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 |
|---|---|---|---|---|---|---|---|
34,985 | RPMI - FBS and PBS - FBS | null | dx.doi.org/10.17504/protocols.io.beehjbb6 | https://www.protocols.io/view/rpmi-fbs-and-pbs-fbs-beehjbb6 | Marco Cosentino, Elisa Storelli, Alessandra Luini, Emanuela Rasini, Massimiliano Legnaro, Marco Ferrari, Franca Marino | TITLE: RPMI - FBS and PBS - FBS
AUTHORS: Marco Cosentino, Elisa Storelli, Alessandra Luini, Emanuela Rasini, Massimiliano Legnaro, Marco Ferrari, Franca Marino
[STEPS] | [] |
101,200 | Tissue Processing | 0 | dx.doi.org/10.17504/protocols.io.bp2l622zzgqe/v1 | https://www.protocols.io/view/tissue-processing-de3q3gmw | daniel.dautan daniel, Per Svenningsson | TITLE: Tissue Processing
AUTHORS: daniel.dautan daniel, Per Svenningsson
[DESCRIPTION]
Protocol for processing mouse tissue for immunohistochemistry.
[STEPS]
1. After completion of live experiments, anesthetize the mouse with institution-approved substance at correct dosage.
2. Ensure the mouse is deeply anesthetize... | ["After completion of live experiments, anesthetize the mouse with institution-approved substance at correct dosage.", "Ensure the mouse is deeply anesthetized via the toe-pinch test and that there is no reaction. Place the mouse with its chest facing up above a basin to capture blood, and secure the paws so that the b... |
27,583 | Antibody Purification and Labeling | null | dx.doi.org/10.17504/protocols.io.667hhhn | null | Maya Brewer, Yuantee Zhu, Danielle Gutierrez, Jeff Spraggins, Mark de Caestecker | TITLE: Antibody Purification and Labeling
AUTHORS: Maya Brewer, Yuantee Zhu, Danielle Gutierrez, Jeff Spraggins, Mark de Caestecker
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the process for antibody purification and subsequent labeling for direct immunofluorescence.</di... | ["[Antibody Purification]\nFor all preparations: this is to remove BSA, azide, or glycine that are often added by the manufacturer. If the antibody has nothing added, skip the purification step.\u0006", "[Antibody Purification]\nAssemble Amicon Pro Affinity Concentrator by carefully attaching the Amicon Ultra device to... |
52,203 | Amylase activity | 1 | null | https://www.protocols.io/view/amylase-activity-bw8jphun | Bjorn Bartholdy, a.g.henry | TITLE: Amylase activity
AUTHORS: Bjorn Bartholdy, a.g.henry
[DESCRIPTION]
This protocol is a scaled-down, modified version of the Enzymatic Assay of α-Amylase (EC 3.2.1.1) found here.
[BEFORE_START]
All instances of dH2O can be replaced with ultrapure water.
[STEPS]
SECTION: Prepare solutions
1. 0.5% Potato starc... | ["[Prepare solutions] 0.5% Potato starch solution\n\nadd a small amount of dH2O to a beaker\nadd 0.5 Mass Percent 0.5% (w/v) potato starch\nBoil for 15 min while stirring\nTake off heat and leave at room temperature\nAdd dH2O to final volume\nContinuous stirring throughout the assay", "[Prepare solutions] 0.2% Maltose... |
80,172 | Mortality in patients with COVID-19 versus non-COVID-19- related acute respiratory distress syndrome: A single center retrospective observational cohort study | 1 | dx.doi.org/10.17504/protocols.io.bp2l6961rlqe/v1 | https://www.protocols.io/view/mortality-in-patients-with-covid-19-versus-non-cov-csikwccw | Yu-Hsiang Hsieh, Han-Shui Hsu | TITLE: Mortality in patients with COVID-19 versus non-COVID-19- related acute respiratory distress syndrome: A single center retrospective observational cohort study
AUTHORS: Yu-Hsiang Hsieh, Han-Shui Hsu
[DESCRIPTION]
The pathophysiology of coronavirus disease-2019 (COVID-19)-related acute respiratory distress syndro... | ["Study population\nThis single center retrospective observational cohort study included patients with COVID-19 and non-COVID-19-related ARDS that required invasive mechanical ventilation. \n\nAll patients with COVID-19 had positive real-time polymerase chain reaction (RT-PCR) results for severe acute respiratory syndr... |
73,687 | Assembly: Chronic recoverable Neuropixels in mice | 1 | null | https://www.protocols.io/view/assembly-chronic-recoverable-neuropixels-in-mice-cj7xurpn | 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... |
88,806 | Carver et al., Aged Brain Spatial Profiling - GeoMx | 1 | dx.doi.org/10.17504/protocols.io.261gedwndv47/v2 | https://www.protocols.io/view/carver-et-al-aged-brain-spatial-profiling-geomx-c2yeyfte | Chase Carver | TITLE: Carver et al., Aged Brain Spatial Profiling - GeoMx
AUTHORS: Chase Carver
[DESCRIPTION]
This protocol provides the staining process for GeoMx digital spatial profiling of mouse brain used in in Carver et al., "Senescent- and disease-associated microglia are modifiable features of aged brain white matter". T
S... | ["[GeoMx slide preparation] For FFPE sections, follow procedures found in document including summaries here:\n1) Slide Preparation\n2) Bake slides\n3) Deparaffinize and rehydrate FFPE tissue sections\n4) Perform target retrieval\n5) Expose RNA targets\n6) Postfix: preserve tissue morphology for soft tissues\n7) In si... |
36,387 | In vivo Nanopool: Pooled sgRNA competition assays to evaluate in vivo cancer dependencies | 1 | null | https://www.protocols.io/view/in-vivo-nanopool-pooled-sgrna-competition-assays-t-bfsbjnan | Thomas Skipper, Daniel Bondeson, Brenton Paolella, Francisca Vazquez | TITLE: In vivo Nanopool: Pooled sgRNA competition assays to evaluate in vivo cancer dependencies
AUTHORS: Thomas Skipper, Daniel Bondeson, Brenton Paolella, Francisca Vazquez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">sgRNA competition assays with constitutive Cas9 systems allow for rapid de-ri... | ["[Develop cell line model]\nChoose dependent cell lines using the Cancer Dependency Map portal. Search the literature to determine whether the cell lines proliferate subcutaenously in vivo.", "[Develop cell line model]\nPlate and infect cell lines of interest to assess Cas9 expression.", "[Develop cell line model]\nIn... |
108,717 | SA-B-Gal Activity | 0 | dx.doi.org/10.17504/protocols.io.3byl49n8ogo5/v1 | https://www.protocols.io/view/sa-b-gal-activity-dnem5bc6 | Karyna Tarasova, Sinan Gültekin, iris.gerner Gerner, Florien Jenner | TITLE: SA-B-Gal Activity
AUTHORS: Karyna Tarasova, Sinan Gültekin, iris.gerner Gerner, Florien Jenner
[DESCRIPTION]
To measure cellular senescence
[STEPS]
SECTION: Senescence associated SA--Galactosidase Activity
1.
SECTION: Senescence associated SA--Galactosidase Activity
1.1. The cells were washed twice with ice... | ["[Senescence associated SA--Galactosidase Activity]", "[Senescence associated SA--Galactosidase Activity] The cells were washed twice with ice cold PBS and then incubated with 60µL of cell lysis buffer\nprovided with the cellular senescence assay kit (Fluorometric format) (Cell Biolabs, USA) for 10 minutes at 4 ºC."... |
70,350 | Phylogenetic Analysis of Complete Bovine Coronavirus Genome Sequences | 5 | dx.doi.org/10.17504/protocols.io.kqdg3pyeql25/v3 | https://www.protocols.io/view/phylogenetic-analysis-of-complete-bovine-coronavir-cgxntxme | Aspen M Workman, Tara G. McDaneld, Gregory P Harhay, Subha Das, John Dustin Loy, Benjamin M. Hause | TITLE: Phylogenetic Analysis of Complete Bovine Coronavirus Genome Sequences
AUTHORS: Aspen M Workman, Tara G. McDaneld, Gregory P Harhay, Subha Das, John Dustin Loy, Benjamin M. Hause
[DESCRIPTION]
Bovine coronavirus (BCoV) has spilled over to many species, including humans, where the host range variant coronaviru... | ["[Software]", "[Software]", "[Software]", "[MAFFT Alignment] Align using MAFFT v7.450\n\nThe sequences were aligned using the MAFFT accuracy methods ---globalpair as defined in the mafft manual page below \n\n \n\n\nKeep in mind ...\n\nThe commands below generate files that contain both STDOUT (mafft output to th... |
null | null | null | dx.doi.org/10.17504/protocols.io.ktwcwpe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>GoldBio's simple His-Tag column prep protocol is a quick and easy method to pouring and packing an agarose resin column.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
45,222 | test 12/4 protocol | 1 | null | https://www.protocols.io/view/test-12-4-protocol-bqeemtbe | Maria Guliakina | TITLE: test 12/4 protocol
AUTHORS: Maria Guliakina
[STEPS]
?. 68test You disposal strongly quitting his endeavor two settling him. Manners ham him hearted hundred expense. Get open game him what hour more part. Adapted as smiling of females oh me journey exposed concern. Met come add cold calm rose mile what. Tiled m... | ["68test You disposal strongly quitting his endeavor two settling him. Manners ham him hearted hundred expense. Get open game him what hour more part. Adapted as smiling of females oh me journey exposed concern. Met come add cold calm rose mile what. Tiled manor court at built by place fanny. Discretion at be an so dec... |
107,014 | Mod3D Live Cell Chambers and holders 3D printing and Assembly | 1 | dx.doi.org/10.17504/protocols.io.n92ldz587v5b/v3 | https://www.protocols.io/view/mod3d-live-cell-chambers-and-holders-3d-printing-a-dkre4v3e | Ray Truant, Siobhan Goss, Siobhan Goss, Kaitlyn Neuman, Christina Yi Peng, Celeste Suart, Nola Begeja, Max Davide Truant | TITLE: Mod3D Live Cell Chambers and holders 3D printing and Assembly
AUTHORS: Ray Truant, Siobhan Goss, Siobhan Goss, Kaitlyn Neuman, Christina Yi Peng, Celeste Suart, Nola Begeja, Max Davide Truant
[DESCRIPTION]
Live-cell microscopy imaging typically involves the use of high-quality glass-bottom chambers that allow c... | ["For FDM prints of holders, print at 20% grid infill with a layer height of 0.16 mm on either a Creality Ender 3 or a CR10 printer (Creality, Shenzhen, China) or similar FDM printer. Poly lactic acid (PLA) or Polyethylene terephthalate glycol (PETG) 1.75mm filament should be used. Acrylonitrile butadiene styrene (ABS)... |
34,379 | Reference-independent analysis of RADseq data from a single sample | 1 | dx.doi.org/10.17504/protocols.io.bdtji6kn | https://www.protocols.io/view/reference-independent-analysis-of-radseq-data-from-bdtji6kn | Bradley Till, Claudia Osorio, Rachel Howard-Till | TITLE: Reference-independent analysis of RADseq data from a single sample
AUTHORS: Bradley Till, Claudia Osorio, Rachel Howard-Till
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes the use of freely available software for the reference-independent analysis of RADseq data... | ["Prepare genomic DNA for sequencing.\nThe extraction of genomic DNA of suitable quality and quantity is essential for a successful experiment. We have prepared a detailed protocol for low-cost tissue collection, desiccation, genomic DNA extraction, and concentration that provides DNA suitable for next generation seque... |
78,971 | Mitochondrial complex activity assays | 1 | dx.doi.org/10.17504/protocols.io.eq2ly753elx9/v1 | https://www.protocols.io/view/mitochondrial-complex-activity-assays-crc3v2yn | michela.deleidi, María José Pérez J., Hariam Raji, Pascale Baden, Federico Bertoli | TITLE: Mitochondrial complex activity assays
AUTHORS: michela.deleidi, María José Pérez J., Hariam Raji, Pascale Baden, Federico Bertoli
[DESCRIPTION]
Mitochondria complex activity assays measure the activity levels of the different complexes of the mitochondrial electron transport chain (ETC).
[STEPS]
SECTION: Mit... | ["[Mitochondrial complex activity assays] Isolate mitochondria from HEK cells, iPSC-derived neurons, or midbrain organoids using the Qproteome Mitochondrial isolation kit (QIAGEN, Cat. No. / ID: 37612) according to manufacturer's instructions.", "[Mitochondrial complex activity assays] Measure Complex I (NADH oxidase/... |
40,481 | V.2 - Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and SARS-CoV-2 (4S)" method | 4 | dx.doi.org/10.17504/protocols.io.bjr9km96 | https://www.protocols.io/view/v-2-direct-wastewater-rna-capture-and-purification-bjr9km96 | Oscar Whitney, Basem Al-Shayeb, Alex Crits-Cristoph, Mira Chaplin, Vinson Fan, Hannah Greenwald, Adrian Hinkle, Rose Kantor, Lauren Kennedy, Anna Maurer, Robert Tjian, Kara L. Nelson, UC Berkeley Wastewater-based epidemiology consortium | TITLE: V.2 - Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and SARS-CoV-2 (4S)" method
AUTHORS: Oscar Whitney, Basem Al-Shayeb, Alex Crits-Cristoph, Mira Chaplin, Vinson Fan, Hannah Greenwald, Adrian Hinkle, Rose Kantor, Lauren Kennedy, Anna Maurer, Robert Tjian, Kara L. Nelson, UC Berkel... | ["[Preparing RNA wash buffers]\nPrepareeach of two wash buffers - Wash buffer #1 (4S-WB1) and #2 (4S-WB2), for later use during cleanup of RNA bound to silica columns.\n1 L", "[Preparing RNA wash buffers]\n4S-WB1 composition: ABCD1ReagentOriginal molarity/%Final molarity/%Volume per liter of buffer2NaCl5 M1.5 M300 mL... |
79,006 | Tetiaroa Vegetation Sampling | 1 | dx.doi.org/10.17504/protocols.io.261ge314yl47/v1 | https://www.protocols.io/view/tetiaroa-vegetation-sampling-crd6v29e | Sage Moloney, Kenechi Elvis Obiorah, Erica Garibay, Allea Eimers | TITLE: Tetiaroa Vegetation Sampling
AUTHORS: Sage Moloney, Kenechi Elvis Obiorah, Erica Garibay, Allea Eimers
[DESCRIPTION]
Measurement of seedling recruitment for four native woody species, the shade cover of four herbaceous plant species, and coconuts on the Motu Ahuroa in Tetiaroa were conducted by students with th... | ["Find the marked transects using a GPS and/or flag markers.", "Use the measuring tape to lay out a 25 m transect from the first marker to its respective end marker.", "Beginning with left or right side of the transect, measure a 1mx1m plot.", "Within this 1m^2 plot:", "For woody seedlings: identify and count seedlings... |
36,635 | SPARC Cat - Sham Control Chronic Implant Cat 4, Day 30 | 1 | dx.doi.org/10.17504/protocols.io.bfz3jp8n | https://www.protocols.io/view/sparc-cat-sham-control-chronic-implant-cat-4-day-3-bfz3jp8n | Brett Hanzlicek, Anna Rietsch, Margot Damaser | TITLE: SPARC Cat - Sham Control Chronic Implant Cat 4, 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 implant cat experiment (Day 30-terminal) for cystotomy (bladder surgery). The ... | ["[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... |
64,537 | ONT Basecalling, Demultiplexing, and Analysis for Fungal Barcodes | 5 | dx.doi.org/10.17504/protocols.io.dm6gpbm88lzp/v1 | https://www.protocols.io/view/ont-basecalling-demultiplexing-and-analysis-for-fu-ca9zsh76 | Stephen Douglas Russell | TITLE: ONT Basecalling, Demultiplexing, and Analysis for Fungal Barcodes
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
This protocol assumes that your MinION run has been completed and the data from the run has been saved. It should take you from raw data to useable FASTA files for each of your fungal barcodes.... | ["For a Flongle cell with 1.15Gb of bases and 1.18M reads, this command takes about 37 minutes to run. Example output:\n\n\n \n\nSometimes after the run I need to restart the CPU before this command runs successfully.", "This protocol assumes the experiment name is \"FirstRun.\"\n\nCreate a new working folder on the de... |
66,356 | Review Ikaria Lean Belly Juice [UK, US, AU] Report | 4 | dx.doi.org/10.17504/protocols.io.kxygxzbzdv8j/v1 | https://www.protocols.io/view/review-ikaria-lean-belly-juice-uk-us-au-report-cc2usyew | Ikarialean Mart | TITLE: Review Ikaria Lean Belly Juice [UK, US, AU] Report
AUTHORS: Ikarialean Mart
[DESCRIPTION]
Ikaria Lean Belly Juice
[STEPS]
SECTION: Ikaria Lean Belly Juice Complant Us Costumers
1. Ikaria Lean Belly Juice comes in a powdered form that is easy to dissolve and mix into any liquid. It comes in a jar, with 30 dose... | ["[Ikaria Lean Belly Juice Complant Us Costumers] Ikaria Lean Belly Juice comes in a powdered form that is easy to dissolve and mix into any liquid. It comes in a jar, with 30 doses inside. The daily dosage is only a scoop, mixed in any drink of your choice. This formula is prepared in a GMP-certified facility using mo... |
95,926 | GENERATING THE POOLED SINGLE GUIDE RNA LIBRARIES | 0 | null | https://www.protocols.io/view/generating-the-pooled-single-guide-rna-libraries-c9wwz7fe | Helaine Graziele Santos Vieira, Helen E. King, Renuka Ravi Gupta, Nona Farbehi, hendersa, Vikram Khurana, Gist Croft, Lorenz Studer, Joseph Powell | TITLE: GENERATING THE POOLED SINGLE GUIDE RNA LIBRARIES
AUTHORS: Helaine Graziele Santos Vieira, Helen E. King, Renuka Ravi Gupta, Nona Farbehi, hendersa, Vikram Khurana, Gist Croft, Lorenz Studer, Joseph Powell
[DESCRIPTION]
This protocol outlines the designing, cloning, and next-generation sequencing (NGS) of a pool... | ["[Synthesizing sgRNA oligonucleotides] The library oligo pool was designed in silico by the Weatheritt Lab (Garvan) and was ordered from Twist Bioscience. We utilised two in-silico tools FlashFry4 and CRISPRDO2, for guide design. Per gene, we designed two dual guides containing two sgRNAs targeting the interest gene. ... |
80,504 | Protocol for Detection and Analysis of Cyclic RNA Using RT-PCR | 4 | dx.doi.org/10.17504/protocols.io.5jyl8jzodg2w/v1 | https://www.protocols.io/view/protocol-for-detection-and-analysis-of-cyclic-rna-csuywexw | creative-biogene | TITLE: Protocol for Detection and Analysis of Cyclic RNA Using RT-PCR
AUTHORS: creative-biogene
[DESCRIPTION]
This protocol describes the design of divergent primers which face away from each other on the linear RNA, so that they can only amplify the circRNAs, and not the linear RNAs with the same sequence.
[STEPS]
S... | ["[Experiment Summary] This protocol describes the design of divergent primers which face away from each other on the linear RNA, so that they can only amplify the circRNAs, and not the linear RNAs with the same sequence. The PCR amplicon for the detection of circRNAs using divergent primers spans the backsplice juncti... |
49,344 | Prepare bovine coronavirus (BCoV) solution | 4 | dx.doi.org/10.17504/protocols.io.bue8nthw | https://www.protocols.io/view/prepare-bovine-coronavirus-bcov-solution-bue8nthw | Adélaïde Roguet, Shuchen Feng | TITLE: Prepare bovine coronavirus (BCoV) solution
AUTHORS: Adélaïde Roguet, Shuchen Feng
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Prepare bovine coronavirus (BCoV) solution from vaccine</span></div></div>
[STEPS]
?. [Prepare the BCoV solution]
Resuspend one ... | ["[Prepare the BCoV solution]\nResuspend one vial of using 1 to 3 mL of 1xTE buffer.", "[Prepare the BCoV solution]\nGently vortex, avoiding foaming.", "[Prepare the BCoV solution]\nAliquot 40-200 µL of the BCoV solution into 600 μL low-binding tubes.\nThe volume aliquoted depends on the number of samples that have to ... |
null | null | null | dx.doi.org/10.17504/protocols.io.srped5n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>S1 Table. Pooled counts of Blue-fronted Amazons. Counts were performed in five roosts by month in the southern Pantanal of Brazil from July 2004 to July 2009. “Roost” is the roost id (1-5), “all.parrots” refers to the number of parrots arriving at roosts irrespective of the g... | [] |
22,673 | Transcriptome profiling of brain and lung under Dip2a regulation | null | dx.doi.org/10.17504/protocols.io.2drga56 | null | rajiv kumar sah, Yang Anlan, Fatoumata Binta Bah, Salah Adlat, Ameer Ali | TITLE: Transcriptome profiling of brain and lung under Dip2a regulation
AUTHORS: rajiv kumar sah, Yang Anlan, Fatoumata Binta Bah, Salah Adlat, Ameer Ali
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Total RNA from brain and lung of E19.5 Dip2a</span><span style = "vertical-align:super;">-/-... | ["[Sample collection protocol]\nDip2a heterozygous mice (Dip2a+/-) were intercrossed, female mice checked for presence of copulation plug (Vaginal plug) and designated as E0.5 day. At age of E19.5, pregnant dams were euthanized and embryos were collected on ice-cold 1X PBS. Brains and lungs were dissected out from each... |
102,453 | Crystallisation of MERS-CoV Mpro | 1 | dx.doi.org/10.17504/protocols.io.8epv5rn84g1b/v1 | https://www.protocols.io/view/crystallisation-of-mers-cov-mpro-dgav3se6 | blake.h.balcomb, Peter Marples, Lizbé Koekemoer, Daren Fearon, Charlie Tomlinson | TITLE: Crystallisation of MERS-CoV Mpro
AUTHORS: blake.h.balcomb, Peter Marples, Lizbé Koekemoer, Daren Fearon, Charlie Tomlinson
[DESCRIPTION]
The COVID-19 pandemic has highlighted the need to identify novel therapeutic interventions and strategies for pandemic preparedness. Other than Severe Acute Respiratory Syndr... | ["[Crystallisation experiment] Protein and buffer requirements:\n32 µL17 mg/mL \n3.36 mL \n14.4 µL seeds, dilution 1:1000", "[Crystallisation experiment] Dispense 35 µL into SwissCI 3 lens plate reservoir wells using a 100 µl multi-channel pipette.\nDispense 150 nL17 mg/mL to each lens using the SPT mosquito.\nDi... |
16,300 | The reconstruction of a single lens microscope. Reviving the Leeuwenhoek’s microscope. | null | null | null | Daniela Flores, Timothy Marzullo | TITLE: The reconstruction of a single lens microscope. Reviving the Leeuwenhoek’s microscope.
AUTHORS: Daniela Flores, Timothy Marzullo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Antonie Van Leeuwenhoek (1632-1723), is considered the father of microscopy and microbiology, due to the developmen... | ["BEFORE TO START: You need:A high temperature flame- it can be a bunsten lighter or a camping torch (propane/isobutene mix).Solid glass filament, like borosilicate glass filament, crystal glass or soda lime glass.Basic Needle noise pliers, like typical laboratory pliers or forceps.Plain glass slideOnionCotton swabMeth... |
null | null | null | dx.doi.org/10.17504/protocols.io.hrjb54n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is used to clarify the process of RNA extration for our R. crenulata genome.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
75,785 | General freezing protocol for HEK-Blue cells | 4 | null | https://www.protocols.io/view/general-freezing-protocol-for-hek-blue-cells-cm9hu936 | Andreas Sagen | TITLE: General freezing protocol for HEK-Blue cells
AUTHORS: Andreas Sagen
[DESCRIPTION]
HEK-Blue is a product from Invivogen, which provide reporter cells for endotoxin-testing among others. Here is a generalized protocol for freezing cells with reporter characteristics. This protocol differ significantly from Invivo... | ["[Concentrated complete freeze medium (CCMF)] Pre-prepare freezing medium. While you could create freeze medium outright, and suspend the cells directly in it, it is recommended to minimize the exposure time of cells with DMSO. To do this, the cells are initially resuspended and counted in serum-free medium. This give... |
52,284 | Whole-cell proteomics and Analysis by Tandem Mass Tagging-based proteomics | 4 | dx.doi.org/10.17504/protocols.io.bxa4pigw | https://www.protocols.io/view/whole-cell-proteomics-and-analysis-by-tandem-mass-bxa4pigw | Felix Kraus, Sharan Swarup, Vinay V. Eapen, J. Wade Harper wade_harper@hms.harvard.edu | TITLE: Whole-cell proteomics and Analysis by Tandem Mass Tagging-based proteomics
AUTHORS: Felix Kraus, Sharan Swarup, Vinay V. Eapen, J. Wade Harper wade_harper@hms.harvard.edu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The analysis of relative protein abundance has emerged as an importa... | ["[Harvest, precipitation and digestion]\nFor whole proteome analysis, is required for each replicate. Lyse cells in lysis buffer and pass them through a 21G needle 10 times. Alternatively, lyse cells bysonication as per manufactures instructions.\n[of protein lysate]", "[Harvest, precipitation and digestion]\nCentri... |
86,200 | Inducing proteostasis stress using G-TPP | 1 | dx.doi.org/10.17504/protocols.io.dm6gp3jypvzp/v2 | https://www.protocols.io/view/inducing-proteostasis-stress-using-g-tpp-cyeyxtfw | Louise Uoselis | TITLE: Inducing proteostasis stress using G-TPP
AUTHORS: Louise Uoselis
[DESCRIPTION]
Inducing proteostasis stress in HeLa cells with G-TPP to analyse proteostasis protection and repair.
[STEPS]
SECTION: Day 1
1. Seed cells in standard growth media, aiming for a density of ~80-90% the following day.
SECTION: Day 3
4... | ["[Day 1] Seed cells in standard growth media, aiming for a density of ~80-90% the following day.", "[Day 3] Harvest the G-TPP treated samples and DMSO control samples after the desired incubation period (eg. 2 – 12 h).", "[Day 2] Feed cells for 60 min prior to starting treatment by aspirating the media from each well ... |
37,283 | cDNA Synthesis | null | dx.doi.org/10.17504/protocols.io.bgnbjvan | https://www.protocols.io/view/cdna-synthesis-bgnbjvan | Allen Institute for Brain Science | TITLE: cDNA Synthesis
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the synthesis of first-strand cDNA from total RNA using the Invitrogen SuperScript III Reverse Transcriptase system.</div><div class = "text-block"><span style = "... | [] |
50,497 | How to create baseurl for OAI-PMH harvesting with OpenRefine | 5 | dx.doi.org/10.17504/protocols.io.bvi9n4h6 | https://www.protocols.io/view/how-to-create-baseurl-for-oai-pmh-harvesting-with-bvi9n4h6 | Andrea Marchitelli, Carlo Bianchini, Alessandra Moi | TITLE: How to create baseurl for OAI-PMH harvesting with OpenRefine
AUTHORS: Andrea Marchitelli, Carlo Bianchini, Alessandra Moi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the method for creating baseurl for harvesting an OAI-PMH repository from a list of identifiers.<... | ["Open the OpeRefine project containing the list of OAI identifiers prepared for harvesting.The list can be prepared by following the directions in the linked protocol How to import OAI-PMH identifiers into OpenRefine.\n{\"blocks\":[{\"key\":\"52lge\",\"text\":\"Protocollo per importare in OpenRefine una lista di ident... |
93,200 | Southern blot | 4 | dx.doi.org/10.17504/protocols.io.bp2l6xe6dlqe/v1 | https://www.protocols.io/view/southern-blot-c69qzh5w | Oriol Busquets, Frank Soldner | TITLE: Southern blot
AUTHORS: Oriol Busquets, Frank Soldner
[DESCRIPTION]
This protocol describes a southern blot analysis adapted from standard protocols (https://cshprotocols.cshlp.org/content/2021/7/pdb.top100396#cited-by) to validate the structural integrity and exclude the loss of heterozygosity (LOH) at a genomi... | ["[Buffers] Prepare the following buffers:", "[Generation of Southern blot probes] To generate southern blot probes use AccuPrime‱ Taq DNA Polymerase, high fidelity; ThermoFisher.12346086 on WIBR3 (parental; RRID:CVCL_9767) gDNA using primers described above.", "[Buffers] 20X SSC buffer: 3M NaCl, 0.3M sodium citrate.",... |
null | null | null | dx.doi.org/10.17504/protocols.io.rjxd4pn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Pregnant women are excluded from many, if not most, clinical trials. Although there are several potential scientific justifications for this exclusion (such as the often unknown effects of the normal physiological changes of pregnancy on drug metabolism), the primary rational... | ["{\"blocks\":[{\"key\":\"ao18p\",\"text\":\"Project Summary\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[{\"offset\":0,\"length\":15,\"style\":\"bold\"}],\"entityRanges\":[],\"data\":[]},{\"key\":\"8btso\",\"text\":\"Pregnancy Testing in Clinical Trials\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRa... |
49,315 | CTAB genomic DNA extraction from Arabidopsis leaf material | 1 | dx.doi.org/10.17504/protocols.io.8epv5y2dl1bz/v3 | https://www.protocols.io/view/ctab-genomic-dna-extraction-from-arabidopsis-leaf-buebntan | Diep R Ganguly, Pip Wilson, Gonzalo Estavillo, Xin Hou, Barry Pogson | TITLE: CTAB genomic DNA extraction from Arabidopsis leaf material
AUTHORS: Diep R Ganguly, Pip Wilson, Gonzalo Estavillo, Xin Hou, Barry Pogson
[DESCRIPTION]
CTAB-based extraction of genomic DNA from Arabidopsis leaf tissue.
[BEFORE_START]
Ensure you grind your leaf tissue into a fine powder using mortar and pestle o... | ["[Cell lysis] Aliquot required volume of CTAB buffer and heat in water bath at 60 ºC for 5-10 minutes immediately before use.", "[Cell lysis] Cool samples to room temperature .", "[Phase separation] Add 300 µL chloroform and mix thoroughly with a vortex or vigorous shaking for 15 seconds.", "[Phase separation] Centrif... |
63,871 | Eagle Hemp CBD Gummies For Sleep, Anxiety, Calm and Immunity | 1 | dx.doi.org/10.17504/protocols.io.eq2lyn2kwvx9/v1 | https://www.protocols.io/view/eagle-hemp-cbd-gummies-for-sleep-anxiety-calm-and-cak7sczn | viaketobenefit | TITLE: Eagle Hemp CBD Gummies For Sleep, Anxiety, Calm and Immunity
AUTHORS: viaketobenefit
[DESCRIPTION]
Cannabidiol (CBD) is a characteristic piece of the hemp plant. It has turned into a profoundly examined subject in regards to the propriety of accomplishing general wellbeing. The turmoil comes from not having t... | [] |
49,932 | Study Protocol: The Association of Preoperative Opioid Use and Patient Outcomes | 1 | dx.doi.org/10.17504/protocols.io.buzknx4w | https://www.protocols.io/view/study-protocol-the-association-of-preoperative-opi-buzknx4w | Bethany Kavalakatt, Vidhya Gunaseelan, Mark C Bicket | TITLE: Study Protocol: The Association of Preoperative Opioid Use and Patient Outcomes
AUTHORS: Bethany Kavalakatt, Vidhya Gunaseelan, Mark C Bicket
[DESCRIPTION]
The objective of this retrospective cohort study is to investigate the differences in clinical and patient-reported outcomes among patients after surgery ba... | ["[Brief Rationale and Hypothesis] This study examines the question of how outcomes reported by patients after surgery for pain, satisfaction, regret of undergoing surgery, and quality of life as well as clinical outcomes differ among patients based on the exposure of opioids in the year before surgery. \n\nIn general,... |
null | null | null | dx.doi.org/10.17504/protocols.io.cdms45 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is the protocol for the Gibson Assembly using the Gibson Assembly® Cloning Kit (E5510).
[GUIDELINES]
<strong>Optimal Quantities<br /><br /></strong>NEB recommends a total of 0.02–0.5 pmols of DNA fragments when 1 or 2 fragments are being assembled into a vec... | [] |
61,920 | Oprah Keto Help You Lose Weight Online Order! | 1 | dx.doi.org/10.17504/protocols.io.kqdg3p37el25/v1 | https://www.protocols.io/view/oprah-keto-help-you-lose-weight-online-order-b8p8rvrw | dfkosxwea | TITLE: Oprah Keto Help You Lose Weight Online Order!
AUTHORS: dfkosxwea
[DESCRIPTION]
Supplement Review - Oprah Keto
Category - Weight Loss
Main Benefit - Fat Burn and Weight Loss
Ingredients - BHB (Beta-Hydroxybutyrate)
Precaution - Not for Pregnant Ladies and Children
Side Effects - Not Yet Reported
Dosage - As Pr... | [] |
35,298 | Opentrons COVID-19 testing (RT-qPCR path, Station C, 24+3+1 sample special) | null | dx.doi.org/10.17504/protocols.io.beqajdse | null | Max Marrone | TITLE: Opentrons COVID-19 testing (RT-qPCR path, Station C, 24+3+1 sample special)
AUTHORS: Max Marrone
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Prepare the reagent tube rack.In an Opentrons 24 tube rack, place the following reagents from the BP Genomics 2019-nCoV Detection Assay kit, prepared accor... | ["Prepare the reagent tube rack.In an Opentrons 24 tube rack, place the following reagents from the BP Genomics 2019-nCoV Detection Assay kit, prepared according to the kit's instructions.Well A1: Well B1: Well B3: Well D3: (Positive Control Template diluted to 200 copies per µL, per BP Genomics' instructions) ABCDE... |
36,146 | Isocitrate dehydrogenase | null | dx.doi.org/10.17504/protocols.io.bfisjkee | https://www.protocols.io/view/isocitrate-dehydrogenase-bfisjkee | Kimberly Chapman, Parith Wongkittichote | TITLE: Isocitrate dehydrogenase
AUTHORS: Kimberly Chapman, Parith Wongkittichote
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Isocitrate dehydrogenase is an enzyme which converts isocitrate to 2-oxoglutarate in the TCA cycle. IDH2 uses NADP and IDH3 uses NAD.</div><div class = "text-block">Our I... | ["Prepare the IDH buffer new (Place on ice)", "To make 10 mL IDH buffer10 mM potassium phosphtate pH 7.4 (200 μL 0.5 M potasium phosphate pH 7.4), 2 mM MgCl2 (20μL 1M MgCl2), 1mM NADP (100 μL 100mM NADP)5mM isocitrate (50 μL 1M isocitrate)Add water to make 10 mL after pH ing to 7.4", "Prepare mitochondrial lysates per... |
45,493 | Preparation of Suppressor tRNA | 1 | dx.doi.org/10.17504/protocols.io.bqnvmve6 | https://www.protocols.io/view/preparation-of-suppressor-trna-bqnvmve6 | Anne Zemella, Theresa Richter, Lena Thoring, Stefan Kubick | TITLE: Preparation of Suppressor tRNA
AUTHORS: Anne Zemella, Theresa Richter, Lena Thoring, Stefan Kubick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">This is part 3.2 of the "A Combined Cell-Free Protein Synthesis and Fluorescence-Based Approach to Investigate G... | ["[3.2.1 Generation of PCR Product]\nFor specific and homogenous 3’-ends of the suppressor tRNA, an additional PCR step before transcription reaction is included. Therefore, the reverse primer contains a 2’-OMe-group to prevent unspecific nucleotides at the 3’-end of the tRNA that can be added by the T7 polymerase duri... |
90,817 | Preparation of an Enriched Synaptic Vesicle Fraction | 1 | dx.doi.org/10.17504/protocols.io.3byl4qr62vo5/v1 | https://www.protocols.io/view/preparation-of-an-enriched-synaptic-vesicle-fracti-c4w9yxh6 | Leonardo A Parra-Rivas | TITLE: Preparation of an Enriched Synaptic Vesicle Fraction
AUTHORS: Leonardo A Parra-Rivas
[DESCRIPTION]
Preparation of an Enriched Synaptic Vesicle Fraction
[STEPS]
1. Mouse brain tissue was homogenized in a buffer containing 0.32 M sucrose in PBS, supplemented with protease/phosphatase inhibitors.
2. The ho... | ["Mouse brain tissue was homogenized in a buffer containing 0.32 M sucrose in PBS, supplemented with protease/phosphatase inhibitors.", "The homogenate was centrifuged at 1,000 × g for 10 min at 4 °C to\nremove nuclei and cellular debris (P1). The supernatant (S1) was centrifuged at\n15,000 × g for 15min at 4 °C to yie... |
null | null | null | dx.doi.org/10.17504/protocols.io.rwvd7e6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol details the Ponisio Lab's collecting protocol for the 2017 Sky Islands season. Insects were collected into cyanide kill jars and pinned later the same day.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.dpi5kd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Marker genes for viruses are typically amplified from aquatic samples to determine whether specific viruses are present in the sample, or to examine the diversity of a group of related viruses. In this [protocol], we will provide an overview of common methods used to amplify, cl... | [] |
39,670 | PMN- 04 - Measurement of Intracellular Reactive Oxygen Species (ROS) levels in Human PMN | 4 | dx.doi.org/10.17504/protocols.io.biywkfxe | https://www.protocols.io/view/pmn-04-measurement-of-intracellular-reactive-oxyge-biywkfxe | Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino | TITLE: PMN- 04 - Measurement of Intracellular Reactive Oxygen Species (ROS) levels in Human PMN
AUTHORS: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">List of published work using... | ["Suspend isolated PMN 1x106 cells/ml in HBSS/HEPES medium.", "Add 2x106 cells in 2 mL of HBSS/HEPES for each tube.", "Incubate for with 2 Micromolar (µM) of C-DCFH-DA in the dark at (Dubnoff Bath).\n37 °C", "Wash twice with of HBSS/HEPES.Each time centrifuge at\n2 mL\nCentrifuge: 400 34, 5 min", "Aspirate supernata... |
77,847 | 96-well plate cell growth optimization for integrated live-cell and endpoint viability drug screening assay | 4 | dx.doi.org/10.17504/protocols.io.eq2ly7qpqlx9/v1 | https://www.protocols.io/view/96-well-plate-cell-growth-optimization-for-integra-cp9xvr7n | Rolando DZ Lyles, M Julia Martinez, Benjamin Sherman, Kerry Burnstein | TITLE: 96-well plate cell growth optimization for integrated live-cell and endpoint viability drug screening assay
AUTHORS: Rolando DZ Lyles, M Julia Martinez, Benjamin Sherman, Kerry Burnstein
[DESCRIPTION]
This protocol details the cell growth optimization for integrated live-cell and endpoint viablility drug screen... | ["[Day 1: Prepare cell lines for seeding into 96-well plates for optimization] In a sterile tissue culture hood, aspirate media from t75-flask.", "[Day 1: Prepare cell lines for seeding into 96-well plates for optimization] Perform a wash with 5 mL Phosphate Buffered Saline (PBS) (Hyclone, Cat# SH30028.02).", "[Day 1: ... |
66,020 | Tree Mapping for Leaf Collection Guidelines (Mont Mégantic only) | 1 | dx.doi.org/10.17504/protocols.io.kxygxe97ov8j/v2 | https://www.protocols.io/view/tree-mapping-for-leaf-collection-guidelines-mont-m-ccqcsvsw | Anna L Crofts, Sabine St-Jean | TITLE: Tree Mapping for Leaf Collection Guidelines (Mont Mégantic only)
AUTHORS: Anna L Crofts, Sabine St-Jean
[DESCRIPTION]
Here, we describe the protocol used by the Canadian Airborne Biodiversity Observatory (CABO) at Parc National du Mont Mégantic, a forested study site in southeastern Québec, to select trees for ... | ["[Tree Selection] Systematically select individuals that meet the leaf-level measurement requirements1 across the majority of species that occur within the park2. Specifically, selected individuals should: \n\nHave mature, healthy, and fully sunlit (exposed to >3hrs of sunlight per day) leaves,\nNot exceed a height be... |
80,824 | Qualitative methods | 1 | dx.doi.org/10.17504/protocols.io.bp2l6952zlqe/v1 | https://www.protocols.io/view/qualitative-methods-cs6ywhfw | Kajiru Gad Kilonzo, Stefanie J. Krauth, Jo Halliday, Clive Kelly, Stefan Siebert, Gloria Temu, Christopher Bunn, Nateiya M Yongolo, Sally Wyke, Emma McIntosh, Blandina Mmbaga | TITLE: Qualitative methods
AUTHORS: Kajiru Gad Kilonzo, Stefanie J. Krauth, Jo Halliday, Clive Kelly, Stefan Siebert, Gloria Temu, Christopher Bunn, Nateiya M Yongolo, Sally Wyke, Emma McIntosh, Blandina Mmbaga
[DESCRIPTION]
This protocol details qualitative methods.
[STEPS]
SECTION: Qualitative methods
1. Qualitati... | ["[Qualitative methods] Qualitative research will be conducted in two phases to address research questions 1 and 2. First, rapid ethnographic assessments (21) (REA) within pre-survey pilot sub samples will identify how people talk about and classify joint pain. Terminologies used will inform subsequent studies.", "[Qua... |
51,221 | AlphaHOR-RES: a method for enriching centromeric DNA | 4 | dx.doi.org/10.17504/protocols.io.bv9vn966 | https://www.protocols.io/view/alphahor-res-a-method-for-enriching-centromeric-dn-bv9vn966 | Nicolas Altemose, Annie Maslan, Owen Smith, Kousik Sundararajan, Rachel Brown, Aaron Straight, Aaron Streets | TITLE: AlphaHOR-RES: a method for enriching centromeric DNA
AUTHORS: Nicolas Altemose, Annie Maslan, Owen Smith, Kousik Sundararajan, Rachel Brown, Aaron Straight, Aaron Streets
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Directed Methylation and Long-read sequencing (DiMeLo-seq) can be used to... | ["Extract genomic DNA from ~25 million cells using an NEB High Molecular Weight DNA extraction kit with 300 rpm agitation during lysis.", "Elute DNA in 300 μL elution buffer and allow to relax at 4ºC for 2 days. DNA will remain viscous until it is digested.", "Once fully relaxed/solubilized, add 37 μL NEBuffer 2.1, 100... |
100,186 | Protocols for "Functional efficacy of the MAO-B inhibitor safinamide in murine substantia nigra pars compacta dopaminergic neurons in vitro: a comparative study with tranylcypromine" | 0 | dx.doi.org/10.17504/protocols.io.e6nvw1jwzlmk/v1 | https://www.protocols.io/view/protocols-for-34-functional-efficacy-of-the-mao-b-dd3228qe | Nicola Biagio Mercuri | TITLE: Protocols for "Functional efficacy of the MAO-B inhibitor safinamide in murine substantia nigra pars compacta dopaminergic neurons in vitro: a comparative study with tranylcypromine"
AUTHORS: Nicola Biagio Mercuri
[DESCRIPTION]
Methodological collection for electrophysiological investigations of neurona... | [] |
88,041 | Stowers Institute for Medical Research Rodent Facility Environmental Summary | 1 | dx.doi.org/10.17504/protocols.io.3byl4qwnzvo5/v1 | https://www.protocols.io/view/stowers-institute-for-medical-research-rodent-faci-cz8hx9t6 | Debra Dukes, Michael Elmore | TITLE: Stowers Institute for Medical Research Rodent Facility Environmental Summary
AUTHORS: Debra Dukes, Michael Elmore
[DESCRIPTION]
Mice (Mus Musculus) are the most common research organisms used in biomedical research. We have
housed and maintained a variety of strains at the Stowers Institute for Medical Researc... | [] |
56,055 | Estimate phospholipids from microalgae | 4 | null | https://www.protocols.io/view/estimate-phospholipids-from-microalgae-b2yxqfxn | Yingyu Hu | TITLE: Estimate phospholipids from microalgae
AUTHORS: Yingyu Hu
[DESCRIPTION]
Here we describe a protocol to estimate phospholipids from microalgae.
After the extraction and measurement of total lipids from microalgae, the rest of lipids extract is dried by nitrogen flow and then dried with magnesium sulphate at 90... | ["[Prepare phospholipids sample] Dry remaining organic phase extract of total lipids at 37 °C under a stream of N2 gas (<2 psi)", "[High temperature dry combust] Use diamond pen to engrave the sample vials with numbers. Log number and sample code.", "[High temperature dry combust] 0.17 M MgSO4 reagent:\nDissolve 1.023 ... |
62,836 | Preparing ONT-tagged Primers and Master Mix for Fungal DNA Barcoding | 4 | null | https://www.protocols.io/view/preparing-ont-tagged-primers-and-master-mix-for-fu-b9kur4ww | Stephen Douglas Russell | TITLE: Preparing ONT-tagged Primers and Master Mix for Fungal DNA Barcoding
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
ONT primer preparation has two specific aspects that are unique when comparing to Sanger sequencing protocols. The first is that each primer needs to be "tagged" - a unique ~10-15bp sequence... | ["[Ordering ONT-tagged Primers] - Determine how many unique primers you need to order. Ex - If you are planning to utilize a Flongle cell with up to 480 specimens, you would need to order five unique forward ONT-tagged primers. If you hope to use a 10.9 cell with 10,000+ specimens, you would need to order at least 105 ... |
62,520 | Microglia isolation from mouse and culture (modified from UCSD) | 1 | dx.doi.org/10.17504/protocols.io.kqdg3p7bel25/v1 | https://www.protocols.io/view/microglia-isolation-from-mouse-and-culture-modifie-b9ayr2fw | rabdelha | TITLE: Microglia isolation from mouse and culture (modified from UCSD)
AUTHORS: rabdelha
[DESCRIPTION]
This protocol details microglia isolation from mouse and culture (modified from UCSD).
[GUIDELINES]
General notes
(Maximum 6 mice per preparation; protocol described below for 6 brains; ~300,000 cells per 7/week... | ["[Microglia isolation from mouse and culture (modified from UCSD)] Deeply anaesthetize with CO2.", "[Microglia isolation from mouse and culture (modified from UCSD)] Can also use euthanasia.", "[Microglia isolation from mouse and culture (modified from UCSD)] Perfuse intracardially with ice-cold PBS (~10 to 20ml, live... |
54,178 | Experiment 1 | 1 | null | https://www.protocols.io/view/experiment-1-by6apzae | Dikla Perez , Yael Steinhart , Amir Grinstein , Meike Morren (Vrije Universiteit) | TITLE: Experiment 1
AUTHORS: Dikla Perez , Yael Steinhart , Amir Grinstein , Meike Morren (Vrije Universiteit)
[DESCRIPTION]
In this experiment, we aimed to provide evidence regarding the effect of expected product visibility on consumers’ likelihood of engaging in consistent behavior when they are faced with two sequ... | ["Experimental design:\n We have employed two expected-visibility conditions (high vs. low) in a between-subjects design.", "Sample\nn = 179 residents of major cities (64.8% women, Mage = 29.22, SDage = 4.45) were paid to take part in an online experiment. Participants were each randomly assigned to one of two expected... |
99,198 | A new protocol for multispecies bacterial infections in zebrafish and their monitoring through automated image analysis | 0 | dx.doi.org/10.17504/protocols.io.rm7vzjybxlx1/v1 | https://www.protocols.io/view/a-new-protocol-for-multispecies-bacterial-infectio-dc462yze | Désirée A. Schmitz, Tobias Wechsler, Hongwei Bran Li, Bjoern H. Menze, Rolf Kümmerli | TITLE: A new protocol for multispecies bacterial infections in zebrafish and their monitoring through automated image analysis
AUTHORS: Désirée A. Schmitz, Tobias Wechsler, Hongwei Bran Li, Bjoern H. Menze, Rolf Kümmerli
[DESCRIPTION]
The zebrafish Danio rerio has become a popular model host to explore disease patholo... | [] |
36,652 | SPARC Cat acute UroMOCA implantation | 1 | dx.doi.org/10.17504/protocols.io.bf2kjqcw | https://www.protocols.io/view/sparc-cat-acute-uromoca-implantation-bf2kjqcw | Anna Rietsch, Brett Hanzlicek, Margot Damaser, Dennis Bourbeau | TITLE: SPARC Cat acute UroMOCA implantation
AUTHORS: Anna Rietsch, Brett Hanzlicek, Margot Damaser, Dennis Bourbeau
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a procedure for an acute wired UroMOCA implant cat experiment. A cystotomy is performed and an active, wired (for power) UroMO... | ["[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... |
86,263 | SW-4 SWAB TESTING | 4 | dx.doi.org/10.17504/protocols.io.n2bvj38mnlk5/v1 | https://www.protocols.io/view/sw-4-swab-testing-cygxxtxn | REDI-NET Consortium | TITLE: SW-4 SWAB TESTING
AUTHORS: REDI-NET Consortium
[DESCRIPTION]
This protocol details standard operating procedure for swab testing.
[BEFORE_START]
BEFORE START
Check the DNA and RNA concentrations in each sample of total nucleic acid (TNA) extraction.
If the concentrations are detectable, choose the sequencing... | ["[gDNA PREPARATION] When the RNA concentration of the sample is lower than the detectable range of the Qubit High Sensitivity Assay (<0.01 ng/µl), the sample is subjected to gDNA sequencing. The cDNA synthesis can be skipped.", "[gDNA PREPARATION] When the DNA concentration >10 ng/ul, calculate the required volume of ... |
70,695 | METATAC V.1 | 4 | dx.doi.org/10.17504/protocols.io.kqdg36x51g25/v2 | https://www.protocols.io/view/metatac-v-1-chaft2bn | Honggui Wu, Xiang Li, Fanchong Jian, Ayijiang Yisimayi, X. Sunney Xie | TITLE: METATAC V.1
AUTHORS: Honggui Wu, Xiang Li, Fanchong Jian, Ayijiang Yisimayi, X. Sunney Xie
[DESCRIPTION]
Abstract
Here we describe a protocol for multiplexed end-tagging amplification of transposase accessible chromatin (METATAC), a high-sensitivity single-cell ATAC-seq technique with the help of META chemis... | ["[REAGENT SETUP] Prepare METATAC Reagents", "[REAGENT SETUP] 5 mL ATAC resuspension buffer (ATAC-RSB)\nMix 50 µL 1 M Tris-HCl pH 7.5, 10 µL 5 M NaCl, 15 µL 1 M MgCl2, and bring the final volume to 5 mL with nuclease-free H2O. Store the buffer at -20 °C for up to several months.", "[REAGENT SETUP] 200 µL Omni-ATAC lys... |
46,298 | A Brief Look of the Evolutionary History of Cardiolipin Synthesis Pathway | 4 | null | https://www.protocols.io/view/a-brief-look-of-the-evolutionary-history-of-cardio-brf2m3qe | 181830691 | TITLE: A Brief Look of the Evolutionary History of Cardiolipin Synthesis Pathway
AUTHORS: 181830691
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Cardiolipin is an important structural and functional component of the mitochondrial intima of eukaryotic cells and the bacterial membrane of prokaryot... | [] |
78,060 | Bulk RNA sequencing analysis | 5 | dx.doi.org/10.17504/protocols.io.yxmvm2m55g3p/v1 | https://www.protocols.io/view/bulk-rna-sequencing-analysis-cqgkvtuw | Raquel Garza | TITLE: Bulk RNA sequencing analysis
AUTHORS: Raquel Garza
[DESCRIPTION]
This protocol describes the steps for the bioinformatical analysis of bulk RNA sequencing with a focus on evolutionary young L1s.
[STEPS]
SECTION: TE subfamily quantification
1. Reads were mapped using STAR aligner (version 2.6.0c; RRID:SCR_00446... | ["[TE subfamily quantification] Reads were mapped using STAR aligner (version 2.6.0c; RRID:SCR_004463) with an hg38 index and gencode annotation as the guide GTF (--sjdbGTFfile), allowing for a maximum of 100 multi mapping loci (--outFilterMultimapNmax 100) and 200 anchors (--winAnchorMultimapNmax). The rest of the par... |
72,183 | Evaluation of miniaturized Illumina DNA preparation protocols for SARS-CoV-2 whole genome sequencing protocol | 4 | dx.doi.org/10.17504/protocols.io.n92ldpp8nl5b/v1 | https://www.protocols.io/view/evaluation-of-miniaturized-illumina-dna-preparatio-ciqxudxn | Sureshnee Pillay, James Emmanuel San, Derek Tshiabuila, Yeshnee Naidoo, Yusasha Pillay, Akhil Maharaj, Ugochukwu J. Anyaneji, Eduan Wilkinson, Houriiyah Tegally, Richard J. Lessells, Cheryl Baxter, Tulio de Oliveira, Jennifer Giandhari | TITLE: Evaluation of miniaturized Illumina DNA preparation protocols for SARS-CoV-2 whole genome sequencing protocol
AUTHORS: Sureshnee Pillay, James Emmanuel San, Derek Tshiabuila, Yeshnee Naidoo, Yusasha Pillay, Akhil Maharaj, Ugochukwu J. Anyaneji, Eduan Wilkinson, Houriiyah Tegally, Richard J. Lessells, Cheryl Baxt... | ["[cDNA] Prepare the cDNA master mix in the pre-PCR clean room. The master mix hood must be decontaminated before and after use with 10% extran and 70% ethanol, and sterilised with ultraviolet light (UV).", "[cDNA] Mix the following components in a labeled 1.5ml tube:\n\n \n Component Volume (ul) 50μM R... |
94,732 | Sinai SCENT TMC - Olink Assay using Proseek® Multiplex 96x96 Kit (Juno Biomark System) | 4 | null | https://www.protocols.io/view/sinai-scent-tmc-olink-assay-using-proseek-multiple-c8rkzv4w | Hui Xie, Manishkumar Patel | TITLE: Sinai SCENT TMC - Olink Assay using Proseek® Multiplex 96x96 Kit (Juno Biomark System)
AUTHORS: Hui Xie, Manishkumar Patel
[DESCRIPTION]
To describe the measurement procedure of 92 protein biomarkers in 1 μL sample volume through Proseek® Multiplex 96×96 Olink. The Proseek reagents are based on PEA, a Proximity... | ["[Sample preparation Notes] The serum and plasma samples for the Olink Inflammation and Immuno-Oncology panel are run neatly. However, every panel has different Sample Preparation requirements for different sample matrices. For example:\n\nSerum and Plasma samples for the Olink CVD III panel should be diluted 1:100 us... |
null | null | null | dx.doi.org/10.17504/protocols.io.cdts6m | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Phenol/chloroform extraction is an easy way to remove proteins from your nucleic acid samples and can be carried out in a manner that is very close to quantitative. Nucleic acids remain in the aqueous phase and proteins separate into the organic phase or lie at the phase interfa... | [] |
86,158 | Processing frozen cells for population-scale SQK-LSK114 Oxford Nanopore long-read DNA sequencing SOP | 1 | dx.doi.org/10.17504/protocols.io.6qpvr347bvmk/v1 | https://www.protocols.io/view/processing-frozen-cells-for-population-scale-sqk-l-cydnxs5e | Guillaume Cogan, Pilar Alvarez Jerez, Laksh Malik, Cornelis Blauwendraat, Kimberley J Billingsley | TITLE: Processing frozen cells for population-scale SQK-LSK114 Oxford Nanopore long-read DNA sequencing SOP
AUTHORS: Guillaume Cogan, Pilar Alvarez Jerez, Laksh Malik, Cornelis Blauwendraat, Kimberley J Billingsley
[DESCRIPTION]
Abstract
As part of the GP2 initiative we will generate long-read sequencing data for ~100... | ["Part 1: Extracting Cell DNA (~2 hours per 8 samples)\n\nFrom: PacBio HMW DNA Extraction Cultured Cells Protocol\n\nCell Input Requirements: 1x106 – 2,5x106 diploid human cells or equivalent \nCell counts should be accurately determined using a hemocytometer or cell counter. \nCell pellets should be frozen dry with as... |
90,512 | 605CefT - Resting Medium (no selection) | 4 | null | https://www.protocols.io/view/605ceft-resting-medium-no-selection-c4mqyu5w | leiboffs | TITLE: 605CefT - Resting Medium (no selection)
AUTHORS: leiboffs
[DESCRIPTION]
This is part of the Leiboff Lab maize transformation protocol for somatic embryogenesis of B104 immature embryos. This protocol is a combination of Chen et al. 2022 and Kang et al. 2022 with some modifications based on material availability... | ["[Planning] Estimate the volume of 605CefT you will need based on the following:\n\n \n\nMake sure to round up! Check the table below to plan your media", "[Mixing Heat-Stable Ingredients] Retrieve the following heat-stable ingredients:\n605 Medium - Stored in Main Lab, 4C Refrigerator, Top Shelf\nCasin Hydrolysate -... |
52,087 | iNDI Maintenance protocol of iPSCs Version 1 | 4 | dx.doi.org/10.17504/protocols.io.n2bvjxm2nlk5/v1 | https://www.protocols.io/view/indi-maintenance-protocol-of-ipscs-version-1-bw4xpgxn | michael.ward , Erika Lara Flores, Mark Cookson | TITLE: iNDI Maintenance protocol of iPSCs Version 1
AUTHORS: michael.ward , Erika Lara Flores, Mark Cookson
[DESCRIPTION]
IPSC maintenance protocol
Matrigel procedure for coating plates
Vitronectin procedure for coating plates
Thawing iPSC
Splitting and Passaging iPSC
Freezing iPSC
[STEPS]
SECTION: Matrigel Coat... | ["[Matrigel Coating] Aliquot concentrated Matrigel:\nGradually thaw a 5ml bottle of Matrigel on ice in a Styrofoam container\nPre-chill labeled Eppendorf tubes by placing in a cool rack on ice. \nBefore pipetting concentrated Matrigel into pre-chilled tubes, chill a 1 ml pipet tip by pipetting ice-cold KnockOut™ DMEM/F... |
38,847 | Restriction enzyme & gel electrophoresis | 1 | null | https://www.protocols.io/view/restriction-enzyme-amp-gel-electrophoresis-bh67j9hn | Hung Liang Pai | TITLE: Restriction enzyme & gel electrophoresis
AUTHORS: Hung Liang Pai
[STEPS]
?. [Preparation]
Set the dry bath incubator,
37 °C
?. [Preparation]
Take 10x buffer from the to thaw.
[fridge]
?. [Protocol-Restriction enzyme]
To add DNA for each sample into each eppendorf, calculate the required DNA volume for each s... | ["[Preparation]\nSet the dry bath incubator,\n37 °C", "[Preparation]\nTake 10x buffer from the to thaw.\n[fridge]", "[Protocol-Restriction enzyme]\nTo add DNA for each sample into each eppendorf, calculate the required DNA volume for each sample. The volume is decided by the formula below:Volume(sample)= / concentra... |
75,160 | Cardiac Action Potential Restitution Protocol | 4 | dx.doi.org/10.17504/protocols.io.yxmvm2pwbg3p/v1 | https://www.protocols.io/view/cardiac-action-potential-restitution-protocol-cmmyu47w | Shailesh Agarwal, Chase Fiore, Robert Harvey | TITLE: Cardiac Action Potential Restitution Protocol
AUTHORS: Shailesh Agarwal, Chase Fiore, Robert Harvey
[DESCRIPTION]
This protocol describes an approach that can be used to quantifiy the rate dependence of cardiac action potential duration.
[STEPS]
1. Membrane potentials were recorded from isolated pig ventricula... | ["Membrane potentials were recorded from isolated pig ventricular myocytes using the whole-cell configuration of the patch clamp technique.", "Isolated cells were placed in a perfusion chamber on the stage of an inverted microscope and bathed in an extracellular solution containing (in mM) NaCl 140, KCl 5.4, CaCl22.5, ... |
78,658 | Harvest of adherend cells from Cytodex® 1 beads | 4 | dx.doi.org/10.17504/protocols.io.6qpvr4w7pgmk/v1 | https://www.protocols.io/view/harvest-of-adherend-cells-from-cytodex-1-beads-cq3avyie | David König, Kim Kremser, Sina Bartfeld, shirin.kadler | TITLE: Harvest of adherend cells from Cytodex® 1 beads
AUTHORS: David König, Kim Kremser, Sina Bartfeld, shirin.kadler
[DESCRIPTION]
Expanding adherend cells to quanteties suitable for cell therapy is a subject of increasing relevance.
Variouse cell types either autolog or allogen - could in future be used for medical... | ["[sampling] withdraw homogenized cell solution from culture vessel\nand transfer to centrifuge tube 10-50 mL", "[Micro carrier solving] add 0.1 % volume of dextranase (v/v)", "[Micro carrier solving] transfer samples to a tube rotator and place in an incubator 10 rpm, 60 min, 37 °C", "[Micro carrier solving] take out... |
53,658 | Inoculating mungbean with Curtobacterium flaccumfaciens pv. flaccumfaciens (Cff) for tan spot disease assessment | 4 | dx.doi.org/10.17504/protocols.io.bym2pu8e | https://www.protocols.io/view/inoculating-mungbean-with-curtobacterium-flaccumfa-bym2pu8e | Niloofar Vaghefi | TITLE: Inoculating mungbean with Curtobacterium flaccumfaciens pv. flaccumfaciens (Cff) for tan spot disease assessment
AUTHORS: Niloofar Vaghefi
[DESCRIPTION]
This protocol provides a method for inoculating mungbean (Vigna radiata) with Curtobacterium flaccumfaciens pv. flaccumfaciens (Cff); a seedborne bacterial pa... | ["[Mungbean seed sterilization] To ensure mungbean seeds are disease-free, germinate the seed on Nutrient Agar (NA) before planting, as described below.\n\nConduct this step 25 days before the planned inoculation date. \n\nNote: The protocol and timeline described here is based on plant incubation in a Controlled Envir... |
11,606 | 3D Nanofibrillar Cellulose hydrogel platform for long-term human islet culture | null | dx.doi.org/10.17504/protocols.io.pjwdkpe | null | Yi-Ju Chen, Ben Z. Stanger | TITLE: 3D Nanofibrillar Cellulose hydrogel platform for long-term human islet culture
AUTHORS: Yi-Ju Chen, Ben Z. Stanger
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>It remains a challenge to maintain human islets </span><span style = "font-style:italic;">ex vivo</span><span> to provide a ... | ["[Preparation of the nanofibrillar cellulose (NFC) hydrogel ]\nWeigh the needed amount of NFC hydrogel (Growdex®) and mix it with CIT culture media at 1:1 ratio by vortexing to make a 0.75% (w/v) hydrogel.\nThe NFC hydrogel (Growdex®) purchased from UPM Biochemicals is 1.5%. For example, weigh 0.5g of NFC hydrogel (Gr... |
40,482 | Protein isolation from the extract of coelomic fluid of the Lumbricus terrestris. | 4 | dx.doi.org/10.17504/protocols.io.bjsaknae | https://www.protocols.io/view/protein-isolation-from-the-extract-of-coelomic-flu-bjsaknae | Angel Justiz-Vaillant | TITLE: Protein isolation from the extract of coelomic fluid of the Lumbricus terrestris.
AUTHORS: Angel Justiz-Vaillant
[STEPS]
?. Six earthworms, Lumbricus terrestris, after removal from the earth are placed in a 15 ml glass tube and washed thoroughly with PBS, pH 7.4.
?. The body of the annelid is pierced with an 1... | ["Six earthworms, Lumbricus terrestris, after removal from the earth are placed in a 15 ml glass tube and washed thoroughly with PBS, pH 7.4.", "The body of the annelid is pierced with an 18-gauge needle.", "The coelomic fluid content of the annelid is added to 2 ml of PBS, pH 7.4.", "After incubation at 4oC for 1h, 0.... |
null | null | null | dx.doi.org/10.17504/protocols.io.egpbbvn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol is used for investigating biotin-BSM binding to streptavidin on QCM-D sensors.
[STEPS]
?.
?.
?.
?.
?. | [] |
48,486 | Test with subprotocols | 1 | null | https://www.protocols.io/view/test-with-subprotocols-btkenkte | Lenny Teytelman | TITLE: Test with subprotocols
AUTHORS: Lenny Teytelman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a test.</div></div>
[STEPS]
?. [Day 1: Sample Prep]
This section has instructions for sample processing and preparation.
?. [Day 2: Culturing]
valuesvalues * 215=A2*217=A3*219=A4*2
valuesv... | ["[Day 1: Sample Prep]\nThis section has instructions for sample processing and preparation.", "[Day 2: Culturing]\nvaluesvalues * 215=A2*217=A3*219=A4*2\nvaluesvalues * 215=A2*217=A3*219=A4*2", "[Day 2: Culturing]"] |
14,828 | T cell cytotoxicity (xCELLigence platform) | 1 | dx.doi.org/10.17504/protocols.io.sqkeduw | https://www.protocols.io/view/t-cell-cytotoxicity-xcelligence-platform-sqkeduw | Kristin Anderson | TITLE: T cell cytotoxicity (xCELLigence platform)
AUTHORS: Kristin Anderson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the steps for preparing cellular cytotoxicity assays using the xCELLigence platform.</div><div class = "text-block">In brief: For impedance assays, 10e5 ... | ["Add 50ul media to each well of the E-VIEW plate (use 'inverse pipetting' technique to avoid bubbles in the wells), place the plate in the xCELLigence MP cradle, and run the setup step of the xCELLigence software to confirm all the wells and connections on the cradle are functioning properly.", "Resuspend adherent tum... |
28,870 | En face preparation and quantification of aortic surface area covered by atherosclerotic lesions | null | dx.doi.org/10.17504/protocols.io.8fehtje | null | Jan Breslow, Daniel Teupser | TITLE: En face preparation and quantification of aortic surface area covered by atherosclerotic lesions
AUTHORS: Jan Breslow, Daniel Teupser
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This protocol describes how t... | ["[Aortic Surface Lesion Area Quantitation by the En Face Method:]\nMice are fasted prior to sacrifice.", "[Aortic Surface Lesion Area Quantitation by the En Face Method:]\nThe mice are weighed prior to euthanasia.", "[Aortic Surface Lesion Area Quantitation by the En Face Method:]\nThe mice are euthanized with an over... |
null | null | null | dx.doi.org/10.17504/protocols.io.ii2ccge | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div title="Page 1">
<div>
<div>
<p>Please contact Dr. Steven Wilhelm (wilhelm@utk.edu) or Samantha Coy (srose16@utk.edu) for additional information regarding this protocol.</p>
<p> </p>
<p>De-MetaST-BLAST, written in C++, is a script that can validate degenerate primers by perf... | [] |
88,514 | Molecular Dynamics Simulations | 4 | null | https://www.protocols.io/view/molecular-dynamics-simulations-c2paydie | Annan SI Cook, Shanlin Rao | TITLE: Molecular Dynamics Simulations
AUTHORS: Annan SI Cook, Shanlin Rao
[DESCRIPTION]
This protocol details molecular dynamics simulations of PI3KC3-C1 on a lipid membrane.
[STEPS]
SECTION: Model Preparation
1. Prepare all-atom structural models of PI3KC3-C1 based on the active conformation with missing regions pre... | ["[Model Preparation] Prepare all-atom structural models of PI3KC3-C1 based on the active conformation with missing regions predicted by AlphaFold-Multimer 2.2.", "[Model Preparation] Assign protonation states to amino acid side chains based on pKa predictions by PROPKA.", "[Parameterize ATP] Parameterize a molecule of... |
68,013 | Protocol for DNA Extraction from Tepary Bean | 4 | dx.doi.org/10.17504/protocols.io.dm6gpb78plzp/v1 | https://www.protocols.io/view/protocol-for-dna-extraction-from-tepary-bean-cenmtdc6 | Aparna Srinivasan, Magdalena M Julkowska | TITLE: Protocol for DNA Extraction from Tepary Bean
AUTHORS: Aparna Srinivasan, Magdalena M Julkowska
[DESCRIPTION]
Protocol to extract high quality DNA from Tepary Bean leaves using modified CTAB method.
[STEPS]
SECTION: Collection of leaf sample
1.
Collect 100 mg of young leaf from Tepary Bean plants in a 2ml eppe... | ["[Collection of leaf sample] Collect 100 mg of young leaf from Tepary Bean plants in a 2ml eppendorf tubes containing two sterile glass beads and freeze immediately in liquid nitrogen.", "[DNA Extraction] Add equal volume of Phenol: Chloroform (phenol:chloroform kit), and vortex well.\n \n\nCentrifuge at 14000 rpm f... |
100,139 | Whole-cell patch-clamp in vitro | 0 | dx.doi.org/10.17504/protocols.io.n2bvjn84pgk5/v1 | https://www.protocols.io/view/whole-cell-patch-clamp-in-vitro-dd2j28cn | Nicola Biagio Mercuri | TITLE: Whole-cell patch-clamp in vitro
AUTHORS: Nicola Biagio Mercuri
[DESCRIPTION]
Evoked firing of single neurons
[STEPS]
SECTION: Patch-clamp recordings
1. A single slice is transferred to a submerged recording chamber (2.5–3 ml/min, 33.5°C), on the stage
of an upright microscope equipped for infrared video micros... | ["[Patch-clamp recordings] A single slice is transferred to a submerged recording chamber (2.5–3 ml/min, 33.5°C), on the stage\nof an upright microscope equipped for infrared video microscopy (Hamamatsu, Tokyo), allowing direct visualization of the recorded neurons.", "[Patch-clamp recordings] Neurons were recorded in ... |
27,443 | UC Davis - Tissue TG & TC Protocol | null | dx.doi.org/10.17504/protocols.io.62thgen | null | Peter Havel | TITLE: UC Davis - Tissue TG & TC Protocol
AUTHORS: Peter Havel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">
The lipid extraction method is based on work by Folch 1957. Tissue is homogenized and put into a 2:1 chloro... | ["Weigh out tissue (minimum of 50 mg) accurately and record, then transfer to a mortar and pestle along with 2 g of sodium sulfate (Fisher S415-212). Grind the tissue with the mortar and pestle until completely homogenous with salt.", "Transfer homogenized mix to a 16×125 mm screw-cap glass tube (Fisher 14-959-35A) usi... |
94,913 | Combinatorial selective ER-phagy remodels the ER during neurogenesis | 2 | dx.doi.org/10.17504/protocols.io.81wgbx13nlpk/v3 | https://www.protocols.io/view/combinatorial-selective-er-phagy-remodels-the-er-d-c8w9zxh6 | Melissa Hoyer, Cristina Capitanio, Ian R. Smith, Julia C. Paoli, Anna Bieber, Yizhi Jiang, Joao A. Paulo, Florian Wilfling, Brenda A. Schulman, Harper JW | TITLE: Combinatorial selective ER-phagy remodels the ER during neurogenesis
AUTHORS: Melissa Hoyer, Cristina Capitanio, Ian R. Smith, Julia C. Paoli, Anna Bieber, Yizhi Jiang, Joao A. Paulo, Florian Wilfling, Brenda A. Schulman, Harper JW
[DESCRIPTION]
The endoplasmic reticulum (ER) employs a diverse proteome landscap... | [] |
44,321 | qPCR Quantify cDNA, PCR, and Reaction Cleanup | 4 | dx.doi.org/10.17504/protocols.io.bph9mj96 | https://www.protocols.io/view/qpcr-quantify-cdna-pcr-and-reaction-cleanup-bph9mj96 | Eric L. Van Nostrand, Thai B. Nguyen, Chelsea Gelboin-Burkhart, Ruth Wang, Steven M. Blue, Gabriel A. Pratt, Ashley L. Louie, Gene W. Yeo | TITLE: qPCR Quantify cDNA, PCR, and Reaction Cleanup
AUTHORS: Eric L. Van Nostrand, Thai B. Nguyen, Chelsea Gelboin-Burkhart, Ruth Wang, Steven M. Blue, Gabriel A. Pratt, Ashley L. Louie, Gene W. Yeo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Profiling of RNA binding protein targets in vivo pro... | ["[Prepare qPCR Master Mix; 9 μL Per Sample]\nPrepare qPCR Master Mix; 9 μL Per Sample: AB1qPCR 2× master mix5.0 μL2H2O3.6 μL3qPCR primer mix0.4 μL (10 μM each qPCR-grade D5x/D7x mix)\nAB1qPCR 2× master mix5.0 μL2H2O3.6 μL3qPCR primer mix0.4 μL (10 μM each qPCR-grade D5x/D7x mix)", "[Prepare qPCR Master Mix; 9 μL Per ... |
38,020 | HBSS/HEPES for ROS measurement in PMN | 3 | dx.doi.org/10.17504/protocols.io.bhdcj22w | https://www.protocols.io/view/hbss-hepes-for-ros-measurement-in-pmn-bhdcj22w | Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino | TITLE: HBSS/HEPES for ROS measurement in PMN
AUTHORS: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
[STEPS] | [] |
57,201 | Modified Illumina DNA Prep (M) Tagmentation Library Preparation for cDNA amplicons from wastewater | 1 | dx.doi.org/10.17504/protocols.io.b34rqqv6 | https://www.protocols.io/view/modified-illumina-dna-prep-m-tagmentation-library-b34rqqv6 | Padmini Ramachandran, Tamara Walsky, Amanda Windsor, Maria Hoffmann, Chris Grim | TITLE: Modified Illumina DNA Prep (M) Tagmentation Library Preparation for cDNA amplicons from wastewater
AUTHORS: Padmini Ramachandran, Tamara Walsky, Amanda Windsor, Maria Hoffmann, Chris Grim
[DESCRIPTION]
This procedure outlines the protocol for sequencing of VarSkip Short SARS-CoV-2 cDNA amplicons using th... | ["[Dilute and Tagment Input DNA] Bring BLT (stored in refrigerator) and TB1 (stored in freezer) to room temperature. \n\n\n\nEnsure that BLT is stored upright at all times, so that the beads remain submerged in the\nbuffer", "[Dilute and Tagment Input DNA] Label a 96-well PCR plate with the Run ID.", "[Dilute and Tagm... |
97,854 | Preparation, Processing and Preservation of Surgical Kidney Resections for Multiomic Studies | 1 | dx.doi.org/10.17504/protocols.io.261ge56zdg47/v1 | https://www.protocols.io/view/preparation-processing-and-preservation-of-surgica-dbs62nhe | Sanjay Jain, Amanda Knoten, Kristy Conlon | TITLE: Preparation, Processing and Preservation of Surgical Kidney Resections for Multiomic Studies
AUTHORS: Sanjay Jain, Amanda Knoten, Kristy Conlon
[DESCRIPTION]
Multiomic technologies are increasingly being used on human samples and generating multidimensional data. Preanalytical and tissue procurement factors can... | ["[Preparation: Obtaining Consent and Preparing to Collect the Kidney] Identify the potential nephrectomy case.", "[Preparation: Obtaining Consent and Preparing to Collect the Kidney] Request permission from the urologist to speak with the patient about possible consent.", "[Preparation: Obtaining Consent and Preparing... |
60,259 | Inorganic polyphosphate from microalgae: A DAPI-based estimation in microtiter plate | 1 | null | https://www.protocols.io/view/inorganic-polyphosphate-from-microalgae-a-dapi-bas-b64brgsn | Yingyu Hu, Zoe V Finkel | TITLE: Inorganic polyphosphate from microalgae: A DAPI-based estimation in microtiter plate
AUTHORS: Yingyu Hu, Zoe V Finkel
[DESCRIPTION]
The DAPI-based fluorometric estimation of polyphosphate from microalgae has been widely used in field samples since the method was published by Martin P. et al., where fluoresce... | ["[Sample collection] Filter microalgae in liquid media onto precombusted GFF filters, using gentle vacuum pressure (5 inches Hg).", "[Sample collection] Rinse sample with filtered seawater", "[Sample collection] Place sample filters in cryogenic vials", "[Sample collection] Filter blank media (without cells) through p... |
59,875 | Single-Cell Isolation of Human Articular Cartilage | 5 | dx.doi.org/10.17504/protocols.io.14egn765qv5d/v1 | https://www.protocols.io/view/single-cell-isolation-of-human-articular-cartilage-b6qbrdsn | hswahn , Martin Lotz | TITLE: Single-Cell Isolation of Human Articular Cartilage
AUTHORS: hswahn , Martin Lotz
[DESCRIPTION]
This is a protocol that describes the process of isolating single cells from healthy knee cartilage for single cell RNAseq.
[STEPS]
1. ~1.5 g of articular cartilage from healthy donor knees (grades 0-1) is resected... | ["~1.5 g of articular cartilage from healthy donor knees (grades 0-1) is resected from the medial condyle of the proximal femur. For details regarding the tissue harvesting procedure please see \ndx.doi.org/10.17504/protocols.io.14egn7996v5d/v1.", "Cartilage shavings are washed with Room temperature Dulbecco's Phosphat... |
107,384 | Microsphere Synthesis | 0 | null | https://www.protocols.io/view/microsphere-synthesis-dk4y4yxw | Matthew Woodworth | TITLE: Microsphere Synthesis
AUTHORS: Matthew Woodworth
[DESCRIPTION]
Microspheres are micron- sized plastic beads that have been used in drug delivery systems, typically with poly-lactide:glycolide (PLGA). The PLGA beads are able to encapsulate small molecules and they will degrade over time, releasing the drug. Syn... | ["[Dissolving PLA] Depending on the amount weighted, calculate the amount of DCM needed. The final concentration of PLA in DCM is 50 mg/mL", "[Dissolving PLA] Collect PLA and record the weight. Aim for 0.5-1 gram.", "[Dissolving PLA] In either a glass scintillation vial or a glass pyrex bottle, add the PLA to the DCM. ... |
90,584 | Protocol to isolate and fix nuclei from flash frozen mouse adrenal glands for IGVF | 4 | null | https://www.protocols.io/view/protocol-to-isolate-and-fix-nuclei-from-flash-froz-c4pyyvpw | Elisabeth Rebboah | TITLE: Protocol to isolate and fix nuclei from flash frozen mouse adrenal glands for IGVF
AUTHORS: Elisabeth Rebboah
[DESCRIPTION]
This protocol describes isolation of nuclei from left and right 10 week old mouse adrenal glands from 8 founder strains (B6J, AJ, 129S1J, NZOJ, WSBJ, NODJ, PWKJ, and CASTJ), preparation of... | ["[Setup] Label tubes.", "[Setup] Pre-chill centrifuge to 4C.", "[Setup] Prepare ice buckets.", "[Setup] Prepare 35 ml lysis buffer on ice in a 50 mL conical tube. Distribute 2 mL into 8 gentleMACS C Tubes on ice. Add 175 ul RNase inhibitor to the lysis buffer aliquot the day of the experiment.", "[Setup] Prepare 3.5 m... |
28,545 | 2ndline_sh_and_VL | null | dx.doi.org/10.17504/protocols.io.749hqz6 | null | Rahel Bircher | TITLE: 2ndline_sh_and_VL
AUTHORS: Rahel Bircher
[STEPS] | [] |
25,254 | Loop L1 (odd level) type IIS cloning - pCk-ye vectors | null | dx.doi.org/10.17504/protocols.io.4wegxbe | null | Eftychis Frangedakis, Susana Sauret-Gueto, Anthony West, Nicola Patron, marta tomaselli, Marius Rebmann, Jim Haseloff | TITLE: Loop L1 (odd level) type IIS cloning - pCk-ye vectors
AUTHORS: Eftychis Frangedakis, Susana Sauret-Gueto, Anthony West, Nicola Patron, marta tomaselli, Marius Rebmann, Jim Haseloff
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol based on:</div><div class = "text-block"><a href="http:... | ["Determine the concentrations of the DNA parts by spectrophotometry (Nanodrop).", ". Prepare Loop assembly Level 1 reaction master mix (MM) according to Table, if four or less number of parts are assembled into a pCk-pe vector. AB1 Components\n Volume (μL)\n 2 Sterile water \n 3 \n 3 10x T4 ligase buffer ... |
80,831 | Cell culture of J774A.1 cells | 4 | dx.doi.org/10.17504/protocols.io.q26g7ye1qgwz/v1 | https://www.protocols.io/view/cell-culture-of-j774a-1-cells-cs67whhn | Lisa Börmel, Sijia Liao, Maria Wallert, Stefan Lorkowski | TITLE: Cell culture of J774A.1 cells
AUTHORS: Lisa Börmel, Sijia Liao, Maria Wallert, Stefan Lorkowski
[DESCRIPTION]
The J774 tumor arose in a female BALB/c/NIH mouse with a reticulum cell sarcoma during a plasmacytoma induction program in 1968 [1]. The original tumor from which the cells designated J774A.1 were isola... | ["[Thaw J774A.1 cells] Transfer the cryotube with the cell suspension from the liquid nitrogen tank to the cell culture on ice.\n\nNote: When handling with liquid nitrogen, wear protective goggles, gloves and a gown, otherwise cold burn may occur.", "[Thaw J774A.1 cells] Thaw the cells immediately in a 37 °C water bath... |
107,089 | Viral Titer Quantification by Digital Droplet PCR | 0 | dx.doi.org/10.17504/protocols.io.3byl498p2go5/v1 | https://www.protocols.io/view/viral-titer-quantification-by-digital-droplet-pcr-dktr4wm6 | Allen Institute | TITLE: Viral Titer Quantification by Digital Droplet PCR
AUTHORS: Allen Institute
[DESCRIPTION]
This protocol can be used to test Viral titer of
rAAV viral vectors.
[STEPS] | [] |
40,787 | ELISA for quantification of IL-25 in human serum. | 6 | dx.doi.org/10.17504/protocols.io.bj3tkqnn | https://www.protocols.io/view/elisa-for-quantification-of-il-25-in-human-serum-bj3tkqnn | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-25 in human serum.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells. ... | ["An anti-human IL-25 coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.", "Add 50 µl of human serum. Human IL-25 present in the serum sample binds to antibodies adsorbed into the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and... |
42,056 | Massive Parallel Reporter Assay (MPRA) | 4 | null | https://www.protocols.io/view/massive-parallel-reporter-assay-mpra-bmbgk2jw | Gracie Gordon, Nadav Ahituv | TITLE: Massive Parallel Reporter Assay (MPRA)
AUTHORS: Gracie Gordon, Nadav Ahituv
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Massively parallel reporter assays (MPRAs) can simultaneously measure the function of thousands of candidate regulatory sequences (CRSs) in a quantitative manner. In thi... | ["[Library Amplification]\nSet up the first-round PCR reaction. This reaction adds a vector overhang sequence upstream andminimal promoter and adaptor sequences downstream of the CRSs ABC1ReagentVolume (μL)Final conc2Agilent oligonucleotide (100 nM)21nM3NEBNext High-Fidelity 2× PCR Master Mix1001x45BC-AG-f01 (100 μM)1... |
51,851 | CTAB genomic DNA-extraction | 4 | dx.doi.org/10.17504/protocols.io.bwvjpe4n | https://www.protocols.io/view/ctab-genomic-dna-extraction-bwvjpe4n | Michael Burgis | TITLE: CTAB genomic DNA-extraction
AUTHORS: Michael Burgis
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for the isolation of genomic DNA for a wide range of plant species.</div><div class = "text-block">This protocol is based on a paper published by Aboul-Maaty et al. 2019 (https://doi.... | ["[Buffer preparation]\n3X Extraction buffer (autoclaved): 3% CTAB (w/v), 1.4M NaCl, 0.8M Tris-HCl pH 8.0, 0.5M EDTA pH 8.03M Potassium acetate6M NaCl1x TE Buffer (autoclaved): 10mM Tris-HCl pH 8.0, 1mM EDTA pH 8.0", "[Grinding plant sample]\nPreheat 3x Extraction buffer in water bath at 65°C. Add 0.3% 2-β-mercaptoetha... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.