| We studied the FLT3 inhibitor SGI-7079 in two human acute myeloid leukaemia cell lines that carry the FLT3-ITD mutation, MOLM13 and MV4-11 (written MV411 in the files). Cultures of each cell line were treated in vitro with 10 nM SGI-7079 or with the DMSO vehicle and harvested after 24 hours, so all samples come from one time point. The treatment is in the `treatment` column, DMSO for the vehicle control and SGI7079 for SGI-7079; the `group` column repeats these labels. The cell line is in the `cell_type` column, MOLM13 or MV411 (`tissue` and `specimen` repeat it), and `cell_line_treatment` simply joins the two labels, for example MOLM13_SGI7079. | |
| There are three replicate cultures for every cell line and treatment, 12 samples in all, so each cell line contributes three DMSO and three SGI7079 cultures. The six samples of a cell line all derive from that one line and share its genetic background. The numbers _01 to _03 in `sample_id` only count the cultures within each cell line and treatment; there is no record that cultures with the same number were handled together. Each culture gave one library, so there are no technical replicates. No processing or sequencing batch is recorded, and we know of no other variable that matters; the remaining columns are GEO annotations. | |
| The data are bulk mRNA-seq (oligo-dT selected), given as the submitters' integer gene-level counts for Ensembl genes from a HISAT2 and StringTie pipeline. | |
| Our question is which genes SGI-7079 changes compared with DMSO on average over the two cell lines: the SGI7079 versus DMSO difference within MOLM13 and the same difference within MV4-11, averaged with the two cell lines weighted equally. All 12 samples are part of the analysis. | |