CAGE - What can it do for you?
- Highly sensitive and accurate quantitative transcriptome analysis not only as a gene, but as a Transcription Start Site (TSS).
- Reliable way to discover Transcription Factor binding motif based on the true TSS nearby the actual promoter.
- Unique and powerful tool to discover alternative promoters for all endogenous genes.
- Help you to discover new biomarker and/or bidirectional enhancer RNA.
- Clarifying the heterogeneity and complexity of transcriptomes from the view of Cause of Transcription instead of expression profiling.
- Linking expression values to promoter sites for a better understanding of how signaling pathways regulate transcription.
- PCR-free operation procedures provide unbiased quantification of transcript amount.
Difference from RNA-Seq and other gene expression 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.
|de novo Gene Finding||good||good||good||N/A|
|Gene Expression Quantification||superior*1 1
*1 free of PCR bias unaffected by gene size
|Determining Promoter Site||superior||average||N/A||N/A|
|Motif Finding for Transcription Factor Binding Site||superior||average||average*2 2
*2 depending on known 5' end sequence information
*3 depending on known 5' end sequence information
|Identification of Bidirectional Enhancer RNA||superior||N/A||N/A||N/A|
|Determining Transcription Start/1st Exon Site||superior||average||N/A||N/A|
|Determining Gene Structure (intron/exon, alternative splicing variants)||N/A||average*43
*4 depending on sequence depth
|Duration of Work Process||average||average||average||good|
|Library Preparation Complicatedness||Long Time 4 (8 days)||average||average||easy|
|Data Analysis Tools||average||good||average||good|
("N/A" means not applicable)
- 1 free of PCR bias and unaffected by gene size
- 2 depending on known 5' end sequence information
- 3 depending on sequence depth
- 4 8 days
What is the CAGE method?
Cap Analysis of Gene Expression (CAGE) is a method for promoter identification and transcription profiling developed by RIKEN (Patent Number: US 6174669, US 6221599, US8809518, etc.). CAGE utilizes a “cap-trapping” technology based on the biotinylation of the 7-methylguanosine cap of Pol II transcripts, to pull down the 5’-complete cDNAs reversely transcribed from the captured transcripts. Through a massive parallel sequencing of the 5’ end of cDNA and analysis of the sequenced tags, transcription start sites and transcripts amount are inferred on a genome-wide scale. Thus, CAGE provides an effective genome-wide transcriptional profiling as an alternative to microarray and RNA-seq.
We are offering CAGE library preparation service with or without sequencing & basic bioinformatics analysis.
|Total RNA required||3 μg of total RNA/sample for PCR free CAGE library||If possible, please provide 12μg of total RNA for PCR free CAGE library preparation service.
CAGE library can be prepared from few 100ng of total RNA, by adding PCR amplification.
|RNA entry QC||Bioanalyzer||We perform entry QC on all samples.|
|DNA amount of CAGE library||Several ng||DNA fragments ready for illumine NGS sequencer.|
|Sequencing platform||Illumina NextSeq 500|
|Number of reads per sample guaranteed||15M reads/sample|
|Optional extra sequencing||Number of lanes per sample||Additional reads are available with additional charge.|
|Mapping rate||About 75% of tags map to unique mapping position||4 M mappable CAGE tags / sample is guaranteed.|
|Sequence data||Provided with Illumina file format||Delimited text files holding sequence information and quality scores.|
|Data Analysis||Mapping positions, Read count quantification, CTSS clustering, Differential expression analysis, Gene Ontology enrichment analysis and Transcriptional Factor binding motif search||Tables/flat files: number of raw reads, number of extracted tags, number of mapped tags, etc.|