Newsletter Archive: 2017

The 4DN Data Release and Use Policy has been approved and released (check it on 4DN web portal)

Outreach and in-reach slides: OH prepared slides for any consortium members to change and use for 4DN outreach and in-reach activities

Outreach slides

In-reach slides

The first education video produced by 4DN has been released on YouTube. 4DN Imaging Workshop: Toward Microscopy Standardization

Thanks to Dr. Grunwald for authorizing OH to make the video.

Welcome to contact OH to submit or recommend 4DN related education and outreach videos.

Release of cell line SOP on 4DN web portal. Click on each cell line to access the SOPs and other information.

2017 4DN Annual Meeting Report.

2017 4DN Annual Meeting survey results. Thanks for your feedback.

Microscope Calibration Project: a new joint project in Imaging Data Standards and Joint Analysis working group

Scientific Webinar Series this Month:

October 27, 2017

Presenter: Adan Horta (Columbia University) - Interchromosomal Interactions as a Source of Neuronal Diversity

Presenter: Horng Ou (Salk Institute) - Visualizing chromatin ultrastructure in interphase and mitotic cells by ChromEMT

2017 4DN Annual Meeting was successfully held in Bethesda on September 17 - 20

Please complete the 2017 4DN Annual Meeting Survey before Oct 12. Your feedbacks are greatly appreciated!

A quick guide to 4DN visualization software: Plot a course through the genome

The 4D Nucleome perspective paper published in Nature: The 4D nucleome project

2017 4DN Annual Meeting is coming on September 17 - 20:

Registration and abstract submission ended on August 15

278 members registered

128 abstracts submitted

4DN Opportunity Pool Initiative announces 2017 Transformative Collaborative Project Awards

The EFMA office will be holding an informational webinar on the EFRI FY2018 solicitation on September 7th, 2017, 1 p.m. Eastern Daylight Time

The topics of the FY18 EFRI solicitation are:

Chromatin and Epigenetic Engineering (CEE)

Continuum, Compliant, and Configurable Soft Robotics Engineering (C3 SoRo)

Registration details for the webinar are available here.

Scientific Webinar Series this Month:

Presenter: Kit S. Lam (University of California Davis) - The use of OBOC combinatorial library method to discover Genetically Encoded Small Illuminants for cellular imaging

Presenter: Suhas Rao (Stanford University) - Tracking the 4D nucleome during cohesin loss and recovery

Reminder: Last 2 weeks for registration of 2017 Annual Meeting

Registration deadline is August 15, 2017. Register here: https://4dn-annual-meetings.fluidreview.com

Abstract and poster submission deadline is also August 15, 2017.

Check more information about abstract submission, poster submission, and hotel booking on the wiki page: https://sites.google.com/a/4dnucleome.org/4d-nucleome-wiki/meetings-and-committees/2017-4d-nucleome-annual-meeting

Invitation: WORKSHOP (EXTRA SESSION FOLLOWING THE 2017 4DN MEETING)

Topic: Integrated Approaches for Spatial and Temporal Mapping of Gene Activity in Cells and Tissues

Time: 1:00 to 5:00 PM, Sept 20, 2017

Location: Conference Room B, Neuroscience Center, 6001 Executive Blvd

Session Chairs: Rob Singer, Joan Ritland and Richard Conroy

ISMB Tutorial: 3D Genome Data Processing, Analysis, and Visualization Tutorial

https://github.com/hms-dbmi/3d-genome-processing-tutorial

Scientific Webinar Series this Month:

July 28, 2017

Presenter: Rupesh Amin (Juno Therapeutics) - Engineering a Tethering System to Dissect Gene Regulation in Mouse Embryonic Stem Cells

Presenter: Maximiliaan Huisman (University of Massachusetts Medical School) - Cryo-FM: moving towards single-basepair resolution in fluorescence microscopy

Reminder of 2017 Annual Meeting registration

Registration deadline is August 15, 2017. Register here: https://4dn-annual-meetings.fluidreview.com

Abstract and poster submission deadline is August 15, 2017.

Check more information about abstract submission, poster submission, and hotel booking on the wiki page: https://sites.google.com/a/4dnucleome.org/4d-nucleome-wiki/meetings-and-committees/2017-4d-nucleome-annual-meeting

New Upcoming Education and Outreach Event

Chromatin Architecture and Chromosome Organization (March 23 - 27, 2018)

Scientific Organizers: Edith Heard and Peter Fraser

Location: Whistler, British Columbia, Canada

Scientific Webinar Series this Month:

June 23, 2017

Presenter: Cory Lindsay (Scripps Research Institute) - Analysis of the nuclear lamina by proteomics and proximity labeling

Presenter: Takashi Fukaya (Princeton University) - Visualization of trans-homologue enhancer-promoter interaction in living Drosophila embryos

2017 4D Nucleome Annual Meeting

Registration opens and the deadline is August 15, 2017. Register here: https://4dn-annual-meetings.fluidreview.com

Check more information about abstract submission, poster submission, and hotel booking on the wiki page: https://sites.google.com/a/4dnucleome.org/4d-nucleome-wiki/meetings-and-committees/2017-4d-nucleome-annual-meeting

4DN Investigator Featured on “Science Happens!” Watch Dr. Job Dekker describe how the folding of DNA strands holds cues to human health here.

Conversations: A Guide to Packing Your DNA. Cell editor Marta Koch and the 4D Nucleome grantees Drs. Job Dekker, Mitchell Guttman, and Stavros Lomvardas discuss the organization of genetic material in the nucleus, how it occurs, and why it matters. Find it here.

Scientific Webinar Series this Month:

May 26, 2017

Presenter: Vishnu Dileep (Florida State University) - Measuring genome-wide replication timing in single cells

Presenter: Yaniv Lubling (Weizmann Institute of Science, Israel) - Cell cycle dynamics of chromosomal organization at single-cell resolution

2017 4D Nucleome Annual Meeting

Dates: Sept 17 - 20, 2017

Location: Bethesda North Marriott Hotel & Conference Center, 5701 Marinelli Road North Bethesda, Maryland 20852, USA

The 2017 4D Nucleome Annual Meeting is a closed meeting for the 4DN funded PIs and associates.Attendees are responsible for all their travel and lodging expenses.

2017 4D Nucleome Annual Meeting information will be posted to the 4DN WIKI

An “Education and Outreach” page launched on the 4DN Portal. It includes information for 4DN related tutorials and meetings. Thanks to 4DN consortium members, a total of 4 workshops and conference tutorials were given in 2016. In addition to 4DN annual meeting, 4DN consortium members will organize two conferences and one tutorial in 2017.

Members from three groups in 4DN (Leonid Mirny, Nils Gehlenborg, and Jian Ma) will jointly offer a data analysis tutorial during ISMB 2017 conference: https://www.iscb.org/ismbeccb2017-program/tutorials#a3

4DN consortium's twitter account is 4DNucleome; please feel free to use @4DNucleome to emphasize that this tweet is related to 4DN.

4DN web portal featured new software tools, including HiGlass and 3D Genome Browser, as well as the previously featured WashU Genome Browser. See more at: http://www.4dnucleome.org/software.html

Ordering information for HAP1 cells have been updated to the Cell Repository wiki page, thanks to Bas van Steensel. To date (April 17, 2017), a total of 13 4DN cell lines have become available.

A new working group “Joint 4D Nucleome Analysis” is formed. Job Dekker and Feng Yue will serve as co-chairs of this working group. Read about the objective, experimental design, and timeline of this working group. Find more information on the wiki Joint 4DN Analysis page.

Scientific Webinar Series this Month:

April 28, 2017

Presenter: Yongdae Shin (Princeton University) - Optical control of intracellular phase transitions

Presenter: Yodai Takei (Caltech) - Multiplexed dynamic imaging of genomic loci by combined CRISPR imaging and DNA sequential FISH

4DN membership and contact information.

The latest 4DN network contact list is now updated in March 2017. NIH 4DN funded PIs are responsible for keeping the member information of their 4DN funded group current (PIs: please see 4DN wiki → PIs and associates on how to update member information).

4DN wiki accounts and “4DN network contact list” have been synchronized. Ambiguous accounts that cannot be validated by the 4DN network contact list have been removed.

Email groups for 4DN network and each Working Group have been organized to facilitate communication across subgroups of the consortium. Please check 4DN wiki (Email groups) for detail.

The bioRxiv has created a channel for our preprints, which can be accessed here: http://connect.biorxiv.org/relate/content/66. The content of the channel is manually curated. If you notice that one of your preprints is missing or incorrectly assigned to the list, please contact nils@hms.harvard.edu or leonid@mit.edu. The fastest way to get your preprint included is to forward a link as soon as it has appeared on the bioRxiv.

Scientific Webinar Series this Month:

March 24, 2017

Presenter: Naoki Kubo (UCSD) - Analysis of Chromatin Organization after Acute Loss of CTCF in Mouse Embryonic Stem Cells

Presenter: Anders Sejr Hansen (UC Berkeley) - CTCF and cohesin regulate chromatin loop stability with distinct dynamics

WiCell International Ordering Process (H1) is ready and available on 4DN Cell Repository.

The 4DN Hi-C data generation protocol has been approved.

Latest 4DN Pre-prints and news feed are now available on the 4DN Portal homepage.

The 4D Nucleome Project perspective paper has been submitted.

Scientific Webinar Series this Month:

February 24, 2017

Presenter: Anastassia Vertii (UMASS) - High-resolution mapping of nucleolar-associated chromatin in mouse cells

Presenter: Sofia Quinodoz (CalTech) - Mapping RNA and DNA in higher-order nuclear structures

The 4DN pre-prints are now accessible through the 4DN Portal, under Publications → 4DN pre-prints. Note that only the pre-prints that are released on a public repository are accessible through the 4DN Portal.

Scientific Webinar Series this Month:

January 27, 2017

Presenter: Ewan Birney - ChromoTrace: Simulation and reconstruction of 3D chromosome configuration by super-resolution microscopy.

Presenter: Nan Hua - 3D genome structure calculation by data integration.

Tier I cells are available to order, for more information on how to order, check the Cell Repository wiki page.

The 2017 4DN Annual Meeting will be in Bethesda, MD on September 17-20, 2017 at the North Bethesda Marriott Hotel and Conference Center. More information regarding the meeting will be available soon.

NEW OH contact email - oh@4dnucleome.org. Emails sent to 4dnucleome@gmail.com will be forwarded to the new email. Announcements should be sent the new 4DN Network email 4dn-network@4dnucleome.org

The Organizational Hub has updated the 4DN contact members list, after receiving the input from almost all contact PIs. 4DN Members updated Contact list is here 4DN NETWORK LIST.

The 4DN eGrant system for the Transformative Collaborative Project Award (TCPA) has been posted in the web portal - http://www.4dnucleome.org/tcpa.html.

Don't forget to check the 4D Nucleome Twitter, Facebook, and Linkedin accounts.