Figure 3 | Scientific Reports

Figure 3

From: Transcriptome analysis of developing lens reveals abundance of novel transcripts and extensive splicing alterations

Figure 3

Completely novel transcripts (CNTs) with high conservation score (phastCons Score > 0.8), and expressed in atleast one developmental stage are shown across the panels. Expression profiles are normalized by the maximum expression level of a given transcript across stages and hierarchically clustered using Cluster 3.0 and visualized as a heatmap using Java Treeview. Samples from E15.5 that came from a different study than the rest of the samples were excluded from this expression analysis in order to avoid the batch effect. Heat maps showing the expression profiles of (a) 647 completely novel (novelty score ≥ 70%) transcripts hierarchically clustered with representative transcript groups expressed (b) in only one specific developmental stage and (c) in all the developmental stages. Novelty score (NS) and phastCons score (PS) indices for transcripts are also shown in as an additional scale bar in each heat map. (d) RT-PCR analysis validates expression of two CNTs with a predicted ORF (MSTRG.8249.1 and MSTRG.18685.1) and two CNTs with no known ORF (MSTRG.17446.1 and MSTRG.21639.1) in E15.5, P0 and P10 lenses. Note that MSTRG.17446.1 is undetected in this analysis at stage E15.5. Hprt represents a loading control. Negative control is included for all CNTs tested where the RT-PCR reaction was performed using the same primers as for the CNTs but without any cDNA. Full-length gels are included in Supplementary Information file.