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Supplemental Material for Brekke et al., 2021

dataset
posted on 09.03.2021, 16:42 by Thomas D. Brekke, Emily C. Moore, Shane C. Campbell-Staton, Colin M. Callahan, Zachary A. Cheviron, Jeffrey M. Good

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)


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 P. campbelli and P. sungorus, , 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 et al. 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 P. sungorus 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.

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Article title

X chromosome-dependent disruption of placental regulatory networks in hybrid dwarf hamsters

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