Supplemental Material for Brekke et al., 2021

Spreadsheet with data for Brekke et al, "X chromosome-dependent disruption of placental regulatory networks in hybrid dwarf hamsters." Tabs include the RAD-based genetic map (Table S1 in the text) with placental phenotypes included; the imputed genotype for every individual for all map-placed genes; the cpm-normalized gene expression data used in analyses in the paper for both the parental species and reciprocal intercrosses (F1 data) and the backcross (BC); connectivity data from the top 500 genes in the BC down regulated module; and the intermediate analysis for calculating the expression interaction score (EI)<br>Table S1. A full description of all RAD markers including their ID, the linkage group they are found on, genetic position in centiMorgans, the position and polarization of the diagnostic SNV between <i>P. campbelli </i>and <i>P. sungorus, </i>, and the sequence of the marker which always begin with TGCAGG (the restriction-enzyme cut-site of SbfI, i.e.: CC_TGCA^GG). SNVs in the sequence are denoted with standard IUPAC ambiguity codes.Table S2. WGCNA modules generated from F1 and pure species placental gene expression data. Color names are arbitrarily and randomly generated by the program, and have no additional meaning. The upregulated and downregulated modules are discussed in the manuscript are indicated as such. Counts of genes in each module, correspondence with previous pairwise analysis (Brekke<i> et al.</i> 2016), association with inheritance pattern and phenotypes, and enrichment for candidate imprinted genes indicated.Table S3. WGCNA modules generated from BC placental gene expression data. Color names are arbitrarily and randomly generated by the program, and do not correspond with the arbitrarily assigned names for to the F1 analysis. The upregulated and downregulated modules are discussed in the manuscript are indicated as such. Counts of genes in each module, correspondence with F1 network analysis, association with phenotypes, and enrichment for candidate imprinted genes are indicated.Table S4. A full description of the genetic locations of each gene from that was captured and associated with the map. Columns are: Linkage group (LG), position in centiMorgans (cM), gene name from the <i>P. sungorus</i> transcriptome (Trinity_Component), the exon that the SNP appears in (exon), the position of the SNP in the exon (snp_pos_in_exon), the gene name (Associated_Gene_Name), and the mouse ensemble gene ID of that gene (Ensembl_Gene_ID).Table S5. SRA sequence accession numbers for each individual by sequence type.

本数据集为布雷克等人（Brekke et al.）发表于论文《杂交矮仓鼠X染色体依赖性胎盘调控网络紊乱》（X chromosome-dependent disruption of placental regulatory networks in hybrid dwarf hamsters）的配套电子表格数据。该电子表格包含以下工作表：1. 纳入胎盘表型信息的RAD（限制性位点关联DNA，Restriction-site Associated DNA）遗传图谱（即文中表S1）；2. 所有图谱定位基因在各受试个体中的推定基因型；3. 本论文分析所用的CPM（每百万片段转录本，counts per million）标准化基因表达数据，涵盖亲本物种、正反交F1代以及回交（BC）群体；4. 回交群体下调共表达模块中排名前500的基因的连接数据；5. 用于计算表达互作得分（expression interaction score, EI）的中间分析结果。

表S1：所有RAD标记的完整说明，包括标记ID、所属连锁群、以厘摩（centiMorgan, cM）为单位的遗传位置、坎贝尔侏儒仓鼠（*P. campbelli*）与西伯利亚侏儒仓鼠（*P. sungorus*）间诊断性单核苷酸变异（Single Nucleotide Variant, SNV）的位置与极化方向，以及始终以TGCAGG开头的标记序列（SbfI限制性内切酶的酶切位点，即CC_TGCA^GG）。序列中的SNV采用标准IUPAC歧义代码标注。

表S2：基于F1代与纯合亲本物种胎盘基因表达数据构建的WGCNA（加权基因共表达网络分析，Weighted Gene Co-expression Network Analysis）模块。模块颜色由程序随机生成，无额外生物学含义。论文中讨论的上调与下调模块已标注。表格包含各模块的基因数量、与此前成对分析（Brekke et al. 2016）的对应关系、与遗传模式及表型的关联，以及候选印记基因的富集情况。

表S3：基于回交（BC）群体胎盘基因表达数据构建的WGCNA模块。模块颜色由程序随机生成，与F1代分析所用的颜色命名无对应关系。论文中讨论的上调与下调模块已标注。表格包含各模块的基因数量、与F1代共表达网络分析的对应关系、与表型的关联，以及候选印记基因的富集情况。

表S4：所有被捕获并锚定至遗传图谱的基因的遗传位置完整说明。各列信息依次为：连锁群（LG）、以厘摩为单位的位置、西伯利亚侏儒仓鼠（*P. sungorus*）转录组中的基因名称（Trinity_Component）、SNP所在外显子（exon）、SNP在外显子中的位置（snp_pos_in_exon）、基因名（Associated_Gene_Name），以及该基因的小鼠Ensembl基因ID（Ensembl_Gene_ID）。

表S5：按测序类型分类的所有受试个体的SRA（序列读取存档，Sequence Read Archive）序列登录号。