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Authors: Roey Angel, Eva Petrova, Ana Lara-Rodriguez
Group: SoWa RI Anaerobic and Molecular Microbiology (public)
Summary: The following protocol is intended for the quantification of RNA using Quant-iT™ RiboGreen™ RNA Assay Kit (ThermoFisher). This protocol is a simplified and condensed version of the full protocol from the manufacturer.The procedure described here is for 96 reactions. If samples are run in duplicates, then this should allow quantifying 40 samples.

Proper citation: Roey Angel, Eva Petrova, Ana Lara-Rodriguez 2020. Quant-iT™ RiboGreen™ RNA Quantification. protocols.io https://dx.doi.org/10.17504/protocols.io.bfbxjipn Copy   

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Authors: Ken Christensen

Proper citation: Ken Christensen 2020. Bacterial Transformation - Mix & Go Competent Cells - CHEM 584 . protocols.io https://dx.doi.org/10.17504/protocols.io.bj2tkqen Copy   

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Authors: 181830691 , FDF

Proper citation: 181830691 , FDF 2020. A Brief Look of Univariate Analysis. protocols.io https:// Copy   

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Authors: Jacob Beal, Traci Haddock-Angelli, Markus Gershater, Vishal Sanchania, Russell Buckley-Taylor, Geoff Baldwin, Natalie Farny, Richard Tennant, Paul Rutten
Group: iGEM Measurement
Summary: You will prepare a dilution series of ​monodisperse silica microspheres and measure the ​Abs​600 in your plate reader. The size and optical characteristics of these microspheres are similar to cells, and there is a known amount of particles per volume. This measurement will allow you to construct a standard curve of particle concentration which can be used to convert 600 nm absorbance measurements into an estimated equivalent number of cells.

Proper citation: Jacob Beal, Traci Haddock-Angelli, Markus Gershater, Vishal Sanchania, Russell Buckley-Taylor, Geoff Baldwin, Natalie Farny, Richard Tennant, Paul Rutten 2019. Calibration Protocol - Particle Standard Curve with Microspheres. protocols.io https://dx.doi.org/10.17504/protocols.io.5n5g5g6 Copy   

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Authors: Anna Behle, Anika Wiegard
Group: Axmann Lab
Summary: Protocol for semi-dry Western Blot

Proper citation: Anna Behle, Anika Wiegard 2019. Western Blot (semi-dry). protocols.io https://dx.doi.org/10.17504/protocols.io.8fdhti6 Copy   

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Authors: Lauren Segers, Kendall Morris, Donald Bolser
Group: SPARC

Proper citation: Lauren Segers, Kendall Morris, Donald Bolser 2019. Morris USF Lab protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.58vg9w6 Copy   

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Authors: Addgene The Nonprofit Plasmid Repository
Summary: This protocol goes through AAV titration by qPCR using SYBR Green Technology. To see the full abstract and additional resources, visit the Addgene protocol page.Sample DataReferencesAurnhammer C, Haase M, Muether N, Hausl M, Rauschhuber C, Huber I, Nitschko H, Busch U, Sing A, Ehrhardt A, Baiker A. Universal real-time PCR for the detection and quantification of adeno-associated virus serotype 2-derived inverted terminal repeat sequences. Hum Gene Ther Methods. 2012 Feb;23(1):18-28.PMID: 22428977

Proper citation: Addgene The Nonprofit Plasmid Repository 2019. AAV Titration by qPCR Using SYBR Green Technology. protocols.io https://dx.doi.org/10.17504/protocols.io.47kgzkw Copy   

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Authors: Javier Antonio Benavides-Montaño, Javier Antonio Benavides

Proper citation: Javier Antonio Benavides-Montaño, Javier Antonio Benavides 2020. Croprological flotation techniques Tibor-Kassai, 1998. protocols.io https://dx.doi.org/10.17504/protocols.io.bipkkdkw Copy   

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Authors: Steven Wilhelm, Gary Lecleir
Group: The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs)

Proper citation: Steven Wilhelm, Gary Lecleir 2019. Emergency Contacts. protocols.io https://dx.doi.org/10.17504/protocols.io.6c6haze Copy   

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Authors: Alina Avanesyan, Timothy K. Maugel [Laboratory for Biological Ultrastructure, William O. Lamp [Department of Entomology
Summary: In this study, we focused on assessing changes in morphology of (a) the lanternfly mouthparts (stylets and labium), and (b) the lanternfly tarsal tips (arolia and tarsal claws) at each developmental stage

Proper citation: Alina Avanesyan, Timothy K. Maugel [Laboratory for Biological Ultrastructure, William O. Lamp [Department of Entomology 2019. Protocol for dissection and tissue preparation of the spotted lanternfly, Lycorma delicatula (Hemiptera: Fulgoridae) for morphometric analysis and morphological analysis using scanning electron microscopy. protocols.io https://dx.doi.org/10.17504/protocols.io.8tthwnn Copy   

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Authors: Aljoscha Benjamin Hwang, Stefan Boes, Thomas Nyffeler, Guido Schuepfer
Summary: Introduction: As the population ages, Alzheimer's disease and other subtypes of dementia are becoming increasingly prevalent. However, in recent years, diagnosis has often been delayed or not made at all. Thus, improving the rate of diagnosis has become an integral part of national dementia strategies. Although screening for dementia remains controversial, the case is strong for screening for dementia and other forms of cognitive impairment in hospital inpatients. For this reason, the objective of this systematic review was to provide clinicians, who wish to implement screening, an up-to-date choice of cognitive tests with the most extensive evidence base for the use in elective hospital inpatients. Methods: For this systematic review, PubMed, PsycINFO and Cochrane Library were searched by using a multi-concept search strategy. The databases were accessed on April 10, 2019. All cross-sectional studies that utilized brief, multi-domain cognitive tests as index test and a reference standard diagnosis of dementia or mild cognitive impairment as comparator were included. Only studies conducted in the hospital setting, sampling from unselected, elective inpatients older than 65 were considered. Discussion: This is only the study protocol. Results and discussion are pending and will be published after completion of this study.

Proper citation: Aljoscha Benjamin Hwang, Stefan Boes, Thomas Nyffeler, Guido Schuepfer 2019. Validity of screening instruments for the detection of dementia and mild cognitive impairment in hospital inpatients: A systematic review of diagnostic accuracy studies - Study protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.z8zf9x6 Copy   

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Authors: Marie Zikanova
Summary: The purinosome has been observed in a broad spectrum of cells, but some studies claim that it is an artefact of the constructs used for visualization or stress granules resulting from the exposure of cells to nutrient-reduced growth media. Both may be true depending on the method of observation. To clarify this point, we combined two previously used methods, transfection and immunofluorescence, to detect purinosomes in purinosome-free cells deficient in particular DNPS steps (CR-DNPS cells) and in cells deficient in the salvage pathway, which resulted in construction of the purinosome regardless of purine level (CR-HGPRT cells).To restore or disrupt purinosome formation, we transiently transfected CR-DNPS and CR-HGPRT cells with vectors encoding BFP-labelled wild-type (wt) proteins and observed the normalization of purinosome formation. The CR-DNPS cell line transfected with a DNA plasmid encoding an enzyme with zero activity served as a negative control for purinosome formation. 

Proper citation: Marie Zikanova 2018. Study of purinosome assembly in cell-based model systems with de novo purine synthesis and salvage pathway deficiencies. protocols.io https://dx.doi.org/10.17504/protocols.io.qxfdxjn Copy   

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Authors: Benjamin Tully
Group: VERVE Net, ECOGEO
Summary: This protocol details the use of various unix commands commonly used in bioinformatics.

Proper citation: Benjamin Tully 2016. Unix and Bioinformatics. protocols.io https://dx.doi.org/10.17504/protocols.io.eptbdnn Copy   

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Authors: Brent A. Biddy, Wenjun Kong, Kenji Kamimoto, Chuner Guo, Sarah Waye, Tao Sun, Samantha Morris
Group: Morris Lab
Summary: Single-cell technologies are offering unprecedented insight into complex biology, revealing the behavior of rare cell populations that are typically masked in bulk population analyses. One current limitation of single-cell approaches is that lineage relationships are lost as a result of cell processing, restricting interpretations of the data collected. Elegant computational approaches have been developed in an effort to infer these missing observations, but it remains a challenge to reconstruct true reprogramming trajectories using these tools. Although sophisticated lineage tracing solutions to connect cell history with fate are emerging, these protocols are either not compatible with high-throughput scRNA-seq, or require genome editing strategies that are not readily deployed in some systems. Here, our protocol describes a single-cell resolution clonal tracking approach, ‘CellTagging’, based on combinatorial cell indexing, permitting the parallel capture of lineage information and cell identity. CellTagging integrates with high-throughput single-cell RNA-sequencing, where iterative rounds of cell labeling enable the construction of multi-level lineage trees. This straightforward lentiviral-labeling approach can be applied to an array of cell biological applications to simultaneously profile lineage and identity, at single-cell resolution.

Proper citation: Brent A. Biddy, Wenjun Kong, Kenji Kamimoto, Chuner Guo, Sarah Waye, Tao Sun, Samantha Morris 2018. Single-cell mapping of lineage and identity via CellTagging. protocols.io https://dx.doi.org/10.17504/protocols.io.wfefbje Copy   

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Authors: Joao Vitor Molino
Summary: This protocols describe the steps required for the motility quantification in Chlamydomonas reinhardtii.

Proper citation: Joao Vitor Molino 2021. Chlamydomonas reinhardtii cell motility quantification. protocols.io https://dx.doi.org/10.17504/protocols.io.bsw5nfg6 Copy   

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Authors: Edi Santosa
Summary: The corms and leaves of elephant foot yams (Amorphophallus paeoniifolius (Dennst.) Nicolson) are important foods in the local diet in many Asian regions. The crop has high productivity and wide agroecological adaptation and exhibits suitability for the agroforestry system. Although the plant is assumed to reproduce via panmixia, a comprehensive study on the genetic background across regions to enhance wider consumer palatability is still lacking. Here, ten informative microsatellites were analyzed in 29 populations across regions in India, Indonesia and Thailand to understand the genetic diversity, population structure and distribution to improve breeding and conservation programs. The genetic diversity was high among and within regions. Some populations exhibited excess heterozygosity and bottlenecking. Pairwise FST indicated very high genetic differentiation across regions (FST = 0.274), and the Asian population was unlikely to be panmictic. Phylogenetic tree construction grouped the populations according to country of origin with the exception of the Medan population from Indonesia. The current gene flow was apparent within the regions but was restricted among the regions. The present study revealed that Indonesia and Thailand populations could be alternative centers of the gene pool, together with India. Consequently, regional action should be incorporated in genetic conservation and breeding efforts to develop new varieties with global acceptance.

Proper citation: Edi Santosa 2017. DNA preparation of Amorphophallus paeoniifolius for SSR evaluation. protocols.io https://dx.doi.org/10.17504/protocols.io.jjdcki6 Copy   

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Authors: Isabelle Vea, Andrés G. de la Filia, Stevie Bain
Group: Mealybug Team
Summary: Protocol to extract DNA from female mealybug (P.citri) for genomic sequencing.This protocol was established by Stevie Bain and Andres Garcia de la Filia in the Ross lab (University of Edinburgh, IEB), which includes a combination of two kits. I modified it slightly based on Dom Laetsch protocol version 1.1 (Blaxter lab, University of Edinburgh, IEB)Main modifications:13,000 rpm centrifuge at 4deg all the time instead of 13000 rpm at room temperatureAmounts of reagents kept from Andres's protocol but use Cell lysis buffer and Protein precitpitation solution from Qiagen (Dom's)Overnight incubation at 56 is in a heated chambre with a rocking platform to allow gentle mixing All vortexing steps were changed to mixing by inversion and rotation as in Dom's protocol.Beware:RNase A concentration should be 100mg/mL the first time and if there is still RNA left, do a second step of RNase A at 20ug/mL as final concentration

Proper citation: Isabelle Vea, Andrés G. de la Filia, Stevie Bain 2021. DNA extraction protocol for genome sequencing v2.0. protocols.io https://dx.doi.org/10.17504/protocols.io.pvgdn3w Copy   

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Authors: New England Biolabs
Group: New England Biolabs (NEB)
Summary: Radioactive Labeling with T4 Polynucleotide Kinase

Proper citation: New England Biolabs 2015. Radioactive Labeling with T4 PNK (M0201S). protocols.io https://dx.doi.org/10.17504/protocols.io.cp7vrm Copy   

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Authors: Tjusls China

Proper citation: Tjusls China 2019. 13 Gel filtration. protocols.io https://dx.doi.org/10.17504/protocols.io.5fag3ie Copy   

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Authors: Bonnie Hurwitz
Group: Biosys-analytics
Summary: This describes the steps involved in logging into the UA High-Performance Computing (HPC) web-portal for the UA Biosystems Analytics class. The instructors should have already given you access to the HPC, if not contact us.

Proper citation: Bonnie Hurwitz 2019. Login to UA HPC web-portal. protocols.io https://dx.doi.org/10.17504/protocols.io.wv7fe9n Copy   

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