id: ECO:0000310
name: nano-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 reverse transcriptase template switching." [ECO:MCC]
synonym: "nanoCAGE" RELATED [PMID:20543846]
is_a: ECO:0000009 ! transcript expression evidence
relationship: IAO:0000136: GO:0010467 ! is about gene expression
relationship: OBI:0000312: OBI:0001673 ! is_specified_output_of nano-cap analysis of gene expression assay
comment: 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 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 bar code-containing oligonucleotide adaptors. After PCR amplification, the nanoCAGE tags are sequenced by synthesis. NanoCAGE requires as little as 10 nanograms of total RNA.
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Last version checked releases/2019-06-14.
14:06:2019 08:25.
rctauber | Last updated releases/2019-06-14 | |
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