Description
This track displays the location of RNA polyadenylation (polyA) sites based
on high-throughput RNA sequencing using the PolyA-seq protocol.
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, the sum of the reads was attributed to the site with the most reads. 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:
| Sample |
Filtered reads |
| MAQC Universal Human Reference 1 |
5057048 |
| MAQC Universal Human Reference 2 |
5030985 |
| MAQC Brain 1 |
4086039 |
| MAQC Brain 2 |
3921040 |
| Brain |
2980439 |
| Kidney |
4626843 |
| Liver |
5626271 |
| Muscle |
4920121 |
| Testis |
5098780 |
Display Conventions and Configuration
These tracks may be configured in a variety of ways to highlight different
aspects of the displayed data. The graphical configuration options
are shown at the top of the track description page. For more information,
see Configuring
graph-based tracks.
In the full and pack display modes, forward-strand tracks are shown in
red and reverse-strand tracks are shown in black.
In the squish and dense display modes, intensity is represented in grayscale (the darker
the shading, the higher the intensity). To show only selected subtracks, uncheck the boxes next to
the tracks that
you wish to hide.
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 polyA sites. Sites 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.
Credits
These data were generated at Merck Research
Laboratories and submitted by Adnan Derti and Tomas Babak.
Data Release Policy
No restrictions.
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