Heat maps from pathway enrichment analysis of differentially regulated genes during the transport process.

<p>Significantly regulated genes - at each of the time point [immediately after packing (0 h), and at 48 and 72 h during transport] compared to the values prior to transport (basal) - were subjected to pathway enrichment analysis. Pathways which showed an enrichment of P<0.05 in at least one of the time points are displayed. Columns and rows in the heat map indicate time points and pathways, respectively. Color scale represents P values of enrichment test and gray cells indicate P>0.05.</p

Physiological parameters measured in zebrafish at various stages during the transport process and prior to transport.

<p>Whole body cortisol (n = 15), blood glucose (n = 15), whole body ammonia (n = 7) and liver ammonia (n = 7) were analyzed prior to transport (basal), immediately after packing (0 h), and at 48 and 72 h of transport.</p><p>Different letters indicate statistically significant differences among the different time points (P<0.05).</p><p>Values are given as means ± s.e.m.</p

Heat maps from GO enrichment analysis of differentially regulated genes during the transport process.

<p>Significantly regulated genes - at each of the time point [immediately after packing (0 h), and at 48 and 72 h during transport] compared to the values prior to transport (basal) - were subjected to GO enrichment analysis. Representative biological process GO terms with P<0.05 were selected mostly from 3^rd or 4^th levels of GO trees in at least one of the time points. Columns and rows in the heat map indicate time points and GO terms, respectively. Color scale represents P values of enrichment test and gray cells indicate P>0.05.</p

Validation of microarray results by quantitative real time PCR.

<p>Correlation plots indicating the relationship between qPCR results (fold change; Y- axis)) of six selected genes and the corresponding data from microarray analysis (X- axis). Fold changes of genes immediately after packing (0 h), and at 48 and 72 h during transport compared to the values prior to transport (basal) are displayed in the figure. Note that the fold changes for <i>scd</i> are 1/10^th of the actual changes.</p

Expression profiles of representative genes in selected GO categories.

<p>(A) Carbohydrate metabolic process; (B) Lipid metabolic process; (C) Proteolysis; (D) Amino acid metabolic process; and (E) Oxidation-reduction process. Significantly regulated genes –in at least one of the time points [immediately after packing (0 h), and at 48 and 72 h during transport] compared to the values prior to transport (basal) - are displayed in the heat maps. Columns and rows in the heat map indicate time points and genes, respectively. Color scale represents fold changes of gene expression. Genes belonging to more than one GO category is shown only once under a particular GO term. *indicates significant differences (P<0.05) at a particular time point compared to the expression of the respective genes prior to transport (basal).</p

Venn diagrams indicating the differentially expressed genes in the zebrafish liver during the transport process.

<p>The number of upregulated (A) and downregulated (B) genes immediately after packing (0 h) and at 48 and 72 h during transport compared to the values prior to transport (basal) are marked inside each circle. The genes which have ≥2 fold change in at least one of the pair wise comparisons (between the time points) and significantly altered (P<0.05) compared to basal values are included for each time point.</p

Expression profiles of representative genes in selected GO categories.

<p>(A) Response to stress; (B) Response to chemical stimulus; and (C) Cellular homeostasis. Significantly regulated genes – in at least one of the time points [immediately after packing (0 h), and at 48 and 72 h during transport] compared to the values prior to transport (basal) - are displayed in the heat maps. Columns and rows in the heat map indicate time points and genes, respectively. Color scale represents fold changes of gene expression. Genes belonging to more than one GO category is shown only once under a particular GO term. *indicates significant differences (P<0.05) at a particular time point compared to the expression of the respective genes before transport (basal).</p

Electronic Supplementary Materials from Towards population genomics in non-model species with large genomes; a case study of the marine zooplankton <i>Calanus finmarchicus</i>

ddRAD-seq pilot study on Calanus finmarchicus; Protocols of library preparation and capture in Calanus spp.; Custom analyses scripts used for sequence capture data analyses