Single-cell RNA sequencing of MCF-7, T-47D and ZR-75-1 breast cancer cell lines treated with estrogen and progesterone

In order to study transcriptional heterogeneity in response to hormone stimulation in breast cancer, we performed high-throughput single-cell RNA sequencing (scRNA-seq) on 3 breast cancer cell lines that differ in their nuclear receptor expression levels. MCF-7, T-47D and ZR-75-1 cell lines were treated with estrogen and progesterone alone or in combination and collected at different time points. Hash-tagging antibodies were used to identify samples. Overall design: High throughput single cell RNA sequencing (RNA-seq) for MCF-7 (27606 cells ), T-47D (25165 cells ) and ZR-75-1 (21397 cells) breast cancer cell lines treated with estrogen (E2) for 3, 6, 24, 48 and 72 hours (h) or progesterone (PG) for 3 and 48 h or a combination of estrogen and progesterone (E2 + PG) or 3 and 48 h. 2 clones were isolated from MCF-7 and subject to 24h and 48h estrogen treatments to assess for clonal derive effect in gene expression. Single cell RNA sequencing of TAMR (3750 cells), HCI003 (1615 cells) and HCI011 (13470 cells) organoids treated with estrogen. 10X multiomic (scRNA and scATAC) sequencing of MCF7 cells (6438 cells) treated with estrogen.