Nuclear Data Project - Overview

The Nuclear Data Project (NDP) is a dedicated scientific resource for the systematic archiving and analysis of quantitative data pertaining to nuclear architecture. The nucleus is a non-randomly organized organelle, and the spatial distribution, morphology, and dynamic behavior of its sub-nuclear bodies are critical determinants of genomic function. This repository addresses the critical need for a centralized, standardized database of nuclear parameters to facilitate advanced analysis and modeling.

The primary objective of this project is to provide a comprehensive, searchable library of high-resolution datasets, enabling the rigorous investigation of structure-function relationships within the nucleus across various organisms, cell types, and physiological or pathological conditions.

Core Scientific Objectives

  1. Data Curation and Standardization: To acquire, validate, and archive high-quality datasets featuring precise morphometric and spatial data on nuclear bodies (e.g., nucleoli, nuclear speckles, PML bodies, Cajal bodies). All entries are annotated with detailed experimental metadata.
  2. Pattern Identification and Analysis: To serve as a foundational resource for the identification of conserved principles and quantitative patterns governing nuclear organization and the interrelationships between nuclear bodies.
  3. Predictive Model Development: To enable the creation and validation of computational models that predict nuclear architecture based on cellular state, and conversely, to infer cellular conditions from nuclear organization.

Database Access and Utility

The NDP interface allows for complex querying of the database based on multiple orthogonal parameters:

  • Biological Specimen: Organism, cell type, tissue origin, and cell line.
  • Experimental Condition: Cell cycle stage (e.g., G1, S, G2, M), metabolic state, response to stressors (e.g., DNA damage, osmotic shock, transcriptional inhibition), and disease context (e.g., cancer subtype, laminopathy).
  • Nuclear Target: Specific nuclear bodies or structures, with data on protein/composition markers used for identification (e.g., Fibrillarin, SC35, Coilin, SP100).
  • Data Modality: Source microscopy technique (e.g., Confocal, TEM).

Data Specifications

Each dataset within the repository provides downloadable assets in standardized, lossless formats to ensure reproducibility and facilitate computational analysis:

  • Primary Imaging Data: Original, unprocessed image stacks (e.g., .tiff, .czi).
  • Derived Quantitative Data: Coordinate sets (2D/3D), morphometric measurements (volume, sphericity, intensity), and inter-body distance matrices in comma-separated value (.csv) format.
  • Complete Metadata: Adhering to OME standards, including full experimental protocols, acquisition parameters, antibody information (clone, RRID), and contributor affiliation.

Contributing

The scientific community is invited to contribute datasets to enhance the breadth and depth of this resource. Submitted data undergoes a curation process to ensure compliance with project standards for annotation and quality control.

Contact

For inquiries regarding collaboration, data submission, or help, please contact at alexey.nisimov@gmail.com. Please note that the website in its current form is still under development.