Data submission

Accession list

Phase 1 data

DRA accession number	data set	library type	library IDs
DRA000991	Phase1 all FREEZE 1.1 data (Phase 1 main paper set)	Helicos CAGE	1383 libraries in https://fantom5-collaboration.gsc.riken.jp/files/data/shared/FREEZE_PHASE1.1/
DRA001026	Phase1 additional set 1 (non FREEZE1.1 mast cell 4 samples)	Helicos CAGE	CNhs13924, CNhs13925, CNhs13926, CNhs13927 (in FREEZE2)
DRA001027	Phase1 additional set 2 (non FREEZE1.1 T-reg human 4 samples)	Helicos CAGE	CNhs13918, CNhs13919, CNhs13920, CNhs13921 (in FREEZE2)
DRA001028	Phase1 additional set 3 (non FREEZE1.1 T-reg mouse 5 samples)	Helicos CAGE	CNhs13913, CNhs14142, CNhs14158, CNhs14159, CNhs14160 (in FREEZE2)
DRA001101	Phase1 additional set 4 (non FREEZE1.1 enhancer paper samples)	Illumina RNA-Seq	RDhi10000-RDhi10005, RDhi10007-RDhi10012, RDhi10014-RDhi10019, RDhi10058 (in UPDATE22)
		Illumina small RNA-Seq	SRhi10066 (tag: TAGCTT, GGCTAC, CTTGTA), SRhi10010 (tag: TTAGGC, CTTGTA, GTGAAA) (in UPDATE22)

Phase 1.5 data (opened before Phase 2 paper publication)

DRA accession number	data set	library type	library IDs
DRA002216	Phase1.5 set 1 (iPS-related 6 samples)	Helicos CAGE	CNhs14214, CNhs14215, CNhs14216, CNhs14217, CNhs14218, CNhs14219 (in FREEZE2)

Others

DRA accession number	data set	library type	library IDs
DRA001100	Platform comparison	Helicos CAGE	CNhs10325-CNhs10356 (excluding CNhs10333, CNhs10338, CNhs10341, CNhs10346, CNhs10349, CNhs10354)
		Illumina CAGE	J20-DA (tag:ACA,ACG,ACT,AGC,ATC,ATG), J21-DA (tag:ACA,ACG,ACT,ATC,ATG), J48-DA (tag:ACA,ACG,ACT,ATC,ATG), J49-DA (tag:ACA,ACG,ACT,ATC,ATG)
		Illumina RNA-Seq	RNig10094-RNig10098, RNig10100-RNig10106
DRA002420	M. Lizio paper	Illumina CAGE	CThi10038,CThi10039,CThi10077-CThi10086
DRA002468		Illumina ChIP-Seq	PShi10148-10150, PShi10176, PShi10177, PShi10179, PShi10189, PShi10213

We cannot edit the DRA001100 entry (for example, publication) with DRA D-way no more. We need to contact the DRA staffs ( trace@ddbj.nig.ac.jp ), when we need to update.

Paper list

• FANTOM Consortium and the RIKEN PMI and CLST (DGT). A promoter-level mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70.
  doi:10.1038/nature13182 PMID:24670764
  (DRA000991)
• Andersson R et al. An atlas of active enhancers across human cell types and tissues. Nature. 2014 Mar 27;507(7493):455-61.
  doi:10.1038/nature12787 PMID:24670763
  (DRA000991 DRA001101)
• Motakis E et al. Redefinition of the human mast cell transcriptome by deep-CAGE sequencing. Blood. 2014 Mar 26.
  doi:10.1182/blood-2013-02-483792 PMID:24671954
  (DRA000991 DRA001026)
• Schmidl C et al. Transcription and enhancer profiling in human monocyte subsets. Blood. 2014 Mar 26.
  doi:10.1182/blood-2013-02-484181 PMID:24671955
  (DRA000991)
• Schmidl C et al. The enhancer and promoter landscape of human regulatory and conventional T-cell subpopulations. Blood. 2014 Mar 26.
  doi:10.1182/blood-2013-02-486944 PMID:24671953
  (DRA000991 DRA001027)
• Rönnerblad M et al. Analysis of the DNA methylome and transcriptome in granulopoiesis reveal timed changes and dynamic enhancer methylation. Blood. 2014 Mar 26.
  doi:10.1182/blood-2013-02-482893 PMID:24671952
  (no info.)
• Prasad P et al. High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesis. Blood. 2014 Mar 26.
  doi:10.1182/blood-2013-02-483537 PMID:24671951
  (no info.)
• Kawaji H et al. Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing. Genome Res. 2014 Apr;24(4):708-17.
  doi:10.1101/gr.156232.113 PMID:24676093
  (DRA001100)
• Morikawa H et al. Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation. Proc Natl Acad Sci U S A. 2014 Apr 8;111(14):5289-94.
  doi:10.1073/pnas.1312717110 PMID:24706905
  (DRA000868 DRA000991 DRA001028)
• Adam J et al. The Evolution of Human Cells in terms of Protein Innovation. Mol Biol Evol. 2014 Apr 1.
  doi:10.1093/molbev/mst139 PMID:24692656
  (No info.)
• Davis MR et al. Transcriptional profiling of the human fibrillin/LTBP gene family, key regulators of mesenchymal cell functions. Mol Genet Metab. 2013 Dec 16.
  doi:10.1016/j.ymgme.2013.12.006 PMID:24703491
  (unknown)
• Frith MC; the FANTOM consortium. Explaining the correlations among properties of mammalian promoters. Nucleic Acids Res. 2014 Mar 27.
  doi:10.1093/nar/gku115 PMID:24682821
  (No info.)
• Arner E et al. Ceruloplasmin is a novel adipokine which is overexpressed in adipose tissue of obese subjects and in obesity-associated cancer cells. PLoS One. 2014 Mar 27;9(3):e80274.
  doi:10.1371/journal.pone.0080274 PMID:24676332
  (No info.)
• Medvedeva YA et al. Effects of cytosine methylation on transcription factor binding sites. BMC Genomics. 2014 Mar 26;15(1):119.
  doi:10.1186/1471-2164-15-119 PMID:24669864
  (No info.)
• Rye M et al. Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines. BMC Genomics. 2014 Mar 26;15(1):120.
  doi:10.1186/1471-2164-15-120 PMID:24669905
  (No info.)