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