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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58,600 | Poliovirus direct detection and nanopore sequencing (DDNS) FAQs | 3 | dx.doi.org/10.17504/protocols.io.b5ggq3tw | https://www.protocols.io/view/poliovirus-direct-detection-and-nanopore-sequencin-b5ggq3tw | Alex Shaw, Catherine Troman, Joyce Akello, Erika Bujaki, Manasi Majumdar, Javier Martin, Nick Grassly | TITLE: Poliovirus direct detection and nanopore sequencing (DDNS) FAQs
AUTHORS: Alex Shaw, Catherine Troman, Joyce Akello, Erika Bujaki, Manasi Majumdar, Javier Martin, Nick Grassly
[DESCRIPTION]
This short FAQ document summarises the poliovirus direct detection and nanopore sequencing (DDNS) protocol, the equipme... | [] |
92,764 | Fixative preparation for Baermann funnel extraction | 4 | null | https://www.protocols.io/view/fixative-preparation-for-baermann-funnel-extractio-c6t4zeqw | Casey A Schlenker | TITLE: Fixative preparation for Baermann funnel extraction
AUTHORS: Casey A Schlenker
[DESCRIPTION]
Fixative preparation for Baermann funnel extraction
[STEPS]
SECTION: Fixative Preparation
1. Weigh 1.6 g PFA powder
SECTION: Fixative Preparation
2. Dissolve in 20 mL of DI water
SECTION: Fixative Preparation
3. Incu... | ["[Fixative Preparation] Weigh 1.6 g PFA powder", "[Fixative Preparation] Dissolve in 20 mL of DI water", "[Fixative Preparation] Incubate in water bath at 60 °C to help dissolve PFA powder for 40 min", "[Fixative Preparation] Add 20 µL of 1 M NaOH to further help dissolve PFA powder", "[Fixative Preparation] Place bac... |
82,583 | Low-cost museum DNA extraction using magnetic beads | 4 | dx.doi.org/10.17504/protocols.io.4r3l27ebxg1y/v2 | https://www.protocols.click/view/low-cost-museum-dna-extraction-using-magnetic-bead-cuvxww7n | Andie C Hall, Owain N Powell, Piotr Cuber, Ben Price | TITLE: Low-cost museum DNA extraction using magnetic beads
AUTHORS: Andie C Hall, Owain N Powell, Piotr Cuber, Ben Price
[DESCRIPTION]
Modified from Korlevic et al 2021& Rohland et al 2018 for high throughput DNA extraction from historical specimens in natural history collections. Please cite these papers when using t... | ["[buffer preparation] Lysis buffer C\n200mM Tris pH8, 25mM EDTA pH8, 0.05% Tween 20, 0.4mg/ml PK\n\nTo make 10 mL mix together: 7295 µL molecular grade water, 2000 µL 1M Tris pH8, \n500 µL 0.5M EDTA (pH 8), 200 µL Proteinase K (20mg/ml), and 5 µL Tween 20.\n\nThis is sufficient for 1 extraction plate of 95 samples and... |
55,619 | Test original protocol | 1 | dx.doi.org/10.17504/protocols.io.b2jbqcin | https://www.protocols.io/view/test-original-protocol-b2jbqcin | Heather Durai | TITLE: Test original protocol
AUTHORS: Heather Durai
[DESCRIPTION]
test abstract
[STEPS]
1. Test Procedure
2. Test Data Analysis | ["Test Procedure", "Test Data Analysis"] |
46,308 | Rapid Single-Pot Assembly of Modular Chromatin Proteins for Epigenetic Engineering | 4 | dx.doi.org/10.17504/protocols.io.brgcm3sw | https://www.protocols.io/view/rapid-single-pot-assembly-of-modular-chromatin-pro-brgcm3sw | James Priode, Karmella Haynes | TITLE: Rapid Single-Pot Assembly of Modular Chromatin Proteins for Epigenetic Engineering
AUTHORS: James Priode, Karmella Haynes
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Chromatin is the nucleo-protein complex that organizes genomic DNA in the nuclei of eukaryotic cells. Transcriptional... | ["[Preparation of Donor DNA Fragments]\nGeneration of linear donor DNA via Q5 HiFi PCR amplification.", "[Preparation of Donor DNA Fragments]\nObtain template DNA for the module(s) of interest that contains a complete open reading frame (ORF) without stop codons.Ensure that the sequence does not contain any BbsI recogn... |
18,061 | A protocol of molecular detection of phytoplasmas and Xylella spp. in post-entry quarantine for plants. | null | dx.doi.org/10.17504/protocols.io.vvme646 | null | Takao Ito, Ryoji Nakaune | TITLE: A protocol of molecular detection of phytoplasmas and Xylella spp. in post-entry quarantine for plants.
AUTHORS: Takao Ito, Ryoji Nakaune
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In the STEPS, we describe TaqMan multiplex real-time PCR to universally detect phytoplasmas (PP) and Xylell... | ["1. Extraction1.1. Crude extraction1.1.1. Put leaf petioles (＜50mg), a metal beads, and 1mL extraction buffer into a tube.1.1.2. 2,500 rpm 60 sec. (the Multi-beads shocker)1.1.3. 9,000 x g 10min 4C1.1.4. Transfer the supernatant to a new tube. Next steps, or keep it in a freezer.", "1.2. Isopropanol precipitation1.2.1... |
97,999 | Protocol for Nuclei/ Cell Isolation and 10X Genomics Fixed RNA profiling for Human Skeletal Muscle | 0 | dx.doi.org/10.17504/protocols.io.14egn68z6l5d/v1 | https://www.protocols.io/view/protocol-for-nuclei-cell-isolation-and-10x-genomic-dbxp2pmn | Nicolas Martin | TITLE: Protocol for Nuclei/ Cell Isolation and 10X Genomics Fixed RNA profiling for Human Skeletal Muscle
AUTHORS: Nicolas Martin
[DESCRIPTION]
This is the 10X Genomics protocol to fix, dissociate, and profile RNA from human skeletal muscle tissue.
[GUIDELINES]
This protocol needs prior approval by the users' instit... | ["[Cell/Nuclei Isolation Protocol for Human Skeletal Muscle] The protocol CG000553 REV B was used to fix, dissociate, and isolate cells/nuclei from frozen human skeletal muscle with the following modifications: \n\n1) 1 mg / mL of Liberase TH was used for dissociation at Step 2b, Page 6.\n2) Two extra \"spin only\" (i.... |
32,902 | HEK293T Landing Pad Recombination Protocol with Fugene (Based on a 24-well plate) | 1 | dx.doi.org/10.17504/protocols.io.bcdeis3e | https://www.protocols.io/view/hek293t-landing-pad-recombination-protocol-with-fu-bcdeis3e | Sarah Roelle, Kenneth Matreyek | TITLE: HEK293T Landing Pad Recombination Protocol with Fugene (Based on a 24-well plate)
AUTHORS: Sarah Roelle, Kenneth Matreyek
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">For using Fugene 6 to recombine Bxb1 attB plasmids into Bxb1 attP Landing Pads already integrated into HEK 293T cells.</div... | ["[Day 0: Day of transfection]\nTrypsinize and count the cells.", "[Day 0: Day of transfection]\nMake 2 transfection mixtures per sample,Opti1 and Opti2 (DNA volumes should be kept between 1.0 and 5.0 uL, if possible):", "[Day 0: Day of transfection]\nOpti1: +\n[Opti-MEM]\n[Fugene6]", "[Day 0: Day of transfection]\nF... |
87,423 | Computational design of novel nanobodies targeting the receptor binding domain of variants of concern of SARS-CoV-2 | 6 | null | https://www.protocols.io/view/computational-design-of-novel-nanobodies-targeting-czk7x4zn | Phoomintara Longsomboon, Thanyada Rungrotmongkol, Nongluk Plongthongkum, Kittikhun Wangkanont, Peter Wolschann, Rungtiva P. Poo-arporn | TITLE: Computational design of novel nanobodies targeting the receptor binding domain of variants of concern of SARS-CoV-2
AUTHORS: Phoomintara Longsomboon, Thanyada Rungrotmongkol, Nongluk Plongthongkum, Kittikhun Wangkanont, Peter Wolschann, Rungtiva P. Poo-arporn
[DESCRIPTION]
The COVID-19 pandemic has created an... | ["[1. Validation of protein-protein docking server] Prepare the protein datasets consisting of 29 nanobodies (Nbs) and 86 antibodies (Abs) complexed with RBDs from the Protein Data Bank (PDB) (https://www.rcsb.org/) for blind docking.", "[1. Validation of protein-protein docking server] Remove heteroatoms/molecules, in... |
42,189 | Introduction to Bioinformatic Tools | 3 | null | https://www.protocols.io/view/introduction-to-bioinformatic-tools-bmfmk3k6 | TITLE: Introduction to Bioinformatic Tools
AUTHORS:
[STEPS] | [] | |
81,075 | Volume of oils (fatty acids) in coffee and comparison between roast levels | 1 | dx.doi.org/10.17504/protocols.io.14egn2kozg5d/v1 | https://www.protocols.io/view/volume-of-oils-fatty-acids-in-coffee-and-compariso-ctetwjen | Shannon.logan | TITLE: Volume of oils (fatty acids) in coffee and comparison between roast levels
AUTHORS: Shannon.logan
[DESCRIPTION]
Measuring the volume of oils produced in coffee across a range of roasts.
[STEPS]
1. Grind coffee to desired consistency and weigh 20g to put into cafetiere
2. Boil kettle with 250ml of deionised wat... | ["Grind coffee to desired consistency and weigh 20g to put into cafetiere", "Boil kettle with 250ml of deionised water", "Pour boiling water into a beaker and allow to cool to 93 °C, using a digital thermometer to ensure accuracy of temperature.", "Once the water has cooled to the desired temperature, pour into the caf... |
30,045 | Protocol to generate Gastruloids (LSCB, EPFL) | 1 | dx.doi.org/10.17504/protocols.io.9j5h4q6 | https://www.protocols.io/view/protocol-to-generate-gastruloids-lscb-epfl-9j5h4q6 | Stefano Vianello, Mehmet Girgin, Giuliana Rossi, Matthias Lutolf | TITLE: Protocol to generate Gastruloids (LSCB, EPFL)
AUTHORS: Stefano Vianello, Mehmet Girgin, Giuliana Rossi, Matthias Lutolf
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Gastruloid generation protocol as performed in the Lutolf Lab, EPFL.</div><div class = "text-block">For previously published ... | ["[Preparation of the cell suspension]\nUsing a vacuum line+glass pasteur pipette, aspirate out the culture medium and replace with PBS-/- , for a short wash\n3 ml\nWhen removing liquid during washes, do not completely dry out the cells. The surface of the well should still look glossy.", "[Preparation of the cell sus... |
99,749 | Differentiation of Mesenchymal Stromal Cells to Endothelial-like cells in Spheroidal Culture | 0 | dx.doi.org/10.17504/protocols.io.5jyl82m17l2w/v3 | https://www.protocols.io/view/differentiation-of-mesenchymal-stromal-cells-to-en-ddnd25a6 | Simeng Li, Isabel Arias Quiros, Guenther Eissner | TITLE: Differentiation of Mesenchymal Stromal Cells to Endothelial-like cells in Spheroidal Culture
AUTHORS: Simeng Li, Isabel Arias Quiros, Guenther Eissner
[DESCRIPTION]
In this protocol, an easy and cost-friendly method to form mesenchymal stromal cell (MSC) spheroids was specified. The MSC spheroids would form in ... | ["[Mesenchymal stromal cell spheroids formation] Split and resuspend MSC in fully-supplemented MesenCult-ACF plus medium.", "[Mesenchymal stromal cell spheroids formation] Count cells with Trypan blue and dilute cell to 3x10e5/ml or 12x10e5/ml. Cells need to be over 95% viable in order to form spheroids.", "[Mesenchyma... |
29,435 | RNA clean-up by phenol:chloroform | null | dx.doi.org/10.17504/protocols.io.8y3hxyn | null | Daniel Richter | TITLE: RNA clean-up by phenol:chloroform
AUTHORS: Daniel Richter
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Phenol: chloroform extraction to clean up RNA ( e.g. to remove DNAse or DNAse Inactivation Reagent.)
</div><div class = "text-block">Based on phenol/chloroform protocol (http://cshprotoc... | ["Add 40 μL (1/10 of final volume) of 3 M sodium acetate, pH 5.2.\nFinal concentration will be 0.3 M.\n[3 M sodium acetate, pH 5.2]", "Add 880 μL (2x volume) of phenol:chloroform:isoamyl alcohol pH 8.0\n880 µl", "Shake vigorously inside fume hood for 15 seconds.\n[Shake]", "Centrifuge at maximum speed in a microcentrif... |
null | null | null | dx.doi.org/10.17504/protocols.io.nbzdap6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This revisited Thalassiosira pseudonana conjugation protocol builds on the following two protocols: <a href="https://www.protocols.io/view/conjugation-of-thalassiosira-pseudonana-f55bq86" target="_blank">Conjugation of Thalassiosira pseudonana</a> (DOI: dx.doi.org/10.17504/pr... | [] |
85,833 | Whole-Genome Amplification of Respiratory Syncytial Virus (RSV) using Illumina CovidSeq reagents for Next-Generation Sequencing | 4 | null | https://www.protocols.io/view/whole-genome-amplification-of-respiratory-syncytia-cx3hxqj6 | Carlos Davina-Nunez, Sonia Perez-Castro, Montse Godoy-Diz, Benito Regueiro-Garcia | TITLE: Whole-Genome Amplification of Respiratory Syncytial Virus (RSV) using Illumina CovidSeq reagents for Next-Generation Sequencing
AUTHORS: Carlos Davina-Nunez, Sonia Perez-Castro, Montse Godoy-Diz, Benito Regueiro-Garcia
[DESCRIPTION]
This protocol has been tested for amplification of RSV-positive nasopharyngeal ... | ["[Primer pools preparation] Prepare both primer mixes according to Table 1.\n\nFor a final concentration of 10uM: add 1017 ul of Nuclease-Free water to Pool 1 and 1035 ul to Pool 2.", "[RT-PCR] Two Master Mixes must be prepared per sample: one for Pool1 and one for Pool 2 (Table 2). Manipulate reagents according to th... |
80,224 | In vitro transcription of guide RNAs and 5'-triphosphate removal | 1 | dx.doi.org/10.17504/protocols.io.n2bvjyp5vk5w/v16 | https://www.protocols.io/view/in-vitro-transcription-of-guide-rnas-and-5-39-trip-csj8wcrw | Mark Dewitt, Julia Wong, Beeke Wienert, Moritz F Schlapansky, Eric Aird | TITLE: In vitro transcription of guide RNAs and 5'-triphosphate removal
AUTHORS: Mark Dewitt, Julia Wong, Beeke Wienert, Moritz F Schlapansky, Eric Aird
[DESCRIPTION]
sgRNA template assembly, in vitro T7 transcription, and sgRNA column cleanup to remove 5'-triphosphate groups
[GUIDELINES]
The primers used are: o... | ["[Design sgRNA and order PCR oligos] Add the desired protospacer sequence to the T7FwdVarV2 oligo and order the oligo from your favorite oligonucleotide supplier. There are many programs available for protospacer design that attempt to optimize on- and/or off-target activity. Which program is most useful depends upon ... |
24,831 | DNA Ligation | null | dx.doi.org/10.17504/protocols.io.4g7gtzn | null | Addgene The Nonprofit Plasmid Repository | TITLE: DNA Ligation
AUTHORS: Addgene The Nonprofit Plasmid Repository
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is for how to perform DNA ligation. To see the full abstract and other resources, visit </span><a href="https://www.addgene.org/protocols/dna-ligation" style = "t... | ["Before setting up the ligation reaction itself, it is important to determine the amount of cut insert and vector to use for the ligation reaction. The volume of vector DNA and insert DNA used in the ligation will vary depending on the size of each and their concentration. However, for most standard cloning (where the... |
71,454 | Qualitative & Quantitative Assessment of Human Islets Using Dithizone (DTZ) | 4 | dx.doi.org/10.17504/protocols.io.bp2l6bnkkgqe/v4 | https://www.protocols.io/view/qualitative-amp-quantitative-assessment-of-human-i-chz6t79e | Human Islet Phenotyping Program (HIPP) of the IIDP | TITLE: Qualitative & Quantitative Assessment of Human Islets Using Dithizone (DTZ)
AUTHORS: Human Islet Phenotyping Program (HIPP) of the IIDP
[DESCRIPTION]
This Standard Operating Procedure is adapted from the work of the 'National Institutes of Health-Sponsored Clinical Islet Transplantation Consortium Phase 3 T... | ["[Preparation of Working Dithizone] Assemble all items described in Materials section.", "[Preparation of Working Dithizone] Prepare DTZ stain as described below. Observe all safety precautions when working with DMSO.", "[Preparation of Working Dithizone] Wearing gloves, dissolve 50 mg dithizone in 10 mL DMSO.", "[Pre... |
63,298 | A novel laboratory method to simulate climatic stress with successful application to experiments with medically relevant ticks | 4 | dx.doi.org/10.17504/protocols.io.rm7vzyo8rlx1/v3 | https://www.protocols.io/view/a-novel-laboratory-method-to-simulate-climatic-str-b93ar8ie | Sang Hyo Kim, Caleb Nielebeck, Lauren Dedmon, Mark Pangilinan, Jahred Quan, William Ota, Javier D. Monzón | TITLE: A novel laboratory method to simulate climatic stress with successful application to experiments with medically relevant ticks
AUTHORS: Sang Hyo Kim, Caleb Nielebeck, Lauren Dedmon, Mark Pangilinan, Jahred Quan, William Ota, Javier D. Monzón
[DESCRIPTION]
This protocol details a novel method to isolate indivi... | ["[Set up] Place a single tick with one wooden skewer in each tube and seal with a cap, labelling each tube with an individual identifier", "[Set up] Place six tubes in each airtight container along with a humidity pack, labelling each container", "[Set up] Confirm the humidity in one container of each RH level with th... |
67,567 | H&E Staining for 10X Genomics Visium Imaging | 4 | dx.doi.org/10.17504/protocols.io.4r3l2owqqv1y/v1 | https://www.protocols.io/view/h-amp-e-staining-for-10x-genomics-visium-imaging-cd8ps9vn | Stephen Fisher, Marielena Grijalva, Rong Guo, sarahjoh, Hieu Nguyen, John Renz, Jean G Rosario, Steven Rudich, Brian Gregory, Junhyong Kim, Kate O'Neill | TITLE: H&E Staining for 10X Genomics Visium Imaging
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 describes H&E staining of 10X Genomics Visium slides prior to imaging and... | ["[Tissue Fixation] Prechill methanol (40mL/slide, dispensed in a 50-mL centrifuge tube) to -20 °C .", "[Tissue Fixation] Remove slide from -80°C and place on dry ice in a sealed container.", "[Tissue Fixation] Place slide on the Thermocycler Adaptor with the active surface facing up and incubate 1 min at 37 °C .", "[... |
77,255 | Plant Extraction and Fractionation | 1 | dx.doi.org/10.17504/protocols.io.q26g7y6bqgwz/v1 | https://www.protocols.io/view/plant-extraction-and-fractionation-cppfvmjn | Matin Mahmood, Enas Jawad Kadhim, Abdulkareem Hameed Abd | TITLE: Plant Extraction and Fractionation
AUTHORS: Matin Mahmood, Enas Jawad Kadhim, Abdulkareem Hameed Abd
[DESCRIPTION]
Plant extraction is a process that aims to extract certain components present in plants. It is a solid/liquid separation operation: a solid object (the plant) is placed in contact with a fluid (the... | ["Powdered plant materials were defatted with hexane in ratio 1:3 W/V for 24 hr.( 500 gm of plant material with 1500 mL of hexane)", "Allowed to dry at room temperature", "A (500gm) of shade-dried for 12 days.", "Coarsely powdered plant materials", "The defatted plant materials were extracted with (2 Liters) of 80% eth... |
88,896 | Simulating the modal analysis of hyperelastic membranes immersed in fluid using FE software ANSYS | 5 | dx.doi.org/10.17504/protocols.io.bp2l6x7dklqe/v1 | https://www.protocols.io/view/simulating-the-modal-analysis-of-hyperelastic-memb-c228yghw | samuel.vorlet | TITLE: Simulating the modal analysis of hyperelastic membranes immersed in fluid using FE software ANSYS
AUTHORS: samuel.vorlet
[DESCRIPTION]
This protocol provides step-by-step guidelines to perform the modal analysis of pre-strained hyperelastic rectangular membrane accounting for fluid-structure interactions using ... | ["[Hyperelastic material definition using the Mooney-Rivlin formulation from uniaxial test data] Open Engineering Data.", "Ad a new material and define the material name. Verify the units.", "Define the hyperelastic material properties.", "In the Hyperelastic toolbox, choose the Mooney-Rivlin material model with the ap... |
53,030 | Microfluidics 5: PDMS Microchannel Bonding on Glass/PDMS | 1 | dx.doi.org/10.17504/protocols.io.bx2epqbe | https://www.protocols.io/view/microfluidics-5-pdms-microchannel-bonding-on-glass-bx2epqbe | Serhat Sevli, C. Yunus Sahan | TITLE: Microfluidics 5: PDMS Microchannel Bonding on Glass/PDMS
AUTHORS: Serhat Sevli, C. Yunus Sahan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">Microfluidic chips, made of PDMS, are one-side open when fabricated. Another layer of glass, PDMS, o... | ["[Oxygen Plasma Exposure]\n1.0.1. Cured PDMS manufactured at previous steps using lithography or 3D printed molds are cut or removed from the mold and put inside a clean petri dish. Since PDMS is vulnerable to surface adsorption of dust, each must be clean and performed inside cleanroom facilities.1.0.2. NehirBT's air... |
18,925 | iDisco immunolabeling in brown adipose tissue (BAT) | null | dx.doi.org/10.17504/protocols.io.wqmfdu6 | null | Seoeun Lee, Lori Zeltser | TITLE: iDisco immunolabeling in brown adipose tissue (BAT)
AUTHORS: Seoeun Lee, Lori Zeltser
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to stain Brown Adipose Tissue using iDisco protocol and visualize the result via confocal microscope.</div></div>
[STEPS]
?. [Samp... | ["[Sample Collection]\nAnesthetize the mouse, perfuse with 20ml Saline and 4% PFA in 0.1M PB", "[Sample Collection]\nDissect BAT, carefully remove white adipose tissue surrounding the BAT. The two bilateral depots can be left connected or separated, as desired", "[Sample Collection]\nFix in 4% PFA in 0.1M PB at 4°C, ov... |
100,011 | Multiplatform Plant Metabolomics Analysis Protocol for Arabidopsis thaliana | 0 | dx.doi.org/10.17504/protocols.io.n92ld8pn9v5b/v1 | https://www.protocols.io/view/multiplatform-plant-metabolomics-analysis-protocol-ddwj27cn | Akila Wijerathna Yapa, Gabriele Netzel, Venea Dara Daygon, Terra Stark | TITLE: Multiplatform Plant Metabolomics Analysis Protocol for Arabidopsis thaliana
AUTHORS: Akila Wijerathna Yapa, Gabriele Netzel, Venea Dara Daygon, Terra Stark
[DESCRIPTION]
In the pursuit of comprehensive metabolomic profiling, a multiplatform analysis protocol has been developed for Arabidopsis thaliana, utilizin... | ["[1. Extraction and Purification of Intracellular Metabolites] Weigh approximately 25 mg of freeze-dried Arabidopsis thaliana tissues into bead beating tubes. Record the exact weights. Keep samples frozen. °C", "[2. HPLC — Amino Acid Analysis] 25 µL of crude solution of samples are added to 25 µL of 1 mM internal stan... |
38,624 | Fungal CTAB DNA Extraction | 4 | dx.doi.org/10.17504/protocols.io.bhx8j7rw | https://www.protocols.io/view/fungal-ctab-dna-extraction-bhx8j7rw | Derreck Carter-House, Jason Stajich, Sarah Unruh, Tania Kurbessoian | TITLE: Fungal CTAB DNA Extraction
AUTHORS: Derreck Carter-House, Jason Stajich, Sarah Unruh, Tania Kurbessoian
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is a CTAB DNA extraction method for filamentous fungi. Its purpose is to extract high molecular weight genomic DNA for genome ... | ["[DNA Extraction steps]\nEach tube of lysis buffer will be split in half so prepare one tube of lysis buffer for two samples.Prepare Lysis Buffer by adding to each 2mL microcentrifuge tube µL Buffer A, µL Buffer B, µL Buffer C, µL PVP, and Proteinase K to microcentrifuge tube, mix, and then split equally into t... |
73,770 | Deglycosylation of N-glycosylated proteins using PNGase F | 4 | dx.doi.org/10.17504/protocols.io.x54v9dr84g3e/v1 | https://www.protocols.io/view/deglycosylation-of-n-glycosylated-proteins-using-p-ckaiusce | Kaia Kukk | TITLE: Deglycosylation of N-glycosylated proteins using PNGase F
AUTHORS: Kaia Kukk
[DESCRIPTION]
The described protocol was used to confirm that NADPH-cytochrome P450 reductase from Helianthus annuus was N-glycosylated when recombinantly expressed in Pichia pastoris (Komagataella phaffii).
[STEPS]
1. 12,5 µl of yea... | ["12,5 µl of yeast lysate containing sufficient amount of target protein for detecting by Western analysis was pipetted into a tube. Two samples were prepared in parallel, one for negative control without N-glycosidase and the other with PNGase F.", "0,5 µl of 10% sodium dodecyl sulfate (SDS) and 1 µl of 1M dithiothrei... |
49,545 | Collecting samples for Total Organic Carbon (TOC) analysis | 1 | null | https://www.protocols.io/view/collecting-samples-for-total-organic-carbon-toc-an-bumhnu36 | Krista Longnecker | TITLE: Collecting samples for Total Organic Carbon (TOC) analysis
AUTHORS: Krista Longnecker
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes collecting samples for Total Organic Carbon (TOC) analysis. The method is appropriate for samples in oligotrophic marine waters where t... | ["[Collecting samples for Total Organic Carbon (TOC) analysis]\nThe glass vials need to be combusted before use.", "[Collecting samples for Total Organic Carbon (TOC) analysis]\nSet aside the caps that were sent with the vials because they cannot be combusted.", "[Collecting samples for Total Organic Carbon (TOC) analy... |
56,659 | F/2 medium at 27 PSU of salinity from Sea Red salts | 4 | dx.doi.org/10.17504/protocols.io.n92ldzyrxv5b/v1 | https://www.protocols.io/view/f-2-medium-at-27-psu-of-salinity-from-sea-red-sal-b3jtqknn | Estelle Bigeard | TITLE: F/2 medium at 27 PSU of salinity from Sea Red salts
AUTHORS: Estelle Bigeard
[DESCRIPTION]
F/2 medium (Guillard’s Marine Water Enrichment Solution) is used to maintain in culture microalgae (for example, dinoflagellates) and their marine parasites (Alveolates, Syndiniales & perkinsids, Fungi Dinomyces ).
Mo... | ["[Preparation of the (Natural, Controled) Seawater Solution] Be careful : Always use clean and non-toxic utensils for mixing.\n\nNote: Due to possible salt stratification during transport, the entire salt should be mixed before sampling and dissolve it into water.\n\nUse Milli-Q water as distilled water may content so... |
44,270 | BSCI:414--Lab10: Protein Translations and In Frame Insertions | 1 | null | https://www.protocols.io/view/bsci-414-lab10-protein-translations-and-in-frame-i-bpgnmjve | Harley King | TITLE: BSCI:414--Lab10: Protein Translations and In Frame Insertions
AUTHORS: Harley King
[STEPS]
?. [Translate Spike-Sumo into Protein]
Find the plasmid "F20_spike-SUMO/pET28" in Benchling in the BSCI:414 plasmids root folder. Open it. Copy this to a new folder with your name under "BSCI:414 Lab 10."
?. [Translate Sp... | ["[Translate Spike-Sumo into Protein]\nFind the plasmid \"F20_spike-SUMO/pET28\" in Benchling in the BSCI:414 plasmids root folder. Open it. Copy this to a new folder with your name under \"BSCI:414 Lab 10.\"", "[Translate Spike-Sumo into Protein]\nLocate the first \"ATG\" codon after the ribosomal binding site (RBS), ... |
91,208 | DNA extraction and genomic DNA cleanup protocol for soil and other environmental samples | 4 | null | https://www.protocols.io/view/dna-extraction-and-genomic-dna-cleanup-protocol-fo-c5bgy2jw | Timothy J Philpott | TITLE: DNA extraction and genomic DNA cleanup protocol for soil and other environmental samples
AUTHORS: Timothy J Philpott
[DESCRIPTION]
This is a spin column based environmental DNA extraction protocol that has been validated with mineral soil and forest floor samples. The protocol starts with disruption and lysis ... | ["[Reagents] Procure the following reagents before beginning.\n\n Chemical name CAS Molecular weight (g/mol) Sodium phosphate, Na3PO4 7601-54-9 163.94 Guanidium isothiocyanate, GITC 593-84-0 118.16 Sodium chloride, NaCl 7647-14-5 58.44 Tris base ... |
43,576 | Transfer of RNA from Agarose Gels onto Membranes | 4 | dx.doi.org/10.17504/protocols.io.bnsymefw | https://www.protocols.io/view/transfer-of-rna-from-agarose-gels-onto-membranes-bnsymefw | Jonathan Houseley, Cristina Cruz | TITLE: Transfer of RNA from Agarose Gels onto Membranes
AUTHORS: Jonathan Houseley, Cristina Cruz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Over the past decade a plethora of noncoding RNAs (ncRNAs) have been identified, initiating an explosion in RNA research. Although RNA sequencing methods ... | ["[Transfer of RNA from Agarose Gels onto Membranes]\nCut a 15 × 15 cm piece of nylon membrane, two 15 × 15 cm pieces of Whatman paper and a 15 × 46 cm piece of Whatman paper.\n46 cm is just the width of our paper. This piece has to be just long enough to reach the SSC on both sides.", "[Transfer of RNA from Agarose Ge... |
67,153 | Measuring protein concentration using the Merck Millipore Direct Detect Spectrometer | 1 | dx.doi.org/10.17504/protocols.io.8epv598m6g1b/v1 | https://www.protocols.io/view/measuring-protein-concentration-using-the-merck-mi-cdtrs6m6 | ronan.ocualain | TITLE: Measuring protein concentration using the Merck Millipore Direct Detect Spectrometer
AUTHORS: ronan.ocualain
[DESCRIPTION]
This protocol details the procedure of measuring protein concentration using the Millipore Direct Detect spectrometer.
[BEFORE_START]
Initial preparation
Before you begin:
Identify the ... | ["[Loading samples on card:] To measure the protein concentration of your lysate, place a Direct Detect card on a clean, dry surface (spotting trays for cards are available).", "[Loading samples on card:] Label the bottom membrane on the card for blank measurement.", "[Loading samples on card:] Label a clean 0.75 mL Ep... |
57,292 | AAVS1 Knock-in | 4 | dx.doi.org/10.17504/protocols.io.b37kqrkw | https://www.protocols.io/view/aavs1-knock-in-b37kqrkw | Hanqin Li, Dirk Hockemeyer | TITLE: AAVS1 Knock-in
AUTHORS: Hanqin Li, Dirk Hockemeyer
[DESCRIPTION]
This protocol describes the standard procedure to knock-in constructs to the AAVS1 safe harbor locus in hPSCs.
General Notes:
1. The AAVS1 knock-in construct, AAVS1-SA-neo-CAGGS-PE2-2A-GFP, can be found at AddGene (Catalog: 180014, RRID:Addgene... | ["One day before nucleofection, prepare two DR4 MEFs 6-well plates.", "Nucleofection of Cas9/sgRNA RNP (protospacer sequence, ACCCCACAGTGGGGCCACTA) and AAVS1 knock-in targeting vector is performed using the nucleofection of ribonucleoprotein (RNP) into human pluripotent stem cells (hPSCs) protocol as described in the c... |
44,689 | LI Detector Analytical Pipeline | 5 | dx.doi.org/10.17504/protocols.io.3byl4kjd2vo5/v1 | https://www.protocols.io/view/li-detector-analytical-pipeline-bpvrmn56 | Saurin B Parikh | TITLE: LI Detector Analytical Pipeline
AUTHORS: Saurin B Parikh
[DESCRIPTION]
The LI Detector framework consists of integrated experimental and analytical pipelines. A. The pin-copy-upscale experimental pipeline from frozen glycerol stocks (top) to imaging (bottom). Each box represents a pinning step, and the steps... | ["[Files] Plate maps of the starting density plate\nA .xlsx file with one plate per sheet\nCells contain strain-id\nExample", "[Files] Table specifying strain-id to orf-name relationship\nA .xlsx file containing unique strain_id to each orf_name\nFirst column is strain_id\nSecond column is orf_name\nEach strain_id from... |
71,158 | Automated Blood Pressure (Oscillometric Technique) | 1 | dx.doi.org/10.17504/protocols.io.6qpvr4drbgmk/v1 | https://www.protocols.click/view/automated-blood-pressure-oscillometric-technique-chqwt5xe | insightsmovement | TITLE: Automated Blood Pressure (Oscillometric Technique)
AUTHORS: insightsmovement
[DESCRIPTION]
The following SOPs outline how to take a blood pressure measurement using an automated device.
Blood-pressure measurement is warranted in any situation that requires assessment of cardiovascular health, including screeni... | ["[Equipment Required] Validated Oscillometric Device", "[Preparing for the Measurement] Follow the Steps below to help prepare your PPC for measurement:\n\nThe patient’s back and legs should be supported with legs uncrossed and feet resting on a firm surface\n\nThe patient’s arms should be bare to the shoulder the arm... |
76,145 | A new method to refine GWAS results based on the UKBiobank phenotype database | 5 | dx.doi.org/10.17504/protocols.io.ewov1o5nklr2/v1 | https://www.protocols.io/view/a-new-method-to-refine-gwas-results-based-on-the-u-cnkrvcv6 | Davide Noto | TITLE: A new method to refine GWAS results based on the UKBiobank phenotype database
AUTHORS: Davide Noto
[DESCRIPTION]
Genome wide association studies (GWAS) is an untargeted methodology able to identify novel gene variants associated with diseases. Sometimes the gene variants identified by GWAS are located within ge... | ["Description of the Protocol\nThis protocol describes an automated workflow able to enrich the results of a Genome Wide Association Study (GWAS ) obtained from the UK Biobank data. In particular the workflow uses the Single Nucleotide Polymorphisms (SNP) that resulted associated with the investigated trait ( Cardiovas... |
null | null | null | dx.doi.org/10.17504/protocols.io.gxvbxn6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div>
<div>
<div>
<div class="b-start-block editable-content">
<p>This protocol describes MRI and ADHD Quotient Test for Session 8 of the following work:</p>
<p> </p>
<p>David O'Connor, et. al. (2017) The Healthy Brain Network Serial Scanning Initiative. <em>GigaScience...</em><... | [] |
24,273 | a protein precipitation extraction method | null | dx.doi.org/10.17504/protocols.io.3xrgpm6 | null | Idha Arfianti | TITLE: a protein precipitation extraction method
AUTHORS: Idha Arfianti
[STEPS]
?. The frozen plasma was thawed at room temperature (25 ± 1°C).
?. The thawed plasma was vortexed to ensure the sample was homogenous.
?. To each 100 µL plasma sample, 50 µL of internal standard (IS) (containing 2 µg/mL of IS) was added, f... | ["The frozen plasma was thawed at room temperature (25 ± 1°C).", "The thawed plasma was vortexed to ensure the sample was homogenous.", "To each 100 µL plasma sample, 50 µL of internal standard (IS) (containing 2 µg/mL of IS) was added, followed by the addition of 250 µL of acetonitrile (ACN).", "The mixture was vortex... |
16,780 | Genetic diversity and population structure of domestic and wild reindeer (Rangifer tarandus L. 1958): a novel approach using BovineHD BeadChip | null | dx.doi.org/10.17504/protocols.io.umkeu4w | null | Veronika Ruslanovna Kharzinova, Arsen Vladimirovich Dotsev, Tatiana Evgenievna Deniskova, Anastasiya Dmitrievna Solovieva, Valeriy Ivanovich Fedorov, Kasim Anverovich Layshev, Tatiana Michailovna Romanenko, Innokentiy Michailovich Okhlopkov, Klaus Wimmers, Henry Reyer, Gottfried Brem, Natalia Anatolievna Zinovieva | TITLE: Genetic diversity and population structure of domestic and wild reindeer (Rangifer tarandus L. 1958): a novel approach using BovineHD BeadChip
AUTHORS: Veronika Ruslanovna Kharzinova, Arsen Vladimirovich Dotsev, Tatiana Evgenievna Deniskova, Anastasiya Dmitrievna Solovieva, Valeriy Ivanovich Fedorov, Kasim Anver... | ["[Sample collection and preparation of genomic DNA]\nGenomic DNA was extracted from muscle and tissue samples using Nexttec columns (Nexttec Biotechnology GmbH, Germany) following the manufacturer's instructions. The quality of the extracted DNA was examined by electrophoresis using 1 % agarose gels viewed under ultra... |
null | null | null | dx.doi.org/10.17504/protocols.io.ibqcamw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Please contact Dr. Steven Wilhelm (wilhelm@utk.edu) for additional information regarding this protocol</p>
<p> </p>
<p>Modified from Pardee, A. B., F. Jacob, and J. Monod. 1959. The genetic control and cytoplasmic expression of "inducibility" in the synthesis of ß-galactosida... | [] |
28,183 | Purification of RNA from the Aqueous Phase Following TRIzol®/Chloroform Extraction using the Monarch® RNA Cleanup Kits | 1 | null | https://www.protocols.io/view/purification-of-rna-from-the-aqueous-phase-followi-7rxhm7n | New England Biolabs | TITLE: Purification of RNA from the Aqueous Phase Following TRIzol®/Chloroform Extraction using the Monarch® RNA Cleanup Kits
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>RNA isolation reagents containing guanidine thiocyanate and phenol (e.g., TRIzol, RNAzol®,... | ["Re-insert the column into the collection tube. Add RNA Cleanup Wash Buffer and spin for . Discard the flow-through.\n500 µl\nTo save time, spin for 30 seconds, instead of 1 minute.", "Following guanidinium-thiocyanate-phenol-chloroform extraction, carefully transfer the upper aqueous phase into an RNase-free tube (n... |
42,763 | pGEM-T连接 | 4 | null | https://www.protocols.io/view/pgem-t-bmzjk74n | 张 雪 | TITLE: pGEM-T连接
AUTHORS: 张 雪
[STEPS]
?. AB12× ligation buffer（用前振荡混匀）5µl2PCR回收产物3µl3pGEM-T Vector1µl4T4 ligase1µl
on ice
AB12× ligation buffer（用前振荡混匀）5µl2PCR回收产物3µl3pGEM-T Vector1µl4T4 ligase1µl
?. 室温1h（20°C左右，16°C最佳）
16 °C
?. 随后4°C过夜
4 °C | ["AB12× ligation buffer（用前振荡混匀）5µl2PCR回收产物3µl3pGEM-T Vector1µl4T4 ligase1µl\non ice\nAB12× ligation buffer（用前振荡混匀）5µl2PCR回收产物3µl3pGEM-T Vector1µl4T4 ligase1µl", "室温1h（20°C左右，16°C最佳）\n16 °C", "随后4°C过夜\n4 °C"] |
42,316 | Chapter 10: Medications | 4 | null | https://www.protocols.io/view/chapter-10-medications-bmjkk4kw | Kerri Wolter | TITLE: Chapter 10: Medications
AUTHORS: Kerri Wolter
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol provides information about medications for vulture rehabilitation and how to calculate drug dosage.</div></div>
[STEPS]
?. [How to calculate volume of the drug]
Calculate the dose requ... | ["[How to calculate volume of the drug]\nCalculate the dose required by multiplying the required dose rate (mg/kg) by the bird’s weight (kg). This gives you the dose required in mg.", "[How to calculate volume of the drug]\nTo calculate the volume of drug required, you need to divide this value by the drug concentratio... |
71,179 | RNAi imaging | 4 | dx.doi.org/10.17504/protocols.io.q26g7y8wkgwz/v1 | https://www.protocols.io/view/rnai-imaging-chrjt54n | Ben Jenkins | TITLE: RNAi imaging
AUTHORS: Ben Jenkins
[DESCRIPTION]
Imaging of P. bursaria cultures
[STEPS]
SECTION: Preparing plates
1. In a sterile hood, resuspend plate using a multichannel pipette.
#Ensure pipettes do not overlap with multiple Wells
#Pipette up and down ~20 times (10x in the middle, 10x moving clockwise arou... | ["[Preparing plates] In a sterile hood, resuspend plate using a multichannel pipette.\n\n#Ensure pipettes do not overlap with multiple Wells\n#Pipette up and down ~20 times (10x in the middle, 10x moving clockwise around the edge)", "[Preparing plates] Spin plate at 800 x g, 5 min, 4 °C \n\n# 800* (*=xg)\n# Ensure rad ... |
62,956 | ONT Post-PCR Pooling & Purification for Fungal Barcoding | 4 | null | https://www.protocols.io/view/ont-post-pcr-pooling-amp-purification-for-fungal-b-b9qkr5uw | Stephen Douglas Russell | TITLE: ONT Post-PCR Pooling & Purification for Fungal Barcoding
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
Overview: The goals of this protocol are to pool your PCR product into a single 1.5 mL tube and to purify that product using magnetic beads.
Time required: ~45 minutes (mostly waiting)
[STEPS]
SECTI... | ["[PCR Pooling] Using a 10uL multichannel pipette, transfer 2 µL or 3 µL of PCR product from each row of your 96 well plate of PCR amplicons into the corresponding cells of a new eight tube strip. (Ex - If you are transferring 3 plates of amplications, at the conclusion, there should be 108 µL of product in each of th... |
null | null | null | dx.doi.org/10.17504/protocols.io.dfm3k5 | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<strong>Primers:</strong><br /><br />attP_F502: CTC CTC AAC TGC CAG GAC TC (PSS2 target 502bp upstream of att: 90315-90334)<br />attP_R141: CCC AACAAG CTC TCA GGA AG (PSS2 target 141bp downstream of att rev: 91010-91029)<br />... | [] |
69,064 | AAV injection in the nodose ganglia in mouse | 4 | dx.doi.org/10.17504/protocols.io.5qpvobjmdl4o/v1 | https://www.protocols.io/view/aav-injection-in-the-nodose-ganglia-in-mouse-cfpgtmjw | Santiago Unda, Michael G. Kaplitt | TITLE: AAV injection in the nodose ganglia in mouse
AUTHORS: Santiago Unda, Michael G. Kaplitt
[DESCRIPTION]
The gut-brain axis links the visceral organs to the medulla oblongata via the vagus nerve. Accessing to the afferent vagal pathway is important to dissect the role of cell populations in the bidirectional commu... | ["[Preparation of the surgical setup] Turn on the heating pad to 37 °C", "[Preparation of the surgical setup] Position the surgical microscope to be ready when the animal is under anesthesia.", "[Preparation of the surgical setup] Thaw the aliquot of AAV to be used, mix it well, and keep it on ice. \n\nN.B: For intrane... |
28,325 | Rat Brain Tissue RNA Extraction/cDNA Synthesis for qPCR | 1 | null | https://www.protocols.io/view/rat-brain-tissue-rna-extraction-cdna-synthesis-for-7wdhpa6 | Kokila Shankar, Olivier George | TITLE: Rat Brain Tissue RNA Extraction/cDNA Synthesis for qPCR
AUTHORS: Kokila Shankar, Olivier George
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is to obtain cDNA from rat brain tissue micropunches for downstream qPCR. Briefly, RNA will be extracted from brain tissue and wi... | ["Remove tissue samples from and thaw on ice\n-80 °C", "If samples are stored in RNALater ICE, remove from tube and add to each sample. Pipet homogenize until tissue is fully dissolved and leave at RT while working on other samples. Spin samples at 13000 RPM at for and transfer supernatant to new tube.\n300 µl\n4... |
21,243 | HPLC sample prep | null | dx.doi.org/10.17504/protocols.io.yy3fxyn | null | Kaitly Woodard | TITLE: HPLC sample prep
AUTHORS: Kaitly Woodard
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Preparation of blood for hemoglobin separation (ion-exchange and reverse-phase HPLC).</div></div>
[STEPS]
?. Prepare 1.5mL Eppendorf tubes with 200uL of Hemolysate Reagent
?. Add 1uL of blood to tube, an... | ["Prepare 1.5mL Eppendorf tubes with 200uL of Hemolysate Reagent", "Add 1uL of blood to tube, and vortex for 5 seconds.", "Centrifuge at max speed for 10 minutes", "Pipette out 75-100uL of supernatant into HPLC vial, careful not to disturb DNA pellet at the bottom of the tube. If pipette tip appears sticky after remova... |
103,374 | BAF_Protocol_014_TMT-Based proteomics: Isobaric isotope labeling quantitative method | 0 | dx.doi.org/10.17504/protocols.io.rm7vzj77xlx1/v1 | https://www.protocols.io/view/baf-protocol-014-tmt-based-proteomics-isobaric-iso-dg7n3zme | Nicholas Sherman | TITLE: BAF_Protocol_014_TMT-Based proteomics: Isobaric isotope labeling quantitative method
AUTHORS: Nicholas Sherman
[DESCRIPTION]
Labeling samples with TMT, digestion, cleanup and fractionation by high pH. Note that generally you need on the order of 25-100ug protein per plex channel for this to work well.
[STEPS]... | ["[Generate tryptic peptides] Refer to BAF_Protocol_007 Solution Digest with Protein Precipitation for protein extraction, clean-up and trypsin digestion.", "[TMT-Labeling - protocol follows TMTprot 16plex, 1 x 0.5 mg (#A44521), user guide] For complete labeling of lysine and N-termini, use a minimum ratio of 1:5-1:10,... |
62,608 | Lifestyle Keto Gummies - 2022 Price, Side Effects And More Details | 3 | dx.doi.org/10.17504/protocols.io.kxygxzo44v8j/v1 | https://www.protocols.io/view/lifestyle-keto-gummies-2022-price-side-effects-and-b9dqr25w | gumieslifestyle | TITLE: Lifestyle Keto Gummies - 2022 Price, Side Effects And More Details
AUTHORS: gumieslifestyle
[DESCRIPTION]
Official Website - Click Here for Lifestyle Keto Gummies
Availability Of Lifestyle Keto Gummies - Online On Website
Main Benefits - Burn Fat Without Any Side Effect
[STEPS] | [] |
28,335 | MojoSort™ Human CD45 Nanobeads Protocol 1 - CD45 less than 50% | null | dx.doi.org/10.17504/protocols.io.7wphpdn | null | Sam Li | TITLE: MojoSort™ Human CD45 Nanobeads Protocol 1 - CD45 less than 50%
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Product description and procedure summary:</span></div><div class = "text-block"><span style = "font-weight:bold;">If the percentage... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes. Kits for human samples have been optimized for PBMCs, please prepare the cells using a suitable method.", "In the final wash of your sample preparation, resuspend the cells in MojoSort™ Buffer by adding up to 4 mL in a 5 mL (12 x 75 mm) ... |
74,272 | Modified survival (mS) assay | 4 | dx.doi.org/10.17504/protocols.io.81wgb6knylpk/v3 | https://www.protocols.io/view/modified-survival-ms-assay-ckr8uv9w | Eva JP Lievens | TITLE: Modified survival (mS) assay
AUTHORS: Eva JP Lievens
[DESCRIPTION]
This protocol describes a modified survival assay, as presented in the paper "Efficient assays to quantify the life history traits of algal viruses" (Lievens et al. 2023, Applied & Environmental Microbiology, doi.org/10.1128/aem.01659-23). It is... | ["[time point 0 - prepare & aliquot suspensions] Mix virus suspensions at 50000, 5000, 500, or 50 virions/ml.", "[time point 0 - prepare & aliquot suspensions] In two deep well plates (\"1\" and \"2\"), mix viral suspensions so they have a volume of 1.5ml and 50000, 5000, 500, or 50 virions/ml. Avoid reusing ti... |
79,019 | Hematoxyllin-Eosin ( HE ) Staining | 4 | dx.doi.org/10.17504/protocols.io.4r3l27zo3g1y/v1 | https://www.protocols.io/view/hematoxyllin-eosin-he-staining-crejv3cn | Freda Halim | TITLE: Hematoxyllin-Eosin ( HE ) Staining
AUTHORS: Freda Halim
[DESCRIPTION]
This is a protocol to stain tissue with Hematoxyllin-Eosin ( HE ) Staining. We use human breast cancer tissue for running this protocol.
[STEPS]
SECTION: Deparaffinization
1. Incubate slides in Xylol
SECTION: Deparaffinization
2. Incubate sl... | ["[Deparaffinization] Incubate slides in Xylol", "[Deparaffinization] Incubate slides in Xylol", "[Rehydration] Incubate slides in 100% Alcohol", "[Rehydration] Incubate slides in 96% Alcohol", "[Rehydration] Incubate slides in 80% Alcohol", "[Rehydration] Incubate Slides in 70% Alcohol", "[Rehydration] Rinse slides ... |
85,592 | Cryo-FIB Milling protocol for mammalian cells | 4 | null | https://www.protocols.io/view/cryo-fib-milling-protocol-for-mammalian-cells-cxtyxnpw | Josh Hutchings, Tamar Basiashvili, Elizabeth Villa | TITLE: Cryo-FIB Milling protocol for mammalian cells
AUTHORS: Josh Hutchings, Tamar Basiashvili, Elizabeth Villa
[DESCRIPTION]
Cryo-Electron Tomography (Cryo-ET) and Cryo-Focused Ion Beam (Cryo-FIB) milling provides insight into the structure and architecture of various proteins and organelles in cells. Mammalian cell... | ["[1. Before you start] Check the status of the high-pressure LN2 tank. If empty change it. Set the regulator valve to 80psi.", "[3. SEM and FIB Overview images] Move the stage to the Mapping position and drop SEM magnification to the lowest possible magnification. Check the focus and take an overview image and save it... |
28,892 | cpf1 cloning | null | dx.doi.org/10.17504/protocols.io.8f4htqw | null | Jaclyn Winter | TITLE: cpf1 cloning
AUTHORS: Jaclyn Winter
[STEPS] | [] |
54,176 | Testowy protokół | 4 | dx.doi.org/10.17504/protocols.io.by58py9w | https://www.protocols.io/view/testowy-protok-by58py9w | lukasz.lukjaniuk | TITLE: Testowy protokół
AUTHORS: lukasz.lukjaniuk
[DESCRIPTION]
To testowa protokół do zrobienia czegos
[STEPS]
SECTION: Section 1
1. ANB
SECTION: Section 1
2. AScdascd
SECTION: Section 1
3.
SECTION: Section 1
3.1.
SECTION: Section 1
3.2.
SECTION: Section 1
2.1.
4. | ["[Section 1] ANB", "[Section 1] AScdascd", "[Section 1]", "[Section 1]", "[Section 1]", "[Section 1]"] |
57,791 | Harvesting and irradiation of mouse embryonic fibroblasts (MEFs) for hPSC cultures | 4 | dx.doi.org/10.17504/protocols.io.b4n7qvhn | https://www.protocols.io/view/harvesting-and-irradiation-of-mouse-embryonic-fibr-b4n7qvhn | Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner | TITLE: Harvesting and irradiation of mouse embryonic fibroblasts (MEFs) for hPSC cultures
AUTHORS: Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner
[DESCRIPTION]
This protocol describes the process of harvesting and irradiating mouse embryonic fibroblasts (MEFs) to use as feeder cells for human... | ["Wash the plates once with 10 ml DPBS for each 15-cm plate.", "Add 3 ml Trypsin and incubate for in 37°C; 5% CO2 for 10 min", "Add 9 ml MEF medium to neutralize the Trypsin. Collect cell suspension in a 50 ml conical tube.", "Rinse the plate with 9 ml of new MEF medium to collect the remaining cells.", "If there are c... |
43,456 | How to Label a Gel | 3 | null | https://www.protocols.io/view/how-to-label-a-gel-bnn8mdhw | TITLE: How to Label a Gel
AUTHORS:
[STEPS] | [] | |
12,411 | 16S Arc 109F-934R | 1 | dx.doi.org/10.17504/protocols.io.n92ldkq9v5br/v1 | https://www.protocols.io/view/16s-arc-109f-934r-qc3dsyn | Eva Petrova, Roey Angel | TITLE: 16S Arc 109F-934R
AUTHORS: Eva Petrova, Roey Angel
[DESCRIPTION]
Amplification of the marker gene 16S rRNA for general Archaea using primers 109F-934R.
109F or ACK GCT CAG TAA CAC GT (target seq. 109 – 125) Grosskopf et al. (1998),
109F-mod AHD GCT CAG TAA CAC RT (target seq. 109 – 125)... | ["[PCR mixture]", "[PCR program] 1. 94◦C – 4′\n2. x 28 - 32 {\n a. 52◦C – 30′′\n b. 72◦C – 45′′\n c. 94◦C – 30′′\n }\n3. 52◦C – 30′′\n4. 72◦C – 10'"] |
93,720 | surveillance of antimicrobial-resistant bacteria causing community-acquired urinary tract infections in low-income countries | 1 | dx.doi.org/10.17504/protocols.io.kqdg3xdneg25/v1 | https://www.protocols.io/view/surveillance-of-antimicrobial-resistant-bacteria-c-c7ryzm7w | Mtebe Majigo, Stephen Mshana, Erick Komba, nyamburasogone, Mecky Matee | TITLE: surveillance of antimicrobial-resistant bacteria causing community-acquired urinary tract infections in low-income countries
AUTHORS: Mtebe Majigo, Stephen Mshana, Erick Komba, nyamburasogone, Mecky Matee
[DESCRIPTION]
The protocol intends to assist users in designing a sustainable surveillance program for AMR ... | ["TARGET POPULATION AND ENROLMENT CRITERIA\nSampling needs to involve children above two years of age and adults (pregnant and non-pregnant women and men) who are residents of a given surveillance area and passively presenting to a health facility for health care within that same surveillance area to ensure linkage of ... |
101,506 | Tutorial on PARADISe: PARAFAC2-based Deconvolution and Identification System for processing GC–MS data | 0 | null | https://www.protocols.io/view/tutorial-on-paradise-parafac2-based-deconvolution-dfda3i2e | Beatriz Quintanilla-Casas, Rasmus Bro, Jesper Løve Hinrich, Cleo L. Davie-Martin | TITLE: Tutorial on PARADISe: PARAFAC2-based Deconvolution and Identification System for processing GC–MS data
AUTHORS: Beatriz Quintanilla-Casas, Rasmus Bro, Jesper Løve Hinrich, Cleo L. Davie-Martin
[DESCRIPTION]
The present protocol provides general guidelines for users working with PARADISe, a deconvolution and ide... | ["[Load GC-MS data (Data tab)] First-time use\n\nFirstly, it is recommended you define a unique PARADISe session name.", "[Load GC-MS data (Data tab)] In PARADISe, GC-MS data can be imported as:\n\nCDF (Computable Document Format) files: Data tab > Add CDF Files. It is advisable that all files are loaded from the same ... |
70,372 | ADR Assessment of TB Patients IIPHG | 2 | dx.doi.org/10.17504/protocols.io.bp2l69n11lqe/v1 | https://www.protocols.io/view/adr-assessment-of-tb-patients-iiphg-cgyctxsw | Harsh Shah, Sandul Yasobant, Jay Patel, Priya Bhavsar, Deepak Saxena, Somen Saha, Anish Sinha [ Department of Public Health Science | TITLE: ADR Assessment of TB Patients IIPHG
AUTHORS: Harsh Shah, Sandul Yasobant, Jay Patel, Priya Bhavsar, Deepak Saxena, Somen Saha, Anish Sinha [ Department of Public Health Science
[DESCRIPTION]
Tuberculosis (TB) is the second leading cause of death due to infectious diseases globally, and delay in TB care cascade ... | [] |
36,787 | collection with public | 2 | dx.doi.org/10.17504/protocols.io.n2bvjyb4wvk5/v1 | https://www.protocols.io/view/collection-with-public-bf6tjren | Misha Murzin | TITLE: collection with public
AUTHORS: Misha Murzin
[DESCRIPTION]
abstract
[STEPS] | [] |
63,269 | Magnitude of job satisfaction and intention to leave their present job among nurses in selected Federal Hospitals in Addis Ababa, Ethiopia | 2 | dx.doi.org/10.17504/protocols.io.e6nvwkj8wvmk/v2 | https://www.protocols.io/view/magnitude-of-job-satisfaction-and-intention-to-lea-b92dr8a6 | Aynye Woldekiros Negese*, Elsabet Getye2, ziyadahm | TITLE: Magnitude of job satisfaction and intention to leave their present job among nurses in selected Federal Hospitals in Addis Ababa, Ethiopia
AUTHORS: Aynye Woldekiros Negese*, Elsabet Getye2, ziyadahm
[DESCRIPTION]
Background
Job dissatisfaction issues and Health workers’ intention to leave is an increasi... | [] |
53,126 | A method for the temperature-controlled extraction of DNA from ancient bones | 1 | dx.doi.org/10.17504/protocols.io.bx5epq3e | https://www.protocols.io/view/a-method-for-the-temperature-controlled-extraction-bx5epq3e | Elena Essel, Matthias Meyer, Petra Korlevic | TITLE: A method for the temperature-controlled extraction of DNA from ancient bones
AUTHORS: Elena Essel, Matthias Meyer, Petra Korlevic
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We here provide a protocol for the decontamination of ancient bones and teeth that is based on a temperature-cont... | ["[Buffer preparation]\nAll buffers are irradiated with UV-C light at a dose of 7 kJ/cm2 using a cross-linker.", "[Buffer preparation]\nSodium-phosphate buffer (0.5 M sodium phosphate, pH 7.0, 0.1 % Tween 20) is prepared by combining the following reagents:\n49.5 mL\n50 µl", "[Buffer preparation]\nTris-Tween wash buffe... |
25,954 | Marchantia protoplast | null | dx.doi.org/10.17504/protocols.io.5kag4se | null | Eftychis Frangedakis | TITLE: Marchantia protoplast
AUTHORS: Eftychis Frangedakis
[STEPS]
?. Grow gemmae on ½ Gamborg B5 plus vitamins media plates (the plates should be covered like Fig. 1A) for 4 days (Fig. 1B).
?. Add 10 ml of 8% (w/v) mannitol at pH 5.7 on the plate and incubate at room temperature 30min.
?. Prepare 2% Driselase solutio... | ["Grow gemmae on ½ Gamborg B5 plus vitamins media plates (the plates should be covered like Fig. 1A) for 4 days (Fig. 1B).", "Add 10 ml of 8% (w/v) mannitol at pH 5.7 on the plate and incubate at room temperature 30min.", "Prepare 2% Driselase solution: add 0.2 g Driselase in 10 ml 8% mannitol solution and incubate in ... |
101,545 | A selective process for application of EDC and 4-APEBA for cabonyl containing metabolites by MALDI-MSI | 0 | dx.doi.org/10.17504/protocols.io.ewov19d9ylr2/v1 | https://www.protocols.io/view/a-selective-process-for-application-of-edc-and-4-a-dfeh3jb6 | Kevin J Zemaitis, Christopher R Anderton, Dusan Velickovic | TITLE: A selective process for application of EDC and 4-APEBA for cabonyl containing metabolites by MALDI-MSI
AUTHORS: Kevin J Zemaitis, Christopher R Anderton, Dusan Velickovic
[DESCRIPTION]
Herein, we outline the protocol for application of 4-(2-((4-bromophenethyl)dimethylammonium)ethoxy)benzenaminium dibromide (4-A... | ["[Materials for OTCD] All chemicals were used as received without any further purification, and synthesis of 4-APEBA was completed in house:\n\n1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) hydrochloride - CAS Number: 25952-53-8 - Sigma-Aldrich (>98.0%; St. Louis, MO) or Tokyo Chemical Industry Co. (>98.0%; Port... |
31,596 | High resolution labeling of mucosal vagal afferent fibers using Dextran-Biotin with counterstaining | 1 | dx.doi.org/10.17504/protocols.io.bp2l6nx5rgqe/v1 | https://www.protocols.io/view/high-resolution-labeling-of-mucosal-vagal-afferent-ba4kiguw | Terry Powley, Jennifer Mcadams, Robert Phillips, Deborah Jaffey | TITLE: High resolution labeling of mucosal vagal afferent fibers using Dextran-Biotin with counterstaining
AUTHORS: Terry Powley, Jennifer Mcadams, Robert Phillips, Deborah Jaffey
[DESCRIPTION]
This protocol describes the methods used to trace and enable morphometric quantification of vagal afferent neurites in mu... | ["[Animals] Two- to four-month-old male\n \nrats in the weight range of 180g to 360g at the time of tracer injection were housed individually in wire hanging cages or in vented rack plastic cages in an Association for Assessment and Accreditation of Laboratory Animal Care-approved temperature (22–24 °C) and humidity (4... |
62,436 | Setting up the working environment | 5 | dx.doi.org/10.17504/protocols.io.yxmvmn5y5g3p/v1 | https://www.protocols.io/view/setting-up-the-working-environment-b88crzsw | Khalid El Moussaoui | TITLE: Setting up the working environment
AUTHORS: Khalid El Moussaoui
[DESCRIPTION]
This protocol illustrates how to properly configure the work environment. In order to avoid a profusion of error messages, it is strongly recommended to follow this protocol to the letter. Attention: the commands are case sensitive ... | ["[xCode command line tools] Open a terminal window.", "[xCode command line tools] Type the following command in the terminal to install xCode command line tools :\n \nA pop-up window opens, click on install and then accept.", "[Miniconda] Download the installation file (.pkg) by clicking on the following link : https:... |
26,547 | U Michigan - Sirius Red staining | null | dx.doi.org/10.17504/protocols.io.56tg9en | null | Jeff Hodgin | TITLE: U Michigan - Sirius Red staining
AUTHORS: Jeff Hodgin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Picrosirius red staining (also called Sirius red staining) highlights fibrosis by staining collagen (collagen... | ["Wash 2x for 5 min in Xylene", "Wash 2x for 3 min in 100% EtOH", "Wash 1x for 2 min in 95% EtOH", "Wash 1x for 2 min in 80% EtOH", "Wash 1x for 1 min in 70% EtOH", "Wash in running tap water for 3 min", "Incubate in hematoxylin for 8 min.", "Wash in running tap water for 10 min", "Incubate for 60 min in Picrosirius re... |
46,862 | Complete CO-Detection by IndEXing (CODEX) Protocol for FF and FFPE Tissues | 1 | null | https://www.protocols.io/view/complete-co-detection-by-indexing-codex-protocol-f-brznm75e | Sachi Krishna, Domenic Abbondanza, Sami Farhi | TITLE: Complete CO-Detection by IndEXing (CODEX) Protocol for FF and FFPE Tissues
AUTHORS: Sachi Krishna, Domenic Abbondanza, Sami Farhi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol contains the necessary information to run an entire CODEX protocol from tissue staining through imagi... | ["[Pre-Staining (Fresh Frozen)]\nRetrieve coverslip from -80°C freezer and place tissue side up onto a bed of Drierite beads. Determine which side of the coverslip the tissue is located on by gently scraping the corner of the OCT layer. Mark your initials on the corner of the coverslip. Let the coverslip sit on the bea... |
98,628 | Early Longitudinal Imaging in Parkinson’s Progression Markers Initiative Using [18F] AV-133 and DaTscanTM (PPMI Early Imaging) | 0 | dx.doi.org/10.17504/protocols.io.5jyl825j6l2w/v1 | https://www.protocols.io/view/early-longitudinal-imaging-in-parkinson-s-progress-dcjc2uiw | Kenneth Marek | TITLE: Early Longitudinal Imaging in Parkinson’s Progression Markers Initiative Using [18F] AV-133 and DaTscanTM (PPMI Early Imaging)
AUTHORS: Kenneth Marek
[DESCRIPTION]
This protocol details early longitudinal imaging in Parkinson’s progression markers initiative using [18F] AV-133 and DaTscan™ (PPMI Early Imaging).... | ["[PURPOSE OF STUDY] The Parkinson Progression Marker Initiative (PPMI) is a longitudinal, observational, multi-center natural history study to assess progression of clinical features, digital outcomes, and imaging, biologic and genetic markers of Parkinson’s disease (PD) progression in study participants with manifest... |
30,555 | LA Urban Coyote Project Volunteer Training Protocol | null | dx.doi.org/10.17504/protocols.io.933h8qn | null | Justin L Brown, Binta Wold, Rachel N Larson | TITLE: LA Urban Coyote Project Volunteer Training Protocol
AUTHORS: Justin L Brown, Binta Wold, Rachel N Larson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This scat survey protocol has been developed for use by National Park Service staff of the Santa Monica Mountains National Recreation Area t... | [] |
34,453 | Production of Recombinant EnvA Rabies Virus | null | dx.doi.org/10.17504/protocols.io.bdvvi666 | null | Allen Institute for Brain Science | TITLE: Production of Recombinant EnvA Rabies Virus
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used for the large-scale production of EnvA-pseudotyped recombinant rabies virus.</div><div class = "text-block"><span style = "font-weight:b... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.gvubw6w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes the library preparation for Nanopore sequencing according to the SQK-MAP005 protocol. </p>
<p>It accompanies the <em>GigaScience</em> publication:</p>
<p> </p>
<p>Benjamin Istace, et al. (2017) De novo assembly and population genomic survey of natural ... | [] |
78,325 | Bulk in vivo electroporation (single cell) | 4 | dx.doi.org/10.17504/protocols.io.j8nlkwr76l5r/v1 | https://www.protocols.io/view/bulk-in-vivo-electroporation-single-cell-cqqvvvw6 | Anya Suppermpool | TITLE: Bulk in vivo electroporation (single cell)
AUTHORS: Anya Suppermpool
[DESCRIPTION]
This protocol will allow you to express single (or near single/mosaic) cell expression in the tectum of larvae. This protocol is adapted from (Hoegler and Horne, 2010; Nikolaou et al., 2015). If you would like to do focal-electro... | ["[Equipments] Stimulator SD9 (Grass Instruments) - borrow from Isaac Bianco (Ask Isaac before use!)", "[Equipments] Electroporation penTM", "[Equipments] Micro glass needle (0.58mm inside diameter, Sutter Instrument, Germany, BF100-58-15) pulled using a micropipette puller (Model P-87 Sutter Instrument, Germany) – nor... |
108,401 | Mouse brain, gut and plasma collection | 0 | dx.doi.org/10.17504/protocols.io.14egn3pkzl5d/v3 | https://www.protocols.io/view/mouse-brain-gut-and-plasma-collection-dm4r48v6 | Livia Hecke Morais | TITLE: Mouse brain, gut and plasma collection
AUTHORS: Livia Hecke Morais
[DESCRIPTION]
Protocol used in the Mazmanian lab for collecting brain and gut tissues and plasma from mouse for metabolomics.
Note that any protocol involving animals should be approved by your Institutional Animal Care
and Use Committee (IAC... | ["[Mouse brain, gut and plasma collection] Euthanize the mouse inside a fume hood by decapitation using scissors (or by alternative method approved by your IACUC).", "[Mouse brain, gut and plasma collection] Use straight scissors to separate the head from the rest of the body.", "[Mouse brain, gut and plasma collection... |
33,850 | Reducing Power | null | dx.doi.org/10.17504/protocols.io.bda2i2ge | null | Jing Xu | TITLE: Reducing Power
AUTHORS: Jing Xu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The reducing power of samples were assayed using the Guo et al.1 ml of the extractwas added to 2.5 ml of phosphate buffer (0.2 M, pH 6.6) and 2.5 ml of 1% potassium ferricyanide.After 20 min, 2.5 ml of 10% t... | [] |
53,903 | GT-seq Library Preparation Protocol | 1 | dx.doi.org/10.17504/protocols.io.byvppw5n | https://www.protocols.io/view/gt-seq-library-preparation-protocol-byvppw5n | Sarah Chang, Michael Russello | TITLE: GT-seq Library Preparation Protocol
AUTHORS: Sarah Chang, Michael Russello
[DESCRIPTION]
Protocol for Genotyping-in-Thousands by sequencing (GT-seq) library preparation.
[STEPS]
SECTION: Making PCR1 Primer Pools
1. Using a sterile polystyrene reservoir and a multichannel pipette, go column by column for each... | ["[Making PCR1 Primer Pools] Using a sterile polystyrene reservoir and a multichannel pipette, go column by column for each plate of primers. Carefully, and making sure that everything is pipetting okay, add 10 µL of each primer to the middle divet of the reservoir. If you pipette on the sides it can be difficult to g... |
19,941 | Value of Information in Telehealth for Chronic Heart Failure | null | dx.doi.org/10.17504/protocols.io.xqdfms6 | null | Andrija S. Grustam, Nasuh Buyukkaramikli, Ron Koymans, Hubertus J.M. Vrijhoef, Johan L. Severens | TITLE: Value of Information in Telehealth for Chronic Heart Failure
AUTHORS: Andrija S. Grustam, Nasuh Buyukkaramikli, Ron Koymans, Hubertus J.M. Vrijhoef, Johan L. Severens
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Figure 1 - Single loop Monte Carlo scheme fo... | [] |
26,306 | ASTROCYTE PRODUCTION (Support Protocol 7.1) | null | dx.doi.org/10.17504/protocols.io.5xag7ie | null | Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward | TITLE: ASTROCYTE PRODUCTION (Support Protocol 7.1)
AUTHORS: Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward
[STEPS]
?. Use 3 P0 or 1 P1 rat pup per uncoated T75 flask. Meninges should be completely removed from brains, and astrocytes isolated per standard mechanical an... | ["Use 3 P0 or 1 P1 rat pup per uncoated T75 flask. Meninges should be completely removed from brains, and astrocytes isolated per standard mechanical and/or enzymatic dissociation protocols under sterile conditions. Expand astrocytes for 1 week or until confluent in DMEM containing 10 % FBS by volume (astrocyte medium)... |
63,847 | ROTAROD PROTOCOL | 4 | dx.doi.org/10.17504/protocols.io.eq2lyn2ywvx9/v1 | https://www.protocols.io/view/rotarod-protocol-cakfsctn | Michael Lee | TITLE: ROTAROD PROTOCOL
AUTHORS: Michael Lee
[DESCRIPTION]
This protocol details the rotarod test.
[GUIDELINES]
Overview
Run groups of up to 5 animals, in a maximum of 4 groups in a single run of 4 trials (i.e. must have ~15-20 min between trials).
Run 4 trials for every animal each day for 4 days.
Detailed records s... | ["[Set-up] Plug in Rotarod, turn on power switch in back.", "[Set-up] Press mode (F1).", "[Set-up] Press Acceleration (F2).", "[Set-up] Set Ramp Duration to 5 min.", "[Set-up] Press ESC.", "[Set-up] Reverse → No.", "[Set-up] Press Alt → Speed and set to a max. of 50 (default is 80).", "[Set-up] Press Forward, and set t... |
101,137 | SARS-CoV-2 TCID50 | 0 | null | https://www.protocols.io/view/sars-cov-2-tcid50-dezr3f56 | Briana L McGovern | TITLE: SARS-CoV-2 TCID50
AUTHORS: Briana L McGovern
[DESCRIPTION]
Protocol used to titer both animal tissue samples and viral stocks at BSL-3
[STEPS]
SECTION: Seeding
2. The day before the assay, seed Vero-TMPRSS2 cells in 96-well plates @ 2e4 cells/well (2e5 cells/ml).
You can either perform the TCID50 in triplicate... | ["[Seeding] The day before the assay, seed Vero-TMPRSS2 cells in 96-well plates @ 2e4 cells/well (2e5 cells/ml).\nYou can either perform the TCID50 in triplicate, which would have 4 samples per plate\nor 4x, which would have 3 samples per plate. \n\nAlways check the confluency of the cells on the day of the assay. If t... |
50,296 | Glyoxal fixation of mammalian cells for immunofluorescence | 4 | dx.doi.org/10.17504/protocols.io.bvcyn2xw | https://www.protocols.io/view/glyoxal-fixation-of-mammalian-cells-for-immunofluo-bvcyn2xw | Karla LH Feijs | TITLE: Glyoxal fixation of mammalian cells for immunofluorescence
AUTHORS: Karla LH Feijs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is our standard protocol for glyoxal fixation of mammalian cells grown on glass cover slips for immunofluorescence microscopy.</div></div>
[STEPS]
?. [Fix ... | ["[Fix the cells]\nWash the cells with warm DMEM without FCS.", "[Fix the cells]\nAdd 300µl glyoxal solution per well (12-well plate) and incubate on ice for 30 minutes , then at room temperature for 20 minutes .\non ice\n0 Room temperature", "[Fix the cells]\nWash 2 times with PBS", "[Fix the cells]\nAdd 300µl quench... |
53,733 | Immunolabelling and clearing of intact spinal cord for visualization of lower urinary tract afferents | 1 | dx.doi.org/10.17504/protocols.io.byqdpvs6 | https://www.protocols.io/view/immunolabelling-and-clearing-of-intact-spinal-cord-byqdpvs6 | Janet R Keast, Peregrine B Osborne, John-Paul Fuller-Jackson | TITLE: Immunolabelling and clearing of intact spinal cord for visualization of lower urinary tract afferents
AUTHORS: Janet R Keast, Peregrine B Osborne, John-Paul Fuller-Jackson
[DESCRIPTION]
The whole-mount immunolabeling and clearing method (iDISCO) was used to visualize cholera toxin subunit B-labelled lower urin... | ["[Spinal cord preparation] While immersed in phosphate buffered-saline (PBS), pH 7.2, trim nerve roots of fixed spinal cord to within approximately 2 mm of the spinal cord surface to facilitate the identification of segments later following imaging.", "[Bleaching] Wash samples in 1x Dulbecco’s PBS (DPBS)(6 x 15 mins).... |
102,230 | ilastik install and run for Syn Bot (Mac Version) | 0 | dx.doi.org/10.17504/protocols.io.261ge5exjg47/v1 | https://www.protocols.io/view/ilastik-install-and-run-for-syn-bot-mac-version-df3w3qpe | Justin T Savage | TITLE: ilastik install and run for Syn Bot (Mac Version)
AUTHORS: Justin T Savage
[DESCRIPTION]
Video instructions for installing ilastik, training an ilastik project, and using the ilastik project for simple SynBot run for Mac operating system.
[STEPS]
1.
SECTION: Installing ilastik
2. 0:00 - 1:00 Install ila... | ["[Installing ilastik] 0:00 - 1:00 Install ilastik by downloading it from ilastik.org/download and running the installer. To run ilastik after initial installation, right-click the application and click open. You will then be prompted to open the application even though it is from an unrecognized developer.", "[Generat... |
55,562 | Gait and rehabilitation in lower limb amputees: a narrative review | 1 | dx.doi.org/10.17504/protocols.io.b2hiqb4e | https://www.protocols.io/view/gait-and-rehabilitation-in-lower-limb-amputees-a-n-b2hiqb4e | Irene Aprile, Marco Gallotti, Marco Germanotta, Pasquale Alessio Sauchelli | TITLE: Gait and rehabilitation in lower limb amputees: a narrative review
AUTHORS: Irene Aprile, Marco Gallotti, Marco Germanotta, Pasquale Alessio Sauchelli
[DESCRIPTION]
Introduction:Even if gait analysis is a validated outcome measure to assess the effects of a rehabilitation program on gait performance, few artic... | [] |
25,037 | Phenol-Chloroform Extraction for dsRNA Purification | null | dx.doi.org/10.17504/protocols.io.4pmgvk6 | null | Cera Fisher | TITLE: Phenol-Chloroform Extraction for dsRNA Purification
AUTHORS: Cera Fisher
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is the final step in preparing injectable constructs for RNA interference. This protocol starts with a 20 uL T7-polymerase transcription reaction. We use New England B... | ["[Adjust salt conditions]\nAdd 166.6 uL of nuclease free water to each PCR tube. Move 187 uL of liquid to new, labeled 1.5 mL microcentrifuge tube.", "[Extract RNA]\nAdd 200 uL of acid phenol/chloroform (50:50) to each tube. Shake vigorously for 15 seconds.", "[Extract RNA]\nCentrifuge at 4C for 5 minutes at 12,000 * ... |
34,817 | The Cluster Feature of Coalmine Disasters and Earthquakes in China | null | dx.doi.org/10.17504/protocols.io.bd89i9z6 | null | Chen Bo | TITLE: The Cluster Feature of Coalmine Disasters and Earthquakes in China
AUTHORS: Chen Bo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span> Recently, in China, nearly half of coalmine disasters are found to present cluster feature or to be accompanied with earthquakes (<5) nearby, in whic... | [] |
85,858 | sample_prep_serum.nan | 4 | dx.doi.org/10.17504/protocols.io.6qpvr34epvmk/v1 | https://www.protocols.io/view/sample-prep-serum-nan-cx4axqse | NAN KB, Mario Uchimiya, John Glushka, Christopher Esselman, Leandro I Ponce, Laura Morris, Arthur Edison | TITLE: sample_prep_serum.nan
AUTHORS: NAN KB, Mario Uchimiya, John Glushka, Christopher Esselman, Leandro I Ponce, Laura Morris, Arthur Edison
[DESCRIPTION]
This is a modified protocol for a protein precipitation method for plasma/serum samples. This protocol was originally proposed by:
See also:
[STEPS]
17. ... | ["Add 600 µL of 100% cold methanol to 300 µL of samples on ice\nUse 1.5-mL Eppendorf tubes\nKeep methanol cold on ice", "Vortex the samples for 10 s", "Incubate the samples at -20 °C for 20 min", "Centrifuge the samples at 4 °C at for 30 min", "Transfer the supernatants to new 1.5-mL Eppendorf tubes", "Dry the sample... |
20,368 | U Mass - Urea/BUN | null | dx.doi.org/10.17504/protocols.io.x5qfq5w | null | Jason Kim | TITLE: U Mass - Urea/BUN
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. Serum Urea/BUN level... | ["Perform daily quality control assessment of instrumentation before analysis.", "Load each sample into a specialized micro-sample cup for the clinical chemistry analyzer.", "Select Urea/BUN test on display and run the analysis.", "Collect and analyze the data."] |
75,215 | BARseq - BARseq-styled in situ sequencing for barcoded rabies virus | 1 | dx.doi.org/10.17504/protocols.io.n2bvj82q5gk5/v1 | https://www.protocols.io/view/barseq-barseq-styled-in-situ-sequencing-for-barcod-cmppu5mn | Xiaoyin Chen, Mara CP Rue | TITLE: BARseq - BARseq-styled in situ sequencing for barcoded rabies virus
AUTHORS: Xiaoyin Chen, Mara CP Rue
[DESCRIPTION]
This protocol describes the application of BARseq-style in situ sequencing adapted for barcoded rabies virus. Similar procedures for both trans-synaptic tracing and retrograde tracing experiments... | ["[Library preparation] Tissues with barcoded neurons should be cryo-sectioned to 20 μm and mounted on slides. Slides can be stored at -80 °C for up to a month.", "[Library preparation] DAY 1\n\nTake slide(s) out of -80 °C and immerse immediately in 4% paraformaldehyde in 1x PBS (2 slides per 50mL falcon tube, back-to-... |
58,925 | Y Maze Forced Alternation | 4 | dx.doi.org/10.17504/protocols.io.b5smq6c6 | https://www.protocols.io/view/y-maze-forced-alternation-b5smq6c6 | Haley Geertsma | TITLE: Y Maze Forced Alternation
AUTHORS: Haley Geertsma
[DESCRIPTION]
This protocol is used to test mice in the Y Maze Forced Alternation behavioural test.
[STEPS]
1. Habituate mice in a separate room for 60 minutes prior to testing.
2. Confirm testing room lighting is set to 60lux and EthoVision is set up properl... | ["Habituate mice in a separate room for 60 minutes prior to testing.", "Confirm testing room lighting is set to 60lux and EthoVision is set up properly.", "Place mice in Arm 1 (with either Arm 2 or 3 blocked, alternate between mice) and record their movement for 5 minutes.", "After testing, place the mouse back into th... |
28,382 | MojoSort™ Isolation Kits Protocol - 1 | null | dx.doi.org/10.17504/protocols.io.7x6hpre | null | Sam Li | TITLE: MojoSort™ Isolation Kits Protocol - 1
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Product description and procedure summary:</span></div><div class = "text-block"><span>Target cells are depleted by incubating the sample with the biotin ant... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes. Kits for human samples have been optimized for PBMCs, please prepare the cells using a suitable method.", "In the final wash of your sample preparation, resuspend the cells in MojoSort™ Buffer by adding up to 4mL in a 5 mL (12 x 75 mm) p... |
36,565 | Molecular Phenotype Distribution of Single Rat ICN Neurons - Heart B | null | dx.doi.org/10.17504/protocols.io.bfxvjpn6 | https://www.protocols.io/view/molecular-phenotype-distribution-of-single-rat-icn-bfxvjpn6 | Shaina Robbins, Alison Moss, Sean Nieves, Sirisha Achanta | TITLE: Molecular Phenotype Distribution of Single Rat ICN Neurons - Heart B
AUTHORS: Shaina Robbins, Alison Moss, Sean Nieves, Sirisha Achanta
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This collection of protocols were used to obtain the current data for the Blackfynn Dataset Molecular Phenoty... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.fzrbp56 | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
<ul>
<li>Make sure you are using fresh <em>E. coli</em> cells streaked for isolation on LB + antibiotics no more than 1 week from -80°C cryostock.</li>
</ul>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
19,255 | Use of tracer dyes to label neural projections to lower urinary tract organs | null | dx.doi.org/10.17504/protocols.io.w2xfgfn | https://www.protocols.io/view/use-of-tracer-dyes-to-label-neural-projections-to-w2xfgfn | Janet Keast, Peregrine Osborne | TITLE: Use of tracer dyes to label neural projections to lower urinary tract organs
AUTHORS: Janet Keast, Peregrine Osborne
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to visualise sensory and autonomic neurons innervating the bladder body (dome), bladder trigone or proxima... | ["[Preparation for surgery]\nPrepare tracer dye solutions: Fluorogold or Fast Blue (each 2% w/v in sterile water).", "[Preparation for surgery]\nAnesthetise animal (2.5% isoflurane in oxygen, or as required for maintenance)", "[Preparation for surgery]\nApply eye lubricant and place animal on heated pad.", "[Preparatio... |
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