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2012-08-17 DCC Progress

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FINAL Data Freeze Wrap-up

The final freeze went well. Around half of the tracks that had data come in during the freeze are already on public. The DCC ran an audit to see which cell growth protocols and antibody validations were still missing. That list is here. The controlled vocabulary wiki's are still up and available for labs to add any of these missing validations.

ENCODE Transition

Labs should submit any remaining data to GEO. Labs continuing in next phase of ENCODE will want to create track hubs, as this will be part of ENCODE 3 submission process. They should be working with wranglers for guidance on both GEO and hub work.

Data Submission and Track Status

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

Tracks released this month on the UCSC public site

  • Broad Histone (Release 3)
  • Caltech RNA-Seq (Release 4)
  • FSU Repli-chip (Release 2
  • GIS RNA PET (Release 2)
  • HAIB Methyl RRBS (Release 3)
  • RIKEN CAGE Loc (Release 4)
  • UW Affy Exon (Release 4)
  • UW DNaseI DGF (Release 4)
  • UW DNaseI HS (Release 6)
  • UW Histone (Release 5)

Tracks currently under review by the DCC quality group

  • AWG Uniform Processing trackHub made into a public hub
  • SYDH TFBS (Release 3)

Next tracks for review

  • CSHL Long Rna Seq

The complete list of released ENCODE tracks


Data Submissions and Track Status

The latest spreadsheet of Mouse ENCODE experiments submitted to the DCC is: Media:MouseExperiments.2012-08-17.xlsx. Mouse track status from wranglers is here: MM9 Track Status

Tracks released this month on the UCSC public site

  • LICR TFBS (Release 3)
  • PSU DnaseI HS
  • PSU TFBS (Release 2)
  • PSU Histone (Release 2)
  • Stan/Yale RNA-seq (Release 2)
  • Stan/Yale TFBS (Release 4)

Tracks currently under review by the DCC quality group

  • SYDH Histone (Release 2)

Next tracks for review

  • LICR Histone
  • CSHL Long RNA Seq
  • UW Dnase
  • UW DGF

ENCODE data accessioned at GEO this month

  • hg19 wgEncodeCaltechRnaSeq GSE33480 (final)
  • hg19 wgEncodeCshlLongRnaSeq GSE30567 (release 2)
  • hg19 wgEncodeCshlShortRnaSeq GSE24565 (final)
  • hg19 wgEncodeGisChiaPet GSE39495 (final)
  • hg19 wgEncodeHaibMethylRrbs GSE27584 (final)
  • hg19 wgEncodeRikenCage GSE34448 (final)
  • hg19 wgEncodeSydhHistone GSE31755 (final)
  • hg19 wgEncodeUmassDekker5C GSE39510 (final)
  • hg19 wgEncodeUw5C GSE39505 (final)
  • mm9 wgEncodeSydhRnaSeq GSE39619 (final)
  • mm9 wgEncodeSydhTfbs GSE36030 (release 2)
  • mm9 wgEncodeUwRnaSeq - in progress, issues with converted fastqs requiring lab to submit directly (final)
  • mm9 wgEncodePsuRnaSeq - awaiting accession (final)
  • mm9 wgEncodePsuTfbs GSE36029 (final)

in queue:

  • hg19 wgEncodeHaibMethylWgbs
  • mm9 wgEncodePsuDnase
  • mm9 LicrTfbs

Will not be going to GEO:

  • hg19 wgEncodeUncBsuProt
  • hg19 wgEncodeUncBsuProtGenc

The complete list of ENCODE data at GEO

ENCODE and modENCODE Data Listings


Missing cell growth protocols

General: H1-hESC

Tenenbaum: HT-1080

Gilbert: iPS_hFib2_iPS4, iPS_hFib2_iPS5, L1210, EpiSC-5, EpiSC-7, ES-EM5Sox17huCD25, ES-46C, ES-TT2

Missing Antibody Validations


LICR: H3K4me1 (ab8895), H3K4me3 (07-473), H3K27ac (ab4729), H3K27me3 (07-449), H3K36me3 (ab9050), H3K4me2 (ab7766), H3K9ac (ab4441), H3K79me2 (39143), H3K9me3 (ab8898), POL2 (MMS-126R), P300 (sc-585)

Caltech: CEBPB (sc-150), E2F4 (sc-866), FOSL1 (sc-605), Max (sc-197), NRSF, POL2 (MMS-126R), POL2S2 (ab5095), Myogenin (sc-12732), MyoD (sc-32758), SRF (sc-335), TCF12 (sc-357), TCF3 (sc-349), USF1 (sc-229), H3K79me3 (ab2621), H3K4me2 (ab32356), H3K79me2 (ab3594), H3ac (06-599), H3K4me3 (07-473), H3K27me3 (07-449), H3K36me3 (ab9050)

Stanford: H3K4me1 (ab8895), H3K4me3 (07-473), H3K9me3 (ab8898), H3K27ac (ab4729), H3K27me3 (9733S), H3K36me3 (9763S), BHLHE40 (NB100-1800), CHD1 (NB100-60411), CHD2 (ab68301), c-Jun (sc-1694), c-Myc (sc-764), CTCF (sc-15914), E2F4 (sc-866), ETS1 (sc-350), GCN5, HCFC1_(NB100-68209), JunD (sc-74), Max (sc-197), Mxi1 (AF4185), NELFe (sc-32912), Nrf2 (sc-22810), P300 (sc-584), POL2 (MMS-126R), POL2S2 (ab5095), RAD21 (ab992), SMC3 (ab9263), TBP (ab62126), UBF (sc-13125), USF2 (ab60931), ZC3H11A_(NB100-74650), ZKSCAN1 (HPA006672), ZNF384_(HPA004051), ZNF-MIZD-CP1_(ab65767), c-Myb (sc-7874), GATA1, P300 (sc-585)

Yale: H3K4me3 (07-473), CTCF (sc-15914)

PSU: GATA2 (sc-9008), POL24H8 (ab5408), FLI1 (sc-356), H3K4me1 (ab8895), H3K4me3 (07-473), H3K9me3 (ab8898), H3K27me3 (07-449), H3K36me3 (ab9050)

hg18 or hg19

UT-A: CTCF (07-729),c-Myc (sc-764)

USC: c-Fos (sc-7202), H3K9ac (07-352), YY1 (sc-1703) ,TR4

Stanford: c-Myc (sc-764), CTCF (sc-15914), POL2S2 (ab5095), BHLHE40 (NB100-1800), BRCA1 (A300-000A), CDP (sc-6327), CHD2 (ab68301), JunD (sc-74), NF-E2 (sc-22827), P300 (sc-585), P300 (sc-584), SREBP1 (sc-8984), SREBP2 (10007663), WHIP (ab4731), Znf143 (16618-1-AP), ZNF384_(HPA004051), HCFC1_(NB100-68209), PRDM1 (9115), GRp20 (sc-1002), HNF4A (sc-6556), MafF (M8194), PGC1A (sc-13067), GATA1 (sc-266), IRF1 (sc-497), NF-YA, NF-YB, P300 (sc-48343), TBLR1_(NB600-270), ZC3H11A_(NB100-74650), ZNF-MIZD-CP1_(ab65767)

HudsonAlpha: CTCF (sc-5916), FOXA2 (sc-6554), JunD (sc-74), NRSF, P300 (sc-585), PBX3 (sc-891), BATF (sc-100974), BCL11A (ab19489), MEF2C (sc-13268), YY1 (sc-1703), SP2 (sc-643), HEY1 (sc-16424), CTCFL (sc-98982), THAP1 (sc-98174), CTCF (07-729)

Broad: CTCF (07-729), H2AZ (07-594), H3K9ac (ab4441), CHD7 (A301-223A-1), JMJD2A (A300-861A-1), SIRT6 (ab48192), POL2B (MMS-128P), H3K9me1 (ab8896), NSD2 (ab75359), P300 (sc-585)

UW: CTCF (07-729)


Caltech: NRSF, Myogenin (sc-12732), MyoD (sc-32758)

SunyAlbany: CELF1 (05-621), ELAVL1 (SC-5261; 07-1735 is recommended replacement for AB5831), IGF2BP1 (SC-21027), PABPC1 (P6246), RIP input, SLBP (06-1376; 26522; MA156353), T7Tag (AB3790; Nov_69522)

Harvard: GCN5, NF-YA, NF-YB, SPT20, ZZZ3, BDP1 (2663), BRF1 (128), BRF2 (4295), RPC155 (1900), TFIIIC-110 (4286), CCNT2 (sc-12419), GTF2B (sc-225), HMGN3 (NB100-61076), NELFe (sc-32912), SIRT6 (ab48192), c-Fos (sc-7202), c-Myc (sc-764)

GIS-Ruan: CTCF (07-729)

Yale: c-Fos (sc-7202), JunD (sc-74), c-Myc (sc-764), SREBP1 (sc-8984), SREBP2 (10007663), NF-E2 (sc-291)