Additional file 2: Figure S1. of Integration of quantitated expression estimates from polyA-selected and rRNA-depleted RNA-seq libraries

Variance in expression estimates arising from differential transcriptome sampling by polyA+ and ribo-minus RNA selection methods. Figure S2. Variance in TPM estimates by differential transcriptome sampling was effectively negated by the combined use of a filtered reference transcriptome for quantifying expression, and applying a ratio-based correction to the TPM estimates of ribo-minus libraries. Figure S3. Reduction in the absolute difference in TPM estimates from polyA+ and ribo-minus libraries when applying a ratio-based correction to the latter. Figure S4. Tissue tree constructed from the Euclidean distances between uncorrected TPM vectors for two human RNA-seq datasets sequenced with either polyA+ or ribo-minus libraries. Figure S5. Tissue tree constructed from the Euclidean distances between corrected TPM vectors for two human RNA-seq datasets sequenced with either polyA+ or ribo-minus libraries. Figure S6. Comparison of TPM estimates in the adrenal gland, as generated for 19,716 human genes using both polyA-selected and rRNA-depleted libraries. Figure S7. Comparison of TPM estimates in the liver, as generated for 19,716 human genes using both polyA-selected and rRNA-depleted libraries. Figure S8. Comparison of TPM estimates in the ovary, as generated for 19,716 human genes using both polyA-selected and rRNA-depleted libraries. Figure S9. Comparison of TPM estimates in the sigmoid colon, as generated for 19,716 human genes using both polyA-selected and rRNA-depleted libraries. Figure S10. Comparison of TPM estimates in the spleen, as generated for 19,716 human genes using both polyA-selected and rRNA-depleted libraries. Figure S11. Comparison of TPM estimates in the testis, as generated for 19,716 human genes using both polyA-selected and rRNA-depleted libraries. (DOCX 709 kb

Additional file 18: of Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

Table S18. Comparison of co-expression clusters between the RNA-seq atlas and the Lizio, et al. CAGE dataset [53]. (XLSX 108 kb

Additional file 6: of Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

Table S6. Chicken RNA-seq meta-dataset, after the second (and final) iteration of Kallisto. (XLSX 23600 kb

Additional file 12: of Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

Table S12. Tissues whose expression vectors are most strongly correlated with each other. (XLSX 18 kb

Additional file 13: of Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

Table S13. Clusters of co-expressed genes (obtained via network analysis of the RNA-seq meta-dataset), including candidate gene names for unannotated GalGal5 protein-coding genes. (XLSX 1432 kb

Additional file 1: of Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

Table S1. Data sources for creating an RNA-seq meta-atlas. (XLSX 16 kb

Additional file 4: of Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

Table S4. Number of genes with detectable expression, per tissue, after the first iteration of Kallisto. (XLSX 11 kb

Additional file 9: of Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

Table S9. Range of expression estimates, and absolute difference between largest and smallest estimate, after randomly down-sampling the LPS-stimulated BMDM datasets. (XLSX 8074 kb

Additional file 10: of Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

Table S10. GO term enrichment for those subsets of genes whose highest PEM is for a given tissue. (XLSX 63 kb

Additional file 11: of Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

Table S11. All-against-all correlation matrix for each tissue in the meta-dataset. (XLSX 79 kb