Data_Sheet_1_What Makes the Harderian Gland Transcriptome Different From Other Chicken Immune Tissues? A Gene Expression Comparative Analysis.XLSX

<p>The Harderian gland is a sparsely characterized immune tissue known to play an important role in local immunity. The function of the Harderian gland, however, is not clearly defined. Measuring the expression of all genes using RNA-seq enables the identification of genes, pathways, or networks of interest. Our relative RNA-seq expression analysis compared the chicken Harderian gland transcriptome to other important primary and secondary immune tissues including the bursa of Fabricius, thymus, and spleen of non-challenged birds. A total of 2,386 transcripts were identified as highly expressed in the Harderian gland. Gene set enrichment showed the importance of G-protein coupled receptor signaling and several immune pathways. Among the genes highly expressed in the Harderian gland were 48 miRNAs, a category of genetic elements involved in regulation of gene expression. Several identified miRNAs have immune related functions. This analysis gives insight to the unique immune processes inherent in the Harderian gland.</p

Data_Sheet_2_What Makes the Harderian Gland Transcriptome Different From Other Chicken Immune Tissues? A Gene Expression Comparative Analysis.XLSX

<p>The Harderian gland is a sparsely characterized immune tissue known to play an important role in local immunity. The function of the Harderian gland, however, is not clearly defined. Measuring the expression of all genes using RNA-seq enables the identification of genes, pathways, or networks of interest. Our relative RNA-seq expression analysis compared the chicken Harderian gland transcriptome to other important primary and secondary immune tissues including the bursa of Fabricius, thymus, and spleen of non-challenged birds. A total of 2,386 transcripts were identified as highly expressed in the Harderian gland. Gene set enrichment showed the importance of G-protein coupled receptor signaling and several immune pathways. Among the genes highly expressed in the Harderian gland were 48 miRNAs, a category of genetic elements involved in regulation of gene expression. Several identified miRNAs have immune related functions. This analysis gives insight to the unique immune processes inherent in the Harderian gland.</p

Depiction of the cell cycle.

<p>Red arrows indicate parts of the cell cycle affected by heat stress. Red lines indicate transitions between stages of cell cycle. Numbers indicate number of genes at that specific stage of the cell cycle enriched in heat stress as identified by WebGIVI. The stages of cell cycle affected by heat stress include the G1 phase, G1/S phase transition, S phase, and G2/M phase transition.</p

WebGIVI cytoscape output results for thermoneutral transcriptome data from Ross708 liver samples 28 days post-hatch.

<p>Yellow circles indicate Genes and red-outlined circles indicate iTerms. Most common iTerms are associated with proinflammatory response, lipid metabolism, cell cycle and circadian rhythm.</p

Depiction of fatty acid metabolism.

<p><b>6a.</b> Integrated transcriptome and metabolome data and fatty acid metabolism depicting acetyl-coa being transformed into either myristate or palmitate. <b>6b</b> depicts the numerous ways glycerol-3-phosphate can be synthesized as well as the final esterification step to form a complete triacylglycerol.</p

PathRings depiction of liver transcriptome data.

<p>Each segment of the inner ring indicates a pathway. Outer rings equate to more specific pathways. Significance is determined by the Fisher’s Exact test and is indicated by color where blue is insignificant and yellow to maroon is significant (0.025–0.001, respectively). Significantly affected pathways were (M) Metabolism, (CC) Cell Cycle, and (DR) DNA Repair.</p

Free amino acids detected by Metabolon and whether they are enriched in thermoneutral, heat stress, or unchanged between conditions from Ross708 liver samples 28 days post-hatch.

<p>Free amino acids detected by Metabolon and whether they are enriched in thermoneutral, heat stress, or unchanged between conditions from Ross708 liver samples 28 days post-hatch.</p

Depiction of glycogenolysis and gluconeogenesis pathways with integrated metabolomic and transcriptomic data from Ross708 liver samples 28 days post-hatch.

<p>The rectangles indicate metabolites and the arrows indicate genes. The legend indicates whether a gene or metabolite was detected and if it was up in heat stress or unchanged between conditions.</p

Spearman correlation network for samples treated with LPS at time point 2h.

<p>(A) The complete network showing interaction between genes at 0 hours after LPS treatment. Highly connected hubs includes <i>TLR4</i>, <i>IFNB</i>, <i>MyD88</i>, <i>IL8</i>, and <i>HSPA14</i>. (B) Cluster 1 from MCODE network clustering algorithm showing the interaction between <i>IL8</i>, <i>IL1B</i>, <i>CCL5</i>, <i>CCL4</i>, <i>iNOS</i>, <i>JUN</i>, and HSPA14 after ignoring the hairball to the right of <i>HSPA14</i>. The cluster shows interaction between immune response genes from LPS stimulation.</p

Spearman correlation network for samples treated with at time point 2h.

<p>(A) The complete network showing interaction between genes at 0 hours after heat stress treatment. Highly connected hubs includes <i>iNOS</i>, <i>IL8</i>, <i>CD40</i>, and <i>HSPA14</i>. (B) Cluster 2 from MCODE network clustering algorithm showing the interaction between <i>iNOS</i>, <i>IFNB</i>, <i>CASP9</i>, <i>CASP3</i>, <i>HSPA14</i>, <i>IFNG</i>, and <i>MAPK9</i>. The cluster shows interaction between multiple mechanisms during response to heat stress.</p