Additional file 1 of Dynamics of rumen gene expression, microbiome colonization, and their interplay in goats
Creators: name: Pan, Xiangyu
name: Li, Zongjun
name: Li, Bibo
name: Zhao, Chen
name: Wang, Yu
name: Chen, Yulin
name: Jiang, Yu
Publisher: name: figshare
Year: 2021
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics

description: Additional file 1: Figure S1. Unsupervised hierarchical clustering analysis showing the relationships among 21 transcriptomic samples in goats and a heatmap showing the pairwise Pearson correlations. Figure S2. WGCNA of postnatal rumen development transcriptomes. Figure S3. Barplots showing the top 10 GO enrichment terms in each host module. Figure S4. Top 20 microbial abundance at the phylum level at each time point. Figure S5. Top 20 microbial abundance at the genus level at each time point. Figure S6. Unsupervised hierarchical clustering analysis showing the relationships among 17 metagenomic samples in goats and a heatmap showing the pairwise Pearson correlations. Figure S7. The clustering tree of 1782 genus on the determination of the optimal soft threshold power for rumen microbiome modules. Figure S8. WGCNA of postnatal rumen development metagenomes. Figure S9. Correlations of host modules with microbial modules at genus level. Figure S10. The tests on the determination of the optimal soft threshold power for rumen host modules. Figure S11. The clustering tree of 2035 DEGs on the determination of the optimal soft threshold power for rumen modules. Figure S12. The tests on the determination of the optimal soft threshold power for rumen microbiome modules in genus level. Table S1. Statistical data for 21 rumen transcriptome samples in goats. Table S2. GO enrichment analysis of 852 DEGs between d 7 vs. d 1 during rumen development. Table S3. GO enrichment analysis of 285 DEGs between d 14 vs. d 7 during rumen development. Table S4. GO enrichment analysis of 358 DEGs between d 21 vs. d 14 during rumen development. Table S5. GO enrichment analysis of 458 DEGs between d 28 vs. d 21 during rumen development. Table S6. GO enrichment analysis of 791 DEGs between d 42 vs. d 28 during rumen development. Table S7. GO enrichment analysis of 535 DEGs between d 56 vs. d 42 during rumen development. Table S8. GO enrichment analysis of 1032 DEGs in the first phase during rumen development. Table S9. GO enrichment analysis of 1509 DEGs in the second phase during rumen development. Table S10. KEGG enrichment results for the DEGs during early rumen development in the first phase. Table S11. KEGG enrichment results for the DEGs during early rumen development in the second phase. Table S12. Spearman’s correlation coefficient and P value of each host module with age. Table S13. Statistical data for the metagenomics raw data. Table S14. Statistical data for metagenomics assembly (contig-level). Table S15. Statistical data for metagenomics assembly (scaffold-level). Table S16. Statistical data for non-redundant gene catalog annotation. Table S17. The relative abundance of KEGG pathway abundance (Mean ± SEM) at the third level during the early rumen development. Table S18. KEGG enrichment results for the rumen metagenome in two phases. Table S20. Spearman’s correlation coefficient and P value of the first eigenvector from the PCA of each host module with microbial alpha diversity index. Table S21. Ingredients and nutrients of the experimental diets.