Supplemental Material for Robinson et al., 2019

Supplementary
Table 1. Average fold-change for GO categories that were significantly enriched
with genes down- and up-regulated in expression in response to acute stress for
control (CO), embryonic (E), post-hatch (PH) and embryonic post-hatch (EPH)
treated fish. Significance was tested using 1-tailed
chi-square test with Yates’ correction for continuity, P<0.05.

Supplementary
Figure 1. Volcano plots of adjusted P-values
(Padj) and log fold change
in expression (log2FC) in response to acute stress (ie. 0 versus 3
hours post stress). Separate plots are for control (A)
embryonic (B) post hatch (C) and embryonic post hatch (D) experimental
treatments. Red points show genes with Padj
< 0.05 while green points show genes with Padj < 0.05 and log2FC > 1.

Supplementary
Figure 2. Pearson correlation analyses of fold difference in expression between
treatments and response to acute stress after treatments. CO,
E, PH and EPH refer to control, embryo, post-hatch and embryo post-hatch
treatments respectively.

Supplementary
Figure 3. Box plots of changes in the expression of T-cell receptor (transcript
XLOC_015821) for control (CO), embryonic (E), post-hatch (PH) and embryonic
post-hatch (EPH) treated fish and map of methylation differences between
treatments 0 hrs pre-acute stress (stars). The gene
expression response for EPH treated fish (from 0 to 3 hrs after acute stress)
is shown as green bars positioned at the start and end of the gene transcript.

Supplementary
Figure 4. Box plots of changes in the expression of Toll-like receptor 3
(transcript XLOC_022410) for control (CO), embryonic (E), post-hatch (PH) and
embryonic post-hatch (EPH) treated fish and map of methylation differences
between treatments 0 hrs pre-acute stress (stars). The
gene expression response for EPH treated fish (from 0 to 3 hrs after acute
stress) is shown as green bars positioned at the start and end of the gene
transcript.

Supplementary
Figure 5. Box plots of changes in the expression of Immunoglobulin H locus B
(transcript XLOC_022187) for control (CO), embryonic (E), post-hatch (PH) and
embryonic post-hatch (EPH) treated fish and map of methylation differences
between treatments 0 hrs pre-acute stress (stars). The
gene expression response for EPH treated fish (from 0 to 3 hrs after acute
stress) is shown as green bars positioned at the start and end of the gene
transcript.

Supplementary
Figure 6. Box plots of changes in the expression of ATP Binding Cassette (ABC
membrane transporters) (transcript XLOC_014577) for control (CO), embryonic
(E), post-hatch (PH) and embryonic post-hatch (EPH) treated fish and map of methylation
differences between treatments 0 hrs pre-acute stress (stars). The
gene expression response for EPH treated fish (from 0 to 3 hrs after acute
stress) is shown as green bars positioned at the start and end of the gene
transcript.

File (.gff) giving annotation used to derive the gene counts. The creation of this file is described in Moghadam et al. (2017).