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