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Authors: Norio Yamamoto, Takahisa Ogawa, Masahiro Banno, Jun Watanabe, Tomoyuki Noda, Haggai Schermann, Toshifumi Ozaki
Proper citation: Norio Yamamoto, Takahisa Ogawa, Masahiro Banno, Jun Watanabe, Tomoyuki Noda, Haggai Schermann, Toshifumi Ozaki 2020. Protocol : Cement augmentation of internal fixation for trochanteric fracture: systematic review and meta-analysis. protocols.io dx.doi.org/10.17504/protocols.io.biggkbtw Copy
Authors: bionano genomics
Proper citation: bionano genomics 2019. HMW DNA extraction from Caenorhabditis pellets for long read sequencing. protocols.io dx.doi.org/10.17504/protocols.io.642hgye Copy
Authors: Celeste Karch, Rita Martinez, Jacob Marsh
Group: Neurodegeneration Method Development Community
Proper citation: Celeste Karch, Rita Martinez, Jacob Marsh 2019. iPSC Restriction Digest: For Screening Edited Clones. protocols.io dx.doi.org/10.17504/protocols.io.x8sfrwe Copy
Authors: G-Biosciences
Group: G-Biosciences
Summary: The Non-Interfering™ Protein Assay is a colorimetric assay for determining protein concentrations in protein loading buffer (Laemmli buffer), high β-mercaptoethanol concentrations, and in lipid and vesicle preparations.
Proper citation: G-Biosciences 2016. A Non-Interfering™ (NI) Protein Assay. protocols.io dx.doi.org/10.17504/protocols.io.e9sbh6e Copy
Authors: New England Biolabs
Group: New England Biolabs (NEB)
Summary: The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina contains the enzymes and buffers required to convert a broad range of input amounts of RNA into high quality directional (strand-specific) libraries for next-generation sequencing on the Illumina platform. The fast, user-friendly workflow has minimal hands-on time and is compatible with poly(A) mRNA enrichment and rRNA depletion methods.
Proper citation: New England Biolabs 2018. Protocol for use with rRNA Depleted FFPE RNA and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760, E7765). protocols.io dx.doi.org/10.17504/protocols.io.ubaesie Copy
Authors: Steven Burgess
Group: OpenPlant Project, Plantae
Proper citation: Steven Burgess 2016. Phosphate solution. protocols.io dx.doi.org/10.17504/protocols.io.fctbiwn Copy
Authors: Carmen Sancho, Regina Hoo, Roser Vento-Tormo
Group: Vento-Tormo
Summary: This protocol is for enrichment of fetal gonadal cells
Proper citation: Carmen Sancho, Regina Hoo, Roser Vento-Tormo 2021. Human embryonic gonad dissociation with Collagenase IV. protocols.io dx.doi.org/10.17504/protocols.io.btjznkp6 Copy
Authors: Sam Li
Group: BioLegend
Proper citation: Sam Li 2019. LEGEND MAX™ Human α-Synuclein ELISA Kit Protocol. protocols.io dx.doi.org/10.17504/protocols.io.98th9wn Copy
Authors: Joost Mansour, Fabrice Not
Group: Ecology of Marine Plankton (ECOMAP) team - Roscoff, Symbiosis Model Systems
Summary: Many marine protists are not culturable and therefore challenging to study, nonetheless, they are essential in all marine ecosystems. The development of single-cell techniques is allowing for more marine protists to be studied. Thereby Cultivation-independent studies are essential for the study of organisms sensitive to the sampling procedure, such as Radiolaria.This method describes the means to acquire clean isolated single-cells from plankton nets for physiological and/or transcriptomic analysis. The isolation of cells in this protocol is followed by preparing the cells for RNA extraction (protocol: Single-cell total RNA extraction from marine protists (e.g. Acantharia, Strombidium cf basimorphum, and Prymnesium parvum)).
Proper citation: Joost Mansour, Fabrice Not 2021. Isolation of clean single-cell samples for physiological or molecular experiments (Radiolaria, Acantharia). protocols.io dx.doi.org/10.17504/protocols.io.bqvrmw56 Copy
Authors: John Tyson
Summary: Old-School Phenol/Chloroform Genomic HMW DNA PreparationIn order to mitigate damage/shearing of genomic DNA we have avoided kits etc. that employ beads or a matrix that your DNA must associate with or sieve through (blend :o)). We have not gone the whole hog at this point and used nuclei preps, dialysis or plug extractions etc. as we have found that material produced from a simple and rapid phenol/chloroform prep is more than adequate and high yielding. We have done some limited salting out experiments as a substitute for the phenol/chloroform approach but have some remaining questions around size and stability in the fridge for extended periods that need resolving. We will be revisiting this.The jumping off point for us was using methods detailed in “Molecular Cloning: A laboratory Manual” by Sambrooke and Russell. If you are at a large institution there will probably be copies around on people’s shelves or in the library collecting dust. It’s time to dust those off, they have been patiently waiting for their day in the sun again :o)). Chapter 6 is a good place to start. This approach produces DNA that is more than large enough for any nanopore sequencing currently.
Proper citation: John Tyson 2020. Phenol/Chloroform Genomic DNA extraction from Tissue Culture cells. protocols.io dx.doi.org/10.17504/protocols.io.7ejhjcn Copy
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. IL-31 is produced mainly by Th2 cells and dendritic cells. It is a proinflammatory cytokine and a chemotactic factor that direct polymorphonuclear cells, monocytes, and T cells to inflammatory lesions. IL-31 induces chemokines production and synthesis of IL-6, IL-16, and IL-32. [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-31 in human serum.. protocols.io dx.doi.org/10.17504/protocols.io.bj34kqqw Copy
Authors: Laura Sánchez
Group: AEGIS - Madrid iGEM 2019
Summary: Molecular cloning system
Proper citation: Laura Sánchez 2019. MoClo reaction. protocols.io dx.doi.org/10.17504/protocols.io.8j8hurw Copy
Authors: Alessio Papini and Ugo Santosuosso, University of Florence, Italy, [email protected]
Summary: Use of geographic profiling for finding first introduction point of a biological invasion
Proper citation: Alessio Papini and Ugo Santosuosso, University of Florence, Italy, [email protected] 2017. Geographic profiling of invading species. protocols.io dx.doi.org/10.17504/protocols.io.kytcxwn Copy
Authors: Ed Leiter
Group: Diabetic Complications Consortium
Summary: This protocol describes a number of the measurements that are made on the mouse anatomy.Edited by: DiaComp MembershipDiabetic Complications:
Proper citation: Ed Leiter 2019. Morphometry: Mouse. protocols.io dx.doi.org/10.17504/protocols.io.7rhhm36 Copy
Authors: Alexandre Paix, Yuemeng Wang, Harold E. Smith, Chih-Yung S. Lee, Deepika Calidas, Tu Lu, Jarrett Smith, Helen Schmidt, Michael W. Krause, and Geraldine Seydoux
Group: Genetics
Summary: This protocols is from:Alexandre Paix, et al. (2014) Scalable and Versatile Genome Editing Using Linear DNAs with Microhomology to Cas9 Sites in Caenorhabditis elegans. Genetics 198:1347-1356;doi:10.1534/genetics.114.170423Please see the full manuscript or additional details
Proper citation: Alexandre Paix, Yuemeng Wang, Harold E. Smith, Chih-Yung S. Lee, Deepika Calidas, Tu Lu, Jarrett Smith, Helen Schmidt, Michael W. Krause, and Geraldine Seydoux 2015. Seamless editing of the C. elegans genome using CRISPR/Cas9. protocols.io dx.doi.org/10.17504/protocols.io.dw67hd Copy
Authors: Sam Li
Group: BioLegend
Summary: BioLegend MojoSort™ nanobeads work in commonly used separation columns, based on our internal research as well as validation by external testing by academic labs. This simple protocol consists of following the MojoSort™ protocol to label the cells with pre-diluted MojoSort™ reagents and using the columns as indicated by the manufacturer.Note: Due to the properties of our beads, it may be possible to use far fewer beads and less antibody cocktail that with other commercial suppliers. We recommend a titration to find the best dilution factor. However, as a general rule, dilutions ranging from 1:2 to 1:10 for the antibody cocktail can be used. Dilutions ranging from 1:5 to 1:20 for the Streptavidin Nanobeads can be used. Please contact BioLegend Technical Service ([email protected]) if further assistance is needed.
Proper citation: Sam Li 2019. MojoSort™ Mouse NK Cell Isolation Kit Column Protocol. protocols.io dx.doi.org/10.17504/protocols.io.7bhhij6 Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol outlines strategies to solve common problems that occur when setting up the TissueCyte 1000 system for normal operation.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 2020. TissueCyte Troubleshooting Guide. protocols.io dx.doi.org/10.17504/protocols.io.bdpsi5ne Copy
Authors: Amritpal Singh Brar, Mridula Gupta, Gurmeet kaur, Suneet Pandher, Satnam Singh
Summary: Amrasca biguttula biguttula (Ishida) commonly known as cotton leafhopper is a serious pest of cotton and okra. Nutritional requirements or growth physiology for this insect has not been much known till date. We developed artificial membrane feeding method for leafhopper which can be further used for RNA interference studies. Main components of this diet were L-cysteine (5.0 mg), glycine (2.0 mg), nicotinic acid (1.0 mg), sucrose (500 mg), K2HPO4(50 mg), ZnCl2 (0.04 mg), Thiamine HCl (0.25 mg), Vitamin B6 (0.25 mg), Becosules capsule powder (Pfizer Limited, USA) (2.0 mg), Green food dye (GanpatiSyn Food Colour, India) (2.0 mg) per 10ml of autoclaved double distilled water. To make diet accessible to the cotton leafhoppers the 1.5 ml of Microcentrifuge tube’s (MCT) cap (Tarsons Products Pvt. Ltd. India) was removed and diet was filled in 2 layers of parafilm sachet (diet was poured on first layer of parafilm on cap and covered with another layer of stretched parafilm) into cap. The MCT’s was cut 1/4th from bottom end, which was covered with muslin cloth (40 count mesh size). This MCTs with leafhopper was kept in incubator at 65-70% RH, 14:10 h light and dark photoperiod and 27± 2°C.
Proper citation: Amritpal Singh Brar, Mridula Gupta, Gurmeet kaur, Suneet Pandher, Satnam Singh 2018. Modified diet assay for studying feeding RNAi in cotton leafhopper, Amrasca biguttula biguttula. protocols.io dx.doi.org/10.17504/protocols.io.ksgcwbw Copy
Authors: Caroline Green
Summary: Escherichia Coli, also known as E. coli, is the most widely studied prokaryotic model organism, and an important species in the field of biotechnology and microbiology, where it has served as the host organism for the majority of work with recombinant DNA. Typically, E. coli expression is the first choice for protein expression and protein product in E. coli is fast, convenient, well established and always with high yields.Experiment PrinciplePlasmid DNA or recombinant DNA adhered to the surface of bacterial cells; 42 °C heat treatment for a short time to promote the absorption of DNA and then cultivate a generation in the non-selective medium; when the antibiotic gene on the plasmid expressed, it can be placed in the medium containing antibiotics.Experimental MaterialsPlasmid DNA, recombinant DNAReagents, kitsLB medium, Distilled water, IPTG, X-gal, AmpicillinEquipmentVortex mixer, Micro-pipettes, Pipette tip, Centrifuge tube, Double-sided micro-centrifuge tube rack, Dry air bath, Constant temperature water bath, Ice maker, Constant temperature shaker, Petri dishes, Clean bench, Alcohol lights, Glass sticks, Constant temperature incubatorOperating MethodAdjust the temperature of the constant temperature water bath to 42°C Geta tube (100 μl) of the competent bacteria from the -70 °C ultrafilter freezer and immediately melt with a finger and insert it into ice and ice for 5 to 10 minutes Add 5 μl of the attached plasmid mixture (DNA content of no more than 100 ng), gently shakeandplace on ice for 20 min Gently shakeand insertinto the 42 °C water bath 1 ~ 2 min for heat shock, and then quickly put back to the ice; put it aside for 3 ~ 5 min Add 500 μl of LB medium (without antibiotics) to each of the tubes in a clean bench and mix them gently onto a shaker of 37 °Cfor 1 h In the clean bench, take the above conversion mixture 100-300 μl, respectively, to the appropriate solid LB plateculture dish containing antibiotics; coat evenly with alcohol lamp burned glass If the carrier and host bacteria are suitable for blue-white screening, drop 40 μl of 2% X-gal, 8 μl of 20% IPTG on the plate and coat evenlywith alcohol lamp burned glass Mark on a coated dish and place in a 37 °Cincubator for 30 to 60 min until the liquid on the surface penetrates into the culture medium and thenplace in the 37 °C incubator overnight Spray 70% ethanol on the bacteria-contaminated table, dry the table, write an experimental reportGeta tube (100 μl) of the competent bacteria from the -70 °C ultrafilter freezer and immediately melt with a finger and insert it into ice and ice for 5 to 10 minutes Add 5 μl of the attached plasmid mixture (DNA content of no more than 100 ng), gently shakeandplace on ice for 20 min Gently shakeand insertinto the 42 °C water bath 1 ~ 2 min for heat shock, and then quickly put back to the ice; put it aside for 3 ~ 5 min Add 500 μl of LB medium (without antibiotics) to each of the tubes in a clean bench and mix them gently onto a shaker of 37 °Cfor 1 h In the clean bench, take the above conversion mixture 100-300 μl, respectively, to the appropriate solid LB plateculture dish containing antibiotics; coat evenly with alcohol lamp burned glass If the carrier and host bacteria are suitable for blue-white screening, drop 40 μl of 2% X-gal, 8 μl of 20% IPTG on the plate and coat evenlywith alcohol lamp burned glass Mark on a coated dish and place in a 37 °Cincubator for 30 to 60 min until the liquid on the surface penetrates into the culture medium and thenplace in the 37 °C incubator overnight Spray 70% ethanol on the bacteria-contaminated table, dry the table, write an experimental reportAdd 5 μl of the attached plasmid mixture (DNA content of no more than 100 ng), gently shakeandplace on ice for 20 min Gently shakeand insertinto the 42 °C water bath 1 ~ 2 min for heat shock, and then quickly put back to the ice; put it aside for 3 ~ 5 min Add 500 μl of LB medium (without antibiotics) to each of the tubes in a clean bench and mix them gently onto a shaker of 37 °Cfor 1 h In the clean bench, take the above conversion mixture 100-300 μl, respectively, to the appropriate solid LB plateculture dish containing antibiotics; coat evenly with alcohol lamp burned glass If the carrier and host bacteria are suitable for blue-white screening, drop 40 μl of 2% X-gal, 8 μl of 20% IPTG on the plate and coat evenlywith alcohol lamp burned glass Mark on a coated dish and place in a 37 °Cincubator for 30 to 60 min until the liquid on the surface penetrates into the culture medium and thenplace in the 37 °C incubator overnight Spray 70% ethanol on the bacteria-contaminated table, dry the table, write an experimental reportGently shakeand insertinto the 42 °C water bath 1 ~ 2 min for heat shock, and then quickly put back to the ice; put it aside for 3 ~ 5 min Add 500 μl of LB medium (without antibiotics) to each of the tubes in a clean bench and mix them gently onto a shaker of 37 °Cfor 1 h In the clean bench, take the above conversion mixture 100-300 μl, respectively, to the appropriate solid LB plateculture dish containing antibiotics; coat evenly with alcohol lamp burned glass If the carrier and host bacteria are suitable for blue-white screening, drop 40 μl of 2% X-gal, 8 μl of 20% IPTG on the plate and coat evenlywith alcohol lamp burned glass Mark on a coated dish and place in a 37 °Cincubator for 30 to 60 min until the liquid on the surface penetrates into the culture medium and thenplace in the 37 °C incubator overnight Spray 70% ethanol on the bacteria-contaminated table, dry the table, write an experimental reportAdd 500 μl of LB medium (without antibiotics) to each of the tubes in a clean bench and mix them gently onto a shaker of 37 °Cfor 1 h In the clean bench, take the above conversion mixture 100-300 μl, respectively, to the appropriate solid LB plateculture dish containing antibiotics; coat evenly with alcohol lamp burned glass If the carrier and host bacteria are suitable for blue-white screening, drop 40 μl of 2% X-gal, 8 μl of 20% IPTG on the plate and coat evenlywith alcohol lamp burned glass Mark on a coated dish and place in a 37 °Cincubator for 30 to 60 min until the liquid on the surface penetrates into the culture medium and thenplace in the 37 °C incubator overnight Spray 70% ethanol on the bacteria-contaminated table, dry the table, write an experimental reportIn the clean bench, take the above conversion mixture 100-300 μl, respectively, to the appropriate solid LB plateculture dish containing antibiotics; coat evenly with alcohol lamp burned glass If the carrier and host bacteria are suitable for blue-white screening, drop 40 μl of 2% X-gal, 8 μl of 20% IPTG on the plate and coat evenlywith alcohol lamp burned glass Mark on a coated dish and place in a 37 °Cincubator for 30 to 60 min until the liquid on the surface penetrates into the culture medium and thenplace in the 37 °C incubator overnight Spray 70% ethanol on the bacteria-contaminated table, dry the table, write an experimental reportIf the carrier and host bacteria are suitable for blue-white screening, drop 40 μl of 2% X-gal, 8 μl of 20% IPTG on the plate and coat evenlywith alcohol lamp burned glass Mark on a coated dish and place in a 37 °Cincubator for 30 to 60 min until the liquid on the surface penetrates into the culture medium and thenplace in the 37 °C incubator overnight Spray 70% ethanol on the bacteria-contaminated table, dry the table, write an experimental reportMark on a coated dish and place in a 37 °Cincubator for 30 to 60 min until the liquid on the surface penetrates into the culture medium and thenplace in the 37 °C incubator overnight Spray 70% ethanol on the bacteria-contaminated table, dry the table, write an experimental reportCollected by Creative BioMart.
Proper citation: Caroline Green 2017. Escherichia Coli Transformation Experiment Guide. protocols.io dx.doi.org/10.17504/protocols.io.i4tcgwn Copy
Authors: New England Biolabs
Group: New England Biolabs (NEB)
Summary: This is the PCR protocol for Phusion® High-Fidelity DNA Polymerase (M0530)
Proper citation: New England Biolabs 2015. PCR with Phusion® Polymerase (M0530). protocols.io dx.doi.org/10.17504/protocols.io.cdjs4m Copy
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