New Term Proposal: CAGE
submitted by Delph almost 8 years ago

Proposal Details

Reason for Change In the next version of ANISEED database (be careful, new url : http://www.aniseed.cnrs.fr/) we will represent this type of experiment. comment: The cDNA synthesis was carried out by using a 25-?g mRNA and first-strand cDNA primer (oligo dT12-18) with SuperScript II RT in the presence of trehalose and sorbitol. Subsequently, full-length cDNA was selected 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 adjacent to the 5’ ends.MmeI cleaves cDNAs at a sequence 20 and 18 nucleotide away (3’) from its recognition site, creating a two base overhang. After amplification, the sequencing tags are concatenated for high-throughput sequencing. Resulting sort reads are aligned against a reference genome, and downstream analysis is performed.
Contact Info Delphine.DAUGA@ibdml.univmed.fr
Preferred Name CAGE
Provisional id
Parent
Synonyms cap analysis of gene expression EXACT [PMID: 16489339]
Definition A type of transcript expression evidence based on high-throughput (HT) sequencing of 5’ end of cDNA molecule.[ECO:MCC]
mchibucos almost 8 years ago
"ECO:0000309 cap analysis of gene expression" is defined as: "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."