Selected STEM profiles. The five most abundant patterns of changes in transcript abundance through time, ranked by decreasing number of transcripts. Stem pattern 31, which is discussed in the text, is also shown below the dashed line. The full set of STEM profiles are shown in Additional file 4. The vertical axis is relative transcript abundance. The horizontal axis is developmental time, with the 6 time points arranged consecutively on the horizontal axis of each plot, from the first time point (2 HPF) on the left and the last (10 DPF) on the right.