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

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 All Sequence Tech hCAGE 
Category
tissue 
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  Category↓1 Sequence Tech↓2   Track Name↓3  
dense
 Configure
 tissue  hCAGE  amygdala, adult, donor8633_CNhs14182_14610-159A2_forward    Schema 
dense
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 tissue  hCAGE  amygdala, adult, donor8633_CNhs14182_14610-159A2_reverse    Schema 
dense
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 tissue  hCAGE  caudate nucleus, adult, donor8633_CNhs14174_10390-105I3_forward    Schema 
dense
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 tissue  hCAGE  caudate nucleus, adult, donor8633_CNhs14174_10390-105I3_reverse    Schema 
dense
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 tissue  hCAGE  cerebellum, adult, donor8633_CNhs14176_10392-105I5_forward    Schema 
dense
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 tissue  hCAGE  cerebellum, adult, donor8633_CNhs14176_10392-105I5_reverse    Schema 
dense
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 tissue  hCAGE  globus pallidus, adult, donor8633_CNhs14171_10387-105H9_forward    Schema 
dense
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 tissue  hCAGE  globus pallidus, adult, donor8633_CNhs14171_10387-105H9_reverse    Schema 
dense
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 tissue  hCAGE  hippocampus, adult, donor8633_CNhs14180_10396-105I9_forward    Schema 
dense
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 tissue  hCAGE  hippocampus, adult, donor8633_CNhs14180_10396-105I9_reverse    Schema 
dense
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 tissue  hCAGE  locus coeruleus, adult, donor8633_CNhs14172_10388-105I1_forward    Schema 
dense
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 tissue  hCAGE  locus coeruleus, adult, donor8633_CNhs14172_10388-105I1_reverse    Schema 
dense
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 tissue  hCAGE  medial frontal gyrus, adult, donor8633_CNhs14177_10393-105I6_forward    Schema 
dense
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 tissue  hCAGE  medial frontal gyrus, adult, donor8633_CNhs14177_10393-105I6_reverse    Schema 
dense
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 tissue  hCAGE  medial temporal gyrus, adult, donor8633_CNhs14179_10395-105I8_forward    Schema 
dense
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 tissue  hCAGE  medial temporal gyrus, adult, donor8633_CNhs14179_10395-105I8_reverse    Schema 
dense
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 tissue  hCAGE  medulla oblongata, adult, donor8633_CNhs14175_10391-105I4_forward    Schema 
dense
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 tissue  hCAGE  medulla oblongata, adult, donor8633_CNhs14175_10391-105I4_reverse    Schema 
dense
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 tissue  hCAGE  occipital cortex, adult, donor8633_CNhs14169_10385-105H7_forward    Schema 
dense
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 tissue  hCAGE  occipital cortex, adult, donor8633_CNhs14169_10385-105H7_reverse    Schema 
dense
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 tissue  hCAGE  parietal gyrus, adult, donor8633_CNhs14181_14609-159A1_forward    Schema 
dense
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 tissue  hCAGE  parietal gyrus, adult, donor8633_CNhs14181_14609-159A1_reverse    Schema 
dense
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 tissue  hCAGE  putamen, adult, donor8633_CNhs14178_10394-105I7_forward    Schema 
dense
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 tissue  hCAGE  putamen, adult, donor8633_CNhs14178_10394-105I7_reverse    Schema 
dense
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 tissue  hCAGE  spinal cord, adult, donor8633_CNhs14168_10384-105H6_forward    Schema 
dense
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 tissue  hCAGE  spinal cord, adult, donor8633_CNhs14168_10384-105H6_reverse    Schema 
dense
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 tissue  hCAGE  substantia nigra, adult, donor8633_CNhs14173_10389-105I2_forward    Schema 
dense
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 tissue  hCAGE  substantia nigra, adult, donor8633_CNhs14173_10389-105I2_reverse    Schema 
dense
 Configure
 tissue  hCAGE  thalamus, adult, donor8633_CNhs14170_10386-105H8_forward    Schema 
dense
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 tissue  hCAGE  thalamus, adult, donor8633_CNhs14170_10386-105H8_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]