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Authors: Louise Lantier
Group: Mouse Metabolic Phenotyping Centers
Summary: Summary: The exercise stress test is a maximal exercise test used to calculate VO2 max. Mice are run to complete exhaustion as the treadmill speed is increased every three minutes (See table 1). During the test, direct measurements of the oxygen consumption and carbon dioxide output by the mouse are made, which are then used to calculate VO2 max, VCO2, and RER. VO2 max refers to the maximum amount of oxygen that the mouse can utilize during maximal exercise.

Proper citation: Louise Lantier 2019. Vandy - Exercise Stress Test. protocols.io https://dx.doi.org/10.17504/protocols.io.yxcfxiw Copy   

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Authors: Anup Sood, Eric Williams, Liz McDonough
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community, GE Research
Summary: The purpose of the protocol is to purify antibodies that will be conjugated to Cy dyes as per the Cell DIVE™ technology. Affinity chromatography will be used to remove impurities from the vendor antibody to enable conjugation.

Proper citation: Anup Sood, Eric Williams, Liz McDonough 2021. Cell DIVE™ Platform | Antibody Purification Chemistry. protocols.io https://dx.doi.org/10.17504/protocols.io.bpx9mpr6 Copy   

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Authors: Addgene The Nonprofit Plasmid Repository
Summary: This protocol is for restriction digest of plasmid DNA. To see the full abstract and additional resources, please visit http://www.addgene.org/plasmid_protocols/restriction_digest/.

Proper citation: Addgene The Nonprofit Plasmid Repository 2019. Restriction Digest of Plasmid DNA. protocols.io https://dx.doi.org/10.17504/protocols.io.63shgne Copy   

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Authors: Dina Stensen, Anne-Sofie Furberg, Karina Olsen, Gunnar Skov Simonsen, Johanna UE Sollid, Lars Småbrekke, Guri Grimnes, Cristopher Sievert Nielsen
Summary: The aim of the study is to evaluate prevalence of Staphylococcus aureus in a youth population. This samples will be connected to other possible riskfactors for Staphylococcus aureus carriage.

Proper citation: Dina Stensen, Anne-Sofie Furberg, Karina Olsen, Gunnar Skov Simonsen, Johanna UE Sollid, Lars Småbrekke, Guri Grimnes, Cristopher Sievert Nielsen 2019. Protocol for sampling and transport of nose- and thoratsamples in the Fit Futures study. protocols.io https://dx.doi.org/10.17504/protocols.io.2j5gcq6 Copy   

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Authors: Anastasios Tsaousis
Group: Protist Research to Optimize Tools in Genetics (PROT-G)

Proper citation: Anastasios Tsaousis 2017. Transfection of Naegleria gruberi. protocols.io https://dx.doi.org/10.17504/protocols.io.hpub5nw Copy   

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Authors: Gary Lecleir, Steven Wilhelm
Group: The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs)
Summary: Welcome to the Wilhelm Lab. This short training is to help orient those that are learning how to work in a laboratory environment as well as help those that are joining our lab to become acquainted with our procedures.

Proper citation: Gary Lecleir, Steven Wilhelm 2019. UTK Laboratory Orientation/Training. protocols.io https://dx.doi.org/10.17504/protocols.io.6c3hayn Copy   

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Authors: Thomas Ashhurst, Darren A. Cox, Adrian L. Smith, Nicholas J. C. King
Group: Immune Dynamics
Summary: Cell counting is a critical step to determine the number of live leukocytes (white blood cells, WBC) and erythrocytes (red blood cells, RBC) per femur, and is accurately performed using a microscope and haemocytometer. This step allows enables the distribution of a specific number of cells per well in the staining plate. Some researchers prefer to perform an erythrocyte (or red blood cell, RBC) lysis prior to counting, as some researchers are concerned about misidentifying erythrocytes as leukocytes during counting. This RBC lysis removes all erythrocytes prior to counting, resulting in easier counting of leukocytes. However, we have found that differentiating leukocytes from erythrocytes is straight forward at a higher magnification based on size (erythrocytes are smallest), colour (erythrocytes are red in colour), and birefringence (leukocytes exhibit birefringence, erythrocytes do not). Additionally, RBC lysis prior to cell staining will have a small impact on CD115 staining levels (see protocol notes). To circumvent the need for RBC lysis prior to staining, we count the number of leukocytes (and erythrocytes) in the centre square only, at a high magnification. Alternatively, an automated cell counter can be used to speed up counting. However, care must be taken to ensure that any automated cell counter is accurately performing counts, as most automated cell counters are calibrated to human blood cells.

Proper citation: Thomas Ashhurst, Darren A. Cox, Adrian L. Smith, Nicholas J. C. King 2021. Cell counting with a haemocytometer (with mouse bone marrow example). protocols.io https://dx.doi.org/10.17504/protocols.io.btqgnmtw Copy   

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Authors: Betty San Martín, Lisette Lapierre, Marcela Fresno, Javiera Cornejo

Proper citation: Betty San Martín, Lisette Lapierre, Marcela Fresno, Javiera Cornejo 2019. Determination of florfenicol and florfenicol amine in fish plasma (Salmo salar) through HPLC MS/MS. protocols.io https://dx.doi.org/10.17504/protocols.io.zhdf326 Copy   

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Authors: Sara H Rouhanifard, Ian A Mellis, Margaret Dunagin, Sareh Bayatpour, Orsolya Symmons, Allison Cote, Arjun Raj
Group: Human Cell Atlas Method Development Community
Summary: Non-enzymatic, high-gain signal amplification methods with single-cell, single-molecule resolution are in great need. We present click-amplifying FISH (clampFISH) for the fluorescent detection of RNA that combines the specificity of oligonucleotides with bioorthogonal click chemistry in order to achieve high specificity and extremely high-gain (>400x) signal amplification. We show that clampFISH signal enables detection with low magnification microscopy and separation of cells by RNA levels via flow cytometry. Additionally, we show that the modular design of clampFISH probes enables multiplexing, that the locking mechanism prevents probe detachment in expansion microscopy, and that clampFISH works in tissue samples.

Proper citation: Sara H Rouhanifard, Ian A Mellis, Margaret Dunagin, Sareh Bayatpour, Orsolya Symmons, Allison Cote, Arjun Raj 2018. ClampFISH . protocols.io https://dx.doi.org/10.17504/protocols.io.qeydtfw Copy   

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Authors: Sanjay Srivatsan, Mary Regier

Proper citation: Sanjay Srivatsan, Mary Regier 2021. Creating sci-Space Grids for Spatial Barcoding. protocols.io https:// Copy   

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Authors: Dr. John Smith
Summary: This is an assay describing indirect sandwich ELISA for RDP Ag of SARS-CoV-2. Yadda, yadda, yadda, Yadda, yadda, yadda, Yadda, yadda, yadda, Yadda, yadda, yadda, Yadda, yadda, yadda, Yadda, yadda, yadda, Yadda, yadda, yadda, Yadda, yadda, yadda, Yadda, yadda, yadda, Yadda, yadda, yadda, Yadda, yadda, yadda, Yadda, yadda, yadda, Yadda, yadda, yadda, Yadda, yadda, yadda.

Proper citation: Dr. John Smith 2020. Test-serology-protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bewejfbe Copy   

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Authors: Benjamin Bolduc
Group: VERVE Net, Sullivan Lab, iVirus
Summary: A collection of protocols designed to guide the user in processing a viral metagenome from raw sequence data to assembly, and subsequent analysis. The user uses actual reads from Ocean Sampling Day (2014) and processes them entirely within Cyverse, a NSF-supported cyberinfrastructure.Quality trimming of reads is important!

Proper citation: Benjamin Bolduc 2016. Quality Control of Reads Using Trimmomatic (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.gvybw7w Copy   

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Authors: Michael Bokoch, Claus Niemann, Dieter Adelmann, Rishi Kothari
Group: UCSF Transplant Anesthesia Research Group (TARG)
Summary: Acute kidney injury (AKI), or worsening kidney function, is a common complication after liver transplantation (20-90% in published studies). Patients who experience AKI after liver transplantation have higher mortality, increased graft loss, longer hospital and intensive care unit stays, and more progression to chronic kidney disease compared with those who do not. In this study, half of the participants will have their body temperature cooled to slightly lower than normal (mild hypothermia) for a portion of the liver transplant operation, while the other half will have their body temperature maintained at normal. The study will evaluate if mild hypothermia protects from AKI during liver transplantation.This study is a single-blinded, randomized controlled trial of mild hypothermia during liver transplantation to provide protection from AKI. Participants will be randomized to normothermia (36.5-37.5 °C) versus mild hypothermia (34-35 °C) during a portion of the liver transplant operation. The protocol is based on preliminary data from rodent models showing that hypothermia protects the kidneys from ischemia-reperfusion injury, as well as studies in deceased organ donors showing that cooling improves post-transplant organ function. Temperature will be maintained with standard techniques plus a minimally-invasive esophageal cooling device that is approved by the U.S. Food and Drug Administration. The investigators hypothesize that mild hypothermia will reduce the incidence and severity of AKI after LTx. Standard surrogates (e.g., change in serum creatinine, need for initiation of dialysis) and biomarkers will be used to assess the severity of kidney injury.

Proper citation: Michael Bokoch, Claus Niemann, Dieter Adelmann, Rishi Kothari 2020. Mild Hypothermia to prevent Acute kidney injury in Liver Transplantation (MHALT) Trial - Statistical Analysis Plan for the Interim Analysis, v1.0 . protocols.io https://dx.doi.org/10.17504/protocols.io.bf5kjq4w Copy   

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Authors: Jiaxin Li

Proper citation: Jiaxin Li 2020. Double digested. protocols.io https://dx.doi.org/10.17504/protocols.io.bni6mche Copy   

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Authors: Xiaohua Du, Xia Liu, Mawolo James Blackar, Yingjie Zhou, Haifeng Wang, Fayang Liu, Zhiqing He
Summary: Definition of key termsSpectrophotometry is an experimental technique that is used to measure the concentration of solutes in a specific solution by calculating the amount of light absorbed by those solutes.[1] This technique is powerful because certain compounds will absorb different wavelengths of light at different intensities. By analyzing the light that passes through the solution, you can identify particular dissolved substances in solution and how concentrated those substances are. A automatic analyser (7180) is the device used to analyze solutions in a laboratory research setting.Desecription of Automatic analyserThe Automatic analyser (7180) is a medium-sized biochemistry automatic analyzer.The minimum required amount of reaction solution is smaller due to a new optical design, and running cost is lower and working efficiency higher because the operating unit is usable in the same way as a general-purpose personal computer. Further, this analyzer features a wide range of applications including routine, stat and special analyses.Benefit of Spectrophotometry methodThe usage of Automatic analyser (Hitachi Ltd 7180 Serial, Tokyo, Japan) enabled us to obtained more samples result in less time and this prevented other factors from influencing our tested results.

Proper citation: Xiaohua Du, Xia Liu, Mawolo James Blackar, Yingjie Zhou, Haifeng Wang, Fayang Liu, Zhiqing He 2019. Spectrophotometry method for the detection of Biochemical parameters. protocols.io https://dx.doi.org/10.17504/protocols.io.6wchfaw Copy   

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Authors: Binnypreet Kaur1, 2, Drahomíra Faktorová1, 2, , Priscila Peña-Diaz1 and Julius Lukeš1, 2
Group: Julius Lukes
Summary: E-mail: [email protected]

Proper citation: Binnypreet Kaur1, 2, Drahomíra Faktorová1, 2, , Priscila Peña-Diaz1 and Julius Lukeš1, 2 2018. Diplonema Genomic DNA isolation. protocols.io https://dx.doi.org/10.17504/protocols.io.hfyb3pw Copy   

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Authors: Marcos Otero-Garcia, Inma Cobos
Group: Neurodegeneration Method Development Community
Summary: - Protocol based on Krishnaswami et al., Nat Protoc. 2016, 3:499-524- Used routinely in our lab for the isolation of single nuclei from fresh frozen postmortem brains from subjects with neurodegenerative disorders and healthy controls for single-nucleus RNA-seq- Works also for isolation of nuclei from fresh frozen mouse brains - Used for isolation of all nuclei or antibody-enriched populations (i.e., NeuN+ nuclei)- We always perform and strongly recommend FACS if used for single-nucleus RNA-seq

Proper citation: Marcos Otero-Garcia, Inma Cobos 2019. Isolation of single nuclei from postmortem fresh frozen human brain and immunostaining for NeuN. protocols.io https://dx.doi.org/10.17504/protocols.io.6tuhenw Copy   

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Authors: Yuan Yao, morigen

Proper citation: Yuan Yao, morigen 2018. Flow cytometry. protocols.io https://dx.doi.org/10.17504/protocols.io.p9ndr5e Copy   

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Authors: Etienne Laliberté, Raymond Soffer
Group: Canadian Airborne Biodiversity Observatory
Summary: Here we describe the standardised protocol used by the Canadian Airborne Biodiversity Observatory (CABO) to measure leaf spectral reflectance and transmittance, using an integrating sphere fitted to a portable full-range field spectroradiometer, for the special case where an individual leaf is too small and/or too narrow to entirely cover the reflectance or transmission port of the integrating sphere. Briefly, three arrays of mature, healthy and sunlit leaves from a canopy plant are arranged on a custom sample mount, and are then used for measurements of adaxial reflectance and transmittance. Reflectance measurements are referenced to a calibrated Spectralon® disk and corrected for stray light. Our leaf spectroscopy protocol is an adaptation of that of Noda et al. (2013) to the SVC DC-R/T sphere, and also builds from protocols by the Carnegie Airborne Observatory and the SVC integrating sphere user manual.

Proper citation: Etienne Laliberté, Raymond Soffer 2018. Measuring spectral reflectance and transmittance (350-2500 nm) of small and/or narrow leaves using the Spectra Vista Corporation (SVC) DC-R/T Integrating Sphere. protocols.io https://dx.doi.org/10.17504/protocols.io.qp7dvrn Copy   

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Authors: Lukas Snoek
Group: Spinoza Centre, REC-L
Summary: This is a test

Proper citation: Lukas Snoek 2017. During Data Acquisition. protocols.io https://dx.doi.org/10.17504/protocols.io.jrbcm2n Copy   

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