G2_e11_5_cf_p300 Track Settings
 
GBBT_2_mm_CD1_e11_5_cf_p300_pks_fm

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Data schema/format description and download
Assembly: Mouse Dec. 2011 (GRCm38/mm10)
Data last updated at UCSC: 2014-02-03 11:39:19


Note: These data were converted via liftOver from the July 2007 (NCBI37/mm9) version of the track

Description

Tracks description

- GBBT-2_mm-CD1_e11.5_craniofacial_p300.bed track displays the list of all called peaks after filtering against a number of likely artifacts (see 'rejected peaks' track for details).

Methods

Antibody

An antibody directed against the enhancer-associated p300 protein was used (Santa Cruz: SC-585). This antibody has previously been validated as a mark associated with in vivo enhancers (Nature 457:854-8)

Tissue

Craniofacial tissue was dissected from ~100 mouse embryos (CD-1 strain) at e11.5. Embryo stage was determined based on time since mating. Only embryos whose overall craniofacial morphology was consistent with a developmental stage of e11.0-e12.0 were used.

Sequencing and Data Analysis

Short-read data was generated using the Illumina GAII sequencing platform. Reads were mapped to the genome and peaks were called using the MACS algorithm (Genome Biol.9:R137).

Data Set Properties

Uniquely Mapped Reads: 6'159'862

Called Peaks: 1'510

Peaks <1kb away from transcription start sites (TSS): 25%

Peaks 1-10kb away from TSS: 17.5%

Peaks 10-100kb away from TSS: 41.1%

Peaks >100kb away from TSS: 16.4%

Credits

This data was generated by the Visel laboratory (Lawrence Berkeley National Laboratory). Questions and comments should be directed to Axel Visel.

Facebase Project Details

References

Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M. Source Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature. 2009 Feb 12;457(7231):854-8.

Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myer Source Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. Epub 2008 Sep 17.