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March 2012 Data Freeze

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The current ENCODE data freeze will be March 31, 2012 12:00 AM PST. The data submission pipeline will close for a period after the deadline.

Goals and Policy

This Freeze is for both Mouse and Human data and is the cut off for the cross analysis with modENCODE. The Mouse group is having a soft freeze goal of Feb 15, 2012. The Human group is having a soft freeze date of Mar 1, 2012. These dates are for the groups and will only be supported by the DCC having the metaData up to date at those times. The actual ENCODE Freeze will be March 31,2012 at 12:00 AM PST. For the West coast labs that will seem like March 30,2012. March 31 is a Saturday. The pipeline will be closing that Friday night/Saturday morning at midnight, and will remain closed for a period of time (est. 2 weeks) so that wranglers can focus on vetting, configuring and associating metadata to freeze submissions.

MOUSE: As this Freeze for the Mouse group should be ALL data, the pipeline will not accept mm9 after March 31, 2012 12:00 AM PST without special handling from your wrangler.

Freeze Progress

Latest spreadsheet of submitted experiments: Media:EncodeExperimentsHg19.2010-02-09.xlsx

Expectations for the Freeze

Below is a qualitative status and plan for each ENCODE composite track that the DCC is currently working on or expects. It is for communication between the wranglers and key lab contacts about the state of submissions for each composite. Please correct the Current Status both immediately and as plans change.

Lab Composite Release Status Freeze Plan
Broad BroadHistone 2 Displayed Displayed (need controls and 1 approved antibody)
Broad BroadHss 1 Released None expected
FSU FsuRepliSeq 1 New 8 data sets
FSU MOUSE FsuRepliSeq 1 New ? data sets
GENCODE GENCODE 10 Released None expected
GIS GisChiaPet 1 Displayed 2 data sets
HudsonAlpha CaltechRnaSeq 3 New Possibly HAIB to add A549??, Replacement bigwigs coming
HudsonAlpha CaltechSingleRnaSeq 1 Proposed Straight to GEO
HudsonAlpha HaibBisulfite 1 Displayed 2 data sets
HudsonAlpha HaibGenotype 2 Released None expected
HudsonAlpha HaibMethyl450 2 Released None expected
HudsonAlpha HaibRnaSeq 1 Released 2 replacement files
HudsonAlpha HaibRrbs 3 New 10-25 data sets
HudsonAlpha HaibTfbs 2 Released 10-20 data sets for release 3
Licr MOUSE LicrHistone 2 Displayed 30 data sets
Licr MOUSE LicrRnaSeq 2 Displayed 19 data sets
Licr MOUSE LicrTfbs 2 Displayed 32 data sets
OpenChrom DukeAffyExonArray Reviewing
OpenChrom OpenChromDnase Displayed
OpenChrom OpenChromFaire Displayed (on experiment revoked)
OpenChrom OpenChromSynth Released
OpenChrom OpenChromTfbs Displayed
PSU MOUSE CaltechHistone 1 Released None expected
PSU MOUSE CaltechRnaSeq 1 New 10 data sets
PSU MOUSE CaltechTfbs 2 Displayed 5 data sets
PSU MOUSE Psu5c 1 New 2 data sets
PSU MOUSE PsuDnaseSeq 1 New ? data sets
PSU MOUSE PsuHistone 1 Reviewing 8 data sets expected by Freeze, possible 2nd release
PSU MOUSE PsuRnaSeq 1 New  ? data sets, what will all data be submitted by Caltech
PSU MOUSE PsuTfbs 1 Reviewing 25 data sets expected by Freeze, possible 2nd release
SYDH MOUSE SydhHistone 2 New 15 data sets between TFBS and Histone Track
SYDH MOUSE SydhRnaSeq 1 Displayed Waiting on second replicates
SYDH MOUSE SydhTfbs 3 Displayed 15 data sets between TFBS and Histone Track
SYDH SydhHistone 2 New 7-8 data sets
SYDH SydhTfbs 2 Displayed 40-50 data sets with release in Feb and release 3 after freeze
SYDH YaleRnaSeq 2 New Replacement data and outstanding issues
Transcriptome CshlLongRnaSeq 2 Submitting 60 data sets
Transcriptome CshlShortRnaSeq 3 Submitting 60 data sets for release 3
Transcriptome GisRnaPet 2 Submitting 12 data sets and some corrections
Transcriptome MOUSE CshlLongRnaSeq 1 Submitting 18 data sets
Transcriptome RikenCage 3 New 11? data sets
UChicago UchicagoTfbs 2 New 15 data sets
Umass Umass5c 1 Reviewing None expected
UNC UncProteoGenomics 2 Submitting 4 data sets
UW MOUSE UwDnase1HS 2 Displayed 36 data sets
UW MOUSE UwDnaseDGF 1 Displayed 2 data sets
UW MOUSE UwRnaSeq 1 Displayed Data replicates
UW MOUSE UwTfbs 1 New ? data sets
UW Uw5c 2 New ? data sets
UW UwAffyExon 2 Released 8 data sets
UW UwCTCF 3 Displayed None expected
UW UwDnase1HS 4 Displayed 36 data sets
UW UwDnaseDGF 3 Displayed 18 data sets
UW UwHistone 3 Displayed 12 data sets
UW UwRepliSeq 1 Reviewing None expected
UW UwRnaSeq 0 New 24 data sets

Data Approval Calls

Will we need this?

Transcriptome, HAIB, SYDH, Caltech have regular calls, We should get some scheduled for Duke, UW, and Licr