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 |
|---|---|---|---|---|---|---|---|
76,717 | Dispensing C. elegans to 96 well tracking plate using Integra VIAFILL | 4 | dx.doi.org/10.17504/protocols.io.261ge396yl47/v2 | https://www.protocols.io/view/dispensing-c-elegans-to-96-well-tracking-plate-usi-cn6mvhc6 | e.warren | TITLE: Dispensing C. elegans to 96 well tracking plate using Integra VIAFILL
AUTHORS: e.warren
[DESCRIPTION]
Protocol for dispensing C. elegans into 96 well plates using the Interga VIAFILL dispenser. Bleach synchronized C. elegans should be prepared in advance. The X,Y,Z positions for dispensing can be adjusted accor... | ["[Configure the Integra VIAFILL] Insert a small cassette into the machine.", "[Configure the Integra VIAFILL] Create a new program (alternatively open a perviously saved program \"WORMS ELLIE\")", "[Configure the Integra VIAFILL] Select\nMode: Repeat Dispense\nTubing: 8 channel small\nPlate: 96 \nVolume: 10 μl\nMap: F... |
87,052 | Multiplex IHC Image Processing V0.2 | 5 | dx.doi.org/10.17504/protocols.io.n92ldmmznl5b/v2 | https://www.protocols.io/view/multiplex-ihc-image-processing-v0-2-cy9kxz4w | Shamilene Sivagnanam, Courtney Betts, Lisa Coussens | TITLE: Multiplex IHC Image Processing V0.2
AUTHORS: Shamilene Sivagnanam, Courtney Betts, Lisa Coussens
[DESCRIPTION]
Understanding immune complexity within the tumor microenvironment provides valuable insight to tumor-immune composition, spatial interactions, and the immune system's reaction to therapy allowing us to... | ["[File prep and Folder Structure] FOLDER AND FILE NAMING CONVENTION\n\nMake sure folder and file naming convention is consistent throughout the entire study. Filenaming convention should be used when saving images during acquisition.", "[File prep and Folder Structure] SET UP FOLDER STRUCTURE\n\nThe pipeline is optima... |
24,045 | Growing bacteria in Superbroth (“thick food”) | null | dx.doi.org/10.17504/protocols.io.3qmgmu6 | null | Cristian Riccio | TITLE: Growing bacteria in Superbroth (“thick food”)
AUTHORS: Cristian Riccio
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol shows you how to prepare "thick food" to grow </span><span style = "font-style:italic;">C. elegans</span><span> at higher densities.</span></div></div>
[... | ["[Prepare Super Broth]\nAdd 1 bottle (100 ml) K-orthophosphates to each bottle of Super Broth (900 ml)", "[Prepare starter culture]\nAdd 30 ml of Super Broth (plus K-orthophosphates) to a 100 ml flask. Inoculate Escherichia coli HB101 (also works with E. coli OP50, Acinetobacter schindleri, Bacillus pumilus and Pseudo... |
108,567 | Indications and prescriptions of penicillins in a population of Colombia: A cross-sectional study | 0 | dx.doi.org/10.17504/protocols.io.4r3l2qk3pl1y/v1 | https://www.protocols.io/view/indications-and-prescriptions-of-penicillins-in-a-dm9x497n | Jorge Machado Alba | TITLE: Indications and prescriptions of penicillins in a population of Colombia: A cross-sectional study
AUTHORS: Jorge Machado Alba
[DESCRIPTION]
Introduction: Inappropriate
use of antibiotics plays a key role in increasing bacterial resistance, which
is a global problem that has increased over time.
Objective: To
... | [] |
101,517 | DENV2 NS2B-NS3 protease co-expression construct small scale expression and purification protocol | 1 | dx.doi.org/10.17504/protocols.io.rm7vzj362lx1/v3 | https://www.protocols.io/view/denv2-ns2b-ns3-protease-co-expression-construct-sm-dfdm3i46 | Korvus Wang, michael fairhead, Eleanor Williams | TITLE: DENV2 NS2B-NS3 protease co-expression construct small scale expression and purification protocol
AUTHORS: Korvus Wang, michael fairhead, Eleanor Williams
[DESCRIPTION]
This protocol details the co-expression and purification of DENV2 NS2B-NS3 protease coexpression construct bearing a N-terminal His-GST tag at s... | ["[Plasmid Transformation] DVNS2B3 N-terminal His-GST tagged co-expression construct was inoculated from its BL21(DE3)-RR glycerol stock.", "[Protein expression] When the OD600 approximately 1.8, add 1mM IPTG. Lower the temperature and shaker speed to . Incubate overnight.", "[Protein Purifcation] Perform IMAC to extr... |
81,482 | Preparing a 3D Printed Implant for Acute In Vivo Electrophysiology | 1 | dx.doi.org/10.17504/protocols.io.6qpvr4jmogmk/v1 | https://www.protocols.io/view/preparing-a-3d-printed-implant-for-acute-in-vivo-e-cttiwnke | Xinxin Yin, Anna Lakunina, Josh Siegle | TITLE: Preparing a 3D Printed Implant for Acute In Vivo Electrophysiology
AUTHORS: Xinxin Yin, Anna Lakunina, Josh Siegle
[DESCRIPTION]
When performing acute electrophysiology experiments in mice, replacing the skull with a 3D printed implant several weeks in advance can substantially improve recording quality. Prior ... | ["[Coat the implant] Prepare the . Put the solid putty on a flat surface (like the bottom of a glass beaker) and heat the putty in the micro-wave oven. Check the softness of the putty every 30 s to prevent overheating. Stop heating when the putty is hot to the touch and easily malleable.", "[Coat the implant] Manipul... |
84,056 | Genotyping protocol for mice | 1 | dx.doi.org/10.17504/protocols.io.kxygx3mjwg8j/v1 | https://www.protocols.click/view/genotyping-protocol-for-mice-cwbyxapw | vanessa promes | TITLE: Genotyping protocol for mice
AUTHORS: vanessa promes
[DESCRIPTION]
This protocol describes the general method to genotype the mice.
[STEPS]
SECTION: DNA Extraction
1. Obtain tail sample from mice.
SECTION: DNA Extraction
2. Add 100 µL of NaOH into tail sample and place in hot plate at 100C for 10 min. Vortex s... | ["[DNA Extraction] Obtain tail sample from mice.", "[DNA Extraction] Add 100 µL of NaOH into tail sample and place in hot plate at 100C for 10 min. Vortex sample and place in hot plate once more for 10 min.", "[DNA Extraction] Add 50 µL of 1M Tris pH 8.0 to neutralize extraction", "[DNA Extraction] Spin for 20,000xg fo... |
40,408 | Quick'n'Dirty electrocompetent E. coli cells | 4 | dx.doi.org/10.17504/protocols.io.bjpykmpw | https://www.protocols.io/view/quick-39-n-39-dirty-electrocompetent-e-coli-cells-bjpykmpw | Elisa Granato | TITLE: Quick'n'Dirty electrocompetent E. coli cells
AUTHORS: Elisa Granato
[STEPS]
?. Using a sterile toothpick, pipette tip or similar, pick up some cell material from the agar plate. How much, you ask? So that you have a visible amount on the tip but not more than that (better to have fewer cells than too m... | ["Using a sterile toothpick, pipette tip or similar, pick up some cell material from the agar plate. How much, you ask? So that you have a visible amount on the tip but not more than that (better to have fewer cells than too many). Probably around 2 µL volume of material. I don't know, I've never measured it. A tiny li... |
68,483 | Miniprep (NEB Monarch) | 4 | null | https://www.protocols.io/view/miniprep-neb-monarch-ce5btg2n | Brian Teague | TITLE: Miniprep (NEB Monarch)
AUTHORS: Brian Teague
[DESCRIPTION]
We transformed E. coli bacteria with our plasmid in order to make more of it -- to use the bacteria as highly accurate DNA copiers. Now that we've grown a bunch of E. coli, we need to get the plasmid DNA back out. That's the point of a miniprep.
... | ["[Harvest the E.coli culture] Transfer 1.5 mLof bacterial culture to a microcentrifuge tube. Centrifuge 16000 x g, 30 s", "[Harvest the E.coli culture] Remove the supernatant using a micropipettor and discard in the biological waste container. Try to get as much as you can without disturbing the pellet.", "[Harvest th... |
null | null | null | dx.doi.org/10.17504/protocols.io.nxadfie | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes protein extraction steps from mouse aorta or vascular smooth muscle cell sample for Western blot. The lysis buffer use is a SMAD lysys buffer adopted from Beaufort et al (2014).</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
41,143 | Enzyme linked immunosorbent assay (ELISA) for determining the plasma or serum concentration of IL-33 in humans. | 4 | dx.doi.org/10.17504/protocols.io.bkexktfn | https://www.protocols.io/view/enzyme-linked-immunosorbent-assay-elisa-for-deter-bkexktfn | Angel Justiz-Vaillant | TITLE: Enzyme linked immunosorbent assay (ELISA) for determining the plasma or serum concentration of IL-33 in humans.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Ninety-six well ELISA plates are coated with monoclonal anti-human antibodies to interleukin-33 (IL-33).
?.... | ["Ninety-six well ELISA plates are coated with monoclonal anti-human antibodies to interleukin-33 (IL-33).", "Patient serum samples are added to the plates.", "The plate is incubate x 1.30 hour at RT.", "The plate is washed 4 times with PBS-tween buffer.", "The wells are incubated with a biotin conjugated anti-human IL... |
null | null | null | dx.doi.org/10.17504/protocols.io.g5yby7w | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?. | [] |
38,567 | Freezing worms | 4 | dx.doi.org/10.17504/protocols.io.bhwfj7bn | https://www.protocols.io/view/freezing-worms-bhwfj7bn | Priota Islam | TITLE: Freezing worms
AUTHORS: Priota Islam
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Caenorhabditis elegans can be frozen and stored for long term storage in liquid nitrogen (−196 °C) and at -80C. The keys to a successful freeze are using animals at the correct stage of development, the addit... | ["[Steps]\nPrepare at least 2 maintenance plates (60mm) with plenty of L1 and L2. The easiest way is to chunk the desired strains onto 2 plates and leave them in the 20C incubator for 4-5days (or until the worms reach a starved state with no food on the plate)", "[Steps]\nLabel the freezing tubes (cryovials) with the s... |
100,825 | River biofilms sampling for both downstream DNA analysis and microscopic counts | 1 | dx.doi.org/10.17504/protocols.io.e6nvw9mjdgmk/v2 | https://www.protocols.io/view/river-biofilms-sampling-for-both-downstream-dna-an-depz3dp6 | Frederic Rimet, Marine Vautier, Rainer Kurmayer, Nico Salmaso, Camilla Capelli, Agnès Bouchez, Peter Hufnagl, Isabelle Domaizon | TITLE: River biofilms sampling for both downstream DNA analysis and microscopic counts
AUTHORS: Frederic Rimet, Marine Vautier, Rainer Kurmayer, Nico Salmaso, Camilla Capelli, Agnès Bouchez, Peter Hufnagl, Isabelle Domaizon
[DESCRIPTION]
The objective of this protocol is to provide a reliable and replicable method fo... | ["[When & where to sample] Choice of the sampling season an period\n- Season: \nSampling in the framework of national river monitoring networks is usually carried out during low flow season, optimally during the natural low-water period of the respective water body under clear water conditions (i.e. summer in Eu... |
37,026 | Anchorage-independent growth assay or Soft Agar assay | null | dx.doi.org/10.17504/protocols.io.bgeajtae | https://www.protocols.io/view/anchorage-independent-growth-assay-or-soft-agar-as-bgeajtae | Marzia Ognibene | TITLE: Anchorage-independent growth assay or Soft Agar assay
AUTHORS: Marzia Ognibene
[STEPS]
?. Prepare 5% SeaKem low gelling agarose in distilled water and autoclave it.
?. Warm 10% serum media in 48 °C water bath
?. Melt the agar in microwave for some minutes. Be sure to mark the level of agar prior to heating so t... | ["Prepare 5% SeaKem low gelling agarose in distilled water and autoclave it.", "Warm 10% serum media in 48 °C water bath", "Melt the agar in microwave for some minutes. Be sure to mark the level of agar prior to heating so the level can be brought back up with distilled water, to maintain the correct concentration of a... |
98,606 | kpoint Inhibitors Combined with Radiotherapy or Chemoradiotherapy for Advanced Non-Small Cell Lung Cancer: A Systematic Review and Single-Arm Meta-Analysis | 0 | dx.doi.org/10.17504/protocols.io.261ge54njg47/v1 | https://www.protocols.io/view/kpoint-inhibitors-combined-with-radiotherapy-or-ch-dcin2ude | ran cui, ran cui | TITLE: kpoint Inhibitors Combined with Radiotherapy or Chemoradiotherapy for Advanced Non-Small Cell Lung Cancer: A Systematic Review and Single-Arm Meta-Analysis
AUTHORS: ran cui, ran cui
[DESCRIPTION]
Background: The recent usage of immunotherapy combined with chemoradiotherapy has improved survival in advanced non-... | ["[steps] Develop a research question and hypothesis:Clearly define the research question and hypothesis for the meta-analysis, focusing on the efficacy and safety of concurrent immune checkpoint inhibitors combined with radiotherapy or chemoradiotherapy for advanced non-small cell lung cancer.", "[steps] Register the ... |
38,978 | Soil_property_data_for_cocci_model | 3 | dx.doi.org/10.17504/protocols.io.bibakaie | https://www.protocols.io/view/soil-property-data-for-cocci-model-bibakaie | Robert Dobos, Orion Z. McCotter, Brendan R. Jackson, Kaitlin Benedict | TITLE: Soil_property_data_for_cocci_model
AUTHORS: Robert Dobos, Orion Z. McCotter, Brendan R. Jackson, Kaitlin Benedict
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This spreadsheet contains the soil property data extracted by the data extraction property scripts used by the cocci habitat suitab... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.udwes7e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Background: Until recently many researchers have examined energy and fatigue as opposite ends of a bipolar spectrum rather than two separate unipolar moods. Studies have also focused on a single variable to study these mood states rather than examining multiple variables simulta... | ["Obtain written informed consent", "[Measure weight and body composition using the Tanita TBF-410-GS]", "[Measure height using a standard stadiometer]", "[Complete surveys] Complete the following surveys\nPittsburgh Sleep Quality Inventory\nO'Connor Trait and State Mental and Physical Fatigue and Energy Survey\nRapid ... |
40,566 | A simple method for purification of immunoglobulin-Y (IgY). | 6 | dx.doi.org/10.17504/protocols.io.bjuwknxe | https://www.protocols.io/view/a-simple-method-for-purification-of-immunoglobulin-bjuwknxe | Angel Justiz-Vaillant | TITLE: A simple method for purification of immunoglobulin-Y (IgY).
AUTHORS: Angel Justiz-Vaillant
[STEPS]
?. Separate egg yolk from the egg white.
?. Add ten parts of distilled water to one part egg yolk.
?. Mix and stir slowly for 6.30 h at 4°C.
?. Centrifuge at 10 000 × g, at 4°C for 27 min to precipitate the lipid... | ["Separate egg yolk from the egg white.", "Add ten parts of distilled water to one part egg yolk.", "Mix and stir slowly for 6.30 h at 4°C.", "Centrifuge at 10 000 × g, at 4°C for 27 min to precipitate the lipids.", "Collect the supernatant containing the IgY.", "Slowly add potassium sulfate to the preparation or speci... |
94,763 | DAB Staining | 4 | dx.doi.org/10.17504/protocols.io.n2bvj34zplk5/v1 | https://www.protocols.io/view/dab-staining-c8sjzwcn | daniel.dautan, Per Svenningsson | TITLE: DAB Staining
AUTHORS: daniel.dautan, Per Svenningsson
[DESCRIPTION]
3, 3'-diaminobenzidine (DAB) staining of mouse brain tissue
[GUIDELINES]
All steps should be done on an orbital shaker.
[STEPS]
SECTION: Staining/Mounting Process
1. Wash freshly sectioned slices of tissue 2-3 times with 1X PBS to remove OCT.... | ["[Staining/Mounting Process] Wash freshly sectioned slices of tissue 2-3 times with 1X PBS to remove OCT.", "[Staining/Mounting Process] Quench sections for 15 min in 3 mL of quenching solution (0.1 mL 30% H2O2, 0.1 mL methanol, and 0.8 mL 1X PBS).", "[Staining/Mounting Process] Wash 4-5 times in 1X PBS.", "[Staining/... |
21,351 | Cell lysis, detergent-free | null | dx.doi.org/10.17504/protocols.io.y4ffytn | null | Teesha Luehr | TITLE: Cell lysis, detergent-free
AUTHORS: Teesha Luehr
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Detergents are generally not compatible with mass spectrometers, so this is a detergent-free method of cell lysis that is compatible with mass spectrometry. Since this protocol does not have a pre... | ["[Growing Cells]\nCulture HeLa cells in Dulbecco's modified Eagle's medium (DMEM) containing 10% FBS, 20mM glutamine, and 1% PenStrep.", "[Cell Lysis]\nResuspend the cell pellet(s) in\n[ice cold Milli-Q water]\nPerform the lysis and digestion in the . The lysis volumes, sonification, and digestion require the larger... |
35,130 | Protocol for introducing fluorescently labeled CRISPR/Cas9 RNP complex into heterotrophic dinoflagellates | null | dx.doi.org/10.17504/protocols.io.bei2jcge | null | Brittany Sprecher, Huan Zhang, Senjie Lin | TITLE: Protocol for introducing fluorescently labeled CRISPR/Cas9 RNP complex into heterotrophic dinoflagellates
AUTHORS: Brittany Sprecher, Huan Zhang, Senjie Lin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Introducing CRISPR/Cas9 machinery into the cell as RNP complexes reduces the number of s... | ["[1.\tPrepare the RNP complex from IDT]\nCombine 1 uL Alt-R™ CRISPR/Cas9 tracrRNA – ATTO™ 550 (100 uM) + 1 L Alt-R™ CRISPR/Cas9 crRNA (100 uM) + 18 uL IDT Nuclease Free Buffer", "[1.\tPrepare the RNP complex from IDT]\nIncubate at 95˚C for 5 minutes, let cool to room temperature on bench", "[1.\tPrepare the RNP comple... |
77,846 | Automation, live-cell imaging, and endpoint cell viability for 96-well plate drug screens | 2 | dx.doi.org/10.17504/protocols.io.x54v9dojzg3e/v1 | https://www.protocols.io/view/automation-live-cell-imaging-and-endpoint-cell-via-cp9wvr7e | Rolando DZ Lyles, M Julia Martinez, Benjamin Sherman, Kerry Burnstein | TITLE: Automation, live-cell imaging, and endpoint cell viability for 96-well plate drug screens
AUTHORS: Rolando DZ Lyles, M Julia Martinez, Benjamin Sherman, Kerry Burnstein
[DESCRIPTION]
To streamline the identification of potentially active cancer therapeutics, here we describe a highly adaptable semi-automated ap... | [] |
78,517 | Cyano_Interlab_study_protocols | 2 | dx.doi.org/10.17504/protocols.io.3byl4j69rlo5/v1 | https://www.protocols.io/view/cyano-interlab-study-protocols-cqwvvxe6 | maurice.mager1808 | TITLE: Cyano_Interlab_study_protocols
AUTHORS: maurice.mager1808
[DESCRIPTION]
All protocols used during the interlaboratory study published by Mager et al. 2023.
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ruid6ue | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The ROS measurements of the supernatant is performed by using DCF-DA, 2’,7’- dichlorofluorescein diacetate, a fluorescent probe for the assay. The formation of the oxidized fluorescent derivative (DCF) is monitored at excitation and emission wavelengths of 488 and 525 nm, res... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.sz2ef8e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>DNA-Blot genotyping of </strong><strong><em>Trypanosoma cruzi </em></strong><strong>Discrete Typing Units (DTU) with radiolabeled probes</strong></p>
[BEFORE_START]
<p><span style="font-weight: 400;">1. Prepare solutions:</span></p>
<ul>
<li style="font-weight: 400;... | [] |
44,478 | GHRU (Genomic Surveillance of Antimicrobial Resistance) Retrospective 1 Bioinformatics Methods | 5 | null | https://www.protocols.io/view/ghru-genomic-surveillance-of-antimicrobial-resista-bpn6mmhe | Anthony Underwood | TITLE: GHRU (Genomic Surveillance of Antimicrobial Resistance) Retrospective 1 Bioinformatics Methods
AUTHORS: Anthony Underwood
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A description of the pipelines used for analysing genome data from the retrospective 1 project of the NIHR Global Health Re... | ["De novo assemblyreads trimming and adapter removal using trimmomatic (0.38) [3], read correction using lighter (1.1.1) [4], downsampling to 100x coverage using seqtk (1.3) [5], read merging using flash (1.2.11) [6], assembly using SPAdes (3.12.0) [7]. Quality control was performed using fastqc (0.11.8) [8], multiq... |
86,130 | Immunohistochemistry for p-eIF2a and eIF2a, v.230804 | 1 | null | https://www.protocols.io/view/immunohistochemistry-for-p-eif2a-and-eif2a-v-23080-cycsxswe | elanalockshin | TITLE: Immunohistochemistry for p-eIF2a and eIF2a, v.230804
AUTHORS: elanalockshin
[DESCRIPTION]
Authors:
Callie Eatman, Elana Lockshin with recommendations from Xinlu Ding, Dan lab, UC-Berkeley
Calakos lab
Duke University
[STEPS]
SECTION: Reagents
1.
phospho-eIF2a antibody: Abcam ab32157
eIF2a antibody: Cell s... | ["[Reagents] phospho-eIF2a antibody: Abcam ab32157\n\n\neIF2a antibody: Cell signaling #5324", "[Tissue Prep] Brains are stored in 4% PFA for 24hrs in 4C before storage in 1xPBS in 4C until sectioning\nBrain is sectioned in 1xPBS bath into 40um slices using Vibratome.\nSlices are stored in 0.03% Sodium Azide in 1xPBS i... |
null | null | null | dx.doi.org/10.17504/protocols.io.puednte | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<h3>Antibiotic Concentrations</h3>
<table>
<thead>
<tr>
<th>Antibiotic</th>
<th>Recommended Stock Concentration</th>
<th>Recommended Working Concentration</th>
</tr>
</thead>
<tbody>
<tr>
<td>Ampicillin</td>
<td>100 mg/mL</td>
<td>100 µg/mL</td>
</tr>
<tr>
<td>Bleocin</td>
<td>5... | [] |
81,725 | Immunohistochemistry | 4 | dx.doi.org/10.17504/protocols.io.j8nlkwxxwl5r/v1 | https://www.protocols.io/view/immunohistochemistry-ct25wqg6 | Miguel Chuapoco | TITLE: Immunohistochemistry
AUTHORS: Miguel Chuapoco
[DESCRIPTION]
Outlines procedures to perform immunohistochemistry on tissue that had been treated with AAV.
[STEPS]
SECTION: Tissue slicing via vibratome (mice and rhesus macaque)
1. All tissue should be stored in PBS prior to slicing and further processing. Remo... | ["[Tissue slicing via vibratome (mice and rhesus macaque)] All tissue should be stored in PBS prior to slicing and further processing. Remove tissue and prepare for mounting. For mouse brain, we separate each half hemisphere. Rhesus macaque brain was separated into 4 mm thick coronal blocks. For all other tissue (e.g. ... |
45,293 | Protocol: Schonger & Sele, How to better communicate the exponential growth of infectious diseases, PLOS ONE 15(12), 2020. | 3 | dx.doi.org/10.17504/protocols.io.bqgmmtu6 | https://www.protocols.io/view/protocol-schonger-amp-sele-how-to-better-communica-bqgmmtu6 | Martin Schonger, Daniela Sele | TITLE: Protocol: Schonger & Sele, How to better communicate the exponential growth of infectious diseases, PLOS ONE 15(12), 2020.
AUTHORS: Martin Schonger, Daniela Sele
[STEPS] | [] |
77,128 | PIP MRI Magnetization Transfer Ratio (MTR) Measurement of Myelofibrosis in Mouse Tibia | 1 | dx.doi.org/10.17504/protocols.io.5jyl8jwy8g2w/v1 | https://www.protocols.io/view/pip-mri-magnetization-transfer-ratio-mtr-measureme-cpjgvkjw | Thomas L Chenevert | TITLE: PIP MRI Magnetization Transfer Ratio (MTR) Measurement of Myelofibrosis in Mouse Tibia
AUTHORS: Thomas L Chenevert
[DESCRIPTION]
The goal of this Co-Clinical Imaging Research Program (CIRP) pre-clinical imaging protocol (PIP) is to provide detailed description of key steps used to achieve a stated level of tech... | [] |
87,510 | Uncovering the Citation Landscape: Exploring OpenCitations COCI, OpenCitations Meta, and ERIH-PLUS in Social Sciences and Humanities Journals - Workflow | 5 | dx.doi.org/10.17504/protocols.io.n92ldpeenl5b/v5 | https://www.protocols.io/view/uncovering-the-citation-landscape-exploring-openci-czpwx5pe | Marta Soricetti, Sara Vellone, Olga Pagnotta, Lorenzo Paolini | TITLE: Uncovering the Citation Landscape: Exploring OpenCitations COCI, OpenCitations Meta, and ERIH-PLUS in Social Sciences and Humanities Journals - Workflow
AUTHORS: Marta Soricetti, Sara Vellone, Olga Pagnotta, Lorenzo Paolini
[DESCRIPTION]
Purpose
The main purpose of this research is to answer to three different... | ["[Processing of Input Data] We tried to define a mapping of the datasets to understand what are the information that the three datasets have in common. By looking at the data and the columns' names, we have identified the following:\n \nTaking as a starting point META, we have identified the COCI columns \"citing\" an... |
26,157 | Prepare NGM plates for nematode, with peptone, without fungizone | null | dx.doi.org/10.17504/protocols.io.5smg6c6 | null | Cancer Research UK / Wellcome Gurdon Institute media kitchen | TITLE: Prepare NGM plates for nematode, with peptone, without fungizone
AUTHORS: Cancer Research UK / Wellcome Gurdon Institute media kitchen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Prepare NGM plates for nematodes, with peptone, without fungizone</div></div>
[STEPS]
?.
?. ABC1Ingredients ... | ["ABC1Ingredients Quantity2NaCl 3g3bacto peptone 2.5g4Agar 17g5Double\n distilled H2O972ml\nABC1Ingredients Quantity2NaCl 3g3bacto peptone 2.5g4Agar 17g5Double\n distilled H2O972ml", "A1Measure 972ml \n double distilled H2O and put in a 1L duran bottle with a magnetic flea2Add 3g NaCl, 2.5g bacto peptone and st... |
82,166 | Phytoplankton Storm Simulation | 4 | null | https://www.protocols.click/view/phytoplankton-storm-simulation-cugwwtxe | AB | TITLE: Phytoplankton Storm Simulation
AUTHORS: AB
[DESCRIPTION]
Lab processing guide for phytoplankton culture experiments
[STEPS]
SECTION: Pre-Experimental Prep
1. Prior to the experiment you should prepare all treatment container. Be sure they are acid washed and you have plenty of nutrient
SECTION: Experimental L... | ["[Pre-Experimental Prep] Prior to the experiment you should prepare all treatment container. Be sure they are acid washed and you have plenty of nutrient", "[Experimental Layout] Treatments should be assigned to a Latin Square design in a 5x5 grid\n\n \n\nTreatments:\nA - Control\nB - Low Storm (50% salinity reduction... |
88,908 | Diamond XChem Seeding Protocol | 4 | dx.doi.org/10.17504/protocols.io.kxygx3nwog8j/v1 | https://www.protocols.io/view/diamond-xchem-seeding-protocol-c23kygkw | Peter Marples, daren.fearon, Charlie Tomlinson | TITLE: Diamond XChem Seeding Protocol
AUTHORS: Peter Marples, daren.fearon, Charlie Tomlinson
[DESCRIPTION]
The use of seeding in protein crystallisation is a highly effective method for increasing the quantity of usable crystals from a single plate and can be crucial for obtaining crystals in a highly reproducible m... | ["[Equiptment needed] Formulatrix Protein Crystallization Imager\nSPT mosquito \nP10 pipette\nSwissCI 3 lens plate [UVXPO-3LENS3W96T-PS3W96T-UVP]\nSeed beads [Hampton HR4-782]\nCrystalline material\nVortex\n0.5 mL Eppendorf tubes [Eppendorf Catalog No. 0030121023]", "[Seeding experiment] Produce crystals to use for see... |
63,390 | TRIM CLINICAL KETO REVIEWS – DOES IT REALLY WORK OR SCAM PILLS? READ IT BEFORE BUY! | 3 | dx.doi.org/10.17504/protocols.io.36wgq7y93vk5/v1 | https://www.protocols.io/view/trim-clinical-keto-reviews-does-it-really-work-or-b956r89e | Trim Clinical Keto | TITLE: TRIM CLINICAL KETO REVIEWS – DOES IT REALLY WORK OR SCAM PILLS? READ IT BEFORE BUY!
AUTHORS: Trim Clinical Keto
[DESCRIPTION]
Trim Clinical Keto Reviews: Pills can make your weight reduction routine simpler than any time in recent memory! This effective recipe has the ability to drive your body into ketosis.
... | [] |
25,790 | 11 Concentration and fluid exchanging | null | dx.doi.org/10.17504/protocols.io.5e6g3he | null | TJUSLS China | TITLE: 11 Concentration and fluid exchanging
AUTHORS: TJUSLS China
[STEPS]
?. [Concentrate]
1. The default concentrator is already inactive.2. Pre-cool the Thermo centrifuge to 4 °C in advance.3. Pour the protein solution to be concentrated into a concentrating tube, level it with the trim tube, place it in a Thermo c... | ["[Concentrate]\n1. The default concentrator is already inactive.2. Pre-cool the Thermo centrifuge to 4 °C in advance.3. Pour the protein solution to be concentrated into a concentrating tube, level it with the trim tube, place it in a Thermo centrifuge at 3400 rpm, stop at half an hour, pour off the effluent, and add ... |
null | null | null | dx.doi.org/10.17504/protocols.io.kzqcx5w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is kit-free and can be used to isolate high quality genomic DNA of predominantly <em>Symbiodinium</em> from symbiotic Aiptasia which can be used as e.g. PCR template for genotyping.</p>
<p> </p>
<p> It is based on the method described in Coffroth et al., 1992.</... | [] |
96,981 | Large volume viral RNA extraction using MagMAX Viral RNA Isolation Kit | 0 | null | https://www.protocols.io/view/large-volume-viral-rna-extraction-using-magmax-vir-daxv2fn6 | Erika Bujaki, Thomas Wilton, Dimitra Klapsa, Alison Tedcastle, Joyce Akello, Nick Grassly, Javier Martin | TITLE: Large volume viral RNA extraction using MagMAX Viral RNA Isolation Kit
AUTHORS: Erika Bujaki, Thomas Wilton, Dimitra Klapsa, Alison Tedcastle, Joyce Akello, Nick Grassly, Javier Martin
[DESCRIPTION]
This method describes large volume nucleic acid purification from sewage concentrates starting with 1.2 mL of sam... | ["Sample Processing", "Workflow A - Automated extraction", "Wash Solution 1\n Add indicated volume of 100% Isopropanol to the bottle of Wash Solution 1 Concentrate.\n Mix well by inverting at least 5 times and mark bottle to indicate that the alcohol was added.", "Reagent\npreparation", "Wash Solution 2\n\nAdd indica... |
72,727 | Use of a FlowCam for descriptive measurements of Aureococcus anophagefferens live culture cells | 1 | dx.doi.org/10.17504/protocols.io.14egn2336g5d/v1 | https://www.protocols.io/view/use-of-a-flowcam-for-descriptive-measurements-of-a-ci9xuh7n | Emily E. Chase, Laura Smith, Alex Truchon, Steven W Wilhelm | TITLE: Use of a FlowCam for descriptive measurements of Aureococcus anophagefferens live culture cells
AUTHORS: Emily E. Chase, Laura Smith, Alex Truchon, Steven W Wilhelm
[DESCRIPTION]
A protocol for acquiring an array of descriptive statistics (e.g., cell count, cell diameter, cell volume) for a monoculture of Aureo... | ["[SAMPLE AND CONTEXT FILE PREPARATION] Aureococcus anophagefferens cells are retrieved from a culture for measuring. At least 500 μL are required for each sample.", "[SAMPLE DESCRIPTIVE STATISTICS ACQUISITION] Following set-up of the FlowCam by manufacturer's instructions (using the 20✕ objective, 20✕ flow cells, and ... |
46,719 | Artificial seawater | 4 | dx.doi.org/10.17504/protocols.io.bru7m6zn | https://www.protocols.io/view/artificial-seawater-bru7m6zn | Simon Blanchoud | TITLE: Artificial seawater
AUTHORS: Simon Blanchoud
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Three alternative solutions for artificial seawater (ASW) have been tested successfully on our </span><span style = "font-style:italic;">Botrylloides</span><span> colonies. For routine work, we ... | ["[2X CSS]\nsea salt in H2O.\n70 g\n1 L", "[2X CSS]\nMix to dissolve.", "[2X CSS]\nFilter at 10 µm", "[10x CSHP]\nTo prepare 10X CSHP take NaCl262.9g4.5MKCl7.4g100mMCaCl29.9g90mMMgCl2 6H2O60.9g300mMMgSO4 7H2O39.4g160mMH2O1000ml\nNaCl262.9g4.5MKCl7.4g100mMCaCl29.9g90mMMgCl2 6H2O60.9g300mMMgSO4 7H2O39.4g160mMH2O1000ml",... |
60,839 | Donor Eligibility Criteria and Pancreas Recovery for HuBMAP TMC-PNNL-UF | 1 | dx.doi.org/10.17504/protocols.io.yxmvmnye5g3p/v2 | https://www.protocols.io/view/donor-eligibility-criteria-and-pancreas-recovery-f-b7nfrmbn | Jing Chen, Martha Campbell-Thompson, Clayton E Mathews | TITLE: Donor Eligibility Criteria and Pancreas Recovery for HuBMAP TMC-PNNL-UF
AUTHORS: Jing Chen, Martha Campbell-Thompson, Clayton E Mathews
[DESCRIPTION]
This document outlines inclusion and exclusion criteria for pancreas donors for the Human BioMolecular Atlas Program (HuBMAP) by the Tissue Mapping Center (TM... | ["Acceptance Criteria", "Inclusions\nAge range: 18-40 years\nEqual number of female and male donors will be accepted \nAll race and ethnicity are eligible\nBMI <28\t\nCause of death due to brain death (excludes donor after cardiac death (DCD))\nICU time <6 days\nReason pancreas was declined for transplantation may fact... |
107,030 | KAPP-Sen TMC: Placenta tissue blocks paraffin embedding | 0 | dx.doi.org/10.17504/protocols.io.261ge51bjg47/v1 | https://www.protocols.io/view/kapp-sen-tmc-placenta-tissue-blocks-paraffin-embed-dkrw4v7e | Ramalakshmi Ramasamy, Anne Marchini, Tim Adams, Elaine Bechtel, Lesley Bechtold | TITLE: KAPP-Sen TMC: Placenta tissue blocks paraffin embedding
AUTHORS: Ramalakshmi Ramasamy, Anne Marchini, Tim Adams, Elaine Bechtel, Lesley Bechtold
[DESCRIPTION]
Placenta formalin-fixed tissue blocks paraffin embedding at JAX Bar Harbor Histology Services.
[STEPS]
1. Procedure addition between sample collection a... | ["Procedure addition between sample collection at Mayo Clinic and JAX Bar Harbor Histology Services processing:", "Samples were received from Mayo Clinic in 10% NBF on ice.", "Formalin was replaced with 70% Ethanol and left overnight at room temperature.", "Samples were shipped at room temperature to JAX Bar Harbor His... |
104,647 | USDA LTAR Common Experiment measurement: Best practices for collection, handling, and analyses of water quantity measurements | 0 | dx.doi.org/10.17504/protocols.io.eq2lyw14wvx9/v1 | https://www.protocols.io/view/usda-ltar-common-experiment-measurement-best-pract-diff4bjn | Claire Baffaut, Harry Schomberg, Michael H. Cosh, Andrew M O'Reilly, Amartya Saha, Nicanor Z. Saliendra, Adam Schreiner-McGraw, Keirith A. Snyder | TITLE: USDA LTAR Common Experiment measurement: Best practices for collection, handling, and analyses of water quantity measurements
AUTHORS: Claire Baffaut, Harry Schomberg, Michael H. Cosh, Andrew M O'Reilly, Amartya Saha, Nicanor Z. Saliendra, Adam Schreiner-McGraw, Keirith A. Snyder
[DESCRIPTION]
Although each of ... | ["[Placement and site maintenance] Avoid placing monitoring equipment in areas regularly trafficked by farm vehicles.", "[Placement and site maintenance] Mark any equipment with flagging and/or signs notifying of its location.", "[Placement and site maintenance] Avoid placing monitoring equipment in areas prone to freq... |
71,489 | DNA - Ball Python DNA Amplification with TFEC primers | 4 | dx.doi.org/10.17504/protocols.io.3byl4jb78lo5/v1 | https://www.protocols.io/view/dna-ball-python-dna-amplification-with-tfec-primer-ch29t8h6 | Jose Avila Cervantes | TITLE: DNA - Ball Python DNA Amplification with TFEC primers
AUTHORS: Jose Avila Cervantes
[DESCRIPTION]
PCR amplification with Tfec set Exon 5 to genotype Piedball morph in Ball python (Python regius)
LEFT PRIMER AACTCAGAGCACTCCATGACC
RIGHT PRIMER CAGGTGTGCCCCTTTCATAA
[STEPS]
1. REAGENTS
10X PCR Buffe... | ["REAGENTS\n10X PCR Buffer\nMgSO420 millimolar (mM) \nTaq Polymerase 5U/ul\nPrimer Tfec exon5 Left 10 micromolar (µM) \nPrimer Tfec exon5 Right 10 micromolar (µM) \nDNTP's 10 micromolar (µM) \nUltra Pure Water\n100bp ladder (100-2,000 bp)\nSYBR Safe DNA stain\nLoading dye\nAgarose", "EQUIPMENT\nDNA LoBind tubes 1.5mL\n... |
38,975 | 2020_cocci_mapping_export_western_USA | 3 | dx.doi.org/10.17504/protocols.io.bia7kahn | https://www.protocols.io/view/2020-cocci-mapping-export-western-usa-bia7kahn | Robert Dobos | TITLE: 2020_cocci_mapping_export_western_USA
AUTHORS: Robert Dobos
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This spreadsheet contains map unit agggregated output of the cocci soil habitat model. Table headers are State, Area Symbol, Area Name, Map Unit Name, Map Unit Acres, Max HSI, and Muk... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.dys7wd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This buffer is used to stabilize samples for archiving and subsequentgenomic DNA extraction. <br /><br />SDS is dissolved to a concentration of 1% (w/v) in DNAB (DNA buffer: 0.4 M NaCl + 0.05 M EDTA in MilliQ water). The buffer may need to be warmed for SDS to completely dissolv... | [] |
39,866 | Frozen Tissue Nuclei Extraction (for 10xV3 snSEQ) | 1 | dx.doi.org/10.17504/protocols.io.bi62khge | https://www.protocols.io/view/frozen-tissue-nuclei-extraction-for-10xv3-snseq-bi62khge | Carly Martin, Abdul Abdul, Charles Vanderburg, Naeem Nadaf, Ashley Feirrera, Evan Macosko | TITLE: Frozen Tissue Nuclei Extraction (for 10xV3 snSEQ)
AUTHORS: Carly Martin, Abdul Abdul, Charles Vanderburg, Naeem Nadaf, Ashley Feirrera, Evan Macosko
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for extraction of nuclei from frozen tissue in preparation for single-nuclei sequencing... | ["Nuclei Extraction protocol, optimized for small tissue piecesMacosko Lab, Stanley Center, Broad Institute", "Dissociation Buffer: DBA stock of 500mls of Dissociation Buffer (DB) using ultrapure nuclease-free water and these reagents:Na2SO4 - 5.83 gK2SO4 - 2.615 gGlucose - 0.905 gHEPES - 1.2 gMgCl2- 2.... |
58,070 | HyDrop-RNA v1.0 | 1 | dx.doi.org/10.17504/protocols.io.b4xwqxpe | https://www.protocols.io/view/hydrop-rna-v1-0-b4xwqxpe | Florian De Rop, Suresh Poovathingal, Stein Aerts | TITLE: HyDrop-RNA v1.0
AUTHORS: Florian De Rop, Suresh Poovathingal, Stein Aerts
[DESCRIPTION]
Step-by-step protocol for performing HyDrop-RNA. The duration of each step assumes an experienced protocol user. For a first-time user, we recommend doubling the expected time for each step.
[STEPS]
SECTION: Microfluidic... | ["[Microfluidics Preparation] Setting up the Microfluidic Framework\nThese steps need to happen in advance before the run can be started, as time between the preparation of the cell resuspension in RT mix and actual encapsulation needs to be minimised to preserve cell viability.", "[Microfluidics Preparation] Boot up ... |
90,462 | Morphology of gracilis muscle and the topographic anatomy of its neurovascular pedicles | 1 | dx.doi.org/10.17504/protocols.io.e6nvwdm6dlmk/v1 | https://www.protocols.io/view/morphology-of-gracilis-muscle-and-the-topographic-c4j6yure | chettiar ganesh kumar, Bv Murlimanju | TITLE: Morphology of gracilis muscle and the topographic anatomy of its neurovascular pedicles
AUTHORS: chettiar ganesh kumar, Bv Murlimanju
[DESCRIPTION]
Gracilis
is often utilized as a graft in the procedures of reconstruction and functioning
muscle transfer.1 It is excellent for the closure of recto-vaginal
and r... | ["[Morphology of gracilis muscle and the topographic anatomy of its neurovascular pedicles] Morphology of gracilis muscle and the\ntopographic anatomy of its neurovascular pedicles"] |
91,286 | Thawing of cryopreserved hPSC | 4 | dx.doi.org/10.17504/protocols.io.e6nvwd282lmk/v1 | https://www.protocols.io/view/thawing-of-cryopreserved-hpsc-c5dwy27e | Valeria Fernandez Vallone, Lyn Healy, Nathalie Lefort, Katarzyna Ludwik, Tamer Onder, Lisa Pavinato, Fatma Visal FVO OKUR, Harald Stachelscheid | TITLE: Thawing of cryopreserved hPSC
AUTHORS: Valeria Fernandez Vallone, Lyn Healy, Nathalie Lefort, Katarzyna Ludwik, Tamer Onder, Lisa Pavinato, Fatma Visal FVO OKUR, Harald Stachelscheid
[DESCRIPTION]
This protocol describes thawing of hPSC.
[GUIDELINES]
Thawing procedure is described for one cryovial. The protoco... | ["[hPSC thawing] Remove cryovial containing frozen hPSC from liquid N2.", "[hPSC thawing] Sanitize the tube with 70 % volume ethanol.", "[hPSC thawing] Using 2 mL pipette transfer slowly hPSC suspension from the cryovial to a 15 mL conical tube.", "[hPSC thawing] Dropwise add 10 mL of culture media supplemented with su... |
58,850 | Efficient realization of quantum primitives for Shor's algorithm using PennyLane library | 5 | dx.doi.org/10.17504/protocols.io.b5qaq5se | https://www.protocols.io/view/efficient-realization-of-quantum-primitives-for-sh-b5qaq5se | Anatoly Antipov, Evgeniy Kiktenko, Aleksey Fedorov | TITLE: Efficient realization of quantum primitives for Shor's algorithm using PennyLane library
AUTHORS: Anatoly Antipov, Evgeniy Kiktenko, Aleksey Fedorov
[DESCRIPTION]
The following protocol describes how to use a software package
containing implementations of various quantum gates and well-known quantum
algor... | ["First of all, you should install the PennyLane library using the regular python environment and set up the Jupyter Notebook's environment", "Content of the Github repository should be uploaded on your PC via the following link:\n\nhttps://github.com/Anatoly-Antipov/QuantumOperations\n\nFiles with the extension \".py\... |
59,914 | DNA extraction from dermatophytes using the Macherey-Nagel NucleoSpin™ Blood QuickPure kit (REF: 740569) | 4 | dx.doi.org/10.17504/protocols.io.e6nvwkbpzvmk/v1 | https://www.protocols.io/view/dna-extraction-from-dermatophytes-using-the-macher-b6rird4e | Khalid El Moussaoui | TITLE: DNA extraction from dermatophytes using the Macherey-Nagel NucleoSpin™ Blood QuickPure kit (REF: 740569)
AUTHORS: Khalid El Moussaoui
[DESCRIPTION]
This protocol describes the steps necessary to extract and purify genomic DNA from dermatophytes (and more specifically from dermatophytes of the genus Trichophyto... | ["[Medium preparation] Dissolve 30 g of in \n1 L of and let mix on the heated magnetic stirrer for 5 min (temperature and mixing speed knob at mid-step).", "[Medium preparation] Cover the flask with glass wool and aluminium foil. Autoclave it at 121 °C for 30 min.", "[Cultivation of the strains] After allowing to ... |
26,372 | Prepare NGM plates with Amphotericin B | null | dx.doi.org/10.17504/protocols.io.5zcg72w | null | Research Cancer UK / Wellcome Gurdon Institute media kitchen | TITLE: Prepare NGM plates with Amphotericin B
AUTHORS: Research Cancer UK / Wellcome Gurdon Institute media kitchen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Prepare NGM plates with amphotericin B</div><div class = "text-block"><span>From "</span><a href="https://www.thermofisher.com/order/cat... | ["ABCD1Ingredients Quantity2NGM Media 1L3Cholesterol 5mg/ml1ml41M CaCl21ml51M MgSO41ml61M KH2PO425ml7Petri dish30mmas required8 50mmas required9 90mmas required10Fungizone400 microlitres 1 microtubbe\nABCD1Ingredients Quantity2NGM Media 1L3Cholesterol 5mg/ml1ml41M CaCl21ml51M MgSO41ml61M KH2PO425ml7Petri dish30mmas... |
28,614 | Cell cultures, transfection and treatments | 1 | dx.doi.org/10.17504/protocols.io.77ehrje | https://www.protocols.io/view/cell-cultures-transfection-and-treatments-77ehrje | Federico Herrera | TITLE: Cell cultures, transfection and treatments
AUTHORS: Federico Herrera
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Human glioblastoma U251 cells and rat brain glioma C6 cells were grown to confluence in Dulbecco´s Minimal Essential Medium (DMEM) supplemented with 10% (v/v )fetal bovin... | [] |
38,695 | Enzyme linked immunosorbent assays (ELISAs) for mouse IL-10, IL-6, IL-1β and TNF-α | 6 | dx.doi.org/10.17504/protocols.io.bh2fj8bn | https://www.protocols.io/view/enzyme-linked-immunosorbent-assays-elisas-for-mous-bh2fj8bn | Anja De Lange, Avril Walters, Nai-Jen Hsu, Muazzam Jacobs, Joseph V Raimondo | TITLE: Enzyme linked immunosorbent assays (ELISAs) for mouse IL-10, IL-6, IL-1β and TNF-α
AUTHORS: Anja De Lange, Avril Walters, Nai-Jen Hsu, Muazzam Jacobs, Joseph V Raimondo
[STEPS]
?. Acquire the necessary reagents and antibodies.
?. Salts (all available from Sigma-Aldrich):34.56 g Na2HPO4192 g NaCl5.76 g of KH2PO4... | ["Acquire the necessary reagents and antibodies.", "Salts (all available from Sigma-Aldrich):34.56 g Na2HPO4192 g NaCl5.76 g of KH2PO44.8 g of KCl2.23 g NaN30.12 g MgCl2.6H2OOther reagents for solutions (all available from Sigma-Aldrich):10 ml Tween 2025 g BSA14.6 ml di-ethanolamine37 % HCL (about 10 ml)", "Prepare sto... |
55,438 | COVID-19: Hospital pharmacological treatment according to geographic region in Colombia | 1 | dx.doi.org/10.17504/protocols.io.b2dnqa5e | https://www.protocols.io/view/covid-19-hospital-pharmacological-treatment-accord-b2dnqa5e | Jorge Machado Alba | TITLE: COVID-19: Hospital pharmacological treatment according to geographic region in Colombia
AUTHORS: Jorge Machado Alba
[DESCRIPTION]
Introduction: The impact of COVID-19 prompted a race to find a treatment that would reduce its mortality. Most studies have not shown favorable results for many of these drug... | [] |
87,010 | FLIM-FRET analyses with mCitrine-mScarlet-I transiently expressed in N. benthamiana | 4 | dx.doi.org/10.17504/protocols.io.6qpvr38epvmk/v1 | https://www.protocols.io/view/flim-fret-analyses-with-mcitrine-mscarlet-i-transi-cy8axzse | Elena-Kristin.Petutschnig, leon.pierdzig, Josephine Mittendorf, Jule Meret Niebisch, Volker Lipka | TITLE: FLIM-FRET analyses with mCitrine-mScarlet-I transiently expressed in N. benthamiana
AUTHORS: Elena-Kristin.Petutschnig, leon.pierdzig, Josephine Mittendorf, Jule Meret Niebisch, Volker Lipka
[DESCRIPTION]
Elucidating protein-protein interactions is crucial for our understanding of molecular processes within li... | ["[Agrobacterium transformation] Transform suitable Agrobacterium tumefaciens strain and select transformants on LB plates containing appropriate antibiotics.\nFor the control constructs pGreenII-0229-p35S-mCitrine, pGreenII-0229-p35S-mScarlet-I and pGreenII-0229-p35S-mCitrine-mScarlet-I transform Agrobacterium tumefac... |
null | null | null | dx.doi.org/10.17504/protocols.io.ehubb6w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol provides method for KEGG Analysis, Gene Ontology Analysis, and Operational Protein Family Analysis. Based on the methods from the following publication: <br /><br />Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.crev3d | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Protocol for using Mouse-FMRP antibody follow immunoprecipitation of FMRP using a rabbit antibody such as Abcam #17722
[GUIDELINES]
This protocol is still in progress, will be updated periodically.
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
39,203 | Root nitrate influx | 4 | dx.doi.org/10.17504/protocols.io.biibkcan | https://www.protocols.io/view/root-nitrate-influx-biibkcan | Prajakta Bendre, Vanessa Melino | TITLE: Root nitrate influx
AUTHORS: Prajakta Bendre, Vanessa Melino
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><pre><code><div class = "text-blocks"></div></code></pre></div><div class = "text-block"><div class = "justify" style = "text-align:justify"><span>Nitrogen (N) in the form of nitrate ... | ["Grow barley plants hydroponically according to the desired growth conditions.", "Prepare the set up by pre-filling 50 ml centrifuge tubes with solutions (1-4 above) and aerate.", "[DAY 18]\n18- day old barley plants were removed from their collars and two plants were bundled together at the stem. These two barley pla... |
null | null | null | dx.doi.org/10.17504/protocols.io.exqbfmw | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<strong>Reagent List:</strong><br />
<ul>
<li>Cell Staining Buffer (BioLegend Cat. No. 420201)</li>
<li>Red Cell Lysis Buffer (BioLegend Cat. No. 420301)</li>
<li>7-AAD Viability Staining Solution (BioLegend Cat. No. 420403)</li>
<li>TruStain FcX™ (anti-CD16/32, BioLegend Cat. No... | [] |
92,138 | ORFanID Web-based Search Engine to Identify Orphan and Taxonomically Restricted Genes | 1 | dx.doi.org/10.17504/protocols.io.14egn37jql5d/v2 | https://www.protocols.io/view/orfanid-web-based-search-engine-to-identify-orphan-c58iy9ue | Thushara Galbadage, Vinodh Gunasekera, Emanuel Tundrea, Richard S. Gunasekera | TITLE: ORFanID Web-based Search Engine to Identify Orphan and Taxonomically Restricted Genes
AUTHORS: Thushara Galbadage, Vinodh Gunasekera, Emanuel Tundrea, Richard S. Gunasekera
[DESCRIPTION]
ORFanID is a web-based software engine designed to identify ORFan genes from genomes of interest; from a given list of DNA or... | ["[Accessing ORFanID] Navigate to ORFanID's webpage at http://www.orfangenes.com/", "[Accessing ORFanID] Click \"Get Started\" on the home page to access the search system.", "[Input Methods] Choose between searching for a gene sequence or using an accession number. For instance, to search a Homo sapiens sample, use th... |
68,366 | Transformation | 4 | dx.doi.org/10.17504/protocols.io.36wgq7xpyvk5/v1 | https://www.protocols.io/view/transformation-cezntf5e | Ana Belem García González, Georgina Diego, Irán Alessandra Chaparro Rodríguez, Jair Alexis Gardea Sáenz | TITLE: Transformation
AUTHORS: Ana Belem García González, Georgina Diego, Irán Alessandra Chaparro Rodríguez, Jair Alexis Gardea Sáenz
[DESCRIPTION]
A protocol for transforming E. coli cells is shown.
[STEPS]
SECTION: Transformation
1. Mix 50 µLof fresh competent cells with2 µLof genetic material (softly without pipe... | ["[Transformation] Mix 50 µLof fresh competent cells with2 µLof genetic material (softly without pipetting) in a sterile 1.5 mL Eppendorf tube.", "[Transformation] Incubate on ice for 30 min", "[Transformation] Apply thermal shock in a water bath at 42 °Cfor 30 s", "[Transformation] Immediately, put on ice", "[Transfor... |
24,272 | Genome-wide SNP data unveil admixture of Chinese indigenous chicken breeds with commercial breeds | null | dx.doi.org/10.17504/protocols.io.3xqgpmw | null | Changsheng Nie | TITLE: Genome-wide SNP data unveil admixture of Chinese indigenous chicken breeds with commercial breeds
AUTHORS: Changsheng Nie
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In this study, we aimed to evaluate the genetic diversity and population structure of eight chicken breeds (including conse... | ["# Documentation#Pairwise LD measures for multiple SNPs (genome-wide)#source: http://zzz.bwh.harvard.edu/plink/ld.shtmlplink --file mydata --r2#running ADMIXTURE in multithreaded mode#source: http://software.genetics.ucla.edu/admixture/admixture-manual.pdfadmixture ~Data/dataset.bed 3 -j4for K in 1 2 3 4 5; \\do admix... |
64,377 | Vissentials Max BHB Reviews It Gives You Slim & Trim Figure Buy It Now | 3 | dx.doi.org/10.17504/protocols.io.8epv59opng1b/v1 | https://www.protocols.io/view/vissentials-max-bhb-reviews-it-gives-you-slim-amp-ca4zsgx6 | StednKih | TITLE: Vissentials Max BHB Reviews It Gives You Slim & Trim Figure Buy It Now
AUTHORS: StednKih
[DESCRIPTION]
-->Vissentials Max BHB Reviews It Gives You Slim & Trim Figure Buy It Now
[STEPS] | [] |
35,797 | Dissociation of Anopheles sp midgut into single-cell suspension for scRNAseq | 1 | dx.doi.org/10.17504/protocols.io.j8nlke246l5r/v1 | https://www.protocols.io/view/dissociation-of-anopheles-sp-midgut-into-single-ce-be7vjhn6 | Silvain Pinaud, Virginia.Howick, Mara Lawniczak | TITLE: Dissociation of Anopheles sp midgut into single-cell suspension for scRNAseq
AUTHORS: Silvain Pinaud, Virginia.Howick, Mara Lawniczak
[DESCRIPTION]
Dissociation of Anopheles sp midgut into a single-cell suspension for scRNAseq
Here, we develop a method of cold dissociation for the mosquito midgut and salivar... | ["[Prepare dissociation buffer] Dissociation will be carry on in chambered slides that allow to handle low volume (<400µL) for the dissociation while being monitoring under a microscope.\n\nNB: The dissociation needs to be visually monitored using a microscope to check the proportion of single cells vs surrounding debr... |
73,215 | P9b Generación informe anual Garantía de Calidad | 1 | dx.doi.org/10.17504/protocols.io.n2bvj8nybgk5/v1 | https://www.protocols.io/view/p9b-generaci-n-informe-anual-garant-a-de-calidad-cjq7umzn | cgarcia | TITLE: P9b Generación informe anual Garantía de Calidad
AUTHORS: cgarcia
[DESCRIPTION]
Procedimiento de Generación informe anual revisión garantía de calidad
[STEPS]
SECTION: P9b Generación informe anual Garantía de Calidad
1. PROCEDIMIENTO DE GENERACIÓN INFORME ANUAL REVISIÓN GARANTÍA DE CALIDAD
Desde la EIDUCAM, e... | ["[P9b Generación informe anual Garantía de Calidad] PROCEDIMIENTO DE GENERACIÓN INFORME ANUAL REVISIÓN GARANTÍA DE CALIDAD\nDesde la EIDUCAM, es necesario establecer mecanismos de control que permitan a las Comisiones Académicas revisar diferentes aspectos relacionados con el desarrollo de nuestros Programas de Doctor... |
32,296 | Wuhan coronavirus (2019-nCoV) real-time RT-PCR ORF1ab 2020 (Wuhan-ORF1ab) | null | dx.doi.org/10.17504/protocols.io.bbsginbw | null | Judy A. Northill, Ian Mackay | TITLE: Wuhan coronavirus (2019-nCoV) real-time RT-PCR ORF1ab 2020 (Wuhan-ORF1ab)
AUTHORS: Judy A. Northill, Ian Mackay
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><ul style = "list-style-type:disc;"><li style = "counter-reset:ol0;list-style-type:disc;"><span>A real-time RT-PCR to detect the "nov... | ["[Mix]\nOligonucleotides ABC1Oligo NameSequence 5'-3'Location based on NC_045512*2WuhanORF1ab-FAATCCACCTGCTCTACAAGATG5455-54763WuhanORF1ab-RCATCACCTAACTCACCTACTGTC5566-55444WuhanORF1ab-P6FAM-AGCTTCACCAGCCCTTGCTCT-BHQ15505-5485\nABC1Oligo NameSequence 5'-3'Location based on NC_045512*2WuhanORF1ab-FAATCCACCTGCTCTACAAGA... |
62,994 | VitalCare Nutrition Keto Gummies - World #1 Weight Loss Supplement | 3 | dx.doi.org/10.17504/protocols.io.x54v9ywr4g3e/v1 | https://www.protocols.io/view/vitalcare-nutrition-keto-gummies-world-1-weight-lo-b9rsr56e | G A | TITLE: VitalCare Nutrition Keto Gummies - World #1 Weight Loss Supplement
AUTHORS: G A
[DESCRIPTION]
That means, when we run out - which we expect will occur in the following week or somewhere in the vicinity - you're in really bad shape. In this way, don't pass up a great opportunity! Request today and guarantee the... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.hvcb62w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Luminex Milliplex Cardiovascular Disease 3-plex Panel 2 instructions per manufacturer.</p>
[STEPS]
?.
?. | [] |
43,875 | Bioinformatics Analysis | 4 | dx.doi.org/10.17504/protocols.io.bn4bmgsn | https://www.protocols.io/view/bioinformatics-analysis-bn4bmgsn | Vasso Makrantoni, Daniel Robertson, Adele L. Marston | TITLE: Bioinformatics Analysis
AUTHORS: Vasso Makrantoni, Daniel Robertson, Adele L. Marston
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A plethora of biological processes like gene transcription, DNA replication, DNA recombination, and chromosome segregation are mediated through protein–DNA int... | ["[Bioinformatics Analysis]\nCarry out all data processing on an Ubuntu 16.04 (xenial) operating system. Perform basecalls using Illumina Real-Time Analysis (RTA2) software on the MiniSeq System. Use FastQC to assess the quality of the raw sequence data (fastq reads), with fastq-screen used to detect any unwanted conta... |
64,792 | Geocarto International manuscript data | 3 | dx.doi.org/10.17504/protocols.io.5jyl89j77v2w/v2 | https://www.protocols.io/view/geocarto-international-manuscript-data-cbhysj7w | Pshegusov R.H., Chadaeva V.A. | TITLE: Geocarto International manuscript data
AUTHORS: Pshegusov R.H., Chadaeva V.A.
[DESCRIPTION]
This paper presents an approach to studying rangeland degradation by integrating remote sensing data, geographic information systems, and ecological niche theory. The document provides information about the source dat... | [] |
25,823 | ISOLATION AND VALIDATION OF CLONAL TRANSGENIC LINES (Basic Protocol 4) | null | dx.doi.org/10.17504/protocols.io.5f7g3rn | null | Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward | TITLE: ISOLATION AND VALIDATION OF CLONAL TRANSGENIC LINES (Basic Protocol 4)
AUTHORS: Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>While transgenic populations may be enriched to near-purity u... | ["[Serial Dilution]\nPrepare one well of 80 % confluent post-transfected cells from a 6-well plate as for an Accutase split (see Basic Protocol 1, Step-case 'EDTA-mediated removal of spontaneously differentiating cells', step 20).\nClonal isolation may be performed immediately after transfection; however, permitting ou... |
null | null | null | dx.doi.org/10.17504/protocols.io.dqn5vd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in "<a href="https://www.protocols.io/view/Obtaining-pure-cyanophage-stocks-liquid-assay-dqm5u5" target="_blank">Obtaining pure cyanophage stocks (liquid assay)</a>"
[STEPS]
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.h65b9g6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
73,325 | Multi-dimensional potential factors associated with COVID-19 vaccine booster acceptance among the Bangladeshi people: a cross-sectional study | 1 | dx.doi.org/10.17504/protocols.io.j8nlkw88wl5r/v1 | https://www.protocols.io/view/multi-dimensional-potential-factors-associated-wit-cjumunu6 | dn.roy | TITLE: Multi-dimensional potential factors associated with COVID-19 vaccine booster acceptance among the Bangladeshi people: a cross-sectional study
AUTHORS: dn.roy
[DESCRIPTION]
This protocol designed to assess the COVID-19 booster vaccine acceptance and identify the multi-dimensional potential factors influencing bo... | [] |
99,220 | Sucrose lysis buffer | 1 | null | https://www.protocols.io/view/sucrose-lysis-buffer-dc5u2y6w | Colleen Kellogg | TITLE: Sucrose lysis buffer
AUTHORS: Colleen Kellogg
[DESCRIPTION]
This protocol describes the preparation of sucrose lysis buffer to preserve DNA on sterivex filters. The protocol is part of the Hakai Institute's pipeline to analyze microbial and environmental DNA from seawater samples and is implemented as a standar... | ["[METHODS] Filter-sterilize and label bottle.", "[METHODS] Top up water to 500 mL. (no need to pH this one!)", "[METHODS] Add a stir bar and dissolve all powder.", "[METHODS] Add milliQ water to about the 400 mL line.", "[METHODS] Add 25 mL of 1 Molarity (M) Tris to the beaker.\n\nCalculation of Tris or EDTA:\nUse the... |
79,716 | Assessment of prepulse inhibition (PPI) of the acoustic startle reflex in rodents | 5 | dx.doi.org/10.17504/protocols.io.5qpvor4o7v4o/v1 | https://www.protocols.io/view/assessment-of-prepulse-inhibition-ppi-of-the-acous-cr4cv8sw | Franciele Kich Giongo, Matheus Gallas-Lopes, Ana P Herrmann | TITLE: Assessment of prepulse inhibition (PPI) of the acoustic startle reflex in rodents
AUTHORS: Franciele Kich Giongo, Matheus Gallas-Lopes, Ana P Herrmann
[DESCRIPTION]
The acoustic startle reflex is an automatic and involuntary response that occurs in humans and other animals when they are exposed to sudden and in... | ["[Setting up the protocol] To create a new protocol, click on the logo in the upper left corner and select \"Edit\" and then \"Procedure\".\n\n \nTo create a new prepulse protocol, select \"Create a new procedure file starting with a standard PPI block\" and name the protocol.\n\n \nIf you already have a saved proto... |
35,283 | Artificial Cerebrospinal Fluid III (ACSF.III) | null | dx.doi.org/10.17504/protocols.io.beptjdnn | null | Allen Institute for Brain Science | TITLE: Artificial Cerebrospinal Fluid III (ACSF.III)
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Artificial Cerebrospinal Fluid III (ACSF.III) is used for applications including tissue bath solution during electrophysiological recording.</div><div class... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.guibwue | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Purpose:</strong> To quantify virus-like particles in culture or environmental samples.</p>
<p><strong>Summary:</strong> Host cells and virus-like particles are enumerated from the same glutaraldehyde-fixed sample. For virus counts, an aliquot is diluted in 0.02-µm-fi... | [] |
69,444 | Setting a sequencing run with a nanopore MinION and the Rapid Sequencing gDNA kit (SQK-RAD004) | 4 | dx.doi.org/10.17504/protocols.io.4r3l2oy53v1y/v3 | https://www.protocols.io/view/setting-a-sequencing-run-with-a-nanopore-minion-an-cf3ctqiw | Narjol Gonzalez-Escalona | TITLE: Setting a sequencing run with a nanopore MinION and the Rapid Sequencing gDNA kit (SQK-RAD004)
AUTHORS: Narjol Gonzalez-Escalona
[DESCRIPTION]
This protocol is to help in setting up a MinION sequencing run using the rapid sequencing kit from Nanopore (SQK-RAD004). It contains all steps and material need for a s... | ["[Preparation of the DNA Library:] Thaw all reagents in box 1 and 2 of the RAD004 kit.", "[Preparation of the DNA Library:] Take a flow cell from 4-8 °C and leave it at room temperature (RT).", "[Preparation of the DNA Library:] Prepare the DNA to the suggested concentration of 400 ng total in 7.5 µL, or a concentrat... |
73,885 | FAME analysis of pollen fatty acids | 1 | dx.doi.org/10.17504/protocols.io.dm6gpj935gzp/v1 | https://www.protocols.io/view/fame-analysis-of-pollen-fatty-acids-ckd5us86 | Mark J. Carroll | TITLE: FAME analysis of pollen fatty acids
AUTHORS: Mark J. Carroll
[DESCRIPTION]
This protocol uses FAME (Fatty Acid Methyl Esterification) techniques adapted from Seppanen-Laasko et al., 2002 to quantify fatty acid contents in small samples (10 mg) of anther pollen, corbicular pollen, or stored pollen. Pollen is ini... | ["Add 1mm zirconia beads to a 2 mL homogenizer tube and fill tube 1/4 full for each pollen sample. Keep the amount the same among samples and standards.", "Add 10.0 mg pollen (usually about 1-2 mg lipid equivalent) to the homogenizer tube.", "[Folch Extraction and Partition of Fatty Acids] Add 1000 µL 2:1 chloroform: m... |
57,189 | Matrigel coating cell culture plates | 4 | null | https://www.protocols.io/view/matrigel-coating-cell-culture-plates-b34dqqs6 | JUSTIN.MCDONOUGH | TITLE: Matrigel coating cell culture plates
AUTHORS: JUSTIN.MCDONOUGH
[DESCRIPTION]
Matrigel is used to pre-coat cell culture dishes and provide an attachment surface for feeder-free human iPS cells to replicate on.
We use Matrigel from Corning (product number) that is provided in a glass bottle as a concentrated l... | ["24W plate: In an appropriate-sized tube, prepare enough 1X Matrigel to distribute 300-500ul of solution to each well of the 24W plate as needed.", "Working quickly, dilute cold 40X Matrigel 1:40 in cold DMEM/F12. This works out to 25ul of 40X Matrigel for every 1ml of DMEM/F12", "Mix by pipetting and distribute 300-... |
94,192 | Optical densitometry of tyrosine hydroxylase fibers | 4 | dx.doi.org/10.17504/protocols.io.kqdg3xo71g25/v1 | https://www.protocols.io/view/optical-densitometry-of-tyrosine-hydroxylase-fiber-c78qzrvw | mariangela.massarocenere | TITLE: Optical densitometry of tyrosine hydroxylase fibers
AUTHORS: mariangela.massarocenere
[DESCRIPTION]
Protocol for quantifying TH+ fibers in rat striatum and substantia nigra pars reticulata (SNpr)
[STEPS]
1. Acquire images with a light microscope of immunostained serial coronal sections covering the caudo-rostr... | ["Acquire images with a light microscope of immunostained serial coronal sections covering the caudo-rostral of the brain regions (3sections/animal for striatum and SNpr)", "Open ImageJ (RRID:SCR_003070,https://imagej.net/)", "Calibrate grey mean values for standard optical density values", "Open 8-bit images in ImageJ... |
99,872 | PBS with 0.1% Sodium Azide | 1 | dx.doi.org/10.17504/protocols.io.rm7vz8q28vx1/v2 | https://www.protocols.io/view/pbs-with-0-1-sodium-azide-ddr8259w | Allen Institute for Brain Science | TITLE: PBS with 0.1% Sodium Azide
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
This protocol describes the method for preparing PBS with 0.1% Sodium Azide for storage and/or processing of fixed tissue.
Note: Research reported in this publication was supported by the National Institute Of Mental Health of ... | [] |
88,265 | DNA EXTRACTION Protocol Template | 1 | null | https://www.protocols.io/view/dna-extraction-protocol-template-c2fhybj6 | Kathleen Pitz, Raissa.meyer | TITLE: DNA EXTRACTION Protocol Template
AUTHORS: Kathleen Pitz, Raissa.meyer
[DESCRIPTION]
A protocol template created through the BeBOP project for DNA Extraction.
[STEPS]
SECTION: Protocol Template
1. Minimum Information about an Omics Protocol (MIOP)
See https://github.com/BeBOP-OBON/miop/blob/main/model/schema/t... | ["[Protocol Template] Minimum Information about an Omics Protocol (MIOP)\n\nSee https://github.com/BeBOP-OBON/miop/blob/main/model/schema/terms.yaml for list and definitions.\n\n\n\n \nMIOP Term\nValue\n \nmethodology category\n\n \nproject\n\n \npurpose\n\n \nanalyses\n\n \ngeographic location\n\n \nbroad-scale env... |
52,093 | Long-read plant genome assembly and annotation: scaffolding | 5 | null | https://www.protocols.io/view/long-read-plant-genome-assembly-and-annotation-sca-bw45pgy6 | Scott Ferguson, Ashley Jones, Justin Borevitz | TITLE: Long-read plant genome assembly and annotation: scaffolding
AUTHORS: Scott Ferguson, Ashley Jones, Justin Borevitz
[DESCRIPTION]
With the introduction of long-read, third generation sequencing (e.g. Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) and associated bioinformatics tools, we ca... | ["[Genome scaffolding] Currently your genome will not exist as full chromosomes, rather as fragmented sections of chromosomes. To increase the utility of your genome scaffolding is performed. Scaffolding attempts to find how your sequences should be joined to form full chromosomes and joins them. There are a number of ... |
52,561 | Intracardial perfusion for electrophysiology in rat | 4 | dx.doi.org/10.17504/protocols.io.81wgb7ey3vpk/v2 | https://www.protocols.io/view/intracardial-perfusion-for-electrophysiology-in-ra-bxjrpkm6 | Alicia Avelar | TITLE: Intracardial perfusion for electrophysiology in rat
AUTHORS: Alicia Avelar
[DESCRIPTION]
This protocol is to use for clearing blood from the brain and helping to maintain viable cells for electrophysiology experiments. No PFA or any tools that have had contact with PFA should be used. This intracranial perfusi... | ["[Anesthesia] anesthetize rat with isoflurane anesthesia machine.", "[Anesthesia] when rat is lying down immobile, doesn’t right it’s position when moved, and is breathing slowly put isoflurane nose cone on rat and test for pain with forceps toe pinch of both feet", "[Surgery and intracranial perfusion] open rat thora... |
20,950 | During data acquisition | null | dx.doi.org/10.17504/protocols.io.ypwfvpe | null | Lukas Snoek, Tinka Beemsterboer | TITLE: During data acquisition
AUTHORS: Lukas Snoek, Tinka Beemsterboer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol lists all the steps necessary to run your MRI experiment/data acquisition safely and in a way that yields high-quality data. Moreover, if you use the centre's QC/prep... | ["[Create new examination]\nAfter you've made sure your exam cards are BIDS-compatible, you can create a new examination by clicking on 'Patients' in the menu bar and subsequently on 'New administration'. Here, you have to fill in some information about the participant. An example can be found in the image below:Fill i... |
22,301 | Semi-thin section analysis | null | dx.doi.org/10.17504/protocols.io.zz5f786 | null | Sue Lin | TITLE: Semi-thin section analysis
AUTHORS: Sue Lin
[STEPS]
?. Double fixation: The specimen was first fixed with 2.5% glutaraldehyde in phosphate buffer (pH7.0) for more than 4 hours; washed three times in the phosphate buffer; then postfixed with 1% OsO4 in phosphate buffer (pH7.0) for 1 hour and washed three times i... | ["Double fixation: The specimen was first fixed with 2.5% glutaraldehyde in phosphate buffer (pH7.0) for more than 4 hours; washed three times in the phosphate buffer; then postfixed with 1% OsO4 in phosphate buffer (pH7.0) for 1 hour and washed three times in the phosphate buffer.", "Dehydration: The specimen was firs... |
51,688 | Cyanobacteria Encapsulation in Sepiolite-Alginate Beads | 6 | dx.doi.org/10.17504/protocols.io.bwqgpdtw | https://www.protocols.io/view/cyanobacteria-encapsulation-in-sepiolite-alginate-bwqgpdtw | Jorge Fernández Méndez, celiamm | TITLE: Cyanobacteria Encapsulation in Sepiolite-Alginate Beads
AUTHORS: Jorge Fernández Méndez, celiamm
[DESCRIPTION]
Cyanobacteria can be encapsulated in biohybrid materials, with components such as biopolymers and clays, as in this case. With alginate (biopolymer) and sepiolite (clay that provides better biocomp... | ["[Solutions preparation] IMPORTANT: the amounts used are the experimental ones did it experimentally, it could change. \n\nHaving different options to do the alginate: sepiolite solutions, best of all are explained.\n\nFirst, produce a 8 % (v/v) suspension of alginate. It is IMPORTANT to mention that it is difficult t... |
28,120 | Hybridization chain reaction (HCR) protocol for tails of mouse embryos | null | dx.doi.org/10.17504/protocols.io.7pyhmpw | null | Paul Gerald Layague Sanchez, Hidenobu Miyazawa, Molecular Instruments | TITLE: Hybridization chain reaction (HCR) protocol for tails of mouse embryos
AUTHORS: Paul Gerald Layague Sanchez, Hidenobu Miyazawa, Molecular Instruments
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is for the in situ hybridization chain reaction (HCR) of intact tails (somi... | ["[Day 3: Rehydration of samples and HCR detection stage ]\nRehydrate samples (one sample per PCR tube, capacity = max) with a series of graded methanol : PBST (PBS + 0.1% Tween) washes.100% methanol 75% methanol : 25% PBST 50% methanol : 50% PBST 25% methanol : 75% PBST 100% PBST 100% PBST\n200 µl", "[Day 3: Rehydrat... |
78,063 | Single cell/nuclei RNAseq analysis | 5 | dx.doi.org/10.17504/protocols.io.n2bvj8bzbgk5/v1 | https://www.protocols.io/view/single-cell-nuclei-rnaseq-analysis-cqgpvtvn | Raquel Garza | TITLE: Single cell/nuclei RNAseq analysis
AUTHORS: Raquel Garza
[DESCRIPTION]
This protocol describes the process for the single cell/nuclei RNA sequencing data of the manuscript "L1retrotransposons drive human neuronal transcriptome complexity and functional diversification " from fetal forebrain and adult prefrontal... | ["[Preprocessing] The raw base calls were demultiplexed and converted to sample-specific fastq files using 10x Genomics Cell Ranger mkfastq (version 3.1.0; RRID:SCR_017344).", "[Gene expression] Cell Ranger count was run with default settings, using an mRNA reference for single-cell samples and a pre-mRNA reference (ge... |
31,106 | SPARC - Preparation of Plasma Samples from Rats | 1 | dx.doi.org/10.17504/protocols.io.261geodpol47/v1 | https://www.protocols.io/view/sparc-preparation-of-plasma-samples-from-rats-bamaic2e | J Paul Robinson | TITLE: SPARC - Preparation of Plasma Samples from Rats
AUTHORS: J Paul Robinson
[DESCRIPTION]
Objective: To collect plasma from live rat experiments for storage at -20˚C for further hormone assays.
[STEPS]
1. Turn on the Hettich Mikro 22R refrigerated centrifuge so it can begin to cool down to 4 °C.
2. Add 15 ... | ["Turn on the Hettich Mikro 22R refrigerated centrifuge so it can begin to cool down to 4 °C.", "Add 15 µL of Protease Inhibitor Cocktail to each of 5 Culex tubes (Vial Clear 8mm Crimp Rnd Bottom \n300 µl Lot:0000071223 MicroLiter Wheaton Company) \n \nFirmly place cap (Snap Cap 8mm, Natural with Cut T/S Septa Lot 000... |
28,215 | Preparing and running a tricine-urea gel | null | dx.doi.org/10.17504/protocols.io.7sxhnfn | null | Robert Hooftman | TITLE: Preparing and running a tricine-urea gel
AUTHORS: Robert Hooftman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In this protocol, the preparation and running of a tricine-urea gel will be explained.</div></div>
[STEPS]
?. Make 3X gel buffer. For the gel buffer, the following is needed: AB... | ["Make 3X gel buffer. For the gel buffer, the following is needed: AB1Ingredients Gel Buffer (3x) 2Tris 3 M 3SDS 0.3 % Then use HCl to set the pH of this solution to 8.45\nAB1Ingredients Gel Buffer (3x) 2Tris 3 M 3SDS 0.3 % ", "Make AB-6 solution by dissolvi... |
63,928 | Jimmy Moore Keto Reviews 2022″ Side Effects, Best Results, Works & Buy! | 3 | dx.doi.org/10.17504/protocols.io.5jyl89k38v2w/v1 | https://www.protocols.io/view/jimmy-moore-keto-reviews-2022-side-effects-best-re-canysdfw | jimmymooreketopills | TITLE: Jimmy Moore Keto Reviews 2022″ Side Effects, Best Results, Works & Buy!
AUTHORS: jimmymooreketopills
[DESCRIPTION]
Jimmy Moore Keto - The keto diet has gotten the standard all insanely standard in each of the a few years, and there's a major consideration or that. Today, we empower you about another updat... | [] |
20,367 | U Mass - Triglyceride | null | dx.doi.org/10.17504/protocols.io.x5pfq5n | null | Jason Kim | TITLE: U Mass - Triglyceride
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This experiment involves a spectrophotometric measurement using Roche Cobas Clinical Chemistry Analyzer. Triglyceride lev... | ["Perform daily quality control assessment of instrumentation before analysis.", "Load each sample into a specialized micro-sample cup for the clinical chemistry analyzer.", "Select Triglyceride test on display and run the analysis.", "Collect and analyze the data."] |
92,396 | Counting Cells Using Cellaca MX | 4 | dx.doi.org/10.17504/protocols.io.bp2l6xz85lqe/v1 | https://www.protocols.io/view/counting-cells-using-cellaca-mx-c6gkzbuw | Ksenija Sabic | TITLE: Counting Cells Using Cellaca MX
AUTHORS: Ksenija Sabic
[DESCRIPTION]
WIP
[STEPS] | [] |
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