Figure 1.
Distribution of transcript entries and total transcript counts over different tag abundance categories.
Categories of transcript abundance were assigned by setting the lower limit of the count number that includes the transcript as a category member. The percentages of total transcript counts and number of different transcript entries per category are plotted on a logarithmic scale (base 10).
Figure 2.
Real-time validation of RNA-seq data.
The relative expression level of the genes selected was shown in log2 fold change as compared with a housekeeping gene, ef1a (10680.1 RKPM).
Figure 3.
Gene ontology slim classification for the entire swimbladder transcriptome under Biological process, Molecular function and Cellular component classifications.
Slim classifications of the total ZGC database entries and swimbladder transcriptome are represented by blue and red bars, respectively. Astrid is used to label significantly enriched categories in the swimbladder (FDR<0.01).
Figure 4.
Gene ontology classification (a) and energy distribution (b) of the swimbladder transcriptome.
Gene ontology classification and energy distribution are based on GO Slim classification of molecular functions. Genes without gene ontology information constitute 40% of the total swimbladder transcriptome and they were not included in the pie chart.
Table 1.
Top 50 enriched Unigenes in the swimbladder with annotation.
Table 2.
Top 20 enriched transcription factors in the swimbladder.
Figure 5.
Expression of hoxc4a, hoxc6a and hoxc8a in developing zebrafish swimbladder. (a, e, i, m).
Expression of hoxc4a in the swimbladder at 36 hpf (a), 60 hpf (e) and 72 hpf (i, m). (b, f, j, n) Expression of hoxc6a in the swimbladder at 36 hpf (b), 60 hpf (f) and 72 hpf (j, n). (c, g, k, o) Expression of hoxc8a in the swimbladder at 36 hpf (c), 60 hpf (g) and 72 hpf (k, o). (d, h, l, p) Expression of foxf1 in the swimbladder at 36 hpf (d), 60 hpf (h), and 72 hpf (l, p). Panels (a–l) are lateral view of embryos after whole mount in situ hybridization and panels (m–p) are cross-sections of in situ hybridized embryos. Swimbladder is indicated by red dashed-line circles or red arrows. Numbers are used to mark the position of somite 1–4.
Figure 6.
Comparison of zebrafish and human (a) or mouse (b) transcriptome tissues by GSEA.
Each intersection of the two zebrafish and human or mouse tissues was split into two cells. Upper cell shows NES, and lower cell shows the corresponding FDR. **: very significant (p<0.001), *: significant (p<0.05).