CAGE 0-24 hr Embryo (read density)

CAGE sequencing of mixed embryo 5' ends (Celniker project)

General Description

To map transcription start sites (TSSs) genome-wide, we perform CAGE (Cap Analysis of Gene Expression). These CAGE tags are 27-nt sequences that are derived from mRNAs and other long capped transcripts in the vicinity of the 5' cap site. Their mapping onto the genome sequence defines TSSs. CAGE libraries are constructed from first-strand cDNA selected through a biotinylated cap. Second-strand synthesis is dependent upon ligation to the first-strand full-length cDNA of a primer that contains a restriction site for a type II endonuclease allowing the cleavage of 5' 27-bp tags from the resulting cDNA. These short fragments are sequenced using the Illumina GA platform.


  1. Sample preparation: CAGE library preparation, CAGE library sequencing
  2. Data Analysis: StatMap alignment, Histogram of CAGE start sites

Sample Details

  1. Samples: Celniker/RNA:83
  2. External Links: SRX015329

Related modENCODE submissions:

Release Date: 2010-02-15