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4dn:phase1:data_submission_and_release [2019/02/13 13:35]
127.0.0.1 external edit 		4dn:phase1:data_submission_and_release [2025/04/22 16:21] (current)
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 +====== 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).
 +
 +------------------------------------------------------------------------------------------
 +
 +{{medialist>​4dn:​data_submission_and_release:​}}
 +
  
4dn/phase1/data_submission_and_release.1550093733.txt.gz · Last modified: 2025/04/22 16:21 (external edit)

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