nanoCAGE™/CAGE™scan Library : Overview

nanoCAGE™ Library

With a sensitivity one thousand times higher than CAGE, nanoCAGE presents powerful new possibilities for the analysis of small-sized samples as little as 500 ng of total RNA. NanoCAGE/CAGEscan overcomes the difficulty of obtaining large quantity of cells for studying and future diagnosing diseases such as cancer and neuron.

As the joint developer with RIKEN of the technology, DNAFORM nanoCAGE/CAGEscan library preparation service provides the end-to-end solution for gemone-wide semi-quantitative expression analysis including library construction, high-throughput sequencing on the Illumina HiSeq platforms and comprehensive data analysis.

nanoCAGE/CAGEscan is a modified technique of CAGE, Cap Analysis fo Gene Expression, that enables genome-wide promoer analysis of small-amount of samples. nanoCAGE/CAGEscan, as well as CAGE, is a tag-based gene expression analysis. Template-switching reaction and csemisuppressive PCR in combined with CAGE, realized significant reduction of sample required. CAGEscaand basically 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. Several articles performing transcriptome analysis with nanoCAGE in human and mouse has been published.


  • Genome-wide gene expression analysis with tiny samples
  • Prediction of promoter sites with small amount of sample
  • Semi-quantitative gene expession profiling

What can nanoCAGE/CAGEscan offers

  • Overcoming limiting sample :Only 500 ng of total RNA is required.
  • New data:Enabling analysis of 3'-end at once.
  • Unique data:CAGE enables experimental identification of transcriptional start sites and quantification of promoter activity.
  • Wide dynamic range:CAGE also enables detection of rare transcripts.

How to choose CAGE and nanoCAGE/CAGEscan

Library Advantage Disadvantage
CAGE Quantitative expression profile without PCR bias 5 μg of total RNA is reqired
  • Only 500 ng of total RNA is required.
  • 3'-end analysis with the same library is possible
PCR step during the library preparation may cause PCR biases on the expression profile.

nanoCAGE™/CAGE™scan Library Service

Technical details

Item Specification Comment
Total RNA requirements 500 nanogram Total RNA preferable
RNA entry QC Agarose gel with the bioanalyzer We perform entry QC on all samples
CAGE library deliverable several nanograms DNA fragments purification with gel
Sequencing platform Illumina
Number of reads per channel guaranteed 4,000,000 reads/channell Standard conditions: 1 Channel per sample. Additional sequences can be obtained at extra charges.
Optional sequencing Number of channels per analysis 1 sample/1 channel is standard. Addtional channel needs addtional carge.
Data analysis Extract tags from reads -> mapping tags to genome -> clustering tags based on genome locations and window size. Standard approach. Clustering results may vary with window size. Different option is available.
Mapping rate About 50% of tags map to unique mapping position One experiment should provide the customer with at least 1,000,000 mappable CAGE tags.
Sequence data Provided with Illumina file format Delimited text files holding sequence information and quality scores.
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 nanoCAGE/CAGEscan library preparation in a flat text file format.