22,613 | Before data acquisition -- Start MRI Project Spinoza REC | null | dx.doi.org/10.17504/protocols.io.2bvgan6 | null | Tinka Beemsterboer, Lukas Snoek, H.Steven Scholte | TITLE: Before data acquisition -- Start MRI Project Spinoza REC
AUTHORS: Tinka Beemsterboer, Lukas Snoek, H.Steven Scholte
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Dear researcher,</div><div class = "text-block">This protocol outlines the steps to start an MRI project at the Spinoza Centre Ro... | ["Apply for a calpendo User Account.The PI and all other researchers, research assistants and interns of the project should apply for a user account in Calpendo.Go to the link https://spinozarec.calpendo.com.Calpendo is the Calendar and user registration system used by Spinoza REC. Apart from booking registrations, Spi... |
108,154 | Wie bewerten psychiatrische Gutachterinnen und Gutachter die Arbeit mit einer Softwarelösung zur Gutachtenerstellung? – Eine Studie zum Nutzererleben einer neuen digitalen Anwendung. Studienprotokoll. | 0 | dx.doi.org/10.17504/protocols.io.261ge5b7wg47/v1 | https://www.protocols.io/view/wie-bewerten-psychiatrische-gutachterinnen-und-gut-dmu246ye | Johanna Ristau, Yves Lehmkuhl, Jana Vachek, Rosa Abel, André Schmoller, Patrick Ristau | TITLE: Wie bewerten psychiatrische Gutachterinnen und Gutachter die Arbeit mit einer Softwarelösung zur Gutachtenerstellung? – Eine Studie zum Nutzererleben einer neuen digitalen Anwendung. Studienprotokoll.
AUTHORS: Johanna Ristau, Yves Lehmkuhl, Jana Vachek, Rosa Abel, André Schmoller, Patrick Ristau
[DESCRIPTION]... | ["[Einleitung] Psychische Erkrankungen sind in Deutschland weit verbreitet. Die Daten der aktuellsten repräsentativen Studie zur psychischen Gesundheit der Allgemeinbevölkerung des Robert-Koch-Instituts von 2008-2011 ergaben, dass jedes Jahr etwa 28 Prozent der Erwachsenen von einer psychischen Erkrankung betroffen sin... |
null | null | null | dx.doi.org/10.17504/protocols.io.jepcjdn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
45,102 | test rating | 1 | null | https://www.protocols.io/view/test-rating-bqanmsde | asfasas | TITLE: test rating
AUTHORS: asfasas
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.esvbee6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For more information and for the Spanish version of this protocol, please see <a href="http://www.wilsonsayreslab.org/blog/2016/3/17/hzp6ve4a7d56mpzg7obagpisba7c2a" target="_blank">here</a>.<br /><br />The protocol is based on: <a href="http://www.scientificamerican.com/article/... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.dmj44m | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This mixture is used in the <a href="https://www.protocols.io/view/CsCl-Step-Gradient-to-Purify-Phage-c4zyx5?step=4" target="_blank">CsCl Step Gradient to Purify Phage Protocol<br /></a>
[GUIDELINES]
<br /><strong>Grams of CsCl to be added to Buffer</strong><br /><br />
<table ... | [] |
96,726 | Donor Selection Criteria for Adipose, Liver & Blood Procurement -- University of Minnesota Human TMC | 1 | dx.doi.org/10.17504/protocols.io.rm7vzxw4xgx1/v1 | https://www.protocols.io/view/donor-selection-criteria-for-adipose-liver-amp-blo-dapw2dpe | Sayeed Ikramuddin, Laura Niedernhofer | TITLE: Donor Selection Criteria for Adipose, Liver & Blood Procurement -- University of Minnesota Human TMC
AUTHORS: Sayeed Ikramuddin, Laura Niedernhofer
[DESCRIPTION]
This document outlines the inclusion and exclusion criteria for donors of adipose (visceral, subcutenous) and blood for the SenNet Consortium prog... | ["[Inclusion Criteria] Age 18 years old or older", "[Exclusion Criteria] Pregnancy or nursing -- Pregnancy is routinely an exclusion for surgery. If patients are scheduled for surgery, they receive a pregnancy test per clinical care. The study team will utilize the results available in the medical record to determine e... |
33,900 | TIM, a Targeted Insertional Mutagenesis method utilizing CRISPR/Cas9 in Chlamydomonas reinhardtii | null | dx.doi.org/10.17504/protocols.io.bdcki2uw | https://www.protocols.io/view/tim-a-targeted-insertional-mutagenesis-method-util-bdcki2uw | Tyler Picariello, Yuqing Hou, Tomohiro Kubo, Nathan A. McNeill, Haru-aki Yanagisawa, Toshiyuki Oda, George B. Witman | TITLE: TIM, a Targeted Insertional Mutagenesis method utilizing CRISPR/Cas9 in Chlamydomonas reinhardtii
AUTHORS: Tyler Picariello, Yuqing Hou, Tomohiro Kubo, Nathan A. McNeill, Haru-aki Yanagisawa, Toshiyuki Oda, George B. Witman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Generation and ... | ["[gRNA design]\ngRNA should target an exon in the first 2/3 of the gene of interest to increase the chance of generating a null mutation.", "[gRNA design]\ngRNA design websites: IDT: https://www.idtdna.com/site/order/designtool/index/CRISPR_CUSTOM -or- CRISPR direct: http://crispr.dbcls.jp.", "[Donor DNA preparation]\... |
90,115 | Dough Rise Assay | 1 | dx.doi.org/10.17504/protocols.io.n2bvj3z2wlk5/v1 | https://www.protocols.io/view/dough-rise-assay-c39byr2n | Natalie Kruglyak, Erin Li, Chantle R Swichkow | TITLE: Dough Rise Assay
AUTHORS: Natalie Kruglyak, Erin Li, Chantle R Swichkow
[DESCRIPTION]
This protocol presents an accessible method for actively evaluating dough rise phenotypes in various yeast strains and yeast/bacteria combinations. As dough rise is a pivotal element in bread-making, this approach simplifies a... | ["[Reducing Microbial Load by Autoclaving Flour] Combine unbleached All-Purpose flour and Stone Ground Whole Wheat flour in equal proportions.", "[Reducing Microbial Load by Autoclaving Flour] Autoclave the flour for 20 minutes using the gravity cycle setting.", "[Reducing Microbial Load by Autoclaving Flour] Ensure th... |
79,200 | ECIS Data Analysis for Stimulation of Human Pulmonary Microvascular Endothelial Cells (HPMECs) with Human Serum | 4 | null | https://www.protocols.io/view/ecis-data-analysis-for-stimulation-of-human-pulmon-crj8v4rw | Michael Bokoch | TITLE: ECIS Data Analysis for Stimulation of Human Pulmonary Microvascular Endothelial Cells (HPMECs) with Human Serum
AUTHORS: Michael Bokoch
[DESCRIPTION]
Sera from patients in our UCSF Liver Transplant Biobank are used to stimulate human pulmonary microvascular endothelial cells (HPMECs) grown to confluency on ECIS... | ["[ECIS Data Analysis for HPMEC stimulation by Liver Biobank Sera] Determine Difference in Area-under-the-Curve (Normalized Resistance at 4000 Hz)\nTo be calculated after recording full ECIS curve after stimulation with human serum from liver transplant (LT) patients.\n\nGoal: To calculate the difference in AUC between... |
null | null | null | dx.doi.org/10.17504/protocols.io.e9dbh26 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is for processing 20x10<sup>6</sup> cells (or ~100µl wet cell pellet). It can be scaled up and down accordingly.</p>
<p> </p>
<p>This is part of the <a href="https://www.protocols.io/view/Collection-of-FOCUS-SubCell-Protocols-For-the-Enri-e9ebh3e" target="_blank... | [] |
65,037 | C4 ZipTip Solid Phase Extraction | 1 | null | https://www.protocols.io/view/c4-ziptip-solid-phase-extraction-cbrmsm46 | Lauren Adams | TITLE: C4 ZipTip Solid Phase Extraction
AUTHORS: Lauren Adams
[DESCRIPTION]
Solid phase extraction for clean-up and concentration of proteins prior to introduction into the mass spectrometer.
[STEPS]
1. Activate Ziptip by pipetting 10 µL of C4 ZipTip Activation Buffer and discarding onto a Kimwipe for a total of 6... | ["Activate Ziptip by pipetting 10 µL of C4 ZipTip Activation Buffer and discarding onto a Kimwipe for a total of 6 times.", "Equilibrate the Ziptip by pipetting 10 µL of C4 ZipTip Equilibration/Wash Buffer and discarding onto a Kimwipe for a total of 6 times.", "Remove C4 Ziptip from p20 pipette and place safely back i... |
46,883 | Western Blot Protocol | 1 | null | https://www.protocols.io/view/western-blot-protocol-br2bm8an | Victoria Beja-Glasser | TITLE: Western Blot Protocol
AUTHORS: Victoria Beja-Glasser
[STEPS]
?. [Protein lysis]
Made lysis buffer. o 1:100 DF PPI enzyme in RIPA buffer
?. [Protein lysis]
Placed brains on metal tube holder, which is on ice, and added 500µL lysis buffer. Transferred brain and lysis buffer to thehomogenizer, then homogeniz... | ["[Protein lysis]\nMade lysis buffer. o 1:100 DF PPI enzyme in RIPA buffer", "[Protein lysis]\nPlaced brains on metal tube holder, which is on ice, and added 500µL lysis buffer. Transferred brain and lysis buffer to thehomogenizer, then homogenized with equipment on Minqing's/Tobias's bench.", "[Protein lysis]\nT... |
88,604 | High-throughput sequencing (HTS) oligos and methods to prepare oligos for HTS applications | 4 | dx.doi.org/10.17504/protocols.io.5jyl8pez7g2w/v1 | https://www.protocols.io/view/high-throughput-sequencing-hts-oligos-and-methods-c2r4yd8w | John B. Ridenour, Rafal Donczew | TITLE: High-throughput sequencing (HTS) oligos and methods to prepare oligos for HTS applications
AUTHORS: John B. Ridenour, Rafal Donczew
[DESCRIPTION]
In this protocol, we provide sequences of oligos used for high-throughput sequencing (HTS) applications and describe methods for preparing the oligos for HTS applica... | ["[Preparation of Y-yoke adapters] Briefly centrifuge the lyophilized adapter oligos at room temperature.", "[Preparation of Y-yoke adapters] Prepare a 100 µM stock of each adapter oligo. Add TLEN buffer at a volume 10 times the nmol of the oligo. For example, if the quantity of a given adapter oligo is nmol, add 1265 ... |
88,603 | Case Selection | 1 | dx.doi.org/10.17504/protocols.io.14egn34qql5d/v1 | https://www.protocols.io/view/case-selection-c2r3yd8n | Chase Carver | TITLE: Case Selection
AUTHORS: Chase Carver
[DESCRIPTION]
This protocol provides the basis for aged mouse acquisition and selection for brain tissue collection.
[STEPS]
SECTION: Case selection of aged mice
1. C57BL/6 Mice were acquired from the National Institute of Aging between 20-22 months old. The mice were house... | ["[Case selection of aged mice] C57BL/6 Mice were acquired from the National Institute of Aging between 20-22 months old. The mice were housed in the vivarium for at least 2 weeks prior to tissue collection\nMice that demonstrated severe dermatitis were excluded from the study. Mice that exhibit overt splenomegaly at t... |
53,530 | Calibration of glass electrode half-cells | 6 | dx.doi.org/10.17504/protocols.io.byh2pt8e | https://www.protocols.io/view/calibration-of-glass-electrode-half-cells-byh2pt8e | Agnes Heering, Ivo Leito, Markus Lahe, Martin Vilbaste | TITLE: Calibration of glass electrode half-cells
AUTHORS: Agnes Heering, Ivo Leito, Markus Lahe, Martin Vilbaste
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpose of this document is give glass-electrode half-cell calibration procedure with aqueous buffers.</div></div>
[STEPS]
?. [Softwar... | ["[Software]\nStart Quick IV Measurement Software.\nComputer cannot go to sleep during measurements or the communication between computer and instruments is lost and data collection stops.", "[Software]\nOn the left hand pick Function “Source & Sampling”.\nAlternatively, open previously saved QIVM file with measurement... |
12,665 | Gait analysis using augmented reality markers | null | dx.doi.org/10.17504/protocols.io.qkzdux6 | null | Gergely Nagymáté, Rita M Kiss | TITLE: Gait analysis using augmented reality markers
AUTHORS: Gergely Nagymáté, Rita M Kiss
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The protocol provides guidelines, preparation and execution instructions to perform and process a gait analysis trial by a novel motion capture method using vir... | ["Attach the AR markers on the corresponding body segments (for gait analysis: pelvis, thighs and legs)", "Start recording and perform anatomical calibration on the subject using the pointer after palpating the calibrated anatomical points.", "Record the gait trial.", "Upload the video takes to a computer.", "The calib... |
99,215 | Let’s Play! An Antidote to Solitary, Serious, Unsurprising Fieldwork | 0 | null | https://www.protocols.io/view/let-s-play-an-antidote-to-solitary-serious-unsurpr-dc5p2y5n | Kassandra Spooner-Lockyer, nick smith, Jean Chia, Noha Fikry Ismail | TITLE: Let’s Play! An Antidote to Solitary, Serious, Unsurprising Fieldwork
AUTHORS: Kassandra Spooner-Lockyer, nick smith, Jean Chia, Noha Fikry Ismail
[DESCRIPTION]
A component of ethnographic fieldwork consists in noticing empirical phenomena through a range of documentary and sensorial modalities. What gets notice... | ["[Broken Telephone] Draft a “Call to fieldwork” & circulate it in your trusted circles of researchers & ethnographers (on Threads, Instagram, listservs)", "[Broken Telephone] Assemble your players; 3-5 researchers engaging in fieldwork.", "[Broken Telephone] Meet over whatever platform is most suitable, zoom, teams, d... |
28,955 | Streptavidin immovilization stress test | null | dx.doi.org/10.17504/protocols.io.8h3ht8n | null | Jorge Fernández | TITLE: Streptavidin immovilization stress test
AUTHORS: Jorge Fernández
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The following protocol was performed to test the affinity of the protein streptavidin for the nitrocellulose when applied a continuous flow of solvent.</div></div>
[STEPS]
?. Cut ... | ["Cut the FF80HP nitrocellulose membranes in 2 rectangles of 0.8cm x 4 cm dimensions. Repeat this procedure with the FF170HP nitrocellulose to obtain a total of 4 nitrocellulose pieces.", "Stamp the microfluidic design, following the protocol microfluidic channels wax priming on:One piece of the FF170Hp nitrocellulos... |
42,212 | Quantification of the molar concentration of the NGS libraries by qPCR | 4 | dx.doi.org/10.17504/protocols.io.bmgck3sw | https://www.protocols.io/view/quantification-of-the-molar-concentration-of-the-n-bmgck3sw | Yoko Kato-Unoki | TITLE: Quantification of the molar concentration of the NGS libraries by qPCR
AUTHORS: Yoko Kato-Unoki
[STEPS]
?. Using the NGS library concentration obtained from the Agilent BioAnalyzer, dilute the libraries to 100 pg/μl with 10 mM Tris-HCl, pH 8.0. Then prepare a 1:10000 dilution of each diluted library (final con... | ["Using the NGS library concentration obtained from the Agilent BioAnalyzer, dilute the libraries to 100 pg/μl with 10 mM Tris-HCl, pH 8.0. Then prepare a 1:10000 dilution of each diluted library (final concentration, 0.01 pg/μl) by conducting 10-fold dilution series using 10 mM Tris-HCl, pH 8.0.*If the library concent... |
29,220 | Magnetic Beads Cell Separation | null | dx.doi.org/10.17504/protocols.io.8schwaw | null | Laura Sánchez, Claudia Troncone Clemente | TITLE: Magnetic Beads Cell Separation
AUTHORS: Laura Sánchez, Claudia Troncone Clemente
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The aim of this protocol is to separate the aptamers that bind to the cells from the ones that don't. The cells used have a histidin tag that attaches to the beads'... | ["[Separation with the MagneHis+]\nPrepare the magnetic module: remove the magnetic plate and load the necessary number of 1.5-mL microcentrifuge tubes.", "[Separation with the MagneHis+]\nPrepare fresh cultured E. coli samples with cell concentrations of 106 CFU/mL in PBS:", "[Separation with the MagneHis+]\nAdd 1 mL ... |
null | null | null | dx.doi.org/10.17504/protocols.io.fjmbkk6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.g3fbyjn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
105,304 | SHARE-seq protocol v2.2 | 4 | null | https://www.protocols.io/view/share-seq-protocol-v2-2-di3y4gpw | Amelia Hall | TITLE: SHARE-seq protocol v2.2
AUTHORS: Amelia Hall
[DESCRIPTION]
An updated version of the protocol SHARE-seq, as used by the Epigenomics Platform and Gene Regulation Observatory at the Broad Institute in the service of data production for the IGVF project. Link to the original paper and protocol here: https://www.s... | ["[1.1 Ordering Oligo Plates and oligos for plate production] One of the more involved aspects of SHARE-seq (and SPLiT-seq) is properly making the oligo hybridization 96 well plates - this section covers that in detail before moving into any of the day to day aspects of this protocol (those start at step 24, in section... |
null | null | null | dx.doi.org/10.17504/protocols.io.c5vy65 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This shows how to make 1M Tris.
[GUIDELINES]
test
[STEPS]
?.
?. | [] |
51,972 | Resting-state Functional Magnetic Resonance Imaging Under Fast and Fed States in Healthy Human Subjects and Gastroparetic Patients | 1 | dx.doi.org/10.17504/protocols.io.bp2l6bw9rgqe/v1 | https://www.protocols.io/view/resting-state-functional-magnetic-resonance-imagin-bwzcpf2w | Kun-Han Lu, Kristine Mosier, John Wo, Terry Powley | TITLE: Resting-state Functional Magnetic Resonance Imaging Under Fast and Fed States in Healthy Human Subjects and Gastroparetic Patients
AUTHORS: Kun-Han Lu, Kristine Mosier, John Wo, Terry Powley
[DESCRIPTION]
This protocol described the steps to acquire and analyze resting-state functional magnetic resonance imagi... | ["[Subjects] Twenty healthy subjects (14 females; 6 males) and 15 gastroparetic patients (11 females; 4 males) participated in this study under research protocols approved by the Institutional Review Board at Purdue University and Indiana University School of Medicine. All healthy subjects did not have a prior diagnosi... |
53,335 | Unified pH measurement | 6 | dx.doi.org/10.17504/protocols.io.bybxpspn | https://www.protocols.io/view/unified-ph-measurement-bybxpspn | Agnes Heering, Ivo Leito, Markus Lahe, Martin Vilbaste | TITLE: Unified pH measurement
AUTHORS: Agnes Heering, Ivo Leito, Markus Lahe, Martin Vilbaste
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The purpose of this document is to present technical guidance of measuring pH</span><span style = "vertical-align:sub;">abs</span><span style = "vertic... | ["[Filling the cell]\n25 °C\nThe side ports must be open.", "[Filling the cell]\nFill capillary with a syringe or pipette with the ionic liquid, so that the level of ionic liquid is 1 mm to 2 mm below the bottoms of the measurement compartments.\n0.1 mL\nIonic liquid has high viscosity, therefore flows very slowly, and... |
44,721 | RNA Direct Lysis Method | 4 | null | https://www.protocols.io/view/rna-direct-lysis-method-bpwrmpd6 | Elizabeth Fozo | TITLE: RNA Direct Lysis Method
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">RNA Direct Lysis method</div><div class = "text-block">(from Masse and Gottesman. 2003 Genes and Development. 17:2374-2383) (notes and italics are from E. Fozo by Selene Hess)</div></div>
[STEPS]
... | ["[Steps]\nGrow cells to desired OD.", "[Steps]\nAt desired OD, remove 750 ml of cells to a tube at 65°C containing 500 ml acid:phenol-chloroform with 100 ml of direct lysis solution (SET-UP at least 25 minutes prior to harvesting to ensure the components are at 65°C). Vortex to mix, and place the tube back at 65°C for... |
42,005 | COVID-19 Addgene Operating Procedures | 3 | dx.doi.org/10.17504/protocols.io.bk9vkz66 | https://www.protocols.io/view/covid-19-addgene-operating-procedures-bk9vkz66 | Joanne Kamens, Addgene The Nonprofit Plasmid Repository | TITLE: COVID-19 Addgene Operating Procedures
AUTHORS: Joanne Kamens, Addgene The Nonprofit Plasmid Repository
[STEPS] | [] |
64,674 | Generation of E. coli MG1655 whole cell lysate for proteomics applications | 1 | null | https://www.protocols.io/view/generation-of-e-coli-mg1655-whole-cell-lysate-for-cbeasjae | David Butcher | TITLE: Generation of E. coli MG1655 whole cell lysate for proteomics applications
AUTHORS: David Butcher
[DESCRIPTION]
This protocol describes the culture of E. coli MG1655 from a glycerol stock solution and subsequent lysis. It is intended for generating small quantities of whole cell lysate from cells grown in nutri... | ["[Cell culture] Seal lids of Bio-Reaction tubes with Parafilm (or swap for lids without pores) and freeze cell pellets at -80 °C until ready to perform lysis (or at least one hour).", "[Cell culture] Centrifuge tubes at 4000 x g, 15 min, 4 °C, then decant culture medium from each tube leaving pellet behind.", "[Cell c... |
null | null | null | dx.doi.org/10.17504/protocols.io.nmadc2e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The following procedure provides guidelines for isolating cells from whole blood using <a href="https://www.stemcell.com/products/brands/rosettesep.html?utm_source=protocolsio&utm_medium=referral" target="_blank" rel="noopener noreferrer">RosetteSep™</a>, an immunodensity... | [] |
36,590 | Tris Buffered Saline (TBS) | null | dx.doi.org/10.17504/protocols.io.bfynjpve | https://www.protocols.io/view/tris-buffered-saline-tbs-bfynjpve | Neilier Junior | TITLE: Tris Buffered Saline (TBS)
AUTHORS: Neilier Junior
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A buffer solution has the function of resisting changes in pH even when adding powerful acids or bases. However, in the physiological environment the buffered system also provides cofactors for ... | ["[Tris Buffered Saline (TBS)]\nPrepare by dissolving and in .\n10 mM Tris150 mM NaCl\n[of TBS]\n[Tris Base]\n[NaCl]\n[of distilled water]", "[Tris Buffered Saline (TBS)]\nAdjust pH before use.\nTris has a pKa of 8.3. Hence, the buffering capacity at is minimal compared to phosphate buffer (pKa = 7.21)"] |
null | null | null | dx.doi.org/10.17504/protocols.io.dq75zm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in "<a href="https://www.protocols.io/view/Obtaining-pure-cyanophage-stocks-liquid-assay-dqm5u5" target="_blank">Obtaining pure cyanophage stock: plaque purification</a>"
[GUIDELINES]
Use either the <a href="https://www.protocols.io/view/Liquid-Amplification-dq65zd" tar... | [] |
92,643 | Single action sequence reinforcement | 1 | dx.doi.org/10.17504/protocols.io.4r3l221k4l1y/v1 | https://www.protocols.io/view/single-action-sequence-reinforcement-c6qbzdsn | Jonathan Tang | TITLE: Single action sequence reinforcement
AUTHORS: Jonathan Tang
[DESCRIPTION]
Single action sequence reinforcement protocol for mouse studies from Tang et al 2023.
[GUIDELINES]
Individual mice were subjected to a single session of protocol each day, with sessions following each other on consecutive days.
[STEP... | ["[Session 1 + Baseline] Mice were placed in a white open field box for closed loop reinforcement protocol. \nTo acquire baseline behavior, individual mice were allowed to behave freely inside the box for 30 minutes on the first action A reinforcement session.", "After initial behavior acquisition, closed loop reinforc... |
101,794 | Organoid Drug Treatment | 0 | dx.doi.org/10.17504/protocols.io.x54v92rb1l3e/v1 | https://www.protocols.io/view/organoid-drug-treatment-dfna3mae | yzhu | TITLE: Organoid Drug Treatment
AUTHORS: yzhu
[DESCRIPTION]
Protocol for drug experiments of organoid samples
[STEPS]
1. Trypsinize organoids and plate at 30,000 cells/well in 24-well plates
2. Incubate 5-7 days
3. Incubate organoids in a complete medium containing 500 nM JQ1 for 24 hours (JQ cells) or 0.1% v/v DMSO ... | ["Trypsinize organoids and plate at 30,000 cells/well in 24-well plates", "Incubate 5-7 days", "Incubate organoids in a complete medium containing 500 nM JQ1 for 24 hours (JQ cells) or 0.1% v/v DMSO (control cells)", "Harvest organoids in Cell Recovery Solution (Corning) on ice for 1 hour, wash with PBS, and centrifuge... |
77,108 | BONCAT-FACS on river water and sewage effluent samples | 4 | dx.doi.org/10.17504/protocols.io.kxygx91ddg8j/v1 | https://www.protocols.io/view/boncat-facs-on-river-water-and-sewage-effluent-sam-cpiuvkew | Katharine Moss, Tim Goodall, Daniel S Read | TITLE: BONCAT-FACS on river water and sewage effluent samples
AUTHORS: Katharine Moss, Tim Goodall, Daniel S Read
[DESCRIPTION]
Bioorthogonal non-canonical amino acid tagging (BONCAT) is a method for detecting translational activity at the single cell level. Briefly, samples are incubated with a non-canonical amino ac... | ["[Advance reagent preparation] Prepare 100 mg/mL HPG solution by dissolving 100 mg of HPG in 1 mL of MilliQ water. \n\nStore solution at 4 °C in the dark.", "[Advance reagent preparation] To prepare 20 millimolar (mM) CuSO4. 5H2O solution, dissolve 0.5 g of CuSO4. 5H2O in 100 mL of MilliQ water.\n\nStore solution... |
103,165 | Multicolor fluorescence in situ hybridization and analysis | 0 | dx.doi.org/10.17504/protocols.io.3byl4937rgo5/v1 | https://www.protocols.io/view/multicolor-fluorescence-in-situ-hybridization-and-dgy53xy6 | Chuyu Chen | TITLE: Multicolor fluorescence in situ hybridization and analysis
AUTHORS: Chuyu Chen
[DESCRIPTION]
Antipsychotics are known to induce the expression of several immediate early genes (IEGs) via D2R antagonism, which then leads to changes in critical signaling pathways in iSPNs. To define the impact of LRRK2 kinase act... | ["[Fresh Frozen Tissue Prep] Place a piece of aluminum foil into a small Styrofoam container containing dry ice.", "[Fresh Frozen Tissue Prep] Mice were euthanized with carbon dioxide, decapitated, their brains rapidly removed, and placed immediately on foil on dry ice", "[Fresh Frozen Tissue Prep] Pour ~50 mL of 2-met... |
65,359 | Wonder Leaf CBD Oil (NEW 2022!) Does It Work Or Just Scam? | 3 | dx.doi.org/10.17504/protocols.io.n92ldz178v5b/v1 | https://www.protocols.io/view/wonder-leaf-cbd-oil-new-2022-does-it-work-or-just-cb3psqmn | Wonder Leaf CBD Oil | TITLE: Wonder Leaf CBD Oil (NEW 2022!) Does It Work Or Just Scam?
AUTHORS: Wonder Leaf CBD Oil
[DESCRIPTION]
MUST CHECK: *Special Discounted Pricing Available For The First 50 Customers Only! (ORDER Wonder Leaf CBD Oil)
[STEPS] | [] |
56,768 | Integrated Extraction for Cells | 1 | dx.doi.org/10.17504/protocols.io.kqdg3p5bql25/v1 | https://www.protocols.io/view/integrated-extraction-for-cells-b3n8qmhw | Juan Sanchez | TITLE: Integrated Extraction for Cells
AUTHORS: Juan Sanchez
[DESCRIPTION]
This liquid-liquid extraction for cells enables thesimultaneous generation of lipidomics and metabolomics samples for HILIC and C18 chromatography.
[GUIDELINES]
This extraction should be performed in a fume hood.
[STEPS]
1. Cells should arri... | ["Cells should arrive pelleted and frozen from collaborator", "Using wide-mouth pipette wash pellet with 500uL 150 mM ammonium acetate (25x aspirations)", "Centrifuge @ 200 g for 5 min", "Remove supernatant", "Repeat steps 2-4 a second time", "Add 4-6 non-sterile 2.3mm stainless steel beads to the tube.", "Dispense 225... |
59,928 | Design and preparation of synthetic reference peptides for APP/Aβ TOMAHAQ proteomics | 4 | dx.doi.org/10.17504/protocols.io.bp2l6bqk1gqe/v2 | https://www.protocols.io/view/design-and-preparation-of-synthetic-reference-pept-b6ryrd7w | Hankum Park, Frances V Hundley, Harper JW | TITLE: Design and preparation of synthetic reference peptides for APP/Aβ TOMAHAQ proteomics
AUTHORS: Hankum Park, Frances V Hundley, Harper JW
[DESCRIPTION]
TOMAHAQ-based targeted proteomics relies on heavy-labeled reference peptides for multi-plexed quantification of peptides of interest within a set of samples. The ... | ["Design APP peptides corresponding to extracellular and cytosolic regions based on data available in Peptide Atlas which are predicted to have favorable LC-MS properties. See attached Table.", "Design half-tryptic peptides based on the cleavage sites for BACE1 and ϒ-secretase. See attached table.", "Order commercial s... |
94,328 | Phenocycler-Fusion Staining Protocol For FFPE Tissue | 1 | dx.doi.org/10.17504/protocols.io.5jyl8pzodg2w/v1 | https://www.protocols.io/view/phenocycler-fusion-staining-protocol-for-ffpe-tiss-c8cyzsxw | Kyung J Ahn, Shovik Bandyopadhyay, Anusha Thadi, Kai Tan | TITLE: Phenocycler-Fusion Staining Protocol For FFPE Tissue
AUTHORS: Kyung J Ahn, Shovik Bandyopadhyay, Anusha Thadi, Kai Tan
[DESCRIPTION]
This protocol describes the method for antibody staining of FFPE tissues on slides using CODEX barcoded antibodies. The Akoya Phenocycler-Fusion user manual was modified to inclu... | ["[Tissue Pre-treatment] Bake sample slide/s in an incubator at 65°C for 1-3 hours until paraffin thoroughly melts.", "[Tissue Deparaffinization and Hydration] Immerse sample slide/s in a coplin jar containing the following reagents for 5 minutes each: \n\na.Histochoice \nb.Histochoice\nc.100% Ethanol\nd.100% Ethanol\n... |
null | null | null | dx.doi.org/10.17504/protocols.io.ek5bcy6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in <a href="https://www.protocols.io/view/Generating-viral-metagenomes-from-the-coral-holobi-ejgbcjw" target="_blank">Generating viral metagenomes from the coral holobiont</a>.
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
35,594 | Fresh 4% Paraformaldehyde in PBS | null | dx.doi.org/10.17504/protocols.io.bezijf4e | null | Allen Institute for Brain Science | TITLE: Fresh 4% Paraformaldehyde in PBS
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Freshly prepared 4% Paraformaldehyde in PBS is used to fix adult and developing mouse brains during the transcardial perfusion process, as well as for immersion fixation... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.p9vdr66 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes how to perform DNA FISH on dissected tissue of Planococcus citri. While the aim of this experiment was to distinguish localisation of the P. citri endosymbionts in ovarian and bacteriome tissue, the protocol can be easily adjusted for other tissues or ... | [] |
22,844 | Pig-Neural recording and analysis-workflow | null | dx.doi.org/10.17504/protocols.io.2i4gcgw | null | Jeffrey Ardell | TITLE: Pig-Neural recording and analysis-workflow
AUTHORS: Jeffrey Ardell
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Neural analysis using linear micrarray electrodes.</div></div>
[STEPS]
?. Recording and Raw DataNeural data: 16 neural channels from 16 electrodes on the linear microelectrode a... | ["Recording and Raw DataNeural data: 16 neural channels from 16 electrodes on the linear microelectrode array (LMA) were recorded. Electrode 1 is located at the tip of the LMA and it is linearly distributed until electrode 16. Each recorded channel is amplified and converted from analog to digital using CED system and ... |
35,637 | Mixotrophy - Quantification of the percent of phytoplankton cells with preys (e.g. fluorescent microspheres or fluorescently labeled bacteria) | 1 | dx.doi.org/10.17504/protocols.io.be2vjge6 | https://www.protocols.io/view/mixotrophy-quantification-of-the-percent-of-phytop-be2vjge6 | Valeria Jimenez | TITLE: Mixotrophy - Quantification of the percent of phytoplankton cells with preys (e.g. fluorescent microspheres or fluorescently labeled bacteria)
AUTHORS: Valeria Jimenez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This methodology describes a protocol modified from Sherr and Sherr (19... | ["[Experiment Set up and Fixation]\nPrepare your prey (YG-beads or FLBs) stock solution. Vortex vigorously and sonicate the solution for ~60 seconds.", "[Experiment Set up and Fixation]\nTake the phytoplankton flasks under different culture conditions (e.g. phytoplankton incubated in the dark and under nutrient limitat... |
51,215 | How is the practice to use the Risk Of Bias In Non-randomised Studies - of Interventions (ROBINS-I) tool in systematic reviews: a meta-epidemiological study protocol | 1 | dx.doi.org/10.17504/protocols.io.bv9pn95n | https://www.protocols.io/view/how-is-the-practice-to-use-the-risk-of-bias-in-non-bv9pn95n | Masahiro Banno, Yasushi Tsujimoto, Takashi Ariie, Yuji Okazaki, Yoshinosuke Shimamura, Kyosuke Kamijo, Yuki Kataoka | TITLE: How is the practice to use the Risk Of Bias In Non-randomised Studies - of Interventions (ROBINS-I) tool in systematic reviews: a meta-epidemiological study protocol
AUTHORS: Masahiro Banno, Yasushi Tsujimoto, Takashi Ariie, Yuji Okazaki, Yoshinosuke Shimamura, Kyosuke Kamijo, Yuki Kataoka
[DESCRIPTION]
<div cl... | ["[ABSTRACT]\nObjectives. To evaluate the practice to use the Risk Of Bias In Non-randomised Studies - of Interventions (ROBINS-I) tool in systematic reviews (SRs) including non-randomized studies of interventions (NRSI). Methods. This study is a meta-epidemiological study. We will include SRs, which include NRSI, and ... |
87,083 | Using TraceFinder and Excel software to evaluate and report multi-analyte targeted LC-MS data acquired on an ThermoScientific Exploris 240 Orbitrap | 1 | dx.doi.org/10.17504/protocols.io.n92ldm8z7l5b/v1 | https://www.protocols.io/view/using-tracefinder-and-excel-software-to-evaluate-a-czajx2cn | Margaux Billen, Scott G Denham, Joanna P Simpson, Natalie ZM Homer | TITLE: Using TraceFinder and Excel software to evaluate and report multi-analyte targeted LC-MS data acquired on an ThermoScientific Exploris 240 Orbitrap
AUTHORS: Margaux Billen, Scott G Denham, Joanna P Simpson, Natalie ZM Homer
[DESCRIPTION]
In our lab we focus on targeted analysis and have found that acquiring LC-... | ["[Creating a compound database in TraceFinder] In TraceFinder, navigate to the 'Method Development' tab in the bottom left corner of the screen.", "[Creating a compound database in TraceFinder] Select 'Compound Database' on the left-hand side. The screen that pops up looks like this:", "[Creating a processing method i... |
27,988 | SOC Medium | null | dx.doi.org/10.17504/protocols.io.7juhknw | null | Alba Balletbó | TITLE: SOC Medium
AUTHORS: Alba Balletbó
[STEPS]
?. Add SOC medium components in a 1 L autoclavable. SOC medium components (1 L): AB1Tryptone2% w/v2Yeast Extract0.5% w/v3NaCl10 mM4KCl2.5 mM5MgCl2 · 6H2O10 mM6MgSO4 · 6H2O10 mM7Glucose20 mM
AB1Tryptone2% w/v2Yeast Extract0.5% w/v3NaCl10 mM4KCl2.5 mM5MgCl2 · 6H2O10 mM6M... | ["Add SOC medium components in a 1 L autoclavable. SOC medium components (1 L): AB1Tryptone2% w/v2Yeast Extract0.5% w/v3NaCl10 mM4KCl2.5 mM5MgCl2 · 6H2O10 mM6MgSO4 · 6H2O10 mM7Glucose20 mM\nAB1Tryptone2% w/v2Yeast Extract0.5% w/v3NaCl10 mM4KCl2.5 mM5MgCl2 · 6H2O10 mM6MgSO4 · 6H2O10 mM7Glucose20 mM", "Add 1 L of distil... |
100,319 | Phylogenetic Read Placement Protocol | 0 | dx.doi.org/10.17504/protocols.io.4r3l2q24xl1y/v1 | https://www.protocols.io/view/phylogenetic-read-placement-protocol-dd7729rn | Matthew D. Hays, Clara A. Fuchsman | TITLE: Phylogenetic Read Placement Protocol
AUTHORS: Matthew D. Hays, Clara A. Fuchsman
[DESCRIPTION]
This protocol is for phylogenetic read placement of metagenomic reads in as quantitative a manner as possible without addition of known standards. This protocol includes assembly of metagenomes into contigs, creatio... | ["[Naming and counting Metagenomic reads] Rename all the metagenome filenames so that they include\nDepth_Cruise_Station\nThis can be done during the QC step, or by hand", "[Making phylogenetic trees] Collect all available relevant reference sequences from NCBI (or public database of choice) that you want on your tree.... |
22,853 | Amplicon library protocol for metabarcoding-based diet analysis in blue tits (Cyanistes caeruleus) using faecal DNA | 1 | dx.doi.org/10.17504/protocols.io.2jdgci6 | https://www.protocols.io/view/amplicon-library-protocol-for-metabarcoding-based-2jdgci6 | James Nicholls, James Nicholls | TITLE: Amplicon library protocol for metabarcoding-based diet analysis in blue tits (Cyanistes caeruleus) using faecal DNA
AUTHORS: James Nicholls, James Nicholls
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Amplicon library protocol for metabarcoding-based diet ... | ["[Overview of methodology]\nAmplicons were produced using a two stage PCR. The initial PCR used locus-specific primers with 5’ tails containing part of either the Illumina Nextera P5 or P7 adaptor sequence. Reagent concentrations, annealing temperatures and number of PCR cycles varied by locus (see table below). Th... |
50,791 | NEBNext® ARTIC SARS-CoV-2 FS Library Prep Kit (Illumina®) E7658 Express Protocol without PCR Bead Cleanup | 4 | dx.doi.org/10.17504/protocols.io.bvufn6tn | https://www.protocols.io/view/nebnext-artic-sars-cov-2-fs-library-prep-kit-illum-bvufn6tn | New England Biolabs | TITLE: NEBNext® ARTIC SARS-CoV-2 FS Library Prep Kit (Illumina®) E7658 Express Protocol without PCR Bead Cleanup
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details methods for the NEBNext® ARTIC SARS-CoV-2 FS Library Prep Kit (Illumina®), NEB #E7658S/... | ["[cDNA Synthesis]\nGently mix and spin down the LunaScript RT SuperMix reagent. Prepare the cDNA synthesis reaction as described below:COMPONENTVOLUMERNA Sample8 µl\n(lilac) LunaScript RT SuperMix2 µlTotal Volume10 µlFor no template controls, mix the following components: COMPONENTVOLUME(white) Nuclease-free Water8 µl... |
38,437 | Processing of leaf spectra | 1 | dx.doi.org/10.17504/protocols.io.bhsdj6a6 | https://www.protocols.io/view/processing-of-leaf-spectra-bhsdj6a6 | Anna Schweiger, Etienne Laliberté | TITLE: Processing of leaf spectra
AUTHORS: Anna Schweiger, Etienne Laliberté
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Steps for processing leaf spectra measured with an integrating sphere</div></div>
[STEPS]
?. This step is taken care of by the CABO leaf spectra processing pipeline: Absolute... | ["This step is taken care of by the CABO leaf spectra processing pipeline: Absolute reflectance and transmittance are calculated based on the most recent reference panel calibration. Depending on leaf size, calculations for absolute reflectance and transmittance are based on either 17 (Protocol “Measuring large leaves ... |
41,369 | nf-vcf-cataloguer | 5 | dx.doi.org/10.17504/protocols.io.bkmzku76 | https://www.protocols.io/view/nf-vcf-cataloguer-bkmzku76 | Israel Aguilar Ordoñez | TITLE: nf-vcf-cataloguer
AUTHORS: Israel Aguilar Ordoñez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">'nf-vcf-cataloguer' is a tool, implemented in Nextflow, that generates a general table description in TSV format of the description of each category and subgroup of a VCF with the extended annota... | ["[Pre-processing]\nCustom filterRemove the variants that have the AN (total number of alleles in called genotypes) value assigned.Dependencies:\na) Includes sites where the compressed VCF file '.vcf.gz' comply with the AN value.", "[Pre-processing]\nSeparate SNVs and indelsKeep only certain types of variants.Dependenc... |
null | null | null | dx.doi.org/10.17504/protocols.io.c68zhv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This mixture is used for the <a href="https://www.protocols.io/view/DNA-Extraction-Protocol-c32yqd" target="_blank">DNA Extraction Protocol</a>.
[GUIDELINES]
I used 400 µl CsCl purified lysate = add 1 µl of ProtK 20 mg/ml stock (20µg) and 20 µl 10% SDS stock (0.5% final concent... | [] |
28,779 | Preparation of M9 Media | null | dx.doi.org/10.17504/protocols.io.8cjhsun | null | NUS iGEM | TITLE: Preparation of M9 Media
AUTHORS: NUS iGEM
[STEPS]
?. Prepare 5x M9 salt, 1M calcium chloride and magnesium sulfate solutions respectively using the following reagents.
?. Add2% casamino
200 ml
100 ml
100 µl
2 ml
?. Top up with sterile deionized water to make a litre of M9 media. | ["Prepare 5x M9 salt, 1M calcium chloride and magnesium sulfate solutions respectively using the following reagents.", "Add2% casamino\n200 ml\n100 ml\n100 µl\n2 ml", "Top up with sterile deionized water to make a litre of M9 media."] |
62,763 | Apple Keto Gummies Australia Reviews (Australia Consumer) Scam or Legit? Read Price 2022, Side Effects & Ingredients | 3 | dx.doi.org/10.17504/protocols.io.n2bvj6z5xlk5/v1 | https://www.protocols.io/view/apple-keto-gummies-australia-reviews-australia-con-b9ijr4cn | health | TITLE: Apple Keto Gummies Australia Reviews (Australia Consumer) Scam or Legit? Read Price 2022, Side Effects & Ingredients
AUTHORS: health
[DESCRIPTION]
Apple Keto Gummies Australia are just accessible on web-based stages. You should visit to true sites of a few makers and medical care brands. The trustworthy b... | [] |
38,539 | Cryopreservation of tissues for primary cell culture and single cell sequencing | 1 | dx.doi.org/10.17504/protocols.io.bhvjj64n | https://www.protocols.io/view/cryopreservation-of-tissues-for-primary-cell-cultu-bhvjj64n | Harikrishna Nakshatri | TITLE: Cryopreservation of tissues for primary cell culture and single cell sequencing
AUTHORS: Harikrishna Nakshatri
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details the cryopreservation of tissues used for primary cell cultures and single cell sequencing.</div></div>
[STEPS]
... | ["[Freezing Protocol]\nCollect tissues in the Cryoprotective Freezing Medium with ROCK inhibitor.", "[Freezing Protocol]\nResuspend in and + .\n[primary cell medium]\n[cryoprotective freezing medium]\n[ROCK inhibitor]", "[Freezing Protocol]\nAliquot into cryogenic storage vials.", "[Freezing Protocol]\nCells should ... |
68,719 | Cell line construction and maintenance for Lyso-IP with or without genes linked with lysosomal storage disease | 4 | dx.doi.org/10.17504/protocols.io.4r3l2oxqqv1y/v1 | https://www.protocols.io/view/cell-line-construction-and-maintenance-for-lyso-ip-cfcptivn | Sharan Sharan Swarup, Harper JW | TITLE: Cell line construction and maintenance for Lyso-IP with or without genes linked with lysosomal storage disease
AUTHORS: Sharan Sharan Swarup, Harper JW
[DESCRIPTION]
Lyso-IP is a method that allows for the isolation of lysosomes for proteomics and metabolomics using HA-tagged TMEM192 (dx.doi.org/10.17504/pro... | ["[Cell line maintenance] Maintain HeLa cells in Dulbecco’ Modifies Eagles Medium (DMEM) with 10% fetal bovine serum and optional 1% penicillin-streptomycin.", "[Endogenous tagging of TMEM192 with 3xHA] For endogenous tagging of TMEM192 with 3xHA, co-transfect HeLa cells with pX459 containing a gRNA (5’-AGTAGAACGTGAGAG... |
86,658 | CAMbank: cfDNA BCT Field Processing v1 | 4 | null | https://www.protocols.io/view/cambank-cfdna-bct-field-processing-v1-cyvaxw2e | Eliah G Overbey, Krista A Ryon, jak, chm2042 | TITLE: CAMbank: cfDNA BCT Field Processing v1
AUTHORS: Eliah G Overbey, Krista A Ryon, jak, chm2042
[DESCRIPTION]
Field processing of cfDNA BCTs for the Cornell Aerospace Medicine Biobank (CAMbank).
Instructions for preserving: plasma and RBC Pellets.
[STEPS]
SECTION: Perform Venipuncture
1. After venipuncture, inve... | ["[Perform Venipuncture] After venipuncture, invert the tubes gently 8 to 10 times to fully mix tube anticoagulant with blood sample.\n\nStore the tube upright at room temperature until centrifugation.\n\nNote: The tube stabilizes cell-free DNA for up to 14 days at 6 °C to 37 °C and CTCs for up to 7 days at 15 °C to 30... |
75,961 | Preparation of Buffers for PhageFISH protocol | 4 | dx.doi.org/10.17504/protocols.io.dm6gpjop8gzp/v1 | https://www.protocols.io/view/preparation-of-buffers-for-phagefish-protocol-cnezvbf6 | Line Jensen Ostenfeld, Saria Otani | TITLE: Preparation of Buffers for PhageFISH protocol
AUTHORS: Line Jensen Ostenfeld, Saria Otani
[DESCRIPTION]
This protocol details about preparation of various buffers for PhageFISH protocol.
[STEPS]
SECTION: Permeabilisation buffer
1. 50 ml:
PBS [pH 7.5] (10 x) 5 ml Tris-HCl [pH 8.0] (1 M) 5 ml EDTA... | ["[Permeabilisation buffer] 50 ml: \n PBS [pH 7.5] (10 x) 5 ml Tris-HCl [pH 8.0] (1 M) 5 ml EDTA (0.5) 5 ml Water 35 ml Lysozyme \n Permeabilisation mix: Mix PBS, Tris-HCl, EDTA, and water.", "[Permeabilisation buffer] High conc. lysozyme buffer: Dissolve lysozyme in appropriate buffer volume (5... |
null | null | null | dx.doi.org/10.17504/protocols.io.eswbefe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in <a href="https://www.protocols.io/view/CviRI-Purification-From-XZ-6E-Virus-Infected-NC64A-er4bd8w" target="_blank">CviRI Purification From XZ-6E Virus Infected NC64A Chlorella</a>.
[STEPS]
?.
?.
?. | [] |
107,239 | Single-cell Epi2-Seq | 1 | null | https://www.protocols.io/view/single-cell-epi2-seq-dkyf4xtn | Christoph Geisenberger, Jeroen van den Berg, Vincent van Batenburg, Buys De Barbanson, Jeroen de Ridder, Alexander van Oudenaarden | TITLE: Single-cell Epi2-Seq
AUTHORS: Christoph Geisenberger, Jeroen van den Berg, Vincent van Batenburg, Buys De Barbanson, Jeroen de Ridder, Alexander van Oudenaarden
[DESCRIPTION]
Here we describe the full protocol for single-cell Epi2-Seq which enables joint readout of histone modifications and DNA methylation in i... | ["[Preparation of Tet1 Reaction Buffer and Fe2+ solution] Assemble TET1 reaction buffer (volumes are suggestions and can be scaled up or down)", "[Chromatin Immuno-Cleavage (ChIC)] Fixation and permeabilization\nHarvest cells and wash twice with PBS at room temperature (centrifuge 3 min, 500 g to pellet)\nResuspend cel... |
null | null | null | dx.doi.org/10.17504/protocols.io.iq5cdy6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Exclusion criteria: lower limb varices, history of leg surgery, trauma, infection, or thromboembolic events.</p>
<p> </p>
<p>Ultrasound examinations are performed in B-mode technique, equipped with a linear broadband (7.5-14-MHz) transducer. The right femoral vein and the ing... | [] |
95,166 | Sanger Tree of Life HMW DNA Extraction: Modified Omega Bio-Tek E.Z.N.A.® | 1 | dx.doi.org/10.17504/protocols.io.36wgq3wj3lk5/v1 | https://www.protocols.io/view/sanger-tree-of-life-hmw-dna-extraction-modified-om-c866zzhe | Amy Denton, Caroline Howard | TITLE: Sanger Tree of Life HMW DNA Extraction: Modified Omega Bio-Tek E.Z.N.A.®
AUTHORS: Amy Denton, Caroline Howard
[DESCRIPTION]
This protocol describes the manual extraction and SPRI of HMW DNA from fresh frozen jellyfish samples intended for long-read sequencing using a combination of the Omega Bio-Tek E.Z.N.A.® M... | ["[Sample Lysis & Precipitation] Set a heat block to 25 °C.", "[Extraction] Add 600 to 800 μL Sera-Mag™ SpeedBead solution to each sample - the Sera-Mag™ SpeedBead solution should be vortexed before use to ensure that the beads are resuspended.", "[Sample Lysis & Precipitation] Label 1.5 mL BioMasher tubes for ... |
66,355 | BuzzBGone Reviews: We Review The Mosquito Zapper That Everyone Is Talking About! | 1 | dx.doi.org/10.17504/protocols.io.q26g74k4kgwz/v1 | https://www.protocols.io/view/buzzbgone-reviews-we-review-the-mosquito-zapper-th-cc2tsyen | prodentim , Kristina Kitko | TITLE: BuzzBGone Reviews: We Review The Mosquito Zapper That Everyone Is Talking About!
AUTHORS: prodentim , Kristina Kitko
[DESCRIPTION]
dental health
[STEPS]
1.
Everyone is talking about this portable Bug Zapper...but is it worth the hype?
The Buzz B-Gone Zap is a mosquito and insect killing system designed t... | ["Everyone is talking about this portable Bug Zapper...but is it worth the hype?\n\nThe Buzz B-Gone Zap is a mosquito and insect killing system designed to work indoors and outdoors. \n\nThe device uses a light and a grill to kill annoying insects – like mosquitos, flies, and other flying bugs. Bugs see the light and f... |
43,869 | ChIP-seq Library preparation | 4 | dx.doi.org/10.17504/protocols.io.bn35mgq6 | https://www.protocols.io/view/chip-seq-library-preparation-bn35mgq6 | Vasso Makrantoni, Daniel Robertson, Adele L. Marston | TITLE: ChIP-seq Library preparation
AUTHORS: Vasso Makrantoni, Daniel Robertson, Adele L. Marston
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A plethora of biological processes like gene transcription, DNA replication, DNA recombination, and chromosome segregation are mediated through protein–DN... | ["[ChIP-seq Library preparation]\nThere are commercially available kits for generating DNA libraries but it is relatively straightforward and cost effective to create libraries using standard molecular biology reagents and custom oligonucleotides. This protocol can be completed within 1 day, and it comprises five disti... |
19,763 | Dietary Record Protocol: Weighed Food Record and Recall | null | dx.doi.org/10.17504/protocols.io.xitfken | null | Rosalind Susan Gibson, Lisa Anne Houghton, Aly Diana, Sofa Rahmannia, Dimas Erlangga Luftimas, Widya Santi Atmaharmoni, Annisha Fathonah, Wina Nur Sofiah, Istri Nur Indira, Lina Sofiatul Inayah, Afini Dwi Purnamasari, Doni Juliana, Aghnia Husnayiani Suryanto, Raulia Haekal | TITLE: Dietary Record Protocol: Weighed Food Record and Recall
AUTHORS: Rosalind Susan Gibson, Lisa Anne Houghton, Aly Diana, Sofa Rahmannia, Dimas Erlangga Luftimas, Widya Santi Atmaharmoni, Annisha Fathonah, Wina Nur Sofiah, Istri Nur Indira, Lina Sofiatul Inayah, Afini Dwi Purnamasari, Doni Juliana, Aghnia Husnayian... | ["[Recording the Foods and Drinks Consumed]\nUse Weighed Record Form (Form A) and Recipe Form (Form B).", "[Recording the Foods and Drinks Consumed]\nFirst, record mother’s name, ID number,interview date, day of the week and cadre’s name at the top of each page of theweighed food record form. Use a separateset of form... |
null | null | null | dx.doi.org/10.17504/protocols.io.jxbcpin | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
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48,271 | test_CB | 1 | dx.doi.org/10.17504/protocols.io.btdpni5n | https://www.protocols.io/view/test-cb-btdpni5n | Christine Briggs | TITLE: test_CB
AUTHORS: Christine Briggs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a test.</div></div>
[STEPS]
?. [old version. This is empty. I'll fork someone else's protocol here.]
This is a link to the 10x sequencing user guides at https://support.10xgenomics.com/single-cell-gene... | ["[old version. This is empty. I'll fork someone else's protocol here.]\nThis is a link to the 10x sequencing user guides at https://support.10xgenomics.com/single-cell-gene-expression/library-prep/doc/user-guide-chromium-single-cell-3-reagent-kits-user-guide-v2-chemistry"] |
41,191 | GM Covid-19 saliva test (v1) | 4 | dx.doi.org/10.17504/protocols.io.bkgfkttn | https://www.protocols.io/view/gm-covid-19-saliva-test-v1-bkgfkttn | TITLE: GM Covid-19 saliva test (v1)
AUTHORS:
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">GM Covid-19 saliva test is a RT-PCR test intended for qualitative detection of nucleic acids from SARS-CoV-2 in saliva specimen. The test is used for screening purpose under class of "research used only" (... | ["[Setup reaction]\nPrepare PCR master mixSqueeze Bottle A to add all of its liquid into Bottle B; Close lid of Bottle B and shake to mix; Squeeze Bottle B to load one droplet into each PCR tube to setup a 96-well PCR plate.", "[Setup reaction]\nSaliva-PrepSaliva is self-collected into any sterile tubes with screw cap ... | |
90,932 | Immunofluorescence protocol for floating mouse brain sections | 1 | dx.doi.org/10.17504/protocols.io.kxygx31ddg8j/v1 | https://www.protocols.io/view/immunofluorescence-protocol-for-floating-mouse-bra-c42uyyew | Mary Alice Allnutt | TITLE: Immunofluorescence protocol for floating mouse brain sections
AUTHORS: Mary Alice Allnutt
[DESCRIPTION]
This protocol details the immunofluorescence for floating sections.
[STEPS]
SECTION: Sectioning and long-term tissue storage
1. Section the brains at thickness on Leica cryostat (CM1860).
SECTION: Section... | ["[Sectioning and long-term tissue storage] Section the brains at thickness on Leica cryostat (CM1860).", "[Sectioning and long-term tissue storage] Collect the sections in cryoprotectant solution in 12-well plates and store at -20 °C.", "[Sectioning and long-term tissue storage] To make 1000 ml cryoprotectant (from ... |
22,785 | this is a test | null | dx.doi.org/10.17504/protocols.io.2g9gbz6 | https://www.protocols.io/view/this-is-a-test-2g9gbz6 | Anita Bandrowski | TITLE: this is a test
AUTHORS: Anita Bandrowski
[STEPS]
?. step one is a test step
?. step two is also a test | ["step one is a test step", "step two is also a test"] |
62,242 | Availability of Open Citations from Open Journals in Crossref - Protocol | 1 | dx.doi.org/10.17504/protocols.io.kxygxz7ywv8j/v3 | https://www.protocols.io/view/availability-of-open-citations-from-open-journals-b82aryae | Davide Brembilla, Chiara Catizone, Giulia Venditti | TITLE: Availability of Open Citations from Open Journals in Crossref - Protocol
AUTHORS: Davide Brembilla, Chiara Catizone, Giulia Venditti
[DESCRIPTION]
This protocol is for the research about the availability of Open Citations from Open Journals in Crossref.
The goal is to find out how many papers from DOAJ journ... | ["[Data Gathering] We download the DOAJ public data dump containing article metadata in tar.gz format.\nThe dump is structured as a single directory of the form doaj_article_data_[date generated] where are listed files with names of the form article_batch_[number].json. Each file contains up to 100,000 records for a to... |
81,466 | Time-lapse killing assay (spheroid - IncuCyte) | 1 | dx.doi.org/10.17504/protocols.io.6qpvro2m3vmk/v2 | https://www.protocols.io/view/time-lapse-killing-assay-spheroid-incucyte-cts2wnge | Philippa R Kennedy, Peter Hinderlie | TITLE: Time-lapse killing assay (spheroid - IncuCyte)
AUTHORS: Philippa R Kennedy, Peter Hinderlie
[DESCRIPTION]
Many tumors exist in vivo as three-dimensional masses. In order to better model the dynamics of three-dimensional tumor growth and immune cell invasion, cancer cell lines are grown in low-adhesion plates t... | ["Optional: If target cells that form a spheroid are to be themselves monitored by fluorescence, perform this labeling/transfection in advance (see Time-lapse killing assay - monolayer - Incucyte)", "Resuspend target cells in their preferred media. Seed 2x104 target cells in 100 μL/well into a 96 well U-bottom low adhe... |
null | null | null | dx.doi.org/10.17504/protocols.io.fi7bkhn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is the hands-on interactive component to the ECOGEO Workshop Module on Binning.</p>
[BEFORE_START]
<p>Before starting, please visit the ECOGEO website for more information on this "Introduction to Environmental 'Omics" training series. The site contains a pre-packaged v... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.cdns5d | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is the protocol for dephosphorylation of 5'-ends of DNA using AnP (Antarctic Phosphatase - M0289).
[STEPS]
?.
?.
?.
?.
?. | [] |
24,696 | Phagocytosis Bead Conjugation | null | dx.doi.org/10.17504/protocols.io.4cygsxw | null | Andrew Crowley | TITLE: Phagocytosis Bead Conjugation
AUTHORS: Andrew Crowley
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocols for the amine coupling of fluorescent microspheres with antigen or capture reagent for opsonization and phagocytosis</div><div class = "text-block"><span>Quantity as written: approx... | ["[Activation]\nResuspend beads by briefly vortexing; dispense\n[(contains appox. 7 billion beads)]", "[Activation]\nPellet by centrifugation and remove supernatant by pipette", "[Activation]\nResuspend in a total of consisting of: - sulfo-NHS made in MES (pH 5.0) - EDC , made in MES (pH 5.0) - MES (pH... |
null | null | null | dx.doi.org/10.17504/protocols.io.iswcefe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Protocol for blunting ends by 3' overhang removal and fill-in of 3' recessed (5' overhang) ends using T4 DNA Polymerase.
[GUIDELINES]
CAUTION: Elevated temperatures, excessive amounts of enzyme, failure to supplement with dNTPs or long reaction times will result in recessed end... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.pjqdkmw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
30,331 | Patient-Centered Education Bundle on Administration of Venous Thromboembolism Prevention | null | dx.doi.org/10.17504/protocols.io.9u3h6yn | null | Oluwafemi P. Owodunni1, Elliott R. Haut, Dauryne L. Shaffer, Deborah B. Hobson, Jiangxia Wang, Gayane Yenokyan, Peggy S. Kraus, Jonathan K. Aboagye, Katherine L. Florecki, Kristen L.W. Webster, Christine G. Holzmueller, Michael B. Streiff, Brandyn D. Lau | TITLE: Patient-Centered Education Bundle on Administration of Venous Thromboembolism Prevention
AUTHORS: Oluwafemi P. Owodunni1, Elliott R. Haut, Dauryne L. Shaffer, Deborah B. Hobson, Jiangxia Wang, Gayane Yenokyan, Peggy S. Kraus, Jonathan K. Aboagye, Katherine L. Florecki, Kristen L.W. Webster, Christine G. Holzmuel... | [] |
28,714 | OD and GFP Plate Reader Assay (72 h Measurement) | null | dx.doi.org/10.17504/protocols.io.8aihsce | null | Alba Balletbó | TITLE: OD and GFP Plate Reader Assay (72 h Measurement)
AUTHORS: Alba Balletbó
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Fluorescence measurements of Optical Density (OD) and Green fluorescent protein (GFP) in </span><span style = "font-style:italic;">Escherichia coli</span><span style =... | ["[Media Preparation]\nPrepare the following media and autoclave them according to standard procedures. M9TG Media (Without carbon source): AB1ReagentAmmount to add for 50 mL2M9 Salts1X3Tryptone0.5 gM9TG Media (0.5% Glycerol): AB1ReagentAmmount to add for 50 mL2M9 Salts1X3Tryptone0.5 g4Glycerol0.25 gM9TG Media (2% Gl... |
69,692 | Setting a sequencing run with a nanopore MinION and the Rapid Sequencing gDNA kit (SQK-RAD004) | 4 | dx.doi.org/10.17504/protocols.io.4r3l2oy53v1y/v5 | https://www.protocols.io/view/setting-a-sequencing-run-with-a-nanopore-minion-an-cga4tsgw | Narjol Gonzalez-Escalona | TITLE: Setting a sequencing run with a nanopore MinION and the Rapid Sequencing gDNA kit (SQK-RAD004)
AUTHORS: Narjol Gonzalez-Escalona
[DESCRIPTION]
This protocol is to help in setting up a MinION sequencing run using the rapid sequencing kit from Nanopore (SQK-RAD004). It contains all steps and material need for a s... | ["[Preparation of the DNA Library:] Thaw all reagents in box 1 and 2 of the RAD004 kit.", "[Preparation of the DNA Library:] Take a flow cell from 4-8 °C and leave it at room temperature (RT).", "[Preparation of the DNA Library:] Prepare the DNA to a concentration of 400 ng total in 7.5 µL, or a concentration of 54 ng... |
102,379 | Dopamine Activation in the vmPFC: Impact on Impulsive Choice in Social Contexts and Neural Connections | 0 | dx.doi.org/10.17504/protocols.io.q26g7157kgwz/v1 | https://www.protocols.io/view/dopamine-activation-in-the-vmpfc-impact-on-impulsi-df8j3run | Spencer Lee | TITLE: Dopamine Activation in the vmPFC: Impact on Impulsive Choice in Social Contexts and Neural Connections
AUTHORS: Spencer Lee
[DESCRIPTION]
This study protocol details the experimental procedures aimed at assessing the effects of dopamine activation in the vmPFC on impulsive behavior and social interaction. Exper... | ["The first experiment aims to determine the effect of dopamine activation in the vmPFC. Long-Evans rats will be used for this study. The experimental group of rats will undergo a procedure where dopamine in the vmPFC is activated by injecting an amphetamine solution. Both the control group and experimental group will ... |
53,400 | Preparation of polygalacturonic acid (PGA) to study virulence in Erwinia/Pectobacterium | 4 | dx.doi.org/10.17504/protocols.io.bydyps7w | https://www.protocols.io/view/preparation-of-polygalacturonic-acid-pga-to-study-bydyps7w | Pol Nadal Jimenez, Rita S. Valente | TITLE: Preparation of polygalacturonic acid (PGA) to study virulence in Erwinia/Pectobacterium
AUTHORS: Pol Nadal Jimenez, Rita S. Valente
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This medium is used for the growth of Erwinia/Pectobacterium species to ensure that virulence genes are turned O... | ["[2% PGA stock solution preparation]\nWeight of PGA (Sigma, P3850) using a precision scale.\n0.2 g", "[2% PGA stock solution preparation]\nTransfer the powder solution to a (low-thermal-expansion borosilicate glass) beaker.\n100 mL", "[2% PGA stock solution preparation]\nAdd of demineralised water and a (microwav... |
50,943 | Microtiter Dish Biofilm Formation Assay | 4 | null | https://www.protocols.io/view/microtiter-dish-biofilm-formation-assay-bvy7n7zn | George A. O'Toole | TITLE: Microtiter Dish Biofilm Formation Assay
AUTHORS: George A. O'Toole
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Biofilms are communities of microbes attached to surfaces, which can be found in medical, industrial and natural settings. In fact, life in a biofilm probably represents the pred... | ["[Growing a Biofilm]\nGrow a culture of the wild-typePseudomonas aeruginosaor mutant strain over night in a rich medium (i.e. LB)", "[Growing a Biofilm]\nDilute the over night culture 1:100 into fresh medium for biofilm assays. A standard biofilm assay medium forP. aeruginosais M63 minimal medium supplemented with mag... |
54,192 | Preparation of BG-11 liquid media | 4 | dx.doi.org/10.17504/protocols.io.by6qpzdw | https://www.protocols.io/view/preparation-of-bg-11-liquid-media-by6qpzdw | Ashwinuday | TITLE: Preparation of BG-11 liquid media
AUTHORS: Ashwinuday
[DESCRIPTION]
This is for making liquid media of BG-11.
[STEPS]
1. Take the medium in powdered form and mix it with doubly distilled water to just 1/10 th of the total volume.
2. Add a common stock of micronutrients made in ddH2O and mix well.
3. Make up... | ["Take the medium in powdered form and mix it with doubly distilled water to just 1/10 th of the total volume.", "Add a common stock of micronutrients made in ddH2O and mix well.", "Make up the volume to the total and mixed well.", "Adjust the pH on a calibrated pH meter using 1N HCl and /or 1N NaOH. The media was mixe... |
45,060 | Quick Protocol for Monarch® Total RNA Miniprep Kit (NEB #T2010) | 1 | dx.doi.org/10.17504/protocols.io.bp9cmr2w | https://www.protocols.io/view/quick-protocol-for-monarch-total-rna-miniprep-kit-bp9cmr2w | New England Biolabs | TITLE: Quick Protocol for Monarch® Total RNA Miniprep Kit (NEB #T2010)
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Quick Protocol for Monarch® Total RNA Miniprep Kit (</span><a href="https://www.neb.com/products/t2010-monarch-total-rna-miniprep-kit#Product%20I... | ["[PART 1: Sample Disruption and Homogenization]\nPlease select your starting material of the following:- Cultured Mammalian Cells- Mammalian Whole Blood (Fresh or Frozen)- Tissue or Leukocytes- Tough-to-Lyse Samples (bacteria, yeast, plant, etc.) using Mechanical Lysis", "[PART 1: Sample Disruption and Homogenization]... |
95,479 | Quantifying Checking Genomic DNA | 1 | null | https://www.protocols.io/view/quantifying-checking-genomic-dna-c9gxz3xn | Carlos Goller | TITLE: Quantifying Checking Genomic DNA
AUTHORS: Carlos Goller
[DESCRIPTION]
Overview and Goals
Your bacterial isolate has been grown on agar plates, lysed open and genomic DNA has been isolated for sequencing. Next, we need to quantify our DNA yield and assess its integrity. For this, we will use the IMPLEN nano spec... | ["[Activity 1: Quantification of DNA with the IMPLEN Nano Spectrophotometer] Based on the NanoDrop ND-1000 Spectrophotometer Protocol.\n\n \n\n\nBefore starting, watch this 3-minute video: The NanoPhotometer Introduction Video (3:43 min video).", "[Activity 1: Quantification of DNA with the IMPLEN Nano Spectrophotomete... |
46,580 | cDNA synthesis using SuperScript™ IV | 1 | dx.doi.org/10.17504/protocols.io.brqum5ww | https://www.protocols.io/view/cdna-synthesis-using-superscript-iv-brqum5ww | Roey Angel, Eva Petrova | TITLE: cDNA synthesis using SuperScript™ IV
AUTHORS: Roey Angel, Eva Petrova
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The following protocol is intended as a downstream application for our </div><div class = "text-block"><a href="https://www.protocols.io/view/purification-of-rna-from-a-dna-rn... | ["[Primer annealing]\nPrepare the following mixture in a PCR tube:to ( - ; usually for soil extract)or a gene-specific primer ()\n1 µl\n[purified RNA]\n10 pg\n5 µg\n200 ng\n[random hexamers (50 µM)]\n2\n[RNase free water]", "[Primer annealing]\nMix gently and spin down the solution.", "[Primer annealing]\nIncubate th... |
65,526 | Antibiotic treatment of the breadcrumb sponge Halichondria panicea and subsequent recolonization | 4 | dx.doi.org/10.17504/protocols.io.3byl4kpk2vo5/v2 | https://www.protocols.io/view/antibiotic-treatment-of-the-breadcrumb-sponge-hali-cb8wsrxe | Lara Schmittmann, Ute U Hentschel | TITLE: Antibiotic treatment of the breadcrumb sponge Halichondria panicea and subsequent recolonization
AUTHORS: Lara Schmittmann, Ute U Hentschel
[DESCRIPTION]
This protocol generates sponges (Halichondria panicea) with a disturbed microbiome under controlled experimental conditions, in order to study bacterial reco... | ["[Preparation] Autoclaving material prior to use for 15 min at 121°C\nculture bottles\nsilicone tubing (in- and outflow tubes can be connected to culture bottles before autoclaving)\n20 L carboys with tin foil wrapped around lid but don't close lid! otherwise carboys dent when they cool down\nfiltration unit with ins... |
56,751 | General Taq PCR Master Mix -- CHEM 384/584 | 4 | dx.doi.org/10.17504/protocols.io.b3npqmdn | https://www.protocols.io/view/general-taq-pcr-master-mix-chem-384-584-b3npqmdn | Ken Christensen | TITLE: General Taq PCR Master Mix -- CHEM 384/584
AUTHORS: Ken Christensen
[DESCRIPTION]
2X PCR Master Mixes are convenient to use as they include all the necessary PCR components except the template and primers. Most PCR Master Mixes also include agarose gel running dyes and a density reagent that allows direct loa... | ["[Setup Reaction] To a 25 µL aliquot of a 2X Taq PCR Master Mix (e.g. TaqDog, or Sapphire Amp), add template (10-20 µl cleared lysate for colony PCR or 20-50 ng of purified DNA for typical PCR), forward and reverse primers to a final concentration of 200 nanomolar (nM). Adjust final volume to 50 µL with nuclease free... |
53,943 | hyRAD RNA probes preparation and capture | 1 | dx.doi.org/10.17504/protocols.io.bywxpxfn | https://www.protocols.io/view/hyrad-rna-probes-preparation-and-capture-bywxpxfn | Tomasz Suchan, Ludovic Orlando | TITLE: hyRAD RNA probes preparation and capture
AUTHORS: Tomasz Suchan, Ludovic Orlando
[DESCRIPTION]
Supplemental Information for:
Suchan, T., Kusliy, M.A., Khan, N., Chauvey, L., Tonasso-Calvière, L., Schiavinato, S., Southon, J., Keller, M., Kitagawa, K., Krause, J., Bessudnov, A.N., Bessudnov, A.A., Graphodatsky... | ["[Preparation] Choose a few fresh samples coming from different populations (if possible, to capture the diversity of the targeted species). The DNA samples should be diluted to the same concentrations, ideally at 20-50 ng/μl. If you need to sequence the probes library, you should keep the samples separated for the ne... |
35,112 | Visual Cell Sorting | 1 | null | https://www.protocols.io/view/visual-cell-sorting-beigjcbw | Nicholas Hasle, Anthony Cooke, Sanjay Srivatsan, Heather Huang, Jason J. Stephany, Zachary Krieger, Dana Jackson, Weiliang Tang, Sriram Pendyala, Raymond J. Monnat Jr., Cole Trapnell, Emily M. Hatch, Douglas M. Fowler | TITLE: Visual Cell Sorting
AUTHORS: Nicholas Hasle, Anthony Cooke, Sanjay Srivatsan, Heather Huang, Jason J. Stephany, Zachary Krieger, Dana Jackson, Weiliang Tang, Sriram Pendyala, Raymond J. Monnat Jr., Cole Trapnell, Emily M. Hatch, Douglas M. Fowler
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block... | ["[Microscope-based imaging, analysis, and activation]\nPrepare cells for imaging", "[Microscope-based imaging, analysis, and activation]\n24 to 48 hours before imaging, plate cells onto 6-well glass bottom, black walled plates at a density of 50,000 to 200,000 cells per well.", "[Microscope-based imaging, analysis, an... |
74,676 | Multi-dimensional potential factors influencing COVID-19 vaccine booster acceptance and hesitancy among university academic community in Bangladesh: a cross-sectional comparative study | 1 | dx.doi.org/10.17504/protocols.io.5jyl8jeq6g2w/v1 | https://www.protocols.io/view/multi-dimensional-potential-factors-influencing-co-ck6uuzew | dn.roy | TITLE: Multi-dimensional potential factors influencing COVID-19 vaccine booster acceptance and hesitancy among university academic community in Bangladesh: a cross-sectional comparative study
AUTHORS: dn.roy
[DESCRIPTION]
Despite the potential therapeutic benefits of primer vaccine dosage regimens, public perceptions ... | [] |
79,366 | Tetrahydrofuran and Dichloromethane Delipidation of a Whole Mouse Brain | 1 | dx.doi.org/10.17504/protocols.io.36wgqj1kxvk5/v1 | https://www.protocols.click/view/tetrahydrofuran-and-dichloromethane-delipidation-o-crrev53e | Andrew Recknagel, Kevin Cao, Judith Baka, Naveen Ouellette, Molly Logsdon, Jayaram Chandrashekar | TITLE: Tetrahydrofuran and Dichloromethane Delipidation of a Whole Mouse Brain
AUTHORS: Andrew Recknagel, Kevin Cao, Judith Baka, Naveen Ouellette, Molly Logsdon, Jayaram Chandrashekar
[DESCRIPTION]
Organic solvent strategies for whole-brain delipidation involve dehydrating the tissue in a water-miscible solvent follo... | ["[THF and DCM Delipidation of a Whole Mouse Brain] Start with a whole mouse brain perfused with 4% PFA and post-fixed for 180 min to360 min at Room temperature and stored at 4 °C for ~720 min or 720 min, then washed in 1X PBS.", "[THF and DCM Delipidation of a Whole Mouse Brain] Dehydrate through H2O → THF series\nWa... |
39,029 | A step by step guide to using Visual Field Analysis | 3 | dx.doi.org/10.17504/protocols.io.bicvkaw6 | https://www.protocols.io/view/a-step-by-step-guide-to-using-visual-field-analysi-bicvkaw6 | Mathilde Josserand, Bastien Lemaire | TITLE: A step by step guide to using Visual Field Analysis
AUTHORS: Mathilde Josserand, Bastien Lemaire
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In this protocol, we provide a step by step guide to using Visual Field Analysis (VFA) successfully. VFA is a python program based on DeepLabCut to... | [] |
41,630 | nf-100GMX-variant-summarizer | 5 | dx.doi.org/10.17504/protocols.io.bkv6kw9e | https://www.protocols.io/view/nf-100gmx-variant-summarizer-bkv6kw9e | Israel Aguilar Ordoñez | TITLE: nf-100GMX-variant-summarizer
AUTHORS: Israel Aguilar Ordoñez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Nextflow pipeline used to count variants for the 100GMX project</div><div class = "text-block"> 'nf-100GMX-variant-summarizer' is a pipeline tool that counts variants in a VEPextended ... | ["[Branch A]\nProject Counts\na) Count samples and raw stats for all samples.b) Give the total counts data.", "[Branch B]\nNo filter countsDependencies:\na) Filter variants that are not in ClinVar, GWAS Catalog or PGKB.b) Give the total counts data.", "[Branch B]\nNovel countsDependencies:\na) Filter variants without a... |
97,116 | Human Dorsal Root Ganglion bulk ATAC-seq protocol | 0 | dx.doi.org/10.17504/protocols.io.5qpvokx27l4o/v1 | https://www.protocols.io/view/human-dorsal-root-ganglion-bulk-atac-seq-protocol-da342gqw | Úrzula Franco-Enzástiga, Theodore Price | TITLE: Human Dorsal Root Ganglion bulk ATAC-seq protocol
AUTHORS: Úrzula Franco-Enzástiga, Theodore Price
[DESCRIPTION]
In this protocol, we describe how to perform bulk ATAC-seq on fresh human dorsal root ganglia.
[BEFORE_START]
Required PPE: All work must be done wearing appropriate PPE including lab coat and glov... | ["[Tissue harvesting and cleaning procedure] Surgically excised lumbar L4 or L5 human dorsal root ganglia (hDRGs) are obtained from organ donors at Southwest Transplant Alliance (STA) at 2 h post cross-clamp.", "[Nuclei isolation] Cleaned hDRG is placed in an eppendorf tube containing 2 mL of ice-cold nuclei isolation ... |
null | null | null | dx.doi.org/10.17504/protocols.io.gagbsbw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol provides an efficient and reliable technique for obtaining HMW DNA(>1Mb) from animal blood. It accompanies:</p>
<p> </p>
<p>Huang Zhihai, Xu Jiang, Xiao Shuiming, Liao Baosheng, Gao Yuan, Zhai Chaochao, Qiu Xiaohui, Xu Wen, Chen Shilin</p>
<p> (2016): Support... | [] |
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