## Description

The 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:

Species | Sample | Filtered reads
Human | MAQC-UHR1 | 5057048
MAQC-UHR2 | 5030985
MAQC-Brain1 | 4086039
MAQC-Brain2 | 3921040
Brain | 2980439
Kidney | 4626843
Liver | 5626271
Muscle | 4920121
Testis | 5098780
Rhesus | Brain | 2615605
Ileum | 3251495
Kidney | 2666757
Liver | 4299805
Testis | 4836387
Dog | Brain | 4309201
Kidney | 5768315
Testis | 5397546
Mouse | Brain | 1187654
Kidney | 3921370
Liver | 4189409
Muscle | 5517961
Testis | 2364217
Rat | Brain | 5549424
Testis | 7466688

## 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.