Description

This track displays the location of RNA polyadenylation (polyA) sites based on high-throughput RNA sequencing using the PolyA-Seq protocol.

Display Conventions and Configuration

PolyA-Seq data is strand-specific, therefore two tracks are provided for each tissue. PolyA site positions correspond to a single base, namely the ends of read alignments immediately upstream of the polyadenylation site. The data provided in this track consists of filtered polyA sites (see Methods). When multiple sites occurred within a 30-bp window on the same strand, only the site with the most reads was retained. Units are in reads per million (RPM) aligned. To obtain read counts, multiply RPM values by the total number of filtered reads for the corresponding experiment:

Methods

A detailed explanation of the experimental methods is provided at NCBI's Gene Expression Omnibus under accession GSE30198. Briefly, PolyA+ RNA was reverse-transcribed using a T(10)VN primer and strand-specific universal adapters, amplified, and sequenced on an Illumina GAIIx sequencer. Reads were reverse-complemented, aligned to the corresponding reference genome and splice junctions, and retained only if they aligned uniquely. 3' ends of alignments were considered as polyA sites. These were then filtered using downstream base frequency matrices for true- and false-positive sites determined from a modified experiment based on a T(10) primer (i.e., excluding the 3' VN). When multiple filtered sites occurred within a 30-nt window on the same strand, read counts were summed and attributed to the most abundant peak. For each tissue, read counts were then divided by the total number of reads, in millions, from all filtered sites.

Data Release Policy

No restrictions.