This page records which lab will produce data from what technologies.

Results of data generation survey (updated 3/21/2017).

—- The following survey was closed —–

We have created a survey for experimental technologies that may be used in 4DN Network.

PIs: Please click here for a survey of technologies that your group may submit data of.

Here are the summary of survey results:

Sequencing:

1. 3C-seq: Job Dekker,
2. 4C-seq
3. 5C: Job Dekker
4. Hi-C: Paul Kaufman, Rafael Casellas, Job Dekker, John Lis, Chuck Murry
5. ChIA-PET: Yijun Ruan,
6. Capture-Hi-C: Rafael Casellas, Job Dekker, Chuck Murry
7. TCC: Lin Chenì
8. In situ Hi-C: Bill Noble and Christine Disteche, Job Dekker, Chuck Murry
9. Dnase Hi-C: Bill Noble and Christine Disteche, Jay Shendure, Chuck Murry
10. Micro-C: Job Dekker
11. GAM: Ana Pombo
12. COLA
13. Single-cell Hi-C: Job Dekker, Chuck Murry
14. Combinatorial single-cell Hi-C: Bill Noble and Christine Disteche, Jay Shendure, Chuck Murry
15. Split-pool Barcoding: Lin Chen, Mitch Guttman, Job Dekker
16. RICh-PET: Yijun Ruan
17. ChIP RICh-PET: Yijun Ruan
18. Distance Hi-C: John Lis
19. DamID and Single-Cell DamID: Bas van Steensel
20. TSA-Seq: Andrew Belmont
21. Repli-Seq: Dave Gilbert
22. TRIP: Bas van Steensel
23. Photo-crosslinking based TCC: Lin Chen
24. RNA-Seq: Bas van Steensel (mRNA), Chuck Murry
25. Nucleolar-associated DNA: Paul Kaufman
26. ATAC-Seq: Job Dekker, Chuck Murry
27. Single-cell repli-seq: Dave Gilbert

Imaging:

1. RNA FISH: Arjun Raj, Thomas Gregor
2. CryoFM (small images series for proof of concept): David Grunwald
3. Live cell: Mark Groudine, Stanley Qi (genomic loci), Job Dekker (Cas9)
4. Immunostaining: Mark Groudine
5. 4D deconvolved stacks: Mark Groudine
6. FISH: Mark Groudine, Bill Noble and Christine Disteche
7. Time-lapse movies (tif or other formats): Thomas Gregor, Mike Levine
8. Single-molecule tracking: Xavier Darzacq, Thomas Gregor
9. High-throughput imaging: Tom Misteli (spinning disk confocal)
10. Single-live-cell tracking of replication: Dave Gilbert
11. Superresolution microscopy (PALM/STORM): Jonas Ries, Job Dekker
12. HIPmap (FISH): Job Dekker
13. (Unspecified): Thoru Pederson

Proteomics:

1. Mass spectrometry: Larry Gerace, Mitchell Guttman and Hess

Models and others:

1. Custom 3D whole-genome models from ChIA-PET and HiC: Dariusz Plewczynski

Genomic technologies currently in use or being developed in the 4DN network (10/17/2016).

Imaging technologies currently in use or being developed in the 4DN network (being compiled by Clodagh O'shea).