Fig 1.
Schematic of IVT-SAPAS method.
The method mainly includes the steps of RNA fragmentation, two rounds of reverse transcription, PCR and size selection. See the method part for details.
Fig 2.
Characteristics of poly(A) sites.
The reads and poly(A) sites were firstly mapped to the known sites of UCSC and Tian's poly(A) database, and the unmapped were annotated to 3'UTR, intron, CDS, 1kb_downstream and intergenic region. A) Pie-chart of mappig location of reads; B) Distribution of mapping location of poly(A) sites; C) Distribution of poly(A) signals; D) Nucleotide composition flanked poly(A) sites.
Fig 3.
Boxplot of standardized 3'UTR length of genes with tandem APA sites.
To reduce the variance of 3’UTR length across genes, we standardized the length by designating the longest 3’UTR as 1.0 and calculated the weighted mean of 3’UTR length with multiple APA sites for each gene.
Fig 4.
Comparison of TMPRSS3 poly(A) reads distribution between MCF7 and MCF10A.
MCF7 prefers to use the full length transcript compared to MCF10A. The inner graph shows qRT-PCR validation (p<0.01 with t test). Two pair of primers (proximal and distal) were used to measure the expression level of the mRNA isoforms.