Supplemental data to "The site of breast cancer metastases dictates their clonal composition and reversible transcriptomic profile"

Differential expression analyses were completed in edgeR, all of them fitting a generalized log-linear model to uncorrected data using the glmQLfit function. P values were adjusted using BH correction and were filtered using 0.05 thresholds for both P value and FDR. Tests were conducted with the primary as the reference level, this means that positive logFCs denote genes upregulated in the metastatic organ (Direction: "UP" in the file)