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

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  Strand: forward reverse
 All Sequence Tech hCAGE  LQhCAGE 
Category
cellLine 
fractionation 
primaryCell 
tissue 
AoSMC response to FGF2 timecourse 
AoSMC response to IL1b timecourse 
ES to cardiomyocyte timecourse 
Embryoid body to melanocyte timecourse 
Epithelial to mesenchymal timecourse 
Human iPS to neuron (Down's syndrome) 1 timecourse 
Human iPS to neuron (Down's syndrome) 2 timecourse 
Human iPS to neuron (wt) 1 timecourse 
Human iPS to neuron (wt) 2 timecourse 
Lymphatic EC response to VEGFC timecourse 
MCF7 response to EGF timecourse 
MCF7 response to HRG timecourse 
MSC to adipocyte (human) timecourse 
Macrophage influenza infection timecourse 
Macrophage response to LPS timecourse 
Myoblast to myotube (wt and DMD) timecourse 
Preadipocyte to adipocyte timecourse 
Rinderpest infection series timecourse 
Saos calcification timecourse 
other samples in timecourse 
Category
 All Sequence Tech hCAGE  LQhCAGE 
List subtracks: only selected/visible    all    ()
  Category↓1 Sequence Tech↓2   Track Name↓3  
dense
 Configure 		 AoSMC response to FGF2 timecourse  hCAGE  Aortic smooth muscle cell response to FGF2, 00hr00min, biol_rep1 (LK1)_CNhs13339_12642-134G5_forward    Data format 
dense
 Configure 		 AoSMC response to FGF2 timecourse  hCAGE  Aortic smooth muscle cell response to FGF2, 00hr00min, biol_rep1 (LK1)_CNhs13339_12642-134G5_reverse    Data format 
dense
 Configure 		 AoSMC response to FGF2 timecourse  hCAGE  Aortic smooth muscle cell response to FGF2, 00hr00min, biol_rep2 (LK2)_CNhs13358_12740-135I4_forward    Data format 
dense
 Configure 		 AoSMC response to FGF2 timecourse  hCAGE  Aortic smooth muscle cell response to FGF2, 00hr00min, biol_rep2 (LK2)_CNhs13358_12740-135I4_reverse    Data format 
dense
 Configure 		 AoSMC response to IL1b timecourse  hCAGE  Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep1 (LK31)_CNhs13349_12652-134H6_forward    Data format 
dense
 Configure 		 AoSMC response to IL1b timecourse  hCAGE  Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep1 (LK31)_CNhs13349_12652-134H6_reverse    Data format 
dense
 Configure 		 AoSMC response to IL1b timecourse  hCAGE  Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep2 (LK32)_CNhs13369_12750-136A5_forward    Data format 
dense
 Configure 		 AoSMC response to IL1b timecourse  hCAGE  Aortic smooth muscle cell response to IL1b, 00hr00min, biol_rep2 (LK32)_CNhs13369_12750-136A5_reverse    Data format 
dense
 Configure 		 primaryCell  hCAGE  CD14+ Monocytes, donor1_CNhs10852_11224-116B9_forward    Data format 
dense
 Configure 		 primaryCell  hCAGE  CD14+ Monocytes, donor1_CNhs10852_11224-116B9_reverse    Data format 
dense
 Configure 		 primaryCell  hCAGE  CD14+ Monocytes, donor2_CNhs11954_11305-117B9_forward    Data format 
dense
 Configure 		 primaryCell  hCAGE  CD14+ Monocytes, donor2_CNhs11954_11305-117B9_reverse    Data format 
dense
 Configure 		 primaryCell  hCAGE  CD14+ Monocytes, donor3_CNhs11997_11381-118B4_forward    Data format 
dense
 Configure 		 primaryCell  hCAGE  CD14+ Monocytes, donor3_CNhs11997_11381-118B4_reverse    Data format 
dense
 Configure 		 primaryCell  hCAGE  CD4+ T Cells, donor1_CNhs10853_11225-116C1_forward    Data format 
dense
 Configure 		 primaryCell  hCAGE  CD4+ T Cells, donor1_CNhs10853_11225-116C1_reverse    Data format 
dense
 Configure 		 primaryCell  hCAGE  CD4+ T Cells, donor2_CNhs11955_11306-117C1_forward    Data format 
dense
 Configure 		 primaryCell  hCAGE  CD4+ T Cells, donor2_CNhs11955_11306-117C1_reverse    Data format 
dense
 Configure 		 primaryCell  hCAGE  CD4+ T Cells, donor3_CNhs11998_11382-118B5_forward    Data format 
dense
 Configure 		 primaryCell  hCAGE  CD4+ T Cells, donor3_CNhs11998_11382-118B5_reverse    Data format 
    
Source data version: FANTOM5 phase2.5
Assembly: Human Feb. 2009 (GRCh37/hg19)

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]