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Brekke等人发表的题为《杂交侏儒仓鼠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）的研究配套数据电子表格。
该电子表格包含以下工作表：
1. 纳入胎盘表型数据的基于RAD（Restriction site-Associated DNA，限制性酶切位点相关DNA）的遗传图谱（即文中表S1）；
2. 所有图谱定位基因的全部个体推算基因型；
3. 本研究分析所用的每百万片段转录本（CPM，counts per million）标准化基因表达数据，涵盖亲本物种、正反交F1子代以及回交（BC）样本；
4. 回交下调模块中排名前500的基因的共连接性数据；
5. 用于计算表达互作得分（EI，Expression Interaction Score）的中间分析结果。

表S1：所有RAD标记的完整说明，包括标记ID、所在连锁群、以厘摩（cM，centiMorgans）为单位的遗传位置、*P. campbelli*与*P. sungorus*间诊断性单核苷酸变异（SNV，Single Nucleotide Variant）的位置与链极性，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：CC_TGCA^GG）。序列中的SNV采用标准IUPAC歧义编码标注。
表S2：由F1及纯种胎盘基因表达数据生成的加权基因共表达网络分析（WGCNA，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。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、与既往成对分析（Brekke等人，2016年）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：由回交胎盘基因表达数据生成的WGCNA模块。模块颜色由程序随机生成，与F1分析中分配的模块名称无对应关系。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：本次捕获并关联至遗传图谱的各基因的遗传位置完整说明。列信息依次为：连锁群（LG）、以厘摩为单位的遗传位置、*P. sungorus*转录组中的基因名称（Trinity_Component）、单核苷酸多态性（SNP，Single Nucleotide Polymorphism）所在外显子（exon）、SNP在外显子中的位置（snp_pos_in_exon）、关联基因名称（Associated_Gene_Name），以及该基因的小鼠Ensembl基因ID（Ensembl_Gene_ID）。
表S5：按序列类型分类的所有个体的SRA（Sequence Read Archive，序列读取档案）序列登录号。