Supplementary Information

Supplementary Information for

San Roman AK, Skaletsky H, Godfrey AK, Bokil N, Teitz L, Singh I, Blanton LV, Bellott DW, Pyntikova T, Lange J, Koutseva N, Hughes JF, Brown LG, Phou S, Buscetta A, Kruszka P, Banks N, Dutra A, Pak E, Lasutschinkow PC, Keen C, Davis SM, Lin AE, Tartaglia NR, Samango-Sprouse C, Muenke M, Page DC

The human Y and inactive X chromosomes similarly modulate autosomal gene expression

Document S1: Figures S1-S22
Table S1: Metadata for RNA-seq of LCLs or fibroblasts from individuals with naturally occurring variations in chromosome copy number or structure, related to Figures 1, 3, 4, and 5
Table S2: Expression change per copy of Chr X or Chr Y for expressed autosomal genes in LCLs and fibroblasts, related to Figure 1
Table S3: Reanalysis of publicly available data to identify AR and ER direct target genes, related to Figure 1
Table S4: Genes expressed from the active X chromosome only (silenced on Xi) that significantly change in expression in response to Chr X and Chr Y copy number, related to Figure 2
Table S5: Expression change per copy of Chr 21 for expressed autosomal genes in LCLs, related to Figure 3
Table S6: Differential gene expression analysis as a function of DYZ1 depth of coverage, related to Figure 4
Table S7: Sex chromosome structural variant breakpoints and gene content, related to Figures 4 and 5
Table S8: Sequence motifs in promoters of Chr X- and Y-responsive genes in LCLs and fibroblasts, related to Figure 6
Table S9: Genome-wide binding analysis of ZFX across ENCODE cell lines, related to Figure 6
Table S10: Reanalysis of publicly available data to identify ZFX direct target genes, related to Figure 6
Table S11: Expression analysis of ZFX and ZFY CRISPRi knockdowns, related to Figure 6
Table S12: Sequence motifs in promoters of genes affected by ZFX and ZFY knockdowns, related to Figure 6
Table S13: Quantification of genome-wide response to Chr X and Y copy number in LCLs and fibroblasts, related to Figures 1 and 2