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2012-01-20 DCC Progress

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Data Submission and Track Status

The next data freeze for human ENCODE has been set for March 2012. Production groups are encouraged to submit data for this freeze by March 1. A hard freeze date for submission for this freeze is March 31. To facilitate planning and smooth the freeze processing, production groups need to provide their data wrangler with a list of proposed data submissions for the freeze.

The pipeline reporting currently shows 2301 experiments on hg19/GRCh37, an increase of 34 over last month. The most recent spreadsheet of hg19 submissions as reported by the pipeline automation is: Media:EncodeExperimentsHg19.2012-01-20.xlsx.

The real-time reporting is now linked on to the left menu bar for easy access.

Reports from the DCC wranglers regarding hg19 track status are here: HG19 Track Status

Tracks released this month on the UCSC public site

  • RIKEN CAGE Loc
  • UW Affy Exon
  • Caltech RNA-seq (Release 2)
  • UW CTCF Binding (Release 2)

Tracks currently under review by the DCC quality group

  • UW Replication Timing
  • HAIB Genotype (Release 2)

Next tracks for review

  • GENCODE V10
  • Open Chrom Synth (Release 2)

The complete list of released ENCODE tracks

Mouse ENCODE

Data Submissions and Track Status

The automated reporting currently shows 349 experiments, an increase of 89 over last month.

The latest spreadsheet of Mouse ENCODE experiments submitted to the DCC is: Media:MouseExperiments.2012-01-20.xlsx.

Mouse track status from wranglers is here: MM9 Track Status

Tracks released this month on the UCSC public site

  • none

Information needed from Labs

Documentation is needed from these labs:

  • Stam: DNase DGF track, ChIP-Seq TFBS track, RNA-Seq track

Data submission information is needed from these labs:

  • Gilbert Lab

ENCODE data accessioned at GEO this month

New:

Updated:

ENCODE data in GEO process

  • OpenChromFaire

The complete list of ENCODE data at GEO

Other News

The DCC has welcomed a new data wrangler -- Ruihua Fang, who joined our ENCODE team last week. Ruihua has a B.S. in Biochemical Engineering and a PhD in Biochemistry, and did postdoc work in bioinformatics and proteomics at both Harvard Medical School and Pacific Northwest National Laboratory. She also has several years of professional experience in biological data wrangling, mining and analysis at Fred Hutchinson Cancer Research Center and CalTech, including work on the WormBase project. Most recently Ruihua developed a Support Vector Machine (SVM) procedure for the automatic categorization of biomedical literature, and has been working with WormBase, FlyBase and SGD to adopt this procedure for their curation processes.