| We treated MCF-7 human breast cancer cells (estrogen receptor positive) for 24 hours with DMSO vehicle, 1 µM ZN-c5 (an oral selective estrogen receptor degrader) or 1 µM 4-hydroxytamoxifen, after seeding them for 48 hours in phenol red-free medium with charcoal-stripped serum. The treatment is recorded in the `group` column, which holds our groups (`geo_treatment` repeats it): DMSO is the vehicle control, ZN-c5 the degrader and Tamoxifen the 4-hydroxytamoxifen treatment (Ctrl, KP868 and Tamo in the sample names). There are three cultures per treatment, nine samples in all, all harvested after 24 hours of treatment, so there is a single time point. | |
| Each sample is a separate culture given one treatment, made into its own library and sequenced once, so there are no technical replicates, and with a cell line there are no donors or animals. The numbers 1 to 3 in the sample names (JM1 to JM3; Rep1 to Rep3 in `geo_title`) only count the cultures within each treatment; nothing records that cultures with the same number were treated, harvested or processed together. GEO gives all nine samples the same batch label (Mar-20), so no batch differences are recorded, and we know of no other variable that matters; the remaining columns are GEO annotations. | |
| The data are bulk poly(A) RNA-seq from stranded TruSeq mRNA libraries, aligned with HISAT2 and given as gene-level integer counts with Ensembl gene IDs, which the submitters deposited as raw counts. | |
| Our question is which genes are differentially expressed in MCF-7 cells treated with ZN-c5 for 24 hours compared with DMSO-treated cells. All nine samples are part of this question: the Tamoxifen cultures come from the same experiment, even though they are not among the groups being compared. | |