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Authors: Sam Li
Group: BioLegend
Summary: 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.

Proper citation: Sam Li 2019. MojoSort™ Mouse CD4 Nanobeads Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.7wthpen Copy   

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Authors: Marita A. Isokallio, James Stewart
Group: Stewart-Lab MPI-AGE
Summary: 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

Proper citation: 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 Copy   

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Authors: Jernej Turnsek
Summary: 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.

Proper citation: Jernej Turnsek 2020. Pillowcase & rubber band DIY face mask. protocols.io https://dx.doi.org/10.17504/protocols.io.be2mjgc6 Copy   

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Authors: Brandt Pence

Proper citation: Brandt Pence 2018. Glycolysis Stress Test for Monocyte Glycolytic Function. protocols.io https://dx.doi.org/10.17504/protocols.io.ufaetie Copy   

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Authors: Roey Angel, Ana Lara-Rodriguez, Eva Petrova
Group: SoWa RI Anaerobic and Molecular Microbiology (public)

Proper citation: Roey Angel, Ana Lara-Rodriguez, Eva Petrova 2020. TPGY BROTH (TRYPTONE PEPTONE GLUCOSE YEAST EXTRACT BROTH). protocols.io https:// Copy   

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Authors: Faris Ghazal
Summary: 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.

Proper citation: 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 Copy   

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Authors: Ariel Rabines, Rob Lampe, Andrew Allen
Group: A.E. Allen Lab
Summary: 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.

Proper citation: Ariel Rabines, Rob Lampe, Andrew Allen 2020. Sterivex DNA extraction. protocols.io https://dx.doi.org/10.17504/protocols.io.bc2hiyb6 Copy   

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Authors: Maryann C. Gruda, Pamela O’Sullivan, Karl-Gustav Ruggeberg, Tamaz Guliashvili, Andrew R. Scheirer, Thomas D. Golobish, Vincent J. Capponi, Phillip P. Chan
Summary: 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.

Proper citation: 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 Copy   

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Authors: 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
Group: Human Cell Atlas Method Development Community
Summary: 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.

Proper citation: 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 Copy   

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Authors: Dane Lyddiard
Summary: 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.

Proper citation: Dane Lyddiard 2020. Thin Layer Chromatography (TLC) Bioautography. protocols.io https://dx.doi.org/10.17504/protocols.io.bmxik7ke Copy   

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Authors: Rosa Leon
Group: Leon Zayas Lab
Summary: This protocol series will guide students through the experience of analyzing metagenomic data. 

Proper citation: Rosa Leon 2018. BIOL 354W - Research Methods in Advance Microbiology. protocols.io https://dx.doi.org/10.17504/protocols.io.nebdban Copy   

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Authors: Daniel Manrique-Castano

Proper citation: Daniel Manrique-Castano 2021. Protein extraction and BCA assay from MCAS sorted cells. protocols.io https:// Copy   

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Authors: Cheng Song

Proper citation: Cheng Song 2017. Basic components detection of Dendrobium plants. protocols.io https://dx.doi.org/10.17504/protocols.io.h4gb8tw Copy   

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Authors: Bioline
Group: Bioline
Summary: 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.

Proper citation: 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 Copy   

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Authors: Josh Quick

Proper citation: Josh Quick 2020. One-pot native barcoding of amplicons v3 (LoCost). protocols.io https:// Copy   

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Authors: Angel Justiz-Vaillant
Group: University of the West Indies, [email protected]
Summary: 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.

Proper citation: Angel Justiz-Vaillant 2020. Preparation of staphylococcal protein-A conjugated to horseradish peroxidase.. protocols.io https://dx.doi.org/10.17504/protocols.io.bj5ykq7w Copy   

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Authors: Cancer Research UK / Wellcome Gurdon Institute media kitchen
Summary: Prepare 2L of B-Broth for culturing bacteria

Proper citation: 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 Copy   

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Authors: Johannes Wolfram Debler
Summary: A quick guide on how to electroporate your plasmid of interest into electrocompetent Agrobacterium tumefaciens cells.

Proper citation: Johannes Wolfram Debler 2019. Electroporation of Agrobacterium. protocols.io https://dx.doi.org/10.17504/protocols.io.g8ubzww Copy   

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Authors: Kerri Wolter
Group: VulPro

Proper citation: Kerri Wolter 2020. Vulture Rehabilitation Manual. protocols.io https:// Copy   

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Authors: Marda Jorgensen, Maigan Brusko
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community

Proper citation: Marda Jorgensen, Maigan Brusko 2020. HubMap UF TMC Tissue Dissociation to Single Cell. protocols.io https://dx.doi.org/10.17504/protocols.io.bd9vi966 Copy   

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