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Authors: Hannigan GD, Meisel JS, Tyldsley AS, Zheng Q, Hodkinson BP, SanMiguel AJ, Minot S, Bushman FD, Grice EA
Group: VERVE Net, Club Grice
Summary: This collection contains protocols for the computational analysis performed in the paper "The Human Skin dsDNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and its Dynamic Associations with the Host Microbiome". Geoffrey Hannigan and Jacquelyn Meisel are graduate students in Dr. Elizabeth Grice's lab in the Department of Dermatology at the University of Pennsylvania.Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome." mBio 6.5 (2015): e01578-15.

Proper citation: Hannigan GD, Meisel JS, Tyldsley AS, Zheng Q, Hodkinson BP, SanMiguel AJ, Minot S, Bushman FD, Grice EA 2016. The Human Skin dsDNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and its Dynamic Associations with the Host Microbiome. protocols.io https://dx.doi.org/10.17504/protocols.io.ekubcww Copy   

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Authors: Brandt Pence

Proper citation: Brandt Pence 2017. Cell Mito Stress Test for Monocyte Mitochondrial Function. protocols.io https://dx.doi.org/10.17504/protocols.io.kw7cxhn Copy   

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Authors: Lucia Maria Costa Monteiro, Glaura N. O. Cruz, Juliana M. Fontes, Marcia C.B. Boechat
Summary: Congenital Zika Syndrome (CZS) is associated with microcephaly and other malformations of the central nervous system. We identified that some of areas damaged by CZS are also known to influence the neural circuitry controlling the lower urinary tract (1). And decided to investigate neurogenic bladder, in an attempt to identify risk factors and therapeutic modalities that could mitigate the impact of the CZS in infected children.A research protocol was developed based on our experience treating neurogenic bladder in children. And, after ethical approval, tested during urological assessment in patients with confirmed microcephaly due to CZS who were referred to our pediatric urodynamics clinic between June 2016 and May 2017. The protocol consisted of obtaining clinical history, laboratory tests, renal and bladder ultrasound and a urodynamic evaluation. ZIKA virus was previously confirmed by maternal history and positive RT-PCR in babies/mothers. Microcephaly and other central nervous system abnormalities were established based on neurological and image evaluation (CT and/or MRI).The results were submitted for publication and we are waiting the editor’s decision. Neurogenic bladder was confirmed so far in 100% of patients tested, with high-risk urodynamic patterns that may cause renal damage if left untreated. This is a preventable health condition in the setting of Congenital Zika Syndrome. While further investigation is necessary to understand long-term disease behavior, bladder proactive management is paramount to help mitigate disease burden for patients and their families.

Proper citation: Lucia Maria Costa Monteiro, Glaura N. O. Cruz, Juliana M. Fontes, Marcia C.B. Boechat 2018. Criteria to evaluate neurogenic bladder in patients with Congenital Zika Syndrome. protocols.io https://dx.doi.org/10.17504/protocols.io.k5vcy66 Copy   

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Authors: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
Summary: List of published papers using this protocol:- Boydum A.Isolation of mononuclear cells and granulocytes from human blood. Scand.J.Clin.Lab. Invest. 21 (Suppl.97): 77-89, 1968- Alex Mabou Tagne, Franca Marino, Massimiliano Legnaro, Alessandra Luini, Barbara Pacchetti and Marco Cosentino. A Novel Standardized Cannabis sativa L. Extract and Its Constituent Cannabidiol Inhibit Human Polymorphonuclear Leukocyte Functions. Int J Mol Sci2019 Apr; 20(8): 1833. Published online 2019 Apr 13. doi: 10.3390/ijms20081833.- Angela Scanzano, Laura Schembri, Emanuela Rasini, Alessandra Luini, Jessica Dallatorre, Massimiliano Legnaro, Raffaella Bombelli, Terenzio Congiu, Marco Cosentino, Franca Marino. Adrenergic Modulation of Migration, CD11b and CD18 Expression, ROS and interleukin-8 Production by Human Polymorphonuclear Leukocytes. Inflamm Res. 2015 Feb;64(2):127-35. doi: 10.1007/s00011-014-0791-8. Epub 2015 Jan 6.

Proper citation: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino 2020. PMN- 01b - Isolation of Human PMN from Whole Blood. protocols.io https://dx.doi.org/10.17504/protocols.io.bpxymppw Copy   

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Authors: Sam Towarnicki
Group: Cage Studies

Proper citation: Sam Towarnicki 2018. Superoxide levels. protocols.io https://dx.doi.org/10.17504/protocols.io.uftetnn Copy   

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Authors: Liz McDonough, Chrystal Chadwick, Fiona Ginty, Christine Surrette, Anup Sood
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community, GE Research
Summary: This document outlines the workflow for antibody staining, dye inactivation, and imaging as per the Cell DIVE™ technology.

Proper citation: Liz McDonough, Chrystal Chadwick, Fiona Ginty, Christine Surrette, Anup Sood 2020. Cell DIVE™ Platform | Antibody Staining & Imaging. protocols.io https://dx.doi.org/10.17504/protocols.io.bpv6mn9e Copy   

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Authors: Thorsten Langner, Adeline Harant, Sophien Kamoun
Summary: Fungal genomes are highly dynamic and often contain supernumerary mini-chromosomes. However, our knowledge about the role of mini-chromosomes in dynamic genome rearrangements and evolution is scarce. Mini-chromosomes are usually smaller then core-chromosomes and are variable in size and numbers between individuals of a species. Mini-chromosome occurence in fungi is well documented since decades, but many genomic projects have neglected them, mainly because it was technically challenging to identify them in whole genome assemblies. Here we present a protocol for isolation of mini-chromosomes for enrichment sequencing. This allows identification of mini-chromosomes in whole genome assemblies and thus comparative genomics analyses of core- and mini-chromosomes. .justify:after { content: ""; display:inline-block; width: 100%; }

Proper citation: Thorsten Langner, Adeline Harant, Sophien Kamoun 2019. Isolation of supernumerary mini-chromosomes from fungi for enrichment sequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.9t7h6rn Copy   

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Authors: Mark Moosburner, Andrew Allen
Group: A.E. Allen Lab
Summary: The CRISPR-Cas9 gene mutagenesis system was adapted for the marine diatom Phaeodactylum tricornutum (CCAP-1055/1) (Figure 1). Here, Cas9 and sgRNA(s) were delivered to Phaeodactylum by bacterial-conjugation transformation on an episome, or artificial chromosome, that is stably maintained and replicated independently from and with the Phaeodactylum chromosomal DNA. Two sgRNA expression cassettes, sgRNA (1/1) and sgRNA (1/2) were cloned into the episome. The sgRNAs each contain a unique 20-nucleotide spacer sequence that , after sgRNA cassette transcription, guides the Cas9 to a nucleic acid target by complementary binding followed by Cas9 nuclease activity. Two Phaeodactylum genes, Pt_GSII (Gene ID: 51092) and Pt_cGOGAT (Gene ID: 24739), were targeted by each sgRNA, respectively. The following protocol was followed to synthesize spacer sequences and sgRNA expression cassettes

Proper citation: Mark Moosburner, Andrew Allen 2019. GG1 - sgRNA cloning for Phaeodactylum tricornutum. protocols.io https://dx.doi.org/10.17504/protocols.io.4abgsan Copy   

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Authors: Brook C Barajas, Jaisri R Lingappa
Group: Lingappa Lab Group
Summary: Proximity Ligation Protocol with Concurrent IF

Proper citation: Brook C Barajas, Jaisri R Lingappa 2017. Proximity Ligation Protocol with Concurrent Immunofluorescence. protocols.io https://dx.doi.org/10.17504/protocols.io.k7yczpw Copy   

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Authors: Erika Alves dos Santos, Silvio Peroni, Marcos Luiz Mucheroni
Summary: This protocol stablishes a method for selecting journals and articles for composing a research sample based on SCImago Journal and Country Rank – SJR metadata (available from https://www.scimagojr.com/). It might be applied partially or in full, in order to obtain an stratified and representative sample of journals and/or articles, considering a multidisciplinary, as well as a unique discipline approach, according to the main objective(s) of the research in which it will be applied.

Proper citation: Erika Alves dos Santos, Silvio Peroni, Marcos Luiz Mucheroni 2020. Workflow for retrieving all the data of the analysis introduced in the article "Citing and referencing habits in Medicine and Social Sciences journals in 2019". protocols.io https://dx.doi.org/10.17504/protocols.io.bbifikbn Copy   

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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 in 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 than with other commercial suppliers. We recommend a titration to find the best dilution factor. However, as a general rule, dilutions ranging from 1:3 to 1:20 for the Nanobeads can be used. Please contact BioLegend Technical Service ([email protected]) if further assistance is needed.

Proper citation: Sam Li 2020. MojoSort™ Mouse Ig light chain κ Nanobeads Column Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bbueinte Copy   

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Authors: Kalle Pärn, Javier Nunez Fontarnau, Marita A. Isokallio, Timo Sipilä, Elina Kilpelainen, Aarno Palotie, Samuli Ripatti, Priit Palta
Group: FIMM HumGen Sequencing Informatics

Proper citation: Kalle Pärn, Javier Nunez Fontarnau, Marita A. Isokallio, Timo Sipilä, Elina Kilpelainen, Aarno Palotie, Samuli Ripatti, Priit Palta 2018. Genotyping chip data lift-over to reference genome build GRCh38/hg38. protocols.io https://dx.doi.org/10.17504/protocols.io.nqtddwn Copy   

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Authors: Jiri Hulcr, Andrew J. Johnson, Demian F Gomez
Group: Protocols Bark Beetle Mycobiome
Summary: This protocol describes how to rear bark and ambrosia beetles in naturally infested wood. This protocol is part of the Bark Beetle Mycobiome (BBM) Research Coordination Network. For more information on the BBM international network: Hulcr J, Barnes I, De Beer ZW, Duong TA, Gazis R, Johnson AJ, Jusino MA, Kasson MT, Li Y, Lynch S, Mayers C, Musvuugwa T, Roets F, Seltmann KC, Six D, Vanderpool D, & Villari C. 2020. Bark beetle mycobiome: collaboratively defined research priorities on a widespread insect-fungus symbiosis. Symbiosis 81: 101–113 https://doi.org/10.1007/s13199-020-00686-9.

Proper citation: Jiri Hulcr, Andrew J. Johnson, Demian F Gomez 2020. Rearing Bark and Ambrosia Beetles from Naturally Infested Wood. protocols.io https://dx.doi.org/10.17504/protocols.io.bnuhmet6 Copy   

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Authors: SADAM DV SATYANARAYANA
Summary: This is a new protocol for isolation of DNA from from forest soil samples 

Proper citation: SADAM DV SATYANARAYANA 2018. Protocol for Isolation of DNA from forest soil samples. protocols.io https://dx.doi.org/10.17504/protocols.io.s2jegcn Copy   

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Authors: Steven Burgess
Group: Ag SynBio Lab UIUC
Summary: SDS-PAGE gel electrophoresis protocol for analyzing samples from plant leaf tissue via immunofluorescence. In this protocol no Coomassie blue is added to samples, the reason is that this interferes with the fluorescent signal during immunoblot. Instead, samples have already been prepared in Laemmli buffer (minus coomassie, protein extraction procedure), the leading edge of samples can be visualized due to the presence of chlorophyll. Note - When using 15 well, 0.75 mm comb, try to limit the volume loaded to 10 μL to minimize the risk of spillover of protein between wells. - Ensure to wipe the tip on the rim of the sample tube to remove the sample stuck to theoutside of the tip. Literature: http://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_6040.pdfhttps://www.bio-rad.com/webroot/web/pdf/lsr/literature/10026447.pdf

Proper citation: Steven Burgess 2020. SDS-PAGE gel electrophoresis. protocols.io https://dx.doi.org/10.17504/protocols.io.bqiemube Copy   

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Authors: Kelsey Miller
Group: BioLegend

Proper citation: Kelsey Miller 2016. Alpha-Synuclein ELISA Kit Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.e34bgqw Copy   

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Authors: Curtis Huttenhower
Group: VERVE Net, Huttenhower Lab
Summary: In this protocol we show how to perform the taxonomic biomarker discovery operation using LEfSe.

Proper citation: Curtis Huttenhower 2016. Taxonomic biomarker discovery with LEfSe. protocols.io https://dx.doi.org/10.17504/protocols.io.d9699d Copy   

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Authors: Daniel Stukenberg
Summary: This protocol provides a workflow for platereader measuremtns with V. natriegens.

Proper citation: Daniel Stukenberg 2018. Platereader workflow with V. natriegens. protocols.io https://dx.doi.org/10.17504/protocols.io.uy9exz6 Copy   

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Authors: New England Biolabs
Group: New England Biolabs (NEB)
Summary: The NEBNext Ultra II FS DNA Library Prep Kit for Illumina contains the enzymes and buffers required to convert a broad range of input amounts of DNA into high quality libraries for next-generation sequencing on the Illumina platform. The fast, user-friendly workflow also has minimal hands-on time.Note: The Ultra II FS Kit is not compatible with bisulfite conversion workflows.

Proper citation: New England Biolabs 2021. E7805 NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina® Protocol for Large Fragment Sizes (> 550 bp) (Chapter 3). protocols.io https://dx.doi.org/10.17504/protocols.io.n2idgce Copy   

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Authors: Sam Li
Group: BioLegend

Proper citation: Sam Li 2019. Cell Surface Flow Cytometry Staining of Whole Blood. protocols.io https://dx.doi.org/10.17504/protocols.io.babbiain Copy   

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