id float64 1.55k 110k ⌀ | title stringlengths 1 256 ⌀ | template_id float64 0 6 ⌀ | doi stringlengths 39 49 ⌀ | url stringlengths 40 92 ⌀ | authors stringlengths 1 933 ⌀ | protocol_text stringlengths 34 1.08M | steps_list stringlengths 2 269k |
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103,472 | Quantification of Proteins and Genes Associated with Endothelial Cell Function after Different Shear Stress Intensities in vitro | 1 | dx.doi.org/10.17504/protocols.io.ewov1q34kgr2/v2 | https://www.protocols.io/view/quantification-of-proteins-and-genes-associated-wi-dhaq32dw | Daniel Conde, Mario Garcia, Manuel Gomez, Alvaro Gurovich | TITLE: Quantification of Proteins and Genes Associated with Endothelial Cell Function after Different Shear Stress Intensities in vitro
AUTHORS: Daniel Conde, Mario Garcia, Manuel Gomez, Alvaro Gurovich
[DESCRIPTION]
This protocol describes the steps necessary to culture human umbilical vein endothelial cells (HUVEC),... | ["[Huvec Cell Seeding] Notes: This step aims to increase the number of HUVEC in a T-75 flask before seeding them in an Ibidi µ-Slide I Luer with a channel height of 0.2 mm. The following procedures must be performed inside a biosafety cabinet with HEPA-filtered laminar flow. To avoid contamination inside the biosafety ... |
48,537 | Cocaine IV Self-Administration | 1 | null | https://www.protocols.io/view/cocaine-iv-self-administration-btmznk76 | Lani Tieu, Brent Boomhower, Molly Brennan, McKenzie Pavlich, Giordano De Guglielmo, Olivier George | TITLE: Cocaine IV Self-Administration
AUTHORS: Lani Tieu, Brent Boomhower, Molly Brennan, McKenzie Pavlich, Giordano De Guglielmo, Olivier George
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the procedure of conducting intravenous cocaine self-administration for the GWAS... | ["[Session Setup]\nBring animals to the experimentation room where you will run self-administration.", "[Session Setup]\nPick up the animal from its cage and place it in operant chamber.", "[Session Setup]\nWith a microchip reader, scan RFID on the chamber door then scan the rat. Animals must be scanned each test day t... |
87,783 | Spectrum Data Plotter: web based violin, box, dot, and average with error overlaid rich data plots | 5 | dx.doi.org/10.17504/protocols.io.n92ldmr5nl5b/v1 | https://www.protocols.io/view/spectrum-data-plotter-web-based-violin-box-dot-and-czyfx7tn | Joe R Delaney | TITLE: Spectrum Data Plotter: web based violin, box, dot, and average with error overlaid rich data plots
AUTHORS: Joe R Delaney
[DESCRIPTION]
Data scientists have been releasing advanced graphical tools in R packages for many years. Unfortunately, individuals with no coding knowledge are unable to access such tools. ... | ["[Background and use cases] Quick link to tool:\nhttps://delaney.shinyapps.io/Spectrum_Data_Plotter/\n\nInterpretation of data via rich plots is almost as important as the data itself for the advancement of science. As big data becomes more prevalent in scientific studies, there is a diverse need of graphical outputs ... |
26,554 | U Michigan - Mesangial matrix evalutaion | null | dx.doi.org/10.17504/protocols.io.562g9ge | null | Jeff Hodgin, Jharna Saha | TITLE: U Michigan - Mesangial matrix evalutaion
AUTHORS: Jeff Hodgin, Jharna Saha
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Periodic acid-Schiff (PAS) is a staining method used to detect glycogen on formalin-fixe... | ["[Protocol 1: PERIODIC ACID SCHIFF (PAS) STAINING]\n1. Wash 2x 4 minutes in Xylene. 2. Wash in 100% EtOH 2x minutes 3. Wash in 95% EtOH 1x 2minutes. 4. Wash in 70% EtOH 1x 2minutes 5. Rinse in dH2O. 6. Incubate in 0.5% Periodic Acid solution for 5min. 7. Rinse 3x in dH2O. 8. Incubate in Schiff’s reagent for 15minute... |
46,726 | Intracellular Accumulation of HiLyte-488-Aβ42 in DU145 and DU145-TXR Cells | 4 | dx.doi.org/10.17504/protocols.io.brvem63e | https://www.protocols.io/view/intracellular-accumulation-of-hilyte-488-a-42-in-d-brvem63e | Lauren Ammerman | TITLE: Intracellular Accumulation of HiLyte-488-Aβ42 in DU145 and DU145-TXR Cells
AUTHORS: Lauren Ammerman
[DESCRIPTION]
Protocol to facilitate the imaging, and subsequent quantification, of the intracellular accumulation of HiLyte-488-Aβ42 in two cell lines - DU145 (paclitaxel sensitive, non-P-gp-overexpressing hum... | ["[Preparation] Prepare Coverslips and 24-well Plate.\n\nnotes - we chose 24-well plates because the wells were big enough to fit our circular coverglasses. This experiment could be done with larger plates; volumes/solutions should be scaled accordingly. Procedures should be performed in a Cell Culture Hood.\n\nSterili... |
107,434 | Low-cost Tagmentation Library Prep for low-coverage Illumina sequencing | 0 | dx.doi.org/10.17504/protocols.io.6qpvr8zrplmk/v1 | https://www.protocols.io/view/low-cost-tagmentation-library-prep-for-low-coverag-dk6i4zce | Matthew Farnitano, Andrea Sweigart | TITLE: Low-cost Tagmentation Library Prep for low-coverage Illumina sequencing
AUTHORS: Matthew Farnitano, Andrea Sweigart
[DESCRIPTION]
Tagmentation is a popular approach for preparing Illumina sequencing libraries, but kits can be pricey. Using a bulk-prepped and pre-loaded Tn5 tagmentation enzyme, this protocol is ... | ["[Before you start] Obtain Tn5 tagmentation enzyme, pre-loaded with universal adapter sequences. Enzyme purification and loading guidelines are not provided here: see reference Lu et al. (2017).", "[Before you start] Quantify input DNA. We recommend 96-well fluorescence quantification with a plate reader and a kit suc... |
null | null | null | dx.doi.org/10.17504/protocols.io.uquevww | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
M2 medium for co-culturing Cyanobacteria, such as S. elongtatus, together with heterotrophic bacteria
Slighly modified from:
Weiss, Taylor L., Eric J. Young, and Daniel C. Ducat. "A synthetic, light-driven consortium of cyanobacteria and heterotrophic bacteria enables stabl... | ["[Ingredients] {\"blocks\":[{\"key\":\"eotso\",\"text\":\"Add 10 ml 100x M2 (https:\\/\\/www.protocols.io\\/view\\/100x-m2-medium-uqnevve)\\n\\n\\n\\n\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[{\"offset\":19,\"length\":52,\"key\":0}],\"data\":[]}],\"entityMap\":[{\"type\":\"link\",... |
20,139 | Processing Bulk Calling Card Sequencing Data | null | dx.doi.org/10.17504/protocols.io.xwjfpcn | null | Arnav Moudgil, Rob Mitra | TITLE: Processing Bulk Calling Card Sequencing Data
AUTHORS: Arnav Moudgil, Rob Mitra
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Here we present a computational pipeline for processing bulk RNA calling card data. These data will have been generated from transfection/-duction of either und... | ["[Preamble]\nTo illustrate the workflow, let's say that we have performed bulk RNA calling cards on our favorite transcription factor (YFTF) in a human cell line. We have prepared libraries from 10 biological replicates of cells transfected with wild-type piggyBac transposase, and 10 replicates of cells with YFTF-pigg... |
null | null | null | dx.doi.org/10.17504/protocols.io.isxcefn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is the correct protocol if you are using the C2987H cells. If you are using the C2987I cells, please refer to <a href="http://protocols.io/view/High-Efficiency-Transformation-Protocol-C2987I-imst35" target="_blank">this protocol</a>.
[GUIDELINES]
<strong>Transfor... | [] |
69,922 | Rat brain processing for histological analyses (update) | 4 | dx.doi.org/10.17504/protocols.io.e6nvwj61wlmk/v2 | https://www.protocols.io/view/rat-brain-processing-for-histological-analyses-upd-cgiatuae | miquel.vila | TITLE: Rat brain processing for histological analyses (update)
AUTHORS: miquel.vila
[DESCRIPTION]
Protocol for rat brain processing in order to perform histological analyses
[STEPS]
SECTION: Rat perfusion
1. Deeply anesthetize animals with sodium pentobarbital (50 mg/kg, i.p.)
SECTION: Rat perfusion
2. Perfuse throug... | ["[Rat perfusion] Deeply anesthetize animals with sodium pentobarbital (50 mg/kg, i.p.)", "[Rat perfusion] Perfuse through the left ventricle with saline [0.9% (wt/vol)] at room temperature (RT)", "[Rat perfusion] Perfuse again with ice-cold formaldehyde solution 4% in PBS buffered for histology", "[Postfixation] Remov... |
105,223 | Animal Care Protocol: Streblospio benedicti | 0 | dx.doi.org/10.17504/protocols.io.eq2lyw24wvx9/v1 | https://www.protocols.io/view/animal-care-protocol-streblospio-benedicti-dizf4f3n | Kayleigh McHugh | TITLE: Animal Care Protocol: Streblospio benedicti
AUTHORS: Kayleigh McHugh
[DESCRIPTION]
This protocol describes how to collect and care for Streblospio benedicti. This protocol outlines best practices for sample collection, adult worm care, crossing worms, and raising worm larvae to adults. Additionally, we have inf... | [] |
91,651 | CRISPRi tiling screens | 4 | null | https://www.protocols.io/view/crispri-tiling-screens-c5rby52n | Andrea R Daniel | TITLE: CRISPRi tiling screens
AUTHORS: Andrea R Daniel
[DESCRIPTION]
This protocols describes methods for characterizing the activity of dSaCas9 as a repressor using promoter tiling guide RNA screens in primary human T cells.
[STEPS]
SECTION: Primary human CD8+ T cell cultures
1. Isolated CD8+ T cells from individua... | ["[Primary human CD8+ T cell cultures] Isolated CD8+ T cells from individual donors were obtianed directly from vials purchased from StemCell Technologies.", "[Primary human CD8+ T cell cultures] Culture T cells were in PRIME-XV T cell Expansion XSFM (FujiFilm) supplemented with 5% human platelet lysate (Compass Biomed... |
86,893 | HiChIP Protocol using Arima-HiC+ Kits | 4 | dx.doi.org/10.17504/protocols.io.ewov1qq67gr2/v1 | https://www.protocols.io/view/hichip-protocol-using-arima-hic-kits-cy4mxyu6 | Anthony Schmitt, Jon Belton, Sara Tin, Jonathan Kirkland, Derek Reid, Xiang Zhou | TITLE: HiChIP Protocol using Arima-HiC+ Kits
AUTHORS: Anthony Schmitt, Jon Belton, Sara Tin, Jonathan Kirkland, Derek Reid, Xiang Zhou
[DESCRIPTION]
HiChIP Workflow Overview
HiChIP is an experimental workflow that captures the structure (three-dimensional conformation) of genomes associated with a protein of interest.... | ["[Crosslinking – Cell Culture] Input: Cells collected from cell culture\nOutput: Crosslinked cells\n\nBefore you begin: This HiChIP workflow for mammalian cell lines begins with harvesting and crosslinking 12-15 million mammalian cells per biological replicate. Each reaction should only contain crosslinked cells comp... |
17,042 | ChroSpin - ProteinA | null | dx.doi.org/10.17504/protocols.io.uvsew6e | null | David Frommholz, Alexandra Ehl, Nadine Stefanczyk | TITLE: ChroSpin - ProteinA
AUTHORS: David Frommholz, Alexandra Ehl, Nadine Stefanczyk
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Purification Guide for the Isolation of Antibodies with ChroSpin Columns by DALEX Biotech.</span></div><div class = "text-block">Eas... | ["[Load and Wash]\nAdd up to 500 µl sample to the top of the column and incubate the column with end-over-end mixing or occasional inversion for 3 minutes.\nFor fast binding antibodies the incubation time can be decreased to 30 seconds. For slow binding antibodies the incubation time can be increased to 10 minutes. Lon... |
21,198 | Loop and uLoop assembly | null | dx.doi.org/10.17504/protocols.io.yxnfxme | null | Bernardo Pollak | TITLE: Loop and uLoop assembly
AUTHORS: Bernardo Pollak
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is used for performing Type IIS assembly by either </span><span style = "font-style:italic;">BsaI</span><span> or </span><span style = "font-style:italic;">SapI</span><span>-me... | ["[Calculate plasmid target concentrations ]\nThe required concentration for each donor part in ng/μL is plasmid length / 100. That will yield a concentration of 15 fmol/µL. For the receiver plasmid the target concentration is length / 200, yielding 7.5 fmol/µL.", "[Prepare DNA mixture]\nAdd into a PCR tube:1 µL of eac... |
5,340 | Immunoflourescent assay | null | dx.doi.org/10.17504/protocols.io.hf4b3qw | null | Binnypreet Kaur1, 2 , Drahomíra Faktorová1, 2, Priscila Peña-Diaz1 and Julius Lukeš1, 2 | TITLE: Immunoflourescent assay
AUTHORS: Binnypreet Kaur1, 2 , Drahomíra Faktorová1, 2, Priscila Peña-Diaz1 and Julius Lukeš1, 2
[STEPS]
?. Store it in dark at 4°C until use
?. Preferably night before, make 4% paraformaldehyde (w/v) in PBS and incubate O/N at 37°C
?.
?. Spin down the cells 3000RPM for 2min and disca... | ["Store it in dark at 4°C until use", "Preferably night before, make 4% paraformaldehyde (w/v) in PBS and incubate O/N at 37°C", "Spin down the cells 3000RPM for 2min and discard the supernatant in formaldehyde waste", "Mix the pellet with 500ul of fixer in the hood and incubate the slides for 10min in humid dark chamb... |
null | null | null | dx.doi.org/10.17504/protocols.io.qeidtce | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This Real-Time PCR genotyping protocol can be used for the detection of polymorphisms at codons 146 (N/S/D), 211 (R/Q) and 222 (Q/K) in the caprine <em>PRNP</em> gene. We developed four seperate Real-Time PCR reactions with four different Custom TaqMan<sup>® </sup>SNP Genotyp... | [] |
94,680 | Generating Ct cut-off values using gBlocks gene fragments | 4 | null | https://www.protocols.io/view/generating-ct-cut-off-values-using-gblocks-gene-fr-c8pyzvpw | Dilip Abraham, Nick Grassly, Catherine Troman, Jonathan Rigby | TITLE: Generating Ct cut-off values using gBlocks gene fragments
AUTHORS: Dilip Abraham, Nick Grassly, Catherine Troman, Jonathan Rigby
[DESCRIPTION]
The following protocol describes the resuspension, dilution, and qPCR of gBlocks gene fragments. gBlocks gene fragments are synthesised double stranded DNA oligos, which... | ["[g-blocks details] gBlocks gene fragments are synthesised double stranded DNA fragments which contain the sequence for the amplicon of interest, in this case for ttr, staG and tviB in S.Typhi, and HF183 bacteroides.", "[Resuspending and diluting the gblocks] gBlocks are supplied as a lyophilised pellet. Resuspend in ... |
20,511 | Mammalian Cell Staining | null | dx.doi.org/10.17504/protocols.io.x97fr9n | null | Kenneth Schackart | TITLE: Mammalian Cell Staining
AUTHORS: Kenneth Schackart
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details how to stain mammalian cells cultured on a 96-well plate. Actin filaments, focal adhesion sites (as indicated by the presence of vinculin), and nuclei will be stained.</div... | ["[Fix the cells]\nRemove cell culture media.\nYou may wash twice with DPBS at this point.", "[Perforate cell membrane]\nRemove paraformaldehyde solution.", "[Block unspecific binding]\nRemove Triton X-100.", "[Stain actin filaments and focal adhesion sites]\nAdd FITC:TRITC solution\n100 µl", "[Bind anti-vinculin to vi... |
null | null | null | dx.doi.org/10.17504/protocols.io.rfgd3jw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The protein encoded by this gene is proteolytically processed to release a secreted peptide termed endothelin 1. This peptide is a potent vasoconstrictor and is produced by vascular endothelial cells. Endothelin 1 also can affect the central nervous system. Two transcript var... | [] |
26,737 | SPARC - Chronic implantation of gastrointestinal and vagus nerve electrodes in the ferret | null | dx.doi.org/10.17504/protocols.io.6crhav6 | null | Charles C. Horn, Derek M. Miller, Stephanie Fulton, Bill J. Yates, Lee E. Fisher, Ameya C. Nanivadekar | TITLE: SPARC - Chronic implantation of gastrointestinal and vagus nerve electrodes in the ferret
AUTHORS: Charles C. Horn, Derek M. Miller, Stephanie Fulton, Bill J. Yates, Lee E. Fisher, Ameya C. Nanivadekar
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to surgically implant... | ["[Preparation: Before first incision]\nInduce anesthesia with 20mg/kg ketamine (i.m.).", "[First incisions and Tunneling]\nMake incisions in skin on the abdomenal midline (~4 cm) and dorsal neck (~3 cm).", "[First incisions and Tunneling]\nUse a trocar to tunnel under skin from the dorsal neck, along the back, and to ... |
53,125 | Plant contig clustering based assembly (PLCL) pipeline: an efficient long-read assembly tool for plant chloroplast and mitochondrial genomes | 5 | dx.doi.org/10.17504/protocols.io.bx5dpq26 | https://www.protocols.io/view/plant-contig-clustering-based-assembly-plcl-pipeli-bx5dpq26 | Kanae Nishii | TITLE: Plant contig clustering based assembly (PLCL) pipeline: an efficient long-read assembly tool for plant chloroplast and mitochondrial genomes
AUTHORS: Kanae Nishii
[DESCRIPTION]
Third generation NGS long-read sequences become popular for draft genome assembly. Here, we developed an efficient plant chloroplast a... | ["[Pre-starting PLCL pipeline] Download data for Arabidopsis thaliana from NCBI and check their read quality.", "[Pre-starting PLCL pipeline] Quality checking ONT reads with NanoPlot and visualize read length distribution using R ggplot2", "[Pre-starting PLCL pipeline] Download ONT reads", "[Pre-starting PLCL pipeline]... |
88,753 | OSU TriState SenNet Processing and Storing of Normal Donor Lungs | 1 | dx.doi.org/10.17504/protocols.io.8epv5xe16g1b/v1 | https://www.protocols.io/view/osu-tristate-sennet-processing-and-storing-of-norm-c2wryfd6 | Sean D. Stacey, Brenda F. Reader, Lorena Rosas, Victor Peters, Ana L. Mora, mauricio.rojas | TITLE: OSU TriState SenNet Processing and Storing of Normal Donor Lungs
AUTHORS: Sean D. Stacey, Brenda F. Reader, Lorena Rosas, Victor Peters, Ana L. Mora, mauricio.rojas
[DESCRIPTION]
This protocol describes the processing and storing of normal donor lungs by the Comprehensive Transplant Center (CTC) Human Tissue Bi... | ["[Objective] To preserve lung tissue for further downstream cellular, protein, RNA, or DNA analyses.", "[Preparation]", "[Preparation] In the biosafety cell culture hood, place three underpads and all needed equipment, including biohazard receptacles, surgical kits, and specimen holders. Before beginning, check that a... |
95,155 | Catalepsy test in rats | 1 | dx.doi.org/10.17504/protocols.io.q26g7p24kgwz/v1 | https://www.protocols.io/view/catalepsy-test-in-rats-c86tzzen | eduard.bentea, María Sanchiz Calvo, Veerle Baekelandt | TITLE: Catalepsy test in rats
AUTHORS: eduard.bentea, María Sanchiz Calvo, Veerle Baekelandt
[DESCRIPTION]
Protocol for performing the catalepsy bar test in rats. This test evaluates muscular rigidity, and can be used in rat models with motor deficits, such as models of Parkison's disease.
[STEPS]
SECTION: Test
1. Br... | ["[Test] Bring cages to the behavioral room for at least 60 min prior to the test for habituation", "[Test] Place both forepaws of the rat on an horizontal bar elevated so that the rat is in an half rearing position", "[Test] Measure the descent latency, defined as the time it takes for both forepaws to be removed from... |
67,418 | Growth Matrix Male Enhancement Reviews! | 3 | dx.doi.org/10.17504/protocols.io.36wgq7w95vk5/v1 | https://www.protocols.io/view/growth-matrix-male-enhancement-reviews-cd32s8qe | Growth Matrix Male Enhancement | TITLE: Growth Matrix Male Enhancement Reviews!
AUTHORS: Growth Matrix Male Enhancement
[DESCRIPTION]
MUST SEE: (SPECIAL SAVINGS) Click Here to Get Growth Matrix Male Enhancement For an Exclusive Discounted Price
[STEPS] | [] |
37,109 | Viral RNA extraction low-cost protocol optimized for SARS-Cov2 at AGROSAVIA | null | dx.doi.org/10.17504/protocols.io.bggvjtw6 | https://www.protocols.io/view/viral-rna-extraction-low-cost-protocol-optimized-f-bggvjtw6 | Alejandro Caro-Quintero, Roxana Yockteng | TITLE: Viral RNA extraction low-cost protocol optimized for SARS-Cov2 at AGROSAVIA
AUTHORS: Alejandro Caro-Quintero, Roxana Yockteng
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Here we present the second version of an RNA extraction protocol for SARs-cov2 using magnetic beads. This protocol w... | ["Pre-processing of mucous samples.", "Dilute of the sample in of Saline Solution [, vortex mix . Use only of this dilution to star protocol. In step 2.3 add isopropanol after incubation.\n100 µl\n300 µl\n100 µl\n540 µl", "Sample Processing (in 1.5 ml tubes)", "To of GITC buffer add of Proteinase K ], of the sample... |
null | null | null | dx.doi.org/10.17504/protocols.io.jmick4e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>1) DNA was extracted from blood samples at DNA Chip Research Inc.</p>
<p>2) SNP genotyping: using the DigiTag2 assay.</p>
[STEPS]
?.
?. | [] |
85,794 | KAPP-Sen TMC: Dissociation of Pancreatic Islets (recovered) | 1 | dx.doi.org/10.17504/protocols.io.x54v9pyq4g3e/v1 | https://www.protocols.io/view/kapp-sen-tmc-dissociation-of-pancreatic-islets-rec-cx2axqae | Juliana Alcoforado Diniz, Jessica Garofalo, Dylan Baker, Paul Robson | TITLE: KAPP-Sen TMC: Dissociation of Pancreatic Islets (recovered)
AUTHORS: Juliana Alcoforado Diniz, Jessica Garofalo, Dylan Baker, Paul Robson
[DESCRIPTION]
The dispersed samples were shipped cold from PRODOLABS. Prior to scRNA-seq dispersed samples from brain dead donor’s pancreatic islets were recovered and dissoc... | ["[Cell Dissociation with Accutase]", "[Fixation of Cells & Nuclei for Chromium Fixed RNA Profiling] Cells were fixated prior to scRNAseq according to https://dx.doi.org/10.17504/protocols.io.x54v9py5zg3e/v1", "[Cell Dissociation with Accutase] Transfer cell suspension of pure islets to a new 50ml tube. Use additio... |
19,135 | EIT data aquisition in rat sciatic nerve using stimulation of tibial and peroneal branches | null | dx.doi.org/10.17504/protocols.io.ww7ffhn | null | Kirill Aristovich, Matteo Donega, David Holder | TITLE: EIT data aquisition in rat sciatic nerve using stimulation of tibial and peroneal branches
AUTHORS: Kirill Aristovich, Matteo Donega, David Holder
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">High-level protocol to obtain the EIT imaging dataset and reconstruct images for the paper.</div><... | ["[Hardware]\nPrepare nessesary hardware:", "[Neural Interface]\nPrepare neural interface:Follow the instructions in teh paper http://iopscience.iop.org/article/10.1088/1741-2552/aae868\nSome of the chemical components are toxicChemical hood cabinet is required", "[Software]", "[Animal Preparation]\nSprague-Dawley adul... |
106,533 | AAV Production Protocol | 0 | dx.doi.org/10.17504/protocols.io.81wgbzwj3gpk/v1 | https://www.protocols.io/view/aav-production-protocol-dkad4sa6 | Benjamin David Webster Belfort | TITLE: AAV Production Protocol
AUTHORS: Benjamin David Webster Belfort
[DESCRIPTION]
Protocol for the production of adeno-associated viruses by the Arenkiel Lab of Team Schlossmacher.
[STEPS]
SECTION: AAV Production Protocol
1.
SECTION: AAV Production Protocol
2. AAV Production
SECTION: AAV Production Protocol
3. A... | ["[AAV Production Protocol]", "[AAV Production Protocol] AAV Production", "[AAV Production Protocol] All AAVs were packaged in-house by the Texas Children’s Hospital Jan and Dan Duncan Neurological Research Institute’s Neuroconnectivity Core, as described below.", "[AAV Production Protocol] Cell Culture and Transfectio... |
null | null | null | dx.doi.org/10.17504/protocols.io.c48yzv | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
This protocol describes conditions using either ABI reagents or PGC Scientific Reagents. The reactions have been tested on the gradient Eppendorf, the Gene Techne and the ABI 9700 thermal cyclers and all machines use the same cycling conditions.<br /><br />When testing plasmid DN... | [] |
22,143 | 1. RNA isolation for tissue | null | dx.doi.org/10.17504/protocols.io.zu7f6zn | null | Sze-Xian Lim, Chin Yee Tan | TITLE: 1. RNA isolation for tissue
AUTHORS: Sze-Xian Lim, Chin Yee Tan
[STEPS]
?. Homogenization in TriZolAdd 1mL of Trizol reagent per 30mg of tissue and homogenize using handheld homogenizer
?. Incubate at RT for 5 mins to allow nucleoprotein complexes to dissociate
?. Spin down at max speed, chilled centrifuge for ... | ["Homogenization in TriZolAdd 1mL of Trizol reagent per 30mg of tissue and homogenize using handheld homogenizer", "Incubate at RT for 5 mins to allow nucleoprotein complexes to dissociate", "Spin down at max speed, chilled centrifuge for 15 minutes", "Carefully remove the top aqueous phase and transfer to a new Eppend... |
68,273 | Post-Surgical Dissection of Ovaries | 4 | dx.doi.org/10.17504/protocols.io.j8nlkkzn1l5r/v1 | https://www.protocols.io/view/post-surgical-dissection-of-ovaries-cewrtfd6 | Stephen Fisher, Marielena Grijalva, Rong Guo, sarahjoh, Hieu Nguyen, John Renz, Jean G Rosario, Steven Rudich, Brian Gregory, Junhyong Kim, Kate O'Neill | TITLE: Post-Surgical Dissection of Ovaries
AUTHORS: Stephen Fisher, Marielena Grijalva, Rong Guo, sarahjoh, Hieu Nguyen, John Renz, Jean G Rosario, Steven Rudich, Brian Gregory, Junhyong Kim, Kate O'Neill
[DESCRIPTION]
This protocol details dissection of the ovaries in preparation for 10X Visium, 10X Multiomics, patho... | ["Receive excised female reproductive system on ice en bloc. Orient the specimen with the anterior aspect of the uterus facing up based on presence of vesicouterine reflection.", "Using a disposable scalpel, incise the mesovarium. Orient ovary with the uteroovarian ligament on the right, infundibulopelvic ligament on t... |
83,099 | DNA extraction (BOMB) | 4 | dx.doi.org/10.17504/protocols.io.n2bvj6mdnlk5/v5 | https://www.protocols.click/view/dna-extraction-bomb-cvd3w28n | Yin-Tse Huang, Tsu-Chun Hung | TITLE: DNA extraction (BOMB)
AUTHORS: Yin-Tse Huang, Tsu-Chun Hung
[DESCRIPTION]
DNA extraction (BOMB)
[STEPS]
SECTION: Sample Collection
1. Add 200 µL of 0.5 mm beads to 2mL screw tube
SECTION: Sample Collection
2. Add200 µL of 1 mm beads to 2mL screw tube
SECTION: Sample Collection
3. Add870 µL Lysis master m... | ["[Sample Collection] Add 200 µL of 0.5 mm beads to 2mL screw tube", "[Sample Collection] Add200 µL of 1 mm beads to 2mL screw tube", "[Sample Collection] Add870 µL Lysis master mix to 2mL screw tube. The final look:", "[Sample Collection] Collect 20-50 mg of sample to 2mL screw tube", "[Sample crush] Put the 2mL screw... |
41,178 | manu | 1 | dx.doi.org/10.17504/protocols.io.bkf2ktqe | https://www.protocols.io/view/manu-bkf2ktqe | Monica Hassan | TITLE: manu
AUTHORS: Monica Hassan
[STEPS]
?. | [] |
50,279 | Coral Lipid Assay for 96-well plates | 1 | dx.doi.org/10.17504/protocols.io.bvcfn2tn | https://www.protocols.io/view/coral-lipid-assay-for-96-well-plates-bvcfn2tn | Colleen Bove, Justin Baumann | TITLE: Coral Lipid Assay for 96-well plates
AUTHORS: Colleen Bove, Justin Baumann
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is designed to work with coral host tissue slurry that has been processed by airbrushing to remove the tissue from the skeleton and after removal of symbion... | ["[Lipid Extraction]\nPull samples from -80 freezer and allow to thaw (maximum of 24 samples per plate in triplicate)", "[Lipid Extraction]\nVortex sample and transfer 600 μL of coral tissue slurry sample to labelled 1.5 mL tube", "[Lipid Extraction]\nPre-make new 2:1 (CHCl3:CH3OH) stock every day running plates", "[Li... |
null | null | null | dx.doi.org/10.17504/protocols.io.f5ibq4e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 19">
<div class="section">
<div class="layoutArea">
<div class="column">
<p>The ISOLATE II Biofluids RNA Kit isolates total RNA with minimal amounts of genomic DNA contamination using the supplied Genomic DNA Removal Column. However, additional DNas... | [] |
102,386 | αS PFF Uptake Protocol | 0 | dx.doi.org/10.17504/protocols.io.e6nvw1e79lmk/v1 | https://www.protocols.io/view/s-pff-uptake-protocol-df8s3rwe | Scott Vermilyea | TITLE: αS PFF Uptake Protocol
AUTHORS: Scott Vermilyea
[DESCRIPTION]
This protocol details the uptake of αS PFF treatement.
[STEPS]
SECTION: αS PFF Uptake Protocol
1. Exchange fresh culture media to cells.
SECTION: αS PFF Uptake Protocol
2. Prepare αS PFF working solution.
Frozen stock is 5 1527, dilute to 0.25 15... | ["[αS PFF Uptake Protocol] Exchange fresh culture media to cells.", "[αS PFF Uptake Protocol] Prepare αS PFF working solution.\n\nFrozen stock is 5 1527, dilute to 0.25 1527 in sterile PBS followed by sonication (1 Sec ON/ 1 Sec OFF) for 2 min with 20% amplitude.", "[αS PFF Uptake Protocol] Add αS PFF to cells for a f... |
40,345 | Enzyme-linked immunosorbent assay (ELISA) for detection of anti-HIV antibodies (ELISA) developed in various animal species. | 4 | dx.doi.org/10.17504/protocols.io.bjmzkk76 | https://www.protocols.io/view/enzyme-linked-immunosorbent-assay-elisa-for-detect-bjmzkk76 | Angel Justiz-Vaillant | TITLE: Enzyme-linked immunosorbent assay (ELISA) for detection of anti-HIV antibodies (ELISA) developed in various animal species.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Enzyme-linked immunosorbent assay (ELISA) for studying the presence of anti-HIV antibodi... | ["The 96 well polystyrene microplates (U-shaped bottom) were coated with 50 ng of the synthetic gp-120 peptide in coating buffer overnight at 4°C.", "The microplate is washed 4X (PBS-Tween-20) and blocked with 3% non-fat milk in PBS, 25 µl/well, 1h, RT.", "The microplate is washed 4X (PBS-Tween-20) and triplicates of 2... |
42,242 | Whole genome sequencing of respiratory syncytial (RSV) virus from clinical samples with low viral load | 1 | dx.doi.org/10.17504/protocols.io.bmhak32e | https://www.protocols.io/view/whole-genome-sequencing-of-respiratory-syncytial-r-bmhak32e | Stephanie Goya, Gabriel L. Rojo, Mercedes S. Nabaes Jordar, Laura E. Valinotto, Alicia S Mistchenko, Mariana Viegas | TITLE: Whole genome sequencing of respiratory syncytial (RSV) virus from clinical samples with low viral load
AUTHORS: Stephanie Goya, Gabriel L. Rojo, Mercedes S. Nabaes Jordar, Laura E. Valinotto, Alicia S Mistchenko, Mariana Viegas
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Here is a d... | ["[Viral RNA extraction]\nCentrifuge the nasopharyngeal aspirate (NPA) at 5,000 g for 5 min to remove cellular debris.", "[Viral RNA extraction]\nExtract viral RNA from 200 μl of NPA by following the protocol PureLink viral RNA/DNA mini kit (Thermo Fisher Scientific) according the manufacturer’s instructions except for... |
48,741 | PCLS Dehydration | 4 | null | https://www.protocols.io/view/pcls-dehydration-btudnns6 | Morrisey Lab | TITLE: PCLS Dehydration
AUTHORS: Morrisey Lab
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">PCLS Dehydration March</div><div class = "text-block">*done at room temperature*</div><div class = "text-block">*make sure to have 2% PFA and etOH pre-aliquoted at room temp*</div></div>
[STEPS] | [] |
50,377 | Drought stress application for smaller plants based on soil water holding capacity | 4 | dx.doi.org/10.17504/protocols.io.bvfhn3j6 | https://www.protocols.io/view/drought-stress-application-for-smaller-plants-base-bvfhn3j6 | Magdalena Julkowska | TITLE: Drought stress application for smaller plants based on soil water holding capacity
AUTHORS: Magdalena Julkowska
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The method of applying drought stress in the small soil-filled containers for relatively small plants. The described method is wor... | ["[Material preparation]\nPrepare pots with the soil of choice for the experiment. Make sure that each pot is filled with approximately the same amount of soil and that the soil is pushed with approximately the same strength. Make sure to mark the pots with a unique ID for each pot.", "[Material preparation]\nLeave the... |
53,789 | Cyanobacteria Yolk-Shell Preparation | 4 | dx.doi.org/10.17504/protocols.io.byr5pv86 | https://www.protocols.io/view/cyanobacteria-yolk-shell-preparation-byr5pv86 | Jorge Fernández Méndez, Celia Martin Morales | TITLE: Cyanobacteria Yolk-Shell Preparation
AUTHORS: Jorge Fernández Méndez, Celia Martin Morales
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Cyanobacteria as well as other photosynthetic microorganisms can be encapsulated within biohybrid nanomaterials. Cyanobacterial Yolk-shell are biohybrid ... | ["[Cells Pretreatment]\nIn sterility, centrifugue a suffcient ammount of exponentially growing cyanobacteria culture (20 to 100 mL) . OD720 should be between 0.5 to 1. It is recommended to split the culture in two different sterile centrifugue tubes.\nCentrifuge: 2800 33, 10 min", "[Cells Pretreatment]\nIn sterility, ... |
49,977 | pS129 alpha-synuclein Western blot | 1 | dx.doi.org/10.17504/protocols.io.bu2znyf6 | https://www.protocols.io/view/ps129-alpha-synuclein-western-blot-bu2znyf6 | Christopher Burke | TITLE: pS129 alpha-synuclein Western blot
AUTHORS: Christopher Burke
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details the investigation of the amount of total alpha-synuclein and pS129 alpha-synuclein in cells.</div></div>
[STEPS]
?. [DETERGENT-BASED CELL LYSIS]
Add of lysis b... | ["[DETERGENT-BASED CELL LYSIS]\nAdd of lysis buffer to the cell pellet and mix thoroughly by pipetting up and down until the cell pellet is completely resolved into a homogeneous solution.\n100 µl", "[DETERGENT-BASED CELL LYSIS]\nAdjust the lysis buffer volume to the cell pellet size, keep the sample at as soon as th... |
62,621 | Limitless Glucose 1 Review : Blood Sugar (Glucose) Level Lower Than Standard Range? (What They Won’t Share) | 3 | dx.doi.org/10.17504/protocols.io.ewov1n5kogr2/v1 | https://www.protocols.io/view/limitless-glucose-1-review-blood-sugar-glucose-lev-b9d5r286 | Limitless Glucose | TITLE: Limitless Glucose 1 Review : Blood Sugar (Glucose) Level Lower Than Standard Range? (What They Won’t Share)
AUTHORS: Limitless Glucose
[DESCRIPTION]
Limitless Glucose 1
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.inwcdfe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for obtaining high quality RNA from yeast using acid-phenol lysis at 65°C. Modifed from DOI: <a href="https://doi.org/10.1016/S0076-6879(02)50976-9" target="_blank">10.1016/S0076-6879(02)50976-9</a> to use 10-15 ml of yeast culture. Expected yield of 100-200 μg of RN... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.errbd56 | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p><strong>MATERIALS AND ASSAY CONDITIONS:</strong><br /><br /></p>
<p> 1) Virus infected NC64A <em>chlorella</em> or Pbi <em>chlorella</em>, pellets frozen at -80°C</p>
<p> <br /> 2) Buffer A: 10 mM Tris-Acetate, pH 8.0, 10 mM 2-ME, 50 µg/mL PMS... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ntrdem6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Here we present a neural differentiation protocol for generating neural progenitor cells (NPCs) from human induced pluripotent stem cells (hiPSCs). Briefly, human dermal fibroblasts were reprogrammed into hiPSCs via non-integrative reprogramming approach. Subsequently, hiPSCs... | [] |
53,008 | Estimate of fractal dimension of rat tissues submitted to experimental protocols | 5 | dx.doi.org/10.17504/protocols.io.bxzqpp5w | https://www.protocols.io/view/estimate-of-fractal-dimension-of-rat-tissues-submi-bxzqpp5w | Gabriel Cao MD, PhD, Graciela Ottaviano, Francisco Capani PhD | TITLE: Estimate of fractal dimension of rat tissues submitted to experimental protocols
AUTHORS: Gabriel Cao MD, PhD, Graciela Ottaviano, Francisco Capani PhD
[DESCRIPTION]
Those who are dedicated to the analysis of structural changes in tissues have tried, over time, to seek increasingly "more rigorous" methods to be... | ["Histological sections of 0.3 to 0.5 µm are obtained and stained with hematoxylin and eosin.", "Each histological section is photographed in contiguous and successive fields with a total magnification of 100X, obtaining a certain number of digitized images that constitute the map of the tissue surface under study.", "... |
null | null | null | dx.doi.org/10.17504/protocols.io.rctd2wn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.phadj2e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong><u>Goal:</u></strong></p>
<p>Immunohistochemistry (or IHC) is a method for demonstrating the presence and location of molecules in cultured cells.</p>
<p><strong> </strong></p>
<p><strong><u>Solutions and Reagents:</u></strong></p>
<p> </p>
<p><strong>NOTE</strong>: ... | [] |
66,315 | Silver Fox Male Enhancement | 3 | dx.doi.org/10.17504/protocols.io.n2bvj6wxxlk5/v1 | https://www.protocols.io/view/silver-fox-male-enhancement-cczjsx4n | Silver Fox Male Enhancement | TITLE: Silver Fox Male Enhancement
AUTHORS: Silver Fox Male Enhancement
[DESCRIPTION]
Silver Fox Male Enhancement
[STEPS] | [] |
50,611 | MiniXT protocol | 4 | dx.doi.org/10.17504/protocols.io.bvntn5en | https://www.protocols.io/view/minixt-protocol-bvntn5en | Marc-Aurel Fuchs, Arun Mahesh, Clara Radulescu, Deborah Lavin, Fiona Rogan, Julia Miskelly, Stephen Bridgett, David Simpson | TITLE: MiniXT protocol
AUTHORS: Marc-Aurel Fuchs, Arun Mahesh, Clara Radulescu, Deborah Lavin, Fiona Rogan, Julia Miskelly, Stephen Bridgett, David Simpson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>We present the ‘mini-XT’ miniaturized tagmentation-based library preparation protocol used... | ["[cDNA synthesis]\nReagentFor 1 reaction (μL)For 420 reactions (μL, 4 x 96 well plate)Luna RT Supermix2840 Nuclease free water31260\nReagentFor 1 reaction (μL)For 420 reactions (μL, 4 x 96 well plate)Luna RT Supermix2840 Nuclease free water31260", "[cDNA synthesis]\nThaw the RNA samples on ice.", "[cDNA synthesis]\nSh... |
37,277 | SPARC_Bolser_intrathoracic vagotomy and cough | null | dx.doi.org/10.17504/protocols.io.bgm5ju86 | https://www.protocols.io/view/sparc-bolser-intrathoracic-vagotomy-and-cough-bgm5ju86 | Donald Bolser | TITLE: SPARC_Bolser_intrathoracic vagotomy and cough
AUTHORS: Donald Bolser
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Cervical vagotomy sections both lower airway and recurrent laryngeal afferent fibers and eliminates cough induced by stimulation of sensory afferents in the lower trachea and ... | ["Anesthetize animal with 2% sevoflurane. Once anesthetized, wean onto sodium pentobarbital anesthesia (28 mg/kg, iv)", "Place femoral venous and arterial catheters, a urinary catheter, and cannulate trachea. Record arterial blood pressure and end tidal CO2. Periodic arterial blood gases are recorded.", "Place electrom... |
77,123 | NCBI submission protocol for microbial pathogen surveillance | 1 | dx.doi.org/10.17504/protocols.io.4r3l284pql1y/v6 | https://www.protocols.io/view/ncbi-submission-protocol-for-microbial-pathogen-su-cpjbvkin | Ruth Timme, Maria Balkey, Robyn Randolph, Julie Haendiges, Sai Laxmi Gubbala Venkata, William Wolfgang, Tina.Pfefer, Errol Strain | TITLE: NCBI submission protocol for microbial pathogen surveillance
AUTHORS: Ruth Timme, Maria Balkey, Robyn Randolph, Julie Haendiges, Sai Laxmi Gubbala Venkata, William Wolfgang, Tina.Pfefer, Errol Strain
[DESCRIPTION]
PURPOSE: Step-by-step instructions for submitting pathogen whole genome sequence data to NCBI and... | ["[Establish submission environmnet at NCBI] Set up a new NCBI submission environment for your lab:\n\n1.1: Create an NCBI user account\n1.2: Set up an NCBI submission user group for your lab\n1.4: Bookmark the link to your submission portal\n1.5. Identify or establish new BioProjects (detailed in Step 3)\n\n\nReady fo... |
94,536 | Solid phase binding assay - Clusterin binding to Very Low-Density Lipoprotein Receptor (VLDLR) | 1 | dx.doi.org/10.17504/protocols.io.yxmvm36kol3p/v1 | https://www.protocols.io/view/solid-phase-binding-assay-clusterin-binding-to-ver-c8jgzujw | Patricia Yuste-Checa, Andreas Bracher, F Ulrich Hartl | TITLE: Solid phase binding assay - Clusterin binding to Very Low-Density Lipoprotein Receptor (VLDLR)
AUTHORS: Patricia Yuste-Checa, Andreas Bracher, F Ulrich Hartl
[DESCRIPTION]
This protocol details how to monitor Clusterin binding to the Very Low-Density Lipoprotein Receptor (VLDLR) by Enzyme-linked immunosorbent a... | ["[Solid phase binding assay - Clusterin binding to Very Low-Density Lipoprotein Receptor (VLDLR)] Coat the corresponding wells of a 96-well plate (Nunc-Immuno MicroWell 96 well solid plate, MERCK) with 100 µL of TBS-C containing 10 1621 VLDLR ectodomain at 4 °C.", "[Solid phase binding assay - Clusterin binding to V... |
44,783 | Salmonella spp. antibiotic susceptibility testing by the Kirby-Bauer disk diffusion method | 4 | dx.doi.org/10.17504/protocols.io.bpypmpvn | https://www.protocols.io/view/salmonella-spp-antibiotic-susceptibility-testing-b-bpypmpvn | Enrique Delgado | TITLE: Salmonella spp. antibiotic susceptibility testing by the Kirby-Bauer disk diffusion method
AUTHORS: Enrique Delgado
[STEPS]
?. [Refreshment of pure isolates]
Pick growth from pure isolates of samples to be analyzed and from quality control organisms to be included in the AST test. Transfer to sterile assay tube... | ["[Refreshment of pure isolates]\nPick growth from pure isolates of samples to be analyzed and from quality control organisms to be included in the AST test. Transfer to sterile assay tubes containing 10 mL of TSB and place the tubes in a shaking incubator at 35 ºC / 18-24 h / 150 rpm.", "[Refreshment of pure isolates]... |
48,116 | 1808 test 2 | 1 | null | https://www.protocols.io/view/1808-test-2-bs8unhww | Maria Guliakina | TITLE: 1808 test 2
AUTHORS: Maria Guliakina
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">test</div></div>
[STEPS]
?. test | ["test"] |
71,786 | Western Blotting (Fly Heads) | 4 | dx.doi.org/10.17504/protocols.io.8epv5j96jl1b/v2 | https://www.protocols.io/view/western-blotting-fly-heads-ciciuaue | Mel Feany | TITLE: Western Blotting (Fly Heads)
AUTHORS: Mel Feany
[DESCRIPTION]
This protocol describes how to perform a Western Blotting technique using fly heads.
[STEPS]
1. Homogenize desired number of fly heads in 1 X Laemmli sample buffer.
2. Heat samples to 100 °C for 10 min , spin briefly before loading.
3. Load premade... | ["Homogenize desired number of fly heads in 1 X Laemmli sample buffer.", "Heat samples to 100 °C for 10 min , spin briefly before loading.", "Load premade gel into western blotting apparatus. Fill reservoir with Running Buffer:\nRunning Buffer:\n6 g Tris-HCL\n28.9 g glycine\nFill to 1 L with distilled water\nAdd 5 m... |
27,232 | Isolation of nuclei from frozen tissue for ATAC-seq and other epigenomic assays | null | dx.doi.org/10.17504/protocols.io.6t8herw | null | 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]
<div class = "text-blocks"><div class = "text-block">This protocol enables the isolation of nuclei from frozen tissues. These nuclei are suitable for use in A... | ["[Before you start the protocol:]\nAll steps should be performed on ice or at . Pre-chill a swinging bucket centrifuge and a fixed angle centrifuge to 4°C.\n4 °C", "[Before you start the protocol:]\nPre-chill all Dounces and pestles to in a fridge.\n4 °C", "[Before you start the protocol:]\nPre-chill all tubes. For e... |
75,508 | Spatial Transcriptomics for FFPE utilizing 10x Genomics Visium | 4 | dx.doi.org/10.17504/protocols.io.kxygx95ezg8j/v1 | https://www.protocols.io/view/spatial-transcriptomics-for-ffpe-utilizing-10x-gen-cmyuu7ww | Andrew Houston, Siqi Chen, Feng Chen | TITLE: Spatial Transcriptomics for FFPE utilizing 10x Genomics Visium
AUTHORS: Andrew Houston, Siqi Chen, Feng Chen
[DESCRIPTION]
To detect gene expression spatially mapped onto formalin-fixed paraffin-embedded tissue samples adapted from the 10x Genomics Visium FFPE v1 protocol.
[STEPS]
SECTION: Quality Assessment... | ["[Quality Assessment] Follow the tissue preparation guide as outlined below to determine if your starting FFPE tissue block is acceptable for the 10x Visium platform\nStart here\nUtilize Visium Tissue Section Test Slide (PN-2000460) to do a quality assessment of each sample\nBe sure to trim a few sections and place in... |
66,629 | Diaetoxil 600mg Avis- Medical, Prix Pharmacie, Arnaque Forum | 1 | dx.doi.org/10.17504/protocols.io.8epv59qkjg1b/v1 | https://www.protocols.io/view/diaetoxil-600mg-avis-medical-prix-pharmacie-arnaqu-cdbds2i6 | Diaetoxil France | TITLE: Diaetoxil 600mg Avis- Medical, Prix Pharmacie, Arnaque Forum
AUTHORS: Diaetoxil France
[DESCRIPTION]
Diaetoxil est formulé pour déclencher une perte de poids naturelle, ce qui permet aux individus d'avoir un corps maigre et un indice de masse corporelle (IMC) sain. En plus d'augmenter le métabolisme des gr... | [] |
15,126 | Preparation of aqueous extracts of plants | null | dx.doi.org/10.17504/protocols.io.szwef7e | null | Cecilia Mónica Rodríguez García, Leticia Peraza | TITLE: Preparation of aqueous extracts of plants
AUTHORS: Cecilia Mónica Rodríguez García, Leticia Peraza
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Aqueous extracts of plants are a simple, economical and eco-friendly alternative to use as a source of antifungal activity. Here is a protocol for... | ["[Aqueous extract preparation from leaves]\n-Collection and preparation of leaves for dryingCollect fresh leaves from the fieldIn the lab wash them with tap waterRemove excess water with a kitchen centrifuge", "[Aqueous extract preparation from leaves]\n-Drying of leavesDistribute the leaves in cardboard boxesPut them... |
35,290 | Multi-Patch Clamp Recording | null | dx.doi.org/10.17504/protocols.io.bep2jdqe | null | Allen Institute for Brain Science | TITLE: Multi-Patch Clamp Recording
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the process to obtain multiple electrophysiological recordings from postnatal mouse and/or human brain slices.</div><div class = "text-block"><span st... | [] |
47,511 | Interpenetration-between-a-polymer-star-and-a-polymer-brush | 1 | dx.doi.org/10.17504/protocols.io.bsmxnc7n | https://www.protocols.io/view/interpenetration-between-a-polymer-star-and-a-poly-bsmxnc7n | Mike Edwards | TITLE: Interpenetration-between-a-polymer-star-and-a-polymer-brush
AUTHORS: Mike Edwards
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">By means of the density functional theory framework I tackle the long-standing problem of a polymer star interpenetrating with a polymer brush at thermal equilib... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.j6ncrde | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>We use the described methods for determining the internal cellular quota of thiamin and its<br />different phosphorylation states in marine algae, in the below case for the haptophyte Emiliania<br />huxleyi. The chemical assay used – the thiochrome assay - was developed in th... | [] |
68,570 | Isolation of trophoblast organoids from full-term human placenta tissue | 4 | dx.doi.org/10.17504/protocols.io.x54v9y98mg3e/v1 | https://www.protocols.io/view/isolation-of-trophoblast-organoids-from-full-term-ce72thqe | Carolyn Coyne, henry.yang | TITLE: Isolation of trophoblast organoids from full-term human placenta tissue
AUTHORS: Carolyn Coyne, henry.yang
[DESCRIPTION]
This protocol describes the isolation of trophoblast organoids from mid-to-late gestation human placental tissue.
[GUIDELINES]
It is recommended that fresh tissue be used in this isolation... | ["[Step-by-step protocol] Dissect placental chorionic villi. Carefully remove decidua.", "[Step-by-step protocol] Generate very small fragments of tissue.", "[Step-by-step protocol] Place tissue fragments in glass bottle containing wash buffer and a stir bar and wash extensively on a magnetic stirrer (VWR, 76447-030) a... |
85,849 | Mapeamento de literatura sobre o modelo conceitual LRMoo | 1 | dx.doi.org/10.17504/protocols.io.j8nlkow55v5r/v1 | https://www.protocols.io/view/mapeamento-de-literatura-sobre-o-modelo-conceitual-cx3zxqp6 | Isabel C Ayres da Silva Maringelli, fernando modesto | TITLE: Mapeamento de literatura sobre o modelo conceitual LRMoo
AUTHORS: Isabel C Ayres da Silva Maringelli, fernando modesto
[DESCRIPTION]
A pesquisa visa identificar a literatura produzida sobre o modelo LRMoo, bem como os modelos conceituais
elaborados pelo ICOM e IFLA para a área de museus (CIDOC-CRM) e biblioteca... | ["BUSCAS\nRealizar as buscas com a utilização das strings elaboradas nas bases de dados selecionadas.", "SELEÇÃO\nFazer leitura dos títulos e resumos para seleção dos trabalhos.", "EXTRAÇÃO\nFazer leitura do texto integral de todos os trabalhos que tiverem ao menos uma citação dos modelos FRBRoo ou LRMoo.", "SINTETIZAR... |
103,739 | Applying the Mitosis-enabled Anchor-away/Recruiter System (MARS) for conditional protein recruitment to the plasma membrane during mitosis | 0 | dx.doi.org/10.17504/protocols.io.n2bvjnzypgk5/v1 | https://www.protocols.io/view/applying-the-mitosis-enabled-anchor-away-recruiter-dhi334gn | Xiaofu Cao, Jeremy M Baskin | TITLE: Applying the Mitosis-enabled Anchor-away/Recruiter System (MARS) for conditional protein recruitment to the plasma membrane during mitosis
AUTHORS: Xiaofu Cao, Jeremy M Baskin
[DESCRIPTION]
Tools for acute manipulation of protein localization enable elucidation of spatiotemporally defined functions, but their r... | ["[Section I. Cloning of the MARS fusion protein expression plasmid] MARS-related plasmids have been deposited to Addgene and their plasmid numbers are listed in the Materials tab. To fuse a single MARS unit to POI, start with pCDNA3-MARS-p85(iSH2) (Addgene 205236). To fuse the tandem MARS module to POI, start with pCD... |
81,316 | Veggie NEFF media for Tetrahymena thermophila | 4 | dx.doi.org/10.17504/protocols.io.5qpvormbbv4o/v1 | https://www.protocols.io/view/veggie-neff-media-for-tetrahymena-thermophila-ctncwmaw | Luisa F Jimenez-Soto | TITLE: Veggie NEFF media for Tetrahymena thermophila
AUTHORS: Luisa F Jimenez-Soto
[DESCRIPTION]
The ciliate Tetrahymena thermophila has been a research organism used by a great community of scientists including biologist, geneticists and toxicologists. T. thermophila is a bacterial predator; however, we can grow it... | ["[Section 1: NEF veggie media] Prepare 4 bottles of 500 ml volume each. Make sure the bottles are free of detergent rests, by washing at least 4 times with distilled water. Label each bottle with the name of the media: NEFv (NEF veggie)", "[Section 1: NEF veggie media] In a 1 liter graduated cylinder, add a magnet st... |
78,354 | Transplanting Arabidopsis | 1 | null | https://www.protocols.io/view/transplanting-arabidopsis-cqrsvv6e | Lynn Doran, Meghan Burns | TITLE: Transplanting Arabidopsis
AUTHORS: Lynn Doran, Meghan Burns
[DESCRIPTION]
Transplanting Arabidopsis grown from seed on agar plates to soil trays.
[BEFORE_START]
Seedlings will be ready to transplant in approximately 10 to 14 days after planting when they've formed one to two true leaves. Do not wait too l... | ["Look at the Arabidopsis on the agar plate and determine which one looks the best. Typically this means it is the plant with the longest roots and greenest leaves.", "Take a pair of tweezers and place them at the base of the plant. Pull up very slowly, ensuring that all of the roots come out of the agar in one piece."... |
57,790 | Freezing of mouse embryonic fibroblasts (MEFs) for hPSC cultures | 4 | dx.doi.org/10.17504/protocols.io.b4n6qvhe | https://www.protocols.io/view/freezing-of-mouse-embryonic-fibroblasts-mefs-for-h-b4n6qvhe | Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner | TITLE: Freezing of mouse embryonic fibroblasts (MEFs) for hPSC cultures
AUTHORS: Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner
[DESCRIPTION]
This protocol describes the freezing of mouse embryonic fibroblasts (MEFs), which can later be used as feeder cells for human pluripotent stem cell (hP... | ["Wash the plates twice with DPBS", "Add Trypsin (5 ml for 15-cm plate) and incubate for 5 min (37°C; 5% CO2)", "Add 10 ml MEF medium to neutralize the Trypsin and collect the solution into a conical tube.", "Centrifuge the cell suspension at 250 x g, 10 min", "Discard supernatant, and re-suspend the cells in MEF Fre... |
67,010 | SNICR barcode library generation | 4 | dx.doi.org/10.17504/protocols.io.6qpvr659ovmk/v1 | https://www.protocols.io/view/snicr-barcode-library-generation-cdpas5ie | Matt Keefe | TITLE: SNICR barcode library generation
AUTHORS: Matt Keefe
[DESCRIPTION]
SNICR barcodes contain a 10x Capture Sequence (Capture Sequence 2) at the 3' end of the transcript. However, the barcodes are located 3' of a full-length H2B-GFP transcript, and are therefore much longer than typical Capture Sequence expres... | ["[10x steps] DO NOT follow step 2.3B; the SNICR barcodes amplified from Nextera Read 1 are with the rest of the 40uL transcriptomic fraction in 2.3A due to their length.", "Overview\nSNICR barcodes contain a 10x Capture Sequence (Capture Sequence 2) at the 3' end of the transcript. However, the barcodes are located 3'... |
26,046 | Calibration Protocol - Fluorescence Standard Curve with Fluorescein | null | dx.doi.org/10.17504/protocols.io.5n6g5he | null | Geoff Baldwin, Traci Haddock-Angelli, Jacob Beal, Ari Dwijayanti, Marko Storch, Natalie Farny, Richard Tennant, Paul Rutten | TITLE: Calibration Protocol - Fluorescence Standard Curve with Fluorescein
AUTHORS: Geoff Baldwin, Traci Haddock-Angelli, Jacob Beal, Ari Dwijayanti, Marko Storch, Natalie Farny, Richard Tennant, Paul Rutten
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:l... | ["[Prepare the fluorescein stock solution]\nSpin down fluorescein kit tube to make sure pellet is at the bottom of tube", "[Prepare the fluorescein stock solution]\nPrepare 10x fluorescein stock solution (100 μM) by resuspending fluorescein in 1mL of 1X PBS\nIt is important that the fluorescein is properly dissolved. T... |
66,320 | Power Keto Gummies It Rapid Fat-Reducing Formula To Give You Slim Figure | 3 | dx.doi.org/10.17504/protocols.io.kqdg3po6ql25/v1 | https://www.protocols.io/view/power-keto-gummies-it-rapid-fat-reducing-formula-t-cczqsx5w | SayraMcatra | TITLE: Power Keto Gummies It Rapid Fat-Reducing Formula To Give You Slim Figure
AUTHORS: SayraMcatra
[DESCRIPTION]
<!--td {border: 1px solid #ccc;}br {mso-data-placement:same-cell;}-->Power Keto Gummies It Rapid Fat-Reducing Formula To Give You Slim Figure
[STEPS] | [] |
81,603 | Peer support implementation strategy in health: scope review | 1 | dx.doi.org/10.17504/protocols.io.14egn2drzg5d/v1 | https://www.protocols.io/view/34-draft-json-34-34-blocks-34-34-key-34-34-5jj8b-ctxbwpin | Rafael Aiello Bomfim, Jean Ribeiro Leite, Giovana Soares Buzinaro, Jhennyffer Cabral, Hazelelponi Nauman Cerqueira Leite | TITLE: Peer support implementation strategy in health: scope review
AUTHORS: Rafael Aiello Bomfim, Jean Ribeiro Leite, Giovana Soares Buzinaro, Jhennyffer Cabral, Hazelelponi Nauman Cerqueira Leite
[DESCRIPTION]
The use of peer support consists of a strategy that uses non-professionals, raised to the status of "leader... | ["Peer support implementation strategy in health: scope review"] |
25,175 | Inoculum preparation for Mixotrophic culturing | null | dx.doi.org/10.17504/protocols.io.4txgwpn | null | Bruna Emerenciano, Maria Izabel Pereira Batista, Adriano Henrique Rangel | TITLE: Inoculum preparation for Mixotrophic culturing
AUTHORS: Bruna Emerenciano, Maria Izabel Pereira Batista, Adriano Henrique Rangel
[STEPS]
?. Prepare the inoculum from Spirulina platensis strain to inoculate 800 mL of Zarrouk medium contained in 1000 mL Erlenmeyer flask.
?. Supplement the Zarrouk medium with 2.5%... | ["Prepare the inoculum from Spirulina platensis strain to inoculate 800 mL of Zarrouk medium contained in 1000 mL Erlenmeyer flask.", "Supplement the Zarrouk medium with 2.5%, 5.0% and 10% clarified buffalo mozzarella cheese whey. The components of Zarrouk medium (per liter) are as follows: 16.8g NaHCO3, 0.5g K2HPO4, 2... |
63,505 | 2-step PCR mixture and conditions (Barcoded-head primers for seqs pooling) | 4 | null | https://www.protocols.io/view/2-step-pcr-mixture-and-conditions-barcoded-head-pr-b99rr956 | Yin-Tse Huang | TITLE: 2-step PCR mixture and conditions (Barcoded-head primers for seqs pooling)
AUTHORS: Yin-Tse Huang
[DESCRIPTION]
PCR mixture and condition (2X SUPERGREEN PCR MASTER MIX)
[STEPS]
SECTION: For 1' PCR head-primers
2. Prepare 1' PCR master mixutre for head-primers (prepare 1.2X of solutions for pipetting erro... | ["[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] Carry out PCR using the following condition: \n\n1' PCR condition for head-primers", "[For 1... |
98,667 | KAPP-Sen TMC: Term Placenta Subject Selection Criteria | 0 | dx.doi.org/10.17504/protocols.io.4r3l2q4q4l1y/v1 | https://www.protocols.io/view/kapp-sen-tmc-term-placenta-subject-selection-crite-dckj2uun | Sonja Suvakov, Elizabeth Ann L. Enninga, Bridget A. Schley, Janelle Santos, Vesna D. Garovic | TITLE: KAPP-Sen TMC: Term Placenta Subject Selection Criteria
AUTHORS: Sonja Suvakov, Elizabeth Ann L. Enninga, Bridget A. Schley, Janelle Santos, Vesna D. Garovic
[DESCRIPTION]
Patient samples will be obtained during an elected cesarean (c-section) delivery. We will target two groups: Young (n=20, ages 20-30 years) a... | ["Inclusion\nBetween the age of 20-30 or 40-50 years of age\nCurrently having a single birth (e.g. one baby)\nPregnancy is the result of natural conception\nElected for physician to perform a cesarean section for delivery\nPregnancy reaches full term (≥ 37 weeks)", "Exclusion\nPregravid BMI > 35\nAny health conditions ... |
55,830 | Artificial saliva | 6 | dx.doi.org/10.17504/protocols.io.3byl4k1jzvo5/v2 | https://www.protocols.io/view/artificial-saliva-b2rwqd7e | Bjørn Peare Bartholdy, a.g.henry | TITLE: Artificial saliva
AUTHORS: Bjørn Peare Bartholdy, a.g.henry
[DESCRIPTION]
Creating an artificial saliva solution for oral biofilm growth, specifically dental calculus.
This is a modified version of Sissons et al. 1991.
[BEFORE_START]
Mix the solution under a fumehood. It can smell pretty bad.
Also have the i... | ["Add 300 mL distilled (or deionized) dH2O to a 1000 mL beaker, with stirring and heat 60 °C .", "Add:\n\n- 2.5 g \n- 5 g \n- 10 g \n- 5 g \n\nLet the reagents completely dissolve before continuing to the next step", "Add:\n\n- 2.5 g \n- 0.35 g \n- 0.2 g \n- 0.74 g \n- 0.54 g \n- 2.5 mg", "Add the ... |
49,753 | SYBR green RT-PCR assay for the surveillance of SARS-CoV-2 variants of concern | 4 | dx.doi.org/10.17504/protocols.io.butznwp6 | https://www.protocols.io/view/sybr-green-rt-pcr-assay-for-the-surveillance-of-s-butznwp6 | Pedro Cardoso, Fernando do Couto Motta, Marilda Agudo Mendonça Teixeira de Siqueira, Daniela Tupy de Godoy, Rodrigo Brindeiro, Monica Barcellos Arruda, Elisabete Andrade, Marisa Ribeiro, Marcela Fontana-Maurell, Elaine Costa, Daniele Rocha, Patricia Alvarez | TITLE: SYBR green RT-PCR assay for the surveillance of SARS-CoV-2 variants of concern
AUTHORS: Pedro Cardoso, Fernando do Couto Motta, Marilda Agudo Mendonça Teixeira de Siqueira, Daniela Tupy de Godoy, Rodrigo Brindeiro, Monica Barcellos Arruda, Elisabete Andrade, Marisa Ribeiro, Marcela Fontana-Maurell, Elaine Cost... | ["Briefly vortex and centrifuge reagents before use.", "Prepare 10 µM working stocks of the primers.", "Thaw the GoTaq® qPCR Master Mix (Promega), Nuclease-Free Water, and primers working stocks.", "Use the 10 µM working stocks to prepare the mix, containing:Volume (per reaction)final concentrationGoTaq® qPCR Master Mi... |
59,655 | Plant assemble - Plant de novo genome assembly: annotation | 5 | dx.doi.org/10.17504/protocols.io.kqdg36d87g25/v2 | https://www.protocols.io/view/plant-assemble-plant-de-novo-genome-assembly-annot-b6hfrb3n | Scott Ferguson, Ashley Jones, Justin Borevitz | TITLE: Plant assemble - Plant de novo genome assembly: annotation
AUTHORS: Scott Ferguson, Ashley Jones, Justin Borevitz
[DESCRIPTION]
With the advancement of long-read sequencing technologies and associated bioinformatics tools, it has now become possible to de novo assemble complex plant genomes with unrivalled c... | ["[Repeat annotate] Now that your genome is complete we want to find and annotate it for repeat regions. To do this we use EDTA and RepeatMasker. EDTA is first used to build a transposon (TE) sequence library. Next, RepeatMasker is used to find all TE and simple repeats within the genome.", "[Repeat annotate: soft mask... |
22,369 | Biolistic transformation of polar diatom Fragilariopsis cylindrus | null | dx.doi.org/10.17504/protocols.io.z39f8r6 | null | Amanda Hopes, Thomas Mock | TITLE: Biolistic transformation of polar diatom Fragilariopsis cylindrus
AUTHORS: Amanda Hopes, Thomas Mock
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Transformation system for the polar diatom </span><span style = "font-style:italic;">Fragilariopsis cylindrus</span><span> using micropart... | ["Culturing Fragilariopsis cylindrus. Grow Fragilariopsis cylindrus in Aquil media + Si (Price, 1989; https://ncma.bigelow.org/algal-recipes) at 4oC in 24 hour light. When culturing pre-chill the media and keep F. cylindrus on ice. Innoculate cells at a starting concentration of 50,000 cells/ml.", "Making plates for sh... |
92,850 | Novel Clinical Prediction Model: Integrating A2DS2score with 24-hour ASPECTS and Red Cell Distribution Width for EnhancedPrediction of Stroke-Associated Pneumonia following Intravenous Thrombolysis | 1 | dx.doi.org/10.17504/protocols.io.rm7vzxeyrgx1/v1 | https://www.protocols.io/view/novel-clinical-prediction-model-integrating-a2ds2s-c6wszfee | Sarawut Krongsut, Atiwat Soontornpun, Niyada Anusasnee | TITLE: Novel Clinical Prediction Model: Integrating A2DS2score with 24-hour ASPECTS and Red Cell Distribution Width for EnhancedPrediction of Stroke-Associated Pneumonia following Intravenous Thrombolysis
AUTHORS: Sarawut Krongsut, Atiwat Soontornpun, Niyada Anusasnee
[DESCRIPTION]
Background:
Stroke-associated pneumo... | ["Novel Clinical Prediction Model: Integrating A2DS2\nscore with 24-hour ASPECTS and Red Cell Distribution Width for Enhanced\nPrediction of Stroke-Associated Pneumonia following Intravenous Thrombolysis"] |
89,994 | Sleep-Wake Recording in Dan lab | 1 | dx.doi.org/10.17504/protocols.io.x54v9pkd4g3e/v1 | https://www.protocols.io/view/sleep-wake-recording-in-dan-lab-c35iyq4e | Xiaolin Huang | TITLE: Sleep-Wake Recording in Dan lab
AUTHORS: Xiaolin Huang
[DESCRIPTION]
Surgery and Setups for Recording 24-Hour Natural Sleep/Wake Cycles in Mice.
[STEPS]
SECTION: Surgery
1. Mice were anesthetized with 1.5% isoflurane and placed in a stereotaxic frame.
SECTION: Surgery
2. Body temperature was maintained using... | ["[Surgery] Mice were anesthetized with 1.5% isoflurane and placed in a stereotaxic frame.", "[Surgery] Body temperature was maintained using a heating pad.", "[Surgery] The skin was incised to expose the skull after asepsis and connective tissue was\nremoved.", "[Surgery] To implant electroencephalogram (EEG) and elec... |
null | null | null | dx.doi.org/10.17504/protocols.io.uw4exgw | null | null | TITLE: No Title
AUTHORS:
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ev3be8n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
A collection of protocols designed to guide the user in processing a viral metagenome from raw sequence data to assembly, and subsequent analysis. The user uses <em>actual</em> reads from <a href="https://github.com/MicroB3-IS/osd-analysis" target="_blank">Ocean Sampling Day (20... | [] |
58,934 | Mouse Perfusion | 1 | dx.doi.org/10.17504/protocols.io.b5swq6fe | https://www.protocols.io/view/mouse-perfusion-b5swq6fe | Haley Geertsma | TITLE: Mouse Perfusion
AUTHORS: Haley Geertsma
[DESCRIPTION]
This protocol is used to perfuse mice and isolate their brain for cryosectioning.
[STEPS]
1. Sedate mice with 120mg/kg Euthanyl then open their chest cavity to expose their heart.
2. Insert the needle tip into the left ventricle and cut the right atria. B... | ["Sedate mice with 120mg/kg Euthanyl then open their chest cavity to expose their heart.", "Insert the needle tip into the left ventricle and cut the right atria. Begin slowly injecting 10mL 1X phosphate buffered saline (PBS) over 5 minutes.", "Once all of the 1X PBS has been perfused, begin injecting 10mL 4% paraforma... |
77,155 | Analysis of ALEX Movies Containing Low-FRET Efficiency Pairs | 5 | null | https://www.protocols.io/view/analysis-of-alex-movies-containing-low-fret-effici-cpkbvksn | Clark Fritsch | TITLE: Analysis of ALEX Movies Containing Low-FRET Efficiency Pairs
AUTHORS: Clark Fritsch
[DESCRIPTION]
This protocol is meant to describe the procedure needed to detect and analyze pairs of fluorescently-labeled molecules that generate low-FRET efficiencies that might otherwise difficult to detect using the programs... | ["In NIS-Elements, we record our single-molecule FRET movies with a .nd2 file format. However, to analyze our data we must first convert our movies from .nd2 files to .tiff files.", "To convert your ALEX .nd2 files to .tiff files, first open Fiji / ImageJ. Then go to File and open the ND2_tiff1.ijm program that is prov... |
27,229 | Gibson Protocol | null | dx.doi.org/10.17504/protocols.io.6t5heq6 | null | N.J. Hillson | TITLE: Gibson Protocol
AUTHORS: N.J. Hillson
[STEPS]
?. Prepare 6 ml of 5X ISO Buffer in a 15 ml falcon tube as follows:3 ml 1 M Tris-HCl pH 7.5+ 150 ul 2 M MgCl2+ 240 ul 100 mM dNTP mix (25 mM each: dGTP, dCTP, dATP, dTTP)+ 300 ul 1 M DTT+ 1.5 g PEG-8000+ 300 ul 100 mM NAD+ _______dH2O to6 mlStore at -20 C in 320 ml ... | ["Prepare 6 ml of 5X ISO Buffer in a 15 ml falcon tube as follows:3 ml 1 M Tris-HCl pH 7.5+ 150 ul 2 M MgCl2+ 240 ul 100 mM dNTP mix (25 mM each: dGTP, dCTP, dATP, dTTP)+ 300 ul 1 M DTT+ 1.5 g PEG-8000+ 300 ul 100 mM NAD+ _______dH2O to6 mlStore at -20 C in 320 ml aliquots.", "Prepare 1.2 ml of Gibson assembly master m... |
65,205 | Amicon NMWCO Filter Concentration and Buffer Exchange | 1 | null | https://www.protocols.io/view/amicon-nmwco-filter-concentration-and-buffer-excha-cbwvspe6 | Lauren Adams | TITLE: Amicon NMWCO Filter Concentration and Buffer Exchange
AUTHORS: Lauren Adams
[DESCRIPTION]
This Amicon NMWCO filter protocol helps concentration dilute elution fractions containing protein as well as assists with buffer exchange if necessary.
[STEPS]
1. Wash the filter three times with Optima grade water and ... | ["Wash the filter three times with Optima grade water and centrifuging at 14,000 x g. Equilibrate the column by washing once with the same buffer as the elution buffer containing the target protein for ~10-30 minutes or until the volume has decreased.", "Load the elution fraction containing the target protein into the ... |
null | null | null | dx.doi.org/10.17504/protocols.io.fyubpww | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 1">
<div class="layoutArea">
<div class="column">
<p>The SensiFAST™ Probe Hi-ROX One-Step Kit has been formulated for highly reproducible first-strand cDNA synthesis and subsequent real-time PCR in a single tube. The kit is formulated for use with p... | [] |
72,322 | Formatting Data for Use With ebFRET Hidden Markov Modeling Software | 1 | null | https://www.protocols.io/view/formatting-data-for-use-with-ebfret-hidden-markov-civaue2e | Clark Fritsch | TITLE: Formatting Data for Use With ebFRET Hidden Markov Modeling Software
AUTHORS: Clark Fritsch
[DESCRIPTION]
This protocol follows from the "Selecting a Region of Interest for Hidden Markov Modeling using ebFRET" protocol and is the second step towards analyzing your data using Hidden Markov Modeling. This protocol... | ["This protocol is a continuation of the \"Selecting a Region of Interest for Hidden Markov Modeling using ebFRET\" practice protocol.", "To begin this protocol, you should have your \"SavedData.csv\" file and traces in one directory, as shown below:\n\n \n\nIt is likely that when you are doing your real analysis that... |
37,964 | HTAPP_Processing human ovarian cancer ascites to a single-cell suspension for single-cell RNA-seq | 1 | dx.doi.org/10.17504/protocols.io.bhbkj2kw | https://www.protocols.io/view/htapp-processing-human-ovarian-cancer-ascites-to-a-bhbkj2kw | Benjamin Izar, Parin Shah, Mei-Ju Su, Isaac Wakiro, Sara Napolitano, Jingyi Wu, Sébastien Vigneau, Asaf Rotem, Orit Rozenblatt-Rosen, Bruce Johnson, Aviv Regev | TITLE: HTAPP_Processing human ovarian cancer ascites to a single-cell suspension for single-cell RNA-seq
AUTHORS: Benjamin Izar, Parin Shah, Mei-Ju Su, Isaac Wakiro, Sara Napolitano, Jingyi Wu, Sébastien Vigneau, Asaf Rotem, Orit Rozenblatt-Rosen, Bruce Johnson, Aviv Regev
[DESCRIPTION]
<div class = "text-blocks"><div... | ["[Sample Description and Allocation]\nReport sample processing information.\n[Wet Ice]\nSample ID:\nDate:Person Processing:", "[Sample Description and Allocation]\nReport the volume and appearance of the sample, including a picture.\n[Wet Ice]\nSample Volume (mL):Describe Sample Appearance:\nInsert Picture(s) of Sampl... |
30,713 | Collecting Duckweed Samples For Microbial Community Profiling | null | dx.doi.org/10.17504/protocols.io.98zh9x6 | null | Kenneth Acosta | TITLE: Collecting Duckweed Samples For Microbial Community Profiling
AUTHORS: Kenneth Acosta
[STEPS]
?. [Processing Water Samples]
Get 150 mL 0.2 micron filter unit. Lay sterilized miracloth on top of filter unit.
?. [Processing Water Samples]
Collect 150-300 mL of water sample and pour through sterilized Miracloth in... | ["[Processing Water Samples]\nGet 150 mL 0.2 micron filter unit. Lay sterilized miracloth on top of filter unit.", "[Processing Water Samples]\nCollect 150-300 mL of water sample and pour through sterilized Miracloth into filter unit.", "[Processing Water Samples]\nFilter water sample through 0.2 micron filter unit by ... |
null | null | null | dx.doi.org/10.17504/protocols.io.qqidvue | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>We show our protocol to isolate total DNA from blood using QIAGEN DNeasy & Tissue Kit. The DNA can be used for identification of pathogenic bacteria by next generation DNA sequening.</p>
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.fw4bpgw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?. | [] |
89,627 | Multiple Targets Identified via Tagmentation (MulTI-Tag) v1.1 | 4 | dx.doi.org/10.17504/protocols.io.6qpvr4bezgmk/v2 | https://www.protocols.io/view/multiple-targets-identified-via-tagmentation-multi-c3r3ym8n | Michael Meers Lab | TITLE: Multiple Targets Identified via Tagmentation (MulTI-Tag) v1.1
AUTHORS: Michael Meers Lab
[DESCRIPTION]
We introduce a public protocol for Multiple Targets Identified via Tagmentation (MulTI-Tag), a chromatin profiling approach that acertains the genomic enrichment of multiple chromatin protein targets in the sa... | ["[Conjugate generation (4 hours)] Resuspend dehydrated, 5’-aminated (NH2) P5_i5 oligo in 1xPBS at a concentration of 200 µM.", "[Conjugate generation (4 hours)] Resuspend dehydrated Tn5MErev oligo (5'-[phos]CTGTCTCTTATACACATCT-3') in 1xPBS at a concentration of 200 µM.", "[Conjugate generation (4 hours)] Anneal P5_i5 ... |
91,132 | Defining AD and PD risk genes | 5 | dx.doi.org/10.17504/protocols.io.kxygx329zg8j/v1 | https://www.protocols.io/view/defining-ad-and-pd-risk-genes-c484yzyw | Xianjun Dong | TITLE: Defining AD and PD risk genes
AUTHORS: Xianjun Dong
[DESCRIPTION]
This protocol describes the method of how we define AD and PD risk genes based on the publications.
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.harb2d6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The protocol can be used to create and extrude phospholipid liposomes. This extrusion protocol roughly follows <a href="https://avantilipids.com/divisions/equipment/mini-extruder-extrusion-technique/" target="_blank">some guidelines published by the manufacturer</a>. However,... | [] |
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