Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor™ 555 (antibody)

RRID:AB_2535849

This polyclonal secondary targets IgG (H+L)

Anti-Mouse IgG (H+L), F(ab′)2 fragment, CF™350 antibody produced in goat (antibody)

RRID:AB_3095587

This polyclonal secondary targets IgG (H+L)

Anti-Mouse IgG (whole molecule)-Peroxidase antibody produced in goat (antibody)

RRID:AB_258167

This polyclonal targets Mouse IgG (whole molecule)-Peroxidase antibody produced in goat

Anti-Rabbit IgG (whole molecule)-Peroxidase antibody produced in goat (antibody)

RRID:AB_258434

This polyclonal targets Rabbit IgG (whole molecule)-Peroxidase antibody produced in goat

Anti-GFP (antibody)

RRID:AB_390913

This monoclonal targets GFP

GFP (B-2) (antibody)

RRID:AB_627695

This monoclonal targets GFP (B-2)

Anti-polyQ specific Antibody, clone MW1 (antibody)

RRID:AB_2920696

This monoclonal targets polyQ

Anti-Ubiquitin Antibody (P4D1) (antibody)

RRID:AB_628423

This monoclonal targets Ubiquitin

p62 (human) polyclonal antibody (antibody)

RRID:AB_2196009

This polyclonal targets p62

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

RRID:AB_477583

This monoclonal targets alpha-Tubulin

Anti-LC3B antibody produced in rabbit (antibody)

RRID:AB_796155

This unknown targets LC3B

MAP LC3beta (G-9) (antibody)

RRID:AB_11150489

This monoclonal targets MAP LC3beta (G-9)

LC3B Antibody (antibody)

RRID:AB_10003146

This polyclonal targets LC3B

VCP antibody [5] (antibody)

RRID:AB_298039

This monoclonal targets VCP antibody [5]

Beta-Actin Antibody (antibody)

RRID:AB_10664137

This monoclonal targets Beta-Actin

Anti-Myc Tag, clone 4A6 (antibody)

RRID:AB_309938

This monoclonal targets Myc Tag

Halo-WIPI2B WT (plasmid)

RRID:Addgene_175025

mCherry-hLC3B-pcDNA3.1 (plasmid)

RRID:Addgene_40827

ZEISS ZEN Microscopy Software (software resource)

RRID:SCR_013672

User interface software for Carl Zeiss light microscopy imaging systems. ZEN is the universal user interface you will see on every imaging system from ZEISS. After selecting fluorophore, ZEN applies the necessary settings to collect and organize data.

Template-O-Matic Toolbox (software resource)

RRID:SCR_003220

Software toolbox for creating customized pediatric templates. It provides reference data based on imaging data from the NIH study of normal brain development. Using the general linear model, they statistically isolate the influence of external variables of interest on brain structure, allowing us to generate high-quality matched templates for any given group of subjects. The toolbox offers two options: # to create pediatric templates (T1) and tissue maps (GM, WM, and CSF) based on the objective 1 NIH data (n = 404), in the age range of 5-18 years, or # to assess a new reference population with regard to your variables of interest. Of note, this approach is generally applicable and in no way restricted to analyzing pediatric imaging data: for example, if you aim at investigating the effects of aging in elderly subjects, the toolbox will also allow you to create more appropriate reference (if your group is large enough to isolate such effects).

Python Programming Language (software resource)

RRID:SCR_008394

Programming language for all operating systems that lets users work more quickly and integrate their systems more effectively. Often compared to Tcl, Perl, Ruby, Scheme or Java. Some of its key distinguishing features include very clear and readable syntax, strong introspection capabilities, intuitive object orientation, natural expression of procedural code, full modularity, exception-based error handling, high level dynamic data types, extensive standard libraries and third party modules for virtually every task, extensions and modules easily written in C, C (or Java for Python, or .NET languages for IronPython), and embeddable within applications as a scripting interface.

Advanced 3D Visualization and Volume Modeling (software resource)

RRID:SCR_007353

Software tool for visualizing, manipulating, and understanding data from tomography, microscopy, MRI and other imaging processes.Used to import and export options, to processes 3D image filtering and DTI based fiber tracking to visualization, volume and surface rendering, author tools for virtual reality navigation, video generation, and more.

IMOD (software resource)

RRID:SCR_003297

A free, cross-platform set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. IMOD 4.1.8 Is Now Available for Linux, Windows, and Mac OS X

MotionCor2 (software resource)

RRID:SCR_016499

Software tool for anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Used to describe the sample motion as a local deformation that varies smoothly throughout the exposure. A program running on Linux.

MATLAB (software resource)

RRID:SCR_001622

Multi paradigm numerical computing environment and fourth generation programming language developed by MathWorks. Allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages, including C, C++, Java, Fortran and Python. Used to explore and visualize ideas and collaborate across disciplines including signal and image processing, communications, control systems, and computational finance.

pSpCas9(BB)-2A-GFP (PX458) (plasmid)

RRID:Addgene_48138

SerialEM (software resource)

RRID:SCR_017293

Software tool for automated EM data acquisition. Used for efficient tilt series acquisition and interface for image capture, display, and storage and for control of some aspects of microscope function.

Huygens Software (software resource)

RRID:SCR_014237

A set of fluorescence microscope image processing packages which perform image restoration, interactive analysis, and volume visualization of 2D and 3D multi channel microscopy images or time series. The restoration is based on different deconvolution algorithms, that permit the recovery of objects from images that are degraded by blurring and noise. Tutorials and documentation are available on the website.

Perseus (software resource)

RRID:SCR_015753

Software that supports biological and biomedical researchers in interpreting protein quantification, interaction and post-translational modification data. Perseus contains a comprehensive portfolio of statistical tools for high-dimensional omics data analysis covering normalization, pattern recognition, time-series analysis, cross-omics comparisons and multiplehypothesis testing.

Leica DM6 B Upright Microscope (instrument resource)

RRID:SCR_024857

Leica DM6 B Upright Microscope includes the Leica DFC7000 T Camera and LAS X Software.

MaxQuant (software resource)

RRID:SCR_014485

A quantitative proteomics software package for analyzing large-scale mass-spectrometric data sets. It is a set of algorithms that include peak detection and scoring of peptides, mass calibration, database searches for protein identification, protein quantification, and provides summary statistics.

GraphPad Prism (software resource)

RRID:SCR_002798

Statistical analysis software that combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization. Designed for biological research applications in pharmacology, physiology, and other biological fields for data analysis, hypothesis testing, and modeling.

Fiji (software resource)

RRID:SCR_002285

Software package as distribution of ImageJ and ImageJ2 together with Java, Java3D and plugins organized into coherent menu structure. Used to assist research in life sciences.

pLAMP1-mCherry (plasmid)

RRID:Addgene_45147

Benchling (web application)

RRID:SCR_013955

An online resource which helps researchers manage and organize labs and experimental results by supplying molecular biology software tools for experimental design and data analysis. Benchling provides tools for functions such as primer design and colony counting as well as CRISPR guide design and automated Gibson and Golden Gate cloning. Users can take notes in line with data, link data across entries, keep files and data in one place, and manage and keep track of team progress. An enterprise version of Benchling is available for scientists working within an organization with additional administrative, compliance, and security protocols.

px330-mcherry (plasmid)

RRID:Addgene_98750

pMRX-IP-GFP-LC3-RFP (plasmid)

RRID:Addgene_84573

Neuro2a-tNhtt-EGFP-150Q (cell line)

RRID:CVCL_D3YT

Cell line Neuro2a-tNhtt-EGFP-150Q is a Cancer cell line with a species of origin Mus musculus (Mouse)

Neuro2a-tNhtt-EGFP-60Q (cell line)

RRID:CVCL_D3YS

Cell line Neuro2a-tNhtt-EGFP-60Q is a Cancer cell line with a species of origin Mus musculus (Mouse)

HEK293 (cell line)

RRID:CVCL_0045

Cell line HEK293 is a Transformed cell line with a species of origin Homo sapiens (Human)