Bisulfite Sequencing

Cited from the paper "Reduction with age in methylcytosine in the promoter region −224∼−101 of the amyloid precursor protein gene in autopsy human cortex"

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Bisulfite genomic sequencing is a sensitive method for the detection of methylated cytosines. 

In this method, sodium bisulfite (NaHSO3) reacts readily with the 5,6-double bond of cytosine but poorly with methylated cytosine. 

The sulfonated cytosine reaction intermediate is readily deaminated to sulfonated uracil from which the sulfonate group can be removed under alkaline conditions to form uracil that is recognized as a thymine by Taq polymerase.

Therefore, after PCR, cytosine remains only at positions where it is methylated in the starting template DNA. 

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Transcripts Tag 'Basic'

What is the "basic" annotation in the GTF/GFF3?

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The transcripts tagged as "basic" form part of a subset of representative transcripts for each gene. This subset prioritises full-length protein coding transcripts over partial or non-protein coding transcripts within the same gene, and intends to highlight those transcripts that will be useful to the majority of users.
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