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Authors: Ida Barlow, Adam Mcdermott-Rouse, Luigi Feriani
Group: Behavioural Genomics
Summary: Protocol for preparing worms, preparing drug plates, dispensing worms with wormsorter and tracking on Hydra rigs
Proper citation: Ida Barlow, Adam Mcdermott-Rouse, Luigi Feriani 2020. Syngenta drug screen. protocols.io dx.doi.org/10.17504/protocols.io.9vqh65w Copy
Authors: Virginia Weis
Group: Aiptasia-Symbiodiniaceae Model System
Summary: Method to chemically bleach Aiptasia in small volume dishes.
Proper citation: Virginia Weis 2018. Menthol protocol to bleach Aiptasia. protocols.io dx.doi.org/10.17504/protocols.io.immcc46 Copy
Authors: Angel Justiz-Vaillant, Monica F. Smikle
Group: University of the West Indies, [email protected]
Proper citation: Angel Justiz-Vaillant, Monica F. Smikle 2020. Universal sandwich ELISA for investigating the binding of avian immunoglobulins to Streptococcal protein-G (SpG) using anti-IgY-peroxidase conjugate. . protocols.io dx.doi.org/10.17504/protocols.io.bjqvkmw6 Copy
Authors: Adam Hunter
Group: Human Cell Atlas Method Development Community
Proper citation: Adam Hunter 2018. CGAP MACS Live Dead Separation. protocols.io dx.doi.org/10.17504/protocols.io.qz5dx86 Copy
Authors: Qi Wang
Group: BGI, GIGA, GigaScience Press
Summary: Quality control for metagenomics data,including: remove low quality reads and host contamination reads.
Proper citation: Qi Wang 2020. Quality control for metagenomics data. protocols.io dx.doi.org/10.17504/protocols.io.be68jhhw Copy
Authors: Josef Hoff
Summary: Electroporation protocol
Weinstock paper:Matthew T Weinstock, Eric D Hesek,Christopher M Wilson, Daniel G GibsonVibrio natriegens as a fast-growing host for molecular biology
Nature Methods volume 13, pages 849–851 (2016)To prepare before:recovery medium(BHI + v2 salts (204 mM NaCl, 4.2 mM KCl, 23.14mM MgCl2), and 680 mM sucrose) sterile filtration
* i have a box of aliquots in the freezer and pre heat them before use-A vial of competent cells is retrieved from storage at −80 °C and allowed to thaw on ice.-Plasmid DNA and electrocompetent cells are combined and gently mixed in a chilled 1.5-mL microcentrifuge tube. -The cell–DNA suspension is transferred to a chilledelectroporation cuvette with a 0.1-cm gap size.-Cells are electroporated with 900V (in our Electroportor we cant set other parameters )
* in the Weinstock paper they recommend depending on the strain 700-900V, 25 μF and 200 Ω-Cells are immediatelyrecovered in 500 μL preheated (50°C) recovery medium and transferred to a 1,5-mL tube.
* we preheat the media to 50°C because the recovery media is cooled down by pipetting and up taking the chilled cells from the cold cuvettes-The cells are recovered by incubating at 37 °C for 1.5h. ( also put the agar plates for preheating in the incubator at 37°C )-The cells are centrifuged down for one mintute at 3000g. The supernant is then discanted.- the pellet is resuspendet in the leftover oft he media and plated out on warm agar plates containing appropriate antibiotic.
* for Chloramphenicol 2µg/mL ; for Kanamycine 200µg/mL; for Carbenicillin 200µg/mL-The plates are incubated for several hours or overnight at 37 °C for colonies to appear.
Proper citation: Josef Hoff 2018. Electroporation protocol for Vibrio natriegens. protocols.io dx.doi.org/10.17504/protocols.io.u3geyjw Copy
Authors: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen
Group: VERVE Net
Summary: For use in "Isolation of cyanophages by liquid enrichment assay"
Proper citation: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Propagation/Amplification of Lytic Agent. protocols.io dx.doi.org/10.17504/protocols.io.dq85zv Copy
Authors: Deborah Jaffey, Terry Powley, Jennifer Mcadams, Robert Phillips
Group: SPARC
Summary: This protocol describes the methods used to trace and enable morphometric quantification of preganglionic efferent neurites in the rat stomach. A mixture of dextran conjugates was injected into the dorsal motor nucleus of the vagal nerve (dmnX) of young adult Sprague-Dawley rats and after a survival period of 19 days for optimal tracer transport, stomachs were removed and processed as whole mounts. ABC-DAB was used to create a permanent gold-brown stain of all labeled efferent neurites. Subgroups of samples were also counterstained with either the panneuronal chromogen cuprolinic blue or with nNOS antibodies and steel gray chromogen to label nitrergic cells.
Proper citation: Deborah Jaffey, Terry Powley, Jennifer Mcadams, Robert Phillips 2019. High resolution labeling of vagal efferent fibers using Dextran-Biotin with counterstaining. protocols.io dx.doi.org/10.17504/protocols.io.2iqgcdw Copy
Authors: Byung Joon Seung
Summary: In retrospective formalin-fixed paraffin-embedded (FFPE) samples, RNA quality of FFPE tissues showed variation following the storage period and fixation process. So we suggest quantitative analysis by dual detection of target mRNA and housekeeping genes in one section and calculated the target gene/housekeeping gene ratio by two open-source image analysis programs. This assay potentially allows for reliable quantification of mRNA expression levels in retrospective FFPE samples.
Proper citation: Byung Joon Seung 2020. Quantitative analysis method of mRNA expression using dual RNA in situ hybridization by comparison with housekeeping genes. protocols.io dx.doi.org/10.17504/protocols.io.badcia2w Copy
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 2018. Quick Protocol for Monarch® Plasmid Miniprep Kit (NEB #T1010). protocols.io dx.doi.org/10.17504/protocols.io.nytdfwn Copy
Authors: New England Biolabs
Group: New England Biolabs (NEB)
Proper citation: New England Biolabs 2015. NEB 3X SDS Sample Loading Buffer. protocols.io dx.doi.org/10.17504/protocols.io.crcv2v Copy
Authors: Monica Simion, Alexandru Salceanu
Group: Coronavirus Method Development Community, covid19-test, XPRIZE Rapid Covid Testing
Proper citation: Monica Simion, Alexandru Salceanu 2020. microfluidic sars cov 2 lamp protocol. protocols.io dx.doi.org/10.17504/protocols.io.bkjjkukn Copy
Authors: Magdalena Julkowska
Summary: Quick and dirty, but very very fast protocol for DNA isolation. It works beautifully if you have plenty of lines to genotype - example T-DNA insertion lines for validation of your favourite gene.
Proper citation: Magdalena Julkowska 2019. Chelex DNA isolation for quick plant genotyping. protocols.io dx.doi.org/10.17504/protocols.io.pdudi6w Copy
Authors: Anna Wilbrey-Clark, Adam Hunter
Group: Human Cell Atlas Method Development Community
Proper citation: Anna Wilbrey-Clark, Adam Hunter 2019. CGAP Human Lung Dissociation - Tissue Stability Study. protocols.io dx.doi.org/10.17504/protocols.io.34kgquw Copy
Authors: MoBio PowerWater instructions amended with specific instructions
Summary: Procedure for DNA extractions using PowerWater DNA extraction kit from filtered LEO seepage water samples and prelimnary QC by nanodrop
Proper citation: MoBio PowerWater instructions amended with specific instructions 2017. Protocol for LEO filter sample DNA extractions using PowerWater kit. protocols.io dx.doi.org/10.17504/protocols.io.h75b9q6 Copy
Authors: Sarah Hessen-Schmidt
Proper citation: Sarah Hessen-Schmidt 2016. Lysis Buffer (10mM Tris-HCl, 2mM EDTA, 1% SDS). protocols.io dx.doi.org/10.17504/protocols.io.fjqbkmw Copy
Authors: Adebambo, A. O. and Ajibike, A. B.
Proper citation: Adebambo, A. O. and Ajibike, A. B. 2017. DNA extraction from FTA Classical Card. protocols.io dx.doi.org/10.17504/protocols.io.ihvcb66 Copy
Authors: New England Biolabs
Group: New England Biolabs (NEB)
Proper citation: New England Biolabs 2015. BioBrick E0546 Destination Reaction. protocols.io dx.doi.org/10.17504/protocols.io.cpmvk5 Copy
Authors: Peter Havel
Group: Mouse Metabolic Phenotyping Centers
Summary: Glucagon is a 29 amino acid polypeptide processed from proglucagon in pancreatic alpha cells. In intestinal L-cells proglucagon is cleaved into glicentin, corresponding to proglucagon residues no 1-69. Glicentin can further be processed into oxyntomodulin, corresponding to proglucagon residues no 33-69. These peptides are released simultaneously upon stimulation. Moreover, a fragment of glucagon corresponding to its Cterminal part (residues no 19-29), also designated mini-glucagon, is reported to be present in the pancreas in low amounts compared to the total glucagon content. In general, glucagon has an effect opposite that of insulin, i.e. it raises blood glucose levels. It causes the liver to convert glycogen into glucose, which is then released into the blood stream. With longer stimulation, glucagon action in the liver results in a glucose-sparing activation of free fatty acid oxidation and production of ketones. During hypoglycaemia, glucagon secretion offers a protective feedback mechanism, defending the organism against damaging effects of glucose deficiency in the brain and nerves.
Proper citation: Peter Havel 2019. UC Davis - Glucagon. protocols.io dx.doi.org/10.17504/protocols.io.63ihgke Copy
Authors: Remco Stam
Group: Stam Lab
Summary: Protocol for the cultivatio of Alternaria Solani.This protocol has been used for many years at the chair of Phytopathology at the Technical University of Munich.SNA Medium was first described by Nirenberg in 1981.
Proper citation: Remco Stam 2016. Cultivation / Spore Production for Alternaria Solani. protocols.io dx.doi.org/10.17504/protocols.io.fmibk4e Copy
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