Data submission and release

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,

1. 4C-seq

1. 5C: Job Dekker

1. Hi-C: Paul Kaufman, Rafael Casellas, Job Dekker, John Lis, Chuck Murry

1. ChIA-PET: Yijun Ruan,

1. Capture-Hi-C: Rafael Casellas, Job Dekker, Chuck Murry

1. TCC: Lin Chenì

1. In situ Hi-C: Bill Noble and Christine Disteche, Job Dekker, Chuck Murry

1. Dnase Hi-C: Bill Noble and Christine Disteche, Jay Shendure, Chuck Murry

1. Micro-C: Job Dekker

1. GAM: Ana Pombo

1. COLA

1. Single-cell Hi-C: Job Dekker, Chuck Murry

1. Combinatorial single-cell Hi-C: Bill Noble and Christine Disteche, Jay Shendure, Chuck Murry

1. Split-pool Barcoding: Lin Chen, Mitch Guttman, Job Dekker

1. RICh-PET: Yijun Ruan

1. ChIP RICh-PET: Yijun Ruan

1. Distance Hi-C: John Lis

1. DamID and Single-Cell DamID: Bas van Steensel

1. TSA-Seq: Andrew Belmont

1. Repli-Seq: Dave Gilbert

1. TRIP: Bas van Steensel

1. Photo-crosslinking based TCC: Lin Chen

1. RNA-Seq: Bas van Steensel (mRNA), Chuck Murry

1. Nucleolar-associated DNA: Paul Kaufman

1. ATAC-Seq: Job Dekker, Chuck Murry

1. Single-cell repli-seq: Dave Gilbert

Imaging:

1. RNA FISH: Arjun Raj, Thomas Gregor

1. CryoFM (small images series for proof of concept): David Grunwald

1. Live cell: Mark Groudine, Stanley Qi (genomic loci), Job Dekker (Cas9)

1. Immunostaining: Mark Groudine

1. 4D deconvolved stacks: Mark Groudine

1. FISH: Mark Groudine, Bill Noble and Christine Disteche

1. Time-lapse movies (tif or other formats): Thomas Gregor, Mike Levine

1. Single-molecule tracking: Xavier Darzacq, Thomas Gregor

1. High-throughput imaging: Tom Misteli (spinning disk confocal)

1. Single-live-cell tracking of replication: Dave Gilbert

1. Superresolution microscopy (PALM/STORM): Jonas Ries, Job Dekker

1. HIPmap (FISH): Job Dekker

1. (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).