NOTE! This is a read-only copy of the ENCODE2 wiki.
Please go to the ENCODE3 wiki for current information.
March 2012 Data Freeze
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.
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.
|Broad||BroadHistone||2||Displayed||Displayed (need controls and 1 approved antibody)|
|FSU||FsuRepliSeq||1||New||8 data sets|
|FSU||MOUSE FsuRepliSeq||1||New||? data sets|
|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||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||OpenChromFaire||Displayed (on experiment revoked)|
|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|
|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||UwDnase1HS||4||Displayed||36 data sets|
|UW||UwDnaseDGF||3||Displayed||18 data sets|
|UW||UwHistone||3||Displayed||12 data sets|
|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