dkNET Webinar: The 4DN Data Portal - Data, Resources and Tools to Help Elucidate Nuclear Organization in Space and Time 05/10/2024

Presenter: Andrew Schroeder, PhD. Project Manager & Senior Data Curator, 4D Nucleome Data Coordination and Integration Center (4DN-DCIC), Park Lab, Department of Biomedical Informatics, Harvard Medical School

Abstract
The Common Fund 4D Nucleome program, currently in its 9th year, is a consortium of researchers that aims to understand the principles behind the three-dimensional organization of the nucleus and how this organization can change over time to affect a variety of cellular processes. The 4DN Data Portal (data.4dnucleome.org) is an expanding resource hosting data generated by the 4DN Network and other reference nucleomics data sets. The portal provides tools for search, exploration, visualization, and download. An overview of the data portal, highlighting available data, how it can be found, visualized and used for analyses will be presented.



The top 3 key questions that the 4DN data portal can answer:

1. Are there significant sites of long-range chromatin contacts near my gene or region of interest?

2. What omics datasets are available for my tissue of interest?

3. Are there imaging datasets available that are relevant to my tissue of interest?

Upcoming webinars schedule: https://dknet.org/about/webinar

1. May 10, 2024

2. Outline
●Brief introduction to the 4D Nucleome
●Finding data of interest in the portal
●Metadata and visualizing data on the portal
●Downloading Data Files
●Standardized bioinformatics pipelines
●Exploring Data

4. Pongubala and Murre, 2021

5. Imaging
B. Bintu lab, UCSD
Sequencing

6. Sequencing
Chromatin Conformation Capture
in situ Hi-C
Dilution Hi-C
DNase Hi-C
Micro-C, TCC
HiChip
PLAC-seq
ChIA-PET/Drop
Capture Hi-C
GAM
SPRITE
MARGI
4C-seq
DAMID-seq, TSA-seq, repli-seq,
CUT&RUN, ChIP-seq, ATAC-seq,
RNA-seq …
Additional Genomics Assays

7. Imaging
B. Bintu lab, UCSD
Multiplexed FISH
MERFISH, MINA,
OligoFISSEQ, ORCA,
seqFISH+,
OligoSTORM
DNA/RNA FISH,
Imunofluorescence,
SPT, OptoDroplet,
Electron Tomography
Additional Imaging Assays

8. LIVE PORTAL DEMO

https://data.4dnucleome.org

9. Useful Links
4DN Data portal - https://data.4dnucleome.org/
4DN Data Collections - https://data.4dnucleome.org/resources/data-collections
FISH Omics Format RTD - https://fish-omics-format.readthedocs.io/en/latest/
HiGlass tutorial video - https://www.youtube.com/watch?v=LEDaOa3NZtM
4DN-DCIC github - https://github.com/4dn-dcic/
Hi-C pipeline repo - https://github.com/4dn-dcic/docker-4dn-hic
4DN JupyterHub - https://data.4dnucleome.org/tools/jupyterhub
Data Portal Publication - https://pubmed.ncbi.nlm.nih.gov/35501320/
4DN Organizational Hub - https://www.4dnucleome.org/

10. Data portal paper in Nature Communications
Data portal
https://data.4dnucleome
.org/publications/ad9b5
72b-fe5e-4d9f-9ba3-7c6
2ff51ce9d/
Pubmed
https://pubmed.ncbi.nlm
.nih.gov/35501320/
Nature Communications
https://www.nature.com/
articles/s41467-022-296
97-4

11. 4DN-DCIC
DBMI
Peter Park
Utku
Ozturk

12. Please reach out to us with questions,
comments or suggestions

[email protected]