Category:ECO:0000309 ! cap analysis of gene expression evidence

name: cap analysis of gene expression evidence
def: "A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by a cap-trapper system." [ECO:MCC]
synonym: "CAGE" EXACT [PMID:16489339]
is_a: ECO:0000009 ! transcript expression evidence
relationship: IAO:0000136: GO:0010467 ! is about gene expression
relationship: OBI:0000312: OBI:0001674 ! is_specified_output_of cap analysis of gene expression assay
comment: Complementary DNA (cDNA) is synthesized from microgram quantities of mRNA using first-strand cDNA primer (oligo dT12-18) and reverse transcriptase in the presence of trehalose and sorbitol, followed by selection of full-length cDNA with biotinylated cap-trapper. Linkers are attached to the 5' ends of full-length enriched cDNAs to introduce a recognition site for the restriction endonuclease MmeI, which creates a two base overhang. After amplification, sequencing tags are concatenated for high-throughput sequencing. Resulting sort reads are aligned against a reference genome, and downstream analysis is performed.