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| Name | Authors | DOI | Group |
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Associated Publications |
RRIDs used | ||||||
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Treg Polarization of Mouse CD4+ Cells Resource Report Resource Website |
Sam Li | DOI:10.17504/protocols.io.792hr8e | BioLegend | BioLegend | 1 | 2019 | Sam Li 2019. Treg Polarization of Mouse CD4+ Cells. protocols.io https://dx.doi.org/10.17504/protocols.io.792hr8e | 2021-04-15 09:14:33 | ||||
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Grinding Tissue with the Qiagen Tissuelyzer (Soybean, Cowpea, Tobacco) Resource Report Resource Website |
Steven Burgess, Lynn Doran | Ag SynBio Lab UIUC | University of Illinois at Urbana-Champaign, Realizing Increased Photosynthetic Efficiency (RIPE) | 1 | 2021 | Steven Burgess, Lynn Doran 2021. Grinding Tissue with the Qiagen Tissuelyzer (Soybean, Cowpea, Tobacco). protocols.io https:// | 2021-04-15 09:14:33 | |||||
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Protein gel sample preparation Resource Report Resource Website |
Cleo B. | DOI:10.17504/protocols.io.7p9hmr6 | iGEM Wageningen 2019 | Sample preparation for tricine SDS-page gels and polyacrylamide SDS-page gels. | Wageningen University | 2 | 2019 | Cleo B. 2019. Protein gel sample preparation . protocols.io https://dx.doi.org/10.17504/protocols.io.7p9hmr6 | 2021-04-15 09:14:34 | |||
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ChroSpin - ProteinG Resource Report Resource Website |
David Frommholz, Alexandra Ehl, Nadine Stefanczyk | DOI:10.17504/protocols.io.pyfdptn | 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). | DALEX Biotech, DALEX Biotech, DALEX Biotech | https://dalex-biotech.com/ | 1 | 2018 | David Frommholz, Alexandra Ehl, Nadine Stefanczyk 2018. ChroSpin - ProteinG. protocols.io https://dx.doi.org/10.17504/protocols.io.pyfdptn | 2021-04-15 09:14:45 | |||
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mcSCRB-seq protocol Resource Report Resource Website |
Johannes Bagnoli, Christoph Ziegenhain, Aleksandar Janjic, Lucas Esteban Wange, Beate Vieth, Swati Parekh, Johanna Geuder, Ines Hellmann, Wolfgang Enard | DOI:10.17504/protocols.io.p9kdr4w | Human Cell Atlas Method Development Community | 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. | Johannes W. Bagnoli, et al (2018) Sensitive and powerful single-cell RNA sequencing using mcSCRB-seq. Nature Communications 9:2937. doi: 10.1038/s41467-018-05347-6 | Ludwig-Maximilians-Universität München, Ludwig-Maximilians-Universität München, Ludwig-Maximilians-Universität München, Ludwig-Maximilians-Universität München, Ludwig-Maximilians-Universität München, Ludwig-Maximilians-Universität München, Ludwig-Maximilians-Universität München, Ludwig-Maximilians-Universität München, Ludwig-Maximilians-Universität München | https://www.nature.com/articles/s41467-018-05347-6 | 2 | 2018 | 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 | 2021-04-15 09:14:34 | |
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Chondrocyte isolation from human cartilage Resource Report Resource Website |
Sarah Snelling | DOI:10.17504/protocols.io.8uphwvn | 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. | University of Oxford | 1 | 2019 | Sarah Snelling 2019. Chondrocyte isolation from human cartilage. protocols.io https://dx.doi.org/10.17504/protocols.io.8uphwvn | 2021-04-15 09:14:33 | ||||
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SPS-PAGE protein electrophoresis Resource Report Resource Website |
Konstantinos Ragios | DOI:10.17504/protocols.io.775hrq6 | iGEM EPFL | 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. | EPFL - EPF Lausanne | 1 | 2019 | Konstantinos Ragios 2019. SPS-PAGE protein electrophoresis. protocols.io https://dx.doi.org/10.17504/protocols.io.775hrq6 | 2021-04-15 09:14:46 | |||
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Quick Protocol for Monarch® Plasmid Miniprep Kit (NEB #T1010) Resource Report Resource Website |
New England Biolabs | DOI:10.17504/protocols.io.ejybcpw | New England Biolabs (NEB) | This is the quick version of the Monarch® Plasmid DNA Miniprep Kit Protocol (NEB #T1010). For the full protocol, please click here. | New England Biolabs | https://www.neb.com/protocols/2015/12/08/quick-protocol-for-monarch-plasmid-miniprep-kit-t1010 | 1 | 2016 | New England Biolabs 2016. Quick Protocol for Monarch® Plasmid Miniprep Kit (NEB #T1010). protocols.io https://dx.doi.org/10.17504/protocols.io.ejybcpw | 2021-04-15 09:14:45 | ||
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Counting Microalgae Culture Density Resource Report Resource Website |
Jakub Nedbal | DOI:10.17504/protocols.io.bd7wi9pe | 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.. | King's College London | https://app.labstep.com/sharelink/1bfe1dae-317f-460d-a934-6d23c1696ac2 | 1 | 2020 | Jakub Nedbal 2020. Counting Microalgae Culture Density. protocols.io https://dx.doi.org/10.17504/protocols.io.bd7wi9pe | 2021-04-15 09:14:34 | |||
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Phenol Chloroform DNA extraction from polycarbonate filters Resource Report Resource Website |
Ashley Humphrey | DOI:10.17504/protocols.io.ibbcain | Protist Research to Optimize Tools in Genetics (PROT-G), The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs), CyanoHABs | University of Tennessee, Knoxville | 1 | 2017 | Ashley Humphrey 2017. Phenol Chloroform DNA extraction from polycarbonate filters. protocols.io https://dx.doi.org/10.17504/protocols.io.ibbcain | 2021-04-15 09:14:46 | ||||
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Immunofluorescence Microscopy Protocol with Methanol Fixed Cells(about S100A6 in SW480 Cells) Resource Report Resource Website |
Shanshan Feng, Huihong Zhai | DOI:10.17504/protocols.io.mqcc5sw | Feng S, Zhou Q, Yang B, Li Q, Liu A, Zhao Y, Qiu C, Ge J, Zhai H (2018) The effect of S100A6 on nuclear translocation of CacyBP/SIP in colon cancer cells. PLoS ONE 13(3): e0192208. doi: 10.1371/journal.pone.0192208 | Ningxia Medical College, Capital Beijing Friendship Hospital Affiliated to Capital Medical University | https://doi.org/10.1371/journal.pone.0192208 | 1 | 2018 | 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 | 2021-04-15 09:14:34 | |||
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Cell culture Resource Report Resource Website |
Yingchao Xue, Xiping Zhan, Shisheng Sun, Senthilkumar S. Karuppagounder, Shuli Xia, Valina L Dawson, Ted M Dawson, John Laterra, Jianmin Zhang, Mingyao Ying | Neurodegeneration Method Development Community | Department of Immunology, Research Center on Pediatric Development and Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology; Hugo W. Moser Research Institute at Kennedy Krieger, Department of Physiology and Biophysics, Howard University, College of Life Sciences, Northwest University, Department of Neurology, Johns Hopkins University School of Medicine; Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine; Adrienne Helis Malvin Medical Research Foundation, Hugo W. Moser Research Institute at Kennedy Krieger; Department of Neurology, Johns Hopkins University School of Medicine, Department of Neurology, Johns Hopkins University School of Medicine; Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine; Adrienne Helis Malvin Medical Research Foundation; Department of Neuroscience, Johns Hopkins University School of Medicine; Department of Physiology, Johns Hopkins University School of Medicine, Department of Neurology, Johns Hopkins University School of Medicine; Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine; Adrienne Helis Malvin Medical Research Foundation; Department of Neuroscience, Johns Hopkins University School of Medicine; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Hugo W. Moser Research Institute at Kennedy Krieger; Department of Neurology, Johns Hopkins University School of Medicine; Department of Neuroscience, Johns Hopkins University School of Medicine; Department of Oncology, Johns Hopkins University School of Medicine, Department of Immunology, Research Center on Pediatric Development and Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, Hugo W. Moser Research Institute at Kennedy Krieger; Department of Neurology, Johns Hopkins University School of Medicine | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6344911/ | 1 | 2020 | 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:// | 2021-04-15 09:14:33 | ||||
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RNA Isolation from Plant Tissue Protocol 3: CTAB-PVP Method Resource Report Resource Website |
Beijing Genomics Institute | DOI:10.17504/protocols.io.4vygw7w | GigaScience Press, BGI | 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) | Beijing Genomics Institute | 1 | 2019 | 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 | 2021-04-15 09:14:34 | |||
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Two-Bottle Choice Protocol Resource Report Resource Website |
Marcella Hughes, Olivier George | George Lab | University of California, San Diego, University of California, San Diego | 1 | 2020 | Marcella Hughes, Olivier George 2020. Two-Bottle Choice Protocol. protocols.io https:// | 2021-04-15 09:14:46 | |||||
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Extraction and purification of viruses from stream biofilms Resource Report Resource Website |
Meriem Bekliz, Hannes Peter | DOI:10.17504/protocols.io.32qgqdw | 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. | Bekliz M, Brandani J, Bourquin M, Battin TJ, Peter H, Benchmarking protocols for the metagenomic analysis of stream biofilm viromes. PeerJ doi: 10.7717/peerj.8187 | Stream Biofilm and Ecosystem Research Laboratory, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland, EPFL - EPF Lausanne | https://doi.org/10.7717/peerj.8187 | 3 | 2019 | Meriem Bekliz, Hannes Peter 2019. Extraction and purification of viruses from stream biofilms. protocols.io https://dx.doi.org/10.17504/protocols.io.32qgqdw | 2021-04-15 09:14:34 | ||
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MojoSort™ Pan DC Isolation Kit Column Protocol Resource Report Resource Website |
Ken Lau | BioLegend | BioLegend | https://www.biolegend.com/en-us/protocols/mojosort-human-pan-dc-isolation-kit-column-protocol | 2 | 2021 | Ken Lau 2021. MojoSort™ Pan DC Isolation Kit Column Protocol. protocols.io https:// | 2021-04-15 09:14:43 | ||||
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NEBNext® ARTIC SARS-CoV-2 Companion Kit (Oxford Nanopore Technologies®) E7760 Resource Report Resource Website |
New England Biolabs | DOI:10.17504/protocols.io.bsbrnam6 | New England Biolabs (NEB), Coronavirus Method Development Community | This protocol details methods for the NEBNext® ARTIC SARS-CoV-2 Companion Kit (Oxford Nanopore Technologies®), NEB #E7660S/L 24/96 reactions. | New England Biolabs | https://www.neb.com/-/media/nebus/files/manuals/manuale7660a.pdf?rev=4a88553b27064ccdbcdce76d05a2627c&hash=09A89395846012AA8A389C1DCFCE92F8 | 1 | 2021 | 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 | 2021-04-15 09:14:32 | ||
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VBRC Base By Base: Export an image of the alignment Resource Report Resource Website |
Nick Tang | DOI:10.17504/protocols.io.ecnbave | VERVE Net, Upton-Lab | 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 | University of Victoria: Department of Biochemistry and Microbiology | http://athena.bioc.uvic.ca/ | 1 | 2016 | Nick Tang 2016. VBRC Base By Base: Export an image of the alignment. protocols.io https://dx.doi.org/10.17504/protocols.io.ecnbave | 2021-04-15 09:14:43 | ||
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Preparation of cell-free RNAPT7 reactions Resource Report Resource Website |
Anibal Arce Medina, | DOI:10.17504/protocols.io.iekcbcw | Laboratorio de Tecnologias Libres | 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) | , | 1 | 2017 | Anibal Arce Medina, 2017. Preparation of cell-free RNAPT7 reactions. protocols.io https://dx.doi.org/10.17504/protocols.io.iekcbcw | 2021-04-15 09:14:34 | |||
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Lab 4 Notebook Resource Report Resource Website |
UCSC BME 22L | UCSC | 1 | 2020 | 2020. Lab 4 Notebook. protocols.io https:// | 2021-04-15 09:14:33 |
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