Embryonic In Ovo Stimulation-Supplementary Tables and Supplementary Figure

Supplementary Tables (Table S)
Table S1A: MultiQC_FastQC Analysis of Taxonomic Composition in the Microbial Communities of Chicken Caecum from in Ovo Simulation.
Table S1B: Sequencing Data Summary: Raw, Trimmed, and Final Paired Reads for Microbial Composition Analysis.
Table S1C: All statistics are based on contigs of size >= 500 bp, unless otherwise noted (e.g., "# contigs (>= 0 bp)" and "Total length (>= 0 bp)" include all contigs).
Table S2: Taxonomic Composition Identified from Sequencing Data: Raw, Trimmed, and Final Paired Reads of chicken guts obtained from the in ovo simulation with the five treatments.
Table S3: Transcriptome sequencing statistics among the 30 ileum samples (5 groups × 6 repeats; groups comprised negative control (NC), positive control (PC), Quercetin (Q), Vitamin E (VE) and Combined use of Q and VE (Q+VE)) obtained from in ovo embryonic injection chickens with the NC, PC, Q, VE and Q+VE.
Table S4A: Differential expression genes (DEGs) between Positive control group (PC) and Negative control group (NC), genes with|log2 (Fold Change) | > 1 & padj < 0.05 were considered (DEGs). Those of |log2 (Fold Change) with - and + values were down- and up-regulated in PC and NC, respectively.
Table S4B: Differential expression genes (DEGs) between Positive control group (PC) and Quercetin+Vitamin E (Q+VE), genes with|log2 (Fold Change) | > 1 & padj < 0.05 were considered (DEGs). Those of |log2 (Fold Change) with - and + values were down- and up-regulated in Q+VE and PC, respectively.
Table S4C: Differential expression genes (DEGs) between Negative control group (NC) and Quercetin+Vitamin E (Q+VE), genes with|log2 (Fold Change) | > 1 & padj < 0.05 were considered (DEGs). Those of |log2 (Fold Change) with - and + values were down- and up-regulated in NC and Q+VE, respectively.
Table S4D: Differential expression genes (DEGs) between Positive control group (PC) and Quercetin group (Q), genes with|log2 (Fold Change) | > 1 & padj < 0.05 were considered (DEGs). Those of |log2 (Fold Change) with - and + values were down- and up-regulated in PC and Q, respectively.
Table S4E: Differential expression genes (DEGs) between Positive control group (NC) and Vitamin E group (VE), genes with|log2 (Fold Change) | > 1 & padj < 0.05 were considered (DEGs). Those of |log2 (Fold Change) with - and + values were down- and up-regulated in VE and PC, respectively.
Table S4F: Differential expression genes (DEGs) between Negative control group (NC) and Quercetin (Q), genes with|log2 (Fold Change) | > 1 & padj < 0.05 were considered (DEGs).
Table S4G: Differential expression genes (DEGs) between Negative control group (NC) and Vitamin E (VE), genes with|log2 (Fold Change) | > 1 & padj < 0.05 were considered (DEGs).
Table S4H: Differential expression genes (DEGs) between Quercetin (Q) and Vitamin E (VE), genes with|log2 (Fold Change) | > 1 & padj < 0.05 were considered (DEGs).