Data submission: Difference between revisions
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* Prasad P et al. High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesis. Blood. 2014 Mar 26. <br />[http://dx.doi.org/10.1182/blood-2013-02-483537 doi:10.1182/blood-2013-02-483537] [http://www.ncbi.nlm.nih.gov/pubmed/24671951 PMID:24671951] <br />(no info.) |
* Prasad P et al. High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesis. Blood. 2014 Mar 26. <br />[http://dx.doi.org/10.1182/blood-2013-02-483537 doi:10.1182/blood-2013-02-483537] [http://www.ncbi.nlm.nih.gov/pubmed/24671951 PMID:24671951] <br />(no info.) |
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* 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. <br />[http://dx.doi.org/10.1101/gr.156232.113 doi:10.1101/gr.156232.113] [http://www.ncbi.nlm.nih.gov/pubmed/24676093 PMID:24676093] <br />(DRA001100) |
* 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. <br />[http://dx.doi.org/10.1101/gr.156232.113 doi:10.1101/gr.156232.113] [http://www.ncbi.nlm.nih.gov/pubmed/24676093 PMID:24676093] <br />(DRA001100) |
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* Morikawa H et al. Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation. PNAS. 2014. <br />[http://dx.doi.org/10.1073/pnas.1312717110 doi:10.1073/pnas.1312717110] [http://www.ncbi.nlm.nih.gov/pubmed/ PMID: |
* Morikawa H et al. Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation. PNAS. 2014. <br />[http://dx.doi.org/10.1073/pnas.1312717110 doi:10.1073/pnas.1312717110] [http://www.ncbi.nlm.nih.gov/pubmed/24706905 PMID:24706905] <br />(DRA000868 DRA000991 DRA001028) |
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* Adam J et al. The Evolution of Human Cells in terms of Protein Innovation. Mol Biol Evol. 2014 Apr 1. <br />[http://dx.doi.org/10.1093/molbev/mst139 doi:10.1093/molbev/mst139] [http://www.ncbi.nlm.nih.gov/pubmed/24692656 PMID:24692656] <br />(No info.) |
* Adam J et al. The Evolution of Human Cells in terms of Protein Innovation. Mol Biol Evol. 2014 Apr 1. <br />[http://dx.doi.org/10.1093/molbev/mst139 doi:10.1093/molbev/mst139] [http://www.ncbi.nlm.nih.gov/pubmed/24692656 PMID:24692656] <br />(No info.) |
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* 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. <br />[http://dx.doi.org/10.1016/j.ymgme.2013.12.006 doi:10.1016/j.ymgme.2013.12.006] [http://www.ncbi.nlm.nih.gov/pubmed/24703491 PMID:24703491] <br />(unknown) |
* 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. <br />[http://dx.doi.org/10.1016/j.ymgme.2013.12.006 doi:10.1016/j.ymgme.2013.12.006] [http://www.ncbi.nlm.nih.gov/pubmed/24703491 PMID:24703491] <br />(unknown) |
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Revision as of 16:13, 8 April 2014
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) |
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 |
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
(no info.) - 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. PNAS. 2014.
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.)
