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Please go to the ENCODE3 wiki for current information.

2012-07-20 DCC Progress

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FINAL Data Freeze

The final freeze for this phase of ENCODE ends in 12 days. The pipeline will close at midnight PST on July 31, and the DCC will be focusing on data review and release through the month of August. Procedures for data submission after August 1 will be developed by the new DCC, and will be communicated to the labs when they are available.

Data Submission and Track Status

The most recent spreadsheet of hg19 submissions as reported by the pipeline automation is: Media:EncodeExperiments.2012-07-20.xlsx. Pipeline reporting shows a total of 2835 experiments submitted on the hg19 genome assembly (an increase of 90 over last month).

Tracks released this month on the UCSC public site

  • Proteogenomics Hg19 Mapping from ENCODE/Univ. North Carolina/Boise State Univ. (Release 2)
  • Affymetrix Exon Array from ENCODE/University of Washington (Release 3)
  • Transcription Levels Assayed by RNA-seq on 9 Cell Lines from ENCODE
  • Small RNA-seq from ENCODE/Cold Spring Harbor Lab (Release 3)
  • Chromatin Interactions by 5C from ENCODE/Dekker Univ. Mass. (Release 2)
  • Long RNA-seq from ENCODE/Cold Spring Harbor Lab (Release 2)
  • Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard (Release 3) 15 Jun 2012

Tracks currently under review by the DCC quality group

  • HAIB RRBS (Release 3) FINAL
  • UW CTCF Binding (Release 4) FINAL
  • UW DNase I HS (Release 6) FINAL
  • UW Histone (Release 5) FINAL


The complete list of released ENCODE tracks

Mouse ENCODE

Data Submissions and Track Status

The latest spreadsheet of Mouse ENCODE experiments submitted to the DCC is: Media:MouseExperiments.2012-07-20.xlsx. Pipeline reporting shows a total of 537 experiments submitted on the mm9 genome assembly (an increase of 30 over last month).

Tracks released this month on the UCSC public site

  • CSHL Long RNA-Seq FINAL(Release 2)
  • FSU Replication Timing FINAL
  • mm9 Mapability FINAL
  • Stan/Yale TFBS (Release 3)
  • SYDH RNA-Seq (Release 1) FINAL
  • UW RNA-Seq (Release 1) FINAL


The complete list of ENCODE data at GEO

ENCODE and modENCODE Data Listings

Other

  • The Quality Metrics page for Human ENCODE data is under review and will be on the preview browser at week's end. It is accessed from the Data Standards page.