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Authors: Anna Vanclová and Natalia Wandyszewska
Group: Protist Research to Optimize Tools in Genetics (PROT-G)
Summary: This protocol was used to check, whether the DNA can be delivered to Eutreptiella gymnastica.

Proper citation: Anna Vanclová and Natalia Wandyszewska 2017. Experimental check of DNA delivery into E. gymnastica by electroporation. protocols.io https://dx.doi.org/10.17504/protocols.io.hh5b386 Copy   

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Authors: Kokila Shankar, Olivier George
Group: George Lab

Proper citation: Kokila Shankar, Olivier George 2020. qPCR Assay. protocols.io https:// Copy   

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Authors: Steven Burgess
Group: Plantae

Proper citation: Steven Burgess 2018. Fluorescence analysis using CF imager. protocols.io https://dx.doi.org/10.17504/protocols.io.q4hdyt6 Copy   

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Authors: Huang Zhihai, Xu Jiang, Xiao Shuiming, Liao Baosheng, Gao Yuan, Zhai Chaochao, Qiu Xiaohui, Xu Wen, Chen Shilin
Group: GigaScience Press
Summary: These methods accompany:Huang Zhihai, Xu Jiang, Xiao Shuiming, Liao Baosheng, Gao Yuan, Zhai Chaochao, Qiu Xiaohui, Xu Wen, Chen Shilin (2016): Supporting data for 'Comparative optical genome analysis of two Pangolin species Manis pentadactyla and Manis javanica'. GigaScience Database.

Proper citation: Huang Zhihai, Xu Jiang, Xiao Shuiming, Liao Baosheng, Gao Yuan, Zhai Chaochao, Qiu Xiaohui, Xu Wen, Chen Shilin 2016. Comparative optical genome analysis of two Pangolin species Manis pentadactyla and Manis javanica (protocols ). protocols.io https://dx.doi.org/10.17504/protocols.io.gaibsce Copy   

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Authors: Lutz Berwanger
Group: Axmann Lab, CyanoWorld
Summary: This protocol can be used to purifiy DNA-dependent RNA polymerase from Synechococcus elongatus PCC 7942 by heparin and ion-exchange chromatography.

Proper citation: Lutz Berwanger 2018. Purification of DNA-dependent RNA Polymerase from Synechococcus elongatus PCC 7942. protocols.io https://dx.doi.org/10.17504/protocols.io.mpxc5pn Copy   

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Authors: Andreea S
Group: iGEM Groningen 2020
Summary: In order to get a relative estimation of the diffusion of our neuropeptide in the soil we can use a soil thin-layer chromatography. In this experiment, developed by Helling & Turner in 1968, a thin-layer chromatography apparatus is utilized to mimic the environment conditions to a certain extent. Using C14 labeled glycines we can use X-ray to determine the distance traveled by the peptide. Use of a small his-tag is unreliable due to the small length of the peptide. As a control we will use two C14 labeled compounds common in the exudate of the plant: Glucose and Glutamic acid. Glucose is considered to diffuse well in the soil whereas glutamic acid has a lower diffusion coefficient (cm/h).Protocol is adapted from Ravanel and colleagues (1999).

Proper citation: Andreea S 2020. Soil thin-layer chromatography . protocols.io https://dx.doi.org/10.17504/protocols.io.bkcaksse Copy   

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Authors: Joshua Lucate
Group: Bio Basic Inc.
Summary: This protocol is for the extraction and purification of up to 10ug of plasmid DNA. It can be used for the purification of plasmid DNA ranging from 40 bp to 40kbp. 

Proper citation: Joshua Lucate 2016. Plasmid DNA miniprep protocol for EZ-10 Spin Column Plasmid DNA minipreps kit (BS413), 50 preps. protocols.io https://dx.doi.org/10.17504/protocols.io.fwdbpa6 Copy   

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Authors: Jacob Marsh, Celeste Karch
Group: Neurodegeneration Method Development Community
Summary: This protocol is about Maintenance and Expansion of induced pluripotent stem cells.

Proper citation: Jacob Marsh, Celeste Karch 2020. iPSC Cell Culture – Maintenance and Expansion. protocols.io https://dx.doi.org/10.17504/protocols.io.9pwh5pe Copy   

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Authors: Tinka Beemsterboer, Lukas Snoek
Group: Spinoza Centre, REC-L
Summary: Dear researcher,This protocol gives you the steps to start an MRI project at the Spinoza Centre Roeterseiland. If you haven't had contact with Steven Scholte or Tinka Beemsterboer, make sure to contact them before completing this protocol. You can reach us by email:Steven Scholte: [email protected] Beemsterboer: [email protected] you have any suggestions for improving the workflow, don't hesitate to add comments to the steps in the protocol.Hope to see you soon!Spinoza REC Team!Steven Scholte, Tinka Beemsterboer en Lukas Snoek 

Proper citation: Tinka Beemsterboer, Lukas Snoek 2018. Before data acquisition -- Start MRI Project Spinoza REC. protocols.io https://dx.doi.org/10.17504/protocols.io.nj6dcre Copy   

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Authors: Suvi Honkanen, Victor A. S. Jones
Summary: Simplified protocol for Agrobacterium-mediated transformation of haploid liverwort Marchantia polymorpha spores. See the attached file for all steps, notes and information on reagents. Includes protocols for spore collection, storage and sterilisation. By Suvi Honkanen and Victor A. S. Jones. Modified from Ishizaki et al. Plant Cell Physiol. 2008 Jul;49(7):1084-91. doi: 10.1093/pcp/pcn085. Developed at the Dolan lab (The University of Oxford) and at the Small lab (The University of Western Australia).Working on a high-throughput T-DNA mutant screen published in https://doi.org/10.1016/j.cub.2016.09.062 , https://doi.org/10.1016/j.cub.2015.11.042 , https://doi.org/10.7554/eLife.38529 , https://doi.org/10.1242/dev.144287 , https://doi.org/10.1371/journal.pbio.3000560 taught us a thing or two about Marchantia transformation. I have further refined the protocol during my current semi high-throughput project. I hope you find some of this useful.

Proper citation: Suvi Honkanen, Victor A. S. Jones 2020. Simplified protocol for Agrobacterium-mediated transformation of the liverwort Marchantia polymorpha, includes protocols for spore sterilisation. protocols.io https://dx.doi.org/10.17504/protocols.io.ba28ighw Copy   

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Authors: Robbie Martin, Steven W. Wilhelm
Group: The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs)
Summary: Phenol/chloroform-based DNA extraction from cells pre-treated with RNase A, lysozyme, proteinase K, and SDS. The protocol was optimized for extracting DNA from Microcystis aeruginosa, but works well for other cyanobacteria.

Proper citation: Robbie Martin, Steven W. Wilhelm 2018. Phenol/chloroform extraction of DNA from cyanobacteria. protocols.io https://dx.doi.org/10.17504/protocols.io.mszc6f6 Copy   

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Authors: Rob Ward's Lab
Summary: Drosophila melanogaster females' productive system has been an excellent model in studying many developmental events such as stem cell specification and cell migration. The ovaries are composed of a chain of egg chambers starting with the germaruim that buds of stage 1 egg chamber after encapsulated it with follicle cells. Then, stage 1 egg chamber goes under 14 developmental stages. This protocol provides the basic method for both dissecting and immunostaining ovaries. Each step is critical. This protocol is modified from http://www.ncbi.nlm.nih.gov/pubmed/8162854

Proper citation: Rob Ward's Lab 2015. Dissecting and Immunostaining Drosophila melanogaster Egg Chambers. protocols.io https://dx.doi.org/10.17504/protocols.io.cs9wh5 Copy   

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Authors: Muofhe Tshibalanganda, Anton Du Plessis, Stephan Le Roux, Paul Papka
Summary: This protocol described the steps used to inspect the Gallium targets used in particle accelerators. These targets are metal disks filled with Gallium, and laser welded on the edges. Various production quality issues may be present - the microCT process needs to be a standard, routine methodology for direct comparison among all such data sets. This protocol sets out the exact steps used for this analysis type.

Proper citation: Muofhe Tshibalanganda, Anton Du Plessis, Stephan Le Roux, Paul Papka 2019. Protocol for microCT inspection of Gallium particle accelerator targets. protocols.io https://dx.doi.org/10.17504/protocols.io.ychfst6 Copy   

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Authors: Dr. Steven Wilhelm, Samantha Coy
Group: Protist Research to Optimize Tools in Genetics (PROT-G), The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs), Samantha R Coy's Protocols
Summary: Van Etten, J. (n.d.). Formulation of Modified Bold's Basal Medium (MBBM). Retrieved from http://ncv.unl.edu/vanettenlab/ Contact Dr. Steven Wilhelm ([email protected]) or Samantha Coy ([email protected]) for additional information regarding this protocol.

Proper citation: Dr. Steven Wilhelm, Samantha Coy 2017. MBBM Stock Solutions. protocols.io https://dx.doi.org/10.17504/protocols.io.hgtb3wn Copy   

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Authors: Nikki Freed, Olin Silander
Group: Coronavirus Method Development Community
Summary: To enable faster, easier sequencing of SARS-COV2 genomes with fewer steps than current methods, we use multiplexed 1200 base pair PCR amplicons with the Oxford Nanopore RAPID barcoding kit (RBK004). This is a modification of the ARTIC amplicon V3 sequencing protocol for MinION for nCoV-2019 developed by Josh Quick, which produces 400 base pair amplicons and uses the Oxford Nanopore Ligation barcoding kit (LSK-109). We have increased the size of the amplicons to 1200bp and use the RAPID barcode kit (RBK004), which enables requires less time and fewer reagents than the LSK-109 protocol. The amplicons produced in this protocol could also be used for Illumina sequencing. Primers were all designed using Primal Scheme: http://primal.zibraproject.org/, described here https://www.nature.com/articles/nprot.2017.066.Primer sequences are here: https://docs.google.com/spreadsheets/d/1M5I_C56ZC8_2Ycgm9EFieVlVNqxsP7dXAnGoBZy3nDo/edit?usp=sharingThe primer scheme .bed and .tsv files necessary for the ARTIC variant calling pipeline are at Zenodo: https://zenodo.org/record/3897530#.Xv5EFpMzadYVersion history: V4: updated .bed and .tsv file link to point to Zenodo (and not google drive). V1-V3: included primers sequences in the protocol, fixed step 17.12 from elute in "molecular grade water or Elution buffer" to elute in "10 mM Tris-HCl pH 8.0 with 50 mM NaCl", as suggested on the Oxford Nanopore protocol, changed images from ARTIC protocol image to our own.

Proper citation: Nikki Freed, Olin Silander 2020. nCoV-2019 sequencing protocol (RAPID barcoding, 1200bp amplicon). protocols.io https://dx.doi.org/10.17504/protocols.io.bh7hj9j6 Copy   

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Authors: philippe.bechtold
Group: XPRIZE Rapid Covid Testing

Proper citation: philippe.bechtold 2020. Thermal cycling of the PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.bk6jkzcn Copy   

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Authors: Jiao Wang

Proper citation: Jiao Wang 2017. Computational prediction of the molecular mechanisms involved in migration. protocols.io https://dx.doi.org/10.17504/protocols.io.iapcadn Copy   

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Authors: Masumi Eto, Shuichi Katsuki, Yoshinori Tanaka, Kosuke Takeya

Proper citation: Masumi Eto, Shuichi Katsuki, Yoshinori Tanaka, Kosuke Takeya 2020. Kinase-activity tagged (KAT) western blotting. protocols.io https://dx.doi.org/10.17504/protocols.io.bhpzj5p6 Copy   

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Authors: Marda Jorgensen, Michelle Daniel
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: Version 11 of the antibody labelling protocol published by Fluidigm.

Proper citation: Marda Jorgensen, Michelle Daniel 2020. Maxpar Antibody Labeling for Imaging Mass Cytometry. protocols.io https://dx.doi.org/10.17504/protocols.io.bf5jjq4n Copy   

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Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol describes the process for diaminobenzidine (DAB) detection of biocytin filled cells. This protocol is optimized for use with brain slices cut at 350 µm thick, in which cells are first filled with biocytin (i.e., post-electrophysiological recording), fixed in 4% PFA/2.5% glutaraldehyde, and transferred to PBS until ready to stain.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. DAB Detection of Biocytin Labeled Tissue. protocols.io https://dx.doi.org/10.17504/protocols.io.bg5yjy7w Copy   

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