Addgene (tool)

RRID:SCR_002037

Non-profit plasmid repository dedicated to helping scientists around the world share high-quality plasmids. Facilitates archiving and distributing DNA-based research reagents and associated data to scientists worldwide. 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.

EuroBioBank (tool)

RRID:SCR_003599

The EuroBioBank network is the first operating network of biobanks in Europe providing human DNA, cell and tissue samples as a service to the scientific community conducting research on rare diseases. It is the only network dedicated to rare disease research in Europe. By creating a critical mass of collections and facilitating the exchange of biological material, the EuroBioBank network helps accelerate research on these diseases. * Over 440,000 samples are available across the network and can be requested via the online catalogue. Approximately 13,000 samples are collected each year and 7,000 samples distributed in Europe and beyond. The biological samples are obtained from patients affected by rare diseases, including rare neuromuscular disorders. * The EuroBioBank Network is currently composed of 18 members, of which 16 biobanks from 8 European countries (France, Germany, Hungary, Italy, Malta, Slovenia, Spain and the United-Kingdom) as well as Israel and Canada. Goals * Identify and localize biological material of interest to researchers * Build a critical mass of rare disease sample collections * Distribute high quality material and associated data to users * Promote best-practice guidelines for biobanking activities * Disseminate knowledge and know-how to the scientific community through training courses * Enhance collaboration with the medical and scientific community in the field of rare diseases EuroBioBank acts as a clearing house or virtual bank, with all samples listed in the central online catalogue remaining in the possession of the member biobanks, where they are located and can be requested. The network was established by patients and researchers to facilitate research on rare diseases by guaranteeing quick and easy access to samples via an online catalogue. The catalogue lists the samples available throughout the EuroBioBank network by type of biomaterial. A search engine enables a search by disease or by bank contact. Once a sample has been located in the catalogue, it can be requested by email. Therefore, the biological material is exchanged faster. If a sample does not appear in the EuroBioBank catalogue, help can be provided to further search it at: eurobiobank (at) telethon.it Funding and Collaboration Originally funded by the EC between 2003-2006, the EuroBioBank received further EC support between 2007-2011 within the European Network of Excellence TREAT-NMD (FP6), which covered the cost sustained by Eurordis for the network coordination and website hosting. Each biobank of the network is financed by its own Institution or charitable organization. As of January 2012, the Fondazione Telethon provides the administrative support for coordinating the EuroBioBank network and hosting the website.

NICHD Brain and Tissue Bank for Developmental Disorders (tool)

RRID:SCR_003601

The objective of this human tissue repository is to systematically collect, store, and distribute brain and other tissues for research dedicated to the improved understanding, care, and treatment of individuals with developmental disorders. Brain sections are primarily frozen in isopentane / dry ice. Tissues are stored in 10% formalin and frozen at -85 degrees C. Of special interest are individuals with Down syndrome and other chromosomal defects, mitochondrial encephalopathies, phenylketonuria and other aminoacidopathies, maternal PKU, Rett syndrome, leukodystrophies, lysosomal disorders, dyslexia, autism, and other neurodevelopmental disorders. The brain and tissue banks have extensive experience in arranging for the rapid retrieval of tissue upon the death of individuals who die while at home, in hospitals or hospice care. As a special service, the brain and tissue banks are able to assist researchers who are working with patients who intend to donate tissues at the time of their death. Immediately after retrieval of the tissue, the brain and tissue banks will forward needed tissue to the referring investigators and ensure proper storage and cataloging of any additional tissues as part of the brain and tissue banks. The recipient of tissue and the brain and tissue banks are required to sign a Tissue Transfer Agreement before any tissues are transferred.

GeneTools (tool)

RRID:SCR_005663

Web-service providing access to database that brings together information from broad range of resources. Web application for functional annotation and statistical hypothesis testing. Provides tools for analysis of genomic and microarray data. Collection of tools include Bibliographic Information,Databases,Gene Annotation,Gene Regulation, Microarray,Proteins,Sequence Manipulation - Nucleic Acids,Sequence Manipulation - Protein, Systems Biology.

Biological General Repository for Interaction Datasets (BioGRID) (tool)

RRID:SCR_007393

Curated protein-protein and genetic interaction repository of raw protein and genetic interactions from major model organism species, with data compiled through comprehensive curation efforts.

Allen Human Brain Atlas: BrainSpan (Atlas of the Developing Brain) (tool)

RRID:SCR_008083

Atlas of developing human brain for studying transcriptional mechanisms involved in human brain development. Consists of RNA sequencing and exon microarray data profiling up to sixteen cortical and subcortical structures across full course of human brain development, high resolution neuroanatomical transcriptional profiles of about 300 distinct structures spanning entire brain for four midgestional prenatal specimens, in situ hybridization image data covering selected genes and brain regions in developing and adult human brain, reference atlas in full color with high resolution anatomic reference atlases of prenatal (two stages) and adult human brain along with supporting histology, magnetic resonance imaging (MRI) and diffusion weighted imaging (DWI) data.

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.

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.

ImageScope (tool)

RRID:SCR_014311

Slide image modification software that allows the user to adjust the magnification, compare slides, pan and zoom, annotate specific areas, and perform image analysis of digital slides. Users can create macros and algorithms to automate analysis and create plots, respectively.

GRatio for ImageJ (tool)

RRID:SCR_015580

ImageJ plugin that performs semiautomated analysis of randomly selected sets of nervous system fibers.

Microsoft Excel (tool)

RRID:SCR_016137

Software application with data analysis tools and spreadsheet templates to track and visualize data. It is used to manage and process data.

Knockout Mouse Project Repository (tool)

RRID:SCR_007318

Repository of mouse vectors, ES cells, mice, embryos, and sperm generated by NIH KOMP Mutagenesis Project. In addition, KOMP Repository offers services in support of KOMP products, including ES cell microinjection, vector cloning, post-insertional modification of cloned ES cells, cryopreservation, assisted reproduction techniques (IVF, ICSI) and mouse breeding, pathology services, phenotyping services, etc. KOMP Repository is final component of more than $50 million trans-NIH initiative to increase availability of genetically altered mice and related materials. The University of California, Davis (UC Davis) and Children''s Hospital Oakland Research Institute (CHORI) in Oakland, Calif., are collaborating to preserve, protect, and make available about 8,500 types of knockout mice and related products available to research community. Products are generated by two KOMP mutagenesis teams (CSD consortium and Regeneron Inc). All KOMP products generated by CSD consortium and Regeneron are available through KOMP Repository. Notice as of December 19, 2019: Materials from KOMP Repository have been deposited into MMRRC, including all mouse models and mouse embryonic stem cell lines. Eventually www.komp.org will be sunsetting, and IMSR will remove KOMP Repository listings, since they were double listed in MMRRC. MMRRC will contain the most accurate and up to date resource models.

pCXLE-hOCT3/4-shp53-F (tool)

RRID:Addgene_27077

pCXLE-hSK (tool)

RRID:Addgene_27078

pCXLE-hUL (tool)

RRID:Addgene_27080

pCXLE-EGFP (tool)

RRID:Addgene_27082

Alexa Fluor® 594 AffiniPure Donkey Anti-Rabbit IgG (H+L) (antibody)

RRID:AB_2340621

This polyclonal targets IgG (H+L)

Anti-GFP (antibody)

RRID:AB_390913

This monoclonal targets GFP

GFAP, rabbit polyclonal, Cat# RPCA-GFAP (antibody)

RRID:AB_2572310

This polyclonal targets GFAP

Biotin-SP-AffiniPure F(ab')2 Fragment Goat Anti-Mouse IgG (H+L) (min X Hu,Bov,Hrs,Rb,Sw Sr Prot) (antibody)

RRID:AB_2338585

This unknown targets Mouse IgG (H+L)

Biotin-SP-conjugated AffiniPure Anti-Sheep IgG (H+L) (antibody)

RRID:AB_2340715

This polyclonal targets

Alexa Fluor 594-AffiniPure Donkey Anti-Sheep IgG (H+L) (antibody)

RRID:AB_2340747

This unknown targets Sheep IgG (H+L)

Mouse Anti-Human SATB family member 2 (SATB2) Monoclonal Antibody, Unconjugated, Clone SATBA4B10 (antibody)

RRID:AB_1029576

This monoclonal targets Human SATB family member 2 (SATB2)

Anti-Microtubule-Associated Protein 2 (MAP2) (antibody)

RRID:AB_11213363

This polyclonal targets Microtubule-Associated Protein 2 (MAP2)

Alexa Fluor 594-AffiniPure Donkey Anti-Goat IgG (H+L) (antibody)

RRID:AB_2340432

This unknown targets Goat IgG (H+L)

DNAJC30 Antibody (antibody)

RRID:AB_11040278

This unknown targets DNAJC30

Monoclonal ANTI-FLAG® M2 antibody produced in mouse (antibody)

RRID:AB_262044

This monoclonal targets FLAG

2′,3′-cyclic-nucleotide 3′-phosphodiesterase CNP, chicken polyclonal, Cat# CPCA-CNP (antibody)

RRID:AB_2572249

This polyclonal targets CNP

Mouse Anti-Neurofilament 70 kD Monoclonal antibody, Unconjugated, Clone da2 (antibody)

RRID:AB_94285

This monoclonal targets Neurofilament 70 kD

Alexa Fluor 647-AffiniPure Donkey Anti-Goat IgG (H+L) (antibody)

RRID:AB_2340436

This unknown targets Goat IgG (H+L)

Ctip2 antibody [25B6] - ChIP Grade (antibody)

RRID:AB_2064130

This monoclonal targets Ctip2

Aldehyde dehydrogenase H1L1 ALDH1L1, mouse monoclonal, Cat# MCA-4A12 (antibody)

RRID:AB_2572221

This monoclonal targets ALDH1L1

ATP synthase Immunocapture antibody [12F4AD8AF8] (antibody)

RRID:AB_10866627

This monoclonal targets ATP synthase Immunocapture antibody [12F4AD8AF8]

Goat Anti-Human Gad1 / gad67 Polyclonal antibody, Unconjugated (antibody)

RRID:AB_2107724

This polyclonal targets Human GAD1 / GAD67

Peroxidase-AffiniPure Goat Anti-Mouse IgG (H + L) (antibody)

RRID:AB_10015289

This polyclonal targets IgG (H + L)

Biotin-SP-AffiniPure Donkey Anti-Goat IgG (H+L) (antibody)

RRID:AB_2340396

This unknown targets Goat IgG (H+L)

Stemgent?????????????? Purified Rabbit anti-Mouse/Human Nanog Antibody (antibody)

RRID:AB_2298294

This monoclonal targets NANOG

CDP (M-222) (antibody)

RRID:AB_2261231

This polyclonal targets CUX1

ChromPure Mouse IgG, whole molecule (antibody)

RRID:AB_2337188

This unknown targets Mouse IgG, whole molecule

Anti-Glial Fibrillary Acidic Protein antibody produced in rabbit (antibody)

RRID:AB_477035

This polyclonal targets Glial Fibrillary Acidic Protein

TBR-1 (M-200) (antibody)

RRID:AB_2287060

This polyclonal targets TBR-1 (M-200)

Glyceraldehyde 3-Phosphate Dehydrogenase GAPDH, mouse monoclonal, Cat# MCA-1D4 (antibody)

RRID:AB_2107599

This monoclonal targets GAPDH

DNAJC30 Antibody (antibody)

RRID:AB_2095222

This unknown targets DNAJC30

WBSCR16 Polyclonal Antibody (antibody)

RRID:AB_2634109

This unknown targets WBSCR16

TWEAKR Antibody (antibody)

RRID:AB_1085912

This monoclonal targets Fn14 / TWEAK Receptor

Peroxidase-AffiniPure Goat Anti-Rabbit IgG (H+L) (antibody)

RRID:AB_2313567

This polyclonal targets IgG (H+L)

Anti-Human TRA-1-60 Affinity Purified Monoclonal Antibody, Unconjugated (antibody)

RRID:AB_1512170

This monoclonal targets Human TRA-1-60

Biotin-SP-AffiniPure Donkey Anti-Mouse IgG (H+L) (min X Bov,Ck,Gt,GP,Hms,Hrs,Hu,Rb,Shp Sr Prot) (antibody)

RRID:AB_2307438

This polyclonal targets Mouse

Alexa Fluor 488-AffiniPure Donkey Anti-Mouse IgG (H+L) (min X Bov,Ck,Gt,GP,Sy Hms,Hrs,Hu,Rb,Shp Sr Prot) (antibody)

RRID:AB_2340846

This unknown targets Mouse IgG (H+L)

DAVID (software resource)

RRID:SCR_001881

Bioinformatics resource system including web server and web service for functional annotation and enrichment analyses of gene lists. Consists of comprehensive knowledgebase and set of functional analysis tools. Includes gene centered database integrating heterogeneous gene annotation resources to facilitate high throughput gene functional analysis.

Axograph (software resource)

RRID:SCR_014284

A software tool which provides a means to acquire and analyze time-series data, as well as a direct route to publication quality graphics. It provides a variety of graph styles and automated, extended, and/or customizable analyses.

Jalview (software resource)

RRID:SCR_006459

A free program for multiple sequence alignment editing, visualisation and analysis that is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation. Jalview has built in DNA, RNA and protein sequence and structure visualisation and analysis capabilities. It uses Jmol to view 3D structures, and VARNA to display RNA secondary structure.

HEK293T (cell line)

RRID:CVCL_0063

Cell line HEK293T is a Transformed cell line with a species of origin Homo sapiens (Human)

Clustal Omega (software resource)

RRID:SCR_001591

Software package as multiple sequence alignment tool that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. Accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/Clustal, GCG/MSF, RSF.

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.

ReNcell CX (cell line)

RRID:CVCL_E922

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

Cytoscape (software resource)

RRID:SCR_003032

Software platform for complex network analysis and visualization. Used for visualization of molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.

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.

REViGO (service resource)

RRID:SCR_005825

Web server that summarizes lists of Gene Ontology terms by removing redundant terms and visualizing the remaining ones in scatterplots, interactive graphs, treemaps, or tag clouds. Platform: Online tool

Neurolucida (software resource)

RRID:SCR_001775

Neurolucida is advanced scientific software for brain mapping, neuron reconstruction, anatomical mapping, and morphometry. Since its debut more than 20 years ago, Neurolucida has continued to evolve and has become the worldwide gold-standard for neuron reconstruction and 3D mapping. Neurolucida has the flexibility to handle data in many formats: using live images from digital or video cameras; stored image sets from confocal microscopes, electron microscopes, and scanning tomographic sources, or through the microscope oculars using the patented LucividTM. Neurolucida controls a motorized XYZ stage for integrated navigation through tissue sections, allowing for sophisticated analysis from many fields-of-view. Neurolucidas Serial Section Manager integrates unlimited sections into a single data file, maintaining each section in aligned 3D space for full quantitative analysis. Neurolucidas neuron tracing capabilities include 3D measurement and reconstruction of branching processes. Neurolucida also features sophisticated tools for mapping delineate and map anatomical regions for detailed morphometric analyses. Neurolucida uses advanced computer-controlled microscopy techniques to obtain accurate results and speed your work. Plug-in modules are available for confocal and MRI analysis, 3D solid modeling, and virtual slide creation. The user-friendly interface gives you rapid results, allowing you to acquire data and capture the full 3D extent of neurons and brain regions. You can reconstruct neurons or create 3D serial reconstructions directly from slides or acquired images, and Neurolucida offers full microscope control for brightfield, fluorescent, and confocal microscopes. Its added compatibility with 64-bit Microsoft Vista enables reconstructions with even larger images, image stacks, and virtual slides. Adding the Solid Modeling Module allows you to rotate and view your reconstructions in real time. Neurolucida is available in two separate versions Standard and Workstation. The Standard version enables control of microscope hardware, whereas the Workstation version is used for offline analysis away from the microscope. Neurolucida provides quantitative analysis with results presented in graphical or spreadsheet format exportable to Microsoft Excel. Overall, features include: - Tracing Neurons - Anatomical Mapping - Image Processing and Analysis Features - Editing - Morphometric Analysis - Hardware Integration - Cell Analysis - Visualization Features Sponsors: Neurolucida is supported by MBF Bioscience.

ImageJ (software resource)

RRID:SCR_003070

Open source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets.