Transcriptional responses to TGFß1 and conditioned media in mammary epithelial cells
To investigate TGFß1 (a key member of the TGFß superfamily) signaling in non-cancerous and cancerous cells derived from breast epithelium and what further response it might generate, we treated the cells with TGFß1 or with conditioned media. We selected MCF10A non-tumorigenic breast epithelial cells (isolated from the mammary gland with fibrocystic disease) and MCF7 breast adenocarcinoma cells (estrogen receptor-positive, ER+). We followed a regimen of treating the cells for six consecutive days, with daily administration of TGFß1 for two hours. The TGFß1-containing medium was changed to a fresh one, which was collected after another 22 hours (so-called conditioned medium, CM) and administered to other cells. This enabled us to assess the ability of extracellularly secreted molecules to further induce a cellular response (bystander effect). RNA-seq analyses were performed on cells either directly treated with TGFß1 in the above scheme or treated with a conditioned media for 1, 2, 3, 4, 5, or 6 days. The experiment was performed in three biological replicates, and each sample was sequenced separately. RNA-seg analysis in both cell lines allowed us to find the differences and similarities in response to TGFß1 and CM. All 84 libraries were sequenced on Illumina NovaSeq6000 platform, in 2x150 mode, with a coverage of 60M reads/sample.