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Authors: Henri Brunengraber
Group: Mouse Metabolic Phenotyping Centers
Summary: During the course of development or during a diet study the amount of food and body weights are measured 1-2 times per week.

Proper citation: Henri Brunengraber 2019. Case - Measurement of Food Consumption and Body Weight. protocols.io https://dx.doi.org/10.17504/protocols.io.yeqftdw Copy   

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Authors: Angel Justiz-Vaillant
Group: University of the West Indies, [email protected]
Summary: Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells. They play essential roles in the activation and differentiation of immune cells, as well as proliferation, maturation, migration, and adhesion. They also have pro-inflammatory and anti-inflammatory properties. The primary function of interleukins is, therefore, to modulate growth, differentiation, and activation during inflammatory and immune responses. Interleukins consist of a large group of proteins that can elicit many reactions in cells and tissues by binding to high-affinity receptors in cell surfaces. They have both paracrine and autocrine function. Interleukins are also used in animal studies to investigate aspect related to clinical medicine.T cells and stem cells make IL-3. It functions as a multilineage colony-stimulating factor. CD4+T cells (Th2) produce IL-5, and its principal targets are B cells. It causes B-cell growth factor and differentiation and IgA selection. Besides, causes eosinophil activation and increased production of these innate immune cells [1]Reference1. Justiz Vaillant AA, Qurie A. Interleukin. In:StatPearls. Treasure Island (FL): StatPearls Publishing; June 12, 2019.

Proper citation: Angel Justiz-Vaillant 2020. ELISA for quantification of IL-5 in human serum.. protocols.io https://dx.doi.org/10.17504/protocols.io.bj25kqg6 Copy   

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Authors: Natalia Wandyszewska and Vladimir Hampl
Group: Protist Research to Optimize Tools in Genetics (PROT-G)
Summary: The protocol decribes the procedure and results of our attempts to transform several species of marine protists by nucleofection.

Proper citation: Natalia Wandyszewska and Vladimir Hampl 2017. Nucleofection of Pyramimonas parkeae, Chromera velia, Bigellowiella natans, Eutreptiella gymnastica, Neovalkampfia damariscottae. protocols.io https://dx.doi.org/10.17504/protocols.io.ibucanw Copy   

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Authors: Roey Angel, Ana Lara-Rodriguez
Group: SoWa RI Anaerobic and Molecular Microbiology (public)
Summary: For the diferential isolation of Clostridium sp.

Proper citation: Roey Angel, Ana Lara-Rodriguez 2020. WILLIS -HOBBS AGAR. protocols.io https://dx.doi.org/10.17504/protocols.io.3exgjfn Copy   

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Authors: Jakub Nedbal
Summary: This protocol describes autoclaving the Erlenmeyer flasks for sterile microalgae culture. It describes the cleaning and preparation of flasks for autoclaving. In the second part, the protocol describes the method of autoclaving.

Proper citation: Jakub Nedbal 2020. Autoclaving Erlenmeyer Flasks for Sterile Algal Cultures. protocols.io https://dx.doi.org/10.17504/protocols.io.bd2di8a6 Copy   

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Authors: Zhujun Wei
Group: 2020 iGEM NEFU China
Summary: We use this protocol to knock out yhaK in E.coli BW25113

Proper citation: Zhujun Wei 2020. Gene knockout. protocols.io https://dx.doi.org/10.17504/protocols.io.bnygmftw Copy   

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Authors: Nicole A. Pelot, J. Ashley Ezzell, Gabriel B. Goldhagen, Jake E. Cariello, Kara A. Clissold, Warren M. Grill
Group: SPARC
Summary: The protocol describes immunohistochemistry with anti-claudin-1, imaging, image segmentation, and image analysis methods to quantify human vagus nerve morphology.

Proper citation: Nicole A. Pelot, J. Ashley Ezzell, Gabriel B. Goldhagen, Jake E. Cariello, Kara A. Clissold, Warren M. Grill 2020. SPARC_Duke_PelotGrill_OT2-OD025340_HumanVagusNerve_Claudin1IHC_Morphology. protocols.io https://dx.doi.org/10.17504/protocols.io.bh4dj8s6 Copy   

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Authors: Maximilian Krause, Adnan M Niazi
Group: The Nordic Nanopore-Seq Network
Summary: This protocol provides a detailed explanation of of the steps necessary for successful Direct RNA Library preparation for Oxford Nanopore Sequencing. The protocol explains the steps needed for RNA sample preparation based on TRIzol extraction and Poly(A)Purist Mag kit enrichment prior to Direct RNA library preparation protocol. The library preparation protocol is based on the Library preparation protocols for RNA-002 kits, yet offers additional advice on what we think is important for a successful library with minimal RNA degradation.The protocol is used to assess poly(A) tail length using the tailfindr package. The poly(A) tail is a homopolymeric stretch of adenosine at the 3`-end of mature RNA transcripts and its length plays an important role in nuclear export, stability, and translational regulation of mRNA. With the introduction of native RNA sequencing by Oxford Nanopore Technologies (ONT), it is now possible to sequence full-length native RNA. A single long read contains both the transcript and the associated poly(A) tail, thereby making genome-wide transcript-specific poly(A) tail length assessment in native RNA feasible. For more information on tailfindr visit the publication or the GitHub repository

Proper citation: Maximilian Krause, Adnan M Niazi 2019. ONT DirectRNA Library preparation for poly(A) estimation. protocols.io https://dx.doi.org/10.17504/protocols.io.9cjh2un Copy   

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Authors: Ruiyun Bi

Proper citation: Ruiyun Bi 2017. Real-time PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.hu2b6ye Copy   

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Authors: protocols.io team
Group: VERVE Net, protocols.io news, Protist Research to Optimize Tools in Genetics (PROT-G)
Summary: Protocols.io offers extensive flexibility in entering and presenting detailed methods. However, simple suggestions in here can help to make your protocol more useful to you and others. Importantly, easy steps outlined here can greatly increase the visibility of your protocol and ensure that scientists who need can find it.If you have any questions, please feel free to reach out to the protocols.io team by e-mailing us at  info [at] protocols.io. 

Proper citation: protocols.io team 2019. How to make your protocol more reproducible, discoverable, and user-friendly. protocols.io https://dx.doi.org/10.17504/protocols.io.g7vbzn6 Copy   

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Authors: Manuela De Las Casas
Group: AEGIS - Madrid iGEM 2019
Summary: The aim of this protocol is to obtain the purified streptavidin with cellulose binding domains on both sides from the transformed bacteria E. coli. Later on, this protein will be attached to a membrane as part of the detection system. The obtention of the proteins starts at this point with transformed bacteria (E. coli).The previous steps to obtain the transformed bacteria and further steps to use the purified protein do not correspond to this protocol.

Proper citation: Manuela De Las Casas 2019. Streptavidin-CBD purification. protocols.io https://dx.doi.org/10.17504/protocols.io.6e8hbhw Copy   

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Authors: Gordon Wellman
Group: Salt Lab KAUST
Summary: This protocol outlines the preparation of a basic sucrose loading dye 10 X stock solution for gel electrophoresis (DNA/RNA). Orange G runs at approximately 50 bp making this loading dye ideal for small molecular weight polynucleotides. Used mainly as an indicator for approx. 100 bp polynucleotides, where we would like to avoid contamination of small fragments with other loading dyes. It is also useful as an indicator if you have excessive primer-dimer amplification in your PCRs as these usually also run at approx. 50 bp.The origins of this protocol have been lost in the mists of time and this method been handed down from PhD student to PhD student.

Proper citation: Gordon Wellman 2018. 10 X Sucrose Orange G Loading Dye. protocols.io https://dx.doi.org/10.17504/protocols.io.kp7cvrn Copy   

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Authors: Yanru Zhong, Hong Gao, Xiuyan Guo, Yuchu Qin, Meifa Huang, Xiaonan Luo
Summary: In this paper, a set of Dombi power partitioned Heronian mean operators of q-rung orthopair fuzzy numbers (qROFNs) are presented and a multiple attribute group decision making (MAGDM) method based on them is proposed. Firstly, the operational rules of qROFNs based on the Dombi t-conorm and t-norm are introduced. According to these rules, a q-rung orthopair fuzzy Dombi partitioned Heronian Mean operator and its weighted form are then established. To reduce the negative effect of unreasonable attribute values on aggregation result in these operators, a q-rung orthopair fuzzy Dombi power partitioned Heronian mean operator and its weighted form are constructed via combining them with the power average operator of qROFNs. On the basis of the constructed operators, a method to solve the MAGDM problems based qROFNs is designed. Finally, a practical example, a set of experiments, and comparisons are reported to demonstrate the feasibility and effectiveness of the proposed method. The demonstration results show that the method is feasible, effective, and flexible, which has satisfying expressiveness and concurrently can consider the interrelationships between different attributes comprehensively and reduce the negative influence of biased attribute values.

Proper citation: Yanru Zhong, Hong Gao, Xiuyan Guo, Yuchu Qin, Meifa Huang, Xiaonan Luo 2019. MAGDM method based on some qROFDPPHM operators. protocols.io https://dx.doi.org/10.17504/protocols.io.5j2g4qe Copy   

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Authors: Jennifer Brum
Group: VERVE Net, Sullivan Lab
Summary: This protocol describes how to concentrate viruses in liquid samples using an Amicon or Nanosep centrifugal ultrafiltration device. We use Amicons to concentrate medium volumes of samples (10s to 100s of mls) down to a final volume of ~4 ml. We use Nanoseps to concentrate smaller volumes of sample (

Proper citation: Jennifer Brum 2016. Concentrating Viruses with an Amicon or Nanosep Centrifugal Ultrafiltration Device. protocols.io https://dx.doi.org/10.17504/protocols.io.c54y8v Copy   

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Authors: Camilo E. Vital, Jenny D. Gómez, Pedro M. Vidigal, Edvaldo Barros, Claudia S.L. Pontes, Nívea M. Vieira, Humberto J O Ramos
Group: Metabolomics Protocols & Workflows
Summary: Phytohormones play a key role in regulating development and growth, as well as acting on plant responses to biotic and abiotic stresses. The following protocol describes a target specific methodology to obtaining quantitative profiles of phytohormones from plant tissues by ultra-high-performance liquid chromatograph (UHPLC) coupled to mass spectrometry.

Proper citation: Camilo E. Vital, Jenny D. Gómez, Pedro M. Vidigal, Edvaldo Barros, Claudia S.L. Pontes, Nívea M. Vieira, Humberto J O Ramos 2019. PHYTOHORMONE PROFILING BY LIQUID CHROMATOGRAPHY COUPLED TO MASS SPECTROMETRY (LC/MS). protocols.io https://dx.doi.org/10.17504/protocols.io.zgff3tn Copy   

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Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: Protocol allows for rapid generation of 3’ transcriptomic-NGS-ready- single-cell-libraries from pools of cells.Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U19MH114830. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Proper citation: Allen Institute for Brain Science 2021. 10xV3 Genomics Sample Processing Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bq7cmziw Copy   

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Authors: Zhujun Wei
Group: 2020 iGEM NEFU China

Proper citation: Zhujun Wei 2020. DNT Induction. protocols.io https://dx.doi.org/10.17504/protocols.io.bnyfmftn Copy   

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Authors: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
Summary: Separation and purification of PBMC from FRESH BLOOD: list of published work using this protocolKustrimovic, N., Comi, C., Magistrelli, L., Rasini, E., Legnaro, M., Bombelli, R., Aleksic, I., Blandini, F., Minafra, B., Riboldazzi, G., Sturchio, A., Mauri, M., Bono, G., Marino, F., & Cosentino, M. (2018). Parkinson's disease patients have a complex phenotypic and functional Th1 bias: cross-sectional studies of CD4+ Th1/Th2/T17 and Treg in drug-naïve and drug-treated patients. Journal of neuroinflammation, 15(1), 205. https://doi.org/10.1186/s12974-018-1248-8Kustrimovic, N., Rasini, E., Legnaro, M., Bombelli, R., Aleksic, I., Blandini, F., Comi, C., Mauri, M., Minafra, B., Riboldazzi, G., Sanchez-Guajardo, V., Marino, F., & Cosentino, M. (2016). Dopaminergic Receptors on CD4+ T Naive and Memory Lymphocytes Correlate with Motor Impairment in Patients with Parkinson's Disease. Scientific reports, 6, 33738. https://doi.org/10.1038/srep33738Cosentino M., Ferrari M., Kustrimovic N., Rasini E., Marino F. (2015). Influence of dopamine receptor gene polymorphisms on circulating T lymphocytes: A pilot study in healthy subjects. Human immunology, 76, 10, 747-752. https://doi.org/10.1016/j.humimm.2015.09.032

Proper citation: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino 2020. Separation and purification of human PBMC from FRESH BLOOD. protocols.io https://dx.doi.org/10.17504/protocols.io.bfxmjpk6 Copy   

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Authors: Nikita Joshi, Alexander Misharin
Group: Human Cell Atlas Method Development Community
Summary: We aimed to develop a protocol for isolation of the single nuclei from the archival frozen human lung tissue suitable for single cell RNA-seq using standard 10x Genomics chemistry. The protocol utilizes standard nuclei isolation buffer (Nuclei EZ buffer) supplemented with RNase inhibitor and a protease inhibitor. For the homogenization step, we elected to use C Tube and GentleMACS tissue dissociation as a way to standardize the homogenization procedure. To maintain nuclei integrity we skipped washing steps and instead use large volumes of washing buffer and proceed to FACSorting immediately after lysis for nuclei purification.This protocol produces a good yield of nuclei and diverse libraries, with multiple cell types being detected. While the number of detected genes and UMI per nuclei is lower than for single cell RNAseq, it is sufficient for identification of the specific cell types, including rare populations. Moreover, snRNAseq allowed resolution of the cell types that are intimately integrated into the lung matrix and otherwise hard to resolve: fibroblasts and type 1 alveolar epithelial cells.We thank Oni Basu (UChicago), Luciano Martelotto (Monash University), Nicole Abreu (10x Genomics) and Sharmila Chatterjee (10x Genomics) for their advice.

Proper citation: Nikita Joshi, Alexander Misharin 2019. Single-nucleus isolation from frozen human lung tissue for single-nucleus RNA-seq. protocols.io https://dx.doi.org/10.17504/protocols.io.zu8f6zw Copy   

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Authors: M Mehedi Hasan Rocky, Mohammad Amzad Hossain Bhuyan, Shamim Akhtar
Group: Coronavirus Method Development Community
Summary: This protocol describes a simple way to make a mask at home using the cotton or linen woven fabric available in wearable cloth or household napkin. Fabric is soaked in a solution containing the table salt (NaCl) and starch. Starch is used to increase the droplet absorption efficiency of fabric whereas salt is added for improving the virus deactivation system. These simple preparation and wearing techniques will help anyone to prepare a mask for safety during COVID-19 pandemic, especially for those people having masks of little avail or no avail. .justify:after { content: ""; display:inline-block; width: 100%; }

Proper citation: M Mehedi Hasan Rocky, Mohammad Amzad Hossain Bhuyan, Shamim Akhtar 2020. Simple Way to Make Homemade Cloth Masks: Fabrics Treated with NaCl and Starch Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.be9djh26 Copy   

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