CAGE Preparation Kit

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CAGE Preparation Kit

CAGE Preparation Kit is a ready-to-use product that includes reagents* and the protocol necessary for the preparation of a CAGE library, which allows the easy introduction of Cap Analysis of Gene Expression, CAGE, into your R&D.
* Note: Reverse Transcriptase is not inclued.

CAGE 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.

A sequencing run using one channel on the Illumina Sequencer can yield over 4,000,000 reads per sample. Expression profiles obtained from DeepCAGE (i.e., combination of next-generation sequencing with next-generation expressing profiling) will be powerful tools for various gene expression analyses and genome annotation projects.


  • Genome-wide gene-expression analysis
  • Prediction of promoter sites
  • Quantitative mRNA expression profiling

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)
  • "Gene Networks project" by the Ministry of Education, Culture, Sports, Science and Technology

Product specifications

  • The cap-trapper method involves capturing the 5'-cap of mRNA while removing rRNA.
  • The random priming method allows generation of hybridization products from non-coding mRNAs, in addition to those from mRNAs
  • The use of barcodes allows multiplex sequence analysis.
  • Prepared CAGE libraries can be analyzed with an Illumina next-generation DNA sequencer.
  • Note: the CAGE Kit does not contain reverse transcriptase.

For data analysis, Platform system for next-generation sequencing (NGS) data analysis is available at the National Institutes of Genetics.
National Institutes of Genetics > NGS Analysis Platform

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Technical Information

CAGE is a novel approach for identifying promoters and gene expression profiling.
CAGE is based on full-length cDNA library technology for next-generation sequencing technologies, where an adaptor is ligated to the 5’ end of each full-length cDNA. By mapping genomic sequences on the CAGE tags, transcriptional start sites can be identified. Thus, CAGE can be a powerful tool for discovery of novel genes, genome-wide gene-expression profiling, and promoter analysis.

Sample Data Download

Downlod the raw fastq data, processed fastq data, reference genome, and analysis results
* The file may take some time to download as the total data size is 32.6GB.

Difference from RNA-Seq and other gene analysis techniques

Different from Microarray and RNA-seq, CAGE is able to accurately identify transcriptional start sites (TSSs) and the corresponding promoter regions through sequencing the 3’ end of cDNA (5’ end of RNA). This makes CAGE a powerful tool to analyze the gene regulation in the TSSs level, enabling analysis of the gene regulated by multiple alternative promoters. Therefore, CAGE can serve as a new perspective approach for genome annotation, by elucidating transcriptional signaling cascades, and performing other functions.

Comparison among major gene expression analysis techniques
CAGE RNA-seq SAGE Microarray
de novo Gene Finding ×
Gene Expression Quantification 1
Determining Promoter Site × ×
Motif Finding for Transcription Factor Binding Site × 2 × 2
Identification of Bidirectional Enhancer RNA × × ×
Determining Transcription Start/1st Exon Site × ×
Determining Gene Structure (intron/exon, alternative splicing variants) × 3 × ×
Duration of Work Process
Library Preparation Complicatedness × 4
Data Analysis Tools
  • 1 free of PCR biasunaffected by gene size
  • 2 depending on known 5' end sequence information
  • 3 depending on sequence depth
  • 4 8 days

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Reagent quantities support 8 library preparations.

  • Item:CAGE Library preparation kit 8 sample version
  • 2,000 USD

Reagent quantities support 48 library preparations.

  • Item:CAGE Library preparation kit 48 sample version
  • 10,000 USD

Shipping and Packing Charge

Domestic Shipment

No additional shipping charge.

Global Shipment

Shipping costs, packaging costs, commission is not included for global delivery. Costs depend on the shipping destination region and product form.
Please refer our price list for shipping and packing charge.
Shipping and Packing Charge

Import duties, taxes, and charges are not included in the item prices or shipping cost. These charges are the customer's responsibility. Please check with your country's customs office to determine what these additional costs will be prior to placing your order. All transactions will be conducted in JPY.

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