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Supplementary Figure 1 EPIGEN_PAPER2_Volcano_Plot_A_c_B_e_C_ph_D_eph.jpg (789.9 kB)

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Supplementary Figure 2 Pearsons.tiff (5.61 MB)

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Supplementary Table 1. Enrichment results pivoted.xlsx (16.06 kB)

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Supplemental Material for Robinson et al., 2019

dataset

posted on 2019-03-18, 14:30 authored by Nicholas Robinson, Hanne Johnsen, Hooman Moghadam, Øivind Andersen, Helge Tveiten

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 (P_adj) 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 P_adj< 0.05 while green points show genes with P_adj< 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).

History

Article title

Early Developmental Stress Affects Subsequent Gene Expression Response to an Acute Stress in Atlantic Salmon: An Approach for Creating Robust Fish for Aquaculture?