Use of DNA sequencing of RNA-derived material to characterize expressed products and their abundances. Tissue composition and developmental stage must be controlled when comparing gene expression across lineages.
A method for detecting differential RNA-modification signals using Gaussian mixture distributions of nanopore current, with condition-specific component proportions. A shifted signal requires biological interpretation as well as statistical separation.[ref]
Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore by Ploy N. Pratanwanich and others. Method overview: shared current distributions and sample-specific modification fractions
A nuclear run-on and capped-end mapping method for characterizing transcription initiation. It is useful for comparing nascent initiation with the surviving mature transcript population.[ref]
Cap analysis of gene expression: sequencing capped RNA ends to characterize start-site usage. Differential survival or capping of transcripts can alter the observed distribution without a matching change in nascent initiation.
Thiol-linked alkylation used with metabolic RNA labelling to identify newly synthesized RNA through characteristic sequencing changes after 4-thiouridine incorporation.[ref]
Profiling RNA from individual isolated cell nucleus preparations. The preparation samples nuclear and often incompletely processed transcripts, so its intron counts are not interchangeable with mature cytoplasmic messenger RNA counts.
Sequencing designed to span long portions of individual RNA molecules or derived Complementary DNA. Linking distant exons on one molecule helps resolve complete transcript isoforms, while per-base errors and sampling depth still require control.
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