Besides short-term non-genomic effects, the G-protein coupled estrogen receptor (GPER) also mediates long-term genomic effects of estrogen. The genomic effects of GPER activation are not completely understood. G1 is a selective GPER agonist, which is popularly used for addressing the effects of GPER activation. Here, we present transcriptomic (RNA-seq) data on MCF-7 cells treated with 100 nM, or 1 µM G1 for a period of 48 h. The data are available from GEO (accession number GSE188706).