Custom CAGE™ Library Preparation & Analysis

CAGE Library

DNAFOM CAGE library preparation services ensure all your bases are covered providing an end-to-end unique transcriptome solution including library construction, sequencing on the Illumina HiSeq platforms and comprehensive data analysis.

CAGE, Cap Analysis of Gene Expression, enables sequencing and mapping of short tags derived from the 5'-end of mRNA, thereby quantifying the frequency of tag sequences. A distinctive feature of CAGE is its capability to accurately identify promoter sites for each transcript and obtain gene expression profiles based on identified promoters.

As genome sequence variations are beginning to be understood on an individual level, attention is now turning to the transcriptome and the effects that differential levels of gene transcription and its promoter activities have on phenotype such as disease susceptibility, cancer progression and biomarker discovery. Expression profiles obtained from CAGE in combination of next-generation sequencing will be powerful tools for various transcriptome projects.


  • Genome-wide gene expression analysis
  • Prediction of promoter position on the genome
  • Quantitative measurement of mRNA expression
  • Biomarker discovery

What CAGE Can Offer You?

  • Unique data:CAGE enables experimental identification of transcriptional start sites and quantification of promoter activity.
  • Wide range of applications:CAGE technology supports transcriptome analysis of a variety of organisms including human and mouse.
  • Wide dynamic range:CAGE also enables detection of rare transcripts.

Examples of actual usage of CAGE

  • "Functional Annotation of Mouse (FANTOM) project" by RIKEN
  • "Encyclopedia of DNA Elements (ENCODE) project" by the National Institute of Health (NIH)
  • "Genome Network Project" by the Ministry of Education, Culture, Sports, Science and Technology

CAGE Library Service Specifications

Technical details

Item Specification Comment
RNA requirements 5 microgram total RNA preferable
RNA QC Bio Analyzer We perform entry QC on all samples
CAGE library deliverable several nanograms Gel purified DNA fragments
Sequencing platform Illumina
Number of reads per channel guaranteed 4,000,000 reads/channel Standard conditions: 1 Channel per sample. Additional sequences can be obtained at extra charges.
Data analysis Extract tags from reads>>>mapping tags to genome>>>clustering tags based on genome locations and window size. Standard approach. Mapping procedures may have to developed for genomes other than human and mouse.
Mapping rates About 50% of tags map to unique mapping position One experiment should provide the customer with at least 1,000,000 mappable CAGE tags.
Description of deliverables: Sequencing data Illumina files Delimited text files holding sequence information and quality scores.
Description of deliverables: Data analysis Mapping positions Tables/flat files: number of raw reads, number of extracted tags, number of mapped tags.

  • Estimated Turn-around-times: About 2 months.
  • Documentation: Report on CAGE library preparation in a flat text file format.