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 |
|---|---|---|---|---|---|---|---|
28,187 | Bimanual Interference Experimental Paradigm | 1 | dx.doi.org/10.17504/protocols.io.7r3hm8n | https://www.protocols.io/view/bimanual-interference-experimental-paradigm-7r3hm8n | Rini Varghese, Robert L. Sainburg, Carolee J Winstein | TITLE: Bimanual Interference Experimental Paradigm
AUTHORS: Rini Varghese, Robert L. Sainburg, Carolee J Winstein
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"> Successful bimanual coordination is accomplished by overcoming a variety of cognitive, perceptual and neuromotor constraints, e.g. hig... | ["[Task Setup]\nTASK SETUPThe task goal is to move to the target quickly and accurately in a single uncorrected motion. ♣ AppearanceWithin each trial, the participant sees on the virtualization mirror —Start circle: - diameter = 1 cm (v) - color = greenConcentric target circle: ... |
61,310 | Stroke volume and cardiac output during 6 minute-walk tests are strong predictors of maximal oxygen uptake in people with stroke | 1 | dx.doi.org/10.17504/protocols.io.b746rqze | https://www.protocols.io/view/stroke-volume-and-cardiac-output-during-6-minute-w-b746rqze | Fangliu, Alice YM YM YM Jones, Raymond Tsang, Fubing Zha, Mingchao Zhou, Kaiwen Xue, Zeyu Zhang, Yulong Wang | TITLE: Stroke volume and cardiac output during 6 minute-walk tests are strong predictors of maximal oxygen uptake in people with stroke
AUTHORS: Fangliu, Alice YM YM YM Jones, Raymond Tsang, Fubing Zha, Mingchao Zhou, Kaiwen Xue, Zeyu Zhang, Yulong Wang
[DESCRIPTION]
The 6-minute walk test (6MWT) is a field test commo... | ["People diagnosed with stroke and receiving treatment at the Second People’s Hospital, Shenzhen, China, were invited to participate in the study through in-hospital poster advertising. The inclusion criteria were: (1) age ≥ 18 years, (2) clinically diagnosed with ischemic and/or hemorrhagic stroke, (3) period since st... |
18,566 | Detection and quantification of Candida spp. from subgingival areas | null | dx.doi.org/10.17504/protocols.io.wdefa3e | null | Sanja Petrovic, Milena Radunovic, Ana Pucar | TITLE: Detection and quantification of Candida spp. from subgingival areas
AUTHORS: Sanja Petrovic, Milena Radunovic, Ana Pucar
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Detection and quantification of Candida spp. from subgingival areas using two methods- sterile periodontal curette and steri... | ["1. The first day- clinical periodontal examination (full mouth examination at six sites per tooth) in order to diagnose chronic periodontitis and detect the deepest periodontal pocket (with the highest PPD value).", "-Record plaque index (Silness-Löe), bleeding on probing (BOP), periodontal pocket depth (PPD) and cli... |
32,906 | Quasi-periodic migration of single cells on short microlanes | null | dx.doi.org/10.17504/protocols.io.bcdiis4e | null | Fang Zhou | TITLE: Quasi-periodic migration of single cells on short microlanes
AUTHORS: Fang Zhou
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><h1><span style = ":justify;">Cell migration on microlanes represents a suitable and simple platform for the exploration of the molecular mechanisms underlying cell ... | ["Preparation of micropatterns.", "Production of stamp masters by photolithoraphy1). A silicon wafer was coated with TI Prime adhesion promoter and then baked on a heating plate. Settings of spincoating: firstly 500 rpm for 5s, then 5000 rpm for 30sSettings of baking: 120 °C for 2 mins2). The wafer was further spincoat... |
54,903 | Backflush of Dead-end Ultrafilter | 1 | dx.doi.org/10.17504/protocols.io.14egnzp6yg5d/v1 | https://www.protocols.io/view/backflush-of-dead-end-ultrafilter-bzuxp6xn | Andrea Ottesen, Brandon Kocurek | TITLE: Backflush of Dead-end Ultrafilter
AUTHORS: Andrea Ottesen, Brandon Kocurek
[DESCRIPTION]
The backflush procedure pushes out all the cells and particles that were captured during the pumping procedure. It is most easily carried out in the lab with established (pump holding equipment) or ad hoc installation... | ["[Backflush Station Set Up] Open the side port of the \"top\" of the ultrafilter by removing the cap. Push the freshly cut tubing on the side port all the way to where the port meets the ultrafilter. Feed the tubing through the peristatic pump and place the end of the tubing into the backflush solution.", "[Backflush ... |
64,169 | Isolation of nuclei from frozen tissue for ATAC-seq and other epigenomic assays | 1 | dx.doi.org/10.17504/protocols.io.ewov1nm2kgr2/v1 | https://www.protocols.io/view/isolation-of-nuclei-from-frozen-tissue-for-atac-se-cawhsfb6 | Ryan Corces, William J. Greenleaf, Howard Y. Chang | TITLE: Isolation of nuclei from frozen tissue for ATAC-seq and other epigenomic assays
AUTHORS: Ryan Corces, William J. Greenleaf, Howard Y. Chang
[DESCRIPTION]
This protocol enables the isolation of nuclei from frozen tissues. These nuclei are suitable for use in ATAC-seq, single-cell ATAC-seq, ChIP-seq, HiC/3C, and... | ["[Before you start the protocol:] All steps should be performed on ice or at 4 °C. Pre-chill a swinging bucket centrifuge and a fixed angle centrifuge to 4°C.", "[Before you start the protocol:] Pre-chill all Dounces and pestles to 4 °C in a fridge.", "[Before you start the protocol:] Pre-chill all tubes. For each sam... |
42,596 | Amplicon Library Preparation | 1 | dx.doi.org/10.17504/protocols.io.bmuck6sw | https://www.protocols.io/view/amplicon-library-preparation-bmuck6sw | Ariel Rabines, Rob Lampe, Andrew Allen | TITLE: Amplicon Library Preparation
AUTHORS: Ariel Rabines, Rob Lampe, Andrew Allen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">18S and 16S amplicon library preparation protocol.</div><div class = "text-block">DNA or RNA is usually extracted with our automated protocols from sterivex but other t... | ["Setup a PCR reaction as follows: AB1Reagent1x reaction (uL)25x buffer5.03F + R primer combined (10 uM)1.04DNA polymerase0.255Template (10 pg - 500 ng)1.0 - 2.06Molecular grade H2Oto 25 uL\n25 µl\nAB1Reagent1x reaction (uL)25x buffer5.03F + R primer combined (10 uM)1.04DNA polymerase0.255Template (10 pg - 500 ng)1.0... |
43,719 | Enzyme–Ligand Interaction Monitored by Synchrotron Radiation Circular Dichroism | 2 | dx.doi.org/10.17504/protocols.io.bnxfmfjn | https://www.protocols.io/view/enzyme-ligand-interaction-monitored-by-synchrotron-bnxfmfjn | Rohanah Hussain, Charlotte S. Hughes, Giuliano Siligardi | TITLE: Enzyme–Ligand Interaction Monitored by Synchrotron Radiation Circular Dichroism
AUTHORS: Rohanah Hussain, Charlotte S. Hughes, Giuliano Siligardi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">CD spectroscopy is the essential tool to quickly ascertain in the far-UV region the global confor... | [] |
69,628 | Mollusk pedal mucus effects on epilithic biofilms | 4 | dx.doi.org/10.17504/protocols.io.5qpvoy3bdg4o/v2 | https://www.protocols.io/view/mollusk-pedal-mucus-effects-on-epilithic-biofilms-cf84tryw | Clara Maria Arboleda-Baena, Claudia Pareja, Isadora Pla, Ramiro Logares, Rodrigo De La Iglesia, Sergio A. Navarrete | TITLE: Mollusk pedal mucus effects on epilithic biofilms
AUTHORS: Clara Maria Arboleda-Baena, Claudia Pareja, Isadora Pla, Ramiro Logares, Rodrigo De La Iglesia, Sergio A. Navarrete
[DESCRIPTION]
Protocol used in the article “Hidden interactions in the intertidal rocky shore: variation in pedal mucus microbiota among ... | ["We cultured epilithic biofilms in K medium (Keller et al. 1987) on a cover glass slide inside a Polycarbonate cell culture plate of 6-Wells, for one week.", "During nocturnal low tides, we collected animals of each mollusk species from wave-exposed platforms, brought them to the laboratory in coolers, and then placed... |
53,026 | Microfluidics 4: PDMS Chip Soft Lithography | 1 | dx.doi.org/10.17504/protocols.io.bx2apqae | https://www.protocols.io/view/microfluidics-4-pdms-chip-soft-lithography-bx2apqae | Serhat Sevli, C. Yunus Sahan | TITLE: Microfluidics 4: PDMS Chip Soft Lithography
AUTHORS: Serhat Sevli, C. Yunus Sahan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">Microfluidics materials are of various types and application-specific. PDMS is one of the most preferred and cost... | ["[PDMS on mold]\n2.0.1. Pour the mixture into the mold.", "[Stock of PDMS]\n3.0.1. The excess of mixed PDMS (but not heated) can be stored in a refrigerator (+4°C) for up to one week.3.0.2. Just take from the refrigerator and pour on a new mold and incubate.\nA longer duration for storage is not suggested since PDMS c... |
null | null | null | dx.doi.org/10.17504/protocols.io.e4cbgsw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Rapid, Sensitive and Reversible Protein Stain For PVDF and Nitrocellulose Membranes.</p>
<p> </p>
<p>(These instructions are for a single 8 x 8 cm membrane. Increase the reagent volumes with larger membranes.)</p>
[GUIDELINES]
<p><strong>INTRODUCTION</strong></p>
<p>Swift™ ... | [] |
65,029 | Fixation and imaging of HeLa cells after mitochondrial depolarization (Provisional unformatted) | 4 | null | https://www.protocols.io/view/fixation-and-imaging-of-hela-cells-after-mitochond-cbrdsm26 | OLIVIA HARDING, holzbaur | TITLE: Fixation and imaging of HeLa cells after mitochondrial depolarization (Provisional unformatted)
AUTHORS: OLIVIA HARDING, holzbaur
[DESCRIPTION]
Ectopic expression of p62/SQSTM1 often induces puncta formation and poor cell health due to p62’s proclivity to multimerize and form filaments. We used the cell fix... | ["Keywords\n Mitochondrial depolarization | paraformaldehyde fixation | confocal imaging\n Guidelines \nThis protocol was adapted from a previous protocol for similar techniques\n (see dx.doi.org/10.17504/protocols.io.bujsnune\nHere we use a primary antibody to a mitochondrial pr otein, HSP60, in\n order to identify mi... |
63,358 | Photorepair Fluence Response Protocol | 1 | dx.doi.org/10.17504/protocols.io.6qpvr671bvmk/v1 | https://www.protocols.io/view/photorepair-fluence-response-protocol-b946r8ze | Daniel Ma, David McDonald, NATALIE HULL | TITLE: Photorepair Fluence Response Protocol
AUTHORS: Daniel Ma, David McDonald, NATALIE HULL
[DESCRIPTION]
Photorepair light exposures are performed on microorganism samples following UV light exposure (i.e. UV disinfection) to determine microorganism regrowth and repair kinetics. Photorepair is a light-dependent, en... | ["[Introduction and Pre-Experiment] The photorepair fluence response protocol is based on Bohrerova and Linden (2007).\n \nTo perform the photorepair fluence response experiment, you will first need to perform a UV fluence response experiment after the references below. Photorepair experiments and sample handling must ... |
null | null | null | dx.doi.org/10.17504/protocols.io.j8hcrt6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
92,918 | 16S and GyrB bacterial amplification | 1 | dx.doi.org/10.17504/protocols.io.36wgq31nylk5/v1 | https://www.protocols.io/view/16s-and-gyrb-bacterial-amplification-c6ywzfxe | Robert Nichols | TITLE: 16S and GyrB bacterial amplification
AUTHORS: Robert Nichols
[DESCRIPTION]
This protocol is used for the amplification of the bacterial gyrB gene and the 16S gene for both PacBio Sequel II and Illumina MiSeq sequencing. This protocol is used in the paper titled Long-read Sequencing Increases the Accuracy and Sp... | ["[Prepare DNA for Amplification] Thaw the isolated DNA", "[Prepare DNA for Amplification] Measure DNA concentration on the Nanodrop\n\nThis requires only 1 µL of isolated DNA. Concentration values typically range from 100 ng/μl to 400 ng/μl. In addition, the NanoDrop gives only an estimate of the total DNA concentr... |
null | null | null | dx.doi.org/10.17504/protocols.io.ftnbnme | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A protocol for isolation of protoplast from plant cells adapted from Yoo et al. 2007 (http://www.nature.com/nprot/journal/v2/n7/full/nprot.2007.199.htm). Procedure was optimized for use on <em>Arabidopsis thaliana</em> tissue.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
... | [] |
82,482 | U54 SCENT Normal Lung Autopsy Tissue Collection Procedure | 1 | null | https://www.protocols.click/view/u54-scent-normal-lung-autopsy-tissue-collection-pr-cusswwee | Carolyn Glass, andrew.nixon, Mary Jordan* | TITLE: U54 SCENT Normal Lung Autopsy Tissue Collection Procedure
AUTHORS: Carolyn Glass, andrew.nixon, Mary Jordan*
[DESCRIPTION]
This document outlines the required criteria and collection protocol for normal lung specimen acquisition from autopsy at Duke University Hospital through the Biorepository and Precision Pa... | ["[Collection Protocol] U54 Clinical Research Coordinator will access Microsoft Teams DUH Decedent Care - Labs Autopsy Team.", "[Collection Protocol] U54 Clinical Research Coordinator will screen the afternoon prior for upcoming autopsy collections that fit inclusion and exclusion criteria.", "[Collection Protocol] U54... |
35,865 | Sample prep - Stanford TMC | 1 | dx.doi.org/10.17504/protocols.io.be9zjh76 | https://www.protocols.io/view/sample-prep-stanford-tmc-be9zjh76 | John Hickey | TITLE: Sample prep - Stanford TMC
AUTHORS: John Hickey
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>See our detailed protocol published with the following title: </span><span style = "font-weight:bold;">CODEX multiplexed tissue imaging with DNA-conjugated antibodies.</span></div></div>
[ST... | ["See our detailed protocol published with the following title: CODEX multiplexed tissue imaging with DNA-conjugated antibodies."] |
93,031 | Protocol for bioequivalence analysis in studies with two treatments (design 2x2x2, 2x3x3 and 2x2x4) using the R Studio software | 5 | dx.doi.org/10.17504/protocols.io.q26g7p7d1gwz/v1 | https://www.protocols.io/view/protocol-for-bioequivalence-analysis-in-studies-wi-c64fzgtn | Leandro do Prado Assunção, Laura Raniere Borges dos Anjos | TITLE: Protocol for bioequivalence analysis in studies with two treatments (design 2x2x2, 2x3x3 and 2x2x4) using the R Studio software
AUTHORS: Leandro do Prado Assunção, Laura Raniere Borges dos Anjos
[DESCRIPTION]
Research and development (R&D) of new drugs is a complex process that requires high financial investmen... | ["[Installing the packages] The default function in R Studio to install packages is install.packages(\"Name\"). Run the code.", "[Installing the packages] Command:\n\ninstall.packages(\"readxl\")\ninstall.packages(\"dplyr\")\ninstall.packages(\"PKNCA\")\ninstall.packages(\"stringr\")\ninstall.packages(\"ggplot2\")\nins... |
47,743 | Protein-A_Protein-LG Sandwich ELISA | 1 | dx.doi.org/10.17504/protocols.io.bsu7nezn | https://www.protocols.io/view/protein-a-protein-lg-sandwich-elisa-bsu7nezn | Angel Justiz-Vaillant | TITLE: Protein-A_Protein-LG Sandwich ELISA
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This ELISA was used to study the interactions between Staphylococcal protein-A (SpA) and protein-LA (SpLG) with different immunoglobulin preparations of mammalian and avian spec... | ["Thisc ELISA was used to study the interactions between Staphylococcal protein-A (SpA) and protein-LG (SpLG) with different immunoglobulin preparations from mammalian and avian species. The 96 well microtiter plate was coated overnight at 4°C with 2 µg/µl per well of SpA in carbonate-bicarbonate buffer pH 9.6.", "The ... |
27,163 | Epigenomic profiling of neuroblastoma cell lines | null | dx.doi.org/10.17504/protocols.io.6r3hd8n | null | Kristen Upton, Robyn T. Sussman, Khushbu Patel, Gregory P. Way, Rebecca N. Adams, Gregory I. Sacks, Rebecca N. Adams, Paolo Fortina, John M. Maris, Jo Lynne Rokita | TITLE: Epigenomic profiling of neuroblastoma cell lines
AUTHORS: Kristen Upton, Robyn T. Sussman, Khushbu Patel, Gregory P. Way, Rebecca N. Adams, Gregory I. Sacks, Rebecca N. Adams, Paolo Fortina, John M. Maris, Jo Lynne Rokita
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol explains ... | [] |
105,011 | Pole Test Assessment | 4 | dx.doi.org/10.17504/protocols.io.n92ld8j87v5b/v1 | https://www.protocols.io/view/pole-test-assessment-dist4een | Ian N Krout, Alexandria White, Tim Sampson | TITLE: Pole Test Assessment
AUTHORS: Ian N Krout, Alexandria White, Tim Sampson
[DESCRIPTION]
Pole descent
This test measures the time for mice to descend a 24-inch pole wrapped in mesh. Mice were trained
for two days with three trials: 1) placed head down ⅓ of the height from the
base, 2) placed head down ⅔ of the he... | ["[Pole set-up] Find a metal pole 1cm in diameter with a height of ~50-60cm. This should have a base that is able to fit inside of a standard mouse cage.", "[Training Day 1] Determine the order of assessment that you will use for the length of the training and assessment, record this in lab notebook.", "[Assessment (t... |
49,130 | Cryostat Sectioning of Tissues for 3D Multimodal Molecular Imaging | 1 | dx.doi.org/10.17504/protocols.io.bt8inrue | https://www.protocols.io/view/cryostat-sectioning-of-tissues-for-3d-multimodal-m-bt8inrue | David Anderson, Elizabeth Neumann, Jamie Allen, Maya Brewer, Danielle Gutierrez, Jeff Spraggins | TITLE: Cryostat Sectioning of Tissues for 3D Multimodal Molecular Imaging
AUTHORS: David Anderson, Elizabeth Neumann, Jamie Allen, Maya Brewer, Danielle Gutierrez, Jeff Spraggins
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Scope: </div><div class = "text-block">Protocol for sectioning flash froz... | ["Set the cryostat temperatures:Internal: -21oCObject: -10oC to -20oC (based on tissue type)", "Carefully remove blade from container and wipe with ethanol and a lint free wipe. Insert blade and lock into place.", "Mount sample onto the cryostat chuck using OCT in the desired orientation. A flat surface can be sh... |
66,030 | Automated DNA/RNA Extractions from a stony coral (Acropora palmata) using ZymoBIOMICS DNA/RNA Magbead Kit and the Kingfisher Flex | 4 | dx.doi.org/10.17504/protocols.io.bp2l61wykvqe/v2 | https://www.protocols.io/view/automated-dna-rna-extractions-from-a-stony-coral-a-ccqnsvve | Benjamin D Young | TITLE: Automated DNA/RNA Extractions from a stony coral (Acropora palmata) using ZymoBIOMICS DNA/RNA Magbead Kit and the Kingfisher Flex
AUTHORS: Benjamin D Young
[DESCRIPTION]
This is the protocol used to extract DNA and RNA from the same piece of coral tissue and skeleton using the Zymo DNA/RNA MagBead and ZymoBIOM... | ["[Coral Tissue Sampling and Storage] For each sample, bonecutters and tweezers were cleaned with 80% bleach and then flame sterilized with 70% ethanol. The bench space was also cleaned between each sample with 80% bleach and 70% ethanol.", "[Coral Tissue Sampling and Storage] All coral samples were stored in 2ml cryo ... |
12,685 | Axolotl blastema dissociation into single cell suspension | null | dx.doi.org/10.17504/protocols.io.qmmdu46 | null | Nicholas Leigh | TITLE: Axolotl blastema dissociation into single cell suspension
AUTHORS: Nicholas Leigh
[DESCRIPTION]
<p>This protocol is designed to obtain blastema cells (and wound epidermis if left attached) into a single cell suspension. It was specifically designed for single cell RNA sequencing, but can be used for other appli... | ["[Tissue collection and enzymatic digestion]\nNarcotize animals in 0.1% Tricaine prepared in 40% Holtfreter's.\nAfter survival surgeries always keep animals overnight in 40% Holtfreter's supplemented with 0.5% sulfamerazine.", "[Tissue collection and enzymatic digestion]\nDilute 10X HBSS with UltraPure H2O to 0.7X HBS... |
null | null | null | dx.doi.org/10.17504/protocols.io.djn4md | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
From Sullivan M., Lindell D., Lee J., Thompson L., Bielawski J., Chisholm S. <a href="http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0040234" target="_blank">Prevalence and Evolution of Core Photosystem II Genes in Marine Cyanobacterial Viruses and Their Ho... | [] |
67,138 | Nanopore (SQK-LSK109) without barcode | 4 | dx.doi.org/10.17504/protocols.io.5qpvob837l4o/v2 | https://www.protocols.io/view/nanopore-sqk-lsk109-without-barcode-cdtas6ie | Wen-Ting Zeng | TITLE: Nanopore (SQK-LSK109) without barcode
AUTHORS: Wen-Ting Zeng
[DESCRIPTION]
Nanopore (SQK-LSK109) without barcode
[STEPS]
SECTION: Step1. DNA repair and end-prep
1. In a 200μl PCR tube, mix the following:
SECTION: Step1. DNA repair and end-prep
1.1. Ensure the components are thoroughly mixed by pipett... | ["[Step1. DNA repair and end-prep] In a 200μl PCR tube, mix the following:", "[Step1. DNA repair and end-prep] Ensure the components are thoroughly mixed by pipetting, and spin down.", "[Step1. DNA repair and end-prep] Using a thermal cycler, incubate at 20 °C for 30 min and 65 °C for 30 min. Hold at 4 °C \n1.2", "[Ste... |
28,570 | Xylem inoculation with flg22 | null | dx.doi.org/10.17504/protocols.io.752hq8e | null | Cleo Bagchus | TITLE: Xylem inoculation with flg22
AUTHORS: Cleo Bagchus
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Protocol can be used after: Plant Infection with </span><span style = "font-style:italic;">Xanthomonas Campestris </span><span>Campestris</span></div></div>
[STEPS]
?. [Day 1]
Place of ... | ["[Day 1]\nPlace of flg22 3 cm above the lesion on the central vein of the leaf.\n15 µl", "[Day 1]\nWith the needle puncture through the droplet into the central vein three times. Do not puncture the leaf completely. Due to a difference in pressure, the droplet should be sucked into the xylem.", "[Day 1]\nPlace a seco... |
94,600 | Formation and isolation of Clu phospholipid particles | 1 | dx.doi.org/10.17504/protocols.io.bp2l6x59zlqe/v1 | https://www.protocols.io/view/formation-and-isolation-of-clu-phospholipid-partic-c8mgzu3w | Patricia Yuste-Checa, Andreas Bracher, F Ulrich Hartl | TITLE: Formation and isolation of Clu phospholipid particles
AUTHORS: Patricia Yuste-Checa, Andreas Bracher, F Ulrich Hartl
[DESCRIPTION]
This protocol details how to efficiently make in vitro and isolate Clu-phospholipid particles using purified Clusterin from HEK293E cells (dx.doi.org/10.17504/protocols.io.bvvkn64w)... | ["[Formation of Clu-phospholipid particles] Prepare 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) stock solution: 5-25 mg/ml DMPC in 3:1 Chloroform:Methanol and store it at -80 °C.", "[Formation of Clu-phospholipid particles] Transfer the corresponding amount of DMPC solution to a glass vial and remove the solvent... |
69,659 | Immunohistochemical labelling of the innervation of dissected human colon wholemounts | 1 | dx.doi.org/10.17504/protocols.io.n92ldpb47l5b/v1 | https://www.protocols.io/view/immunohistochemical-labelling-of-the-innervation-o-cf93tr8n | Bao Nan CHEN, Adam HUMENICK, Simon Brookes | TITLE: Immunohistochemical labelling of the innervation of dissected human colon wholemounts
AUTHORS: Bao Nan CHEN, Adam HUMENICK, Simon Brookes
[DESCRIPTION]
This protocol outlines basic methods to localise neurochemical markers in dissected wholemount specimens of human colon using fluorescence immunohistochemical m... | ["All handling of un-fixed human tissue is exclusively done by staff trained in occupational health and safety requirements for handling hazardous material, wearing appropriate PPE (gloves, gowns and masks) and working in areas designated for human tissue.Users of this protocol should check local requirements with thei... |
43,624 | Artificial Pith Gallery (APG) construction | 3 | dx.doi.org/10.17504/protocols.io.bnugmetw | https://www.protocols.io/view/artificial-pith-gallery-apg-construction-bnugmetw | James Skelton, Jiri Hulcr | TITLE: Artificial Pith Gallery (APG) construction
AUTHORS: James Skelton, Jiri Hulcr
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to rear ambrosia beetles with the fungus of your choice. Could be used for just rearing beetles, or growing fungi on natural substrate. </d... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.gqnbvve | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
94,043 | Quantification of tissue creatine content using capillary electrophoresis | 4 | null | https://www.protocols.io/view/quantification-of-tissue-creatine-content-using-ca-c733zqqn | Jane Choi, Angelo Bautista, Peter G Arthur, J. Jane Pillow | TITLE: Quantification of tissue creatine content using capillary electrophoresis
AUTHORS: Jane Choi, Angelo Bautista, Peter G Arthur, J. Jane Pillow
[DESCRIPTION]
The current protocol describes an alternative method for creatine quantification in biological tissue samples using capillary electrophoresis, with high sep... | ["[Preparation of buffers] Prepare the stock phosphate buffer (PB) 200 millimolar (mM) pH 6", "[Preparation of buffers] pH the solution to 6.0 with concentrated NaOH", "[Preparation of buffers] top up the volume to 50 mL with ddH2O (ideally using a volumetric flask)", "[Preparation of buffers] filter sterilise the solu... |
74,211 | TEST - manual DNA Purification via magnetic beads | 4 | null | https://www.protocols.io/view/test-manual-dna-purification-via-magnetic-beads-ckqbuvsn | Carla Jungkunz | TITLE: TEST - manual DNA Purification via magnetic beads
AUTHORS: Carla Jungkunz
[DESCRIPTION]
manual purification of DNA/PCRs via magnetic beads
[BEFORE_START]
bring magnetic beads to room temperature (at least 30min)
[STEPS]
SECTION: prepare magnetic beads
1. 30 min bring magnetic beads to room temperature (RT)
... | ["[prepare magnetic beads] 30 min bring magnetic beads to room temperature (RT)", "[Binding of DNA] Add beads ... |
66,558 | TEA BURN | 3 | dx.doi.org/10.17504/protocols.io.6qpvr6n73vmk/v1 | https://www.protocols.io/view/tea-burn-cc86szze | Tea Pavlek | TITLE: TEA BURN
AUTHORS: Tea Pavlek
[DESCRIPTION]
LSDFLAS
[STEPS] | [] |
18,490 | Long term Cryopreservation of Chloroviruses by Infection of Chlorella | null | dx.doi.org/10.17504/protocols.io.wa2fage | null | Samantha Coy, Alyssa Alsante, Steven Wilhelm | TITLE: Long term Cryopreservation of Chloroviruses by Infection of Chlorella
AUTHORS: Samantha Coy, Alyssa Alsante, Steven Wilhelm
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Contact Dr. Steven Wilhelm (wilhelm@utk.edu) or Samantha Coy (srose16@vols.utk.edu) for additional information regarding ... | ["[Pre-cryopreservation]\nConfirm that the lysate (PBCV-1 in this case) is not contaminated with microbiota (e.g. heterotrophic bacteria) as these will degrade the virus population.", "[Pre-cryopreservation]\nPerform a plaque assay to determine the plaque forming units (PFU/mL) of the virus to determine the volume requ... |
71,261 | Plate Streaking | 1 | null | https://www.protocols.io/view/plate-streaking-cht5t6q6 | Carlos Goller, Carly Sjogren | TITLE: Plate Streaking
AUTHORS: Carlos Goller, Carly Sjogren
[DESCRIPTION]
Overview and Goals
Streaking bacteria on agar plates allows scientists to obtain isolated colonies of bacteria. An isolated colony provides up to 10^8 bacteria cells that are genetically identical. This is why we call them clones or refer to th... | ["[Procedure for plate streaking] Obtain a fresh petri dish containing TSA media.", "[Procedure for plate streaking] Label the bottom of the plate (the side containing TSA media) keeping to the circumference (write on the edge, not in the center) with your bacterial isolate#, your Team#, your initials and today's date... |
35,877 | Viral inactivation of clinical samples | null | dx.doi.org/10.17504/protocols.io.bfadjia6 | https://www.protocols.io/view/viral-inactivation-of-clinical-samples-bfadjia6 | Tammy Krylova, Tim Budd, Jerome Nicod, Rupert Beale, Simon Caidan | TITLE: Viral inactivation of clinical samples
AUTHORS: Tammy Krylova, Tim Budd, Jerome Nicod, Rupert Beale, Simon Caidan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Purpose of examination / Clinical relevance</span></div><div class = "text-block"><div class = "j... | ["[Inactivation step]\nWarning! Exposure to SARS-CoV-2 can result in COVID-19.➢ All unsealed work must be undertaken in a class I or Class II Microbiological Safety Cabinet (MBSC).\nSingle sample per cycle only!Working with multiple samples might lead to errors in sample identification!➢ Work with only one bagged sampl... |
19,754 | U Cinn - Cholesterol Concentration | null | dx.doi.org/10.17504/protocols.io.xiifkce | null | Patrick Tso, Dana Lee | TITLE: U Cinn - Cholesterol Concentration
AUTHORS: Patrick Tso, Dana Lee
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">In vitro quantification of cholesterol in serum or plasma is determined using an Infinity Total ... | ["Prepare working standards by making a serial dilution of the stock 200mg/dl standard.", "Using a 96 well flat bottom plate, into separate wells, pipette 2μL of deionized water, standard, or sample to be assayed.", "Add 200μL of Reagent (supplied ready to use) to all wells.", "Incubate plate for 5 minutes at 37°C.", "... |
null | null | null | dx.doi.org/10.17504/protocols.io.f5kbq4w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 5">
<div class="section">
<div class="layoutArea">
<div class="column">
<p>The ISOLATE II Biofluids RNA Kit is specially developed for the rapid phenol-free isolation of high quality total RNA from biofluids and viruses. Total RNA can be purified fr... | [] |
48,554 | Primary Lung Fibroblasts (PLF) Plating/Freezing Protocol | 4 | null | https://www.protocols.io/view/primary-lung-fibroblasts-plf-plating-freezing-prot-btninmce | Morrisey Lab | TITLE: Primary Lung Fibroblasts (PLF) Plating/Freezing Protocol
AUTHORS: Morrisey Lab
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Primary Lung Fibroblasts (PLF) Plating/Freezing Protocol</span></div><div class = "text-block"><span style = "font-weight:bold;">PLF... | [] |
38,280 | Antibody lyophilization | 4 | dx.doi.org/10.17504/protocols.io.bhmgj43w | https://www.protocols.io/view/antibody-lyophilization-bhmgj43w | Christine Camacho, Marc Bosse, Sean Bendall, Mike Angelo | TITLE: Antibody lyophilization
AUTHORS: Christine Camacho, Marc Bosse, Sean Bendall, Mike Angelo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details the lyophilization process of stock antibodies using an overnight lyophilization process.</div></div>
[STEPS]
?. [Preparation]
If pr... | ["[Preparation]\nIf processing a large amount of vials, pre-cool extra aluminum tube racks for at least at .\n-80 °C", "[Preparation of 5 µg Antibody Aliquots ]\nSelect antibodies to lyophilize using data provided on MIBItracker.", "[Preparation of 5 µg Antibody Aliquots ]\nMeasure the total volume of each antibody to... |
63,544 | Soil sample(Citizen scientists, Chinese) | 1 | dx.doi.org/10.17504/protocols.io.kqdg3py21l25/v1 | https://www.protocols.io/view/soil-sample-citizen-scientists-chinese-caaysafw | Hsin-Mao Wu | TITLE: Soil sample(Citizen scientists, Chinese)
AUTHORS: Hsin-Mao Wu
[DESCRIPTION]
Soil sample, citizen scientist
[STEPS]
SECTION: 採土
1. 選定地點，分為以下三種
醫院
公園
天然地區
SECTION: 採土
2. 移除表土，取距離土表5~7公分之處的土，裝入塑膠夾鏈袋中
SECTION: 採土
3. 將塑膠袋中的土均勻混合，分別倒入兩個HDPE塑膠罐之中
SECTION: 採土
4. 將HDPE罐子收進袋子中
SECTION: 採土
5. 最後拍兩張照片
| ["[採土] 選定地點，分為以下三種\n醫院\n公園\n天然地區", "[採土] 移除表土，取距離土表5~7公分之處的土，裝入塑膠夾鏈袋中", "[採土] 將塑膠袋中的土均勻混合，分別倒入兩個HDPE塑膠罐之中", "[採土] 將HDPE罐子收進袋子中", "[採土] 最後拍兩張照片"] |
100,089 | Clinical features and management of VEXAS syndrome in critical care: a scoping review protocol | 0 | null | https://www.protocols.io/view/clinical-features-and-management-of-vexas-syndrome-ddyz27x6 | Kasumi Satoh, Yasushi Tsujimoto, Daisuke Kasugai, Kazuki Okura, Takao Ono, Yuki Miyamoto, Tasuku Matsuyama, Taketo Watase, Hajime Nakae, Tadahiro Goto | TITLE: Clinical features and management of VEXAS syndrome in critical care: a scoping review protocol
AUTHORS: Kasumi Satoh, Yasushi Tsujimoto, Daisuke Kasugai, Kazuki Okura, Takao Ono, Yuki Miyamoto, Tasuku Matsuyama, Taketo Watase, Hajime Nakae, Tadahiro Goto
[DESCRIPTION]
Objective: This study aims to understand th... | ["[Introduction] Vacuoles, E1 enzyme, X-linked, Autoinflammatory, Somatic (VEXAS) syndrome is an acquired autoinflammatory disorder that primarily affects men over 50 years of age and was identified in 2020 as a new disease concept associated with mutations in the Ubiquitin-like modifier activating enzyme 1 (UBA1) gene... |
64,108 | DAB ANTIBODY (IHC) STAINING PROTOCOL | 1 | dx.doi.org/10.17504/protocols.io.kxygxzqyzv8j/v1 | https://www.protocols.io/view/dab-antibody-ihc-staining-protocol-caukseuw | Michael Lee | TITLE: DAB ANTIBODY (IHC) STAINING PROTOCOL
AUTHORS: Michael Lee
[DESCRIPTION]
This is the basic protocol for antibody staining of formalin fixed paraffin embedded (FFPE) tissue.
[GUIDELINES]
Principle:
For antibody staining to be successful, most FFPE tissue requires antigen retrieval of some kind. Formalin fixatio... | ["[Deparaffinize tissue: Day 1] 2 options: \n\n1) Either place slides on a slide warmer with temperature set to approx. 57 °C. Leave the slides on the warming plate until the paraffin looks melted on all of the slides (about 10 - 15 min) or 2) Put slides in a 60 °C oven for about 30 min.", "[Deparaffinize tissue: Day ... |
48,057 | Prestwick screen protocol | 4 | null | https://www.protocols.io/view/prestwick-screen-protocol-bs6znhf6 | Ida Barlow, Thomas O'brien | TITLE: Prestwick screen protocol
AUTHORS: Ida Barlow, Thomas O'brien
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Protocol for screening the Prestwick </span><span style = "font-style:italic;">C. elegans</span><span> drug library of 240 drugs at 3 concentrations and imaging under baseline a... | ["[Pick L4 worms for bleaching (-9 days from first day of tracking)]\nPick 10 x N2 L4s onto 8 x 90mm plates (pre-seeded with OP50)", "[Pour 96WPs (up to 3 days before tracking)]\nPrepare 1L low peptone NGM and autoclave\n{\"blocks\":[{\"key\":\"37sqq\",\"text\":\"C. elegans is maintained in the laboratory on Nematode G... |
87,146 | Workflow for beta-range forest plots, bootstrap ridgeline plots, and bootstrap violin plots | 5 | dx.doi.org/10.17504/protocols.io.5qpvorz4dv4o/v2 | https://www.protocols.io/view/workflow-for-beta-range-forest-plots-bootstrap-rid-czcix2ue | Jonathan Fries, Sandra Oberleiter, Jakob Pietschnig | TITLE: Workflow for beta-range forest plots, bootstrap ridgeline plots, and bootstrap violin plots
AUTHORS: Jonathan Fries, Sandra Oberleiter, Jakob Pietschnig
[DESCRIPTION]
Regression is a widely used statistical method in various research areas, such as educational psychology, and it is common to display regression ... | ["[Install and load packages] The following workflow requires the statistical programming environment R (at least version 4.2.2). Before running any command prompts, some packages need to be installed. To this end, we create a vector that contains the respective package names and run a for loop that only installs packa... |
67,412 | https://www.facebook.com/PromaxKeto/ | 3 | dx.doi.org/10.17504/protocols.io.yxmvmnro6g3p/v1 | https://www.protocols.io/view/https-www-facebook-com-promaxketo-cd3us8nw | Ketosis gives off an impression of being an exceptionally fruitful weight reduction technique, yet it is hard to accomplish. | TITLE: https://www.facebook.com/PromaxKeto/
AUTHORS: Ketosis gives off an impression of being an exceptionally fruitful weight reduction technique, yet it is hard to accomplish.
[DESCRIPTION]
Ketosis gives off an impression of being an exceptionally fruitful weight reduction technique, yet it is hard to accomplish.
... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.h3mb8k6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ke3ctgn | null | null | TITLE: No Title
AUTHORS:
[STEPS] | [] |
57,199 | High Throughput SARS-COV-2, PMMOV, and BCoV quantification in settled solids using digital RT-PCR | 1 | dx.doi.org/10.17504/protocols.io.b34pqqvn | https://www.protocols.io/view/high-throughput-sars-cov-2-pmmov-and-bcov-quantifi-b34pqqvn | Aaron Topol (Verily Life Sciences), marlene.wolfe , Brad White (Verily Life Sciences), Krista Wigginton, Alexandria B B Boehm | TITLE: High Throughput SARS-COV-2, PMMOV, and BCoV quantification in settled solids using digital RT-PCR
AUTHORS: Aaron Topol (Verily Life Sciences), marlene.wolfe , Brad White (Verily Life Sciences), Krista Wigginton, Alexandria B B Boehm
[DESCRIPTION]
v3 updates: changes to the S gene primers and probes for detect... | ["[Preparation (both assays)] Retrieve all kit components from the One-Step RT-ddPCR advanced kit for probes from the -20 °C freezer and thaw the components on ice.", "[Preparation (both assays)] Retrieve ddPCR positive control aliquots (50 copies per uL gRNA and 100 copies per µL BCoV and PMMoV gene blocks) from the -... |
93,024 | ONT Sequencing IT/Compute Pop!_OS 22.04 Setup | 5 | dx.doi.org/10.17504/protocols.io.14egn7kzmv5d/v3 | https://www.protocols.io/view/ont-sequencing-it-compute-pop-os-22-04-setup-c638zgrw | Stephen Douglas Russell | TITLE: ONT Sequencing IT/Compute Pop!_OS 22.04 Setup
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
The IT requirements for processing MinION data should be carefully reviewed before purchasing a MinION device. You will want to go with a Linux system. System76 is really the primary/best vendor for laptops. Pay carefu... | ["[Preparing a new CPU for MinION Sequencing] The final setup I went with can be found below. It was expensive (around for the laptop in early 2022), but should be able to achieve live basecalling for two MinION devices at the same time. Overall specs of my laptop: \n\n \n \n\nMinimum IT requirements for MinION from ... |
null | null | null | dx.doi.org/10.17504/protocols.io.ddv265 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<span data-reactid=".0.1.0.1.0.0.0.4.0">Quick and easy method to transform a free plasmid into either budding or fission yeast.</span>
[BEFORE_START]
<span data-reactid=".0.1.0.1.0.0.2.1.1.0">Grow at least a 1 mL liquid yeast culture overnight, or plate yeast on minimal medium ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.fjsbkne | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?. | [] |
75,230 | Nucleofection (Amaxa) and electroporation (Biorad) of hPSCs | 2 | dx.doi.org/10.17504/protocols.io.e6nvwkkewvmk/v2 | https://www.protocols.io/view/nucleofection-amaxa-and-electroporation-biorad-of-cmp6u5re | Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner | TITLE: Nucleofection (Amaxa) and electroporation (Biorad) of hPSCs
AUTHORS: Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner
[DESCRIPTION]
This collection describes the standard procedure for the delivery of plasmids, mRNA or ribonucleoprotein (RNP) into human pluripotent stem cells (hPSCs) usi... | [] |
68,156 | Anthoceros agrestis Bonn (hornwort) transformation v02 | 1 | dx.doi.org/10.17504/protocols.io.kxygxzjydv8j/v1 | https://www.protocols.io/view/anthoceros-agrestis-bonn-hornwort-transformation-v-ces4tegw | Eftychis Frangedakis, Manuel Waller | TITLE: Anthoceros agrestis Bonn (hornwort) transformation v02
AUTHORS: Eftychis Frangedakis, Manuel Waller
[DESCRIPTION]
Anthoceros agrestis Bonn (hornwort) transformation v02
[STEPS]
6. Tissue preparation:
Collect approximately 1 g of thallus tissue grown for 4-6 weeks under low light intensity (approximately... | ["Tissue preparation: \n\nCollect approximately 1 g of thallus tissue grown for 4-6 weeks under low light intensity (approximately 0.1 g of tissue per petri dish - 10 petri dishes in total). Figure1 and Figure 4.1\n\nTransfer the tissue into an empty petri dish, add sterile water until the tissue is covered and fragme... |
50,423 | Determining Protein Concentration of Cell-free Extract | 1 | dx.doi.org/10.17504/protocols.io.bvgxn3xn | https://www.protocols.io/view/determining-protein-concentration-of-cell-free-ext-bvgxn3xn | Weston Kightlinger | TITLE: Determining Protein Concentration of Cell-free Extract
AUTHORS: Weston Kightlinger
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Cell-free protein synthesis reactions require high-quality, active extracts to produce high yields of protein therapeutics, enzymes, antigens, vaccines, and other... | ["[Determining Protein Concentration of Cell-free Extract]\nIn 96 well plate with lid 3370 add of Bradford Reagent to each well.\n250 µl", "[Determining Protein Concentration of Cell-free Extract]\nDilute BSA standards according to the following:", "[Determining Protein Concentration of Cell-free Extract]\nMake a seri... |
28,261 | DNA construct for genetic transformation of the coral symbiotic alga Breviolum sp. | null | dx.doi.org/10.17504/protocols.io.7udhns6 | null | Jun Minagawa | TITLE: DNA construct for genetic transformation of the coral symbiotic alga Breviolum sp.
AUTHORS: Jun Minagawa
[STEPS]
?. | [] |
26,884 | Primer ID MiSeq Library Prep for HIV-1 DR and diversity | null | dx.doi.org/10.17504/protocols.io.6hchb2w | null | Shuntai Zhou | TITLE: Primer ID MiSeq Library Prep for HIV-1 DR and diversity
AUTHORS: Shuntai Zhou
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is the protocol to prepare Primer ID MiSeq sequencing library. Viral RNA was first extracted using QIAamp viral RNA extraction kit. The block of random nucleotid... | ["[Prepare Primer Mix (Optional, only for multiplexed Primer ID library prep)]\nFor multiplexing sequencing, first, prepare Primer Mix.Example (For HIV drug resistance pipeline). ABC1Regions\nDR cDNA primer\nDR F primer\n2PR\nR2614_PID\nF2163AD\n3RT\nR3284_PID11\nF2620_AD\n4INR4752_PID11\nF4383_AD\n5V3\nR7209_PID11V1... |
64,773 | 2-step PCR mixture and conditions (Barcoded-head primers for seqs pooling) | 4 | dx.doi.org/10.17504/protocols.io.j8nlkky3xl5r/v1 | https://www.protocols.io/view/2-step-pcr-mixture-and-conditions-barcoded-head-pr-cbhdsj26 | Yin-Tse Huang, Tsu-Chun Hung | TITLE: 2-step PCR mixture and conditions (Barcoded-head primers for seqs pooling)
AUTHORS: Yin-Tse Huang, Tsu-Chun Hung
[DESCRIPTION]
PCR mixture and condition (2X SUPERGREEN PCR MASTER MIX)
[STEPS]
1. Wear glove, clean up the working bench w. 1% bleach
SECTION: For 1' PCR head-primers
2. Prepare 1' PCR mast... | ["Wear glove, clean up the working bench w. 1% bleach", "[For 1' PCR head-primers] Prepare 1' PCR master mixutre for head-primers (prepare 1.2X of solutions for pipetting error if needed)\n \nPCR mixture for head-primers for each reaction", "[For 1' PCR head-primers] Mix the 1' PCR master mixture gently by pi... |
26,536 | UC Davis - Mouse Model Creation | null | dx.doi.org/10.17504/protocols.io.56gg9bw | null | Kent Lloyd | TITLE: UC Davis - Mouse Model Creation
AUTHORS: Kent Lloyd
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This is a generic protocol for making genetically-altered mouse models for research. Investigators who do not h... | ["Depending on the type of mutant mouse requested, a number of protocols can be used. Investigators should consult with technical assistance staff at the MMPC @ UC Davis to develop their plan for deriving a mutant mouse."] |
103,025 | Shipping live Daphnia | 0 | null | https://www.protocols.io/view/shipping-live-daphnia-dgur3wv6 | Molly Fredericks, Jeffry L. Dudycha, Carla Caceres, Matt Bruner | TITLE: Shipping live Daphnia
AUTHORS: Molly Fredericks, Jeffry L. Dudycha, Carla Caceres, Matt Bruner
[DESCRIPTION]
Background:
Daphnia are small zooplankto... | ["Label 50mL conical/falcon tubes with the species, genotype, and date in which the Daphnia were placed into the tubes.", "Fill up the 50mL conical/falcon tubes with 45ml of filtered lake water or Artificial Daphnia Media (ADaM). Other Daphnia media, such as COMBO, may work.", "Place up to 6 individuals per tube.", "Fe... |
29,379 | Creation of HBSS Wash Buffer | Brusko Lab | null | dx.doi.org/10.17504/protocols.io.8xbhxin | null | Brusko Laboratory, Matthew Brown, Thinzar Pe Myint | TITLE: Creation of HBSS Wash Buffer | Brusko Lab
AUTHORS: Brusko Laboratory, Matthew Brown, Thinzar Pe Myint
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Open a sterile 1 liter (L) Rapid-Flow Sterile Disposable Filter Unit with a 0.2 micrometer (µm) PES Membrane.
?. Remove the lid of the filter flask an... | ["Open a sterile 1 liter (L) Rapid-Flow Sterile Disposable Filter Unit with a 0.2 micrometer (µm) PES Membrane.", "Remove the lid of the filter flask and add of (1x) HBSS to the filter.\n940 ml", "Add a single aliquot of FBS and a aliquot of Penicillin/Streptomycin (Pen/Strep) to the HBSS in the filter system\n50 ... |
76,443 | The annotation pipeline for the genome of a snake | 1 | dx.doi.org/10.17504/protocols.io.4r3l27ez4g1y/v1 | https://www.protocols.io/view/the-annotation-pipeline-for-the-genome-of-a-snake-cnv3ve8n | Boyang Liu, Liangyu Cui, Zhangwen Deng, Yue Ma, Diancheng Yang, Yanan Gong, Yanchun Xu, Shuhui Yang, Song Huang | TITLE: The annotation pipeline for the genome of a snake
AUTHORS: Boyang Liu, Liangyu Cui, Zhangwen Deng, Yue Ma, Diancheng Yang, Yanan Gong, Yanchun Xu, Shuhui Yang, Song Huang
[DESCRIPTION]
Here are detailed methods use for the annotation of various snake genomes.
[STEPS]
SECTION: Repeat annotation_de novo
1. 1) R... | ["[Repeat annotation_de novo] 1) Run RepeatModeler to build a de novo library based on the input assembled genome sequence.\n2) Using the library constructed in step 5 as the database, run RepeatMasker (v. 3.3.0) to find and then classify the repetitive sequences.", "[Repeat annotation_database] Run TRF (v. 4.09), Repe... |
null | null | null | dx.doi.org/10.17504/protocols.io.hnfb5bn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol for isolating environmental DNA from filter membranes is modified from Renshaw et al. 2015.</p>
<p>The room temperature preservation of filtered environmental DNA samples and assimilation into a phenol–chloroform–isoamyl alcohol DNA extraction.</p>
<p>Molecular ... | [] |
28,901 | Western Blot (tank-blot) + Antibody staining | null | dx.doi.org/10.17504/protocols.io.8gdhts6 | null | iGEM Dusseldorf | TITLE: Western Blot (tank-blot) + Antibody staining
AUTHORS: iGEM Dusseldorf
[STEPS]
?. [Western blot]
Create blotting buffer stock containing:100mL 10x SDS running buffer 200mL 100% Methanol700mL H20Fill a tray with blotting buffer
?. [Western blot]
Transfer SDS gel to the blotting buffer
?. [Western blot]
Assemble b... | ["[Western blot]\nCreate blotting buffer stock containing:100mL 10x SDS running buffer 200mL 100% Methanol700mL H20Fill a tray with blotting buffer", "[Western blot]\nTransfer SDS gel to the blotting buffer", "[Western blot]\nAssemble blotting sandwich (take it, soak sponge and place on it, soak filter paper and place ... |
null | null | null | dx.doi.org/10.17504/protocols.io.kp7cvrn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol outlines the preparation of a basic sucrose loading dye 10 X stock solution for gel electrophoresis (DNA/RNA). Orange G runs at approximately 50 bp making this loading dye ideal for small molecular weight polynucleotides. Used mainly as an indicator for approx. ... | [] |
69,317 | NCBI submission protocol for SARS-CoV-2 wastewater data: SRA, BioSample, and BioProject | 1 | dx.doi.org/10.17504/protocols.io.ewov14w27vr2/v8 | https://www.protocols.io/view/ncbi-submission-protocol-for-sars-cov-2-wastewater-cfxdtpi6 | Ruth Timme, Maria Balkey | TITLE: NCBI submission protocol for SARS-CoV-2 wastewater data: SRA, BioSample, and BioProject
AUTHORS: Ruth Timme, Maria Balkey
[DESCRIPTION]
PURPOSE:
This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wa... | ["["Ingredients" to have in place before starting your submissions] Set up a new NCBI submission environment for your lab\n1.1: Create an NCBI user account\n1.2: Set up an NCBI submission user group for your lab\n1.3: Bookmark the link to your Submission Portal\n1.4. Identify or establish new BioProjects (det... |
22,329 | Unroofing mammalian cells for AFM | null | dx.doi.org/10.17504/protocols.io.z2zf8f6 | null | Veronika Cencen | TITLE: Unroofing mammalian cells for AFM
AUTHORS: Veronika Cencen
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS] | [] |
66,216 | Tissue staining for IMC | 4 | null | https://www.protocols.io/view/tissue-staining-for-imc-ccwgsxbw | Santhosh Sivajothi | TITLE: Tissue staining for IMC
AUTHORS: Santhosh Sivajothi
[DESCRIPTION]
FFPE tissue processing for IMC
[STEPS]
1. Warm slide to 60C for 10 mins on a slide heater
2. Dewax the slide in Histoclear for 20 min in the fume hood.
3. Rehydrate the slide in descending grades of ethanol (100%, 95%, 90%, 70%, 50%), 5 min eac... | ["Warm slide to 60C for 10 mins on a slide heater", "Dewax the slide in Histoclear for 20 min in the fume hood.", "Rehydrate the slide in descending grades of ethanol (100%, 95%, 90%, 70%, 50%), 5 min each.", "During rehydration, prepare a coplin jar with 1X antigen retrieval solution and place in pressure cooker to wa... |
94,803 | Stereo-seq cell type abundance analysis | 4 | dx.doi.org/10.17504/protocols.io.14egn3kjzl5d/v1 | https://www.protocols.io/view/stereo-seq-cell-type-abundance-analysis-c8ttzwnn | Peter Kilfeather | TITLE: Stereo-seq cell type abundance analysis
AUTHORS: Peter Kilfeather
[DESCRIPTION]
Stereo-seq cell type abundance analysis from Kilfeather, Khoo et al., 2024
[STEPS]
SECTION: Protocol
1. To test for differential abundance of cell types between age groups, we used mixed effects modelling of associations of single ... | ["[Protocol] To test for differential abundance of cell types between age groups, we used mixed effects modelling of associations of single cells (MASC). MASC tests whether cell type membership of individual cells is influenced by an experimental covariate of interest, while accounting for technical covariates and biol... |
null | null | null | dx.doi.org/10.17504/protocols.io.crzv75 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.imscc6e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Randomized survey study to test whether evidence-based patient information about cancer screening provided upfront to people make them less likely to simply follow a non-evidence-based recommendation of their physician</p>
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.rihd4b6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes how Aiptasia stocks are cared for in the Weis lab. The protocol was last updated in 2018. Most students and postdocs tha have been in the Weis lab have contributed to this protocol in some form or another, and they are too numerous to list.</p>
[BEFOR... | [] |
33,050 | BFM speed recording with back-focal-plane interferometry | 1 | dx.doi.org/10.17504/protocols.io.bch2it8e | https://www.protocols.io/view/bfm-speed-recording-with-back-focal-plane-interfer-bch2it8e | Teuta Pilizota, Ekaterina Krasnopeeva, Jerko Rosko | TITLE: BFM speed recording with back-focal-plane interferometry
AUTHORS: Teuta Pilizota, Ekaterina Krasnopeeva, Jerko Rosko
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The speed of bacterial flagellar motor (BFM) is measured with back-focal-plane interferometry. Heavily attenuated optical trap (... | ["[Preparing the cells]\nGrow cells to the desired OD", "[Preparing the cells]\nTruncate flagellar filaments by passing a bacterial suspension through two syringes with narrow-gauge needles (26 gauge) connected with a plastic tube (“shearing device”) 30-80 times", "[Preparing the slide]\nCoat the surface of the tunnel-... |
24,612 | GG2 - CRISPR-Cas9 episome cloning using red-blue screening for Phaeodactylum tricornutum | null | dx.doi.org/10.17504/protocols.io.4acgsaw | null | Mark Moosburner, Andrew Allen | TITLE: GG2 - CRISPR-Cas9 episome cloning using red-blue screening for Phaeodactylum tricornutum
AUTHORS: Mark Moosburner, Andrew Allen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">To ensure Cas9 activity upon episomal transformation, the 3’ end of the Cas9 coding sequencing was transcriptionally ... | [] |
61,975 | NCBI submission protocol for SARS-CoV-2 wastewater data: SRA, BioSample, and BioProject | 1 | dx.doi.org/10.17504/protocols.io.ewov14w27vr2/v7 | https://www.protocols.io/view/ncbi-submission-protocol-for-sars-cov-2-wastewater-b8rxrv7n | Ruth Timme, Maria Balkey | TITLE: NCBI submission protocol for SARS-CoV-2 wastewater data: SRA, BioSample, and BioProject
AUTHORS: Ruth Timme, Maria Balkey
[DESCRIPTION]
PURPOSE:
This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in ... | ["["Ingredients" to have in place before starting your submissions] Set up a new NCBI submission environment for your lab\n1.1: Create an NCBI user account\n1.2: Set up an NCBI submission user group for your lab\n1.3: Bookmark the link to your Submission Portal\n1.4. Identify or establish new BioProjects (det... |
null | null | null | dx.doi.org/10.17504/protocols.io.nhqdb5w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is for performing CITE-seq and Cell Hashing in parallel. </p>
<p> </p>
<p><strong>CITE-seq: </strong></p>
<p> </p>
<p>Cellular Indexing of Transcriptomes and Epitopes by Sequencing (<a href="https://www.nature.com/articles/nmeth.4380" target="_blank">CITE-seq</a... | [] |
23,618 | Quantitative PCR analysis to assess gene expression changes in hyperglycemic larval zebrafish | null | dx.doi.org/10.17504/protocols.io.3bagiie | null | Sandra Rieger | TITLE: Quantitative PCR analysis to assess gene expression changes in hyperglycemic larval zebrafish
AUTHORS: Sandra Rieger
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block"><span>To assess hyperglycemia in larval zebraf... | ["Preparation of mRNA from larval zebrafish. Pool 10 zebrafish larvae and isolate RNA according to the RNeasy Mini Kit (QIAGEN) manual. Elute final mRNA in 30 μl of RNase-free water.", "Preparation of cDNA from mRNA. Prepare cDNA from isolated mRNA according to the SuperScript®III First-Strand Synthesis System (Life Te... |
30,765 | Pseudorabies virus (PRV) injection into inguinal white adipose tissue | 1 | dx.doi.org/10.17504/protocols.io.baamiac6 | https://www.protocols.io/view/pseudorabies-virus-prv-injection-into-inguinal-whi-baamiac6 | Clara Huesing, Heike Muenzberg, Rui Zhang, Nathan Lee, Emily Qualls-Creekmore, Marie Francois | TITLE: Pseudorabies virus (PRV) injection into inguinal white adipose tissue
AUTHORS: Clara Huesing, Heike Muenzberg, Rui Zhang, Nathan Lee, Emily Qualls-Creekmore, Marie Francois
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We utilize pesudorabies virus (PRV) retrograde tracing in combination wi... | ["[Room preparation]\nTurn on the glass bead sterilizer", "[Room preparation]\nTurn on the two heating pads (stereotaxic platform and designated area for recovery)", "[Room preparation]\nPlace a non-sterile towel on your recovery heating pad and a sterile towel on the stereotaxic platform heating pad", "[Room preparati... |
44,611 | Yeast gDNA extraction | 4 | dx.doi.org/10.17504/protocols.io.bptbmnin | https://www.protocols.io/view/yeast-gdna-extraction-bptbmnin | Joseph Ong | TITLE: Yeast gDNA extraction
AUTHORS: Joseph Ong
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The purpose of this protocol is to describe how to purify genomic (or chromosomal) DNA from yeast. Here, we use </span><span style = "font-style:italic;">Saccharomyces cerevisiae</span><span> strai... | ["[Culturing yeast]\nStreak out yeast from glycerol stock onto YPD and grow at 30 °C for two or three overnights until visible colonies have formed.", "[Culturing yeast]\nSelect 3 separate colonies and grow in 40 mL of YPD (50 g Difco™ YPD dissolved in 1 L of DI water and autoclaved at 120 °C for 15 minutes) in a 50 mL... |
92,353 | Trophoblast Organoid Media (TOM) | 4 | null | https://www.protocols.io/view/trophoblast-organoid-media-tom-c6e9zbh6 | vfarmer | TITLE: Trophoblast Organoid Media (TOM)
AUTHORS: vfarmer
[DESCRIPTION]
Media is also used with flipped TOs. Media can be stored at 4C and used within 1 month.
[STEPS]
SECTION: Recipe
1. In a 50 mL conical add 40 mL of F12/DMEM. Mix in the following components:
SECTION: Recipe
1.1. B27 1 mL
stock is 10X, final is 1X
... | ["[Recipe] In a 50 mL conical add 40 mL of F12/DMEM. Mix in the following components:", "[Recipe] B27 1 mL\n\nstock is 10X, final is 1X\n\nsupplier: ThermoFisher (Gibco), cat#: 17504044", "[Recipe] N-Acetyl-L-Cystine (NAC) 625 µL\n\nstock is 100 mM in H20, final is 1.25 mM\n\nsupplier: Sigma, cat#: A9165", "[Recipe] N2... |
82,331 | Mouse astrocyte territory volume analysis | 3 | dx.doi.org/10.17504/protocols.io.q26g7yoo3gwz/v1 | https://www.protocols.io/view/mouse-astrocyte-territory-volume-analysis-cum3wu8n | Shiyi Wang | TITLE: Mouse astrocyte territory volume analysis
AUTHORS: Shiyi Wang
[DESCRIPTION]
Mouse astrocyte territory volume analysis
[STEPS] | [] |
24,428 | CGAP Human Lung Dissociation - Tissue Stability Study | null | dx.doi.org/10.17504/protocols.io.34kgquw | null | Anna Wilbrey-Clark, Adam Hunter | TITLE: CGAP Human Lung Dissociation - Tissue Stability Study
AUTHORS: Anna Wilbrey-Clark, Adam Hunter
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Cut lung into 1cm x 1cm sections and ensure weight is 0.2-0.5g.
?. Transfer the piece of tissue to a 10cm petri dish and add ~250µl Digestion Medium to cover... | ["Cut lung into 1cm x 1cm sections and ensure weight is 0.2-0.5g.", "Transfer the piece of tissue to a 10cm petri dish and add ~250µl Digestion Medium to cover it. (Digestion medium = DMEM with 1mg/ml collagenase D and 0.1mg/ml DNase I).", "Using two scalpels, chop the piece as finely as possible.", "Add ~2ml of Diges... |
22,494 | The PacBio libraries preparation for the Scapharca broughtonii. | null | dx.doi.org/10.17504/protocols.io.z76f9re | null | Chang-Ming Bai | TITLE: The PacBio libraries preparation for the Scapharca broughtonii.
AUTHORS: Chang-Ming Bai
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is used to outline the process of the PacBio libraries preparation for the </span><span style = "font-style:italic;">Scapharca broughtoni... | ["The genomic DNA was fragmented using a g-TUBE (Covaris, Brighton, UK) to obtain ~20kb frequments, and verified with Agilent Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA, USA).\nThe sizes of the main fragments should >17 Kb.", "End-repair and adaptor-ligation were carried out using SMRTbell Template P... |
35,590 | 384 Well PicoGreen | null | dx.doi.org/10.17504/protocols.io.bezejf3e | null | Allen Institute for Brain Science | TITLE: 384 Well PicoGreen
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Quant-iT™ PicoGreen® dsDNA Assay is used for detection and quantitation of double stranded DNA products. </div><div class = "text-block"><span style = "font-weight:bold;">Note</span><... | [] |
54,948 | Collection of rat vagal tissue samples for TEM imaging | 1 | dx.doi.org/10.17504/protocols.io.bzwcp7aw | https://www.protocols.io/view/collection-of-rat-vagal-tissue-samples-for-tem-ima-bzwcp7aw | Terry Powley, Deborah Jaffey | TITLE: Collection of rat vagal tissue samples for TEM imaging
AUTHORS: Terry Powley, Deborah Jaffey
[DESCRIPTION]
This protocol describes the methods used to generate samples of rat vagus tissue suitable for TEM imaging.
[STEPS]
SECTION: Animals
1.
rats (2–4 months old, male and female) were housed in shoe-box c... | ["[Animals] rats (2–4 months old, male and female) were housed in shoe-box cages with bedding material in an Association for Assessment and Accreditation of Laboratory Animal Care-approved colony room, temperature (22–24°C) and humidity (40%–60%) controlled. The room was maintained on a 12:12 hour light–dark schedule. ... |
79,718 | Neuromelanin quantification in formalin-fixed substantia nigra and locus coeruleus | 4 | dx.doi.org/10.17504/protocols.io.14egn29bpg5d/v1 | https://www.protocols.click/view/neuromelanin-quantification-in-formalin-fixed-subs-cr4ev8te | Dipshay Avi Chand, Miriam Scadeng, Birger Victor Dieriks | TITLE: Neuromelanin quantification in formalin-fixed substantia nigra and locus coeruleus
AUTHORS: Dipshay Avi Chand, Miriam Scadeng, Birger Victor Dieriks
[DESCRIPTION]
There are limited methods for absolute quantification of neuromelanin in brain regions such as the substantia nigra and locus coeruleus. While stereo... | ["[Neuromelanin synthesis] Add 50 mL phosphate buffer, 630 μL dopamine stock solution, 61 μL L-cysteine stock solution, and 250 μL mushroom tyrosinase stock to an Erlenmeyer flask", "[Neuromelanin synthesis] Wrap the flask with aluminium foil and make small holes on top; this protects the reaction from light but allo... |
null | null | null | dx.doi.org/10.17504/protocols.io.ejxbcpn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is the "quick" version of Monarch® PCR & DNA Cleanup Kit (5 μg) Protocol (NEB #T1030). For the full protocol, please click <a href="https://www.neb.com/protocols/2015/11/23/monarch-pcr-and-dna-cleanup-kit-protocol" target="_blank">here</a>.
[BEFORE_START]
Add 4 volumes... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.dpc5iv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol gives a method for prophage induction in marine <em>Synechococcus.<br /><br /></em>Paul, J. H., and M. Weinbauer. 2010. Detection of lysogeny in marine environments, p. 30–33. In S. W. Wilhelm, M. G. Weinbauer, and C. A. Suttle [eds.], Manual of Aquatic Viral Ecolo... | [] |
67,403 | Alpha Extract CBD Oil Canada – Are Any Negative Effects Exist! | 3 | dx.doi.org/10.17504/protocols.io.14egn7dbmv5d/v1 | https://www.protocols.io/view/alpha-extract-cbd-oil-canada-are-any-negative-effe-cd3js8kn | lothairjobin | TITLE: Alpha Extract CBD Oil Canada – Are Any Negative Effects Exist!
AUTHORS: lothairjobin
[DESCRIPTION]
Alpha Extracts CBD Oil
[STEPS] | [] |
99,796 | Aggregated aSyn Dot Blot assay | 1 | dx.doi.org/10.17504/protocols.io.bp2l629x1gqe/v1 | https://www.protocols.io/view/aggregated-asyn-dot-blot-assay-ddpu25nw | rabdelha | TITLE: Aggregated aSyn Dot Blot assay
AUTHORS: rabdelha
[DESCRIPTION]
This protocol details aggregated aSyn Dot Blot assay.
[STEPS]
SECTION: Aggregated aSyn Dot Blot assay
1. Normalize protein samples to equal concentrations between 100 ng-1000 1909 in PBS.
SECTION: Aggregated aSyn Dot Blot assay
2. Carefully spot 1... | ["[Aggregated aSyn Dot Blot assay] Normalize protein samples to equal concentrations between 100 ng-1000 1909 in PBS.", "[Aggregated aSyn Dot Blot assay] Carefully spot 1.5 µL each sample onto dry nitrocellulose ( pores) membrane.", "[Aggregated aSyn Dot Blot assay] Allow moisture to dry for a minute or two.", "[Aggre... |
null | null | null | dx.doi.org/10.17504/protocols.io.erbbd2n | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<strong>Materials</strong><br /><br />1) L broth<br />
<ul>
<li>1.0% Bactro-tryptone</li>
<li>0.5% Bacto-yeast extract</li>
<li>0.5% NaCl</li>
</ul>
After autoclaving, add 1.0 mL of 20% glucose per 100 mL of L broth<br /><br />2) 10mM Tris-HCl, pH 8.0, 50 mM CaCl<sub>2<br /><br /... | [] |
37,915 | UABMC - Norgen Animal Tissue RNA Purification Protocol | 4 | null | https://www.protocols.io/view/uabmc-norgen-animal-tissue-rna-purification-protoc-bg93jz8n | Christopher Willey | TITLE: UABMC - Norgen Animal Tissue RNA Purification Protocol
AUTHORS: Christopher Willey
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Purpose</span></div><div class = "text-block">This procedure describes the purification of RNA from snap frozen animal tissues f... | ["[CELL LYSATE PREPARATION]\nExcise the tissue sample from the animal.", "[CELL LYSATE PREPARATION]\nDetermine the amount of tissue by weighing.", "[CELL LYSATE PREPARATION]\nTransfer the tissue into a mortar that contains an appropriate amount of liquid nitrogen to cover the sample. Grind the tissue thoroughly using a... |
28,294 | DRBUDDI for MRI Processing | null | dx.doi.org/10.17504/protocols.io.7vehn3e | null | Courtney Comrie | TITLE: DRBUDDI for MRI Processing
AUTHORS: Courtney Comrie
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol will provide a basic guide to utilizing the DRBUDDI tool in TORTIOSE.</div><div class = "text-block">Note: Steps may vary based upon image.</div></div>
[STEPS]
?. [Introduction]
... | ["[Introduction]\nDRBUDDI is a EPI distortion correction module in TORTOISE. It bases its corrections by using DTI data pairs (blip up and blip down). When processing MR images DRBUDDI is usually the second step in the pipeline.", "[DRBUDDI]\nIn terminal go to your directory with the DTI data.", "[DRBUDDI]\nType the fo... |
68,488 | Expression and purification of recombinant UvsX recombinase | 1 | dx.doi.org/10.17504/protocols.io.5qpvobemdl4o/v1 | https://www.protocols.io/view/expression-and-purification-of-recombinant-uvsx-re-ce5gtg3w | lucero.merino.c, lucero.mascaro.r | TITLE: Expression and purification of recombinant UvsX recombinase
AUTHORS: lucero.merino.c, lucero.mascaro.r
[DESCRIPTION]
The UvsX is a enzyme that is part for an isothermal DNA amplification based on the recombination process, the RPA reaction.
RPA uses 4 enzymes: UvsX, UvsY, Bsu and Gp32. It's an isothermal ampli... | ["[DAY1: Transformation of competent cells] Quantify the plasmid containing the UvsX recombinase gene and determine the volume that contains 100 ng of the plasmid.", "[DAY1: Transformation of competent cells] Add the resuspension to a LB agar plate with 0.05 mg/mL and spread the recently transformed cells. Incubate pl... |
null | null | null | dx.doi.org/10.17504/protocols.io.hpdb5i6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
60,954 | Coverage of open citations in DOAJ journals | 1 | dx.doi.org/10.17504/protocols.io.n92ldz598v5b/v2 | https://www.protocols.io/view/coverage-of-open-citations-in-doaj-journals-b7r2rm8e | Constance Dami, Alessandro Bertozzi, Chiara Manca, Umut Kucuk | TITLE: Coverage of open citations in DOAJ journals
AUTHORS: Constance Dami, Alessandro Bertozzi, Chiara Manca, Umut Kucuk
[DESCRIPTION]
This is the protocol for the research of the coverage of open citations in DOAJ journals.
Our goal is to find out:
about the coverage of articles from open access journals in DOA... | ["[Data Gathering] We download from the DOAJ Public data dump the article metadata in JSON format in order to collect all the article DOIs in DOAJ (doaj_articles_data.json). Then we open the file inside the python script, as indicated in the code below:\n\n \n\nOnce we have obtained the JSON file, we establish a connec... |
76,622 | Isolation and Culture of Mouse Cortical Neurons | 4 | dx.doi.org/10.17504/protocols.io.x54v9dwezg3e/v1 | https://www.protocols.io/view/isolation-and-culture-of-mouse-cortical-neurons-cn3nvgme | Ashley V Kumar, Patricia Montilla-Perez, Francesca Telese | TITLE: Isolation and Culture of Mouse Cortical Neurons
AUTHORS: Ashley V Kumar, Patricia Montilla-Perez, Francesca Telese
[DESCRIPTION]
We provide a detailed protocol to isolate and culture primary cortical neurons from the cortex of mice at embryonic day 15.5.
[BEFORE_START]
Coat 10cm dishes with Poly-D-Lysine .... | ["[Tissue Dissection] Collect the embryos in a 10 cm Petri dish with ice-cold HBSS-G and cut the heads. Keep the Petri dish on ice while dissecting.", "[Tissue Dissection] Using a microscope, insert the tip of tweezers into the eyes to keep the head fixed, cut up from the cranial floor to the nose, open the skull like... |
88,115 | 603.3 & 604.5_URMC_HTC_Lung and Lobe Processing for SenNet | 4 | dx.doi.org/10.17504/protocols.io.n2bvj395plk5/v1 | https://www.protocols.io/view/603-3-amp-604-5-urmc-htc-lung-and-lobe-processing-c2atyaen | Gloria S Pryhuber, Heidie Huyck | TITLE: 603.3 & 604.5_URMC_HTC_Lung and Lobe Processing for SenNet
AUTHORS: Gloria S Pryhuber, Heidie Huyck
[DESCRIPTION]
Purpose and Scope of the Procedure
Standardize process for processing lung donations into components for storage and distribution
Scope: coordination of receipt and gross dissection of tis... | ["Assemble Team and Materials as needed for processing, to accomplish:\n i.CT Scan\n ii.Separation of Lobes\n iii.Tissue Dissociation\n iv.Formalin Inflation\n v.OCT /CMC Inflation\n vi.Paraformaldehyde Inflation", "Record details of procedures in Worksheets.", "[Unpacking] Shipped package is opened o... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.