CAGE kc167 Nuclear RNA

CAGE sequencing and alignment of Dm Cell Line kc167_Nuclear_RNA 5' ends (Celniker project, Celniker subgroup)


CAGE libraries were created from 5' ends of RNA isolated from the D. melanogaster kc167_Nuclear_RNA (2 reps), sequenced using Illumina GAIIx, and aligned to the D. melanogaster r5 genome using StatMap. Tracks show read alignments and density.
Total read count: 35076598
Mapped read count: 8738414
Alignment rate: 24%

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: Histogram of CAGE start sites
  3. Other Protocols: StatMap alignment

Sample Details

  1. Samples: Celniker/RNA:876 (modENCODE_3970:Celniker/RNA:876), Celniker/RNA:879 (modENCODE_3970:Celniker/RNA:879)
  2. External Links: SRR488274, SRR488276

Referenced modENCODE submissions:

Related modENCODE submissions:

Release Date: 2012-08-15