Supplemental Table 4: List of genes differentially expressed in chicken embryonic gonads with various degrees of feminization after in ovo exposure to ethynylestradiol

Supplemental Table 4 supporting: Keiko Shioda et al. “Transcriptomic and epigenetic preservation of genetic sex identity in estrogen-feminized male chicken embryonic gonads”
Supplemental Table 4: Differentially expressed genes.

Chicken embryos (29 total) were exposed to 20 microgram/egg ethynylestradiol or vehicle oil emulsion from incubation day 6, and their gonads were collected on day 19. This table shows list of differentially expressed genes in chicken embryonic gonads showing various degrees of feminization after exposure to ethynylestradiol determined by RNA-seq. Induction or suppression comparing various degrees of feminization scores (FS= 0,1,2,3) are shown in the tag labels.

Each tag shows a list of DEGs with gene symbols, log2 fold changes (logFC), average log2 counts-per-million expression (logCPM), likelihood ratio statistics (LR) (1), p-values, and false discovery ratio (FDR) (2) calculated based on the generalized linear model (3). DEGs listed in each spreadsheet are selected using criteria indicated in the tags. For example, “FS0 vs FS1” indicates genes differentially expressed between FS=0 and FS=1 gonads. The spreadsheet “FS0 < FS1 or FS2” lists genes whose expression in weaker in FS=0 compared to either FS=1 or FS=2. The spreadsheet “FS0 vs FS1 not FS3 UP” lists genes upregulated in FS=1 compared to FS=0, but genes upregulated in FS=3 compared to FS=0 were removed from this list.

[References]

1. Xu M, Chen L. An empirical likelihood ratio test robust to individual heterogeneity for differential expression analysis of RNA-seq. Brief Bioinform. 2018;19(1):109-117.

2. Reiner A, Yekutieli D, Benjamini Y. Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics. 2003;19(3):368-375.

3. Nikolayeva O, Robinson MD. edgeR for differential RNA-seq and ChIP-seq analysis: an application to stem cell biology. Methods Mol Biol. 2014;1150:45-79.