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Authors: Sam Li
Group: BioLegend

Proper citation: Sam Li 2019. Treg Polarization of Mouse CD4+ Cells. protocols.io https://dx.doi.org/10.17504/protocols.io.792hr8e Copy   

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Authors: Steven Burgess, Lynn Doran
Group: Ag SynBio Lab UIUC

Proper citation: Steven Burgess, Lynn Doran 2021. Grinding Tissue with the Qiagen Tissuelyzer (Soybean, Cowpea, Tobacco). protocols.io https:// Copy   

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Authors: Cleo B.
Group: iGEM Wageningen 2019
Summary: Sample preparation for tricine SDS-page gels and polyacrylamide SDS-page gels.

Proper citation: Cleo B. 2019. Protein gel sample preparation . protocols.io https://dx.doi.org/10.17504/protocols.io.7p9hmr6 Copy   

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Authors: David Frommholz, Alexandra Ehl, Nadine Stefanczyk
Summary: Purification Guide for the Isolation of Antibodies with ChroSpin Columns by DALEX Biotech.Easy and quick small scale antibody purification from various sources and species.Each ChroSpin column has a binding capacity of > 2 mg (tested with human polyclonal Ig, binding varies between species and clones).The proprietary resin does not shrink or swell in aqueous buffers.High pressure stability.pH stability short term 2 - 8, long term 3 - 8.Excellent thermal stability up to 15 minutes at 80 °C in aqueous buffers at neutral pH.Can be dried for long term storage (80 °C for > 2 h).

Proper citation: David Frommholz, Alexandra Ehl, Nadine Stefanczyk 2018. ChroSpin - ProteinG. protocols.io https://dx.doi.org/10.17504/protocols.io.pyfdptn Copy   

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Authors: Johannes Bagnoli, Christoph Ziegenhain, Aleksandar Janjic, Lucas Esteban Wange, Beate Vieth, Swati Parekh, Johanna Geuder, Ines Hellmann, Wolfgang Enard
Group: Human Cell Atlas Method Development Community
Summary: Single-cell RNA sequencing (scRNA-seq) has emerged as a central genome-wide method to characterize cellular identities and processes. Consequently, improving its sensitivity, flexibility and cost-efficiency can advance many research questions. Among the flexible plate-based methods, “Single-Cell RNA-Barcoding and Sequencing” (SCRB-seq) is one of the most sensitive and efficient ones. Here, we systematically evaluated experimental conditions of this protocol and find that adding polyethylene glycol considerably increases sensitivity by enhancing cDNA synthesis. Furthermore, using Terra polymerase increases efficiency due to a more even cDNA amplification that requires less sequencing of libraries. We combined these and other improvements to a new scRNA-seq library protocol we call “molecular crowding SCRB-seq” (mcSCRB-seq), which we show to be  the most sensitive and one of the most efficient and flexible scRNA-seq methods to date.

Proper citation: Johannes Bagnoli, Christoph Ziegenhain, Aleksandar Janjic, Lucas Esteban Wange, Beate Vieth, Swati Parekh, Johanna Geuder, Ines Hellmann, Wolfgang Enard 2018. mcSCRB-seq protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.p9kdr4w Copy   

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Authors: Sarah Snelling
Summary: A standard methodology used within our group for extracting chondrocytes from human cartilage obtained as waste tissue at the time of joint replacement. Chondrocytes obtained through this method are used at P1 (at most P2) for in vitro assays. This is adapted from other published methods based on the requirements of our group for a consistent and straightforward method for obtaining viable cells.

Proper citation: Sarah Snelling 2019. Chondrocyte isolation from human cartilage. protocols.io https://dx.doi.org/10.17504/protocols.io.8uphwvn Copy   

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Authors: Konstantinos Ragios
Group: iGEM EPFL
Summary: SDS-PAGE (sodium dodecyl sulfate–polyacrylamide gel electrophoresis) is a variant of PAGE that allows to separate protein molecules according to their molecular masses under electric field.SDS-PAGE is a discontinuous electrophoretic system developed by Ulrich K. Laemmli which is commonly used as a method to separate proteins with molecular masses between 5 and 250 KDa.In this protocol we will use an already precasted gel.

Proper citation: Konstantinos Ragios 2019. SPS-PAGE protein electrophoresis. protocols.io https://dx.doi.org/10.17504/protocols.io.775hrq6 Copy   

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Authors: New England Biolabs
Group: New England Biolabs (NEB)
Summary: This is the quick version of the Monarch® Plasmid DNA Miniprep Kit Protocol (NEB #T1010). For the full protocol, please click here.

Proper citation: New England Biolabs 2016. Quick Protocol for Monarch® Plasmid Miniprep Kit (NEB #T1010). protocols.io https://dx.doi.org/10.17504/protocols.io.ejybcpw Copy   

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Authors: Jakub Nedbal
Summary: Counting culture cell density offers a reliable way of consistend seeding density for freshly inoculated cultures and allows tracking the growth of the cultures. Cell densiry counting, as described in this protocol, is performed manually under the microscope in a Neubauer hemocytometer..

Proper citation: Jakub Nedbal 2020. Counting Microalgae Culture Density. protocols.io https://dx.doi.org/10.17504/protocols.io.bd7wi9pe Copy   

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Authors: Ashley Humphrey
Group: Protist Research to Optimize Tools in Genetics (PROT-G), The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs), CyanoHABs

Proper citation: Ashley Humphrey 2017. Phenol Chloroform DNA extraction from polycarbonate filters. protocols.io https://dx.doi.org/10.17504/protocols.io.ibbcain Copy   

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Authors: Shanshan Feng, Huihong Zhai

Proper citation: Shanshan Feng, Huihong Zhai 2018. Immunofluorescence Microscopy Protocol with Methanol Fixed Cells(about S100A6 in SW480 Cells). protocols.io https://dx.doi.org/10.17504/protocols.io.mqcc5sw Copy   

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Authors: Yingchao Xue, Xiping Zhan, Shisheng Sun, Senthilkumar S. Karuppagounder, Shuli Xia, Valina L Dawson, Ted M Dawson, John Laterra, Jianmin Zhang, Mingyao Ying
Group: Neurodegeneration Method Development Community

Proper citation: Yingchao Xue, Xiping Zhan, Shisheng Sun, Senthilkumar S. Karuppagounder, Shuli Xia, Valina L Dawson, Ted M Dawson, John Laterra, Jianmin Zhang, Mingyao Ying 2020. Cell culture . protocols.io https:// Copy   

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Authors: Beijing Genomics Institute
Group: GigaScience Press, BGI
Summary: Implemented by: Beijing Genomics InstituteThis protocol is part of a collection of eighteen protocols used to isolate total RNA from plant tissue. (RNA Isolation from Plant Tissue Collection: https://www.protocols.io/view/rna-isolation-from-plant-tissue-439gyr6)

Proper citation: Beijing Genomics Institute 2019. RNA Isolation from Plant Tissue Protocol 3: CTAB-PVP Method. protocols.io https://dx.doi.org/10.17504/protocols.io.4vygw7w Copy   

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Authors: Marcella Hughes, Olivier George
Group: George Lab

Proper citation: Marcella Hughes, Olivier George 2020. Two-Bottle Choice Protocol. protocols.io https:// Copy   

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Authors: Meriem Bekliz, Hannes Peter
Summary: This series of sequential protocols can be used to extract and purify viruses from stream biofilm samples for metagenomic analysis. We compared each critical step of the protocol to alternatives and evaluated their performance using epifluorescence counting of viral-like particles and DNA yields. The pipeline consists of concentration of sample using tangential flow filtration, extraction using tetrasodium pyrophosphate and sonication and purfication using DNase I treatment, filtration, and ultracentrifugation in a sucrose density gradient. Where appropriate, we provide links to similar protocols.

Proper citation: Meriem Bekliz, Hannes Peter 2019. Extraction and purification of viruses from stream biofilms. protocols.io https://dx.doi.org/10.17504/protocols.io.32qgqdw Copy   

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Authors: Ken Lau
Group: BioLegend

Proper citation: Ken Lau 2021. MojoSort™ Pan DC Isolation Kit Column Protocol. protocols.io https:// Copy   

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Authors: New England Biolabs
Group: New England Biolabs (NEB), Coronavirus Method Development Community
Summary: This protocol details methods for the NEBNext® ARTIC SARS-CoV-2 Companion Kit (Oxford Nanopore Technologies®), NEB #E7660S/L 24/96 reactions.

Proper citation: New England Biolabs 2021. NEBNext® ARTIC SARS-CoV-2 Companion Kit (Oxford Nanopore Technologies®) E7760. protocols.io https://dx.doi.org/10.17504/protocols.io.bsbrnam6 Copy   

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Authors: Nick Tang
Group: VERVE Net, Upton-Lab
Summary: Viral Bioinformatic Resource CentreProvide databases of viral genomic information. Please check the Organisms menu to see which viruses we support: we’re now focusing on large DNA viruses The VOCs (Virus Orthologous Clusters) database is at the heart of our system. The database links directly to integrated tools for comparative analyses. VOCs sorts genes into ortholog clusters (e.g. RNA polymerase) to simplify data retrieval. Provide easy access to the genes, gene families, and genomes of the different virus families. via a unique series of powerful Java tools that support multiple computer platforms (see VBRC Tools menu). design and build software to tackle specific bioinformatics/virology problems, often in collaboration with virologists. Rally the research community to provide expert curation of these viral genomes by: Adding value to GenBank sequences through enhancing and updating genome annotations Linking to research reviews/papers for the research community. Collaborate with researchers to help on specific bioinformatics problems, e.g. Custom searches of the databases Building new features into our tools Help with genome annotation

Proper citation: Nick Tang 2016. VBRC Base By Base: Export an image of the alignment. protocols.io https://dx.doi.org/10.17504/protocols.io.ecnbave Copy   

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Authors: Anibal Arce Medina,
Group: Laboratorio de Tecnologias Libres
Summary: This collection contains the protocols and recipes for the preparation of cell-free RNAPT7 transcription/translation coupled reactions.The crude extracts are obtained from IPTG-treated E.coli BL21 DE3 STAR cells. IPTG triggers RNAPT7 expression and accumulation in cells before collection. Reactions take place when the cell extract is mixed with a maltodextrin-based energy solution along with amino acids solution and other salts (Magnesium and Potassium). This system allows transcription/translation coupled reactions from plasmid DNA that contains T7 promoter transcriptional units. In our hands, it has been possible to express different fluorescent reporters, including deGFP which is highly efficient. Products of the reaction can be measured during the whole reaction time in a plate reader with appropriate optic filters, open hardware cameras, and microscopes. When set up correctlly, deGFP fluorescence intensity is detected as fast as ∼30 minutes after the reaction starts and it shows a rapid increase during the first ∼2.5-3.0 hours. The system presented here contains the features highlighted bellow, and is an adaptation of protocols and findings from the following listed papers: 1.- This system uses maltodextrin and Polyphosphate-based energy solution: Kim, H.-C., Kim, T.-W., Kim, D.-M., . Prolonged production of proteins in a cellfree protein synthesis system using polymeric carbohydrates (2011) Caschera, F.; Noireaux, V., A cost-effective polyphosphate-based metabolism fuels an all E. coli cell-free expression system. Metabolic engineering (2015) 2.- The S12 crude extract is prepared from E.coli cells ( expressing Pol T7 ) using bead beater. Sun, Z. Z.; Hayes, C. A.; Shin, J.; Caschera, F.; Murray, R. M.; Noireaux, V., Protocols for implementing an Escherichia coli based TX-TL cell-free expression system for synthetic biology. Journal of visualized experiments (2013) Kim, TW., Kim, HC., Oh, IS. et al. A highly efficient and economical cell-free protein synthesis system using the S12 extract of Escherichia coli. Biotechnol Bioproc E (2008) 3.- The amino acid stock solution contains each amino acid at ∼12 nM in a stable solution: Caschera, V. Noireaux Preparation of amino acid mixtures for cell-free expression systems. Benchmarks (2015)

Proper citation: Anibal Arce Medina, 2017. Preparation of cell-free RNAPT7 reactions. protocols.io https://dx.doi.org/10.17504/protocols.io.iekcbcw Copy   

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Authors:
Group: UCSC BME 22L

Proper citation: 2020. Lab 4 Notebook. protocols.io https:// Copy   

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