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Authors: Li Deng
Group: VERVE Net, Sullivan Lab

Proper citation: Li Deng 2016. SYBR Gold working solutions. protocols.io https://dx.doi.org/10.17504/protocols.io.c7azid Copy   

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Authors: Thuc Nguyen, Emma Garren
Group: CZI Spatial Transcriptomics Protocol Repository
Summary: This protocol describes multiround hybrization of directly-conjugated FISH probes for single molecule RNA detection. Thin tissue sections (10-μm) are placed onto silanized coverslips (24x50) that fit onto an ASI imaging chamber. A SecureSeal chamber is placed around the sections, which act as a reaction chamber and imaging chamber.

Proper citation: Thuc Nguyen, Emma Garren 2019. Single molecule FISH. protocols.io https://dx.doi.org/10.17504/protocols.io.xb2fiqe Copy   

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Authors: Alexandra Ehl, David Frommholz, Nadine Stefanczyk
Summary: Purification Guide for the Isolation of Histidine-tagged Proteins with ChroSpin Columns by DALEX Biotech.ChroSpin-IMAC by DALEX Biotech offers a robust and convenient way to isolate polyhistidine-tagged proteins from bacterial, mammalian, and insect cell cultures.Immobilized metal affinity chromatography (IMAC) is based on the interaction of the imidazole ring of histidine with transition metal ions immobilized on a solid support. Recombinant proteins with a 3 - 10 histidine fusion tag bind to these metal ions while unwanted proteins are removed by washing with excess binding buffer. Elution of the target protein is achieved by the addition of imidazole, EDTA or a low pH. Easy and quick small scale fusion protein purification from various sources.Low metal leaching from column.Tolerates reducing reagents (e.g. DTT up to 10 mM).The proprietary resin does not shrink or swell in aqueous buffers.High pressure stability.pH stability short term 2 - 8, long term 3 - 8.Excellent thermal stability up to 15 minutes at 120 °C in aqueous buffers at neutral pH.Can be dried for long term storage (80 °C for > 2 h).

Proper citation: Alexandra Ehl, David Frommholz, Nadine Stefanczyk 2018. ChroSpin - IMAC. protocols.io https://dx.doi.org/10.17504/protocols.io.tv3en8n Copy   

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Authors: Jessica Riesterer, Erin Stempinski, Claudia Lopez
Group: NCIHTAN
Summary: Tissues, cell monolayers, organoids and xenografts all image differently depending on the sample preparation method utilized. Moreover, the same tissue type from different species may also need different fixation solution and processing methods to have optimal contrast and charge mitigation when the same microscope is used (Borrett & Hughes, 2016; Kizilyaprak, Longo, Daraspe, & Humbel, 2015; Kopek et al., 2017). For example, brain tissue may be processed successfully using a protocol that yields poor images when applied to cancer tissues (unpublished data). Researchers are therefore encouraged to dive into the literature and test new sample preparation protocols for a specific sample-type. Also, and if available, having the ability to evaluate the use of FIB-SEM versus SBF-SEM will help the researcher to design a data collection strategy. The protocols evaluated during development of this workflow included the Dresden protocol (Paridaen, Wilsch-Bräuninger, & Huttner, 2013), Renovo (Mukherjee et al., 2016) and the Hua method (Hua, Laserstein, & Helmstaedter, 2015). We settled on the the Hua method with some modifications as described below, for human cancer biopsies. The final protocol described is sufficient for large format mapping and 3DEM FIB-SEM and SBF-SEM, eliminating the need for multiple samples processed with different protocols. In the case of biopsy tissue, where sample acquisition is limited and precious, flexibility is an important advantage of this workflow.

Proper citation: Jessica Riesterer, Erin Stempinski, Claudia Lopez 2019. Post-Fixation Heavy Metal Staining and Resin Embedding for Electron Microscopy (EM). protocols.io https://dx.doi.org/10.17504/protocols.io.36vgre6 Copy   

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Authors: HANNIGAN GD, GRICE EA, ET AL.
Group: VERVE Net, Club Grice
Summary: This section outlines the analyses we used in our replication cycle section of our report. We first predict how many contigs are potentially of the temperate replication cycle and display this information using a Euler diagram. We then use a relative abundance approach by visualizing the percent of temperate phages present at each site. We end by visualizing the relative abundances of bacteria annotations of the phage contigs. Based on methods from the following publication: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, GRICE EA, ET AL. 2016. Script R11: Replication Cycle. protocols.io https://dx.doi.org/10.17504/protocols.io.ejfbcjn Copy   

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Authors: Thomas Taylor-Clark, Seol-Hee Kim
Group: SPARC
Summary: Mice are euthanized, perfused with fixative and the vagal ganglia extracted. Vagal ganglia are then cyosectioned. Slices are stained for protein expression using immunohistochemistry. Expression of specific proteins and reporter proteins isarevisualized using microscopy.

Proper citation: Thomas Taylor-Clark, Seol-Hee Kim 2019. Dissection and immunohistochemistry of mouse vagal ganglia. protocols.io https://dx.doi.org/10.17504/protocols.io.baumieu6 Copy   

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Authors: Dave Lunt
Group: EvoHull
Summary: Protocol to prepare E. coli supercompetent cells to transform with plasmid/ligation. This protocol is originally derived from Hanahan, D. (1983) J. Mol. Biol. 166:557-580 with some changes. This version works exceptionally well for cloning PCR products where the number of colonies is not expected to be as high as from some ligations. These cells outperform commercially purchased supercompetent cells in my hands.

Proper citation: Dave Lunt 2016. Transformation of supercompetent cells. protocols.io https://dx.doi.org/10.17504/protocols.io.etubenw Copy   

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Authors: Anna Miller

Proper citation: Anna Miller 2020. Rqtl_code. protocols.io https://dx.doi.org/10.17504/protocols.io.bmwtk7en Copy   

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Authors: Lara Ferrero Gomez
Summary: Performing bioassays to assess the larval susceptibility to Temephos

Proper citation: Lara Ferrero Gomez 2020. Protocol Temephos Bioassay. protocols.io https://dx.doi.org/10.17504/protocols.io.bbstinen Copy   

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Authors: Sam Li
Group: BioLegend

Proper citation: Sam Li 2019. Cell Surface Flow Cytometry Staining Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.baa9iah6 Copy   

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Authors: New England Biolabs
Group: New England Biolabs (NEB)
Summary: This is the "quick" version of Monarch® PCR & DNA Cleanup Kit (5 μg) Protocol (NEB #T1030). For the full protocol, please click here.

Proper citation: New England Biolabs 2016. Quick Protocol for Monarch® PCR & DNA Cleanup Kit (5 ?g) (NEB #T1030). protocols.io https://dx.doi.org/10.17504/protocols.io.ejxbcpn Copy   

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Authors: Teesha Luehr
Group: Leonard Foster's Lab
Summary: Detergents are generally not compatible with mass spectrometers, so this is a detergent-free method of cell lysis that is compatible with mass spectrometry. Since this protocol does not have a precipitation step, it saves time and minimizes sample loss as well.

Proper citation: Teesha Luehr 2019. Cell lysis, detergent-free. protocols.io https://dx.doi.org/10.17504/protocols.io.y4ffytn Copy   

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Authors: JCPrice
Group: Chemistry 586 Advanced Biochemical Methods

Proper citation: JCPrice 2020. Bicinchoninic acid Acid Protein Concentration measurement . protocols.io https:// Copy   

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Authors: Mrinalini Watsa, Gideon Erkenswick, Stefan Prost, Aaron Pomerantz
Summary: This collection of protocols are examples of protocols used for education in high throughput sequencing with Oxford Nanopore Technology's MinION sequencer.

Proper citation: Mrinalini Watsa, Gideon Erkenswick, Stefan Prost, Aaron Pomerantz 2019. Field Genomics Protocols. protocols.io https://dx.doi.org/10.17504/protocols.io.9dnh25e Copy   

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Authors: Omar Valencia
Summary: Evaluation of β-diversity partitioning in its spatial species turnover (BJTU) and nestedness (BJNE) components along a latitudinal gradient across.

Proper citation: Omar Valencia 2018. Gamma-diversity partitioning of gobiid fishes (Teleostei: Gobiidae) ensemble along of Eastern Tropical Pacific: biological inventory, latitudinal variation and species turnover. protocols.io https://dx.doi.org/10.17504/protocols.io.sbfeajn Copy   

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Authors: Nus Igem

Proper citation: Nus Igem 2019. Q5 Polymerase PCR Cloning. protocols.io https://dx.doi.org/10.17504/protocols.io.7pqhmmw Copy   

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Authors: Judy Northill, David Warrilow, Ian Mackay
Group: Public Health Virology, Forensic and Scientific Services
Summary: A real-time PCR targeting the DNA-dependent RNA polymerase of Orthopoxviruses.This protocol was designed and developed at this laboratory.

Proper citation: Judy Northill, David Warrilow, Ian Mackay 2018. Orthopoxvirus real-time PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.n43dgyn Copy   

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Authors: Kenneth Schackart, Kattika Kaarj
Group: 481b Laboratory
Summary: This protocol details how to electrospin a PCL:PEG copolymer onto glass cover slip.

Proper citation: Kenneth Schackart, Kattika Kaarj 2019. PCL:PEG Electrospinning. protocols.io https://dx.doi.org/10.17504/protocols.io.yaffsbn Copy   

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Authors: Christopher Bartley
Summary: Transfection of Neuro2a cells with PolyJet

Proper citation: Christopher Bartley 2015. Neuro2a cell DNA plasmid transfection (PolyJet). protocols.io https://dx.doi.org/10.17504/protocols.io.cqmvu5 Copy   

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Authors: Alba Balletbó
Group: iGEM Wageningen 2019
Summary: Fluorescence measurements of Optical Density (OD) and Green fluorescent protein (GFP) in Escherichia coli.

Proper citation: Alba Balletbó 2019. OD and GFP Plate Reader Assay (72 h Measurement). protocols.io https://dx.doi.org/10.17504/protocols.io.8aihsce Copy   

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