====== Data submission and release ======

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

===== Technology Survey and Survey Results =====

[[https://mail.google.com/mail/u/0/#inbox/15af12d5c823cd0f|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.

[[https://www.surveymonkey.com/r/4DN-experimental-survey|PIs: Please click here for a survey of technologies that your group may submit data of.]]

Here are the summary of survey results:

Sequencing:

  - 3C-seq: Job Dekker,

  - 4C-seq

  - 5C: Job Dekker

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

  - ChIA-PET: Yijun Ruan,

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

  - TCC: Lin Chenì

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

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

  - Micro-C: Job Dekker

  - GAM: Ana Pombo

  - COLA

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

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

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

  - RICh-PET: Yijun Ruan

  - ChIP RICh-PET: Yijun Ruan

  - Distance Hi-C: John Lis

  - DamID and Single-Cell DamID: Bas van Steensel

  - TSA-Seq: Andrew Belmont

  - Repli-Seq: Dave Gilbert

  - TRIP: Bas van Steensel

  - Photo-crosslinking based TCC: Lin Chen

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

  - Nucleolar-associated DNA: Paul Kaufman

  - ATAC-Seq: Job Dekker, Chuck Murry

  - Single-cell repli-seq: Dave Gilbert

Imaging:

  - RNA FISH: Arjun Raj, Thomas Gregor

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

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

  - Immunostaining: Mark Groudine

  - 4D deconvolved stacks: Mark Groudine

  - FISH: Mark Groudine, Bill Noble and Christine Disteche

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

  - Single-molecule tracking: Xavier Darzacq, Thomas Gregor

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

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

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

  - HIPmap (FISH): Job Dekker

  - (Unspecified): Thoru Pederson

Proteomics:

  - Mass spectrometry: Larry Gerace, Mitchell Guttman and Hess

Models and others:

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

===== Compilation of Current Technologies Used in the 4DN Network =====

[[https://docs.google.com/document/d/1N8ZgdQen2VFO30vyk4fHlpKko18bZIaYfQdbtordhnU/edit|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).

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