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| Name | Authors | DOI | Group |
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MojoSort™ Mouse CD4 Nanobeads Protocol Resource Report Resource Website |
Sam Li | DOI:10.17504/protocols.io.7wthpen | BioLegend | Product description and procedure summary:The cells targeted by the Nanobeads are either selected or depleted by incubating your sample with the directly conjugated magnetic particles. The magnetically labeled fraction is retained by the use of a magnetic separator. After collection of the targeted cells, downstream applications include functional assays, gene expression, phenotypic characterization, etc. Note: This procedure is optimized for the isolation of 107 to 2 x 108 cells per tube. If working with fewer than 107 cells, keep volumes as indicated for 107 cells. For best results, optimize the conditions to your specific cell number and tissue. Prepare fresh MojoSort™ Buffer solution by diluting the 5X concentrate with sterile distilled water. Scale up volumes if using 14mL tubes and Magnet, and place the tube in the magnet for 10 minutes. | BioLegend | https://www.biolegend.com/protocols/mojosort-mouse-cd4-nanobeads-protocol/4314/ | 1 | 2019 | Sam Li 2019. MojoSort™ Mouse CD4 Nanobeads Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.7wthpen | 2021-04-15 09:15:44 | ||
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Low-frequency variant calling from high-quality mtDNA sequencing data Resource Report Resource Website |
Marita A. Isokallio, James Stewart | DOI:10.17504/protocols.io.nfkdbkw | Stewart-Lab MPI-AGE | High-quality, highly enriched mitochondrial DNA (mtDNA) sample enables detection of extremely low-frequency mtDNA variants. When mtDNA is carefully enriched, fragmented in the presence of EDTA and sequenced with unique dual indices by Illumina HiSeq in paired-end mode, it is possible to reliably detect variants at allele frequencies | Max Planck Instutute for Biology of Ageing, Max Planck Instutute for Biology of Ageing | 1 | 2018 | Marita A. Isokallio, James Stewart 2018. Low-frequency variant calling from high-quality mtDNA sequencing data. protocols.io https://dx.doi.org/10.17504/protocols.io.nfkdbkw | 2021-04-15 09:15:16 | |||
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Pillowcase & rubber band DIY face mask Resource Report Resource Website |
Jernej Turnsek | DOI:10.17504/protocols.io.be2mjgc6 | This protocol describes a very simple way to make a face mask at home using a cotton pillowcase, a (coffee) filter, 2 rubber bands, and a minute of your time.Wearing a face mask helps stop the spread of the new coronavirus. Useful additional resources:1/ Video protocol for a related face mask alternative.2/ More DIY face mask ideas via the Center for Disease Control and Prevention.3/ Pillowcase alternatives and strategies to improve/modify (the effectiveness of) your DIY face mask.4/ Discussion on sneeze/cough droplet ballistics and why wearing a mask, even a DIY cloth-based one without filters, matters. | University of California, Berkeley | 4 | 2020 | Jernej Turnsek 2020. Pillowcase & rubber band DIY face mask. protocols.io https://dx.doi.org/10.17504/protocols.io.be2mjgc6 | 2021-04-15 09:15:16 | ||||
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Glycolysis Stress Test for Monocyte Glycolytic Function Resource Report Resource Website |
Brandt Pence | DOI:10.17504/protocols.io.ufaetie | University of Memphis | 1 | 2018 | Brandt Pence 2018. Glycolysis Stress Test for Monocyte Glycolytic Function. protocols.io https://dx.doi.org/10.17504/protocols.io.ufaetie | 2021-04-15 09:15:16 | |||||
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TPGY BROTH (TRYPTONE PEPTONE GLUCOSE YEAST EXTRACT BROTH) Resource Report Resource Website |
Roey Angel, Ana Lara-Rodriguez, Eva Petrova | SoWa RI Anaerobic and Molecular Microbiology (public) | Soil and Water Research Infrastructure, Soil and Water Research Infrastructure, Soil and Water Research Infrastructure | http://www.himedialabs.com/TD/M969.pdf | 1 | 2020 | Roey Angel, Ana Lara-Rodriguez, Eva Petrova 2020. TPGY BROTH (TRYPTONE PEPTONE GLUCOSE YEAST EXTRACT BROTH). protocols.io https:// | 2021-04-15 09:15:44 | ||||
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The feasibility and outcome of atrial fibrillation screening using intermittent electrocardiogram in a primary health care setting: A cross-sectional study Resource Report Resource Website |
Faris Ghazal | DOI:10.17504/protocols.io.m2fc8bn | BackgroundAtrial fibrillation (AF) is a major risk of ischemic stroke unless treated with anticoagulant. Detection of AF can be difficult because AF is often paroxysmal and asymptomatic. The aim of this study is to develop a screening model for detecting AF in a primary health care setting and to start oral anticoagulant therapy in high risk patients to prevent stroke.Methods and FindingsA cross-sectional study. All of 70- to 74-year-old individuals registered at a single primary health care centre in Stockholm were invited to AF screening upon visiting the centre during a ten-month period. Those who did not have contact with the centre during this period were invited to participate by letter. Intermittent ECG recording, 30 seconds twice a day, using a hand-held Zenicor device over a 2-week period, was offered to participants without AF. Oral anticoagulant therapy was offered to patients with newly detected AF.A total number of 324 (78.1%) out of 415 identified persons participated in the study. The mean age of the participants was 72 years, 52.2% were female and the median CHA2DS2-VASc was 3. Previously diagnosed AF was found in 34 (8.2%) persons in the target population. Among participants without previously known AF, 16 (5.5%) cases of new AF were detected. The final AF prevalence in the target population was 12%. Initiation of oral anticoagulant therapy was successful 88% of patients with newly detected AF.ConclusionsThe AF screening project showed a high participation rate and yielded a high rate of newly discovered AF of which 88% were able to be treated with oral anticoagulant. | Feasibility and outcomes of atrial fibrillation screening using intermittent electrocardiography in a primary healthcare setting: A cross-sectional study | Karolinska Institute Stockholm | 1 | 2018 | Faris Ghazal 2018. The feasibility and outcome of atrial fibrillation screening using intermittent electrocardiogram in a primary health care setting: A cross-sectional study. protocols.io https://dx.doi.org/10.17504/protocols.io.m2fc8bn | 2021-04-15 09:15:16 | |||
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Sterivex DNA extraction Resource Report Resource Website |
Ariel Rabines, Rob Lampe, Andrew Allen | DOI:10.17504/protocols.io.bc2hiyb6 | A.E. Allen Lab | A mostly automated protocol for extraction of genomic DNA from seawater filtered onto a Sterivex filter (Cat. No. SVGP0150). Reagents come from the Macherey-Nagel NucleoMag Plant Kit for DNA purfication (Cat. No. 744400). Automated liquid handling is performed on an eppendorf EpMotion 5075t with multi-channel pipettes. This protocol assumes that the Sterivex is sealed with tube sealant on the male end and a male-luer lock plug on the female end. Using this protocol, we routinely extract ~80 samples at a time.The protocol has been modified to increase to an 800 µL starting volume. This normally results in less Lysis Buffer MC1 and Binding Buffer MC2 than is needed. Extra binding buffer should be purchased separately. The kit manual can be found here: https://www.mn-net.com/media/pdf/09/46/a0/Instruction-NucleoMag-Plant.pdfAdditional notes from the manufacturer on using the kit with the epMotion can be found here: https://www.mn-net.com/media/pdf/95/2c/ef/AN-NucleoMag-Plant-epMotion5075.pdf . Note that we have modifications to their protocol.The epMotion program is attached here. | Scripps Institution of Oceanography, Scripps Institution of Oceanography, Scripps Institution of Oceanography | 2 | 2020 | Ariel Rabines, Rob Lampe, Andrew Allen 2020. Sterivex DNA extraction. protocols.io https://dx.doi.org/10.17504/protocols.io.bc2hiyb6 | 2021-04-15 09:15:44 | |||
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Broad Adsorption Of Sepsis-Related PAMP And DAMP Molecules, Mycotoxins, and Cytokines From Whole Blood Using CytoSorb® Sorbent Porous Polymer Beads Resource Report Resource Website |
Maryann C. Gruda, Pamela O’Sullivan, Karl-Gustav Ruggeberg, Tamaz Guliashvili, Andrew R. Scheirer, Thomas D. Golobish, Vincent J. Capponi, Phillip P. Chan | DOI:10.17504/protocols.io.kurcwv6 | In vitro blood recirculation model through Cytosorb device, including specific blood tubing and peristaltic pump components to analyze removal of key inflammatory mediators and toxins. | Gruda MC, Ruggeberg K, O’Sullivan P, Guliashvili T, Scheirer AR, Golobish TD, Capponi VJ, Chan PP (2018) Broad adsorption of sepsis-related PAMP and DAMP molecules, mycotoxins, and cytokines from whole blood using CytoSorb® sorbent porous polymer beads. PLoS ONE 13(1): e0191676. doi: 10.1371/journal.pone.0191676 | CytoSorbents, Inc. Monmouth Junction, UNITED STATES, , , , , , , | https://doi.org/10.1371/journal.pone.0191676 | 1 | 2018 | Maryann C. Gruda, Pamela O’Sullivan, Karl-Gustav Ruggeberg, Tamaz Guliashvili, Andrew R. Scheirer, Thomas D. Golobish, Vincent J. Capponi, Phillip P. Chan 2018. Broad Adsorption Of Sepsis-Related PAMP And DAMP Molecules, Mycotoxins, and Cytokines From Whole Blood Using CytoSorb® Sorbent Porous Polymer Beads. protocols.io https://dx.doi.org/10.17504/protocols.io.kurcwv6 | 2021-04-15 09:15:42 | ||
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ExFISH - Tissue Slice Resource Report Resource Website |
Fei Chen, Asmamaw T Wassie, Allison J Cote, Anubhav Sinha, Shahar Alon, Shoh Asano, Evan R Daugharthy, Jae-Byum Chang, Adam Marblestone, George M Church, Arjun Raj, Edward S Boyden | DOI:10.17504/protocols.io.n6adhae | Human Cell Atlas Method Development Community | The ability to image RNA identity and location with nanoscale precision in intact tissues is of great interest for defining cell types and states in normal and pathological biological settings. Here, we present a strategy for expansion microscopy of RNA. We developed a small-molecule linker that enables RNA to be covalently attached to a swellable polyelectrolyte gel synthesized throughout a biological specimen. Then, postexpansion, fluorescent in situ hybridization (FISH) imaging of RNA can be performed with high yield and specificity as well as single-molecule precision in both cultured cells and intact brain tissue. Expansion FISH (ExFISH) separates RNAs and supports amplification of single-molecule signals (i.e., via hybridization chain reaction) as well as multiplexed RNA FISH readout. ExFISH thus enables super-resolution imaging of RNA structure and location with diffraction-limited microscopes in thick specimens, such as intact brain tissue and other tissues of importance to biology and medicine. | Massachusetts Institute of Technology, Massachusetts Institute of Technology, University of Pennsylvania, Massachusetts Institute of Technology, Massachusetts Institute of Technology, Massachusetts Institute of Technology, Harvard University, Massachusetts Institute of Technology, Massachusetts Institute of Technology, Harvard University, University of Pennsylvania, Massachusetts Institute of Technology | http://expansionmicroscopy.org/ExFISHV1.0.docx | 1 | 2018 | Fei Chen, Asmamaw T Wassie, Allison J Cote, Anubhav Sinha, Shahar Alon, Shoh Asano, Evan R Daugharthy, Jae-Byum Chang, Adam Marblestone, George M Church, Arjun Raj, Edward S Boyden 2018. ExFISH - Tissue Slice. protocols.io https://dx.doi.org/10.17504/protocols.io.n6adhae | 2021-04-15 09:15:15 | ||
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Thin Layer Chromatography (TLC) Bioautography Resource Report Resource Website |
Dane Lyddiard | DOI:10.17504/protocols.io.bmxik7ke | A TLC bioautography protocol to test the constituents of plant extracts and essential oils for antibacterial activity was adapted and optimised from the methods described in Smith et al. (2007) and Hamburger & Cordell (1987). The protocol described here has been used successfully with a number of non-fastidious organisms, plant extracts and essential oils. The procedure is economical, easy to undertake and the results easily interpreted. In addition to initially screening plants for antibacterial constituents, the TLC bioautography can inform compound isolation work.References:Hamburger, M. O., Cordell, G. A., 1987. A direct Bioautographic TLC assay for compounds possessing antibacterial activity. Journal of Natural Products 50, 19-22.Smith, J. E., Tucker, D., Watson, K., Jones, G. L., 2007. Identification of antibacterial constituents from the indigenous Australian medicinal plant Eremophila duttonii F. Muell. (Myoporaceae). J Ethnopharmacol 112, 386-393. | University of New England, Australia | 2 | 2020 | Dane Lyddiard 2020. Thin Layer Chromatography (TLC) Bioautography. protocols.io https://dx.doi.org/10.17504/protocols.io.bmxik7ke | 2021-04-15 09:15:15 | ||||
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BIOL 354W - Research Methods in Advance Microbiology Resource Report Resource Website |
Rosa Leon | DOI:10.17504/protocols.io.nebdban | Leon Zayas Lab | This protocol series will guide students through the experience of analyzing metagenomic data. | Willamette University | 11 | 2018 | Rosa Leon 2018. BIOL 354W - Research Methods in Advance Microbiology. protocols.io https://dx.doi.org/10.17504/protocols.io.nebdban | 2021-04-15 09:15:15 | |||
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Protein extraction and BCA assay from MCAS sorted cells Resource Report Resource Website |
Daniel Manrique-Castano | Université Laval | 1 | 2021 | Daniel Manrique-Castano 2021. Protein extraction and BCA assay from MCAS sorted cells. protocols.io https:// | 2021-04-15 09:15:15 | ||||||
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Basic components detection of Dendrobium plants Resource Report Resource Website |
Cheng Song | DOI:10.17504/protocols.io.h4gb8tw | 1 | 2017 | Cheng Song 2017. Basic components detection of Dendrobium plants. protocols.io https://dx.doi.org/10.17504/protocols.io.h4gb8tw | 2021-04-15 09:15:43 | ||||||
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Genomic DNA removal and total RNA purification from all types of lysate (ISOLATE II Biofluids RNA Kit) Resource Report Resource Website |
Bioline | DOI:10.17504/protocols.io.f48bqzw | Bioline | The ISOLATE II Biofluids RNA Kit is specially developed for the rapid phenol-free isolation of high quality total RNA from biofluids and viruses. The following protocol is two part. The first part provides a procedure for the removal of genomic DNA applies to all the different types of lysate. Ensure you use the correct column: the Genomic DNA Removal Column has a blue ring. The second part is the protocol for the purification of total RNA apply to all the different types of lysate. Ensure you use the correct column: the ISOLATE II RNA Column has a black ring. | http://www.bioline.com/us/downloads/dl/file/id/3789/isolate_ii_biofluids_rna_kit_product_manual.pdf | 1 | 2016 | Bioline 2016. Genomic DNA removal and total RNA purification from all types of lysate (ISOLATE II Biofluids RNA Kit). protocols.io https://dx.doi.org/10.17504/protocols.io.f48bqzw | 2021-04-15 09:15:16 | |||
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One-pot native barcoding of amplicons v3 (LoCost) Resource Report Resource Website |
Josh Quick | University of Birmingham | http://lab.loman.net/protocols/ | 1 | 2020 | Josh Quick 2020. One-pot native barcoding of amplicons v3 (LoCost). protocols.io https:// | 2021-04-15 09:15:43 | |||||
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Preparation of staphylococcal protein-A conjugated to horseradish peroxidase. Resource Report Resource Website |
Angel Justiz-Vaillant | DOI:10.17504/protocols.io.bj5ykq7w | University of the West Indies, [email protected] | This reagent can be used in ELISA, Western blotting and Dot blot to detect antigens and antibodies. It is important in the immunodiagnosis of infectious diseases. I find this useful in the detection of anti-HIV antibodies by ELISA. | University of the West Indies St. Augustine | 1 | 2020 | Angel Justiz-Vaillant 2020. Preparation of staphylococcal protein-A conjugated to horseradish peroxidase.. protocols.io https://dx.doi.org/10.17504/protocols.io.bj5ykq7w | 2021-04-15 09:15:42 | |||
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Prepare 2L of B-Broth for culturing bacteria Resource Report Resource Website |
Cancer Research UK / Wellcome Gurdon Institute media kitchen | DOI:10.17504/protocols.io.3nmgmc6 | Prepare 2L of B-Broth for culturing bacteria | Cancer Research UK / Wellcome Gurdon Institute | 1 | 2019 | Cancer Research UK / Wellcome Gurdon Institute media kitchen 2019. Prepare 2L of B-Broth for culturing bacteria. protocols.io https://dx.doi.org/10.17504/protocols.io.3nmgmc6 | 2021-04-15 09:15:42 | ||||
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Electroporation of Agrobacterium Resource Report Resource Website |
Johannes Wolfram Debler | DOI:10.17504/protocols.io.g8ubzww | A quick guide on how to electroporate your plasmid of interest into electrocompetent Agrobacterium tumefaciens cells. | Curtin University | 1 | 2019 | Johannes Wolfram Debler 2019. Electroporation of Agrobacterium. protocols.io https://dx.doi.org/10.17504/protocols.io.g8ubzww | 2021-04-15 09:15:43 | ||||
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Vulture Rehabilitation Manual Resource Report Resource Website |
Kerri Wolter | VulPro | VulPro | 1 | 2020 | Kerri Wolter 2020. Vulture Rehabilitation Manual. protocols.io https:// | 2021-04-15 09:15:15 | |||||
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HubMap UF TMC Tissue Dissociation to Single Cell Resource Report Resource Website |
Marda Jorgensen, Maigan Brusko | DOI:10.17504/protocols.io.bd9vi966 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | University of Florida, University of Florida | 1 | 2020 | Marda Jorgensen, Maigan Brusko 2020. HubMap UF TMC Tissue Dissociation to Single Cell. protocols.io https://dx.doi.org/10.17504/protocols.io.bd9vi966 | 2021-04-15 09:15:16 |
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