Data submission: Difference between revisions
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| [http://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA000991 DRA000991] |
| [http://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA000991 DRA000991] |
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| Phase1 all FREEZE 1.1 data (Phase 1 main paper set) |
| Phase1 all FREEZE 1.1 data (Phase 1 main paper set) |
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| Heliscope CAGE |
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| 1383 libraries in https://fantom5-collaboration.gsc.riken.jp/files/data/shared/FREEZE_PHASE1.1/ |
| 1383 libraries in https://fantom5-collaboration.gsc.riken.jp/files/data/shared/FREEZE_PHASE1.1/ |
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| [http://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA001026 DRA001026] |
| [http://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA001026 DRA001026] |
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| Phase1 additional set 1 (non FREEZE1.1 mast cell 4 samples) |
| Phase1 additional set 1 (non FREEZE1.1 mast cell 4 samples) |
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| Heliscope CAGE |
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| CNhs13924, CNhs13925, CNhs13926, CNhs13927 (in FREEZE2) |
| CNhs13924, CNhs13925, CNhs13926, CNhs13927 (in FREEZE2) |
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| [http://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA001027 DRA001027] |
| [http://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA001027 DRA001027] |
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| Phase1 additional set 2 (non FREEZE1.1 T-reg human 4 samples) |
| Phase1 additional set 2 (non FREEZE1.1 T-reg human 4 samples) |
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| Heliscope CAGE |
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| CNhs13918, CNhs13919, CNhs13920, CNhs13921 (in FREEZE2) |
| CNhs13918, CNhs13919, CNhs13920, CNhs13921 (in FREEZE2) |
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| [http://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA001028 |
| [http://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA001028 DRA001028] |
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| Phase1 additional set 3 (non FREEZE1.1 T-reg mouse 5 samples) |
| Phase1 additional set 3 (non FREEZE1.1 T-reg mouse 5 samples) |
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| Heliscope CAGE |
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| CNhs13913, CNhs14142, CNhs14158, CNhs14159, CNhs14160 (in FREEZE2) |
| CNhs13913, CNhs14142, CNhs14158, CNhs14159, CNhs14160 (in FREEZE2) |
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| Illumina small RNA-Seq |
| Illumina small RNA-Seq |
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| SRhi10066 (tag: TAGCTT, GGCTAC, CTTGTA), SRhi10010 (tag: TTAGGC, CTTGTA, GTGAAA) (in UPDATE22) |
| SRhi10066 (tag: TAGCTT, GGCTAC, CTTGTA), SRhi10010 (tag: TTAGGC, CTTGTA, GTGAAA) (in UPDATE22) |
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=== Phase 1.5 data (opened before Phase 2 paper publication) === |
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{| border="1" cellpadding="10" cellspacing="0" |
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! DRA accession number |
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! data set |
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! library type |
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! library IDs |
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|- |
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| [http://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA002216 DRA002216] |
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| Phase1.5 set 1 (iPS-related 6 samples) |
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| Heliscope CAGE |
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| CNhs14214, CNhs14215, CNhs14216, CNhs14217, CNhs14218, CNhs14219 (in FREEZE2) |
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|} |
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=== Phase 2 data === |
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{| border="1" cellpadding="10" cellspacing="0" |
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! DRA accession number |
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! data set |
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! library type |
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! library IDs |
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|- |
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| [http://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA002711 DRA002711] |
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| Phase1.6 set (HiC-related 15 samples) |
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| Heliscope CAGE |
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| CNhs14104-CNhs14113, CNhs14123-CNhs14127 (in FREEZE2) |
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|- |
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| [http://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA002747 DRA002747](human) [http://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA002748 DRA002748](mouse) |
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| Phase2 set (Phase 2 main paper set that have not been deposited in above deposition) |
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| Heliscope CAGE |
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| 1,607 libraries in FREEZE 2 |
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|} |
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=== sRNA data === |
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{| border="1" cellpadding="10" cellspacing="0" |
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! DRA accession number |
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! data set |
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! library type |
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! library IDs |
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|- |
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| [http://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA003769 DRA003769] |
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| Adipogenesis paper |
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| Illumina small RNA-Seq |
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| SRhi10064 (CGTACG, GAGTGG, GGTAGC), SRhi10065 (ATCACG, CGATGT, TTAGGC, TGACCA, ACAGTG, GCCAAT, CAGATC, ACTTGA, GATCAG, TAGCTT, GGCTAC, CTTGTA, AGTCAA, AGTTCC, ATGTCA, CCGTCC, GTAGAG, GTCCGC) [The dataset was eliminated in the revision of the adipose paper.] |
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|- |
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| [http://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA003804 DRA003804](human) [http://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA003807 DRA003807](mouse) |
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| sRNA paper |
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| Illumina small RNA-Seq |
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| 401 libraries in UPDATE_023 (except for DRA003769 and DRA001101) |
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|- |
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|DRA008211 (chicken, dog, rat) |
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| sRNA ZOO paper |
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| Illumina small RNA-Seq |
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| 17 libraries in UPDATE_030 |
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|} |
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=== RNA-Seq data === |
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{| border="1" cellpadding="10" cellspacing="0" |
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! DRA accession number |
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! data set |
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! library type |
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! library IDs |
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|- |
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| [http://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA004790 DRA004790] |
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| RNA-Seq for lncRNA paper |
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| Illumina RNA-Seq |
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| RDhi10006, RDhi10013, RDhi10020, RDhi10051-RDhi10057, RDhi10059-RDhi10099 |
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|} |
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=== CAGEScan data === |
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{| border="1" cellpadding="10" cellspacing="0" |
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! DRA accession number |
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! data set |
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! library type |
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! library IDs |
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|- |
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| [http://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA005606 DRA005606] |
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| Human CAGEScan |
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| CAGEScan |
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| NCig10013-NCig10068, NCig10126-NCig10131 |
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|} |
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=== CAGE data of other species === |
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{| border="1" cellpadding="10" cellspacing="0" |
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! DRA accession number |
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! data set |
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! library type |
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! library IDs |
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|- |
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| [http://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA004812 DRA004812] |
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| chicken CAGE |
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| Heliscope CAGE |
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| CNhs10485, CNhs11292, CNhs11296, CNhs11299, CNhs11306, CNhs11314, CNhs11922, CNhs12735-CNhs12736, CNhs13027-CNhs13030, CNhs13976-CNhs13981, CNhs14200-CNhs14208, CNhs14210-CNhs14213 |
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|- |
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| [http://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA004813 DRA004813] |
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| dog CAGE |
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| Heliscope CAGE |
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| CNhs10590, CNhs10873, CNhs11053, CNhs11066, CNhs11069-CNhs11070, CNhs11291, CNhs11300, CNhs11304, CNhs11308, CNhs11310, CNhs11895, CNhs12204 |
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|- |
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| [http://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA004814 DRA004814] |
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| rat CAGE |
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| Heliscope CAGE |
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| CNhs10614, CNhs11293, CNhs11295, CNhs11298, CNhs11301-CNhs11302, CNhs11307, CNhs11312-CNhs11313, CNhs11315, CNhs12070-CNhs12072 |
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| Line 48: | Line 163: | ||
| rowspan="3" | [http://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA001100 DRA001100] |
| rowspan="3" | [http://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA001100 DRA001100] |
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| rowspan="3" | Platform comparison |
| rowspan="3" | Platform comparison |
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| |
| Heliscope CAGE |
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| CNhs10325-CNhs10356 (excluding CNhs10333, CNhs10338, CNhs10341, CNhs10346, CNhs10349, CNhs10354) |
| CNhs10325-CNhs10356 (excluding CNhs10333, CNhs10338, CNhs10341, CNhs10346, CNhs10349, CNhs10354) |
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|- |
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| Line 56: | Line 171: | ||
| Illumina RNA-Seq |
| Illumina RNA-Seq |
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| RNig10094-RNig10098, RNig10100-RNig10106 |
| RNig10094-RNig10098, RNig10100-RNig10106 |
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|- |
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| DRA002420 |
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| rowspan="2" | M. Lizio paper |
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| Illumina CAGE |
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| CThi10038,CThi10039,CThi10077-CThi10086 |
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|- |
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| DRA002468 |
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| Illumina ChIP-Seq |
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| PShi10148-10150, PShi10176, PShi10177, PShi10179, PShi10189, PShi10213 |
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|- |
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| [http://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA003273 DRA003273] |
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| L. Dieterich paper |
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| Illumina CAGE |
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| CNhi10365, CNhi10366, CNhi10367 (excluding the below entries) |
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|- |
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| DRA004084 |
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| L. Dieterich paper |
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| Illumina CAGE |
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| CNhi10365.ACG, CNhi10365.AGT, CNhi10365.GCG, CNhi10366.ACC, CNhi10366.ATG, CNhi10366.GCG, CNhi10367.ACG, CNhi10367.ATG, CNhi10367.CAC |
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| Line 64: | Line 198: | ||
* FANTOM Consortium and the RIKEN PMI and CLST (DGT). A promoter-level mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70. <br />[http://dx.doi.org/10.1038/nature13182 doi:10.1038/nature13182] [http://www.ncbi.nlm.nih.gov/pubmed/24670764 PMID:24670764] <br />(DRA000991) |
* FANTOM Consortium and the RIKEN PMI and CLST (DGT). A promoter-level mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70. <br />[http://dx.doi.org/10.1038/nature13182 doi:10.1038/nature13182] [http://www.ncbi.nlm.nih.gov/pubmed/24670764 PMID:24670764] <br />(DRA000991) |
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* Andersson R et al. An atlas of active enhancers across human cell types and tissues. Nature. 2014 Mar 27;507(7493):455-61. <br />[http://dx.doi.org/10.1038/nature12787 doi:10.1038/nature12787] [http://www.ncbi.nlm.nih.gov/pubmed/24670763 PMID:24670763] <br />(DRA000991 DRA001101) |
* Andersson R et al. An atlas of active enhancers across human cell types and tissues. Nature. 2014 Mar 27;507(7493):455-61. <br />[http://dx.doi.org/10.1038/nature12787 doi:10.1038/nature12787] [http://www.ncbi.nlm.nih.gov/pubmed/24670763 PMID:24670763] <br />(DRA000991 DRA001101) |
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* Motakis E et al. Redefinition of the human mast cell transcriptome by deep-CAGE sequencing. Blood. 2014 Mar 26. <br />[http://dx.doi.org/10.1182/blood-2013-02-483792 doi:10.1182/blood-2013-02-483792] [http://www.ncbi.nlm.nih.gov/pubmed/24671954 PMID:24671954] <br />( |
* Motakis E et al. Redefinition of the human mast cell transcriptome by deep-CAGE sequencing. Blood. 2014 Mar 26. <br />[http://dx.doi.org/10.1182/blood-2013-02-483792 doi:10.1182/blood-2013-02-483792] [http://www.ncbi.nlm.nih.gov/pubmed/24671954 PMID:24671954] <br />(DRA000991 DRA001026) |
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* Schmidl C et al. Transcription and enhancer profiling in human monocyte subsets. Blood. 2014 Mar 26. <br />[http://dx.doi.org/10.1182/blood-2013-02-484181 doi:10.1182/blood-2013-02-484181] [http://www.ncbi.nlm.nih.gov/pubmed/24671955 PMID:24671955] <br />(DRA000991) |
* Schmidl C et al. Transcription and enhancer profiling in human monocyte subsets. Blood. 2014 Mar 26. <br />[http://dx.doi.org/10.1182/blood-2013-02-484181 doi:10.1182/blood-2013-02-484181] [http://www.ncbi.nlm.nih.gov/pubmed/24671955 PMID:24671955] <br />(DRA000991) |
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* Schmidl C et al. The enhancer and promoter landscape of human regulatory and conventional T-cell subpopulations. Blood. 2014 Mar 26. <br />[http://dx.doi.org/10.1182/blood-2013-02-486944 doi:10.1182/blood-2013-02-486944] [http://www.ncbi.nlm.nih.gov/pubmed/24671953 PMID:24671953] <br />(DRA000991 DRA001027) |
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* Rönnerblad M et al. Analysis of the DNA methylome and transcriptome in granulopoiesis reveal timed changes and dynamic enhancer methylation. Blood. 2014 Mar 26. <br />[http://dx.doi.org/10.1182/blood-2013-02-482893 doi:10.1182/blood-2013-02-482893] [http://www.ncbi.nlm.nih.gov/pubmed/24671952 PMID:24671952] <br />(no info.) |
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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.) |
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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) |
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* 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. <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.) |
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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) |
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* Frith MC; the FANTOM consortium. Explaining the correlations among properties of mammalian promoters. Nucleic Acids Res. 2014 Mar 27. <br />[http://dx.doi.org/10.1093/nar/gku115 doi:10.1093/nar/gku115] [http://www.ncbi.nlm.nih.gov/pubmed/24682821 PMID:24682821] <br />(No info.) |
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* 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. <br />[http://dx.doi.org/10.1371/journal.pone.0080274 doi:10.1371/journal.pone.0080274] [http://www.ncbi.nlm.nih.gov/pubmed/24676332 PMID:24676332] <br />(No info.) |
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* Medvedeva YA et al. Effects of cytosine methylation on transcription factor binding sites. BMC Genomics. 2014 Mar 26;15(1):119. <br />[http://dx.doi.org/10.1186/1471-2164-15-119 doi:10.1186/1471-2164-15-119] [http://www.ncbi.nlm.nih.gov/pubmed/24669864 PMID:24669864] <br />(No info.) |
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* 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. <br /> [http://dx.doi.org/10.1186/1471-2164-15-120 doi:10.1186/1471-2164-15-120] [http://www.ncbi.nlm.nih.gov/pubmed/24669905 PMID:24669905] <br />(No info.) |
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Latest revision as of 15:58, 29 March 2019
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) | Heliscope 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) | Heliscope CAGE | CNhs13924, CNhs13925, CNhs13926, CNhs13927 (in FREEZE2) |
| DRA001027 | Phase1 additional set 2 (non FREEZE1.1 T-reg human 4 samples) | Heliscope CAGE | CNhs13918, CNhs13919, CNhs13920, CNhs13921 (in FREEZE2) |
| DRA001028 | Phase1 additional set 3 (non FREEZE1.1 T-reg mouse 5 samples) | Heliscope 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) | Heliscope CAGE | CNhs14214, CNhs14215, CNhs14216, CNhs14217, CNhs14218, CNhs14219 (in FREEZE2) |
Phase 2 data
| DRA accession number | data set | library type | library IDs |
|---|---|---|---|
| DRA002711 | Phase1.6 set (HiC-related 15 samples) | Heliscope CAGE | CNhs14104-CNhs14113, CNhs14123-CNhs14127 (in FREEZE2) |
| DRA002747(human) DRA002748(mouse) | Phase2 set (Phase 2 main paper set that have not been deposited in above deposition) | Heliscope CAGE | 1,607 libraries in FREEZE 2 |
sRNA data
| DRA accession number | data set | library type | library IDs |
|---|---|---|---|
| DRA003769 | Adipogenesis paper | Illumina small RNA-Seq | SRhi10064 (CGTACG, GAGTGG, GGTAGC), SRhi10065 (ATCACG, CGATGT, TTAGGC, TGACCA, ACAGTG, GCCAAT, CAGATC, ACTTGA, GATCAG, TAGCTT, GGCTAC, CTTGTA, AGTCAA, AGTTCC, ATGTCA, CCGTCC, GTAGAG, GTCCGC) [The dataset was eliminated in the revision of the adipose paper.] |
| DRA003804(human) DRA003807(mouse) | sRNA paper | Illumina small RNA-Seq | 401 libraries in UPDATE_023 (except for DRA003769 and DRA001101) |
| DRA008211 (chicken, dog, rat) | sRNA ZOO paper | Illumina small RNA-Seq | 17 libraries in UPDATE_030 |
RNA-Seq data
| DRA accession number | data set | library type | library IDs |
|---|---|---|---|
| DRA004790 | RNA-Seq for lncRNA paper | Illumina RNA-Seq | RDhi10006, RDhi10013, RDhi10020, RDhi10051-RDhi10057, RDhi10059-RDhi10099 |
CAGEScan data
| DRA accession number | data set | library type | library IDs |
|---|---|---|---|
| DRA005606 | Human CAGEScan | CAGEScan | NCig10013-NCig10068, NCig10126-NCig10131 |
CAGE data of other species
| DRA accession number | data set | library type | library IDs |
|---|---|---|---|
| DRA004812 | chicken CAGE | Heliscope CAGE | CNhs10485, CNhs11292, CNhs11296, CNhs11299, CNhs11306, CNhs11314, CNhs11922, CNhs12735-CNhs12736, CNhs13027-CNhs13030, CNhs13976-CNhs13981, CNhs14200-CNhs14208, CNhs14210-CNhs14213 |
| DRA004813 | dog CAGE | Heliscope CAGE | CNhs10590, CNhs10873, CNhs11053, CNhs11066, CNhs11069-CNhs11070, CNhs11291, CNhs11300, CNhs11304, CNhs11308, CNhs11310, CNhs11895, CNhs12204 |
| DRA004814 | rat CAGE | Heliscope CAGE | CNhs10614, CNhs11293, CNhs11295, CNhs11298, CNhs11301-CNhs11302, CNhs11307, CNhs11312-CNhs11313, CNhs11315, CNhs12070-CNhs12072 |
Others
| DRA accession number | data set | library type | library IDs |
|---|---|---|---|
| DRA001100 | Platform comparison | Heliscope 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 | |
| DRA003273 | L. Dieterich paper | Illumina CAGE | CNhi10365, CNhi10366, CNhi10367 (excluding the below entries) |
| DRA004084 | L. Dieterich paper | Illumina CAGE | CNhi10365.ACG, CNhi10365.AGT, CNhi10365.GCG, CNhi10366.ACC, CNhi10366.ATG, CNhi10366.GCG, CNhi10367.ACG, CNhi10367.ATG, CNhi10367.CAC |
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
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(No info.)
