TSS activity(read counts) Track Settings
 
TSS activity per sample(read counts)

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Category
cellLine 
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qualitycontrol 
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BMM TB activation IFNg timecourse 
BMM TB activation IL13 timecourse 
BMM TB activation IL4 timecourse 
BMM TB activation IL4-IL13 timecourse 
BMM TB infection control timecourse 
ES to neuron timecourse 
J2E erythrocytic differentiation (EPO) timecourse 
MSC to adipocyte (mouse) timecourse 
MSC to osteocyte (mouse) timecourse 
T-cell differentiation timecourse 
Tracheal to ciliated epithelium timecourse 
Trophoblast differentiation timecourse 
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Source data version: FANTOM5 phase2.5
Assembly: Mouse July 2007 (NCBI37/mm9)

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]