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Authors: Daniela Flores, Timothy Marzullo

Proper citation: Daniela Flores, Timothy Marzullo 2018. The reconstruction of a single lens microscope. Reviving the Leeuwenhoek’s microscope. . protocols.io https:// Copy   

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Authors: Alex Zegarra

Proper citation: Alex Zegarra 2020. Plasmid DNA Mini Kit I- Spin Protocol . protocols.io https:// Copy   

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Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: The following are media recipes necessary for isolating and maintaining Synechococcus isolates.

Proper citation: Matthew Sullivan 2016. Media recipes for Synechococcus isolates. protocols.io https://dx.doi.org/10.17504/protocols.io.c9jz4m Copy   

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Authors: Sam Li
Group: BioLegend

Proper citation: Sam Li 2019. Propidium Iodide Cell Cycle Staining Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bacyiaxw Copy   

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Authors: Freddie-Jeanne Richard
Summary: Y choice test designed for terrestrial invertebrase

Proper citation: Freddie-Jeanne Richard 2019. Y Choice test invertebrate. protocols.io https://dx.doi.org/10.17504/protocols.io.vpfe5jn Copy   

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Authors: Tingting Xiang
Group: Aiptasia-Symbiodiniaceae Model System

Proper citation: Tingting Xiang 2018. Isolation of axenic Symbiodinium cultures. protocols.io https://dx.doi.org/10.17504/protocols.io.qxzdxp6 Copy   

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Authors: Hongbo Zhang
Summary: This protocol can be used to isolate single cells from human fetal thigh from age GA6-GA11.

Proper citation: Hongbo Zhang 2018. Single cell isolation from human fetal thigh. protocols.io https://dx.doi.org/10.17504/protocols.io.ta8eihw Copy   

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Authors: Jim Leebens-Mack, Charlotte Carrigan
Group: GigaScience Press
Summary: Protocol implemented by: Jim Leebens-Mack and Charlotte Carrigan The first protocol used for isolation of total RNA was Qiagen’s RNeasy Plant Mini Kit (Qiagen, Valencia, CA). These kits are commercially available and widely used in RNA isolation. For detailed methods associated with this kit we refer readers to the “RNeasy Mini Handbook” available for download at www.qiagen.com. This 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: Jim Leebens-Mack, Charlotte Carrigan 2019. RNA Isolation from Plant Tissue Protocol 1: Qiagen RNeasy Plant Mini Kit. protocols.io https://dx.doi.org/10.17504/protocols.io.4vxgw7n Copy   

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Authors: Michael Economo
Summary: How to make a cleaning solution for cleaning silicon probes

Proper citation: Michael Economo 2019. Electrode cleaning solution. protocols.io https://dx.doi.org/10.17504/protocols.io.8pwhvpe Copy   

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Authors: Pia Elustondo, Claudio Slamovits
Group: Protist Research to Optimize Tools in Genetics (PROT-G)

Proper citation: Pia Elustondo, Claudio Slamovits 2018. Transfection of O. marina using particle bombardment. protocols.io https://dx.doi.org/10.17504/protocols.io.ui7euhn Copy   

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Authors: Kevin Bonham
Summary: For purifying proteins from mammalian cells for analysis by western blot.

Proper citation: Kevin Bonham 2014. Immunoprecipitation / coimmunoiprecipitation (IP / Co-IP) {biochemistry}. protocols.io https://dx.doi.org/10.17504/protocols.io.ccisud Copy   

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Authors: Edvard Grødem, Kieran Sweeney, Megan N. McClean
Summary: Optogenetic systems use light to precisely control and investigate cellular processes. Until recently, there had been few instruments available for applying controlled light doses to cultures of cells. The optoPlate, a programmable array of 192 LEDs, was developed to meet this need. However, LED performance varies and without calibration there are substantial brightness differences between LEDs on an optoPlate. Here we present a method for calibrating an optoPlate that uses a programmable microscope stage and optical power meter to automatically measure all 192 LEDs of an optoPlate. The resulting brightness measurements are used to calculate calibration values that tune the electrical current supplied to each optoPlate LED to reduce brightness variation in optogenetic experiments.

Proper citation: Edvard Grødem, Kieran Sweeney, Megan N. McClean 2020. OptoPlate Calibration protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bivmke46 Copy   

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Authors: Weixue Mu, Jinpu Wei, Ting Yang, Yannan Fan, Le Cheng, Jinlong Yang, Ranchang Mu, Jie Liu, Jianming Zhao, Weibang Sun, Xun Xu, Xin Liu, Radoje Drmanac, Huan Liu
Group: Bauhinia Genome, Plantae, BGI
Summary: RNA extraction of plant tissues (in our case Bauhinia leaves) using a pBIOZOL/CTAB lysis buffer

Proper citation: Weixue Mu, Jinpu Wei, Ting Yang, Yannan Fan, Le Cheng, Jinlong Yang, Ranchang Mu, Jie Liu, Jianming Zhao, Weibang Sun, Xun Xu, Xin Liu, Radoje Drmanac, Huan Liu 2017. RNA extraction for plant samples using CTAB-pBIOZOL. protocols.io https://dx.doi.org/10.17504/protocols.io.gsnbwde Copy   

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Authors: Jacob Heldenbrand, Yingxue Ren, Yan Asmann, Liudmila S. Mainzer

Proper citation: Jacob Heldenbrand, Yingxue Ren, Yan Asmann, Liudmila S. Mainzer 2017. Step-by-Step guide for downloading very large datasets to a supercomputer using the SRA Toolkit . protocols.io https://dx.doi.org/10.17504/protocols.io.kb6csre Copy   

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Authors: Mihir Kekre

Proper citation: Mihir Kekre 2021. C-SOP-901: Preparation of DNA Isolates for Domestic and Overseas Transport. protocols.io https:// Copy   

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Authors: Sabine St-Jean
Group: Canadian Airborne Biodiversity Observatory
Summary: Here we describe the standardised protocol used by the Canadian Airborne Biodiversity Observatory (CABO) to use the Trimble GPS with the NTRIP centimeter-level precision subscription from Cansel to record the precise location of a plot (corner or center) or a plant.

Proper citation: Sabine St-Jean 2020. Trimble GPS Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.9zeh73e Copy   

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Authors: Yves Basset
Summary: Suggested field procedures for collecting soil/litter arthropods in a tropical rainforest for long-term monitoring with DNA metabarcoding.Standardized field protocols to monitor the soil fauna exist but they are not tailored to surveys in tropical rainforests and not designated to obtain samples that can be later processed with metabarcoding. In general, the soil fauna is extracted by Berlese-Tullgren apparatus, while the litter-dwelling and more active fauna is better surveyed with Winkler extractors. Here, we used Berlese-Tullgren which represent the choice method for Collembola but included in our samples both soil and litter.

Proper citation: Yves Basset 2020. Suggested field procedures for collecting soil/litter arthropods in a tropical rainforest for long-term monitoring with DNA metabarcoding. protocols.io https://dx.doi.org/10.17504/protocols.io.bj9gkr3w Copy   

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Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab

Proper citation: Matthew Sullivan 2016. Colony PCR Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.c6czav Copy   

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Authors: Tobias von der Haar

Proper citation: Tobias von der Haar 2019. Site directed mutagenesis by PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.igucbww Copy   

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Authors: G-Biosciences
Group: G-Biosciences
Summary: The OmniPrep™ kit isolates high quality genomic DNA from many different species and tissue types including animal, plant, bacteria, yeast, fungi, whole blood, and cells in culture. DNA can be isolated from samples high in polysaccharides or other contaminants that are difficult to remove from the DNA preparations.This protocol is for use with body fluids (including CSF, plasma, saliva, serum, sputum, synovial fluid, urine and whole blood). Please refer to the appropriate protocol depending on your application.

Proper citation: G-Biosciences 2016. OmniPrep™ For High Quality Genomic DNA Extraction From Body Fluids. protocols.io https://dx.doi.org/10.17504/protocols.io.e6jbhcn Copy   

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