Figure 2

Validation of selected poly(A)+ and poly(A)- transcripts. (a-c) Validation of known poly(A)- transcripts. Y-axis: normalized read densities of each gene from the UCSC genome browser (left panels). Quantitative RT-PCR (qRT-PCR) was performed with independent poly(A)+ and poly(A)- sample preparations, and the relative signals from each enriched RNA preparation were normalized to those in the total RNA preparations from different cell lines (right panels). Note that the signals for poly(A)- transcripts were significantly enriched in the poly(A)- samples. (d-e) Validation of known poly(A)+ transcripts. Normalized read densities (left panels) and qRT-PCRs (right panels) were analyzed as described above. Note that the signals for poly(A)+ transcripts were significantly enriched in the poly(A)+ samples. Grey, poly(A)+ sample from H9 cells; black, poly(A)- sample from H9 cells; pink, poly(A)+ sample from HeLa cells; red, poly(A)- sample from HeLa cells. Dashed lines, the cutoff ratio used to assign poly(A)+ and poly(A)- transcripts (the abundance in either poly(A)+ or poly(A)- fractionation accounts for more than one-third when compared to the total RNA). Gene models are shown beneath the UCSC genome browser screenshots. See text for details. These descriptions are also used for other figures throughout this study. Error bars were calculated from three biological repeats.