TSS activity(TPM) Track Settings
 
TSS activity per sample(TPM)

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Select subtracks by sequence tech and category: (help)

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 All Sequence Tech hCAGE  LQhCAGE 
Category
primaryCell 
tissue 
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  Category↓1 Sequence Tech↓2   Track Name↓3  
dense
 Configure
 primaryCell  hCAGE  Canine Aortic Smooth Muscle cells, donor1_CNhs11895_11297-117B1_forward    Schema 
dense
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 primaryCell  hCAGE  Canine Aortic Smooth Muscle cells, donor1_CNhs11895_11297-117B1_reverse    Schema 
dense
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 primaryCell  hCAGE  Canine Aortic Smooth Muscle cells, donor2_CNhs11300_11374-118A6_forward    Schema 
dense
 Configure
 primaryCell  hCAGE  Canine Aortic Smooth Muscle cells, donor2_CNhs11300_11374-118A6_reverse    Schema 
dense
 Configure
 primaryCell  hCAGE  Canine Aortic Smooth Muscle cells, donor3_CNhs11070_11446-118I6_forward    Schema 
dense
 Configure
 primaryCell  hCAGE  Canine Aortic Smooth Muscle cells, donor3_CNhs11070_11446-118I6_reverse    Schema 
dense
 Configure
 primaryCell  LQhCAGE  Canine Aortic Smooth Muscle cells - differentiated, donor1 _CNhs12204_11470-119C3_forward    Schema 
dense
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 primaryCell  LQhCAGE  Canine Aortic Smooth Muscle cells - differentiated, donor1 _CNhs12204_11470-119C3_reverse    Schema 
dense
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 primaryCell  hCAGE  Canine Aortic Smooth Muscle cells - differentiated, donor2_CNhs11066_11471-119C4_forward    Schema 
dense
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 primaryCell  hCAGE  Canine Aortic Smooth Muscle cells - differentiated, donor2_CNhs11066_11471-119C4_reverse    Schema 
dense
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 primaryCell  hCAGE  Canine Aortic Smooth Muscle cells - differentiated, donor3_CNhs11053_11472-119C5_forward    Schema 
dense
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 primaryCell  hCAGE  Canine Aortic Smooth Muscle cells - differentiated, donor3_CNhs11053_11472-119C5_reverse    Schema 
dense
 Configure
 primaryCell  hCAGE  Canine hepatocytes, donor1_CNhs10873_11244-116E2_forward    Schema 
dense
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 primaryCell  hCAGE  Canine hepatocytes, donor1_CNhs10873_11244-116E2_reverse    Schema 
dense
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 primaryCell  hCAGE  Canine hepatocytes, donor2_CNhs11069_11325-117E2_forward    Schema 
dense
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 primaryCell  hCAGE  Canine hepatocytes, donor2_CNhs11069_11325-117E2_reverse    Schema 
dense
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 primaryCell  hCAGE  Canine hepatocytes, donor3_CNhs11308_11407-118E3_forward    Schema 
dense
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 primaryCell  hCAGE  Canine hepatocytes, donor3_CNhs11308_11407-118E3_reverse    Schema 
dense
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 primaryCell  hCAGE  Canine Mesenchymal stem cells - bone marrow derived, donor1_CNhs11291_11293-117A6_forward    Schema 
dense
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 primaryCell  hCAGE  Canine Mesenchymal stem cells - bone marrow derived, donor1_CNhs11291_11293-117A6_reverse    Schema 
dense
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 primaryCell  hCAGE  Canine Mesenchymal stem cells - bone marrow derived, donor2_CNhs11304_11370-118A2_forward    Schema 
dense
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 primaryCell  hCAGE  Canine Mesenchymal stem cells - bone marrow derived, donor2_CNhs11304_11370-118A2_reverse    Schema 
dense
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 primaryCell  hCAGE  Canine Mesenchymal stem cells - bone marrow derived, donor3_CNhs11310_11442-118I2_forward    Schema 
dense
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 primaryCell  hCAGE  Canine Mesenchymal stem cells - bone marrow derived, donor3_CNhs11310_11442-118I2_reverse    Schema 
dense
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 tissue  hCAGE  Universal RNA - Dog Normal Tissues Biochain, pool1_CNhs10590_10006-101B2_forward    Schema 
dense
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 tissue  hCAGE  Universal RNA - Dog Normal Tissues Biochain, pool1_CNhs10590_10006-101B2_reverse    Schema 
    
Source data version: FANTOM5 phase2.5

Description - FANTOM5

Regulated transcription controls the diversity, developmental pathways, and spatial organization of the hundreds of cell types that make up a mammal. In FANTOM5 ( http://fantom.gsc.riken.jp/5/ ), we mapped transcription start sites (TSS) and their usage in human, mouse, dog, rat, macaque and chicken primary cells, cell lines and tissues to produce a comprehensive overview of gene expression across the human body by using single molecule sequencing. This datahub is set up to provide the TSS activities in individual biological states and the identified regions. Please visit the web site for further data exploration and with details.

Methods

5′-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS activities in the sample. The read counts tracks indicate raw counts of CAGE reads, and the TPM tracks indicate normalized counts as TPM (tags per million).

Categories of individual samples
- Cell Line hCAGE
- Cell Line LQhCAGE
- fractionation hCAGE
- Primary cell hCAGE
- Primary cell LQhCAGE
- Time course hCAGE
- Tissue hCAGE

Credits

Please send us any questions regarding to this trackHub and underlying data.

References

  • The FANTOM5 project
  • Transcribed Enhancer Atlas
  • The FANTOM5 reprocessed data
  • Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, et al. Science. 2015 Feb 27;347(6225): 1010-4. doi: 10.1126/science.1259418. Epub 2015 [PMID: 25678556]
  • Gateways to the FANTOM5 promoter level mammalian expression atlas. Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S, et al. Genome Biol. 2015 Jan 5;16:22. doi: 10.1186/s13059-014-0560-6. [PMID: 25723102]
  • A promoter-level mammalian expression atlas. Forrest ARR, Kawaji H, Rehli M, Baillie JK, de Hoon MJL, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M et al. Nature. 2014 Mar 27;507(7493):462-70. [PMID: 24670764]
  • An atlas of active enhancers across human cell types and tissues. Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, et al. Nature. 2014 Mar 27;507(7493):455-61. [PMID: 24670763]