New Term Proposal: nanoCAGE
submitted by
about 13 years ago
| 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 tag for this term: nanoCAGE captures the 5? ends of molecules by template switching. When polymerizing the cDNA of a capped mRNA, the reverse transcriptase adds extra cytosines that are complementary to the cap. Each 5? full length cDNAs is extended upon hybridization of the riboguanosine-tailed template-switching oligonucleotides to these extra cytosines. In the semisuppressive PCR, the short templates fold intramolecularly and prevent the binding of primers which precludes amplification; longer molecules are less likely to fold and are thus amplified. Templates derived from reaction artifacts form stable homoduplexes, also precluding amplification. After template-switching, semisuppressive PCR and EcoP151 cleavage, 25-bp tags are ligated to barcode-containing oligonucleotide adaptors. After PCR amplification, the nanoCAGE tags are sequenced by synthesis. |
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| Contact Info | Delphine.DAUGA@ibdml.univmed.fr |
| Preferred Name | nanoCAGE |
| Provisional id | |
| Parent | |
| Synonyms | nano-cap analysis of gene expression EXACT [PMID: 21205859] |
| Definition | A type of transcript expression evidence based on high-throughput (HT) sequencing of 5’ end of cDNA molecule from as little as 10ng of total RNA. [ECO:MCC] |
"ECO:0000310 nano-cap analysis of gene expression" is defined: "A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by reverse transcriptase template switching."