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This is a list of tools and resources that we have found mentioned in this publication.


MAFFT (tool)

RRID:SCR_011811

Multiple alignment program for amino acid or nucleotide sequences.

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MP Biomedicals (tool)

RRID:SCR_013308

An Antibody supplier

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MetaMorph Microscopy Automation and Image Analysis Software (tool)

RRID:SCR_002368

Software tool for automated microscope acquisition, device control, and image analysis. Used for integrating dissimilar fluorescent microscope hardware and peripherals into a single custom workstation, while providing all the tools needed to perform analysis of acquired images. Offers user friendly application modules for analysis such as cell signaling, cell counting, and protein expression.

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FastTree (tool)

RRID:SCR_015501

Source code that infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. It uses the Jukes-Cantor or generalized time-reversible (GTR) models of nucleotide evolution and the JTT, WAG, or LG models of amino acid evolution.

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GenScript (tool)

RRID:SCR_002891

Commercial organization which provides life science services and products to researchers. They specialize in gene synthesis, peptide, protein, antibody and preclinical drug development service.

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Adobe Illustrator (tool)

RRID:SCR_010279

Vector graphics software to create digital graphics, illustrations, and typography for several types of media: print, web, interactive, video, and mobile.

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Addgene (tool)

RRID:SCR_002037

A non-profit plasmid repository dedicated to helping scientists around the world share high-quality plasmids.\\n\\nAddgene’s mission is to accelerate research and discovery by improving access to useful research materials and information. We facilitate the sharing of high-quality scientific materials, research reproducibility, and open science by archiving and distributing DNA-based research reagents and associated data to scientists worldwide. Our repository contains over 65,000 plasmids, including special collections on CRISPR, fluorescent proteins, and ready-to-use viral preparations. There is no cost for scientists to deposit plasmids, which saves time and money associated with shipping plasmids themselves. All plasmids are fully sequenced for validation and sequencing data is openly available. We handle the appropriate Material Transfer Agreements (MTA) with institutions, facilitating open exchange and offering intellectual property and liability protection for depositing scientists. Furthermore, we curate free educational resources for the scientific community including a blog, eBooks, video protocols, and detailed molecular biology resources.

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GFP antibody (antibody)

RRID:AB_305564

This polyclonal antibody targets GFP antibody

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PSD95 antibody [6G6-1C9] (antibody)

RRID:AB_303248

This monoclonal antibody targets PSD95 antibody [6G6-1C9]

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MAP2 antibody - Neuronal Marker (antibody)

RRID:AB_2138153

This polyclonal antibody targets MAP2 antibody - Neuronal Marker

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Monoclonal Anti-alpha-Tubulin antibody produced in mouse (antibody)

RRID:AB_477582

This monoclonal antibody targets alpha-Tubulin antibody produced in mouse

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Adobe Photoshop (tool)

RRID:SCR_014199

Software for image processing, analysis, and editing. The software includes features such as touch capabilities, a customizable toolbar, 2D and 3D image merging, and Cloud access and options.

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ImageJ (tool)

RRID:SCR_003070

Software tool as an open source Java-based image processing program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets.

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ZEN Digital Imaging for Light Microscopy (tool)

RRID:SCR_013672

User interface software for Carl Zeiss light microscopy imaging systems. After selecting a fluorophore, ZEN applies the necessary settings to collect and organize data.

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Mascot (tool)

RRID:SCR_014322

A software package and server used to identify and characterize proteins from primary sequence databases using mass spectrometry data. Mascot integrates peptide mass fingerprinting, sequence querying, and MS/MS ion searching in order to search for proteins in databases like SwissProt, NCBInr, EMBL EST divisions, contaminants, and cRAP. If a license is purchased, users may: search data sets that exceed the 1200 spectrum limit of the free version; set up automated, high throughput work; add and edit proteins and quantification methods; and search a preferred collection of sequence databases. The software package works with instruments from AB Sciex, Agilent, Bruker, Jeol, Shimadzu, Thermo Scientific, and Waters.

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