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” <br>Supplemental Table 4: Differentially expressed genes.<br><br>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.<br>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 &lt; 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.<br>[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.

补充表4 支撑文献：Keiko Shioda 等. 《雌激素雌性化的雄性鸡胚胎性腺中转录组与表观遗传组对遗传性别身份的维持》
补充表4：差异表达基因

共纳入29枚鸡胚，于孵化第6天起分别经每枚卵20微克的乙炔雌二醇或溶剂油乳剂处理，并于孵化第19天采集其性腺组织。
本表格展示经RNA测序（RNA-seq）鉴定的、暴露于乙炔雌二醇后呈现不同程度雌性化的鸡胚胎性腺的差异表达基因（differentially expressed genes，DEGs）列表。
标签标注了基于不同雌性化评分（FS=0、1、2、3）组间比较得到的基因诱导或抑制情况。
每个标签下的差异表达基因列表包含基因符号、log2倍变化值（log2 fold change, logFC）、平均log2计数每百万转录本（average log2 counts-per-million, logCPM）、基于广义线性模型（generalized linear model）计算得到的似然比统计量（likelihood ratio statistics, LR）(1)、P值以及错误发现率（false discovery rate, FDR）(2)。
各电子表格中收录的差异表达基因均基于标签所示的筛选标准得到。例如，"FS0 vs FS1"代表FS=0与FS=1性腺组间的差异表达基因。
电子表格"FS0 < FS1 或 FS2"收录了FS=0组的表达水平低于FS=1组或FS=2组的基因。
电子表格"FS0 vs FS1 not FS3 UP"收录了相较于FS=0组在FS=1组中上调的基因，但相较于FS=0组在FS=3组中上调的基因已被排除出该列表。

[参考文献]
1. Xu M, Chen L. 适用于RNA-seq差异表达分析的、对个体异质性具有鲁棒性的经验似然比检验. Brief Bioinform. 2018;19(1):109-117.
2. Reiner A, Yekutieli D, Benjamini Y. 基于错误发现率控制流程鉴定差异表达基因. Bioinformatics. 2003;19(3):368-375.
3. Nikolayeva O, Robinson MD. edgeR在差异RNA-seq与ChIP-seq分析中的应用：以干细胞生物学研究为例. Methods Mol Biol. 2014;1150:45-79.