Discussion of 4DN JAWG Marker Paper Outline: https://docs.google.com/document/d/1TNk17MMvh1iuMugyuU1QImmOYDwojt85f02XdJYw47M/edit

We have created a Slack workspace for 4DN Joint Analysis. We will have more discussion on the marker paper there. You are welcome to join in using the invitation link: https://join.slack.com/t/4dnjawg/shared_invite/enQtODcyNzMwOTg4MDUyLWIxNmQwZjZmMDFkM2RjZmQ4ZjEyMzg4ZTEzZThkOWZkYmY0NmQ1MzJhMmMzYzkxZWFiMjY4OTYyOGIxZTM4M2Y

Presentation by Xiaotao Wang (Yue Lab) and Andy Schroeder (DCIC): Sharing analysis products within the JAWG via the DCIC

Presentation by Ruan Lab: Brief updates on 1) methods comparison; 2) human ChIA-Drop data

Presentation by Dekker Lab: Hi-C protocol parameter sweep

Presentation by Christoph Thieme / Teresa Szczepinska (Pombo, Plewczynski, Nicodemi Labs): GAM versus Hi-C comparisons mESC and H1 hESC

Presentation by Jian Ma: Update on recent progress

Discussion on manuscript coordination

Presentation by Frank Alber: Comparative genome structure analysis (H1/HFF/GM12878)

Annual meeting planning (agenda) https://docs.google.com/document/d/1dGMfu7VUUoMifpCQ19hCom5aVVe7UqWGXJ0i4YRPSFE/edit?ts=5db7287d#heading=h.oplwmnls7v3

Go over planned data sets (listed here and here). https://docs.google.com/spreadsheets/d/1ONfcbvM1iP30vhStJuOemho039hMA0juFvjEU92zse4/edit#gid=0

Google Doc for sharing analysis results. https://docs.google.com/document/d/1-0oWZsmXhEaD20WJNgIt6cgwIi-rhZVCiBDYqxVXQXE/edit?usp=sharing

Perhaps have a plenary session for JAWG, visualization and imaging.

The imaging demo may be open the entire time, not just during the breakout.

Action items:

[Burak] Contact David Grunewald to find out more.

[Feng] Continue scheduling discussion via email.

[Bill] Email to find out what data is on the way. Put a deadline.

[Bill] Schedule presentations for the next three meetings. Frank, Job, Feng (cross-platform comparisons), Jian. Make sure we get important discussions about manuscripts into the agenda for upcoming calls.

1. Presentation by Jennifer E. Phillips-Cremins

2. Discussion of Jie Liu's associate member application (https://drive.google.com/file/d/0B1Uh14Y8H75dVUN4YS1XOU1BaVR5Q0syN3JvMlB2THdDMmJV/view)

3. Outreach session (chaired by Peter Fraser)

Presentation by Dr. Jie Liu for 4DN association member application: Computational methods for high resolution chromatin organization (https://drive.google.com/file/d/1VYwFZ-QQ8fHpOo7Iqv5mZCMEm_nb-eLL/view)

Presentation by Kyle Xiong (Ma Lab): SNIPER - call subcompartments by imputing inter-chromosomal chromatin interactions

Discussion of authorship and data release policy

Discussion of publication of individual datasets by data producers and the use of individual datasets generated by others in the group in publications.

Presentation by Tarik Salameh (Yue Lab): A supervised learning framework for chromatin loop detection in genome-wide contact maps

Presentation by Daniel Capurso (Ruan Lab): Comparative analysis of methods for protein-enriched chromatin interactions

Presentation by Liguo Zhang (Belmont Lab): Development and Application of TSA-Seq 2.0 to Measuring 3D Genome Organization Relative to Nuclear Compartments

Discussion on how to perform the joint analysis as a group.

Proposal to assemble an analysis team with members from interested centers and labs.

Presentation by Dr. Thomas C. Bishop (Louisiana Tech University): G-Dash: A Genome Dashboard Integrating Modeling and Informatics

Presentation by Nils Krietenstein (Rando, Mirny, Dekker Labs): Micro-C vs Hi-C

Presentation by DCIC: Pipelines, visualization, sites supporting joint papers

Discussion on handling co-authorships across JAWG papers

Presentation by Xiaotao Wang (Yue Lab): cross-platform comparisonsOutreach

Presentation by Sheng Zhong: Brief update on analysis of inter-chromosomal interactions

Outreach

Feedback of the Keystone meeting of 2 weeks ago

Kate Rivera (4DN Program Coordinator) has drafted a version of a 4DN brochure. Please have a look, we will go over it and discuss suggestions/modifications.

Retrospective of the last meeting's actions items and their implementation. (minutes of last outreach discussion)

Presentation by Alber/Ma Labs: Structural models vs SPIN

Presentation by Bill/Erez Labs: ENCODE to present their 4D Nucleome related work

Presentation by Xiaotao Wang (Yue Lab): a short update on the cross-platform comparison.

Presentation by Peiyao Zhao (Gilbert Lab): High Res Repli-seq (H1, H9, HCT116, F121-9 ESC and NPC)

Presentation by Tarik Salameh (Yue Lab): PIKACHU: A supervised machine learning method to identify chromatin loops from genome-wide interaction data

Plans for intensifying Outreach activities: https://docs.google.com/document/d/174APgE9ppCWaR0H9OLUjuX7Z0gwx9dL3dsCKzRnaMRQ/edit

Present the Outreach activities google sheet: https://docs.google.com/spreadsheets/d/1b_QkvoI86FSakGteLjYC81Q0hQ92RR_uI8jYN6Rx6mU/edit#gid=1386834576

Presentation by Rando/Mirny/Dekker labs: Micro-C vs Hi-C - long presentation

Presentation by Ruan/Aiden/Dekker/Ren/Ma labs: pull-down vs non-pulldown 3C methods comparisons

Presentation by Guttman lab: ligation vs non-ligation assays (HiC vs SPRITE/GAM)

Presentation by Zhong/Ren labs: RNA-chromatin interactions

Presentation by Pombo/Nicodemi/Ren/Hu labs: Allelic GAM/Hi-C/PLAC-seq + other data (cell line F123)

Presentation by Alber / Data producing labs: Structural modeling

Presentation by Ren/Hu.Pombo/Nicodemi: PLAC-seq - Hi-C - GAM

Burak: No JAWG DCIC data update. Encouraged upcoming JAWG presentations to start with a slide on data availability

Sheng: Gave an outreach activities update. Encouraged conference organizers/attendees to update the worksheet ‘4DN workshops and posters

David Gilbert: Gave an anecdote about a scientific meeting that discouraged a 4DN-specific talk. But urged everyone to do their best to put 4DN affiliation in presentation/posters.

Updates of nuclear speckle project: Belmont/Zhong/Guttman

Updates of SPIN states project: Ma/Belmont/van Steensel/Gilbert

DCIC/Burak Alver to give an update on processed data available for JA for the various groups to use ChIP status

Discussion of the planned presentation schedule: https://docs.google.com/spreadsheets/d/1bpJR_UnFE67P_dqrj0gbPequ_tx0WPmEMTl6hKbgGz0/edit#gid=0

Continue discussion of plans for papers. Discussion on how to coordinate and report updates of ongoing analyses towards these papers to the JAWG/DAWG groups

Update on ENCODE data being generated by ENCODE for 4DN Tier 1 cells (Job and Feng).

Coordination between JAWG/DAWG with the larger outreach strategy discussed at this weeks 4DN Steering Committee call.

Planning of manuscripts. Feng has created a google doc for listing proposed manuscripts. Please add your planned manuscript before the call on Jan 10. We will discuss it at the meeting. Here is the link to the google doc: https://docs.google.com/document/d/1Riv1WeOyHWDAkZn874h87ykHqz0ogotNuaC-cryLtDU/edit

Feedback and discussion of the annual meeting

Discussion of next steps

RFI from groups about publication plans on Joint Analysis projects

Questionnaire Form

Result Table

1. Discussion of the Omics data freeze

1. DCIC updates

1. Summary report from each lab that promised Omics data generation by the January data freeze.

Update from DCIC: data freeze progress - Burak Alver

Discussion of data analysis plans - Job and Feng

A report from the imaging WG and their plans for benchmarking technologies - Imaging WG

Update from microscope calibration efforts - David Grunwald

Scheduling JAWG scientific presentations - Feng and Job

1. Data submission status update

2. Discussion of data analysis plan

3. Scheduling JAWG scientific presentations

4. Discussion of the monthly joint call plan for DAWG and JAWG

1. Presentation by DCIC: Data Processing Pipeline

2. Update and Discussion of ENCODE data generation for 4DN cell lines HFFc6 and Endoderm.

1. Presentation by Wouter de Laat: Multi-contact 4C

2. Microscope calibration project updates (David Grunwald)

1. Presentation by Kami Ahmad: CUT&RUN for chromatin structure

1. Presentation by Karla Neugebauer: The Cell Nucleus under Stress

1. Presentation by Sheng Zhong: Global mapping of RNA-genome interactions

2. Discussion of “Craig’s list for collaborative projects”. https://sites.google.com/a/4dnucleome.org/4d-nucleome-wiki/collaboration-plaza

1. Presentation by Jian Ma: Computational methods for probing nuclear compartmentalization

2. Discussion of “Craig’s list for collaborative projects”. https://sites.google.com/a/4dnucleome.org/4d-nucleome-wiki/collaboration-plaza

1. Presentation by Jie Liu (Noble Lab): Unsupervised Embedding of Single-cell Hi-C Data

2. Discussion of associate member application from Dr. Maxwell Libbrecht. https://drive.google.com/file/d/1D3GAZcfJ4Czz_wkLGKckqDb1T4qV2_un/view

1. Presentation by Alexander Kukalev and Warren Winick-Ng (Pombo Lab): Update on H1 hESC GAM data production and QC

1. Discussion of the 4DN network feedback about the associate member application from Dr. Maxwell Libbrecht.

1. Presentation by Nicola Neretti: Bayesian Estimation of 3D Chromosomal Structure from Single Cell Hi-C Data

1. Discussion of draft analysis design for the integrative analysis. Please add comments to the draft plan in suggesting mode. Link to the google doc.

1. Presentation by Maxwell Libbrecht for 4DN associate member application from Maxwell Libbrecht & Michael Hoffman: Understanding large-scale genome regulation through joint analysis of chromatin state and chromatin conformation

1. Presentation by Dr. Dave Gilbert: 16 fraction repliseq

2. Discussion of associate membership application Drs. Libbrecht and Hoffman

3. Discussion of associate member application by Dr. Kai Tan. https://drive.google.com/file/d/1BvXm6FmlHU9T1oVfE1WzbzEl_udEVOnD/view

1. Presentation by Dr. Kai Tan for 4DN associate member application (https://drive.google.com/file/d/1BvXm6FmlHU9T1oVfE1WzbzEl_udEVOnD/view)

2. Planning of next data freeze: endoderm data

1. Discussion about associate member application by Dr. Kai Tan. Here is the application letter: https://[[http://drive.google.com/file/d/1BvXm6FmlHU9T1oVfE1WzbzEl_udEVOnD/view|drive.google.com/file/d/1BvXm6FmlHU9T1oVfE1WzbzEl_udEVOnD/view]]

2. Scheduling of the first round data analyses

3. Discuss proposals on how to do the integrative analysis: form groups that analyze specific features of the data using multiple approaches.

4. Please read the new associate member application submitted by Dr. Peter Yingxiao Wang. We will discuss it on July 12. Here is the application letter: https://drive.google.com/file/d/1LKhwC0_GHnKwTcb0AT-lHLZthxyZm4Ki/view

1. Discussion about associate member application by Dr. Peter Yingxiao Wang. Here is his application letter. https://drive.google.com/file/d/1LKhwC0_GHnKwTcb0AT-lHLZthxyZm4Ki/view

2. Discussion of presentation list of data analyses by data producers. https://docs.google.com/spreadsheets/d/1bpJR_UnFE67P_dqrj0gbPequ_tx0WPmEMTl6hKbgGz0/edit#gid=0

1. Presentation by Hakan Ozadam and Sergey Venev (Dekker Lab): Compartment, insulation and dot analysis of Hi-C data for H1-ESCs and HFFc6

1. Presentation by Ivan Juric (Ming Hu lab) and Miao Yu (Ren Lab): PLAC-seq analysis

1. Presentation by Christoph Thieme and Alexander Kukalev (Pombo Lab): Comparing chromatin contacts in ESCs by GAM and Hi-C

1. Presentation by Dr. Peter Yingxiao Wang for his associate member application.

2. Discuss how to share the Joint Analysis presentations, including the slides and recordings.

1. Presentation by Daniel Capurso (Ruan Lab): CTCF motif orientation in ChIA-PET loops at different sequencing depths and in different cell types

2. Discuss on associate member application from Dr. Peter Yingxiao Wang

1. Presentation by Da Kuang (Yue Lab): Identifying differential chromatin interactions with triplet network

1. The presentation slides can be shared on 4DN joint analysis wiki page now. If you want to share your slides (including past presentations), please send them to Zhangming (Frank). Email: yanzm@ucsd.edu

2. Presentation by Andrew Belmont and Liguo Zhang (Belmont Lab): TSA-Seq overview and update

1. Presentation by Yuchuan Wang (Jian Ma lab at Carnegie Mellon): Updates on Integrative Analysis of Nuclear Compartmentalization for Joint Analysis Cell Lines

1. Presentation by Gurkan Yardimci (Noble Lab and Shendure Lab): Exploratory analysis of sciHiC data

1. Presentation by Frank Alber: Update on data integration efforts in genome structure analysis of tier 1 cells.

2. Discussion on “planning for the annual meeting” (15 mins)

1. Presentation by Sofi Quinodoz (Guttman Lab): Update on DNA SPRITE of Tier 1 cell lines

1. Go over which presentations are ready for the annual meeting

1. Presentation by Gianluca Pegoraro (IWG): The 4DN Imaging to Omics Working Subgroup

2. Discussion about the annual meeting presentations https://docs.google.com/document/d/1Bn2EWLV81ebqt8A8NYOTY8NtCe6QEKpkGH2pIEDrSy4/edit

1. Presentation by Sheng Zhong: Comparison of RNA-DNA interactions with other 4DN data types

2. Discussion about the annual meeting presentations https://docs.google.com/document/d/1Bn2EWLV81ebqt8A8NYOTY8NtCe6QEKpkGH2pIEDrSy4/edit