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.
CAGE | RNA-seq | SAGE | Microarray | |
de novo Gene Finding | good | good | good | N/A |
---|---|---|---|---|
Gene Expression Quantification | superior*1 1 *1 free of PCR bias unaffected by gene size |
good | good | average |
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 |
average*3 2 *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 |
N/A | N/A |
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.
Specification | Comment | |
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 Illumina NGS sequencer. |
Sequencing platform | Illumina NextSeq 500/2000 | |
Number of reads per sample guaranteed | 15M reads/sample | |
Additional reads are available with additional charge | Number of lanes per sample | |
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. |
Learn More About the Analysis Methodology
See details about sequencing, visualization, and analysis of data.