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ENCODE data submission plans

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OBSOLETE INFO ALERT -- This page is retained for historical purposes

Data Plans

This table summarizes the data submission plans for all ENCODE projects. The Lab link displays the datatype document provided by the ENCODE investigators to NHGRI. Before data can be submitted, a Data Agreement must be developed for each datatype. The status of the data agreements for each lab is shown here. For the latest contact information for the lab PI and staff, see the Contacts page.

Lab #Reps Data ETA 1st Data Data types Bioinformatics Contact Wrangler
Bernstein (Broad) 2 Aug 1 22 ChIP-seq, 2 input ChIP-seq Tarjei Mikkelsen Tim Dreszer
Crawford (Duke) 2-3 Sep 1 ChIP-seq&chip,DNase-seq&chip,FAIRE-seq&chip Terry Furey Tim Dreszer
Gingeras (Affy/CSHL) 1 Aug 1 6 RNA-chip RNA-seq, RNA-chip,CAGE, PET, RIP Roderic Guigo Brian Raney
Hubbard (Sanger) N/A Oct 1 Annotated gene set (Gencode) Felix Kokocinski Brian Raney
Myers (HudsonAlpha,Stanford,Caltech) 2 NOW 7 ChIP-seq, 3 input (K562,GM12878,jurkat), 3 RNA-seq ChIP-seq, RNA-seq, Methyl-seq Rami Rauch Tim Dreszer, Brian Raney (RNA-seq)
Stam (UW) NOW 6 DNase-seq DNase-seq, ChIP-seq, 5C, Deep-seq Richard Sandstrom Tim Dreszer, Brian Raney (5C)]
Snyder (Yale) 3 July 1 2 ChIP-seq, 2 input (Hela +-gIF) ChIP-seq datasubmission@gersteinlab.org Tim Dreszer
Pilot region projects
Dekker (UMass) NOW 4 regions chromosome interactions Bryan Lajoie Kate Rosenbloom
Elnitski (NHGRI) NOW? 44 sites, 3 cell lines Bi-directional promoters; Silencers and Enhancer Blockers Edwin Jacox Tim Dreszer
Margulies (NHGRI) NOW, and July1 multiple alignments and conservation Gayle McEwen Brian Raney
Tenenbaum (SUNY) 3 Aug 1 RIP-chip, RIP-seq, RIP-genechip Ajish George Brian Raney
Weng (BU/UMass 3 Dec 1 TFBS predicted, tested Soo Lee Kate Rosenbloom

#reps - Number of biological replicates
Data ETA - Estimated date of first data submission
Freq - Expected frequency of data submissions
Lab Contact - This should be the person who will be submitting the data sets to the genome browser.
Wrangler - The Genome Browser engineer assigned to ensure your data is properly converted into displayable tracks on the browser.

Current Status of Data Submission and Experiment Progress Chart are also available.

Data submission pipeline testing

Data submission packaging

Seq data handling proposal

Data submission pipeline test instance: http://hgwdev.cse.ucsc.edu:3000

Data submission pipeline production instance: http://encodesubmit.ucsc.edu/

Crawford project data agreement notes