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||○||○||○||×|
|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||△||△ 3||△||○|
|Library Preparation Complicatedness||× 4||△||△||◎|
|Data Analysis Tools||△||○||△||○|
- 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.
|Total RNA required||5 μg / sample||Total RNA preferable|
|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 HiSeq 2000/2500|
|Number of reads per lane guaranteed||75 M reads/lane
Approx. 100 - 150 M reads / lane in average
|Standard conditions: 8 - 12 samples per lane.|
|Optional extra sequencing||Number of lanes per analysis||Additional lanes 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||Tables/flat files: number of raw reads, number of extracted tags, number of mapped tags, etc.|